From b68b1d388e53dd4424968d59e744deae481fdfd7 Mon Sep 17 00:00:00 2001 From: Ino de Bruijn Date: Thu, 12 Mar 2026 18:09:03 -0400 Subject: [PATCH] Re-annotate um_tcga_gdc with vibe-vep --- crdc/gdc/um_tcga_gdc/data_mutations.txt | 1494 ++++++++++++++++++++++- 1 file changed, 1491 insertions(+), 3 deletions(-) diff --git a/crdc/gdc/um_tcga_gdc/data_mutations.txt b/crdc/gdc/um_tcga_gdc/data_mutations.txt index 4cfef1c0fa..7a445914f5 100644 --- a/crdc/gdc/um_tcga_gdc/data_mutations.txt +++ b/crdc/gdc/um_tcga_gdc/data_mutations.txt @@ -1,3 +1,1491 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:7314cf92f21accfc69a6679d817d788038357154d4c6df44ef578c035a85d345 -size 2485706 +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number 1000G_AF 1000G_AFR_AF 1000G_AMR_AF 1000G_EAS_AF 1000G_EUR_AF 1000G_SAS_AF APPRIS Allele Amino_acids BIOTYPE CANONICAL CCDS CDS_position CLIN_SIG CONTEXT COSMIC DISTANCE DOMAINS ENSP ESP_AA_AF ESP_EA_AF EXON Existing_variation FLAGS Feature Feature_type GDC_FILTER GENE_PHENO Gene HGNC_ID HGVS_OFFSET HIGH_INF_POS IMPACT INTRON MANE MAX_AF MAX_AF_POPS MOTIF_NAME MOTIF_POS MOTIF_SCORE_CHANGE One_Consequence PHENO PICK PUBMED PolyPhen RNA_Support RNA_alt_count RNA_depth RNA_ref_count SIFT SOMATIC SWISSPROT SYMBOL SYMBOL_SOURCE TRANSCRIPTION_FACTORS TRANSCRIPT_STRAND TREMBL TSL UNIPARC UNIPROT_ISOFORM VARIANT_CLASS all_effects cDNA_position callers case_id genomic_location_explanation gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF gnomAD_non_cancer_AF gnomAD_non_cancer_AFR_AF gnomAD_non_cancer_AMI_AF gnomAD_non_cancer_AMR_AF gnomAD_non_cancer_ASJ_AF gnomAD_non_cancer_EAS_AF gnomAD_non_cancer_FIN_AF gnomAD_non_cancer_MAX_AF_POPS_adj gnomAD_non_cancer_MAX_AF_adj gnomAD_non_cancer_MID_AF gnomAD_non_cancer_NFE_AF gnomAD_non_cancer_OTH_AF gnomAD_non_cancer_SAS_AF hotspot miRNA n_depth normal_bam_uuid t_depth tumor_bam_uuid Annotation_Status all_effects +LCE3D 84648 BI GRCh38 1 152579792 152579792 + missense_variant Missense_Mutation SNP C C T rs201921868 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 59 32 c.145G>A p.Glu49Lys p.E49K ENST00000368787.4 NM_032563.2 49 Gag/Aag 2/2 P1 T E/K protein_coding YES CCDS1014.1 145/279 GCCCTCGGAGC COSM1256369 Pfam:PF14672;PANTHER:PTHR23263;PANTHER:PTHR23263:SF123;Low_complexity_(Seg):seg ENSP00000357776 2/2 rs201921868;COSV64230604 ENST00000368787 Transcript ENSG00000163202 HGNC:16615 MODERATE NM_032563.2 3.266e-05 gnomAD_SAS missense_variant 0;1 1.0 benign(0.339) Unknown tolerated_low_confidence(0.09) 0;1 Q9BYE3.103 LCE3D HGNC -1 1.0 UPI000006EC48 SNV LCE3D,missense_variant,p.E49K,ENST00000368787,NM_032563.2,c.145G>A,MODERATE,YES,tolerated_low_confidence(0.09),benign(0.339),-1 214/625 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 7.962e-06 0.0 0.0 0.0 0.0 0.0 8.795e-06 0.0 3.266e-05 4.061740037286654e-05 2.4334500267286785e-05 0.0 0.0 0.0 0.0002023470005951 0.0 nfe 6.173789734020829e-05 0.0 6.173789734020829e-05 0.0 0.0 0 65 c9a84256-3c03-426f-be9c-b08f27cbb26d 91 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS LCE3D,missense_variant,p.E49K,ENST00000368787.4,c.145G>A,MODERATE,YES +SELE 6401 BI GRCh38 1 169729197 169729197 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 36 22 c.1079C>A p.Pro360Gln p.P360Q ENST00000333360.12 NM_000450.2 360 cCa/cAa 7/14 P1 T P/Q protein_coding YES CCDS1283.1 1079/1833 AAACTGGGATT Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR19325;PANTHER:PTHR19325:SF493;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000331736 7/14 ENST00000333360 Transcript ENSG00000007908 HGNC:10718 MODERATE NM_000450.2 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) P16581.223 SELE HGNC -1 1.0 UPI000012E44A SNV SELE,missense_variant,p.P360Q,ENST00000333360,NM_000450.2,c.1079C>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;SELE,missense_variant,p.P360Q,ENST00000367776,,c.1079C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;SELE,missense_variant,p.P360Q,ENST00000367777,,c.1079C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;SELE,missense_variant,p.P298Q,ENST00000367775,,c.893C>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;SELE,missense_variant,p.P360Q,ENST00000367774,,c.1079C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;SELE,downstream_gene_variant,,ENST00000609271,,,MODIFIER,,,,-1;C1orf112,intron_variant,,ENST00000498289,,n.851+45265G>T,MODIFIER,,,,1;SELE,downstream_gene_variant,,ENST00000461085,,,MODIFIER,,,,-1 1236/3875 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 50 c9a84256-3c03-426f-be9c-b08f27cbb26d 58 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS SELE,missense_variant,p.P360Q,ENST00000367774.1,c.1079C>A,MODERATE,;SELE,missense_variant,p.P360Q,ENST00000367777.5,c.1079C>A,MODERATE,;SELE,missense_variant,p.P360Q,ENST00000367776.5,c.1079C>A,MODERATE,;SELE,missense_variant,p.P298Q,ENST00000367775.5,c.893C>A,MODERATE,;SELE,missense_variant,p.P360Q,ENST00000333360.12,c.1079C>A,MODERATE,YES;FIRRM,intron_variant,,ENST00000498289.5,n.851+45265G>T,MODIFIER, +EHD3 30845 BI GRCh38 2 31261636 31261636 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 94 121 c.1003C>G p.Leu335Val p.L335V ENST00000322054.10 NM_014600.3 335 Ctg/Gtg 5/6 P1 G L/V protein_coding YES CCDS1774.1 1003/1608 ACAACCTGGCC PANTHER:PTHR11216;PANTHER:PTHR11216:SF127;Gene3D:1.10.268.20;Pfam:PF18150 ENSP00000327116 5/6 ENST00000322054 Transcript ENSG00000013016 HGNC:3244 MODERATE NM_014600.3 missense_variant 1.0 possibly_damaging(0.841) Unknown deleterious(0) Q9NZN3.160 EHD3 HGNC 1 1.0 UPI0000140D07 Q9NZN3-1 SNV EHD3,missense_variant,p.L335V,ENST00000322054,NM_014600.3,c.1003C>G,MODERATE,YES,deleterious(0),possibly_damaging(0.841),1 1473/4825 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 119 c9a84256-3c03-426f-be9c-b08f27cbb26d 215 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS EHD3,missense_variant,p.L335V,ENST00000322054.10,c.1003C>G,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 24 30 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 60 c9a84256-3c03-426f-be9c-b08f27cbb26d 54 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +PAG1 55824 BI GRCh38 8 80976771 80976771 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 104 12 c.1072C>T p.Leu358Phe p.L358F ENST00000220597.4 NM_018440.4 358 Ctc/Ttc 9/9 P1 A L/F protein_coding YES CCDS6227.1 1072/1299 ATAGAGATCAT Pfam:PF15347;PANTHER:PTHR16322;PANTHER:PTHR16322:SF0;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000220597 9/9 ENST00000220597 Transcript ENSG00000076641 HGNC:30043 MODERATE NM_018440.4 missense_variant 1.0 probably_damaging(0.982) Unknown deleterious(0) Q9NWQ8.147 PAG1 HGNC -1 2.0 UPI0000072E56 SNV PAG1,missense_variant,p.L358F,ENST00000220597,NM_018440.4,c.1072C>T,MODERATE,YES,deleterious(0),probably_damaging(0.982),-1;PAG1,upstream_gene_variant,,ENST00000523463,,,MODIFIER,,,,-1 1783/10744 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 59 c9a84256-3c03-426f-be9c-b08f27cbb26d 116 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS PAG1,missense_variant,p.L358F,ENST00000220597.4,c.1072C>T,MODERATE,YES +GLIS3 169792 BI GRCh38 9 4125772 4125772 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 84 69 c.93G>T p.Met31Ile p.M31I ENST00000324333.14 NM_152629.4 31 atG/atT 2/10 A2 A M/I protein_coding CCDS6451.1 93/2328 GCATTCATTGC PANTHER:PTHR45718;PANTHER:PTHR45718:SF1 ENSP00000325494 2/10 ENST00000324333 Transcript 1.0 ENSG00000107249 HGNC:28510 MODERATE missense_variant benign(0.007) Unknown deleterious(0.03) Q8NEA6.149 GLIS3 HGNC -1 A0A0S2Z689.24 1.0 UPI00003675FE Q8NEA6-1 SNV GLIS3,missense_variant,p.M186I,ENST00000381971,NM_001042413.2,c.558G>T,MODERATE,YES,tolerated(0.22),benign(0.015),-1;GLIS3,missense_variant,p.M31I,ENST00000324333,NM_152629.3,c.93G>T,MODERATE,,deleterious(0.03),benign(0.007),-1;GLIS3,missense_variant,p.M186I,ENST00000477901,,c.558G>T,MODERATE,,tolerated(0.21),benign(0.015),-1;GLIS3,missense_variant,p.M186I,ENST00000481827,,c.558G>T,MODERATE,,tolerated(0.21),benign(0.015),-1;GLIS3,missense_variant,p.M31I,ENST00000462164,,c.93G>T,MODERATE,,deleterious(0.03),benign(0.007),-1;GLIS3,missense_variant,p.M31I,ENST00000478315,,c.93G>T,MODERATE,,deleterious(0.03),benign(0.007),-1;GLIS3,missense_variant,p.M31I,ENST00000645097,,c.93G>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.015),-1;GLIS3,missense_variant,p.M31I,ENST00000478844,,c.93G>T,MODERATE,,deleterious(0.03),benign(0.007),-1;GLIS3,intron_variant,,ENST00000473846,,n.356-6891G>T,MODIFIER,,,,-1;GLIS3,intron_variant,,ENST00000490709,,n.417-6891G>T,MODIFIER,,,,-1;GLIS3,intron_variant,,ENST00000645252,,n.152+25168G>T,MODIFIER,,,,-1;GLIS3,intron_variant,,ENST00000491889,,c.389-6891G>T,MODIFIER,,,,-1 287/6667 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 102 c9a84256-3c03-426f-be9c-b08f27cbb26d 153 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS GLIS3,missense_variant,p.M31I,ENST00000645097.1,c.93G>T,MODERATE,;GLIS3,missense_variant,p.M31I,ENST00000683998.1,c.93G>T,MODERATE,;GLIS3,missense_variant,p.M186I,ENST00000481827.5,c.558G>T,MODERATE,;GLIS3,missense_variant,p.M31I,ENST00000462164.5,c.93G>T,MODERATE,;GLIS3,intron_variant,,ENST00000473846.5,n.356-6891G>T,MODIFIER,;GLIS3,missense_variant,p.M186I,ENST00000477901.5,c.558G>T,MODERATE,;GLIS3,missense_variant,p.M31I,ENST00000478315.5,c.93G>T,MODERATE,;GLIS3,missense_variant,p.M31I,ENST00000478844.5,c.93G>T,MODERATE,;GLIS3,intron_variant,,ENST00000490709.1,n.417-6891G>T,MODIFIER,;GLIS3,intron_variant,,ENST00000645252.2,n.152+25168G>T,MODIFIER,;GLIS3,missense_variant,NMD_transcript_variant,p.M31I,ENST00000682846.1,c.93G>T,MODERATE,;GLIS3,missense_variant,p.M31I,ENST00000682749.1,c.93G>T,MODERATE,;GLIS3,intron_variant,NMD_transcript_variant,,ENST00000491889.6,c.389-6891G>T,MODIFIER,;GLIS3,missense_variant,p.M31I,ENST00000324333.14,c.93G>T,MODERATE,;GLIS3,missense_variant,p.M186I,ENST00000381971.8,c.558G>T,MODERATE,YES +GBA2 57704 BI GRCh38 9 35741707 35741707 + missense_variant Missense_Mutation SNP G G A rs762730206 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 74 75 c.751C>T p.Arg251Cys p.R251C ENST00000378103.7 NM_020944.3 251 Cgt/Tgt 4/17 P1 A R/C protein_coding YES CCDS6589.1 751/2784 CTGACGGCAGG PANTHER:PTHR12654:SF0;PANTHER:PTHR12654;PIRSF:PIRSF028944;Pfam:PF12215 ENSP00000367343 4/17 rs762730206;COSV62306157 ENST00000378103 Transcript 1.0 ENSG00000070610 HGNC:18986 MODERATE NM_020944.3 9.923e-05 gnomAD_ASJ missense_variant 0;1 1.0 benign(0.244) Unknown deleterious(0) 0;1 Q9HCG7.143 GBA2 HGNC -1 1.0 UPI0000073FD5 Q9HCG7-1 SNV GBA2,missense_variant,p.R251C,ENST00000378094,NM_001330660.2,c.751C>T,MODERATE,,deleterious(0),probably_damaging(0.963),-1;GBA2,missense_variant,p.R251C,ENST00000378103,NM_020944.3,c.751C>T,MODERATE,YES,deleterious(0),benign(0.244),-1;CREB3,downstream_gene_variant,,ENST00000353704,NM_006368.5,,MODIFIER,YES,,,1;GBA2,upstream_gene_variant,,ENST00000378088,,,MODIFIER,,,,-1;GBA2,non_coding_transcript_exon_variant,,ENST00000467252,,n.323C>T,MODIFIER,,,,-1;GBA2,non_coding_transcript_exon_variant,,ENST00000485259,,n.330C>T,MODIFIER,,,,-1;CREB3,downstream_gene_variant,,ENST00000486056,,,MODIFIER,,,,1;GBA2,upstream_gene_variant,,ENST00000486797,,,MODIFIER,,,,-1;GBA2,upstream_gene_variant,,ENST00000488292,,,MODIFIER,,,,-1;GBA2,downstream_gene_variant,,ENST00000489025,,,MODIFIER,,,,-1 1275/3611 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 7.954e-06 0.0 0.0 9.923e-05 0.0 0.0 8.792e-06 0.0 0.0 6.7616001615533605e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0004960320075042 0.0 0 110 c9a84256-3c03-426f-be9c-b08f27cbb26d 149 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS GBA2,non_coding_transcript_exon_variant,,ENST00000485259.1,n.330C>T,MODIFIER,;GBA2,non_coding_transcript_exon_variant,,ENST00000467252.5,n.323C>T,MODIFIER,;GBA2,missense_variant,p.R251C,ENST00000378094.4,c.751C>T,MODERATE,;GBA2,missense_variant,p.R251C,ENST00000378103.7,c.751C>T,MODERATE,YES +INPP5E 56623 BI GRCh38 9 136438740 136438740 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 9 8 c.680T>G p.Leu227Arg p.L227R ENST00000371712.4 NM_001318502.2 227 cTg/cGg 1/10 P1 C L/R protein_coding YES CCDS7000.1 680/1935 GCACCAGGAGC PANTHER:PTHR46625 ENSP00000360777 1/10 ENST00000371712 Transcript 1.0 ENSG00000148384 HGNC:21474 MODERATE NM_019892.6 missense_variant 1.0 benign(0.06) Unknown tolerated(0.06) Q9NRR6.156 INPP5E HGNC -1 1.0 UPI000014053C Q9NRR6-1 SNV INPP5E,missense_variant,p.L227R,ENST00000371712,NM_001318502.2&NM_019892.6,c.680T>G,MODERATE,YES,tolerated(0.06),benign(0.06),-1;INPP5E,missense_variant,p.L227R,ENST00000676019,,c.680T>G,MODERATE,,deleterious(0.03),possibly_damaging(0.458),-1;SEC16A,downstream_gene_variant,,ENST00000277537,,,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000290037,NM_001276418.1,,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000313050,NM_014866.2,,MODIFIER,YES,,,-1;SEC16A,downstream_gene_variant,,ENST00000313084,,,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000371706,,,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000431893,,,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000453963,,,MODIFIER,,,,-1;INPP5E,upstream_gene_variant,,ENST00000675256,,,MODIFIER,,,,-1;INPP5E,non_coding_transcript_exon_variant,,ENST00000635815,,n.1084T>G,MODIFIER,,,,-1;SEC16A,downstream_gene_variant,,ENST00000467838,,,MODIFIER,,,,-1;INPP5E,upstream_gene_variant,,ENST00000674513,,,MODIFIER,,,,-1 1106/3417 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 22 c9a84256-3c03-426f-be9c-b08f27cbb26d 17 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS INPP5E,non_coding_transcript_exon_variant,,ENST00000635815.1,n.1084T>G,MODIFIER,;INPP5E,missense_variant,p.L227R,ENST00000371712.4,c.680T>G,MODERATE,YES;INPP5E,missense_variant,p.L227R,ENST00000676019.1,c.680T>G,MODERATE, +OR5L2 26338 BI GRCh38 11 55827450 55827450 + missense_variant Missense_Mutation SNP G G T rs1489088383 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 172 40 c.232G>T p.Val78Leu p.V78L ENST00000378397.1 NM_001004739.1 78 Gtg/Ttg 1/1 P1 T V/L protein_coding YES CCDS31511.1 232/936 TAATTGTGCCA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR26452;PANTHER:PTHR26452:SF438;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15410 ENSP00000367650 1/1 rs1489088383 ENST00000378397 Transcript ENSG00000205030 HGNC:8351 MODERATE NM_001004739.1 4.621e-05 gnomAD_FIN missense_variant 1.0 benign(0.023) Unknown tolerated(0.07) Q8NGL0.134 OR5L2 HGNC 1 UPI0000041C49 SNV OR5L2,missense_variant,p.V78L,ENST00000378397,NM_001004739.1,c.232G>T,MODERATE,YES,tolerated(0.07),benign(0.023),1 232/936 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 3.98e-06 0.0 0.0 0.0 0.0 4.621e-05 0.0 0.0 0.0 0 174 c9a84256-3c03-426f-be9c-b08f27cbb26d 212 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS OR5L2,missense_variant,p.V78L,ENST00000378397.1,c.232G>T,MODERATE,YES +SIK3 23387 BI GRCh38 11 116858663 116858663 + missense_variant Missense_Mutation SNP G G T rs746419435 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 47 40 c.2802C>A p.Asp934Glu p.D934E ENST00000445177.6 NM_001366686.3 934 gaC/gaA 21/25 T D/E protein_coding YES 2784/4092 GCCTGGTCGTA PANTHER:PTHR24346;PANTHER:PTHR24346:SF42 ENSP00000391295 21/25 rs746419435 cds_start_NF ENST00000445177 Transcript 1.0 ENSG00000160584 HGNC:29165 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.041) Unknown tolerated_low_confidence(0.3) SIK3 HGNC -1 H0Y4E8.63 5.0 UPI000066D910 SNV SIK3,missense_variant,p.D928E,ENST00000445177,NM_001366686.2,c.2784C>A,MODERATE,YES,tolerated_low_confidence(0.3),benign(0.041),-1;SIK3,missense_variant,p.D886E,ENST00000375300,NM_025164.6&NM_001281748.3,c.2658C>A,MODERATE,,tolerated_low_confidence(0.3),benign(0.169),-1;SIK3,intron_variant,,ENST00000446921,NM_001281749.3,c.2622-144C>A,MODIFIER,,,,-1;SIK3,intron_variant,,ENST00000488337,,n.815-144C>A,MODIFIER,,,,-1;SIK3,non_coding_transcript_exon_variant,,ENST00000480468,,n.488C>A,MODIFIER,,,,-1;SIK3,intron_variant,,ENST00000415541,,c.*2146-144C>A,MODIFIER,,,,-1;SIK3,intron_variant,,ENST00000465421,,n.2064-144C>A,MODIFIER,,,,-1;APOA1-AS,downstream_gene_variant,,ENST00000444200,,,MODIFIER,,,,1;APOA1-AS,downstream_gene_variant,,ENST00000669664,,,MODIFIER,YES,,,1 2782/6331 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 61 c9a84256-3c03-426f-be9c-b08f27cbb26d 87 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS SIK3,non_coding_transcript_exon_variant,,ENST00000480468.1,n.488C>A,MODIFIER,;SIK3,intron_variant,,ENST00000446921.6,c.2622-144C>A,MODIFIER,;SIK3,intron_variant,NMD_transcript_variant,,ENST00000415541.5,c.*2146-144C>A,MODIFIER,;SIK3,intron_variant,,ENST00000465421.5,n.2064-144C>A,MODIFIER,;SIK3,missense_variant,p.D886E,ENST00000375300.6,c.2658C>A,MODERATE,;SIK3,intron_variant,,ENST00000488337.5,n.815-144C>A,MODIFIER,;SIK3,missense_variant,p.D934E,ENST00000445177.6,c.2802C>A,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8KA-01B TCGA-VD-A8KA-10A Somatic 41 29 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 af04ca52-8b71-497e-8135-6ddfca9ab221 0 74 c9a84256-3c03-426f-be9c-b08f27cbb26d 70 896a48cf-49ed-418e-970b-8d77abbe7238 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +BAP1 8314 BI GRCh38 3 52406367 52406367 + stop_gained Nonsense_Mutation SNP G G C TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 1 36 c.669C>G p.Tyr223Ter p.Y223* ENST00000460680.6 NM_004656.4 223 taC/taG 9/17 P1 C Y/* protein_coding YES CCDS2853.1 669/2190 TCGTGGTAGGG CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Superfamily:SSF54001 ENSP00000417132 9/17 COSV56240406 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 stop_gained 1 1.0 Unknown 1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,stop_gained,p.Y223*,ENST00000460680,NM_004656.4,c.669C>G,HIGH,YES,,,-1;BAP1,intron_variant,,ENST00000296288,,c.660-45C>G,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,non_coding_transcript_exon_variant,,ENST00000471532,,n.836C>G,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 799/3600 muse;mutect2;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 0 34 b899781d-8ea5-4b33-8cc6-5905ed911c5a 37 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000471532.5,n.836C>G,MODIFIER,;BAP1,intron_variant,,ENST00000296288.9,c.660-45C>G,MODIFIER,;BAP1,stop_gained,p.Y223*,ENST00000460680.6,c.669C>G,HIGH,YES +BMP1 649 BI GRCh38 8 22201895 22201895 + missense_variant Missense_Mutation SNP G G A rs148552467 TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 14 15 c.2200G>A p.Val734Ile p.V734I ENST00000306385.10 NM_006129.5 734 Gtc/Atc 16/20 P1 A V/I protein_coding YES CCDS6026.1 2200/2961 GCTTCGTCCTC Gene3D:2.10.25.10;Pfam:PF07645;PIRSF:PIRSF001199;PROSITE_patterns:PS01186;PROSITE_profiles:PS50026;PANTHER:PTHR45645;PANTHER:PTHR45645:SF24;SMART:SM00179;SMART:SM00181;Superfamily:SSF57184 ENSP00000305714 0.000227 0.0 16/20 rs148552467 ENST00000306385 Transcript 1.0 ENSG00000168487 HGNC:1067 MODERATE NM_006129.5 0.000227 AA missense_variant 1.0 benign(0.056) Unknown tolerated(0.17) P13497.222 BMP1 HGNC 1 1.0 UPI0000049818 P13497-1 SNV BMP1,missense_variant,p.V734I,ENST00000306385,NM_006129.5,c.2200G>A,MODERATE,YES,tolerated(0.17),benign(0.056),1;BMP1,3_prime_UTR_variant,,ENST00000354870,,c.*1457G>A,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000306349,NM_001199.4,,MODIFIER,,,,1;BMP1,3_prime_UTR_variant,,ENST00000520626,,c.*2732G>A,MODIFIER,,,,1;BMP1,3_prime_UTR_variant,,ENST00000520970,,c.*692G>A,MODIFIER,,,,1;BMP1,3_prime_UTR_variant,,ENST00000520982,,c.*1667G>A,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000471755,,,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000483364,,,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000518913,,,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000521385,,,MODIFIER,,,,1;BMP1,downstream_gene_variant,,ENST00000522332,,,MODIFIER,,,,1 2234/3593 muse;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 3.205e-05 6.227e-05 5.803e-05 0.0 0.0 0.0 4.44e-05 0.0 0.0 4.73120016977191e-05 4.861920024268329e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.171700078994036e-05 0.0 6.171700078994036e-05 0.0004950499860569 0.0 0 17 b899781d-8ea5-4b33-8cc6-5905ed911c5a 29 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS BMP1,missense_variant,p.V734I,ENST00000306385.10,c.2200G>A,MODERATE,YES;BMP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000520982.5,c.*1667G>A,MODIFIER,;BMP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000520626.6,c.*2732G>A,MODIFIER,;BMP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000520970.5,c.*692G>A,MODIFIER,;BMP1,3_prime_UTR_variant,,ENST00000354870.5,c.*1457G>A,MODIFIER, +MYOF 26509 BI GRCh38 10 93408846 93408846 + missense_variant Missense_Mutation SNP C C T rs762578223 TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 43 45 c.670G>A p.Val224Ile p.V224I ENST00000359263.9 NM_013451.4 224 Gtc/Atc 7/54 P4 T V/I protein_coding YES CCDS41551.1 670/6186 ACAGACGTGAA COSM1969981;COSM4182647;COSM4182648 Gene3D:2.60.40.150;Pfam:PF00168;PROSITE_profiles:PS50004;PANTHER:PTHR12546;PANTHER:PTHR12546:SF55;SMART:SM00239;Superfamily:SSF49562;CDD:cd04011 ENSP00000352208 7/54 rs762578223;COSV63700907 ENST00000359263 Transcript ENSG00000138119 HGNC:3656 MODERATE NM_013451.4 0.0001961 gnomAD_SAS missense_variant 0;1 1.0 benign(0.013) Unknown tolerated(0.31) 0;1 Q9NZM1.183 MYOF HGNC -1 1.0 UPI000012FBA1 Q9NZM1-1 SNV MYOF,missense_variant,p.V224I,ENST00000359263,NM_013451.4,c.670G>A,MODERATE,YES,tolerated(0.31),benign(0.013),-1;MYOF,missense_variant,p.V224I,ENST00000358334,NM_133337.3,c.670G>A,MODERATE,,tolerated(0.29),benign(0.015),-1;MYOF,missense_variant,p.V224I,ENST00000371489,,c.670G>A,MODERATE,,tolerated(0.19),benign(0.013),-1 810/6860 muse;mutect2;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 2.404e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0001961 0 66 b899781d-8ea5-4b33-8cc6-5905ed911c5a 88 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS MYOF,missense_variant,p.V224I,ENST00000371489.5,c.670G>A,MODERATE,;MYOF,missense_variant,p.V224I,ENST00000358334.9,c.670G>A,MODERATE,;MYOF,missense_variant,p.V224I,ENST00000359263.9,c.670G>A,MODERATE,YES +DCPS 28960 BI GRCh38 11 126306707 126306707 + stop_gained Nonsense_Mutation DEL C C - novel TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 32 16 c.339del p.Tyr113Ter p.Y113* ENST00000263579.5 NM_001350236.2 113 taC/ta 2/6 P1 - Y/X protein_coding YES CCDS8473.1 339/1014 TATCTACAGCAC PDB-ENSP_mappings:1st0.A;PDB-ENSP_mappings:1st0.B;PDB-ENSP_mappings:1st4.A;PDB-ENSP_mappings:1st4.B;PDB-ENSP_mappings:1xml.A;PDB-ENSP_mappings:1xml.B;PDB-ENSP_mappings:1xmm.A;PDB-ENSP_mappings:1xmm.B;PDB-ENSP_mappings:1xmm.C;PDB-ENSP_mappings:1xmm.D;Gene3D:3.30.200.40;PDB-ENSP_mappings:3bl7.A;PDB-ENSP_mappings:3bl7.B;PDB-ENSP_mappings:3bl9.A;PDB-ENSP_mappings:3bl9.B;PDB-ENSP_mappings:3bla.A;PDB-ENSP_mappings:3bla.B;PDB-ENSP_mappings:4qde.A;PDB-ENSP_mappings:4qde.B;PDB-ENSP_mappings:4qde.C;PDB-ENSP_mappings:4qde.D;PDB-ENSP_mappings:4qdv.A;PDB-ENSP_mappings:4qdv.B;PDB-ENSP_mappings:4qdv.C;PDB-ENSP_mappings:4qdv.D;PDB-ENSP_mappings:4qeb.A;PDB-ENSP_mappings:4qeb.B;PDB-ENSP_mappings:4qeb.C;PDB-ENSP_mappings:4qeb.D;PDB-ENSP_mappings:5osy.A;PDB-ENSP_mappings:5osy.B;Pfam:PF05652;PIRSF:PIRSF028973;PANTHER:PTHR12978;Superfamily:SSF102860 ENSP00000263579 2/6 ENST00000263579 Transcript 1.0 ENSG00000110063 HGNC:29812 HIGH NM_014026.6 frameshift_variant 1.0 Unknown Q96C86.165 DCPS HGNC 1 A0A384MTI8.11 1.0 UPI000006F1CC deletion DCPS,frameshift_variant,p.Y113*,ENST00000263579,NM_001350236.2&NM_014026.6,c.339del,HIGH,YES,,,1;AP001318.2,upstream_gene_variant,,ENST00000524964,,,MODIFIER,,,,-1 360/5427 mutect2;pindel;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 0 35 b899781d-8ea5-4b33-8cc6-5905ed911c5a 48 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS DCPS,stop_gained,p.Y113*,ENST00000263579.5,c.339del,HIGH,YES +C12orf71 728858 BI GRCh38 12 27081268 27081268 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 44 31 c.716A>G p.Lys239Arg p.K239R ENST00000429849.3 NM_001384983.1 239 aAa/aGa 2/2 P1 C K/R protein_coding YES CCDS44851.1 716/810 GACTTTTGGTG Pfam:PF15480;PANTHER:PTHR36462 ENSP00000413728 2/2 ENST00000429849 Transcript ENSG00000214700 HGNC:34452 MODERATE missense_variant 1.0 benign(0.098) Unknown tolerated(0.24) A8MTZ7.71 C12orf71 HGNC -1 2.0 UPI00001D79FA SNV C12orf71,missense_variant,p.K239R,ENST00000429849,NM_001080406.1,c.716A>G,MODERATE,YES,tolerated(0.24),benign(0.098),-1 747/957 muse;mutect2;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 2.027469963650219e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085749995079823e-05 0.0 3.085749995079823e-05 0.0004945599939674 0.0 0 51 b899781d-8ea5-4b33-8cc6-5905ed911c5a 76 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS C12orf71,missense_variant,p.K239R,ENST00000429849.3,c.716A>G,MODERATE,YES +C12orf50 160419 BI GRCh38 12 87998090 87998090 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 24 14 c.234T>A p.His78Gln p.H78Q ENST00000298699.7 NM_152589.3 78 caT/caA 4/13 P1 T H/Q protein_coding YES CCDS9031.1 234/1245 AAAGGATGGTG Pfam:PF17732;PANTHER:PTHR15725;PANTHER:PTHR15725:SF1 ENSP00000298699 4/13 ENST00000298699 Transcript ENSG00000165805 HGNC:26665 MODERATE NM_152589.3 missense_variant 1.0 benign(0.277) Unknown tolerated(0.12) Q8NA57.114 C12orf50 HGNC -1 2.0 UPI0000071382 SNV C12orf50,missense_variant,p.H78Q,ENST00000298699,NM_152589.3,c.234T>A,MODERATE,YES,tolerated(0.12),benign(0.277),-1;C12orf50,missense_variant,p.H78Q,ENST00000550553,NM_001363616.2,c.234T>A,MODERATE,,tolerated(0.06),benign(0.189),-1;C12orf50,missense_variant,p.H78Q,ENST00000551163,,c.234T>A,MODERATE,,deleterious(0.02),benign(0.277),-1;C12orf50,non_coding_transcript_exon_variant,,ENST00000551944,,n.645T>A,MODIFIER,,,,-1 404/1711 muse;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 0 43 b899781d-8ea5-4b33-8cc6-5905ed911c5a 38 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS C12orf50,missense_variant,p.H78Q,ENST00000551163.2,c.234T>A,MODERATE,;C12orf50,non_coding_transcript_exon_variant,,ENST00000551944.1,n.645T>A,MODIFIER,;C12orf50,missense_variant,p.H78Q,ENST00000550553.5,c.234T>A,MODERATE,;C12orf50,missense_variant,p.H78Q,ENST00000298699.7,c.234T>A,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EF-01A TCGA-V4-A9EF-10A Somatic 28 29 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 a18d3ba3-e2f4-4144-9c25-2019cad193f4 0 54 b899781d-8ea5-4b33-8cc6-5905ed911c5a 58 852590cd-efe3-4dff-b358-7ea9a7e66f85 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +PYCR2 29920 BI GRCh38 1 225921259 225921259 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 25 25 c.746G>A p.Gly249Asp p.G249D ENST00000343818.11 NM_013328.4 249 gGc/gAc 6/7 P1 T G/D protein_coding YES CCDS31043.1 746/963 GGAAGCCCCCA Gene3D:1.10.3730.10;HAMAP:MF_01925;Pfam:PF14748;PIRSF:PIRSF000193;PANTHER:PTHR11645;PANTHER:PTHR11645:SF4;Superfamily:SSF48179;TIGRFAM:TIGR00112 ENSP00000342502 6/7 ENST00000343818 Transcript 1.0 ENSG00000143811 HGNC:30262 MODERATE NM_013328.4 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q96C36.162 PYCR2 HGNC -1 A0A0S2Z5U6.30 1.0 UPI000006F2BB SNV PYCR2,missense_variant,p.G249D,ENST00000343818,NM_013328.4,c.746G>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;AL117348.2,missense_variant,p.G175D,ENST00000432920,,c.524G>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.993),-1;PYCR2,missense_variant,p.G175D,ENST00000612039,NM_001271681.1,c.524G>A,MODERATE,,deleterious(0.01),probably_damaging(0.978),-1;PYCR2,missense_variant,p.G248D,ENST00000612651,,c.743G>A,MODERATE,,deleterious(0.01),probably_damaging(1),-1;PYCR2,downstream_gene_variant,,ENST00000472798,,,MODIFIER,,,,-1;PYCR2,downstream_gene_variant,,ENST00000489681,,,MODIFIER,,,,-1;MIR6741,downstream_gene_variant,,ENST00000618782,,,MODIFIER,YES,,,-1;PYCR2,non_coding_transcript_exon_variant,,ENST00000478402,,n.2355G>A,MODIFIER,,,,-1;PYCR2,non_coding_transcript_exon_variant,,ENST00000446534,,n.1304G>A,MODIFIER,,,,-1;PYCR2,non_coding_transcript_exon_variant,,ENST00000466127,,n.463G>A,MODIFIER,,,,-1;PYCR2,downstream_gene_variant,,ENST00000467298,,,MODIFIER,,,,-1 886/1680 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 44 f387bb51-516b-46bc-900b-e5b26cb80086 50 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS PYCR2,non_coding_transcript_exon_variant,,ENST00000446534.1,n.1304G>A,MODIFIER,;PYCR2,non_coding_transcript_exon_variant,,ENST00000466127.1,n.463G>A,MODIFIER,;PYCR2,non_coding_transcript_exon_variant,,ENST00000478402.5,n.2355G>A,MODIFIER,;PYCR2,missense_variant,p.G249D,ENST00000343818.11,c.746G>A,MODERATE,YES;PYCR2,missense_variant,p.G175D,ENST00000612039.4,c.524G>A,MODERATE,;ENSG00000255835,missense_variant,p.G175D,ENST00000432920.2,c.524G>A,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 42 31 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 65 f387bb51-516b-46bc-900b-e5b26cb80086 74 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +DCAF1 9730 BI GRCh38 3 51429369 51429369 + synonymous_variant Silent SNP G G C novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 32 36 c.1569C>G p.Ala523= p.A523= ENST00000423656.5 NM_014703.3 523 gcC/gcG 11/25 A1 C A protein_coding YES CCDS74943.1 1569/4524 CGCAAGGCCAT PANTHER:PTHR13129;Superfamily:SSF48371 ENSP00000393183 11/25 ENST00000423656 Transcript ENSG00000145041 HGNC:30911 LOW synonymous_variant 1.0 Unknown Q9Y4B6.165 DCAF1 HGNC -1 5.0 UPI00000716AC Q9Y4B6-1 SNV DCAF1,synonymous_variant,p.A522=,ENST00000504652,NM_001171904.1&NM_001349171.2,c.1566C>G,LOW,,,,-1;DCAF1,synonymous_variant,p.A523=,ENST00000423656,NM_014703.3&NM_001349170.2&NM_001349168.2&NM_001349169.2,c.1569C>G,LOW,YES,,,-1;DCAF1,intron_variant,,ENST00000335891,,c.673-8419C>G,MODIFIER,,,,-1 1699/5946 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 70 f387bb51-516b-46bc-900b-e5b26cb80086 68 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS DCAF1,synonymous_variant,p.A523=,ENST00000684031.1,c.1569C>G,LOW,YES;DCAF1,synonymous_variant,p.A522=,ENST00000504652.5,c.1566C>G,LOW,;DCAF1,synonymous_variant,p.A523=,ENST00000423656.5,c.1569C>G,LOW, +TMEM39A 55254 BI GRCh38 3 119438101 119438101 + missense_variant,splice_region_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 18 15 c.578T>A p.Phe193Tyr p.F193Y ENST00000319172.10 NM_018266.3 193 tTt/tAt 6/9 P1 T F/Y protein_coding YES CCDS2987.1 578/1467 CACCAAACCTG Transmembrane_helices:TMhelix;PANTHER:PTHR12995:SF3;PANTHER:PTHR12995;Pfam:PF10271 ENSP00000326063 6/9 ENST00000319172 Transcript ENSG00000176142 HGNC:25600 MODERATE NM_018266.3 missense_variant 1.0 probably_damaging(0.973) Unknown deleterious(0.01) Q9NV64.125 TMEM39A HGNC -1 1.0 UPI00000715E5 Q9NV64-1 SNV TMEM39A,missense_variant,p.F193Y,ENST00000319172,NM_018266.3,c.578T>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.973),-1;TMEM39A,missense_variant,p.F39Y,ENST00000491685,,c.116T>A,MODERATE,,deleterious(0),probably_damaging(0.973),-1;TMEM39A,splice_region_variant,,ENST00000486159,,n.659T>A,LOW,,,,-1;TMEM39A,splice_region_variant,,ENST00000438581,,c.*246T>A,LOW,,,,-1;TMEM39A,upstream_gene_variant,,ENST00000468545,,,MODIFIER,,,,-1;TMEM39A,upstream_gene_variant,,ENST00000473684,,,MODIFIER,,,,-1 932/4853 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 32 f387bb51-516b-46bc-900b-e5b26cb80086 33 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS TMEM39A,non_coding_transcript_exon_variant,,ENST00000486159.5,n.659T>A,MODIFIER,;TMEM39A,missense_variant,splice_region_variant,p.F39Y,ENST00000491685.5,c.116T>A,MODERATE,;TMEM39A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000438581.6,c.*246T>A,MODIFIER,;TMEM39A,missense_variant,splice_region_variant,p.F193Y,ENST00000319172.10,c.578T>A,MODERATE,YES +PPID 5481 BI GRCh38 4 158717162 158717162 + synonymous_variant Silent SNP G G A rs747950446 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 57 29 c.372C>T p.Gly124= p.G124= ENST00000307720.4 NM_005038.3 124 ggC/ggT 4/10 P1 A G protein_coding YES CCDS3801.1 372/1113 TTGCGGCCTGC CDD:cd01926;Pfam:PF00160;Gene3D:2.40.100.10;Superfamily:SSF50891;PROSITE_profiles:PS50072;PANTHER:PTHR11071:SF442;PANTHER:PTHR11071;Prints:PR00153 ENSP00000303754 4/10 rs747950446 ENST00000307720 Transcript ENSG00000171497 HGNC:9257 LOW NM_005038.3 5.438e-05 gnomAD_EAS synonymous_variant 1.0 Unknown Q08752.193 PPID HGNC -1 E5KN55.86 1.0 UPI0000128C6B SNV PPID,synonymous_variant,p.G124=,ENST00000307720,NM_005038.3,c.372C>T,LOW,YES,,,-1;PPID,upstream_gene_variant,,ENST00000512699,,,MODIFIER,,,,-1 480/1830 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 3.979e-06 0.0 0.0 0.0 5.438e-05 0.0 0.0 0.0 0.0 0 57 f387bb51-516b-46bc-900b-e5b26cb80086 86 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS PPID,synonymous_variant,p.G124=,ENST00000307720.4,c.372C>T,LOW,YES +TNS3 64759 BI GRCh38 7 47400814 47400814 + missense_variant Missense_Mutation SNP C C G rs1584571629 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 43 13 c.824G>C p.Gly275Ala p.G275A ENST00000311160.14 NM_022748.12 275 gGg/gCg 14/31 P1 G G/A protein_coding YES CCDS5506.2 824/4338 CCTTCCCAAAC PROSITE_profiles:PS51182;PANTHER:PTHR45734;PANTHER:PTHR45734:SF5;Pfam:PF10409;Gene3D:2.60.40.1110;SMART:SM01326;Superfamily:SSF49562 ENSP00000312143 14/31 ENST00000311160 Transcript ENSG00000136205 HGNC:21616 MODERATE NM_022748.12 missense_variant 1.0 benign(0.015) Unknown tolerated(0.08) Q68CZ2.141 TNS3 HGNC -1 1.0 UPI00001AE9DA Q68CZ2-1 SNV TNS3,missense_variant,p.G275A,ENST00000311160,NM_022748.12,c.824G>C,MODERATE,YES,tolerated(0.08),benign(0.015),-1;TNS3,missense_variant,p.G378A,ENST00000457718,,c.1133G>C,MODERATE,,tolerated(0.08),benign(0.012),-1;TNS3,missense_variant,p.G364A,ENST00000450444,,c.1091G>C,MODERATE,,tolerated(0.08),benign(0.015),-1;TNS3,downstream_gene_variant,,ENST00000442536,,,MODIFIER,,,,-1;TNS3,downstream_gene_variant,,ENST00000458317,,,MODIFIER,,,,-1;TNS3,non_coding_transcript_exon_variant,,ENST00000469470,,n.259G>C,MODIFIER,,,,-1;TNS3,upstream_gene_variant,,ENST00000485555,,,MODIFIER,,,,-1 1149/7585 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 48 f387bb51-516b-46bc-900b-e5b26cb80086 56 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS TNS3,non_coding_transcript_exon_variant,,ENST00000469470.1,n.259G>C,MODIFIER,;TNS3,missense_variant,p.G389A,ENST00000705350.1,c.1166G>C,MODERATE,;TNS3,missense_variant,p.G275A,ENST00000311160.14,c.824G>C,MODERATE,YES;TNS3,missense_variant,p.G378A,ENST00000457718.6,c.1133G>C,MODERATE,;TNS3,missense_variant,p.G364A,ENST00000450444.6,c.1091G>C,MODERATE, +ZNF479 90827 BI GRCh38 7 57120662 57120662 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 20 17 c.753C>T p.Ser251= p.S251= ENST00000319636.10 NM_001370129.2 251 agC/agT 4/4 P1 A S protein_coding CCDS43590.1 753/1575 GACCAGCTAAA Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF295;SMART:SM00355;Superfamily:SSF57667 ENSP00000324518 4/4 ENST00000319636 Transcript 1.0 ENSG00000185177 HGNC:23258 LOW synonymous_variant Unknown Q96JC4.154 ZNF479 HGNC -1 1.0 UPI000006E615 SNV ZNF479,synonymous_variant,p.S251=,ENST00000331162,NM_033273.2,c.753C>T,LOW,YES,,,-1;ZNF479,synonymous_variant,p.S251=,ENST00000319636,NM_001370129.1,c.753C>T,LOW,,,,-1 770/1811 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 54 f387bb51-516b-46bc-900b-e5b26cb80086 37 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS ZNF479,synonymous_variant,p.S251=,ENST00000331162.8,c.753C>T,LOW,;ZNF479,synonymous_variant,p.S251=,ENST00000319636.10,c.753C>T,LOW,YES +COL14A1 7373 BI GRCh38 8 120203780 120203780 + missense_variant Missense_Mutation SNP G G A rs1238741811 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 50 13 c.949G>A p.Val317Ile p.V317I ENST00000297848.8 NM_021110.4 317 Gtt/Att 9/48 P4 A V/I protein_coding YES CCDS34938.1 949/5391 ACAATGTTGCC Gene3D:3.40.50.410;Pfam:PF00092;PROSITE_profiles:PS50234;PANTHER:PTHR24020;PANTHER:PTHR24020:SF15;SMART:SM00327;Superfamily:SSF49265;Superfamily:SSF53300;CDD:cd01482 ENSP00000297848 9/48 rs1238741811 ENST00000297848 Transcript 1.0 ENSG00000187955 HGNC:2191 MODERATE NM_021110.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.354) Unknown deleterious(0) Q05707.166 COL14A1 HGNC 1 5.0 UPI000046D377 Q05707-1 SNV COL14A1,missense_variant,p.V317I,ENST00000297848,NM_021110.4,c.949G>A,MODERATE,YES,deleterious(0),benign(0.354),1;COL14A1,missense_variant,p.V317I,ENST00000309791,,c.949G>A,MODERATE,,deleterious(0),probably_damaging(0.948),1;COL14A1,missense_variant,p.V317I,ENST00000537875,,c.949G>A,MODERATE,,deleterious(0),probably_damaging(0.986),1;COL14A1,missense_variant,p.V130I,ENST00000434620,,c.388G>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;COL14A1,missense_variant,p.V74I,ENST00000523142,,c.220G>A,MODERATE,,deleterious(0),probably_damaging(0.985),1;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,,n.1183G>A,MODIFIER,,,,1;COL14A1,missense_variant,p.V317I,ENST00000498051,,c.949G>A,MODERATE,,deleterious(0),probably_damaging(0.986),1 1225/8009 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 26 f387bb51-516b-46bc-900b-e5b26cb80086 63 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS COL14A1,missense_variant,p.V130I,ENST00000434620.5,c.388G>A,MODERATE,;COL14A1,missense_variant,p.C73Y,ENST00000523142.5,c.218G>A,MODERATE,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943.6,n.1183G>A,MODIFIER,;COL14A1,missense_variant,p.V317I,ENST00000309791.8,c.949G>A,MODERATE,;COL14A1,missense_variant,p.V317I,ENST00000297848.8,c.949G>A,MODERATE,YES;COL14A1,missense_variant,p.V317I,ENST00000537875.2,c.949G>A,MODERATE,;COL14A1,missense_variant,NMD_transcript_variant,p.V317I,ENST00000498051.6,c.949G>A,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 37 50 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 78 f387bb51-516b-46bc-900b-e5b26cb80086 87 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +PALM2AKAP2 445815 BI GRCh38 9 110137341 110137341 + synonymous_variant Silent SNP G G T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 52 27 c.1104G>T p.Leu368= p.L368= ENST00000259318.7 NM_001136562.3 368 ctG/ctT 2/4 T L protein_coding CCDS48003.1 1104/2580 CCACTGACTAA PANTHER:PTHR10498;PANTHER:PTHR10498:SF10;MobiDB_lite:mobidb-lite ENSP00000259318 2/4 ENST00000259318 Transcript ENSG00000157654 HGNC:33529 LOW synonymous_variant Unknown Q9Y2D5.167 PALM2AKAP2 HGNC 1 2.0 UPI0000EADF0B SNV PALM2AKAP2,synonymous_variant,p.L599=,ENST00000374530,NM_007203.5,c.1797G>T,LOW,YES,,,1;PALM2AKAP2,synonymous_variant,p.L457=,ENST00000374525,NM_001004065.4,c.1371G>T,LOW,,,,1;PALM2AKAP2,synonymous_variant,p.L599=,ENST00000302798,NM_147150.3,c.1797G>T,LOW,,,,1;PALM2AKAP2,synonymous_variant,p.L457=,ENST00000434623,NM_001198656.1,c.1371G>T,LOW,,,,1;PALM2AKAP2,synonymous_variant,p.L368=,ENST00000259318,NM_001136562.3,c.1104G>T,LOW,,,,1;PALM2AKAP2,synonymous_variant,p.L417=,ENST00000480388,,c.1251G>T,LOW,,,,1;PALM2AKAP2,downstream_gene_variant,,ENST00000413420,,,MODIFIER,,,,1;PALM2AKAP2,downstream_gene_variant,,ENST00000471798,,,MODIFIER,,,,1;PALM2AKAP2,upstream_gene_variant,,ENST00000482335,,,MODIFIER,,,,1;PALM2AKAP2,intron_variant,,ENST00000495980,,c.157-18978G>T,MODIFIER,,,,1 1311/3101 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 66 f387bb51-516b-46bc-900b-e5b26cb80086 79 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS PALM2AKAP2,synonymous_variant,p.L368=,ENST00000259318.7,c.1104G>T,LOW,;PALM2AKAP2,synonymous_variant,p.L417=,ENST00000480388.1,c.1251G>T,LOW,;PALM2AKAP2,intron_variant,NMD_transcript_variant,,ENST00000495980.1,c.157-18978G>T,MODIFIER,;PALM2AKAP2,synonymous_variant,p.L457=,ENST00000374525.5,c.1371G>T,LOW,;PALM2AKAP2,synonymous_variant,p.L457=,ENST00000434623.6,c.1371G>T,LOW,;PALM2AKAP2,synonymous_variant,p.L599=,ENST00000302798.7,c.1797G>T,LOW,;PALM2AKAP2,synonymous_variant,p.L599=,ENST00000374530.8,c.1797G>T,LOW,YES +MYOF 26509 BI GRCh38 10 93431453 93431453 + synonymous_variant Silent SNP C C T rs756928666 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 35 31 c.300G>A p.Pro100= p.P100= ENST00000359263.9 NM_013451.4 100 ccG/ccA 4/54 P4 T P protein_coding YES CCDS41551.1 300/6186 TTGTACGGCAG COSM428152;COSM4816188;COSM4816189;COSM4816190 Gene3D:2.60.40.150;PDB-ENSP_mappings:2dmh.A;PDB-ENSP_mappings:6eel.A;PDB-ENSP_mappings:6eel.B;PDB-ENSP_mappings:6eel.C;Pfam:PF00168;PANTHER:PTHR12546;PANTHER:PTHR12546:SF55;SMART:SM00239;Superfamily:SSF49562;CDD:cd08373 ENSP00000352208 4/54 rs756928666;COSV63700233 ENST00000359263 Transcript ENSG00000138119 HGNC:3656 LOW NM_013451.4 0.0001669 gnomAD_EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q9NZM1.183 MYOF HGNC -1 1.0 UPI000012FBA1 Q9NZM1-1 SNV MYOF,synonymous_variant,p.P100=,ENST00000359263,NM_013451.4,c.300G>A,LOW,YES,,,-1;MYOF,synonymous_variant,p.P100=,ENST00000358334,NM_133337.3,c.300G>A,LOW,,,,-1;MYOF,synonymous_variant,p.P100=,ENST00000371489,,c.300G>A,LOW,,,,-1;MYOF,synonymous_variant,p.P100=,ENST00000371488,,c.300G>A,LOW,,,,-1;MYOF,non_coding_transcript_exon_variant,,ENST00000488645,,n.494G>A,MODIFIER,,,,-1 440/6860 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 2.805e-05 0.0 5.794e-05 0.0 0.0001669 0.0 8.828e-06 0.0 3.268e-05 4.733380046673119e-05 7.29749008314684e-05 0.0 6.631299766013399e-05 0.0 0.0004030629934277 0.0 eas 0.0004030629934277 0.0 1.543260077596642e-05 0.0 0.0 0 48 f387bb51-516b-46bc-900b-e5b26cb80086 66 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS MYOF,non_coding_transcript_exon_variant,,ENST00000488645.1,n.494G>A,MODIFIER,;MYOF,synonymous_variant,p.P100=,ENST00000371488.3,c.300G>A,LOW,;MYOF,synonymous_variant,p.P100=,ENST00000371489.5,c.300G>A,LOW,;MYOF,synonymous_variant,p.P100=,ENST00000358334.9,c.300G>A,LOW,;MYOF,synonymous_variant,p.P100=,ENST00000359263.9,c.300G>A,LOW,YES +CAT 847 BI GRCh38 11 34468309 34468309 + missense_variant Missense_Mutation SNP G G A rs746357360 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 102 69 c.1348G>A p.Val450Met p.V450M ENST00000241052.5 NM_001752.4 450 Gtg/Atg 11/13 P1 A V/M protein_coding YES CCDS7891.1 1348/1584 TGAACGTGCTG PDB-ENSP_mappings:1dgb.A;PDB-ENSP_mappings:1dgb.B;PDB-ENSP_mappings:1dgb.C;PDB-ENSP_mappings:1dgb.D;PDB-ENSP_mappings:1dgf.A;PDB-ENSP_mappings:1dgf.B;PDB-ENSP_mappings:1dgf.C;PDB-ENSP_mappings:1dgf.D;PDB-ENSP_mappings:1dgg.A;PDB-ENSP_mappings:1dgg.B;PDB-ENSP_mappings:1dgg.C;PDB-ENSP_mappings:1dgg.D;PDB-ENSP_mappings:1dgh.A;PDB-ENSP_mappings:1dgh.B;PDB-ENSP_mappings:1dgh.C;PDB-ENSP_mappings:1dgh.D;PDB-ENSP_mappings:1f4j.A;PDB-ENSP_mappings:1f4j.B;PDB-ENSP_mappings:1f4j.C;PDB-ENSP_mappings:1f4j.D;PDB-ENSP_mappings:1qqw.A;PDB-ENSP_mappings:1qqw.B;PDB-ENSP_mappings:1qqw.C;PDB-ENSP_mappings:1qqw.D;CDD:cd08156;Pfam:PF06628;Gene3D:2.40.180.10;PIRSF:PIRSF038928;Superfamily:SSF56634;PROSITE_profiles:PS51402;PANTHER:PTHR11465:SF9;PANTHER:PTHR11465 ENSP00000241052 11/13 rs746357360 ENST00000241052 Transcript 1.0 ENSG00000121691 HGNC:1516 MODERATE NM_001752.4 2.637e-05 gnomAD_NFE missense_variant 1.0 probably_damaging(0.961) Unknown deleterious(0.02) P04040.225 CAT HGNC 1 A0A384P5Q0.8 1.0 UPI000002F090 SNV CAT,missense_variant,p.V450M,ENST00000241052,NM_001752.4,c.1348G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.961),1;CAT,non_coding_transcript_exon_variant,,ENST00000525707,,n.147G>A,MODIFIER,,,,1;CAT,downstream_gene_variant,,ENST00000530343,,,MODIFIER,,,,1;CAT,upstream_gene_variant,,ENST00000534710,,,MODIFIER,,,,1 1428/2291 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 1.193e-05 0.0 0.0 0.0 0.0 0.0 2.637e-05 0.0 0.0 2.7062500521424223e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.173409929033369e-05 0.0 6.173409929033369e-05 0.0 0.0 0 128 f387bb51-516b-46bc-900b-e5b26cb80086 171 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS CAT,non_coding_transcript_exon_variant,,ENST00000525707.2,n.147G>A,MODIFIER,;CAT,missense_variant,p.V450M,ENST00000241052.5,c.1348G>A,MODERATE,YES +NECAP1 25977 BI GRCh38 12 8095681 8095681 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 82 46 c.757G>A p.Gly253Arg p.G253R ENST00000339754.11 NM_015509.4 253 Gga/Aga 7/8 P4 A G/R protein_coding CCDS8589.1 757/828 TGTGGGGAGAC PANTHER:PTHR12847;PANTHER:PTHR12847:SF7 ENSP00000341737 7/8 ENST00000339754 Transcript 1.0 ENSG00000089818 HGNC:24539 MODERATE NM_015509.4 missense_variant probably_damaging(0.984) Unknown deleterious(0) Q8NC96.131 NECAP1 HGNC 1 1.0 UPI000006EB8D Q8NC96-1 SNV NECAP1,missense_variant,p.G253R,ENST00000639955,,c.757G>A,MODERATE,YES,deleterious(0),probably_damaging(0.984),1;NECAP1,missense_variant,p.G253R,ENST00000339754,NM_015509.4,c.757G>A,MODERATE,,deleterious(0),probably_damaging(0.984),1;NECAP1,missense_variant,p.G249R,ENST00000638237,,c.745G>A,MODERATE,,deleterious(0.02),probably_damaging(1),1;NECAP1,missense_variant,p.G157R,ENST00000639167,,c.469G>A,MODERATE,,deleterious(0),probably_damaging(1),1;NECAP1,missense_variant,p.G111R,ENST00000540083,,c.331G>A,MODERATE,,deleterious(0),probably_damaging(0.984),1;NECAP1,missense_variant,p.G86R,ENST00000638334,,c.256G>A,MODERATE,,deleterious(0),probably_damaging(1),1;NECAP1,intron_variant,,ENST00000639811,,c.677-361G>A,MODIFIER,,,,1;NECAP1,downstream_gene_variant,,ENST00000541948,,,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000639595,,c.*97G>A,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000640209,,c.*353G>A,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000450991,,c.*366G>A,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000639038,,c.*353G>A,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000638787,,c.*233G>A,MODIFIER,,,,1;NECAP1,3_prime_UTR_variant,,ENST00000639841,,c.*204G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000640648,,n.3445G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000544891,,n.3147G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000638883,,n.2224G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000640072,,n.1708G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000537796,,n.1678G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000640099,,n.1594G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000640481,,n.1500G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000545807,,n.1721G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000639276,,n.936G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000639071,,n.859G>A,MODIFIER,,,,1;NECAP1,non_coding_transcript_exon_variant,,ENST00000640091,,n.404G>A,MODIFIER,,,,1;AC006511.5,intron_variant,,ENST00000639368,,n.321+5382G>A,MODIFIER,YES,,,1;NECAP1,downstream_gene_variant,,ENST00000542095,,,MODIFIER,,,,1;NECAP1,downstream_gene_variant,,ENST00000546181,,,MODIFIER,,,,1;AC006511.5,upstream_gene_variant,,ENST00000546339,,,MODIFIER,,,,1 772/2634 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 92 f387bb51-516b-46bc-900b-e5b26cb80086 128 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS NECAP1,non_coding_transcript_exon_variant,,ENST00000640091.1,n.404G>A,MODIFIER,;NECAP1,missense_variant,p.G86R,ENST00000638334.1,c.256G>A,MODERATE,;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639841.1,c.*204G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000640072.1,n.1708G>A,MODIFIER,;NECAP1,missense_variant,p.G111R,ENST00000540083.1,c.331G>A,MODERATE,;NECAP1,non_coding_transcript_exon_variant,,ENST00000545807.6,n.1721G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000640481.1,n.1500G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000638883.1,n.2224G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000544891.6,n.3147G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000537796.2,n.1678G>A,MODIFIER,;NECAP1,intron_variant,,ENST00000639811.1,c.677-361G>A,MODIFIER,;NECAP1,missense_variant,p.G157R,ENST00000639167.1,c.469G>A,MODERATE,;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000638787.1,c.*233G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000640099.1,n.1594G>A,MODIFIER,;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000640209.1,c.*353G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000639071.1,n.859G>A,MODIFIER,;NECAP1,missense_variant,p.G253R,ENST00000339754.11,c.757G>A,MODERATE,YES;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639595.1,c.*97G>A,MODIFIER,;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639038.1,c.*353G>A,MODIFIER,;ENSG00000284697,intron_variant,,ENST00000639368.1,n.321+5382G>A,MODIFIER,;NECAP1,non_coding_transcript_exon_variant,,ENST00000639276.1,n.936G>A,MODIFIER,;NECAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000450991.6,c.*366G>A,MODIFIER,;NECAP1,missense_variant,p.G249R,ENST00000638237.1,c.745G>A,MODERATE,;NECAP1,non_coding_transcript_exon_variant,,ENST00000640648.1,n.3445G>A,MODIFIER,;NECAP1,missense_variant,p.G253R,ENST00000639955.1,c.757G>A,MODERATE, +ALOX15 246 BI GRCh38 17 4633480 4633480 + synonymous_variant Silent SNP T T A rs1472437416 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 91 32 c.1182A>T p.Arg394= p.R394= ENST00000293761.8 NM_001140.5 394 cgA/cgT 9/14 P1 A R protein_coding YES CCDS11049.1 1182/1989 GTGTATCGCAG Gene3D:1.20.245.10;Pfam:PF00305;Prints:PR00087;PROSITE_profiles:PS51393;PANTHER:PTHR11771;PANTHER:PTHR11771:SF33;Superfamily:SSF48484 ENSP00000293761 9/14 rs1472437416 ENST00000293761 Transcript ENSG00000161905 HGNC:433 LOW NM_001140.5 0.0001307 gnomAD_SAS synonymous_variant 1.0 Unknown P16050.197 ALOX15 HGNC -1 1.0 UPI000013E118 P16050-1 SNV ALOX15,synonymous_variant,p.R394=,ENST00000293761,NM_001140.5,c.1182A>T,LOW,YES,,,-1;ALOX15,synonymous_variant,p.R355=,ENST00000574640,,c.1065A>T,LOW,,,,-1;ALOX15,synonymous_variant,p.R394=,ENST00000570836,,c.1182A>T,LOW,,,,-1;ALOX15,downstream_gene_variant,,ENST00000576572,,,MODIFIER,,,,-1 1209/2697 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 1.591e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0001307 0 89 f387bb51-516b-46bc-900b-e5b26cb80086 123 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS ALOX15,synonymous_variant,p.R394=,ENST00000570836.6,c.1182A>T,LOW,;ALOX15,synonymous_variant,p.R355=,ENST00000574640.1,c.1065A>T,LOW,;ALOX15,synonymous_variant,p.R394=,ENST00000293761.8,c.1182A>T,LOW,YES +SLFN11 91607 BI GRCh38 17 35352621 35352621 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 36 23 c.2441G>A p.Ser814Asn p.S814N ENST00000308377.8 NM_001387160.1 814 aGc/aAc 5/5 P1 T S/N protein_coding CCDS11294.1 2441/2706 CGGTGCTGACA Gene3D:3.40.50.300;PANTHER:PTHR12155;PANTHER:PTHR12155:SF43;Superfamily:SSF52540 ENSP00000312402 5/5 ENST00000308377 Transcript ENSG00000172716 HGNC:26633 MODERATE missense_variant benign(0.316) Unknown tolerated(0.11) Q7Z7L1.140 SLFN11 HGNC -1 1.0 UPI0000140B0E SNV SLFN11,missense_variant,p.S814N,ENST00000394566,NM_001104590.2&NM_001376008.1&NM_001376011.1&NM_001104588.2&NM_001376007.1&NM_001376010.1&NM_001104587.2,c.2441G>A,MODERATE,YES,tolerated(0.11),benign(0.316),-1;SLFN11,missense_variant,p.S814N,ENST00000308377,NM_152270.4&NM_001376009.1&NM_001104589.2&NM_001376012.1,c.2441G>A,MODERATE,,tolerated(0.11),benign(0.316),-1;SLFN11,3_prime_UTR_variant,,ENST00000592108,,c.*250G>A,MODIFIER,,,,-1 2594/4910 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 58 f387bb51-516b-46bc-900b-e5b26cb80086 59 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS SLFN11,3_prime_UTR_variant,,ENST00000592108.1,c.*250G>A,MODIFIER,;SLFN11,missense_variant,p.S814N,ENST00000308377.8,c.2441G>A,MODERATE,;SLFN11,missense_variant,p.S814N,ENST00000685675.1,c.2441G>A,MODERATE,YES;SLFN11,missense_variant,p.S814N,ENST00000394566.5,c.2441G>A,MODERATE, +DSC1 1823 BI GRCh38 18 31132611 31132611 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 62 28 c.2195del p.Asn732IlefsTer2 p.N732Ifs*2 ENST00000257198.6 NM_024421.2 732 aAt/at 14/16 P1 - N/X protein_coding YES CCDS11894.1 2195/2685 ATTAAATTTTGC Pfam:PF01049;Prints:PR01820;PANTHER:PTHR24025;PANTHER:PTHR24025:SF8 ENSP00000257198 14/16 ENST00000257198 Transcript ENSG00000134765 HGNC:3035 HIGH NM_024421.2 frameshift_variant 1.0 Unknown Q08554.175 DSC1 HGNC -1 2.0 UPI000006DF10 Q08554-1 deletion DSC1,frameshift_variant,p.N732Ifs*2,ENST00000257197,NM_004948.3,c.2195del,HIGH,,,,-1;DSC1,frameshift_variant,p.N732Ifs*2,ENST00000257198,NM_024421.2,c.2195del,HIGH,YES,,,-1;DSCAS,intron_variant,,ENST00000581836,,n.209-18185del,MODIFIER,,,,1;AC012417.1,downstream_gene_variant,,ENST00000582307,,,MODIFIER,YES,,,1;DSCAS,downstream_gene_variant,,ENST00000654403,,,MODIFIER,YES,,,1 2457/4225 mutect2;pindel;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 79 f387bb51-516b-46bc-900b-e5b26cb80086 90 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS DSC1,frameshift_variant,p.N732Ifs*2,ENST00000257197.7,c.2195del,HIGH,;DSC1,frameshift_variant,p.N732Ifs*2,ENST00000257198.6,c.2195del,HIGH,YES;DSCAS,intron_variant,,ENST00000581836.2,n.225-18188del,MODIFIER,YES +KANK3 256949 BI GRCh38 19 8324675 8324675 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 53 29 c.2238G>A p.Arg746= p.R746= ENST00000593649.5 746 cgG/cgA 9/11 P4 T R protein_coding YES 2238/2523 AGCAGCCGCAC Gene3D:1.25.40.20;Pfam:PF13857;PROSITE_profiles:PS50297;PANTHER:PTHR24168;PANTHER:PTHR24168:SF23;SMART:SM00248;Superfamily:SSF48403 ENSP00000470728 9/11 ENST00000593649 Transcript ENSG00000186994 HGNC:24796 LOW synonymous_variant 1.0 Unknown Q6NY19.134 KANK3 HGNC -1 1.0 UPI000024321F Q6NY19-1 SNV KANK3,synonymous_variant,p.R746=,ENST00000330915,NM_198471.3,c.2238G>A,LOW,,,,-1;KANK3,synonymous_variant,p.R746=,ENST00000593649,,c.2238G>A,LOW,YES,,,-1;NDUFA7,upstream_gene_variant,,ENST00000301457,NM_005001.5,,MODIFIER,YES,,,-1;RPS28,downstream_gene_variant,,ENST00000600659,NM_001031.5,,MODIFIER,YES,,,1;RPS28,downstream_gene_variant,,ENST00000417088,,,MODIFIER,,,,1;RPS28,downstream_gene_variant,,ENST00000449223,,,MODIFIER,,,,1;NDUFA7,upstream_gene_variant,,ENST00000593729,,,MODIFIER,,,,-1;NDUFA7,upstream_gene_variant,,ENST00000595856,,,MODIFIER,,,,-1;AC010323.1,upstream_gene_variant,,ENST00000598884,,,MODIFIER,YES,,,-1;NDUFA7,upstream_gene_variant,,ENST00000601101,,,MODIFIER,,,,-1;RPS28,downstream_gene_variant,,ENST00000602140,,,MODIFIER,,,,1 2304/2672 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 68 f387bb51-516b-46bc-900b-e5b26cb80086 82 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS KANK3,synonymous_variant,p.R746=,ENST00000593649.5,c.2238G>A,LOW,;KANK3,synonymous_variant,p.R746=,ENST00000330915.7,c.2238G>A,LOW,YES +OPA3 80207 BI GRCh38 19 45553694 45553694 + synonymous_variant Silent SNP G G A rs1308359391 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 38 3 c.360C>T p.Asn120= p.N120= ENST00000263275.5 NM_025136.4 120 aaC/aaT 2/2 P3 A N protein_coding CCDS12668.1 360/540 AGCGCGTTCCA COSM4079390 Pfam:PF07047;PANTHER:PTHR12499;PANTHER:PTHR12499:SF0 ENSP00000263275 2/2 rs1308359391;COSV54400771 ENST00000263275 Transcript 1.0 ENSG00000125741 HGNC:8142 LOW NM_025136.4 9.581e-06 gnomAD_NFE synonymous_variant 0;1 Unknown 0;1 Q9H6K4.148 OPA3 HGNC -1 1.0 UPI0000130D53 Q9H6K4-1 SNV OPA3,synonymous_variant,p.N120=,ENST00000263275,NM_025136.4,c.360C>T,LOW,,,,-1;OPA3,synonymous_variant,p.N67=,ENST00000544371,,c.201C>T,LOW,,,,-1;OPA3,intron_variant,,ENST00000323060,NM_001017989.3,c.143-24238C>T,MODIFIER,YES,,,-1 398/7811 muse;mutect2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 4.294e-06 0.0 0.0 0.0 0.0 0.0 9.581e-06 0.0 0.0 0 20 f387bb51-516b-46bc-900b-e5b26cb80086 41 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS OPA3,synonymous_variant,p.N67=,ENST00000544371.1,c.201C>T,LOW,;OPA3,synonymous_variant,p.N120=,ENST00000263275.5,c.360C>T,LOW,YES;OPA3,intron_variant,,ENST00000323060.4,c.143-24238C>T,MODIFIER, +CDH4 1002 BI GRCh38 20 61936830 61936830 + missense_variant Missense_Mutation SNP G G A rs780992540 TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 30 3 c.2638G>A p.Val880Ile p.V880I ENST00000614565.5 NM_001794.5 880 Gtc/Atc 16/16 P1 A V/I protein_coding YES CCDS13488.1 2638/2751 GCTCCGTCAGC COSM1028771 Gene3D:4.10.900.10;Pfam:PF01049;PANTHER:PTHR24027;PANTHER:PTHR24027:SF81;Low_complexity_(Seg):seg ENSP00000484928 16/16 rs780992540;COSV64644940 ENST00000614565 Transcript ENSG00000179242 HGNC:1763 MODERATE NM_001794.5 4.628e-05 gnomAD_FIN missense_variant 0;1 1.0 probably_damaging(0.993) Unknown tolerated(0.27) 0;1 P55283.168 CDH4 HGNC 1 1.0 UPI000015FE86 P55283-1 SNV CDH4,missense_variant,p.V880I,ENST00000614565,NM_001794.5,c.2638G>A,MODERATE,YES,tolerated(0.27),probably_damaging(0.993),1;CDH4,missense_variant,p.V786I,ENST00000611855,,c.2356G>A,MODERATE,,tolerated(0.48),benign(0.275),1;CDH4,missense_variant,p.V806I,ENST00000543233,NM_001252339.3&NM_001252338.2,c.2416G>A,MODERATE,,tolerated(0.48),probably_damaging(0.993),1 2891/6678 muse;mutect2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 2.42e-05 0.0 0.0 0.0 0.0 4.628e-05 4.457e-05 0.0 0.0 2.7062100343755446e-05 4.867359893978573e-05 0.0 0.0 0.0 0.0 0.0 afr 4.867359893978573e-05 0.0 1.5436900866916403e-05 0.0004945599939674 0.0 0 32 f387bb51-516b-46bc-900b-e5b26cb80086 33 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS CDH4,missense_variant,p.V806I,ENST00000543233.2,c.2416G>A,MODERATE,;CDH4,missense_variant,p.V786I,ENST00000611855.4,c.2356G>A,MODERATE,;CDH4,missense_variant,p.V880I,ENST00000614565.5,c.2638G>A,MODERATE,YES +ZBTB21 49854 BI GRCh38 21 41991321 41991321 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 65 26 c.2775G>A p.Glu925= p.E925= ENST00000310826.10 NM_001098402.2 925 gaG/gaA 3/3 P1 T E protein_coding YES CCDS13678.1 2775/3201 TGACGCTCCAG Gene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24408;PANTHER:PTHR24408:SF18;SMART:SM00355;Superfamily:SSF57667 ENSP00000308759 3/3 ENST00000310826 Transcript ENSG00000173276 HGNC:13083 LOW NM_001098402.2 synonymous_variant 1.0 Unknown Q9ULJ3.185 ZBTB21 HGNC -1 1.0 UPI000013C34D Q9ULJ3-1 SNV ZBTB21,synonymous_variant,p.E925=,ENST00000310826,NM_001098402.2,c.2775G>A,LOW,YES,,,-1;ZBTB21,synonymous_variant,p.E724=,ENST00000398505,NM_001320729.2&NM_001098403.2,c.2172G>A,LOW,,,,-1;ZBTB21,synonymous_variant,p.E925=,ENST00000398499,NM_001320731.2,c.2775G>A,LOW,,,,-1;ZBTB21,synonymous_variant,p.E925=,ENST00000398511,NM_020727.5,c.2775G>A,LOW,,,,-1;ZBTB21,downstream_gene_variant,,ENST00000398497,,,MODIFIER,,,,-1;ZBTB21,downstream_gene_variant,,ENST00000425521,,,MODIFIER,,,,-1;ZBTB21,downstream_gene_variant,,ENST00000449949,,,MODIFIER,,,,-1;ZBTB21,downstream_gene_variant,,ENST00000465968,,,MODIFIER,,,,-1 2962/7452 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 64 f387bb51-516b-46bc-900b-e5b26cb80086 91 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS ZBTB21,synonymous_variant,p.E925=,ENST00000398511.3,c.2775G>A,LOW,;ZBTB21,synonymous_variant,p.E925=,ENST00000398499.5,c.2775G>A,LOW,;ZBTB21,synonymous_variant,p.E724=,ENST00000398505.7,c.2172G>A,LOW,;ZBTB21,synonymous_variant,p.E925=,ENST00000310826.10,c.2775G>A,LOW,YES +SERPIND1 3053 BI GRCh38 22 20780141 20780141 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 175 162 c.829G>C p.Ala277Pro p.A277P ENST00000215727.10 NM_000185.4 277 Gct/Cct 2/5 P1 C A/P protein_coding YES CCDS13783.1 829/1500 AAGATGCTCTG PDB-ENSP_mappings:1jmj.A;PDB-ENSP_mappings:1jmj.B;PDB-ENSP_mappings:1jmo.A;CDD:cd02047;PANTHER:PTHR11461:SF30;PANTHER:PTHR11461;Gene3D:3.30.497.10;Pfam:PF00079;SMART:SM00093;Superfamily:SSF56574 ENSP00000215727 2/5 ENST00000215727 Transcript 1.0 ENSG00000099937 HGNC:4838 MODERATE NM_000185.4 missense_variant 1.0 benign(0.033) Unknown tolerated(0.25) P05546.212 SERPIND1 HGNC 1 1.0 UPI000012C603 SNV SERPIND1,missense_variant,p.A277P,ENST00000215727,NM_000185.4,c.829G>C,MODERATE,YES,tolerated(0.25),benign(0.033),1;SERPIND1,missense_variant,p.A277P,ENST00000406799,,c.829G>C,MODERATE,,tolerated(0.25),benign(0.033),1;PI4KA,intron_variant,,ENST00000255882,NM_001362863.1&NM_001362862.1&NM_058004.4,c.2328+13052C>G,MODIFIER,YES,,,-1;PI4KA,intron_variant,,ENST00000466162,,n.91+13052C>G,MODIFIER,,,,-1;PI4KA,intron_variant,,ENST00000484220,,n.64+13052C>G,MODIFIER,,,,-1 878/2203 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 259 f387bb51-516b-46bc-900b-e5b26cb80086 338 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS SERPIND1,missense_variant,p.A277P,ENST00000406799.1,c.829G>C,MODERATE,;SERPIND1,missense_variant,p.A277P,ENST00000215727.10,c.829G>C,MODERATE,YES;PI4KA,intron_variant,,ENST00000484220.1,n.64+13052C>G,MODIFIER,;PI4KA,intron_variant,,ENST00000466162.5,n.91+13052C>G,MODIFIER,;PI4KA,intron_variant,,ENST00000255882.11,c.2328+13052C>G,MODIFIER,YES +APEX2 27301 BI GRCh38 X 55006862 55006862 + missense_variant Missense_Mutation SNP C C A TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 38 15 c.984C>A p.Phe328Leu p.F328L ENST00000374987.4 NM_014481.4 328 ttC/ttA 6/6 P1 A F/L protein_coding YES CCDS14365.1 984/1557 CGCTTCCTCCC PANTHER:PTHR22748;PANTHER:PTHR22748:SF4 ENSP00000364126 6/6 COSV58193316 ENST00000374987 Transcript ENSG00000169188 HGNC:17889 MODERATE NM_014481.4 missense_variant 1 1.0 benign(0.037) Unknown tolerated(0.08) 1 Q9UBZ4.162 APEX2 HGNC 1 E5KN95.78 1.0 UPI0000071F5B SNV APEX2,missense_variant,p.F328L,ENST00000374987,NM_014481.4&NM_001271748.2,c.984C>A,MODERATE,YES,tolerated(0.08),benign(0.037),1;ALAS2,downstream_gene_variant,,ENST00000335854,NM_001037967.4,,MODIFIER,,,,-1;ALAS2,downstream_gene_variant,,ENST00000396198,NM_001037968.4,,MODIFIER,,,,-1;ALAS2,downstream_gene_variant,,ENST00000498636,,,MODIFIER,,,,-1;ALAS2,downstream_gene_variant,,ENST00000650242,NM_000032.5,,MODIFIER,YES,,,-1;APEX2,downstream_gene_variant,,ENST00000471758,,,MODIFIER,,,,1 1044/3239 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 42 f387bb51-516b-46bc-900b-e5b26cb80086 53 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS APEX2,missense_variant,p.F328L,ENST00000374987.4,c.984C>A,MODERATE,YES +ARHGAP4 393 BI GRCh38 X 153910344 153910344 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EZ-01A TCGA-V4-A9EZ-10A Somatic 27 26 c.1983G>A p.Gly661= p.G661= ENST00000350060.10 NM_001666.5 661 ggG/ggA 17/22 A2 T G protein_coding CCDS14736.1 1983/2841 GTGGGCCCGAA PROSITE_profiles:PS50238;PANTHER:PTHR14166:SF16;PANTHER:PTHR14166;Pfam:PF00620;Gene3D:1.10.555.10;SMART:SM00324;Superfamily:SSF48350 ENSP00000203786 17/22 ENST00000350060 Transcript ENSG00000089820 HGNC:674 LOW NM_001666.5 synonymous_variant Unknown P98171.185 ARHGAP4 HGNC -1 1.0 UPI000013C648 P98171-1 SNV ARHGAP4,synonymous_variant,p.G701=,ENST00000370028,NM_001164741.2,c.2103G>A,LOW,YES,,,-1;ARHGAP4,synonymous_variant,p.G661=,ENST00000350060,NM_001666.5,c.1983G>A,LOW,,,,-1;ARHGAP4,synonymous_variant,p.G640=,ENST00000370016,,c.1920G>A,LOW,,,,-1;ARHGAP4,synonymous_variant,p.G483=,ENST00000393721,,c.1449G>A,LOW,,,,-1;ARHGAP4,synonymous_variant,p.G150=,ENST00000442172,,c.450G>A,LOW,,,,-1;ARHGAP4,intron_variant,,ENST00000454164,,c.421+162G>A,MODIFIER,,,,-1;AVPR2,downstream_gene_variant,,ENST00000337474,,,MODIFIER,,,,1;AVPR2,downstream_gene_variant,,ENST00000370049,NM_001146151.3,,MODIFIER,,,,1;ARHGAP4,downstream_gene_variant,,ENST00000422918,,,MODIFIER,,,,-1;AVPR2,downstream_gene_variant,,ENST00000430697,,,MODIFIER,YES,,,1;AVPR2,downstream_gene_variant,,ENST00000646375,NM_000054.6,,MODIFIER,,,,1;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000467421,,n.339G>A,MODIFIER,,,,-1;ARHGAP4,3_prime_UTR_variant,,ENST00000404127,,c.*1357G>A,MODIFIER,,,,-1;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000470209,,n.1756G>A,MODIFIER,,,,-1;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494302,,n.1534G>A,MODIFIER,,,,-1;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494397,,n.580G>A,MODIFIER,,,,-1;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000461739,,n.176G>A,MODIFIER,,,,-1;ARHGAP4,intron_variant,,ENST00000420383,,c.1739-259G>A,MODIFIER,,,,-1;AVPR2,downstream_gene_variant,,ENST00000434679,,,MODIFIER,,,,1;ARHGAP4,downstream_gene_variant,,ENST00000463905,,,MODIFIER,,,,-1;U52112.1,upstream_gene_variant,,ENST00000464967,,,MODIFIER,,,,-1;ARHGAP4,upstream_gene_variant,,ENST00000466928,,,MODIFIER,,,,-1;ARHGAP4,downstream_gene_variant,,ENST00000494813,,,MODIFIER,,,,-1;U52112.1,upstream_gene_variant,,ENST00000642393,,,MODIFIER,,,,-1;U52112.1,upstream_gene_variant,,ENST00000646191,,,MODIFIER,YES,,,-1 2045/3254 muse;mutect2;varscan2 39e494bc-7710-4f9f-98b0-0f509f7aef1a 0 34 f387bb51-516b-46bc-900b-e5b26cb80086 53 910b26bb-4bf3-4d8a-b559-2a9769a01db6 SUCCESS ARHGAP4,non_coding_transcript_exon_variant,,ENST00000461739.1,n.176G>A,MODIFIER,;ARHGAP4,missense_variant,p.G150D,ENST00000442172.1,c.449G>A,MODERATE,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000467421.1,n.339G>A,MODIFIER,;ARHGAP4,intron_variant,,ENST00000454164.5,c.421+162G>A,MODIFIER,;ARHGAP4,intron_variant,NMD_transcript_variant,,ENST00000700282.1,c.*379+162G>A,MODIFIER,;ARHGAP4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000404127.6,c.*1357G>A,MODIFIER,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000470209.5,n.1756G>A,MODIFIER,;ARHGAP4,synonymous_variant,p.G640=,ENST00000370016.5,c.1920G>A,LOW,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494302.5,n.1534G>A,MODIFIER,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494397.5,n.580G>A,MODIFIER,;ARHGAP4,synonymous_variant,p.G661=,ENST00000350060.10,c.1983G>A,LOW,YES;ARHGAP4,intron_variant,NMD_transcript_variant,,ENST00000420383.5,c.1739-259G>A,MODIFIER,;ARHGAP4,synonymous_variant,p.G701=,ENST00000370028.7,c.2103G>A,LOW,;ARHGAP4,synonymous_variant,p.G483=,ENST00000393721.5,c.1449G>A,LOW, +AGRN 375790 BI GRCh38 1 1042015 1042015 + missense_variant Missense_Mutation SNP C C T rs1205781353 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 15 c.1237C>T p.Arg413Cys p.R413C ENST00000379370.7 NM_198576.4 413 Cgc/Tgc 7/36 P1 T R/C protein_coding YES CCDS30551.1 1237/6138 GTCCCCGCTGC Gene3D:3.30.60.30;Pfam:PF07648;PROSITE_profiles:PS51465;PANTHER:PTHR10574;PANTHER:PTHR10574:SF288;Superfamily:SSF100895 ENSP00000368678 7/36 rs1205781353 ENST00000379370 Transcript 1.0 ENSG00000188157 HGNC:329 MODERATE NM_198576.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.973) Unknown deleterious(0.01) O00468.192 AGRN HGNC 1 1.0 UPI00001D7C8B O00468-6 SNV AGRN,missense_variant,p.R308C,ENST00000651234,,c.922C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.836),1;AGRN,missense_variant,p.R308C,ENST00000652369,NM_001364727.2,c.922C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.836),1;AGRN,missense_variant,p.R275C,ENST00000620552,NM_001305275.2,c.823C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.88),1;AGRN,missense_variant,p.R413C,ENST00000379370,NM_198576.4,c.1237C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.973),1;AGRN,downstream_gene_variant,,ENST00000469403,,,MODIFIER,,,,1;AGRN,upstream_gene_variant,,ENST00000479707,,,MODIFIER,,,,1 1290/7326 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.760410087736091e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435000022989698e-05 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 50 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AGRN,missense_variant,p.R308C,ENST00000652369.1,c.922C>T,MODERATE,;AGRN,missense_variant,p.R308C,ENST00000651234.1,c.922C>T,MODERATE,;AGRN,missense_variant,p.R275C,ENST00000620552.4,c.823C>T,MODERATE,;AGRN,missense_variant,p.R413C,ENST00000379370.7,c.1237C>T,MODERATE,YES +UBE2J2 118424 BI GRCh38 1 1255391 1255391 + missense_variant Missense_Mutation SNP C C T rs146586696 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 71 12 c.592G>A p.Val198Ile p.V198I ENST00000349431.11 NM_058167.3 198 Gtc/Atc 7/7 P1 T V/I protein_coding CCDS14.1 592/780 CTGGACGAGGT ENSP00000305826 0.000227 0.0 7/7 rs146586696 ENST00000349431 Transcript ENSG00000160087 HGNC:19268 MODERATE NM_058167.3 0.000227 AA missense_variant benign(0.003) Unknown tolerated(0.21) Q8N2K1.158 UBE2J2 HGNC -1 A0A024R075.44 1.0 UPI0000149EE7 Q8N2K1-1 SNV UBE2J2,missense_variant,p.V146I,ENST00000347370,NM_194458.1,c.436G>A,MODERATE,,tolerated(0.36),benign(0.003),-1;UBE2J2,missense_variant,p.V198I,ENST00000349431,NM_058167.3,c.592G>A,MODERATE,,tolerated(0.21),benign(0.003),-1;UBE2J2,missense_variant,p.V146I,ENST00000400929,NM_194457.2,c.436G>A,MODERATE,,tolerated(0.36),benign(0.003),-1;UBE2J2,missense_variant,p.V198I,ENST00000360466,,c.592G>A,MODERATE,,tolerated(0.21),benign(0.003),-1;UBE2J2,missense_variant,p.V214I,ENST00000400930,NM_194315.2,c.640G>A,MODERATE,YES,tolerated(0.21),benign(0.001),-1;UBE2J2,downstream_gene_variant,,ENST00000422076,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000435198,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000502382,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000509720,,,MODIFIER,,,,-1;UBE2J2,non_coding_transcript_exon_variant,,ENST00000467339,,n.388G>A,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000491779,,,MODIFIER,,,,-1;UBE2J2,3_prime_UTR_variant,,ENST00000450390,,c.*653G>A,MODIFIER,,,,-1;UBE2J2,3_prime_UTR_variant,,ENST00000464036,,c.*396G>A,MODIFIER,,,,-1;UBE2J2,3_prime_UTR_variant,,ENST00000473215,,c.*586G>A,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000466752,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000471154,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000477894,,,MODIFIER,,,,-1;UBE2J2,downstream_gene_variant,,ENST00000503294,,,MODIFIER,,,,-1;AL162741.1,upstream_gene_variant,,ENST00000565563,,,MODIFIER,YES,,,-1 781/2260 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.994e-06 0.0 2.893e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 83 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 83 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS UBE2J2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000473215.5,c.*586G>A,MODIFIER,;UBE2J2,non_coding_transcript_exon_variant,,ENST00000467339.1,n.388G>A,MODIFIER,;UBE2J2,missense_variant,p.V214I,ENST00000400930.8,c.640G>A,MODERATE,;UBE2J2,missense_variant,p.V198I,ENST00000360466.6,c.592G>A,MODERATE,;UBE2J2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000464036.5,c.*396G>A,MODIFIER,;UBE2J2,missense_variant,p.V146I,ENST00000400929.6,c.436G>A,MODERATE,;UBE2J2,missense_variant,p.V146I,ENST00000347370.6,c.436G>A,MODERATE,;UBE2J2,missense_variant,p.V198I,ENST00000349431.11,c.592G>A,MODERATE,YES;UBE2J2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000450390.6,c.*653G>A,MODIFIER, +GABRD 2563 BI GRCh38 1 2030070 2030070 + missense_variant Missense_Mutation SNP G G A rs1459168993 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 7 c.1147G>A p.Val383Ile p.V383I ENST00000378585.7 NM_000815.5 383 Gtc/Atc 9/9 P4 A V/I protein_coding CCDS36.1 1147/1359 GCCGCGTCCCG PANTHER:PTHR18945;PANTHER:PTHR18945:SF34;Superfamily:SSF90112;Prints:PR01722 ENSP00000367848 9/9 rs1459168993;COSV66080286 ENST00000378585 Transcript 1.0 ENSG00000187730 HGNC:4084 MODERATE NM_000815.5 2.734e-05 gnomAD_NFE missense_variant 0;1 benign(0.001) Unknown tolerated(0.81) 0;1 O14764.187 GABRD HGNC 1 1.0 UPI0000070D0A SNV GABRD,missense_variant,p.V383I,ENST00000378585,NM_000815.5,c.1147G>A,MODERATE,,tolerated(0.81),benign(0.001),1;GABRD,missense_variant,p.R456H,ENST00000638771,,c.1367G>A,MODERATE,YES,,unknown(0),1;GABRD,missense_variant,p.V360I,ENST00000640949,,c.1078G>A,MODERATE,,tolerated(0.73),benign(0.003),1;GABRD,missense_variant,p.V411I,ENST00000640067,,c.1231G>A,MODERATE,,tolerated(0.85),benign(0.003),1;GABRD,missense_variant,p.V311I,ENST00000640030,,c.931G>A,MODERATE,,tolerated(0.5),benign(0.001),1;GABRD,missense_variant,p.R393H,ENST00000638411,,c.1178G>A,MODERATE,,,unknown(0),1;GABRD,downstream_gene_variant,,ENST00000638763,,,MODIFIER,,,,1;GABRD,downstream_gene_variant,,ENST00000638804,,,MODIFIER,,,,1;GABRD,downstream_gene_variant,,ENST00000640981,,,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000640423,,n.1156G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000639777,,n.1751G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000638604,,n.1706G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000639070,,n.1726G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000640892,,n.1814G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000640317,,n.1496G>A,MODIFIER,,,,1;GABRD,non_coding_transcript_exon_variant,,ENST00000640688,,n.648G>A,MODIFIER,,,,1;GABRD,downstream_gene_variant,,ENST00000639045,,,MODIFIER,,,,1;GABRD,downstream_gene_variant,,ENST00000639935,,,MODIFIER,,,,1 1226/1914 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.228e-05 0.0 0.0 0.0 0.0 0.0 2.734e-05 0.0 0.0 0 46 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GABRD,non_coding_transcript_exon_variant,,ENST00000640688.1,n.648G>A,MODIFIER,;GABRD,non_coding_transcript_exon_variant,,ENST00000640317.1,n.1496G>A,MODIFIER,;GABRD,non_coding_transcript_exon_variant,,ENST00000640892.1,n.1814G>A,MODIFIER,;GABRD,non_coding_transcript_exon_variant,,ENST00000639070.1,n.1726G>A,MODIFIER,;GABRD,non_coding_transcript_exon_variant,,ENST00000639777.1,n.1751G>A,MODIFIER,;GABRD,non_coding_transcript_exon_variant,,ENST00000640423.1,n.1156G>A,MODIFIER,;GABRD,missense_variant,p.V311I,ENST00000640030.1,c.931G>A,MODERATE,;GABRD,missense_variant,p.V360I,ENST00000640949.1,c.1078G>A,MODERATE,;GABRD,missense_variant,p.R456H,ENST00000638771.1,c.1367G>A,MODERATE,;GABRD,missense_variant,p.V411I,ENST00000640067.1,c.1231G>A,MODERATE,;GABRD,non_coding_transcript_exon_variant,,ENST00000638604.1,n.1706G>A,MODIFIER,;GABRD,missense_variant,p.V383I,ENST00000378585.7,c.1147G>A,MODERATE,YES;GABRD,missense_variant,p.R393H,ENST00000638411.1,c.1178G>A,MODERATE, +PANK4 55229 BI GRCh38 1 2514411 2514411 + missense_variant Missense_Mutation SNP G G A rs753091403 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 18 c.1430C>T p.Ala477Val p.A477V ENST00000378466.9 NM_018216.4 477 gCg/gTg 11/19 P1 A A/V protein_coding YES 1430/2322 TCTCCGCCCTC COSM2051264 PANTHER:PTHR12280:SF20;PANTHER:PTHR12280;PIRSF:PIRSF036939;Pfam:PF01937;Gene3D:1.20.1700.10;Superfamily:SSF111321 ENSP00000367727 11/19 rs753091403;COSV65866365 ENST00000378466 Transcript 1.0 ENSG00000157881 HGNC:19366 MODERATE NM_018216.4 9.801e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.968) Unknown deleterious(0.03) 0;1 Q9NVE7.163 PANK4 HGNC -1 1.0 UPI000000DA54 SNV PANK4,missense_variant,p.A477V,ENST00000378466,NM_018216.4,c.1430C>T,MODERATE,YES,deleterious(0.03),probably_damaging(0.968),-1;PANK4,missense_variant,p.A438V,ENST00000435556,,c.1313C>T,MODERATE,,deleterious(0.03),probably_damaging(0.997),-1;PANK4,missense_variant,p.A335V,ENST00000505228,,c.1004C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.696),-1;PANK4,downstream_gene_variant,,ENST00000468002,,,MODIFIER,,,,-1;PANK4,upstream_gene_variant,,ENST00000471361,,,MODIFIER,,,,-1;PANK4,downstream_gene_variant,,ENST00000486396,,,MODIFIER,,,,-1;PANK4,upstream_gene_variant,,ENST00000487804,,,MODIFIER,,,,-1;PANK4,upstream_gene_variant,,ENST00000502512,,,MODIFIER,,,,-1;PANK4,downstream_gene_variant,,ENST00000515423,,,MODIFIER,,,,-1 1439/2641 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.602e-05 0.0 0.0 0.0 0.0 0.0 8.877e-06 0.0 9.801e-05 1.3537700397137089e-05 2.435930036881473e-05 0.0 6.628660048590973e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PANK4,missense_variant,NMD_transcript_variant,p.R335W,ENST00000505228.5,c.1003C>T,MODERATE,;PANK4,missense_variant,p.A438V,ENST00000435556.8,c.1313C>T,MODERATE,;PANK4,missense_variant,p.A477V,ENST00000378466.9,c.1430C>T,MODERATE,YES +CAMTA1 23261 BI GRCh38 1 7670940 7670940 + synonymous_variant Silent SNP G G A rs776020744 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 41 c.2682G>A p.Pro894= p.P894= ENST00000303635.12 NM_015215.4 894 ccG/ccA 10/23 P1 A P protein_coding YES CCDS30576.1 2682/5022 GGCCCGTGGCA PDB-ENSP_mappings:2cxk.A;PDB-ENSP_mappings:2cxk.B;PDB-ENSP_mappings:2cxk.C;PDB-ENSP_mappings:2cxk.D;PDB-ENSP_mappings:2cxk.E;PANTHER:PTHR23335:SF11;PANTHER:PTHR23335;Pfam:PF01833;Gene3D:2.60.40.10;Superfamily:SSF81296 ENSP00000306522 10/23 rs776020744 ENST00000303635 Transcript 1.0 ENSG00000171735 HGNC:18806 LOW NM_015215.4 0.0001088 gnomAD_EAS synonymous_variant 1.0 Unknown Q9Y6Y1.161 CAMTA1 HGNC 1 1.0 UPI00001C1D72 Q9Y6Y1-1 SNV CAMTA1,synonymous_variant,p.P894=,ENST00000303635,NM_015215.4&NM_001349609.2&NM_001349610.2&NM_001349608.2&NM_001349612.2,c.2682G>A,LOW,YES,,,1 2759/8314 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.195e-05 0.0 0.0 0.0 0.0001088 0.0 8.814e-06 0.0 0.0 6.7599498834169935e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 77 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CAMTA1,5_prime_UTR_variant,,ENST00000700421.1,c.-247G>A,MODIFIER,;CAMTA1,5_prime_UTR_variant,,ENST00000700420.1,c.-247G>A,MODIFIER,;CAMTA1,missense_variant,p.V137M,ENST00000700445.1,c.409G>A,MODERATE,;CAMTA1,synonymous_variant,p.P315=,ENST00000700419.1,c.945G>A,LOW,;CAMTA1,synonymous_variant,p.P870=,ENST00000700417.1,c.2610G>A,LOW,;CAMTA1,synonymous_variant,p.P894=,ENST00000476864.2,c.2682G>A,LOW,;CAMTA1,synonymous_variant,p.P864=,ENST00000700415.1,c.2592G>A,LOW,;CAMTA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000700414.1,c.*2533G>A,MODIFIER,;CAMTA1,synonymous_variant,p.P894=,ENST00000303635.12,c.2682G>A,LOW,YES +RERE 473 BI GRCh38 1 8656243 8656243 + missense_variant Missense_Mutation SNP G G A rs772909728 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 103 10 c.55C>T p.Arg19Trp p.R19W ENST00000337907.7 NM_012102.4 19 Cgg/Tgg 3/24 P1 A R/W protein_coding YES CCDS95.1 55/4701 GTCCCGGTCTC MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000338629 3/24 rs772909728 ENST00000337907 Transcript 1.0 ENSG00000142599 HGNC:9965 MODERATE 1.762e-05 gnomAD_NFE missense_variant 1.0 probably_damaging(0.99) Unknown deleterious_low_confidence(0.02) Q9P2R6.180 RERE HGNC -1 1.0 UPI00001419CC Q9P2R6-1 SNV RERE,missense_variant,p.R19W,ENST00000337907,NM_012102.4,c.55C>T,MODERATE,YES,deleterious_low_confidence(0.02),probably_damaging(0.99),-1;RERE,missense_variant,p.R19W,ENST00000400908,NM_001042681.2,c.55C>T,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(0.99),-1;RERE,missense_variant,p.R19W,ENST00000656437,,c.55C>T,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(0.99),-1;RERE,missense_variant,p.R19W,ENST00000659924,,c.55C>T,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(0.996),-1;RERE,missense_variant,p.R19W,ENST00000400907,,c.55C>T,MODERATE,,deleterious_low_confidence(0.01),probably_damaging(0.996),-1;RERE,missense_variant,p.R19W,ENST00000468247,,c.55C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.99),-1;RERE,non_coding_transcript_exon_variant,,ENST00000480342,,n.607C>T,MODIFIER,,,,-1 690/8026 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.965e-06 0.0 0.0 0.0 0.0 0.0 1.762e-05 0.0 0.0 1.3571700037573464e-05 2.443670018692501e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5456000255653635e-05 0.0 0.0 0 134 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 113 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RERE,missense_variant,p.R19W,ENST00000468247.1,c.55C>T,MODERATE,;RERE,missense_variant,p.R19W,ENST00000704050.1,c.55C>T,MODERATE,;RERE,non_coding_transcript_exon_variant,,ENST00000480342.5,n.607C>T,MODIFIER,;RERE,missense_variant,p.R19W,ENST00000659924.1,c.55C>T,MODERATE,;RERE,missense_variant,p.R19W,ENST00000656437.1,c.55C>T,MODERATE,;RERE,missense_variant,p.R19W,ENST00000400907.6,c.55C>T,MODERATE,;RERE,missense_variant,p.R19W,ENST00000400908.7,c.55C>T,MODERATE,YES;RERE,missense_variant,p.R19W,ENST00000337907.7,c.55C>T,MODERATE, +DHRS3 9249 BI GRCh38 1 12617167 12617167 + missense_variant Missense_Mutation SNP C C T rs765594786 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 7 c.182G>A p.Arg61His p.R61H ENST00000616661.5 NM_004753.7 61 cGc/cAc 1/6 P1 T R/H protein_coding YES CCDS146.1 182/909 CGCCGCGCTCC COSM458657 CDD:cd05339;PANTHER:PTHR24322:SF483;PANTHER:PTHR24322;Gene3D:3.40.50.720;Pfam:PF00106;SMART:SM00822;Superfamily:SSF51735 ENSP00000480439 1/6 rs765594786;COSV66108438 ENST00000616661 Transcript 1.0 ENSG00000162496 HGNC:17693 MODERATE NM_004753.7 9.433e-06 gnomAD_NFE missense_variant 0;1 1.0 benign(0.001) Unknown tolerated(0.46) 0;1 O75911.170 DHRS3 HGNC -1 1.0 UPI000006EE74 O75911-1 SNV DHRS3,missense_variant,p.R61H,ENST00000616661,NM_004753.7&NM_001319225.2&NM_001324370.2,c.182G>A,MODERATE,YES,tolerated(0.46),benign(0.001),-1;DHRS3,upstream_gene_variant,,ENST00000464917,,,MODIFIER,,,,-1;DHRS3,upstream_gene_variant,,ENST00000482265,,,MODIFIER,,,,-1;AC254633.1,downstream_gene_variant,,ENST00000606790,,,MODIFIER,YES,,,-1 1044/2201 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.155e-06 0.0 0.0 0.0 0.0 0.0 9.433e-06 0.0 0.0 0 31 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DHRS3,missense_variant,p.R46H,ENST00000714546.1,c.137G>A,MODERATE,;DHRS3,missense_variant,p.R61H,ENST00000616661.5,c.182G>A,MODERATE,YES;DHRS3,missense_variant,p.R46H,ENST00000714544.1,c.137G>A,MODERATE,;DHRS3,missense_variant,p.R46H,ENST00000714545.1,c.137G>A,MODERATE,;DHRS3,intron_variant,,ENST00000714541.1,c.-61+1904G>A,MODIFIER, +ARHGEF10L 55160 BI GRCh38 1 17632390 17632390 + missense_variant Missense_Mutation SNP G G A rs750101839 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 108 12 c.1654G>A p.Gly552Arg p.G552R ENST00000361221.8 NM_018125.4 552 Ggg/Agg 16/29 P4 A G/R protein_coding YES CCDS182.1 1654/3840 ACCGCGGGCAG PANTHER:PTHR12877;PANTHER:PTHR12877:SF16;Pfam:PF19057;Gene3D:2.30.29.30;Superfamily:SSF50729 ENSP00000355060 16/29 rs750101839;COSV51430940 ENST00000361221 Transcript 1.0 ENSG00000074964 HGNC:25540 MODERATE NM_018125.4 6.154e-05 gnomAD_AFR missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q9HCE6.134 ARHGEF10L HGNC 1 1.0 UPI00004CA9C5 Q9HCE6-1 SNV ARHGEF10L,missense_variant,p.G552R,ENST00000361221,NM_018125.4,c.1654G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;ARHGEF10L,missense_variant,p.G513R,ENST00000375415,NM_001011722.2&NM_001319837.1,c.1537G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ARHGEF10L,missense_variant,p.G330R,ENST00000375408,NM_001319838.1&NM_001328124.1,c.988G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ARHGEF10L,non_coding_transcript_exon_variant,,ENST00000469726,,n.1934G>A,MODIFIER,,,,1;ARHGEF10L,upstream_gene_variant,,ENST00000482359,,,MODIFIER,,,,1;ARHGEF10L,missense_variant,p.G96R,ENST00000167825,,c.286G>A,MODERATE,,deleterious(0.01),probably_damaging(1),1 1950/4625 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.954e-06 6.154e-05 0.0 0.0 0.0 0.0 8.791e-06 0.0 0.0 6.760869837307837e-06 2.431910070299637e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 127 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 120 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ARHGEF10L,missense_variant,NMD_transcript_variant,p.G96R,ENST00000167825.5,c.286G>A,MODERATE,;ARHGEF10L,missense_variant,p.G330R,ENST00000375408.7,c.988G>A,MODERATE,;ARHGEF10L,non_coding_transcript_exon_variant,,ENST00000469726.5,n.1934G>A,MODIFIER,;ARHGEF10L,missense_variant,p.G513R,ENST00000375415.5,c.1537G>A,MODERATE,;ARHGEF10L,missense_variant,p.G552R,ENST00000361221.8,c.1654G>A,MODERATE,YES +TAS1R2 80834 BI GRCh38 1 18854585 18854585 + synonymous_variant Silent SNP G G A rs148401055 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 8 c.885C>T p.Gly295= p.G295= ENST00000375371.4 NM_152232.4 295 ggC/ggT 3/6 P1 A G protein_coding YES CCDS187.1 885/2520 ACGGCGCCAGT COSM164794 CDD:cd06363;PANTHER:PTHR14516:SF4;PANTHER:PTHR14516;Gene3D:3.40.50.2300;Pfam:PF01094;Gene3D:3.40.50.2300;Superfamily:SSF53822 ENSP00000364520 0.0 0.0001163 3/6 rs148401055 ENST00000375371 Transcript ENSG00000179002 HGNC:14905 LOW 0.0001633 gnomAD_OTH synonymous_variant 1.0 Unknown Q8TE23.157 TAS1R2 HGNC -1 2.0 UPI0000456168 SNV TAS1R2,synonymous_variant,p.G295=,ENST00000375371,NM_152232.4,c.885C>T,LOW,YES,,,-1 907/2542 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.789e-05 0.0 2.893e-05 0.0 5.441e-05 0.0 2.642e-05 0.0001633 3.267e-05 6.758859854016919e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 18 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TAS1R2,synonymous_variant,p.G295=,ENST00000375371.4,c.885C>T,LOW,YES +EMC1 23065 BI GRCh38 1 19231417 19231417 + synonymous_variant Silent SNP C C T rs150315726 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 9 c.1788G>A p.Ser596= p.S596= ENST00000477853.6 NM_001271428.2 596 tcG/tcA 16/23 P4 T S protein_coding YES CCDS190.1 1788/2982 ATTCCCGACTC PDB-ENSP_mappings:6ww7.A;PANTHER:PTHR21573 ENSP00000420608 0.0004539 0.0 16/23 rs150315726 ENST00000477853 Transcript 1.0 ENSG00000127463 HGNC:28957 LOW NM_015047.3 0.0004539 AA synonymous_variant 1.0 Unknown Q8N766.148 EMC1 HGNC -1 1.0 UPI0000070A23 Q8N766-1 SNV EMC1,synonymous_variant,p.S596=,ENST00000477853,NM_001271428.2&NM_015047.3&NM_001375820.1,c.1788G>A,LOW,YES,,,-1;EMC1,synonymous_variant,p.S595=,ENST00000375199,NM_001271427.2&NM_001375821.1,c.1785G>A,LOW,,,,-1;EMC1,synonymous_variant,p.S574=,ENST00000375208,NM_001271429.2,c.1722G>A,LOW,,,,-1;EMC1,downstream_gene_variant,,ENST00000641089,,,MODIFIER,,,,-1;EMC1,upstream_gene_variant,,ENST00000494770,,,MODIFIER,,,,-1;EMC1-AS1,intron_variant,,ENST00000437898,,n.60-8840C>T,MODIFIER,YES,,,1 1803/6640 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.426e-05 0.0001242 2.966e-05 0.0 0.0 0.0 6.213e-05 0.0001646 0.0 4.734340109280311e-05 0.0001460640050936 0.0 0.0 0.0 0.0 0.0 afr 0.0001460640050936 0.0 1.5433999578817748e-05 0.0 0.0 0 35 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EMC1,synonymous_variant,p.S599=,ENST00000486405.2,c.1797G>A,LOW,;EMC1,synonymous_variant,p.S574=,ENST00000375208.7,c.1722G>A,LOW,;EMC1,synonymous_variant,p.S595=,ENST00000375199.7,c.1785G>A,LOW,;EMC1,non_coding_transcript_exon_variant,,ENST00000693007.1,n.900G>A,MODIFIER,;EMC1,synonymous_variant,NMD_transcript_variant,p.S596=,ENST00000688667.1,c.1788G>A,LOW,;EMC1,synonymous_variant,p.S594=,ENST00000690823.1,c.1782G>A,LOW,;EMC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000685594.1,c.*414G>A,MODIFIER,;EMC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000688332.1,c.*1549G>A,MODIFIER,;EMC1,non_coding_transcript_exon_variant,,ENST00000690451.1,n.3236G>A,MODIFIER,;EMC1,non_coding_transcript_exon_variant,,ENST00000688918.1,n.342G>A,MODIFIER,;EMC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000685099.1,c.*2067G>A,MODIFIER,;EMC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000692207.1,c.*1552G>A,MODIFIER,;EMC1,intron_variant,,ENST00000690732.1,c.1783-454G>A,MODIFIER,;EMC1,synonymous_variant,p.S596=,ENST00000477853.6,c.1788G>A,LOW,YES;EMC1,synonymous_variant,p.S555=,ENST00000688219.1,c.1665G>A,LOW,;EMC1-AS1,intron_variant,,ENST00000437898.3,n.213-8840C>T,MODIFIER,YES +NBPF3 84224 BI GRCh38 1 21483149 21483149 + synonymous_variant Silent SNP C C T rs1160087291 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 37 c.1665C>T p.Asn555= p.N555= ENST00000318249.10 NM_032264.6 555 aaC/aaT 15/15 P4 T N protein_coding YES CCDS216.1 1665/1902 CTCAACGAGGT PROSITE_profiles:PS51316;PANTHER:PTHR14199;PANTHER:PTHR14199:SF18;Pfam:PF06758;SMART:SM01148 ENSP00000316782 15/15 rs1160087291;COSV59057561 ENST00000318249 Transcript ENSG00000142794 HGNC:25076 LOW NM_032264.6 2.891e-05 gnomAD_AMR synonymous_variant 0;1 1.0 Unknown 0;1 Q9H094.127 NBPF3 HGNC 1 1.0 UPI0000037D6C Q9H094-1 SNV NBPF3,synonymous_variant,p.N555=,ENST00000318249,NM_032264.6,c.1665C>T,LOW,YES,,,1;NBPF3,synonymous_variant,p.N543=,ENST00000342104,NM_001256416.4,c.1629C>T,LOW,,,,1;NBPF3,synonymous_variant,p.N485=,ENST00000454000,NM_001256417.4,c.1455C>T,LOW,,,,1;NBPF3,synonymous_variant,p.N499=,ENST00000619554,NM_001377493.1&NM_001330381.3&NM_001377495.1&NM_001377492.1&NM_001377494.1&NM_001377496.1&NM_001377491.1,c.1497C>T,LOW,,,,1;NBPF3,non_coding_transcript_exon_variant,,ENST00000469876,,n.823C>T,MODIFIER,,,,1;NBPF3,downstream_gene_variant,,ENST00000477050,,,MODIFIER,,,,1;NBPF3,3_prime_UTR_variant,,ENST00000318220,,c.*2032C>T,MODIFIER,,,,1;NBPF3,3_prime_UTR_variant,,ENST00000434838,,c.*2253C>T,MODIFIER,,,,1 2016/3767 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.604e-05 0.0 2.891e-05 0.0 0.0 0.0 2.663e-05 0.0 0.0 0 146 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 75 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NBPF3,non_coding_transcript_exon_variant,,ENST00000469876.5,n.823C>T,MODIFIER,;NBPF3,synonymous_variant,p.N499=,ENST00000619554.1,c.1497C>T,LOW,;NBPF3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000434838.6,c.*2253C>T,MODIFIER,;NBPF3,synonymous_variant,p.N543=,ENST00000342104.9,c.1629C>T,LOW,;NBPF3,synonymous_variant,p.N555=,ENST00000318249.10,c.1665C>T,LOW,YES;NBPF3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000318220.10,c.*2032C>T,MODIFIER,;NBPF3,synonymous_variant,p.N485=,ENST00000454000.6,c.1455C>T,LOW, +HSPG2 3339 BI GRCh38 1 21850169 21850169 + missense_variant Missense_Mutation SNP G G A rs1160285381 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 12 c.7318C>T p.Arg2440Trp p.R2440W ENST00000374695.8 NM_005529.7 2440 Cgg/Tgg 57/97 P1 A R/W protein_coding YES CCDS30625.1 7318/13176 GATCCGGACCG COSM3385772 Gene3D:2.60.40.10;Pfam:PF07679;PROSITE_profiles:PS50835;PANTHER:PTHR11640;PANTHER:PTHR11640;PANTHER:PTHR11640:SF79;PANTHER:PTHR11640:SF79;Superfamily:SSF48726 ENSP00000363827 57/97 rs1160285381;COSV65969175 ENST00000374695 Transcript 1.0 ENSG00000142798 HGNC:5273 MODERATE NM_005529.7 8.863e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.979) Unknown deleterious(0) 0;1 P98160.227 HSPG2 HGNC -1 1.0 UPI0000212778 SNV HSPG2,missense_variant,p.R2440W,ENST00000374695,NM_005529.7&NM_001291860.2,c.7318C>T,MODERATE,YES,deleterious(0),probably_damaging(0.979),-1;HSPG2,upstream_gene_variant,,ENST00000453796,,,MODIFIER,,,,-1;HSPG2,downstream_gene_variant,,ENST00000493940,,,MODIFIER,,,,-1 7411/14341 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.999e-06 0.0 0.0 0.0 0.0 0.0 8.863e-06 0.0 0.0 6.7568498707260005e-06 0.0 0.0 6.621640204684809e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HSPG2,missense_variant,p.R2440W,ENST00000374695.8,c.7318C>T,MODERATE,YES +GRHL3 57822 BI GRCh38 1 24342713 24342713 + missense_variant Missense_Mutation SNP G G A rs1261266801 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 19 c.1226G>A p.Arg409His p.R409H ENST00000350501.9 NM_198174.3 409 cGc/cAc 10/16 A R/H protein_coding YES CCDS252.2 1226/1881 GATGCGCGATG PANTHER:PTHR11037:SF6;PANTHER:PTHR11037;Pfam:PF04516 ENSP00000288955 10/16 rs1261266801 ENST00000350501 Transcript 1.0 ENSG00000158055 HGNC:25839 MODERATE 3.518e-05 gnomAD_NFE missense_variant 1.0 probably_damaging(0.98) Unknown deleterious(0) Q8TE85.140 GRHL3 HGNC 1 2.0 UPI000049DC7B Q8TE85-1 SNV GRHL3,missense_variant,p.R409H,ENST00000361548,NM_198173.3,c.1226G>A,MODERATE,,deleterious(0),probably_damaging(0.966),1;GRHL3,missense_variant,p.R363H,ENST00000356046,NM_001195010.2,c.1088G>A,MODERATE,,deleterious(0),probably_damaging(0.963),1;GRHL3,missense_variant,p.R409H,ENST00000350501,NM_198174.3,c.1226G>A,MODERATE,YES,deleterious(0),probably_damaging(0.98),1;GRHL3,missense_variant,p.R414H,ENST00000236255,NM_021180.3,c.1241G>A,MODERATE,,deleterious(0),probably_damaging(0.966),1;GRHL3,3_prime_UTR_variant,,ENST00000528064,,c.*895G>A,MODIFIER,,,,1;GRHL3,non_coding_transcript_exon_variant,,ENST00000461318,,n.134G>A,MODIFIER,,,,1;GRHL3,downstream_gene_variant,,ENST00000528181,,,MODIFIER,,,,1 1353/2119 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0 0.0 0.0 0.0 0.0 3.518e-05 0.0 0.0 0 105 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GRHL3,missense_variant,p.R316H,ENST00000528064.6,c.947G>A,MODERATE,;GRHL3,missense_variant,p.R414H,ENST00000236255.4,c.1241G>A,MODERATE,;GRHL3,missense_variant,p.R363H,ENST00000524724.6,c.1088G>A,MODERATE,;GRHL3,missense_variant,p.R363H,ENST00000356046.6,c.1088G>A,MODERATE,;GRHL3,missense_variant,p.R409H,ENST00000350501.9,c.1226G>A,MODERATE,;GRHL3,missense_variant,p.R409H,ENST00000461318.2,c.1226G>A,MODERATE,;GRHL3,missense_variant,p.R409H,ENST00000361548.9,c.1226G>A,MODERATE,YES;GRHL3,missense_variant,p.R363H,ENST00000689444.1,c.1088G>A,MODERATE,;GRHL3,missense_variant,p.R316H,ENST00000692334.1,c.947G>A,MODERATE,;GRHL3,missense_variant,p.R316H,ENST00000690803.1,c.947G>A,MODERATE, +TRIM63 84676 BI GRCh38 1 26060279 26060279 + missense_variant Missense_Mutation SNP C C T rs764437396 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 27 c.584G>A p.Arg195His p.R195H ENST00000374272.4 NM_032588.4 195 cGt/cAt 4/9 P1 T R/H protein_coding YES CCDS273.1 584/1062 CTCGACGGGAA PANTHER:PTHR24103;PANTHER:PTHR24103:SF570 ENSP00000363390 4/9 rs764437396 ENST00000374272 Transcript ENSG00000158022 HGNC:16007 MODERATE NM_032588.4 6.153e-05 gnomAD_AFR missense_variant 1.0 benign(0.39) Unknown deleterious(0) Q969Q1.176 TRIM63 HGNC -1 1.0 UPI00000437F6 Q969Q1-1 SNV TRIM63,missense_variant,p.R195H,ENST00000374272,NM_032588.4,c.584G>A,MODERATE,YES,deleterious(0),benign(0.39),-1;TRIM63,downstream_gene_variant,,ENST00000483052,,,MODIFIER,,,,-1 720/1770 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.194e-05 6.153e-05 0.0 0.0 5.437e-05 0.0 8.794e-06 0.0 0.0 2.028229937423021e-05 7.296429976122454e-05 0.0 0.0 0.0 0.0 0.0 afr 7.296429976122454e-05 0.0 0.0 0.0 0.0 0 80 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TRIM63,missense_variant,p.R195H,ENST00000374272.4,c.584G>A,MODERATE,YES +SRSF4 6429 BI GRCh38 1 29149122 29149122 + missense_variant Missense_Mutation SNP C C T rs1447567488 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 146 117 c.773G>A p.Arg258His p.R258H ENST00000373795.7 NM_005626.5 258 cGc/cAc 6/6 P1 T R/H protein_coding YES CCDS333.1 773/1485 GGCTGCGGCTG COSM5053372 Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR23147:SF55;PANTHER:PTHR23147 ENSP00000362900 6/6 rs1447567488;COSV65694535 ENST00000373795 Transcript ENSG00000116350 HGNC:10786 MODERATE NM_005626.5 6.533e-05 gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.858) Unknown deleterious(0.02) 0;1 Q08170.193 SRSF4 HGNC -1 1.0 UPI00001358BF SNV SRSF4,missense_variant,p.R258H,ENST00000373795,NM_005626.5,c.773G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.858),-1;SRSF4,missense_variant,p.R228H,ENST00000466448,,c.683G>A,MODERATE,,tolerated(0.05),probably_damaging(0.933),-1;SRSF4,non_coding_transcript_exon_variant,,ENST00000634348,,n.6859G>A,MODIFIER,,,,-1;AL357500.1,upstream_gene_variant,,ENST00000413004,,,MODIFIER,YES,,,-1 921/2300 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.963e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.533e-05 0 210 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 264 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SRSF4,missense_variant,p.R228H,ENST00000466448.4,c.683G>A,MODERATE,;SRSF4,non_coding_transcript_exon_variant,,ENST00000634348.1,n.6859G>A,MODIFIER,;SRSF4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000691479.1,c.*980G>A,MODIFIER,;SRSF4,missense_variant,p.R258H,ENST00000373795.7,c.773G>A,MODERATE,YES +PTPRU 10076 BI GRCh38 1 29311656 29311656 + missense_variant Missense_Mutation SNP G G A rs752247574 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 26 c.2999G>A p.Arg1000Gln p.R1000Q ENST00000345512.7 NM_005704.5 1000 cGg/cAg 22/31 P4 A R/Q protein_coding YES CCDS334.1 2999/4341 CTCACGGTACT CDD:cd14632;Gene3D:3.90.190.10;Pfam:PF00102;SMART:SM00194;Superfamily:SSF52799;PROSITE_profiles:PS50055;PANTHER:PTHR19134;PANTHER:PTHR19134:SF207 ENSP00000334941 22/31 rs752247574 ENST00000345512 Transcript ENSG00000060656 HGNC:9683 MODERATE 0.0002719 gnomAD_EAS missense_variant 1.0 benign(0.194) Unknown tolerated(0.11) Q92729.192 PTPRU HGNC 1 1.0 UPI000013C57E Q92729-1 SNV PTPRU,missense_variant,p.R990Q,ENST00000373779,NM_133178.4,c.2969G>A,MODERATE,,tolerated(0.11),benign(0.122),1;PTPRU,missense_variant,p.R987Q,ENST00000428026,NM_001195001.2,c.2960G>A,MODERATE,,tolerated(0.13),benign(0.122),1;PTPRU,missense_variant,p.R996Q,ENST00000460170,NM_133177.4,c.2987G>A,MODERATE,,tolerated(0.11),benign(0.122),1;PTPRU,missense_variant,p.R1000Q,ENST00000345512,NM_005704.5,c.2999G>A,MODERATE,YES,tolerated(0.11),benign(0.194),1;PTPRU,non_coding_transcript_exon_variant,,ENST00000415600,,n.1332G>A,MODIFIER,,,,1;PTPRU,non_coding_transcript_exon_variant,,ENST00000526080,,n.213G>A,MODIFIER,,,,1 3128/4470 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.389e-05 0.0 2.893e-05 0.0 0.0002719 0.0 0.0 0.0 0.0 3.378649853402749e-05 2.4303699319716543e-05 0.0 0.0 0.0 0.0006041079759597 0.0 eas 0.0006041079759597 0.0 1.542919926578179e-05 0.0 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PTPRU,non_coding_transcript_exon_variant,,ENST00000526080.1,n.213G>A,MODIFIER,;PTPRU,non_coding_transcript_exon_variant,,ENST00000415600.6,n.1332G>A,MODIFIER,;PTPRU,missense_variant,p.R996Q,ENST00000460170.2,c.2987G>A,MODERATE,;PTPRU,missense_variant,p.R987Q,ENST00000428026.6,c.2960G>A,MODERATE,;PTPRU,missense_variant,p.R990Q,ENST00000373779.8,c.2969G>A,MODERATE,YES;PTPRU,missense_variant,p.R1000Q,ENST00000345512.7,c.2999G>A,MODERATE, +ZSCAN20 7579 BI GRCh38 1 33495249 33495249 + missense_variant Missense_Mutation SNP C C T rs763522543 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 20 c.2905C>T p.Arg969Cys p.R969C ENST00000361328.7 969 Cgt/Tgt 8/8 P1 T R/C protein_coding YES CCDS41300.1 2905/3132 TCTTCCGTGAC Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR23226;PANTHER:PTHR23226:SF220;SMART:SM00355;Superfamily:SSF57667 ENSP00000355053 8/8 rs763522543 ENST00000361328 Transcript ENSG00000121903 HGNC:13093 MODERATE 0.0001976 gnomAD_SAS missense_variant 1.0 probably_damaging(0.993) Unknown deleterious(0) P17040.193 ZSCAN20 HGNC 1 2.0 UPI0000D61EC5 P17040-1 SNV ZSCAN20,missense_variant,p.R969C,ENST00000361328,NM_001377376.1&NM_001377377.1&NM_001377379.1&NM_001377378.1&NM_145238.6,c.2905C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),1;ZSCAN20,downstream_gene_variant,,ENST00000373413,,,MODIFIER,,,,1 3058/4316 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.81e-05 0.0 0.0 0.0 0.0 0.0 8.854e-06 0.0 0.0001976 0 57 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZSCAN20,missense_variant,p.R969C,ENST00000684572.1,c.2905C>T,MODERATE,YES;ZSCAN20,missense_variant,p.R969C,ENST00000361328.7,c.2905C>T,MODERATE, +CSMD2 114784 BI GRCh38 1 33624546 33624546 + synonymous_variant Silent SNP G G A rs761883622 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 45 9 c.5598C>T p.Ile1866= p.I1866= ENST00000373381.9 NM_001281956.2 1866 atC/atT 35/71 A I nonsense_mediated_decay CCDS380.1 5478/10464 ACCACGATCTT COSM3488531;COSM3488532 ENSP00000241312 35/70 rs761883622;COSV53876669 ENST00000241312 Transcript ENSG00000121904 HGNC:19290 LOW 5.787e-05 gnomAD_AMR synonymous_variant 0;1 Unknown 0;1 Q7Z408.146 CSMD2 HGNC -1 1.0 UPI00004561AB Q7Z408-1 SNV CSMD2,synonymous_variant,p.I1866=,ENST00000373381,NM_001281956.2,c.5598C>T,LOW,YES,,,-1;CSMD2,synonymous_variant,p.I1826=,ENST00000619121,,c.5478C>T,LOW,,,,-1;CSMD2,synonymous_variant,p.I1826=,ENST00000373388,NM_052896.4,c.5478C>T,LOW,,,,-1;CSMD2,synonymous_variant,p.I739=,ENST00000373380,,c.2217C>T,LOW,,,,-1;CSMD2,5_prime_UTR_variant,,ENST00000373377,,c.-106C>T,MODIFIER,,,,-1;CSMD2,synonymous_variant,p.I1826=,ENST00000241312,,c.5478C>T,LOW,,,,-1 5507/13108 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.592e-05 0.0 5.787e-05 0.0 0.0 0.0 1.76e-05 0.0 0.0 6.760139967809664e-06 0.0 0.0 6.624269735766575e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 67 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 54 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CSMD2,non_coding_transcript_exon_variant,,ENST00000373377.1,n.401C>T,MODIFIER,;CSMD2,non_coding_transcript_exon_variant,,ENST00000373380.5,n.2438C>T,MODIFIER,;CSMD2,synonymous_variant,p.I1826=,ENST00000373388.7,c.5478C>T,LOW,;CSMD2,synonymous_variant,p.I1826=,ENST00000619121.4,c.5478C>T,LOW,;CSMD2,synonymous_variant,p.I1866=,ENST00000373381.9,c.5598C>T,LOW,YES +DLGAP3 58512 BI GRCh38 1 34900087 34900087 + missense_variant Missense_Mutation SNP C C T rs377551672 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 9 c.1294G>A p.Val432Met p.V432M ENST00000235180.4 432 Gtg/Atg 2/10 P1 T V/M protein_coding CCDS30670.1 1294/2940 GTCCACGCTGG COSM2079939 PANTHER:PTHR12353;PANTHER:PTHR12353:SF4 ENSP00000235180 0.0 0.0001163 2/10 rs377551672 ENST00000235180 Transcript ENSG00000116544 HGNC:30368 MODERATE 0.0001163 EA missense_variant benign(0.025) Unknown tolerated(0.25) O95886.136 DLGAP3 HGNC -1 2.0 UPI00003D4D81 SNV DLGAP3,missense_variant,p.V432M,ENST00000373347,NM_001080418.3,c.1294G>A,MODERATE,YES,tolerated(0.25),benign(0.025),-1;DLGAP3,missense_variant,p.V432M,ENST00000235180,,c.1294G>A,MODERATE,,tolerated(0.25),benign(0.025),-1 1294/3587 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.594e-05 0.0 0.0 0.0 0.0 0.0 3.519e-05 0.0 0.0 1.3518299965653569e-05 0.0 0.0 6.626029789913446e-05 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DLGAP3,missense_variant,p.V432M,ENST00000235180.4,c.1294G>A,MODERATE,;DLGAP3,missense_variant,p.V432M,ENST00000373347.6,c.1294G>A,MODERATE,YES +GRIK3 2899 BI GRCh38 1 36841902 36841902 + missense_variant Missense_Mutation SNP G G A rs376333303 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 47 47 c.1364C>T p.Thr455Met p.T455M ENST00000373091.8 NM_000831.4 455 aCg/aTg 10/16 P1 A T/M protein_coding YES CCDS416.1 1364/2760 ATAGCGTCCTG COSM186834;COSM3751170 Pfam:PF10613;PANTHER:PTHR18966;PANTHER:PTHR18966:SF174;SMART:SM00079;SMART:SM00918;Superfamily:SSF53850;CDD:cd13723 ENSP00000362183 0.0 0.0001163 10/16 rs376333303 ENST00000373091 Transcript ENSG00000163873 HGNC:4581 MODERATE NM_000831.4 0.001155 gnomAD_FIN missense_variant 1.0 benign(0.427) Unknown tolerated(0.13) Q13003.184 GRIK3 HGNC -1 1.0 UPI000013E311 Q13003-1 SNV GRIK3,missense_variant,p.T455M,ENST00000373091,NM_000831.4,c.1364C>T,MODERATE,YES,tolerated(0.13),benign(0.427),-1;GRIK3,missense_variant,p.T455M,ENST00000373093,,c.1364C>T,MODERATE,,tolerated(0.15),possibly_damaging(0.555),-1 1771/9491 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001312 0.0 0.0 0.0 0.0 0.001155 6.154e-05 0.0 3.266e-05 9.463299647904932e-05 2.4320199372596107e-05 0.0 0.0 0.0 0.0002016939979512 0.0009414419764652 fin 0.0009414419764652 0.0 1.5429699487867765e-05 0.0 0.0002085940068354 0 108 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 94 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GRIK3,missense_variant,p.T455M,ENST00000373093.4,c.1364C>T,MODERATE,;GRIK3,missense_variant,p.T455M,ENST00000373091.8,c.1364C>T,MODERATE,YES +COL9A2 1298 BI GRCh38 1 40311131 40311131 + missense_variant Missense_Mutation SNP G G A rs767929481 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 8 c.592C>T p.Arg198Cys p.R198C ENST00000372748.8 NM_001852.4 198 Cgc/Tgc 12/32 P1 A R/C protein_coding YES CCDS450.1 592/2070 CCCGCGTTTGC Pfam:PF01391;PANTHER:PTHR24023;PANTHER:PTHR24023:SF906 ENSP00000361834 12/32 rs767929481 ENST00000372748 Transcript 1.0 ENSG00000049089 HGNC:2218 MODERATE NM_001852.4 6.533e-05 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.659) Unknown deleterious(0.01) Q14055.184 COL9A2 HGNC -1 1.0 UPI0000126D47 SNV COL9A2,missense_variant,p.R198C,ENST00000372748,NM_001852.4,c.592C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.659),-1;COL9A2,missense_variant,p.R104C,ENST00000417105,,c.310C>T,MODERATE,,deleterious(0),possibly_damaging(0.659),-1;COL9A2,downstream_gene_variant,,ENST00000372736,,,MODIFIER,,,,-1;COL9A2,downstream_gene_variant,,ENST00000642679,,,MODIFIER,,,,-1;COL9A2,non_coding_transcript_exon_variant,,ENST00000488463,,n.643C>T,MODIFIER,,,,-1;COL9A2,downstream_gene_variant,,ENST00000490132,,,MODIFIER,,,,-1;COL9A2,non_coding_transcript_exon_variant,,ENST00000482722,,n.895C>T,MODIFIER,,,,-1;COL9A2,downstream_gene_variant,,ENST00000461118,,,MODIFIER,,,,-1;COL9A2,downstream_gene_variant,,ENST00000495948,,,MODIFIER,,,,-1;COL9A2,downstream_gene_variant,,ENST00000496215,,,MODIFIER,,,,-1 681/2852 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0 0.0 0.0 0.0 4.619e-05 8.798e-06 0.0 6.533e-05 2.7042000510846265e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.630059993360192e-05 0.0 4.630059993360192e-05 0.0 0.0002084199950331 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COL9A2,missense_variant,p.R104C,ENST00000417105.6,c.310C>T,MODERATE,;COL9A2,non_coding_transcript_exon_variant,,ENST00000488463.6,n.643C>T,MODIFIER,;COL9A2,non_coding_transcript_exon_variant,,ENST00000482722.5,n.895C>T,MODIFIER,;COL9A2,missense_variant,p.R198C,ENST00000372748.8,c.592C>T,MODERATE,YES +HIVEP3 59269 BI GRCh38 1 41583282 41583282 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 26 c.1516C>T p.Arg506Trp p.R506W ENST00000372583.6 NM_024503.5 506 Cgg/Tgg 4/9 P5 A R/W protein_coding YES CCDS463.1 1516/7221 CTCCCGGTAGA PANTHER:PTHR45944;PANTHER:PTHR45944:SF5;MobiDB_lite:mobidb-lite ENSP00000361664 4/9 ENST00000372583 Transcript ENSG00000127124 HGNC:13561 MODERATE NM_024503.5 missense_variant 1.0 probably_damaging(0.987) Unknown deleterious(0) Q5T1R4.146 HIVEP3 HGNC -1 1.0 UPI000013CC24 Q5T1R4-1 SNV HIVEP3,missense_variant,p.R506W,ENST00000372583,NM_024503.5,c.1516C>T,MODERATE,YES,deleterious(0),probably_damaging(0.987),-1;HIVEP3,missense_variant,p.R506W,ENST00000372584,NM_001127714.3,c.1516C>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1;HIVEP3,missense_variant,p.R506W,ENST00000643665,,c.1516C>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1;AC119676.1,downstream_gene_variant,,ENST00000646142,,,MODIFIER,YES,,,-1;HIVEP3,upstream_gene_variant,,ENST00000460604,,,MODIFIER,,,,-1 2826/12617 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 69 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HIVEP3,missense_variant,p.R506W,ENST00000372584.5,c.1516C>T,MODERATE,;HIVEP3,missense_variant,p.R506W,ENST00000643665.1,c.1516C>T,MODERATE,;HIVEP3,missense_variant,p.R506W,ENST00000372583.6,c.1516C>T,MODERATE,YES +ST3GAL3 6487 BI GRCh38 1 43920545 43920545 + missense_variant Missense_Mutation SNP C C T rs554609799 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 15 c.931C>T p.Arg311Trp p.R311W ENST00000361392.9 NM_174964.4 311 Cgg/Tgg 10/12 0.0002 0.0 0.0 0.001 0.0 0.0 T R/W protein_coding CCDS494.1 931/1173 TGGGCCGGGGG PANTHER:PTHR13713:SF37;PANTHER:PTHR13713;PIRSF:PIRSF005557;Gene3D:3.90.1480.20;Pfam:PF00777 ENSP00000355341 10/12 rs554609799 ENST00000361392 Transcript 1.0 ENSG00000126091 HGNC:10866 MODERATE 0.001 EAS missense_variant probably_damaging(0.989) Unknown deleterious(0) Q11203.185 ST3GAL3 HGNC 1 1.0 UPI0000074408 Q11203-2 SNV ST3GAL3,missense_variant,p.R311W,ENST00000642331,NM_001350619.2,c.931C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;ST3GAL3,missense_variant,p.R296W,ENST00000643252,NM_001350620.2,c.886C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;ST3GAL3,missense_variant,p.R365W,ENST00000262915,NM_174963.5,c.1093C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;ST3GAL3,missense_variant,p.R350W,ENST00000351035,NM_174968.5,c.1048C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;ST3GAL3,missense_variant,p.R296W,ENST00000647148,,c.886C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;ST3GAL3,missense_variant,p.R296W,ENST00000646971,,c.886C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;ST3GAL3,missense_variant,p.R296W,ENST00000644195,,c.886C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;ST3GAL3,missense_variant,p.R311W,ENST00000361392,NM_174964.4,c.931C>T,MODERATE,,deleterious(0),probably_damaging(0.989),1;ST3GAL3,missense_variant,p.R296W,ENST00000645034,,c.886C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;ST3GAL3,missense_variant,p.R296W,ENST00000347631,NM_006279.5,c.886C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;ST3GAL3,missense_variant,p.R327W,ENST00000361746,,c.979C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ST3GAL3,missense_variant,p.R280W,ENST00000646686,NM_001350621.2,c.838C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;ST3GAL3,missense_variant,p.R280W,ENST00000361400,NM_174969.4,c.838C>T,MODERATE,,deleterious(0),probably_damaging(0.967),1;ST3GAL3,missense_variant,p.R265W,ENST00000372374,NM_001270460.2,c.793C>T,MODERATE,,deleterious(0),probably_damaging(0.971),1;ST3GAL3,missense_variant,p.R334W,ENST00000372372,NM_174971.5,c.1000C>T,MODERATE,,deleterious(0),probably_damaging(0.978),1;ST3GAL3,missense_variant,p.R350W,ENST00000372368,,c.1048C>T,MODERATE,,deleterious(0),probably_damaging(0.99),1;ST3GAL3,missense_variant,p.R261W,ENST00000644287,,c.781C>T,MODERATE,,deleterious(0),probably_damaging(0.99),1;ST3GAL3,missense_variant,p.R277W,ENST00000533933,,c.829C>T,MODERATE,,deleterious(0.01),probably_damaging(0.982),1;ST3GAL3,missense_variant,p.R225W,ENST00000332628,,c.673C>T,MODERATE,,deleterious(0),probably_damaging(0.975),1;ST3GAL3,missense_variant,p.R266W,ENST00000372369,NM_001270459.2,c.796C>T,MODERATE,,deleterious(0),probably_damaging(0.981),1;ST3GAL3,missense_variant,p.R95W,ENST00000490502,,c.283C>T,MODERATE,,deleterious(0),probably_damaging(0.99),1;ST3GAL3,intron_variant,,ENST00000330208,NM_001270466.2,c.255-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000335430,NM_001270465.2,c.*23-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000353126,NM_174966.4,c.745-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000361812,,c.443-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000372362,NM_174967.4,c.398-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000372365,,c.*23-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000372366,,c.*23-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000372367,NM_001270463.3,c.555-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000528371,NM_001270464.3,c.510-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000531451,NM_174970.4,c.350-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000531816,,c.255-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000531993,NM_001270462.3,c.604-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000545417,NM_174965.3,c.443-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000642934,NM_001270461.3,c.697-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000644922,,c.712-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000645117,,c.*23-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000647237,NM_001363573.2,c.907-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000647503,,c.440-9587C>T,MODIFIER,,,,1;ST3GAL3,downstream_gene_variant,,ENST00000643989,,,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000461375,,n.848C>T,MODIFIER,,,,1;ST3GAL3,missense_variant,p.R265W,ENST00000646069,,c.793C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;ST3GAL3,synonymous_variant,p.A287=,ENST00000646027,,c.861C>T,LOW,,,,1;ST3GAL3,synonymous_variant,p.A217=,ENST00000530581,,c.651C>T,LOW,,,,1;AL451062.2,3_prime_UTR_variant,,ENST00000645057,,c.*2208C>T,MODIFIER,YES,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000645640,,c.*694C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000645142,,c.*348C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000642949,,c.*348C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000645705,,c.*350C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000645165,,c.*694C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000643283,,c.*348C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000647134,,c.*711C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000647482,,c.*480C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000642504,,c.*711C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000643813,,c.*763C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000645394,,c.*348C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000642194,,c.*83C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000642780,,c.*351C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000469715,,c.*512C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000490541,,c.*663C>T,MODIFIER,,,,1;ST3GAL3,3_prime_UTR_variant,,ENST00000533212,,c.*83C>T,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645670,,n.1444C>T,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000495482,,n.1433C>T,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000644016,,n.856C>T,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645644,,n.848C>T,MODIFIER,,,,1;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645012,,n.534C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000489897,,c.*366-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000533997,,c.*570-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000643597,,c.*189-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000644378,,n.589-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000644645,,c.*210-9587C>T,MODIFIER,,,,1;ST3GAL3,intron_variant,,ENST00000647128,,c.*111-9587C>T,MODIFIER,,,,1;ST3GAL3,downstream_gene_variant,,ENST00000530154,,,MODIFIER,,,,1;ST3GAL3,downstream_gene_variant,,ENST00000646032,,,MODIFIER,,,,1 1117/2297 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.3591000424639788e-05 2.4462999135721475e-05 0.0 0.0 0.0 0.0002056770026683 0.0 0.0 0.0 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ST3GAL3,non_coding_transcript_exon_variant,,ENST00000495482.2,n.1433C>T,MODIFIER,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645670.1,n.1444C>T,MODIFIER,;ST3GAL3,synonymous_variant,p.A94=,ENST00000490502.1,c.282C>T,LOW,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645012.1,n.534C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000644378.1,n.589-9587C>T,MODIFIER,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000644016.1,n.856C>T,MODIFIER,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000645644.1,n.848C>T,MODIFIER,;ST3GAL3,intron_variant,NMD_transcript_variant,,ENST00000644645.1,c.*210-9587C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642780.1,c.*351C>T,MODIFIER,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000461375.2,n.848C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000647503.1,c.440-9587C>T,MODIFIER,;ST3GAL3,synonymous_variant,p.A260=,ENST00000644287.1,c.780C>T,LOW,;ST3GAL3,intron_variant,,ENST00000644922.1,c.712-9587C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643813.1,c.*763C>T,MODIFIER,;ST3GAL3,synonymous_variant,p.A224=,ENST00000332628.11,c.672C>T,LOW,;ST3GAL3,missense_variant,p.R277W,ENST00000533933.6,c.829C>T,MODERATE,;ST3GAL3,intron_variant,,ENST00000645117.1,c.*23-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000372366.6,c.*23-9587C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000490541.6,c.*663C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000531451.5,c.350-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000372362.6,c.398-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000531993.6,c.604-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000372365.5,c.*23-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000372367.5,c.555-9587C>T,MODIFIER,;ST3GAL3,missense_variant,p.R266W,ENST00000372369.5,c.796C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000469715.6,c.*512C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000533212.5,c.*83C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000361812.9,c.443-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000531816.1,c.255-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000528371.5,c.510-9587C>T,MODIFIER,;ST3GAL3,synonymous_variant,NMD_transcript_variant,p.A217=,ENST00000530581.5,c.651C>T,LOW,;ST3GAL3,missense_variant,p.R280W,ENST00000646686.1,c.838C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642194.1,c.*83C>T,MODIFIER,;ST3GAL3,missense_variant,p.R350W,ENST00000372368.7,c.1048C>T,MODERATE,;ST3GAL3,missense_variant,p.R296W,ENST00000644195.1,c.886C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647134.1,c.*711C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645165.1,c.*694C>T,MODIFIER,;ST3GAL3,missense_variant,p.R296W,ENST00000645034.1,c.886C>T,MODERATE,;ST3GAL3,missense_variant,p.R327W,ENST00000361746.9,c.979C>T,MODERATE,;ST3GAL3,intron_variant,NMD_transcript_variant,,ENST00000647128.1,c.*111-9587C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645394.1,c.*348C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647482.1,c.*480C>T,MODIFIER,;ST3GAL3,missense_variant,p.R365W,ENST00000262915.8,c.1093C>T,MODERATE,;ST3GAL3,missense_variant,p.R296W,ENST00000647148.1,c.886C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642504.1,c.*711C>T,MODIFIER,;ST3GAL3,missense_variant,NMD_transcript_variant,p.R265W,ENST00000646069.1,c.793C>T,MODERATE,;ST3GAL3,synonymous_variant,NMD_transcript_variant,p.A287=,ENST00000646027.1,c.861C>T,LOW,;ST3GAL3,missense_variant,p.R296W,ENST00000646971.1,c.886C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645705.1,c.*350C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645142.1,c.*348C>T,MODIFIER,;ST3GAL3,intron_variant,NMD_transcript_variant,,ENST00000489897.6,c.*366-9587C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642949.1,c.*348C>T,MODIFIER,;ST3GAL3,missense_variant,p.R350W,ENST00000351035.8,c.1048C>T,MODERATE,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643283.1,c.*348C>T,MODIFIER,;ST3GAL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645640.1,c.*694C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000642934.1,c.697-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000353126.8,c.745-9587C>T,MODIFIER,;ST3GAL3,intron_variant,NMD_transcript_variant,,ENST00000533997.6,c.*570-9587C>T,MODIFIER,;ST3GAL3,missense_variant,p.R311W,ENST00000361392.9,c.931C>T,MODERATE,;ST3GAL3,intron_variant,,ENST00000647237.1,c.907-9587C>T,MODIFIER,;ST3GAL3,missense_variant,p.R311W,ENST00000642331.1,c.931C>T,MODERATE,;ST3GAL3,missense_variant,p.R265W,ENST00000372374.7,c.793C>T,MODERATE,;ST3GAL3,missense_variant,p.R296W,ENST00000643252.1,c.886C>T,MODERATE,;ST3GAL3,missense_variant,p.R296W,ENST00000347631.8,c.886C>T,MODERATE,YES;ST3GAL3,missense_variant,p.R280W,ENST00000361400.9,c.838C>T,MODERATE,;ST3GAL3,intron_variant,,ENST00000335430.10,c.*23-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000545417.5,c.443-9587C>T,MODIFIER,;ST3GAL3,intron_variant,,ENST00000330208.6,c.255-9587C>T,MODIFIER,;ST3GAL3,missense_variant,p.R334W,ENST00000372372.7,c.1000C>T,MODERATE,;ST3GAL3,intron_variant,NMD_transcript_variant,,ENST00000643597.1,c.*189-9587C>T,MODIFIER,;ENSG00000284989,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645057.1,c.*2208C>T,MODIFIER,YES +SLC6A9 6536 BI GRCh38 1 43997900 43997900 + synonymous_variant Silent SNP G G A rs145370858 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 4 c.1881C>T p.Tyr627= p.Y627= ENST00000360584.6 NM_201649.4 627 taC/taT 13/14 A Y protein_coding YES CCDS41317.1 1881/2121 ATGGCGTAGAG Transmembrane_helices:TMhelix;PROSITE_profiles:PS50267;CDD:cd11498;PANTHER:PTHR11616:SF263;PANTHER:PTHR11616;Pfam:PF00209;Superfamily:SSF161070 ENSP00000353791 0.000227 0.0 13/14 rs145370858 ENST00000360584 Transcript 1.0 ENSG00000196517 HGNC:11056 LOW 0.000227 AA synonymous_variant 1.0 Unknown P48067.166 SLC6A9 HGNC -1 1.0 UPI000053030B P48067-1 SNV SLC6A9,synonymous_variant,p.Y554=,ENST00000372310,NM_001024845.3,c.1662C>T,LOW,,,,-1;SLC6A9,synonymous_variant,p.Y554=,ENST00000673836,NM_001328629.1,c.1662C>T,LOW,,,,-1;SLC6A9,synonymous_variant,p.Y627=,ENST00000360584,NM_201649.4,c.1881C>T,LOW,YES,,,-1;SLC6A9,synonymous_variant,p.Y573=,ENST00000357730,NM_001328627.1&NM_001261380.2&NM_006934.4,c.1719C>T,LOW,,,,-1;SLC6A9,synonymous_variant,p.Y443=,ENST00000475075,NM_001328630.2&NM_001328626.2&NM_001328628.1,c.1329C>T,LOW,,,,-1;SLC6A9,intron_variant,,ENST00000372306,,c.1624+2867C>T,MODIFIER,,,,-1;SLC6A9,intron_variant,,ENST00000372307,,c.1341+2867C>T,MODIFIER,,,,-1;CCDC24,downstream_gene_variant,,ENST00000372318,NM_001349127.1&NM_152499.4&NM_001349128.1&NM_001349129.1,,MODIFIER,YES,,,1;CCDC24,downstream_gene_variant,,ENST00000466180,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000472562,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000479055,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000460543,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000463846,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000485811,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000486064,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000486504,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000490064,,,MODIFIER,,,,1;CCDC24,downstream_gene_variant,,ENST00000490563,,,MODIFIER,,,,1 2073/2330 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.391e-05 6.164e-05 0.0 0.0 0.0 0.0 8.817e-06 0.0 0.0001307 2.027409936999902e-05 4.861690104007721e-05 0.0 6.621640204684809e-05 0.0 0.0 0.0 afr 4.861690104007721e-05 0.0 0.0 0.0 0.0 0 41 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC6A9,synonymous_variant,p.Y573=,ENST00000357730.6,c.1719C>T,LOW,;SLC6A9,synonymous_variant,p.Y627=,ENST00000360584.6,c.1881C>T,LOW,;SLC6A9,synonymous_variant,p.Y443=,ENST00000475075.6,c.1329C>T,LOW,;SLC6A9,synonymous_variant,p.Y554=,ENST00000673836.1,c.1662C>T,LOW,;SLC6A9,synonymous_variant,p.Y554=,ENST00000372310.8,c.1662C>T,LOW,YES;SLC6A9,intron_variant,,ENST00000372306.7,c.1624+2867C>T,MODIFIER,;SLC6A9,intron_variant,,ENST00000372307.7,c.1341+2867C>T,MODIFIER, +CDCP2 200008 BI GRCh38 1 54144713 54144713 + synonymous_variant Silent SNP G G A rs150004831 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 11 12 c.180C>T p.Ile60= p.I60= ENST00000371330.1 NM_201546.4 60 atC/atT 2/4 A I protein_coding CCDS588.2 180/1350 ACCACGATCAG COSM2193645 PROSITE_profiles:PS01180;CDD:cd00041;PANTHER:PTHR45645;Pfam:PF00431;Gene3D:2.60.120.290;SMART:SM00042;Superfamily:SSF49854 ENSP00000360381 0.000227 0.0 2/4 rs150004831 ENST00000371330 Transcript ENSG00000157211 HGNC:27297 LOW 0.000227 AA synonymous_variant Unknown Q5VXM1.114 CDCP2 HGNC -1 2.0 UPI0000458963 Q5VXM1-1 SNV CDCP2,synonymous_variant,p.I60=,ENST00000371330,NM_201546.4,c.180C>T,LOW,,,,-1;CDCP2,synonymous_variant,p.I60=,ENST00000530059,NM_001353655.1,c.180C>T,LOW,YES,,,-1;AL357673.1,non_coding_transcript_exon_variant,,ENST00000525949,,n.193C>T,MODIFIER,,,,-1;AL357673.1,3_prime_UTR_variant,,ENST00000637610,,c.*344C>T,MODIFIER,YES,,,-1;AL357673.1,3_prime_UTR_variant,,ENST00000311841,,c.*528C>T,MODIFIER,,,,-1;AL357673.2,downstream_gene_variant,,ENST00000623663,,,MODIFIER,YES,,,1 1028/2723 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2e-05 0.0001231 0.0 0.0 0.0001087 0.0 0.0 0.0 3.267e-05 5.406139825936407e-05 0.0001701669971225 0.0 0.0 0.0 0.0 0.0 afr 0.0001701669971225 0.0 1.542830068501644e-05 0.0 0.0 0 29 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 23 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000256407,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000311841.7,c.*528C>T,MODIFIER,;ENSG00000256407,non_coding_transcript_exon_variant,,ENST00000525949.1,n.193C>T,MODIFIER,;CDCP2,synonymous_variant,p.I60=,ENST00000371330.1,c.180C>T,LOW,;CDCP2,synonymous_variant,p.I60=,ENST00000530059.3,c.180C>T,LOW,YES;ENSG00000256407,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000637610.1,c.*344C>T,MODIFIER,YES +CACHD1 57685 BI GRCh38 1 64675411 64675411 + missense_variant Missense_Mutation SNP C C T rs182391558 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 77 11 c.2738C>T p.Thr913Met p.T913M ENST00000651257.2 NM_020925.4 913 aCg/aTg 20/27 0.0002 0.0 0.0014 0.0 0.0 0.0 A2 T T/M protein_coding YES 2738/3825 TTTGACGAACC COSM3400948 PANTHER:PTHR10166;PANTHER:PTHR10166:SF40 ENSP00000498498 20/27 rs182391558;COSV51547812 ENST00000651257 Transcript ENSG00000158966 HGNC:29314 MODERATE NM_020925.4 0.0014 AMR missense_variant 0;1 1.0 benign(0.246) Unknown deleterious(0) 0;1 Q5VU97.124 CACHD1 HGNC 1 UPI00015B3BA1 Q5VU97-1 SNV CACHD1,missense_variant,p.T913M,ENST00000651257,NM_020925.4,c.2738C>T,MODERATE,YES,deleterious(0),benign(0.246),1;CACHD1,missense_variant,p.T779M,ENST00000650260,NM_001293274.1,c.2336C>T,MODERATE,,deleterious(0),benign(0.246),1;CACHD1,missense_variant,p.T862M,ENST00000290039,,c.2585C>T,MODERATE,,deleterious(0),benign(0.246),1;CACHD1,non_coding_transcript_exon_variant,,ENST00000495994,,n.2968C>T,MODIFIER,,,,1;CACHD1,non_coding_transcript_exon_variant,,ENST00000470527,,n.2676C>T,MODIFIER,,,,1 3354/5933 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.994e-05 0.0 5.814e-05 0.0 5.442e-05 0.0 8.814e-06 0.0 3.273e-05 2.02863993763458e-05 0.0 0.0 6.626910180784762e-05 0.0 0.0 0.0 nfe 3.086420110776089e-05 0.0 3.086420110776089e-05 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 88 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CACHD1,non_coding_transcript_exon_variant,,ENST00000470527.1,n.2676C>T,MODIFIER,;CACHD1,non_coding_transcript_exon_variant,,ENST00000495994.5,n.2968C>T,MODIFIER,;CACHD1,missense_variant,p.T779M,ENST00000650260.1,c.2336C>T,MODERATE,;CACHD1,missense_variant,p.T862M,ENST00000290039.6,c.2585C>T,MODERATE,;CACHD1,missense_variant,p.T913M,ENST00000651257.2,c.2738C>T,MODERATE,YES +CLCA1 1179 BI GRCh38 1 86494297 86494297 + synonymous_variant Silent SNP G G A rs899149911 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 19 c.1791G>A p.Thr597= p.T597= ENST00000234701.7 597 acG/acA 12/15 P1 A T protein_coding YES CCDS709.1 1791/2745 AAAACGAACAA COSM3419537 TIGRFAM:TIGR00868;PANTHER:PTHR10579:SF2;PANTHER:PTHR10579 ENSP00000234701 12/15 rs899149911;COSV52327435 ENST00000234701 Transcript ENSG00000016490 HGNC:2015 LOW synonymous_variant 0;1 1.0 Unknown 0;1 A8K7I4.105 CLCA1 HGNC 1 1.0 UPI00001AE689 SNV CLCA1,synonymous_variant,p.T597=,ENST00000234701,,c.1791G>A,LOW,YES,,,1;CLCA1,synonymous_variant,p.T597=,ENST00000394711,NM_001285.4,c.1791G>A,LOW,,,,1 2142/3310 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 43 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CLCA1,synonymous_variant,p.T597=,ENST00000394711.2,c.1791G>A,LOW,YES;CLCA1,synonymous_variant,p.T597=,ENST00000234701.7,c.1791G>A,LOW, +NOTCH2 4853 BI GRCh38 1 119963578 119963578 + synonymous_variant Silent SNP C C T rs369028361 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 168 11 c.1911G>A p.Thr637= p.T637= ENST00000256646.7 NM_024408.4 637 acG/acA 11/34 P1 T T protein_coding YES CCDS908.1 1911/7416 CCTGACGTGCC CDD:cd00054;Gene3D:2.10.25.10;PIRSF:PIRSF002279;Pfam:PF00008;SMART:SM00179;SMART:SM00181;Superfamily:SSF57184;PROSITE_profiles:PS50026;PANTHER:PTHR24033;PANTHER:PTHR24033:SF157;PROSITE_patterns:PS00022 ENSP00000256646 0.0 0.0001163 11/34 rs369028361 ENST00000256646 Transcript 1.0 ENSG00000134250 HGNC:7882 LOW NM_024408.4 0.0001163 EA synonymous_variant 1.0 Unknown Q04721.230 NOTCH2 HGNC -1 1.0 UPI000013CF1D SNV NOTCH2,synonymous_variant,p.T637=,ENST00000256646,NM_024408.4&NM_001200001.1,c.1911G>A,LOW,YES,,,-1;NOTCH2,synonymous_variant,p.T598=,ENST00000579475,,c.1794G>A,LOW,,,,-1;NOTCH2,3_prime_UTR_variant,,ENST00000640021,,c.*1035G>A,MODIFIER,,,,-1;NOTCH2,non_coding_transcript_exon_variant,,ENST00000479412,,n.2049G>A,MODIFIER,,,,-1 2167/11425 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.195e-05 0.0 0.0 0.0 0.0 0.0 2.648e-05 0.0 0.0 2.0278799638617784e-05 4.8626301577314734e-05 0.0 0.0 0.0 0.0 0.0 afr 4.8626301577314734e-05 0.0 1.5431100109708495e-05 0.0 0.0 0 195 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 180 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NOTCH2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000640021.1,c.*1035G>A,MODIFIER,;NOTCH2,non_coding_transcript_exon_variant,,ENST00000479412.2,n.2049G>A,MODIFIER,;NOTCH2,synonymous_variant,p.T637=,ENST00000256646.7,c.1911G>A,LOW,YES +TCHH 7062 BI GRCh38 1 152109157 152109157 + missense_variant Missense_Mutation SNP G G A rs780658407 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 204 22 c.4060C>T p.Arg1354Cys p.R1354C ENST00000614923.2 1354 Cgc/Tgc 2/2 P1 A R/C protein_coding CCDS41396.1 4060/5832 GCGGCGCAGCG COSM895994 PANTHER:PTHR34855;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000357794 2/2 rs780658407;COSV64278195 ENST00000368804 Transcript 1.0 ENSG00000159450 HGNC:11791 MODERATE 1.766e-05 gnomAD_NFE missense_variant 0;1 benign(0.025) Unknown deleterious_low_confidence(0) 0;1 Q07283.169 TCHH HGNC -1 5.0 UPI0000458A5E SNV TCHH,missense_variant,p.R1354C,ENST00000614923,NM_007113.3,c.4060C>T,MODERATE,YES,deleterious_low_confidence(0),benign(0.025),-1;TCHH,missense_variant,p.R1354C,ENST00000368804,,c.4060C>T,MODERATE,,deleterious_low_confidence(0),benign(0.025),-1 4060/6900 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.015e-06 0.0 0.0 0.0 0.0 0.0 1.766e-05 0.0 0.0 6.779389877920039e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5461200746358372e-05 0.0 0.0 0 214 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 226 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TCHH,missense_variant,p.R1354C,ENST00000614923.2,c.4060C>T,MODERATE,YES +EFNA4 1945 BI GRCh38 1 155068970 155068970 + missense_variant Missense_Mutation SNP G G A rs200331554 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 11 c.587G>A p.Arg196His p.R196H ENST00000368409.8 NM_005227.3 196 cGt/cAt 4/4 A2 A R/H protein_coding CCDS1089.1 587/606 TCTTCGTCTTC COSM4022934 PANTHER:PTHR11304;PANTHER:PTHR11304:SF42;Low_complexity_(Seg):seg ENSP00000357394 4/4 rs200331554;COSV63018009 ENST00000368409 Transcript ENSG00000243364 HGNC:3224 MODERATE NM_005227.3 0.0001386 gnomAD_FIN missense_variant 0;1 probably_damaging(0.987) Unknown deleterious_low_confidence(0.04) 0;1 P52798.172 EFNA4 HGNC 1 1.0 UPI0000129C90 P52798-1 SNV EFNA4,missense_variant,p.R196H,ENST00000368409,NM_005227.3,c.587G>A,MODERATE,,deleterious_low_confidence(0.04),probably_damaging(0.987),1;EFNA4,intron_variant,,ENST00000359751,NM_182690.3,c.470-29G>A,MODIFIER,,,,1;EFNA4,intron_variant,,ENST00000427683,NM_182689.2,c.470-49G>A,MODIFIER,YES,,,1;AL691442.1,intron_variant,,ENST00000505139,,c.113+5034G>A,MODIFIER,YES,,,1 671/1254 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.786e-05 0.0 0.0 0.0 0.0 0.0001386 2.64e-05 0.0 3.269e-05 6.0879101511090994e-05 4.868079849984497e-05 0.0 0.0 0.0 0.0 0.00028328600456 fin 0.00028328600456 0.0 6.173409929033369e-05 0.0 0.0 0 78 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 49 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EFNA4,intron_variant,,ENST00000427683.2,c.470-49G>A,MODIFIER,;EFNA4-EFNA3,intron_variant,,ENST00000505139.1,c.113+5034G>A,MODIFIER,YES;EFNA4,missense_variant,p.R196H,ENST00000368409.8,c.587G>A,MODERATE,YES;EFNA4,intron_variant,,ENST00000359751.8,c.470-29G>A,MODIFIER, +THBS3 7059 BI GRCh38 1 155198098 155198098 + missense_variant Missense_Mutation SNP C C T rs373078740 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 26 4 c.2197G>A p.Val733Ile p.V733I ENST00000368378.7 NM_007112.5 733 Gtc/Atc 18/23 P1 T V/I protein_coding YES CCDS1099.1 2197/2871 CAGGACGACGG Gene3D:2.60.120.200;PROSITE_profiles:PS51236;PANTHER:PTHR10199;PANTHER:PTHR10199:SF89;Superfamily:SSF49899 ENSP00000357362 18/23 rs373078740 ENST00000368378 Transcript ENSG00000169231 HGNC:11787 MODERATE NM_007112.5 6.533e-05 gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(0.29) P49746.185 THBS3 HGNC -1 1.0 UPI000013776E P49746-1 SNV THBS3,missense_variant,p.V724I,ENST00000541576,NM_001252607.1,c.2170G>A,MODERATE,,tolerated(0.29),benign(0),-1;THBS3,missense_variant,p.V733I,ENST00000368378,NM_007112.5,c.2197G>A,MODERATE,YES,tolerated(0.29),benign(0),-1;THBS3,missense_variant,p.V262I,ENST00000541990,,c.784G>A,MODERATE,,tolerated(0.55),benign(0),-1;THBS3,missense_variant,p.V613I,ENST00000457183,NM_001252608.2,c.1837G>A,MODERATE,,tolerated(0.3),benign(0),-1;MIR92B,downstream_gene_variant,,ENST00000607575,,,MODIFIER,YES,,,1;THBS3,non_coding_transcript_exon_variant,,ENST00000465596,,n.462G>A,MODIFIER,,,,-1;THBS3,downstream_gene_variant,,ENST00000460050,,,MODIFIER,,,,-1;THBS3,downstream_gene_variant,,ENST00000486260,,,MODIFIER,,,,-1;THBS3,3_prime_UTR_variant,,ENST00000428962,,c.*519G>A,MODIFIER,,,,-1;THBS3,upstream_gene_variant,,ENST00000469769,,,MODIFIER,,,,-1;THBS3,downstream_gene_variant,,ENST00000496332,,,MODIFIER,,,,-1;THBS3,upstream_gene_variant,,ENST00000498500,,,MODIFIER,,,,-1;THBS3-AS1,intron_variant,,ENST00000447623,,n.533-305C>T,MODIFIER,YES,,,1;THBS3-AS1,upstream_gene_variant,,ENST00000422665,,,MODIFIER,,,,1;THBS3-AS1,upstream_gene_variant,,ENST00000430312,,,MODIFIER,,,,1;THBS3-AS1,upstream_gene_variant,,ENST00000436772,,,MODIFIER,,,,1;THBS3-AS1,upstream_gene_variant,,ENST00000453136,,,MODIFIER,,,,1;THBS3-AS1,upstream_gene_variant,,ENST00000454348,,,MODIFIER,,,,1 2218/3145 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.387e-05 0.0 0.0 0.0 5.437e-05 4.619e-05 1.759e-05 0.0 6.533e-05 1.3521000255423132e-05 2.4328499421244487e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002083330036839 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS THBS3,non_coding_transcript_exon_variant,,ENST00000465596.1,n.462G>A,MODIFIER,;THBS3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000428962.2,c.*519G>A,MODIFIER,;THBS3,missense_variant,p.V262I,ENST00000541990.5,c.784G>A,MODERATE,;THBS3,missense_variant,p.V613I,ENST00000457183.6,c.1837G>A,MODERATE,;THBS3,missense_variant,p.V724I,ENST00000541576.5,c.2170G>A,MODERATE,;THBS3,missense_variant,p.V733I,ENST00000368378.7,c.2197G>A,MODERATE,YES;THBS3-AS1,intron_variant,,ENST00000702887.1,n.399-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000453136.6,n.284-2074C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702355.1,n.403-246C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702905.1,n.430-246C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702560.1,n.536-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702269.1,n.369-246C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000687157.1,n.488-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000701421.1,n.536-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000690090.1,n.668+134C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000436772.3,n.373-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702425.1,n.110-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702879.1,n.377-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702699.1,n.377-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000686282.1,n.540-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000701341.1,n.540-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000702000.1,n.539+1081C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000685687.1,n.540-305C>T,MODIFIER,YES;THBS3-AS1,intron_variant,,ENST00000422665.2,n.496-305C>T,MODIFIER,;THBS3-AS1,intron_variant,,ENST00000447623.4,n.541-305C>T,MODIFIER, +KIRREL1 55243 BI GRCh38 1 158078073 158078073 + synonymous_variant Silent SNP C C T rs746915018 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 53 49 c.285C>T p.Asp95= p.D95= ENST00000359209.11 NM_018240.7 95 gaC/gaT 3/15 P1 T D protein_coding YES CCDS1172.2 285/2274 GACGACGCCTC Gene3D:2.60.40.10;Pfam:PF07679;PROSITE_profiles:PS50835;PANTHER:PTHR11640;PANTHER:PTHR11640:SF14;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726 ENSP00000352138 3/15 rs746915018 ENST00000359209 Transcript ENSG00000183853 HGNC:15734 LOW NM_018240.7 0.0001087 gnomAD_EAS synonymous_variant 1.0 Unknown Q96J84.164 KIRREL1 HGNC 1 1.0 UPI0000443FBD Q96J84-1 SNV KIRREL1,synonymous_variant,p.D95=,ENST00000359209,NM_018240.7,c.285C>T,LOW,YES,,,1;KIRREL1,synonymous_variant,p.D34=,ENST00000360089,,c.102C>T,LOW,,,,1;KIRREL1,intron_variant,,ENST00000368173,NM_001286349.1,c.53-6349C>T,MODIFIER,,,,1 317/7448 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.579e-05 6.152e-05 2.892e-05 0.0 0.0001087 0.0 4.396e-05 0.0 0.0 4.0568498661741614e-05 2.4329699954250827e-05 0.0 0.0 0.0 0.0002017759979935 0.0 nfe 6.172269786475226e-05 0.0 6.172269786475226e-05 0.0 0.0 0 107 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 102 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KIRREL1,synonymous_variant,p.D95=,ENST00000359209.11,c.285C>T,LOW,YES;KIRREL1,synonymous_variant,p.D34=,ENST00000360089.8,c.102C>T,LOW,;KIRREL1,intron_variant,,ENST00000368173.7,c.53-6349C>T,MODIFIER, +ATP1A2 477 BI GRCh38 1 160135874 160135874 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 22 c.2320G>A p.Ala774Thr p.A774T ENST00000361216.8 NM_000702.4 774 Gcc/Acc 17/23 P1 A A/T protein_coding YES CCDS1196.1 2320/3063 CCATCGCCTAC COSM4806973 Gene3D:1.20.1110.10;PANTHER:PTHR43294;PANTHER:PTHR43294:SF6;Superfamily:SSF81665;TIGRFAM:TIGR01106;TIGRFAM:TIGR01494;CDD:cd02608 ENSP00000354490 17/23 COSV63402254 ENST00000361216 Transcript 1.0 ENSG00000018625 HGNC:800 MODERATE NM_000702.4 missense_variant 1 1.0 benign(0.054) Unknown deleterious(0.04) 1 P50993.202 ATP1A2 HGNC 1 A0A0S2Z3W6.35 1.0 UPI0000124FC1 SNV ATP1A2,missense_variant,p.A774T,ENST00000361216,NM_000702.4,c.2320G>A,MODERATE,YES,deleterious(0.04),benign(0.054),1;ATP1A2,missense_variant,p.A485T,ENST00000447527,,c.1453G>A,MODERATE,,deleterious(0.03),benign(0.043),1;ATP1A2,missense_variant,p.A774T,ENST00000392233,,c.2320G>A,MODERATE,,deleterious(0.04),benign(0.054),1;ATP1A2,upstream_gene_variant,,ENST00000459972,,,MODIFIER,,,,1;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,,n.2423G>A,MODIFIER,,,,1;ATP1A2,upstream_gene_variant,,ENST00000463989,,,MODIFIER,,,,1 2423/5435 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 148 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 85 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ATP1A2,synonymous_variant,p.S484=,ENST00000447527.1,c.1452G>A,LOW,;ATP1A2,missense_variant,p.A774T,ENST00000392233.7,c.2320G>A,MODERATE,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488.5,n.2423G>A,MODIFIER,;ATP1A2,missense_variant,p.A774T,ENST00000361216.8,c.2320G>A,MODERATE,YES +NOS1AP 9722 BI GRCh38 1 162367162 162367162 + missense_variant Missense_Mutation SNP G G A rs760300331 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 51 32 c.1216G>A p.Ala406Thr p.A406T ENST00000361897.10 NM_014697.3 406 Gcg/Acg 10/10 A A/T protein_coding YES CCDS1237.1 1216/1521 TGGGCGCGGGC PANTHER:PTHR11232;PANTHER:PTHR11232:SF39 ENSP00000355133 10/10 rs760300331;COSV62639941 ENST00000361897 Transcript 1.0 ENSG00000198929 HGNC:16859 MODERATE NM_014697.3 2.893e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.01) Unknown tolerated_low_confidence(0.65) 0;1 O75052.149 NOS1AP HGNC 1 1.0 UPI000019C573 O75052-1 SNV NOS1AP,missense_variant,p.A111T,ENST00000493151,NM_001126060.1,c.331G>A,MODERATE,,tolerated(0.59),benign(0.001),1;NOS1AP,missense_variant,p.A406T,ENST00000361897,NM_014697.3,c.1216G>A,MODERATE,YES,tolerated_low_confidence(0.65),benign(0.01),1;NOS1AP,missense_variant,p.A401T,ENST00000530878,NM_001164757.2,c.1201G>A,MODERATE,,tolerated(0.63),benign(0.01),1;NOS1AP,missense_variant,p.A62T,ENST00000464284,,c.184G>A,MODERATE,,tolerated_low_confidence(0.73),benign(0.01),1;AL512785.2,missense_variant,p.A62T,ENST00000431696,,c.184G>A,MODERATE,,tolerated(0.7),benign(0.294),1;AL512785.2,5_prime_UTR_variant,,ENST00000420220,,c.-54G>A,MODIFIER,YES,,,1;NOS1AP,non_coding_transcript_exon_variant,,ENST00000454693,,n.140G>A,MODIFIER,,,,1;NOS1AP,3_prime_UTR_variant,,ENST00000430120,,c.*264G>A,MODIFIER,,,,1;AL512785.2,upstream_gene_variant,,ENST00000367932,,,MODIFIER,,,,1 1703/5016 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.989e-06 0.0 2.893e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 102 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 83 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000254706,5_prime_UTR_variant,,ENST00000420220.1,c.-54G>A,MODIFIER,YES;NOS1AP,non_coding_transcript_exon_variant,,ENST00000454693.1,n.140G>A,MODIFIER,;ENSG00000254706,missense_variant,p.A62T,ENST00000431696.1,c.184G>A,MODERATE,;NOS1AP,missense_variant,p.A111T,ENST00000493151.1,c.331G>A,MODERATE,;NOS1AP,missense_variant,p.A62T,ENST00000464284.1,c.184G>A,MODERATE,;NOS1AP,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000430120.3,c.*264G>A,MODIFIER,;NOS1AP,missense_variant,p.A401T,ENST00000530878.5,c.1201G>A,MODERATE,;NOS1AP,missense_variant,p.A406T,ENST00000361897.10,c.1216G>A,MODERATE,YES +GPA33 10223 BI GRCh38 1 167055070 167055070 + missense_variant Missense_Mutation SNP C C T rs767074475 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 6 c.733G>A p.Val245Met p.V245M ENST00000367868.4 NM_005814.3 245 Gtg/Atg 6/7 P1 T V/M protein_coding YES CCDS1258.1 733/960 AACCACGCCCA PANTHER:PTHR44969;PANTHER:PTHR44969:SF1;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000356842 6/7 rs767074475 ENST00000367868 Transcript ENSG00000143167 HGNC:4445 MODERATE NM_005814.3 3.518e-05 gnomAD_NFE missense_variant 1.0 benign(0.044) Unknown deleterious(0.03) Q99795.174 GPA33 HGNC -1 1.0 UPI000012502D SNV GPA33,missense_variant,p.V245M,ENST00000367868,NM_005814.3,c.733G>A,MODERATE,YES,deleterious(0.03),benign(0.044),-1;GPA33,non_coding_transcript_exon_variant,,ENST00000527955,,n.824G>A,MODIFIER,,,,-1;AL158837.1,intron_variant,,ENST00000417644,,n.216+2304C>T,MODIFIER,YES,,,1 823/2548 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.992e-05 0.0 2.892e-05 0.0 0.0 0.0 3.518e-05 0.0 0.0 2.027769915002864e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.628919850802049e-05 0.0 4.628919850802049e-05 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 24 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GPA33,non_coding_transcript_exon_variant,,ENST00000527955.5,n.824G>A,MODIFIER,;GPA33,missense_variant,p.V245M,ENST00000367868.4,c.733G>A,MODERATE,YES;ENSG00000227907,intron_variant,,ENST00000417644.1,n.216+2304C>T,MODIFIER,YES +FMO3 2328 BI GRCh38 1 171117113 171117113 + missense_variant Missense_Mutation SNP G G A rs751472166 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 27 c.1270G>A p.Glu424Lys p.E424K ENST00000367755.9 NM_001002294.3 424 Gag/Aag 9/9 P1 A E/K protein_coding YES CCDS1292.1 1270/1599 AAAGCGAGACC COSM1689161 Gene3D:3.50.50.60;Pfam:PF00743;PIRSF:PIRSF000332;Prints:PR01123;PANTHER:PTHR23023;PANTHER:PTHR23023:SF44;Superfamily:SSF51905 ENSP00000356729 9/9 rs751472166;COSV63008674 ENST00000367755 Transcript 1.0 ENSG00000007933 HGNC:3771 MODERATE NM_001002294.3 2.893e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.003) Unknown tolerated(0.37) 0;1 P31513.196 FMO3 HGNC 1 A0A024R8Z4.50 1.0 UPI000016A103 SNV FMO3,missense_variant,p.E424K,ENST00000367755,NM_001002294.3&NM_001319174.2&NM_001319173.2&NM_006894.6,c.1270G>A,MODERATE,YES,tolerated(0.37),benign(0.003),1;BX284613.2,intron_variant,,ENST00000653116,,n.542+50991C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000664920,,n.681+4637C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000669750,,n.533+50991C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000670085,,n.371+50991C>T,MODIFIER,YES,,,-1 1353/2059 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.965e-06 0.0 2.893e-05 0.0 0.0 0.0 8.815e-06 0.0 0.0 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FMO3,missense_variant,p.E424K,ENST00000367755.9,c.1270G>A,MODERATE,YES;ENSG00000231424,intron_variant,,ENST00000653116.1,n.542+50991C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000664920.1,n.681+4637C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000670085.1,n.371+50991C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000669750.1,n.533+50991C>T,MODIFIER,YES +FMO2 2327 BI GRCh38 1 171205611 171205611 + missense_variant Missense_Mutation SNP G G A rs187393653 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 18 15 c.1160G>A p.Arg387His p.R387H ENST00000209929.10 NM_001365900.1 387 cGt/cAt 7/9 P1 A R/H protein_coding YES CCDS1293.2 1160/1608 AGCTCGTTGGG Gene3D:3.50.50.60;Pfam:PF00743;PIRSF:PIRSF000332;Prints:PR00370;PANTHER:PTHR23023;PANTHER:PTHR23023:SF84;Superfamily:SSF51905 ENSP00000209929 7/9 rs187393653;COSV52950089;COSV99269261 ENST00000209929 Transcript ENSG00000094963 HGNC:3770 MODERATE NM_001460.5 0.000202 gnomAD_SAS missense_variant 0;1;1 1.0 possibly_damaging(0.888) Unknown deleterious(0.01) 0;1;1 Q99518.185 FMO2 HGNC 1 1.0 UPI0000ED9123 SNV FMO2,missense_variant,p.R387H,ENST00000209929,NM_001365900.1&NM_001460.5&NM_001301347.2,c.1160G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.888),1;FMO2,downstream_gene_variant,,ENST00000489354,,,MODIFIER,,,,1;FMO2,3_prime_UTR_variant,,ENST00000529935,,c.*483G>A,MODIFIER,,,,1;FMO2,upstream_gene_variant,,ENST00000488431,,,MODIFIER,,,,1;AL021026.1,intron_variant,,ENST00000422841,,n.289-1623C>T,MODIFIER,YES,,,-1;AL021026.1,intron_variant,,ENST00000445290,,n.139-6096C>T,MODIFIER,,,,-1;AL021026.1,intron_variant,,ENST00000445909,,n.76-1623C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000653116,,n.458-37423C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000664920,,n.483-37423C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000669750,,n.449-37423C>T,MODIFIER,,,,-1;BX284613.2,intron_variant,,ENST00000670085,,n.287-37423C>T,MODIFIER,YES,,,-1 1226/5215 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.144e-05 6.218e-05 0.0 0.0 0.0 0.0 6.406e-05 0.0001689 0.000202 7.438359898515046e-05 2.4328499421244487e-05 0.0 0.0001326610072283 0.0 0.0 0.0 amr 0.0001326610072283 0.0 0.0001234639930771 0.0 0.0 0 35 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000225243,intron_variant,,ENST00000445909.5,n.76-1623C>T,MODIFIER,;ENSG00000225243,intron_variant,,ENST00000445290.1,n.139-6096C>T,MODIFIER,YES;ENSG00000225243,intron_variant,,ENST00000422841.5,n.289-1623C>T,MODIFIER,;FMO2,missense_variant,p.R387H,ENST00000209929.10,c.1160G>A,MODERATE,YES;FMO2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000529935.5,c.*483G>A,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000653116.1,n.458-37423C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000664920.1,n.483-37423C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000670085.1,n.287-37423C>T,MODIFIER,;ENSG00000231424,intron_variant,,ENST00000669750.1,n.449-37423C>T,MODIFIER,YES +ADIPOR1 51094 BI GRCh38 1 202950953 202950953 + missense_variant Missense_Mutation SNP G G A rs766587890 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 27 c.118C>T p.Arg40Trp p.R40W ENST00000340990.10 NM_001290629.1 40 Cgg/Tgg 2/8 P1 A R/W protein_coding YES CCDS1430.1 118/1128 TACCCGTTTGC PANTHER:PTHR20855;PANTHER:PTHR20855:SF40;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000341785 2/8 rs766587890;COSV61851334 ENST00000340990 Transcript ENSG00000159346 HGNC:24040 MODERATE NM_015999.6 missense_variant 0;1 1.0 benign(0.075) Unknown deleterious(0.02) 0;1 Q96A54.148 ADIPOR1 HGNC -1 1.0 UPI000003779A SNV ADIPOR1,missense_variant,p.R40W,ENST00000340990,NM_001290629.1&NM_001290557.1&NM_001290553.1&NM_015999.6,c.118C>T,MODERATE,YES,deleterious(0.02),benign(0.075),-1;ADIPOR1,missense_variant,p.R40W,ENST00000367254,,c.118C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.9),-1;ADIPOR1,missense_variant,p.R40W,ENST00000417068,,c.118C>T,MODERATE,,deleterious(0.02),benign(0.075),-1;ADIPOR1,missense_variant,p.R40W,ENST00000426229,,c.118C>T,MODERATE,,deleterious(0.02),benign(0.075),-1 340/2091 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.0285100617911667e-05 0.0 0.0 0.0 0.0 0.0002018569939536 0.0 nfe 3.086320066358894e-05 0.0 3.086320066358894e-05 0.0 0.0 0 93 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ADIPOR1,missense_variant,p.R40W,ENST00000426229.1,c.118C>T,MODERATE,;ADIPOR1,missense_variant,p.R40W,ENST00000417068.5,c.118C>T,MODERATE,;ADIPOR1,missense_variant,p.R40W,ENST00000367254.7,c.118C>T,MODERATE,;ADIPOR1,missense_variant,p.R40W,ENST00000340990.10,c.118C>T,MODERATE,YES +CHIT1 1118 BI GRCh38 1 203225707 203225707 + synonymous_variant Silent SNP G G A rs1330040380 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 9 c.219C>T p.Asp73= p.D73= ENST00000367229.6 NM_003465.3 73 gaC/gaT 3/11 P1 A D protein_coding YES CCDS1436.1 219/1401 GTCTCGTCATT PDB-ENSP_mappings:1guv.A;PDB-ENSP_mappings:1hki.A;PDB-ENSP_mappings:1hkj.A;PDB-ENSP_mappings:1hkk.A;PDB-ENSP_mappings:1hkm.A;PDB-ENSP_mappings:1lg1.A;PDB-ENSP_mappings:1lg2.A;PDB-ENSP_mappings:1lq0.A;PDB-ENSP_mappings:1waw.A;PDB-ENSP_mappings:1wb0.A;Gene3D:3.20.20.80;PDB-ENSP_mappings:4wjx.A;PDB-ENSP_mappings:4wk9.A;PDB-ENSP_mappings:4wka.A;PDB-ENSP_mappings:4wkf.A;PDB-ENSP_mappings:4wkh.A;PDB-ENSP_mappings:5hbf.A;PDB-ENSP_mappings:5hbf.B;PDB-ENSP_mappings:5nr8.A;PDB-ENSP_mappings:5nra.A;PDB-ENSP_mappings:5nrf.A;PDB-ENSP_mappings:6jjr.A;PDB-ENSP_mappings:6jk6.A;Pfam:PF00704;PANTHER:PTHR11177;PANTHER:PTHR11177:SF248;SMART:SM00636;Superfamily:SSF51445;CDD:cd02872 ENSP00000356198 3/11 rs1330040380;COSV55149024 ENST00000367229 Transcript 1.0 ENSG00000133063 HGNC:1936 LOW NM_003465.3 8.791e-06 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q13231.191 CHIT1 HGNC -1 1.0 UPI00000399C1 Q13231-1 SNV CHIT1,synonymous_variant,p.D73=,ENST00000367229,NM_003465.3,c.219C>T,LOW,YES,,,-1;CHIT1,synonymous_variant,p.D73=,ENST00000255427,NM_001256125.2,c.219C>T,LOW,,,,-1;CHIT1,non_coding_transcript_exon_variant,,ENST00000484834,,n.4576C>T,MODIFIER,,,,-1;CHIT1,non_coding_transcript_exon_variant,,ENST00000513472,,n.415C>T,MODIFIER,,,,-1;CHIT1,upstream_gene_variant,,ENST00000506427,,,MODIFIER,,,,-1;CHIT1,synonymous_variant,p.D73=,ENST00000491855,,c.219C>T,LOW,,,,-1;CHIT1,synonymous_variant,p.D73=,ENST00000503786,,c.219C>T,LOW,,,,-1 256/2248 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.791e-06 0.0 0.0 1.3526499969884752e-05 2.4339200535905547e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 65 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CHIT1,non_coding_transcript_exon_variant,,ENST00000513472.5,n.415C>T,MODIFIER,;CHIT1,synonymous_variant,NMD_transcript_variant,p.D73=,ENST00000503786.1,c.219C>T,LOW,;CHIT1,synonymous_variant,NMD_transcript_variant,p.D73=,ENST00000491855.5,c.219C>T,LOW,;CHIT1,synonymous_variant,p.D73=,ENST00000255427.7,c.219C>T,LOW,;CHIT1,synonymous_variant,p.D73=,ENST00000367229.6,c.219C>T,LOW,YES;CHIT1,non_coding_transcript_exon_variant,,ENST00000484834.5,n.4576C>T,MODIFIER, +CNTN2 6900 BI GRCh38 1 205067175 205067175 + missense_variant Missense_Mutation SNP C C T rs756558390 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 56 7 c.2050C>T p.Arg684Trp p.R684W ENST00000331830.7 NM_005076.5 684 Cgg/Tgg 16/23 P2 T R/W protein_coding CCDS1449.1 2050/3123 AGTTCCGGGTC Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR10075;PANTHER:PTHR10075:SF55;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000330633 16/23 rs756558390 ENST00000331830 Transcript 1.0 ENSG00000184144 HGNC:2172 MODERATE NM_005076.5 9.927e-05 gnomAD_ASJ missense_variant probably_damaging(0.999) Unknown deleterious(0) Q02246.194 CNTN2 HGNC 1 A1ML24.3 1.0 UPI00001266A5 SNV CNTN2,missense_variant,p.R684W,ENST00000331830,NM_005076.5,c.2050C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R508W,ENST00000636312,,c.1522C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R684W,ENST00000638378,NM_001346083.2,c.2050C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R684W,ENST00000640428,,c.2050C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;CNTN2,missense_variant,p.R97W,ENST00000638577,,c.289C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,non_coding_transcript_exon_variant,,ENST00000636641,,n.462C>T,MODIFIER,,,,1;CNTN2,missense_variant,p.R684W,ENST00000640326,,c.2050C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R684W,ENST00000639971,,c.2050C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R684W,ENST00000639302,,c.2050C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CNTN2,missense_variant,p.R415W,ENST00000639122,,c.1243C>T,MODERATE,,deleterious(0),probably_damaging(1),1;CNTN2,3_prime_UTR_variant,,ENST00000640352,,c.*2848C>T,MODIFIER,,,,1;CNTN2,3_prime_UTR_variant,,ENST00000639843,,c.*374C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,,n.2042C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000525433,,n.932C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,,n.2969C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000639023,,n.1741C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000639788,,n.209C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000638715,,n.323C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000638449,,n.1105C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000638980,,n.1094C>T,MODIFIER,,,,1;CNTN2,non_coding_transcript_exon_variant,,ENST00000638050,,n.121C>T,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000527340,,,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000530117,,,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000530594,,,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000639156,,,MODIFIER,,,,1;CNTN2,upstream_gene_variant,,ENST00000639354,,,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000639503,,,MODIFIER,,,,1;CNTN2,downstream_gene_variant,,ENST00000639831,,,MODIFIER,,,,1;CNTN2,upstream_gene_variant,,ENST00000640227,,,MODIFIER,,,,1 2319/7916 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.978e-06 0.0 0.0 9.927e-05 0.0 0.0 0.0 0.0 0.0 6.7616001615533605e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 94 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 63 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CNTN2,non_coding_transcript_exon_variant,,ENST00000638050.2,n.121C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000639788.1,n.209C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000638715.1,n.323C>T,MODIFIER,;CNTN2,missense_variant,p.P96L,ENST00000638577.1,c.287C>T,MODERATE,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636641.2,n.462C>T,MODIFIER,;CNTN2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639843.1,c.*374C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000525433.2,n.932C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000638980.1,n.1094C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000638449.1,n.1105C>T,MODIFIER,;CNTN2,missense_variant,NMD_transcript_variant,p.P414L,ENST00000639122.1,c.1241C>T,MODERATE,;CNTN2,missense_variant,p.P507L,ENST00000636312.2,c.1520C>T,MODERATE,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872.6,n.2042C>T,MODIFIER,;CNTN2,non_coding_transcript_exon_variant,,ENST00000639023.1,n.1741C>T,MODIFIER,;CNTN2,missense_variant,NMD_transcript_variant,p.R684W,ENST00000639971.1,c.2050C>T,MODERATE,;CNTN2,missense_variant,NMD_transcript_variant,p.R684W,ENST00000640326.1,c.2050C>T,MODERATE,;CNTN2,missense_variant,p.R684W,ENST00000331830.7,c.2050C>T,MODERATE,YES;CNTN2,missense_variant,NMD_transcript_variant,p.R684W,ENST00000639302.1,c.2050C>T,MODERATE,;CNTN2,missense_variant,p.R684W,ENST00000640428.1,c.2050C>T,MODERATE,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809.2,n.2969C>T,MODIFIER,;CNTN2,missense_variant,p.R684W,ENST00000638378.1,c.2050C>T,MODERATE,;CNTN2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000640352.1,c.*2848C>T,MODIFIER, +C1orf116 79098 BI GRCh38 1 207027583 207027583 + missense_variant Missense_Mutation SNP G G T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 46 4 c.16C>A p.Leu6Met p.L6M ENST00000359470.6 NM_023938.6 6 Ctg/Atg 2/4 P1 T L/M protein_coding YES CCDS1475.1 16/1806 CCACAGCTCCC PANTHER:PTHR21555;MobiDB_lite:mobidb-lite ENSP00000352447 2/4 ENST00000359470 Transcript ENSG00000182795 HGNC:28667 MODERATE NM_023938.6 missense_variant 1.0 probably_damaging(0.991) Unknown deleterious(0.01) Q9BW04.134 C1orf116 HGNC -1 1.0 UPI000013E1EF Q9BW04-1 SNV C1orf116,missense_variant,p.L6M,ENST00000359470,NM_023938.6,c.16C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.991),-1;C1orf116,intron_variant,,ENST00000461135,NM_001083924.2,c.-633-2519C>A,MODIFIER,,,,-1 275/5501 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 49 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS C1orf116,intron_variant,,ENST00000461135.2,c.-633-2519C>A,MODIFIER,;C1orf116,missense_variant,p.L6M,ENST00000359470.6,c.16C>A,MODERATE,YES +CENPF 1063 BI GRCh38 1 214642777 214642777 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 18 c.4439G>A p.Cys1480Tyr p.C1480Y ENST00000366955.8 NM_016343.4 1480 tGt/tAt 12/20 P1 A C/Y protein_coding YES CCDS31023.1 4439/9345 CTCTTGTGTGC PANTHER:PTHR18874;Low_complexity_(Seg):seg ENSP00000355922 12/20 ENST00000366955 Transcript 1.0 ENSG00000117724 HGNC:1857 MODERATE NM_016343.4 missense_variant 1.0 possibly_damaging(0.583) Unknown tolerated(0.24) P49454.200 CENPF HGNC 1 1.0 UPI00001AE985 SNV CENPF,missense_variant,p.C1480Y,ENST00000366955,NM_016343.4,c.4439G>A,MODERATE,YES,tolerated(0.24),possibly_damaging(0.583),1 4607/10290 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 63 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CENPF,missense_variant,p.C1480Y,ENST00000706765.1,c.4439G>A,MODERATE,;CENPF,missense_variant,p.C1480Y,ENST00000366955.8,c.4439G>A,MODERATE,YES +OBSCN 84033 BI GRCh38 1 228317745 228317745 + missense_variant Missense_Mutation SNP C C T rs528758181 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 28 c.13843C>T p.Arg4615Trp p.R4615W ENST00000422127.5 NM_001098623.2 4615 Cgg/Tgg 52/105 0.0002 0.0 0.0 0.0 0.001 0.0 T R/W protein_coding CCDS58065.1 13843/23907 CAGTGCGGCTT Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR44888;PANTHER:PTHR44888:SF2;Superfamily:SSF49265 ENSP00000409493 52/105 rs528758181 ENST00000422127 Transcript ENSG00000154358 HGNC:15719 MODERATE 0.001 EUR missense_variant benign(0.425) Unknown deleterious(0.02) Q5VST9.183 OBSCN HGNC 1 5.0 UPI0001838884 Q5VST9-1 SNV OBSCN,missense_variant,p.R5572W,ENST00000570156,NM_001271223.2,c.16714C>T,MODERATE,YES,deleterious(0.04),possibly_damaging(0.757),1;OBSCN,missense_variant,p.R5130W,ENST00000662438,,c.15388C>T,MODERATE,,deleterious(0.03),probably_damaging(0.936),1;OBSCN,missense_variant,p.R4615W,ENST00000422127,NM_001098623.2,c.13843C>T,MODERATE,,deleterious(0.02),benign(0.425),1;OBSCN,missense_variant,p.R4615W,ENST00000636476,,c.13843C>T,MODERATE,,,possibly_damaging(0.629),1;OBSCN,missense_variant,p.R4615W,ENST00000284548,NM_052843.4,c.13843C>T,MODERATE,,deleterious(0.04),possibly_damaging(0.629),1;OBSCN,downstream_gene_variant,,ENST00000660857,,,MODIFIER,,,,1 13917/24060 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.48e-05 6.86e-05 2.905e-05 0.0 5.583e-05 0.0 9.327e-06 0.0 6.555e-05 2.027929986070376e-05 0.0 0.0 0.0 0.0 0.000201613001991 0.0 nfe 3.0868999601807445e-05 0.0 3.0868999601807445e-05 0.0 0.0 0 67 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 60 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS OBSCN,missense_variant,p.R4615W,ENST00000636476.2,c.13843C>T,MODERATE,;OBSCN,missense_variant,p.R5130W,ENST00000662438.1,c.15388C>T,MODERATE,;OBSCN,missense_variant,p.R4615W,ENST00000422127.5,c.13843C>T,MODERATE,;OBSCN,missense_variant,p.R4615W,ENST00000284548.16,c.13843C>T,MODERATE,;OBSCN,missense_variant,p.R5572W,ENST00000680850.1,c.16714C>T,MODERATE,YES;OBSCN,missense_variant,p.R5572W,ENST00000570156.7,c.16714C>T,MODERATE, +GALNT2 2590 BI GRCh38 1 230236034 230236034 + missense_variant Missense_Mutation SNP G G A rs151140953 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 8 c.395G>A p.Arg132Gln p.R132Q ENST00000366672.5 NM_001291866.2 132 cGg/cAg 4/16 P1 A R/Q protein_coding YES CCDS1582.1 395/1716 GTGGCGGGTGG PDB-ENSP_mappings:2ffu.A;PDB-ENSP_mappings:2ffv.A;PDB-ENSP_mappings:2ffv.B;Gene3D:3.90.550.10;PDB-ENSP_mappings:4d0t.A;PDB-ENSP_mappings:4d0t.B;PDB-ENSP_mappings:4d0t.C;PDB-ENSP_mappings:4d0t.D;PDB-ENSP_mappings:4d0t.E;PDB-ENSP_mappings:4d0t.F;PDB-ENSP_mappings:4d0z.A;PDB-ENSP_mappings:4d0z.B;PDB-ENSP_mappings:4d0z.C;PDB-ENSP_mappings:4d0z.D;PDB-ENSP_mappings:4d0z.E;PDB-ENSP_mappings:4d0z.F;PDB-ENSP_mappings:4d11.A;PDB-ENSP_mappings:4d11.B;PDB-ENSP_mappings:4d11.C;PDB-ENSP_mappings:4d11.D;PDB-ENSP_mappings:4d11.E;PDB-ENSP_mappings:4d11.F;PDB-ENSP_mappings:5ajn.A;PDB-ENSP_mappings:5ajo.A;PDB-ENSP_mappings:5ajp.A;PDB-ENSP_mappings:5fv9.A;PDB-ENSP_mappings:5fv9.B;PDB-ENSP_mappings:5fv9.C;PDB-ENSP_mappings:5fv9.D;PDB-ENSP_mappings:5fv9.E;PDB-ENSP_mappings:5fv9.F;PDB-ENSP_mappings:5ndf.A;PDB-ENSP_mappings:5ndf.B;PDB-ENSP_mappings:5ndf.C;PDB-ENSP_mappings:5ndf.D;PDB-ENSP_mappings:5ndf.E;PDB-ENSP_mappings:5ndf.F;PDB-ENSP_mappings:6e7i.A;PDB-ENSP_mappings:6egs.A;PDB-ENSP_mappings:6egs.B;PDB-ENSP_mappings:6nqt.A;PDB-ENSP_mappings:6nqt.B;PDB-ENSP_mappings:6nqt.C;PDB-ENSP_mappings:6nqt.D;PDB-ENSP_mappings:6nqt.E;PDB-ENSP_mappings:6nqt.F;PANTHER:PTHR11675;PANTHER:PTHR11675:SF49;Superfamily:SSF53448 ENSP00000355632 0.000227 0.0 4/16 rs151140953 ENST00000366672 Transcript 1.0 ENSG00000143641 HGNC:4124 MODERATE NM_004481.5 0.000227 AA missense_variant 1.0 benign(0.003) Unknown tolerated(0.63) Q10471.185 GALNT2 HGNC 1 A0A1L7NY50.19 1.0 UPI0000074053 Q10471-1 SNV GALNT2,missense_variant,p.R132Q,ENST00000366672,NM_001291866.2&NM_004481.5,c.395G>A,MODERATE,YES,tolerated(0.63),benign(0.003),1;GALNT2,non_coding_transcript_exon_variant,,ENST00000494106,,n.358G>A,MODIFIER,,,,1 438/4423 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.204e-05 6.239e-05 2.902e-05 0.0 0.0 0.0 2.658e-05 0.0 9.823e-05 6.76023000778514e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 36 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GALNT2,missense_variant,p.R132Q,ENST00000366672.5,c.395G>A,MODERATE,YES;GALNT2,non_coding_transcript_exon_variant,,ENST00000494106.1,n.358G>A,MODIFIER, +COG2 22796 BI GRCh38 1 230683588 230683588 + missense_variant Missense_Mutation SNP C C T rs753073596 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 27 c.1181C>T p.Ala394Val p.A394V ENST00000366669.9 NM_007357.3 394 gCg/gTg 11/18 P4 T A/V protein_coding YES CCDS1584.1 1181/2217 AATAGCGGGAT COSM5447023 PANTHER:PTHR12961 ENSP00000355629 11/18 rs753073596;COSV64187943 ENST00000366669 Transcript 1.0 ENSG00000135775 HGNC:6546 MODERATE NM_007357.3 0.0001087 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.932) Unknown deleterious(0.03) 0;1 Q14746.164 COG2 HGNC 1 B1ALW7.98 1.0 UPI0000127E38 Q14746-1 SNV COG2,missense_variant,p.A335V,ENST00000534989,,c.1004C>T,MODERATE,,deleterious(0.03),probably_damaging(0.932),1;COG2,missense_variant,p.A394V,ENST00000366669,NM_007357.3,c.1181C>T,MODERATE,YES,deleterious(0.03),probably_damaging(0.932),1;COG2,missense_variant,p.A394V,ENST00000366668,NM_001145036.2,c.1181C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.859),1;COG2,upstream_gene_variant,,ENST00000482012,,,MODIFIER,,,,1;COG2,upstream_gene_variant,,ENST00000490900,,,MODIFIER,,,,1;COG2,3_prime_UTR_variant,,ENST00000468893,,c.*1039C>T,MODIFIER,,,,1;COG2,downstream_gene_variant,,ENST00000494371,,,MODIFIER,,,,1 1307/2932 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.99e-05 0.0 0.0 0.0 0.0001087 0.0 8.793e-06 0.0 6.533e-05 0 90 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 69 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COG2,missense_variant,p.A335V,ENST00000534989.1,c.1004C>T,MODERATE,;COG2,missense_variant,p.A394V,ENST00000366668.7,c.1181C>T,MODERATE,;COG2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000468893.6,c.*1039C>T,MODIFIER,;COG2,missense_variant,p.A394V,ENST00000366669.9,c.1181C>T,MODERATE,YES +SLC35F3 148641 BI GRCh38 1 234231557 234231557 + missense_variant Missense_Mutation SNP G G A rs530447111 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 67 56 c.217G>A p.Val73Met p.V73M ENST00000366617.3 NM_001300845.2 73 Gtg/Atg 2/7 0.0002 0.0008 0.0 0.0 0.0 0.0 A1 A V/M protein_coding CCDS73050.1 217/1266 CGGTCGTGCTG Pfam:PF00892;PANTHER:PTHR19346;PANTHER:PTHR19346:SF3;Transmembrane_helices:TMhelix;CDD:cd19065 ENSP00000355576 2/7 rs530447111;COSV104426931;COSV64021032 ENST00000366617 Transcript ENSG00000183780 HGNC:23616 MODERATE 0.0008 AFR missense_variant 0;1;1 possibly_damaging(0.721) Unknown deleterious(0.01) 0;1;1 Q8IY50.109 SLC35F3 HGNC 1 1.0 UPI00001AF636 Q8IY50-1 SNV SLC35F3,missense_variant,p.V142M,ENST00000366618,NM_173508.4,c.424G>A,MODERATE,YES,deleterious(0.05),possibly_damaging(0.517),1;SLC35F3,missense_variant,p.V73M,ENST00000366617,NM_001300845.1,c.217G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.721),1 445/2762 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.976e-06 6.158e-05 0.0 0.0 0.0 0.0 8.84e-06 0.0 0.0 6.758580184396124e-06 2.4310800654347983e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 149 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 123 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC35F3,missense_variant,p.V73M,ENST00000366617.3,c.217G>A,MODERATE,;SLC35F3,missense_variant,p.V142M,ENST00000366618.8,c.424G>A,MODERATE,YES +LYST 1130 BI GRCh38 1 235664617 235664617 + synonymous_variant Silent SNP G G A rs757560834 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 9 c.11043C>T p.Gly3681= p.G3681= ENST00000389793.7 NM_001301365.1 3681 ggC/ggT 51/53 P1 A G protein_coding YES CCDS31062.1 11043/11406 CCTCCGCCAGC Gene3D:2.130.10.10;PROSITE_profiles:PS50294;PANTHER:PTHR13743;PANTHER:PTHR13743:SF86;SMART:SM00320;Superfamily:SSF50978 ENSP00000374443 51/53 rs757560834 ENST00000389793 Transcript 1.0 ENSG00000143669 HGNC:1968 LOW NM_000081.4 9.805e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q99698.188 LYST HGNC -1 5.0 UPI000020509E Q99698-1 SNV LYST,synonymous_variant,p.G3681=,ENST00000389793,NM_001301365.1&NM_000081.4,c.11043C>T,LOW,YES,,,-1;LYST,3_prime_UTR_variant,,ENST00000389794,,c.*6467C>T,MODIFIER,,,,-1;LYST,non_coding_transcript_exon_variant,,ENST00000473037,,n.6033C>T,MODIFIER,,,,-1 11204/13466 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.197e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 9.805e-05 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LYST,intron_variant,NMD_transcript_variant,,ENST00000697240.1,c.3173-63C>T,MODIFIER,;LYST,non_coding_transcript_exon_variant,,ENST00000697239.1,n.437C>T,MODIFIER,;LYST,non_coding_transcript_exon_variant,,ENST00000697238.1,n.197C>T,MODIFIER,;LYST,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697237.1,c.*1000C>T,MODIFIER,;LYST,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697236.1,c.*1471C>T,MODIFIER,;LYST,synonymous_variant,p.G531=,ENST00000697235.1,c.1593C>T,LOW,;LYST,non_coding_transcript_exon_variant,,ENST00000462376.2,n.2453C>T,MODIFIER,;LYST,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697178.1,c.*7029C>T,MODIFIER,;LYST,non_coding_transcript_exon_variant,,ENST00000473037.5,n.6033C>T,MODIFIER,;LYST,synonymous_variant,p.G3681=,ENST00000389793.7,c.11043C>T,LOW,YES +RYR2 6262 BI GRCh38 1 237707047 237707047 + missense_variant Missense_Mutation SNP C C T rs747271394 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 34 c.9679C>T p.Arg3227Cys p.R3227C ENST00000366574.7 NM_001035.3 3227 Cgc/Tgc 68/105 P1 T R/C protein_coding YES CCDS55691.1 9679/14904 GCATTCGCTAC COSM906241 PANTHER:PTHR12864;PANTHER:PTHR12864:SF45 ENSP00000355533 68/105 rs747271394;COSV63695082 ENST00000366574 Transcript 1.0 ENSG00000198626 HGNC:10484 MODERATE NM_001035.3 6.536e-05 gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.81) Unknown deleterious(0) 0;1 Q92736.216 RYR2 HGNC 1 1.0 UPI0000DD0308 Q92736-1 SNV RYR2,missense_variant,p.R3227C,ENST00000366574,NM_001035.3,c.9679C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.81),1;RYR2,missense_variant,p.R3211C,ENST00000360064,,c.9631C>T,MODERATE,,deleterious(0),probably_damaging(0.932),1;RYR2,missense_variant,p.R624C,ENST00000659194,,c.1870C>T,MODERATE,,deleterious(0),probably_damaging(0.911),1;RYR2,upstream_gene_variant,,ENST00000660292,,,MODIFIER,,,,1;RYR2,upstream_gene_variant,,ENST00000661330,,,MODIFIER,,,,1;RYR2,3_prime_UTR_variant,,ENST00000609119,,c.*714C>T,MODIFIER,,,,1 10017/16583 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.204e-05 0.0 0.0 0.0 0.0 0.0 8.86e-06 0.0 6.536e-05 6.763059900549706e-06 0.0 0.0 6.628660048590973e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 84 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 64 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RYR2,missense_variant,p.R2572C,ENST00000714022.1,c.7714C>T,MODERATE,;RYR2,missense_variant,p.R3227C,ENST00000661330.2,c.9679C>T,MODERATE,;RYR2,missense_variant,p.R3215C,ENST00000714019.1,c.9643C>T,MODERATE,;RYR2,missense_variant,p.R3227C,ENST00000659194.3,c.9679C>T,MODERATE,;RYR2,missense_variant,p.R3227C,ENST00000366574.7,c.9679C>T,MODERATE,YES;RYR2,missense_variant,p.R3227C,ENST00000660292.2,c.9679C>T,MODERATE,;RYR2,missense_variant,p.R3190C,ENST00000714018.1,c.9568C>T,MODERATE,;RYR2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000609119.2,c.*714C>T,MODIFIER,;RYR2,missense_variant,p.R3227C,ENST00000714021.1,c.9679C>T,MODERATE, +GREB1 9687 BI GRCh38 2 11634329 11634329 + synonymous_variant Silent SNP C C T rs368127534 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 7 5 c.5190C>T p.Asn1730= p.N1730= ENST00000234142.9 1730 aaC/aaT 28/32 P1 T N protein_coding CCDS42655.1 5190/5850 CAGAACGTGCA COSM1494620 Pfam:PF15782;PANTHER:PTHR15720;PANTHER:PTHR15720:SF13 ENSP00000234142 28/32 rs368127534;COSV52180306 ENST00000234142 Transcript ENSG00000196208 HGNC:24885 LOW 0.0001657 gnomAD_OTH synonymous_variant 0;1 Unknown 0;1 Q4ZG55.99 GREB1 HGNC 1 1.0 UPI0000163937 Q4ZG55-1 SNV GREB1,synonymous_variant,p.N1730=,ENST00000381486,NM_014668.4,c.5190C>T,LOW,YES,,,1;GREB1,synonymous_variant,p.N1730=,ENST00000234142,,c.5190C>T,LOW,,,,1;GREB1,synonymous_variant,p.N728=,ENST00000396123,,c.2184C>T,LOW,,,,1 5452/8444 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.047e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0001657 3.269e-05 1.351730043097632e-05 4.863099820795469e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863099820795469e-05 0.0 0.0 0.0 0.0 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GREB1,synonymous_variant,p.N728=,ENST00000396123.2,c.2184C>T,LOW,;GREB1,synonymous_variant,p.N1730=,ENST00000234142.9,c.5190C>T,LOW,;GREB1,synonymous_variant,p.N1730=,ENST00000381486.7,c.5190C>T,LOW,YES +EIF2AK2 5610 BI GRCh38 2 37122654 37122654 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 19 c.919C>T p.Arg307Cys p.R307C ENST00000233057.9 NM_001135651.3 307 Cgt/Tgt 12/17 P1 A R/C protein_coding YES CCDS1786.1 919/1656 TTCACGCTCCG COSM84586 PDB-ENSP_mappings:2a19.B;PDB-ENSP_mappings:2a19.C;PDB-ENSP_mappings:2a1a.B;PDB-ENSP_mappings:3uiu.A;PDB-ENSP_mappings:3uiu.B;PDB-ENSP_mappings:6d3k.A;PDB-ENSP_mappings:6d3k.B;PDB-ENSP_mappings:6d3k.C;PDB-ENSP_mappings:6d3l.A;Coiled-coils_(Ncoils):Coil;PROSITE_profiles:PS50011;CDD:cd14047;PANTHER:PTHR11042:SF90;PANTHER:PTHR11042;Gene3D:3.30.200.20;Pfam:PF00069;SMART:SM00220;Superfamily:SSF56112 ENSP00000233057 12/17 COSV51794332 ENST00000233057 Transcript 1.0 ENSG00000055332 HGNC:9437 MODERATE NM_001135651.3 missense_variant 1 1.0 probably_damaging(0.999) Unknown deleterious(0) 1 P19525.232 EIF2AK2 HGNC -1 2.0 UPI000000D925 P19525-1 SNV EIF2AK2,missense_variant,p.R307C,ENST00000233057,NM_001135651.3,c.919C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;EIF2AK2,missense_variant,p.R307C,ENST00000395127,NM_002759.3,c.919C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;EIF2AK2,missense_variant,p.R266C,ENST00000405334,NM_001135652.2,c.796C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;EIF2AK2,missense_variant,p.R307C,ENST00000647926,,c.919C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1 1175/9975 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 67 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EIF2AK2,intron_variant,,ENST00000411537.7,n.1120-2515C>T,MODIFIER,;EIF2AK2,missense_variant,p.R266C,ENST00000405334.5,c.796C>T,MODERATE,;EIF2AK2,missense_variant,p.R307C,ENST00000395127.6,c.919C>T,MODERATE,;EIF2AK2,missense_variant,NMD_transcript_variant,p.R307C,ENST00000647926.1,c.919C>T,MODERATE,;EIF2AK2,missense_variant,p.R307C,ENST00000681516.1,c.919C>T,MODERATE,;EIF2AK2,missense_variant,p.R307C,ENST00000679507.1,c.919C>T,MODERATE,;EIF2AK2,missense_variant,p.R307C,ENST00000681463.1,c.919C>T,MODERATE,;EIF2AK2,non_coding_transcript_exon_variant,,ENST00000681329.1,n.1258C>T,MODIFIER,;EIF2AK2,missense_variant,p.R307C,ENST00000681507.1,c.919C>T,MODERATE,;EIF2AK2,missense_variant,p.R250C,ENST00000680273.1,c.748C>T,MODERATE,;EIF2AK2,missense_variant,p.R307C,ENST00000233057.9,c.919C>T,MODERATE,YES;EIF2AK2,missense_variant,p.R307C,ENST00000679979.1,c.919C>T,MODERATE, +STON1-GTF2A1L 286749 BI GRCh38 2 48582292 48582292 + synonymous_variant Silent SNP G G A rs370458736 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 32 c.1659G>A p.Ala553= p.A553= ENST00000394754.5 NM_172311.3 553 gcG/gcA 2/11 P1 A A protein_coding CCDS1841.1 1659/2208 TTGGCGCAGAG COSM4094499;COSM4094500 PROSITE_profiles:PS51072;CDD:cd09262;PANTHER:PTHR10529;PANTHER:PTHR10529:SF339;Pfam:PF00928;PIRSF:PIRSF037099;Gene3D:2.60.40.1170;Superfamily:SSF49447 ENSP00000385273 0.0 0.0001163 2/4 rs370458736;COSV100561493 ENST00000404752 Transcript ENSG00000243244 HGNC:17003 LOW NM_006873.4 0.0001634 gnomAD_OTH synonymous_variant 0;1 Unknown 0;1 Q9Y6Q2.154 STON1 HGNC 1 1.0 UPI000006E627 Q9Y6Q2-1 SNV STON1,synonymous_variant,p.A553=,ENST00000406226,NM_001198595.1,c.1659G>A,LOW,YES,,,1;STON1,synonymous_variant,p.A553=,ENST00000649748,,c.1659G>A,LOW,,,,1;STON1,synonymous_variant,p.A553=,ENST00000404752,NM_006873.4,c.1659G>A,LOW,,,,1;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000394754,NM_172311.3,c.1659G>A,LOW,YES,,,1;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000405008,,c.1659G>A,LOW,,,,1;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000402114,NM_001198593.1,c.1659G>A,LOW,,,,1;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000394751,NM_001198594.1,c.1659G>A,LOW,,,,1;STON1,upstream_gene_variant,,ENST00000444932,,,MODIFIER,,,,1 1769/5529 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.22e-05 0.000123 2.891e-05 0.0 5.437e-05 9.24e-05 3.592e-05 0.0001634 6.533e-05 2.027899972745217e-05 4.863809954258613e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863809954258613e-05 0.0 1.5429699487867765e-05 0.0 0.0 0 92 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 74 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000394751.5,c.1659G>A,LOW,;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000394754.5,c.1659G>A,LOW,YES;STON1,synonymous_variant,p.A553=,ENST00000406226.1,c.1659G>A,LOW,;STON1,synonymous_variant,p.A553=,ENST00000404752.6,c.1659G>A,LOW,YES;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000405008.5,c.1659G>A,LOW,;STON1-GTF2A1L,synonymous_variant,p.A553=,ENST00000402114.6,c.1659G>A,LOW,;STON1,synonymous_variant,p.A553=,ENST00000649748.1,c.1659G>A,LOW, +DUSP11 8446 BI GRCh38 2 73774981 73774981 + stop_gained Nonsense_Mutation SNP G G A rs754705080 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 16 c.241C>T p.Arg81Ter p.R81* ENST00000272444.8 NM_003584.2 128 Cga/Tga 3/9 P1 A R/* protein_coding YES CCDS1928.2 382/1134 TTCTCGGATTT COSM1022860;COSM4873993 PDB-ENSP_mappings:4jmj.A;PDB-ENSP_mappings:4mbb.A;PDB-ENSP_mappings:4nyh.A;PDB-ENSP_mappings:4nyh.B;PDB-ENSP_mappings:4nyh.C;CDD:cd17665;PANTHER:PTHR10367:SF9;PANTHER:PTHR10367;Gene3D:3.90.190.10;SMART:SM00195;Superfamily:SSF52799 ENSP00000272444 3/9 rs754705080;COSV55595147;COSV99730981 ENST00000272444 Transcript ENSG00000144048 HGNC:3066 HIGH 8.807e-06 gnomAD_NFE stop_gained 0;1;1 1.0 Unknown 0;1;1 O75319.165 DUSP11 HGNC -1 1.0 UPI0000EE25F4 O75319-1 SNV DUSP11,stop_gained,p.R128*,ENST00000443070,,c.382C>T,HIGH,,,,-1;DUSP11,stop_gained,p.R128*,ENST00000272444,NM_003584.2,c.382C>T,HIGH,YES,,,-1;DUSP11,stop_gained,p.R79*,ENST00000452812,,c.235C>T,HIGH,,,,-1;DUSP11,non_coding_transcript_exon_variant,,ENST00000480948,,n.145C>T,MODIFIER,,,,-1;DUSP11,non_coding_transcript_exon_variant,,ENST00000477458,,n.252C>T,MODIFIER,,,,-1 424/1653 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.986e-06 0.0 0.0 0.0 0.0 0.0 8.807e-06 0.0 0.0 1.353229981759796e-05 2.4362900148844343e-05 0.0 0.0 0.0 0.0 0.0 0.0032894699834287 0.0 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DUSP11,stop_gained,p.R81*,ENST00000696057.1,c.241C>T,HIGH,;DUSP11,stop_gained,p.R79*,ENST00000452812.1,c.235C>T,HIGH,;DUSP11,stop_gained,p.R81*,ENST00000443070.5,c.241C>T,HIGH,;DUSP11,non_coding_transcript_exon_variant,,ENST00000477458.1,n.252C>T,MODIFIER,;DUSP11,non_coding_transcript_exon_variant,,ENST00000480948.5,n.145C>T,MODIFIER,;DUSP11,stop_gained,p.R81*,ENST00000696056.1,c.241C>T,HIGH,;DUSP11,stop_gained,p.R81*,ENST00000696055.1,c.241C>T,HIGH,;DUSP11,stop_gained,NMD_transcript_variant,p.R81*,ENST00000696054.1,c.241C>T,HIGH,;DUSP11,stop_gained,p.R81*,ENST00000696053.1,c.241C>T,HIGH,;DUSP11,stop_gained,p.R37*,ENST00000696052.1,c.109C>T,HIGH,;DUSP11,stop_gained,p.R81*,ENST00000272444.8,c.241C>T,HIGH,YES;DUSP11,non_coding_transcript_exon_variant,,ENST00000696051.1,n.347C>T,MODIFIER,;DUSP11,stop_gained,NMD_transcript_variant,p.R81*,ENST00000696050.1,c.241C>T,HIGH, +DCTN1 1639 BI GRCh38 2 74366609 74366609 + synonymous_variant Silent SNP C C T rs1473795697 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 85 54 c.2478G>A p.Thr826= p.T826= ENST00000361874.8 826 acG/acA 22/31 P4 T T protein_coding YES CCDS1939.1 2478/3837 AGGAGCGTGTC PANTHER:PTHR18916;PANTHER:PTHR18916:SF75 ENSP00000354791 22/32 rs1473795697 ENST00000361874 Transcript 1.0 ENSG00000204843 HGNC:2711 LOW 0.0001447 gnomAD_AMR synonymous_variant 1.0 Unknown Q14203.203 DCTN1 HGNC -1 1.0 UPI0000129A25 Q14203-1 SNV DCTN1,synonymous_variant,p.T826=,ENST00000361874,NM_004082.5,c.2478G>A,LOW,YES,,,-1;DCTN1,synonymous_variant,p.T809=,ENST00000628224,,c.2427G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T819=,ENST00000394003,NM_001190837.2,c.2457G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T789=,ENST00000409240,NM_001190836.2,c.2367G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T809=,ENST00000409868,NM_001378992.1&NM_001378991.1,c.2427G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T692=,ENST00000633691,NM_023019.4,c.2076G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T692=,ENST00000409438,NM_001135041.3,c.2076G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T806=,ENST00000409567,NM_001135040.3,c.2418G>A,LOW,,,,-1;DCTN1,intron_variant,,ENST00000495643,,n.494+174G>A,MODIFIER,,,,-1;DCTN1,intron_variant,,ENST00000497666,,n.96+2691G>A,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000463583,,,MODIFIER,,,,-1;DCTN1,synonymous_variant,p.T789=,ENST00000434055,,c.2367G>A,LOW,,,,-1;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,,n.3457G>A,MODIFIER,,,,-1;AC006030.1,upstream_gene_variant,,ENST00000451608,,,MODIFIER,YES,,,-1;DCTN1,downstream_gene_variant,,ENST00000470351,,,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000477966,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000491465,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000492717,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000495895,,,MODIFIER,,,,-1 2796/4500 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.006e-05 0.0 0.0001447 0.0 0.0 0.0 0.0 0.0 0.0 1.3513000340026338e-05 0.0 0.0 0.0 0.0003028470091521 0.0 0.0 0.0 1.5427300240844488e-05 0.0 0.0 0 180 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 139 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DCTN1,intron_variant,,ENST00000495643.1,n.494+174G>A,MODIFIER,;DCTN1,synonymous_variant,p.T806=,ENST00000409567.7,c.2418G>A,LOW,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110.5,n.3457G>A,MODIFIER,;DCTN1,synonymous_variant,p.T809=,ENST00000409868.5,c.2427G>A,LOW,;DCTN1,synonymous_variant,p.T692=,ENST00000633691.1,c.2076G>A,LOW,;DCTN1,synonymous_variant,p.T692=,ENST00000409438.5,c.2076G>A,LOW,;DCTN1,synonymous_variant,p.T789=,ENST00000409240.5,c.2367G>A,LOW,;DCTN1,synonymous_variant,NMD_transcript_variant,p.T789=,ENST00000434055.5,c.2367G>A,LOW,;DCTN1,intron_variant,,ENST00000497666.1,n.96+2691G>A,MODIFIER,;DCTN1,synonymous_variant,p.T809=,ENST00000680606.1,c.2427G>A,LOW,;DCTN1,synonymous_variant,p.T826=,ENST00000628224.3,c.2478G>A,LOW,YES;DCTN1,synonymous_variant,p.T826=,ENST00000361874.8,c.2478G>A,LOW,;DCTN1,synonymous_variant,p.T819=,ENST00000394003.7,c.2457G>A,LOW, +DCTN1 1639 BI GRCh38 2 74369357 74369357 + synonymous_variant Silent SNP C C T rs777762235 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 7 c.1527G>A p.Thr509= p.T509= ENST00000361874.8 509 acG/acA 14/31 P4 T T protein_coding YES CCDS1939.1 1527/3837 GCAACCGTCTC Coiled-coils_(Ncoils):Coil;PANTHER:PTHR18916;PANTHER:PTHR18916:SF75 ENSP00000354791 14/32 rs777762235 ENST00000361874 Transcript 1.0 ENSG00000204843 HGNC:2711 LOW 8.796e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q14203.203 DCTN1 HGNC -1 1.0 UPI0000129A25 Q14203-1 SNV DCTN1,synonymous_variant,p.T509=,ENST00000361874,NM_004082.5,c.1527G>A,LOW,YES,,,-1;DCTN1,synonymous_variant,p.T492=,ENST00000628224,,c.1476G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T502=,ENST00000394003,NM_001190837.2,c.1506G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T472=,ENST00000409240,NM_001190836.2,c.1416G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T492=,ENST00000409868,NM_001378992.1&NM_001378991.1,c.1476G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T375=,ENST00000633691,NM_023019.4,c.1125G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T375=,ENST00000409438,NM_001135041.3,c.1125G>A,LOW,,,,-1;DCTN1,synonymous_variant,p.T489=,ENST00000409567,NM_001135040.3,c.1467G>A,LOW,,,,-1;DCTN1,downstream_gene_variant,,ENST00000458655,,,MODIFIER,,,,-1;DCTN1,non_coding_transcript_exon_variant,,ENST00000497666,,n.39G>A,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000463583,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000495643,,,MODIFIER,,,,-1;DCTN1,synonymous_variant,p.T472=,ENST00000434055,,c.1416G>A,LOW,,,,-1;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,,n.1748G>A,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000462813,,,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000470351,,,MODIFIER,,,,-1;DCTN1,downstream_gene_variant,,ENST00000477966,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000491465,,,MODIFIER,,,,-1;DCTN1,upstream_gene_variant,,ENST00000495895,,,MODIFIER,,,,-1 1845/4500 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.978e-06 0.0 0.0 0.0 0.0 0.0 8.796e-06 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DCTN1,synonymous_variant,p.T489=,ENST00000409567.7,c.1467G>A,LOW,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110.5,n.1748G>A,MODIFIER,;DCTN1,synonymous_variant,p.T492=,ENST00000409868.5,c.1476G>A,LOW,;DCTN1,synonymous_variant,p.T375=,ENST00000633691.1,c.1125G>A,LOW,;DCTN1,synonymous_variant,p.T375=,ENST00000409438.5,c.1125G>A,LOW,;DCTN1,synonymous_variant,p.T472=,ENST00000409240.5,c.1416G>A,LOW,;DCTN1,synonymous_variant,NMD_transcript_variant,p.T472=,ENST00000434055.5,c.1416G>A,LOW,;DCTN1,non_coding_transcript_exon_variant,,ENST00000497666.1,n.39G>A,MODIFIER,;DCTN1,synonymous_variant,p.T492=,ENST00000680606.1,c.1476G>A,LOW,;DCTN1,synonymous_variant,p.T509=,ENST00000628224.3,c.1527G>A,LOW,YES;DCTN1,synonymous_variant,p.T509=,ENST00000361874.8,c.1527G>A,LOW,;DCTN1,synonymous_variant,p.T502=,ENST00000394003.7,c.1506G>A,LOW, +BUB1 699 BI GRCh38 2 110655794 110655794 + synonymous_variant Silent SNP C C T rs772143908 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 114 12 c.1821G>A p.Ala607= p.A607= ENST00000302759.11 NM_004336.5 607 gcG/gcA 16/25 P1 T A protein_coding YES CCDS33273.1 1821/3258 GTAGACGCAAG PANTHER:PTHR14030;PANTHER:PTHR14030:SF8 ENSP00000302530 16/25 rs772143908;COSV100241428 ENST00000302759 Transcript 1.0 ENSG00000169679 HGNC:1148 LOW NM_004336.5 1.759e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 O43683.193 BUB1 HGNC -1 1.0 UPI00000012C4 O43683-1 SNV BUB1,synonymous_variant,p.A607=,ENST00000302759,NM_004336.5,c.1821G>A,LOW,YES,,,-1;BUB1,synonymous_variant,p.A587=,ENST00000535254,NM_001278616.1,c.1761G>A,LOW,,,,-1;BUB1,synonymous_variant,p.A607=,ENST00000409311,NM_001278617.1,c.1821G>A,LOW,,,,-1;BUB1,downstream_gene_variant,,ENST00000666956,,,MODIFIER,,,,-1;BUB1,synonymous_variant,p.A94=,ENST00000671097,,c.282G>A,LOW,,,,-1;BUB1,non_coding_transcript_exon_variant,,ENST00000466333,,n.1854G>A,MODIFIER,,,,-1 1889/3762 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.956e-06 0.0 0.0 0.0 0.0 0.0 1.759e-05 0.0 0.0 2.0306999431340955e-05 0.0 0.0 6.639219645876437e-05 0.0 0.0 9.439310088055208e-05 0.0 1.543970029160846e-05 0.0 0.0 0 146 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 126 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BUB1,non_coding_transcript_exon_variant,,ENST00000466333.5,n.1854G>A,MODIFIER,;BUB1,synonymous_variant,p.A607=,ENST00000409311.5,c.1821G>A,LOW,;BUB1,missense_variant,NMD_transcript_variant,p.R94H,ENST00000671097.1,c.281G>A,MODERATE,;BUB1,synonymous_variant,p.A587=,ENST00000535254.6,c.1761G>A,LOW,;BUB1,synonymous_variant,p.A607=,ENST00000302759.11,c.1821G>A,LOW,YES +MERTK 10461 BI GRCh38 2 111947478 111947478 + missense_variant Missense_Mutation SNP C C T rs765685308 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 26 c.668C>T p.Pro223Leu p.P223L ENST00000295408.9 NM_006343.3 223 cCg/cTg 4/19 P1 T P/L protein_coding YES CCDS2094.1 668/3000 GGGCCCGCCTG PANTHER:PTHR24416;PANTHER:PTHR24416:SF257;PROSITE_profiles:PS50835;Superfamily:SSF48726;SMART:SM00409;Pfam:PF13927;Gene3D:2.60.40.10;CDD:cd05749 ENSP00000295408 4/19 rs765685308 ENST00000295408 Transcript 1.0 ENSG00000153208 HGNC:7027 MODERATE NM_006343.3 6.152e-05 gnomAD_AFR missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0) Q12866.211 MERTK HGNC 1 1.0 UPI000013E252 SNV MERTK,missense_variant,p.P223L,ENST00000295408,NM_006343.3,c.668C>T,MODERATE,YES,deleterious(0),probably_damaging(0.994),1;MERTK,missense_variant,p.P223L,ENST00000421804,,c.668C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;MERTK,missense_variant,p.P47L,ENST00000409780,,c.140C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;MERTK,5_prime_UTR_variant,,ENST00000616902,,c.-548C>T,MODIFIER,,,,1;MERTK,3_prime_UTR_variant,,ENST00000439966,,c.*141C>T,MODIFIER,,,,1;SLC30A6P1,downstream_gene_variant,,ENST00000447549,,,MODIFIER,YES,,,-1 797/3826 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.193e-05 6.152e-05 0.0 0.0 0.0 0.0 1.759e-05 0.0 0.0 6.761139957234263e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542919926578179e-05 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MERTK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000439966.5,c.*141C>T,MODIFIER,;MERTK,missense_variant,p.P47L,ENST00000409780.5,c.140C>T,MODERATE,;MERTK,missense_variant,p.P223L,ENST00000295408.9,c.668C>T,MODERATE,YES +PSD4 23550 BI GRCh38 2 113183214 113183214 + missense_variant Missense_Mutation SNP C C T rs201700173 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 21 c.758C>T p.Ala253Val p.A253V ENST00000245796.11 NM_012455.3 253 gCg/gTg 2/17 P4 T A/V protein_coding YES CCDS33276.1 758/3171 CCTGGCGAGTC COSM1005671 PANTHER:PTHR10663;PANTHER:PTHR10663:SF338 ENSP00000245796 2/17 rs201700173;COSV55525638 ENST00000245796 Transcript ENSG00000125637 HGNC:19096 MODERATE NM_012455.3 5.437e-05 gnomAD_EAS missense_variant 0;1 1.0 benign(0) Unknown deleterious_low_confidence(0) 0;1 Q8NDX1.142 PSD4 HGNC 1 1.0 UPI00004A0748 Q8NDX1-1 SNV PSD4,missense_variant,p.A253V,ENST00000245796,NM_012455.3,c.758C>T,MODERATE,YES,deleterious_low_confidence(0),benign(0),1;PSD4,missense_variant,p.A253V,ENST00000441564,,c.758C>T,MODERATE,,deleterious_low_confidence(0),benign(0),1;PSD4,intron_variant,,ENST00000485525,,n.84-1743C>T,MODIFIER,,,,1;PSD4,downstream_gene_variant,,ENST00000465917,,,MODIFIER,,,,1;PSD4,non_coding_transcript_exon_variant,,ENST00000418251,,n.944C>T,MODIFIER,,,,1;PSD4,upstream_gene_variant,,ENST00000409656,,,MODIFIER,,,,1 953/11342 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.988e-05 0.0 0.0 0.0 5.437e-05 0.0 2.638e-05 0.0 3.266e-05 3.379890040378086e-05 0.0 0.0 0.0 0.0 0.0004030629934277 0.0 eas 0.0004030629934277 0.0032894699834287 1.5433099179062992e-05 0.0 0.0002082470018649 0 68 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PSD4,missense_variant,p.A253V,ENST00000441564.7,c.758C>T,MODERATE,;PSD4,non_coding_transcript_exon_variant,,ENST00000418251.6,n.944C>T,MODIFIER,;PSD4,intron_variant,,ENST00000485525.5,n.84-1743C>T,MODIFIER,;PSD4,missense_variant,p.A253V,ENST00000245796.11,c.758C>T,MODERATE,YES +CNTNAP5 129684 BI GRCh38 2 124446912 124446912 + missense_variant Missense_Mutation SNP C C T rs375042758 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 13 c.893C>T p.Thr298Met p.T298M ENST00000431078.1 NM_130773.4 298 aCg/aTg 6/24 P1 T T/M protein_coding YES CCDS46401.1 893/3921 CGAGACGGATG COSM122251 PROSITE_profiles:PS50025;CDD:cd00110;PANTHER:PTHR15036;PANTHER:PTHR15036:SF37;Gene3D:2.60.120.200;Pfam:PF02210;SMART:SM00282;Superfamily:SSF49899 ENSP00000399013 0.0 0.0001169 6/24 rs375042758 ENST00000431078 Transcript ENSG00000155052 HGNC:18748 MODERATE 0.0001169 EA missense_variant 1.0 possibly_damaging(0.549) Unknown tolerated(0.21) Q8WYK1.128 CNTNAP5 HGNC 1 1.0 UPI0000071988 SNV CNTNAP5,missense_variant,p.T298M,ENST00000431078,NM_001367498.1&NM_130773.4,c.893C>T,MODERATE,YES,tolerated(0.21),possibly_damaging(0.549),1 1257/5284 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.611e-05 0.0 0.0 0.0 0.0 4.648e-05 1.782e-05 0.0 3.271e-05 2.704090002225712e-05 0.0 0.0 0.0001987279974855 0.0 0.0 0.0 amr 0.0001987279974855 0.0 1.5428800907102413e-05 0.0 0.0 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CNTNAP5,missense_variant,p.T298M,ENST00000431078.1,c.893C>T,MODERATE,;CNTNAP5,missense_variant,p.T298M,ENST00000682447.1,c.893C>T,MODERATE,YES +IMP4 92856 BI GRCh38 2 130345790 130345790 + missense_variant Missense_Mutation SNP G G A rs11542413 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 28 c.451G>A p.Val151Ile p.V151I ENST00000259239.8 NM_001371725.1 151 Gtc/Atc 6/9 0.0002 0.0 0.0014 0.0 0.0 0.0 P1 A V/I protein_coding YES CCDS2160.1 451/876 TCATCGTCAGC PROSITE_profiles:PS50833;PANTHER:PTHR22734:SF2;PANTHER:PTHR22734;Pfam:PF04427;Gene3D:3.40.50.10480;SMART:SM00879;Superfamily:SSF52954 ENSP00000259239 6/9 rs11542413 ENST00000259239 Transcript ENSG00000136718 HGNC:30856 MODERATE NM_033416.3 0.0014 AMR missense_variant 1.0 benign(0.085) Unknown tolerated(0.65) Q96G21.139 IMP4 HGNC 1 1.0 UPI0000071F26 SNV IMP4,missense_variant,p.V151I,ENST00000259239,NM_001371725.1&NM_033416.3&NM_001371726.1&NM_001371728.1&NM_001320305.2&NM_001320304.2,c.451G>A,MODERATE,YES,tolerated(0.65),benign(0.085),1;IMP4,missense_variant,p.V151I,ENST00000409935,,c.451G>A,MODERATE,,tolerated(0.67),possibly_damaging(0.462),1;IMP4,missense_variant,p.V96I,ENST00000428740,NM_001320307.2&NM_001320306.2,c.286G>A,MODERATE,,tolerated(0.71),benign(0.05),1;IMP4,missense_variant,p.V140I,ENST00000452955,,c.418G>A,MODERATE,,tolerated(0.61),benign(0.03),1;IMP4,missense_variant,p.V66I,ENST00000409649,NM_001320309.2&NM_001371730.1&NM_001320310.2&NM_001320311.2&NM_001371733.1&NM_001371732.1&NM_001371734.1&NM_001371731.1,c.196G>A,MODERATE,,tolerated(0.72),benign(0.085),1;CCDC115,upstream_gene_variant,,ENST00000259229,NM_001321119.2&NM_032357.4,,MODIFIER,YES,,,-1;CCDC115,upstream_gene_variant,,ENST00000409127,NM_001321118.1,,MODIFIER,,,,-1;IMP4,non_coding_transcript_exon_variant,,ENST00000460766,,n.612G>A,MODIFIER,,,,1;IMP4,non_coding_transcript_exon_variant,,ENST00000464432,,n.571G>A,MODIFIER,,,,1;IMP4,non_coding_transcript_exon_variant,,ENST00000473689,,n.567G>A,MODIFIER,,,,1;IMP4,non_coding_transcript_exon_variant,,ENST00000490895,,n.598G>A,MODIFIER,,,,1;IMP4,non_coding_transcript_exon_variant,,ENST00000460100,,n.79G>A,MODIFIER,,,,1;IMP4,non_coding_transcript_exon_variant,,ENST00000462357,,n.70G>A,MODIFIER,,,,1;IMP4,intron_variant,,ENST00000462392,,n.628+91G>A,MODIFIER,,,,1;CCDC115,upstream_gene_variant,,ENST00000442217,,,MODIFIER,,,,-1;IMP4,downstream_gene_variant,,ENST00000456713,,,MODIFIER,,,,1;CCDC115,upstream_gene_variant,,ENST00000465315,,,MODIFIER,,,,-1;IMP4,downstream_gene_variant,,ENST00000470672,,,MODIFIER,,,,1;IMP4,upstream_gene_variant,,ENST00000475074,,,MODIFIER,,,,1;IMP4,downstream_gene_variant,,ENST00000477375,,,MODIFIER,,,,1;IMP4,downstream_gene_variant,,ENST00000495606,,,MODIFIER,,,,1;CCDC115,upstream_gene_variant,,ENST00000651709,,,MODIFIER,,,,-1 487/2411 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.385e-05 0.0 0.0002024 0.0 0.0001087 0.0 0.0 0.0 6.533e-05 6.084040069254115e-05 0.0 0.0 0.0005301519995555 0.0 0.0 0.0 amr 0.0005301519995555 0.0 1.5430699932039715e-05 0.0 0.0 0 63 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IMP4,non_coding_transcript_exon_variant,,ENST00000462357.1,n.70G>A,MODIFIER,;IMP4,non_coding_transcript_exon_variant,,ENST00000460100.1,n.79G>A,MODIFIER,;IMP4,synonymous_variant,p.S139=,ENST00000452955.1,c.417G>A,LOW,;IMP4,missense_variant,p.V96I,ENST00000428740.5,c.286G>A,MODERATE,;IMP4,non_coding_transcript_exon_variant,,ENST00000460766.5,n.612G>A,MODIFIER,;IMP4,missense_variant,p.V66I,ENST00000409649.5,c.196G>A,MODERATE,;IMP4,missense_variant,p.V151I,ENST00000259239.8,c.451G>A,MODERATE,YES;IMP4,non_coding_transcript_exon_variant,,ENST00000473689.5,n.567G>A,MODIFIER,;IMP4,non_coding_transcript_exon_variant,,ENST00000464432.5,n.571G>A,MODIFIER,;IMP4,intron_variant,,ENST00000462392.5,n.628+91G>A,MODIFIER,;IMP4,non_coding_transcript_exon_variant,,ENST00000490895.5,n.598G>A,MODIFIER,;IMP4,missense_variant,p.V151I,ENST00000409935.5,c.451G>A,MODERATE, +MAP3K19 80122 BI GRCh38 2 134981281 134981281 + missense_variant Missense_Mutation SNP G G A rs749899105 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 44 46 c.3460C>T p.Arg1154Cys p.R1154C ENST00000375845.8 NM_001321177.2 1154 Cgt/Tgt 9/10 A2 A R/C protein_coding CCDS2176.2 3460/3987 AAAACGGTTTA Superfamily:SSF56112;SMART:SM00220;Gene3D:1.10.510.10;Pfam:PF00069;PANTHER:PTHR45832;PANTHER:PTHR45832:SF5;CDD:cd06631;PROSITE_profiles:PS50011 ENSP00000365005 9/10 rs749899105 ENST00000375845 Transcript ENSG00000176601 HGNC:26249 MODERATE 0.0001845 gnomAD_AFR missense_variant probably_damaging(0.999) Unknown deleterious(0) Q56UN5.134 MAP3K19 HGNC -1 1.0 UPI00004F77F2 Q56UN5-1 SNV MAP3K19,missense_variant,p.R1154C,ENST00000392915,,c.3460C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;MAP3K19,missense_variant,p.R1154C,ENST00000375845,NM_025052.4&NM_001321177.1,c.3460C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;MAP3K19,missense_variant,p.R1041C,ENST00000358371,NM_001018044.2,c.3121C>T,MODERATE,,deleterious(0),probably_damaging(0.996),-1;MAP3K19,missense_variant,p.R544C,ENST00000437365,,c.1630C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;MAP3K19,missense_variant,p.R336C,ENST00000375844,NM_001018046.2,c.1006C>T,MODERATE,,deleterious(0),probably_damaging(0.99),-1;MAP3K19,missense_variant,p.R288C,ENST00000392918,NM_001018047.2,c.862C>T,MODERATE,,deleterious(0),probably_damaging(0.99),-1;MAP3K19,missense_variant,p.R286C,ENST00000392917,NM_001282883.1,c.856C>T,MODERATE,,deleterious(0),probably_damaging(0.981),-1;MAP3K19,downstream_gene_variant,,ENST00000637841,,,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,,n.3783C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661220,,n.363C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000669737,,n.293C>T,MODIFIER,,,,-1;MAP3K19,3_prime_UTR_variant,,ENST00000662522,,c.*2810C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000669521,,n.372C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000668969,,n.593C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661533,,n.512C>T,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000478805,,n.538C>T,MODIFIER,,,,-1 3491/4369 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0001845 0.0 9.921e-05 0.0 0.0 0.0 0.0 0.0 4.057450132677332e-05 0.0001216430027852 0.0 0.0 0.0 0.0 0.0 afr 0.0001216430027852 0.0 1.5433499356731772e-05 0.0 0.0 0 96 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 90 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAP3K19,non_coding_transcript_exon_variant,,ENST00000669737.1,n.293C>T,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025.2,n.3783C>T,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000478805.1,n.538C>T,MODIFIER,;MAP3K19,missense_variant,p.R544C,ENST00000437365.2,c.1630C>T,MODERATE,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000669521.1,n.372C>T,MODIFIER,;MAP3K19,missense_variant,p.R288C,ENST00000392918.7,c.862C>T,MODERATE,;MAP3K19,missense_variant,p.R286C,ENST00000392917.8,c.856C>T,MODERATE,;MAP3K19,missense_variant,p.R336C,ENST00000375844.7,c.1006C>T,MODERATE,;MAP3K19,missense_variant,p.R1154C,ENST00000375845.8,c.3460C>T,MODERATE,;MAP3K19,missense_variant,p.R1154C,ENST00000392915.7,c.3460C>T,MODERATE,YES;MAP3K19,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000662522.1,c.*2810C>T,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661533.1,n.512C>T,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000668969.1,n.593C>T,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661220.1,n.363C>T,MODIFIER,;MAP3K19,missense_variant,p.R1041C,ENST00000358371.9,c.3121C>T,MODERATE, +NEB 4703 BI GRCh38 2 151492472 151492472 + missense_variant Missense_Mutation SNP C C T rs745615279 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 56 16 c.24788G>A p.Arg8263Gln p.R8263Q ENST00000397345.8 NM_001164508.2 8263 cGg/cAg 177/182 T R/Q protein_coding 19220/20010 GTTTCCGGAAA COSM4537979;COSM4537980;COSM4537981 PROSITE_profiles:PS51216;PANTHER:PTHR11039:SF37;PANTHER:PTHR11039;SMART:SM00227 ENSP00000172853 144/149 rs745615279;COSV51441238;COSV51460697 ENST00000172853 Transcript 1.0 ENSG00000183091 HGNC:7720 MODERATE 5.572e-05 gnomAD_EAS missense_variant 0;1;1 possibly_damaging(0.703) Unknown tolerated(0.06) 0;1;1 P20929.192 NEB HGNC -1 1.0 UPI0000212787 P20929-1 SNV NEB,missense_variant,p.R8298Q,ENST00000618972,NM_001271208.2,c.24893G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.996),-1;NEB,missense_variant,p.R8263Q,ENST00000397345,NM_001164508.1,c.24788G>A,MODERATE,,deleterious(0.02),probably_damaging(0.935),-1;NEB,missense_variant,p.R8263Q,ENST00000427231,NM_001164507.1,c.24788G>A,MODERATE,,deleterious(0.03),probably_damaging(0.991),-1;NEB,missense_variant,p.R8263Q,ENST00000603639,,c.24788G>A,MODERATE,,deleterious(0.02),probably_damaging(0.935),-1;NEB,missense_variant,p.R8263Q,ENST00000604864,,c.24788G>A,MODERATE,,deleterious(0.03),probably_damaging(0.991),-1;NEB,missense_variant,p.R6407Q,ENST00000409198,NM_004543.5,c.19220G>A,MODERATE,,tolerated(0.07),probably_damaging(0.948),-1;NEB,missense_variant,p.R6407Q,ENST00000172853,,c.19220G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.703),-1;NEB,missense_variant,p.R2745Q,ENST00000413693,,c.8234G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.494),-1;NEB,missense_variant,p.R397Q,ENST00000397337,,c.1190G>A,MODERATE,,tolerated(0.12),probably_damaging(0.998),-1;NEB,missense_variant,p.R504Q,ENST00000434685,,c.1511G>A,MODERATE,,tolerated(0.45),probably_damaging(0.959),-1;NEB,downstream_gene_variant,,ENST00000421461,,,MODIFIER,,,,-1;NEB,downstream_gene_variant,,ENST00000424585,,,MODIFIER,,,,-1;NEB,non_coding_transcript_exon_variant,,ENST00000498015,,n.248G>A,MODIFIER,,,,-1;RIF1,intron_variant,,ENST00000457745,,n.481-2757C>T,MODIFIER,,,,1;RIF1,upstream_gene_variant,,ENST00000484077,,,MODIFIER,,,,1;NEB,non_coding_transcript_exon_variant,,ENST00000497809,,n.825G>A,MODIFIER,,,,-1;RIF1,intron_variant,,ENST00000454583,,c.*416-2757C>T,MODIFIER,,,,1 19423/20634 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.023e-06 0.0 0.0 0.0 5.572e-05 0.0 0.0 0.0 0.0 0 73 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NEB,non_coding_transcript_exon_variant,,ENST00000498015.2,n.248G>A,MODIFIER,;NEB,non_coding_transcript_exon_variant,,ENST00000497809.1,n.825G>A,MODIFIER,;RIF1,intron_variant,,ENST00000457745.1,n.481-2757C>T,MODIFIER,;NEB,missense_variant,p.G463R,ENST00000688578.1,c.1387G>A,MODERATE,;NEB,missense_variant,p.G2165R,ENST00000690043.1,c.6493G>A,MODERATE,;NEB,missense_variant,p.G1033R,ENST00000434685.6,c.3097G>A,MODERATE,;NEB,non_coding_transcript_exon_variant,,ENST00000689642.1,n.607G>A,MODIFIER,;NEB,non_coding_transcript_exon_variant,,ENST00000693000.1,n.2679G>A,MODIFIER,;NEB,missense_variant,p.R2745Q,ENST00000413693.5,c.8234G>A,MODERATE,;NEB,missense_variant,p.R8263Q,ENST00000397345.8,c.24788G>A,MODERATE,YES;NEB,missense_variant,p.G397R,ENST00000397337.6,c.1189G>A,MODERATE,;NEB,missense_variant,p.R8263Q,ENST00000427231.7,c.24788G>A,MODERATE,;NEB,missense_variant,p.R6407Q,ENST00000409198.5,c.19220G>A,MODERATE,;RIF1,intron_variant,NMD_transcript_variant,,ENST00000454583.6,c.*416-2757C>T,MODIFIER, +SCN2A 6326 BI GRCh38 2 165354394 165354394 + missense_variant Missense_Mutation SNP C C T TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 8 c.3122C>T p.Pro1041Leu p.P1041L ENST00000283256.10 NM_021007.3 1041 cCg/cTg 17/27 P1 T P/L protein_coding CCDS33314.1 3122/6018 TAAACCGCTTG COSM1264993;COSM1264994 PDB-ENSP_mappings:6j8e.A;PANTHER:PTHR10037;PANTHER:PTHR10037:SF278;Pfam:PF06512 ENSP00000283256 17/27 COSV51840749 ENST00000283256 Transcript 1.0 ENSG00000136531 HGNC:10588 MODERATE missense_variant 1 benign(0.149) Unknown deleterious(0.03) 1 Q99250.207 SCN2A HGNC 1 1.0 UPI00001279C9 Q99250-1 SNV SCN2A,missense_variant,p.P1041L,ENST00000636071,NM_001040143.2,c.3122C>T,MODERATE,YES,deleterious(0.03),benign(0.006),1;SCN2A,missense_variant,p.P909L,ENST00000636985,,c.2726C>T,MODERATE,,deleterious(0.03),benign(0.149),1;SCN2A,missense_variant,p.P1041L,ENST00000375437,NM_001040142.2,c.3122C>T,MODERATE,,deleterious(0.03),benign(0.149),1;SCN2A,missense_variant,p.P1041L,ENST00000283256,NM_021007.3,c.3122C>T,MODERATE,,deleterious(0.03),benign(0.149),1;SCN2A,missense_variant,p.P1041L,ENST00000637266,NM_001371247.1,c.3122C>T,MODERATE,,deleterious(0.03),benign(0.149),1;SCN2A,missense_variant,p.P1041L,ENST00000631182,NM_001371246.1,c.3122C>T,MODERATE,,deleterious(0.03),benign(0.006),1;SCN2A,missense_variant,p.P325L,ENST00000674133,,c.974C>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.254),1;SCN2A,3_prime_UTR_variant,,ENST00000636662,,c.*3645C>T,MODIFIER,,,,1;SCN2A,3_prime_UTR_variant,,ENST00000636384,,c.*1109C>T,MODIFIER,,,,1;SCN2A,3_prime_UTR_variant,,ENST00000636769,,c.*1064C>T,MODIFIER,,,,1;SCN2A,3_prime_UTR_variant,,ENST00000636135,,c.*1441C>T,MODIFIER,,,,1;SCN2A,3_prime_UTR_variant,,ENST00000673831,,c.*475C>T,MODIFIER,,,,1;SCN2A,3_prime_UTR_variant,,ENST00000673883,,c.*264C>T,MODIFIER,,,,1;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,,n.3265C>T,MODIFIER,,,,1 3278/8660 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673883.1,c.*264C>T,MODIFIER,;SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673831.1,c.*475C>T,MODIFIER,;SCN2A,missense_variant,NMD_transcript_variant,p.R325C,ENST00000674133.1,c.973C>T,MODERATE,;SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636769.1,c.*1064C>T,MODIFIER,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032.4,n.3265C>T,MODIFIER,;SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636662.2,c.*3645C>T,MODIFIER,;SCN2A,missense_variant,p.P1041L,ENST00000283256.10,c.3122C>T,MODERATE,;SCN2A,missense_variant,p.P1041L,ENST00000637266.2,c.3122C>T,MODERATE,;SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636135.1,c.*1441C>T,MODIFIER,;SCN2A,missense_variant,p.P909L,ENST00000636985.2,c.2726C>T,MODERATE,;SCN2A,missense_variant,p.P1041L,ENST00000636071.2,c.3122C>T,MODERATE,;SCN2A,missense_variant,p.P1041L,ENST00000375437.7,c.3122C>T,MODERATE,YES;SCN2A,missense_variant,p.P1041L,ENST00000631182.3,c.3122C>T,MODERATE,;SCN2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636384.2,c.*1109C>T,MODIFIER, +LRP2 4036 BI GRCh38 2 169156288 169156288 + missense_variant Missense_Mutation SNP C C T rs867978150 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 61 9 c.12137G>A p.Arg4046Gln p.R4046Q ENST00000649046.1 NM_004525.3 4046 cGa/cAa 65/79 P1 T R/Q protein_coding YES CCDS2232.1 12137/13968 CACATCGTTTT CDD:cd00054;Pfam:PF07645;Gene3D:2.10.25.10;SMART:SM00179;SMART:SM00181;PROSITE_profiles:PS50026;PANTHER:PTHR46513:SF21;PANTHER:PTHR46513 ENSP00000496870 65/79 rs867978150 ENST00000649046 Transcript 1.0 ENSG00000081479 HGNC:6694 MODERATE NM_004525.3 missense_variant 1.0 benign(0.029) Unknown tolerated(0.51) P98164.202 LRP2 HGNC -1 UPI0000141BA5 SNV LRP2,missense_variant,p.R4046Q,ENST00000649046,NM_004525.3,c.12137G>A,MODERATE,YES,tolerated(0.51),benign(0.029),-1;LRP2,missense_variant,p.R1013Q,ENST00000649153,,c.3038G>A,MODERATE,,tolerated(0.64),benign(0.343),-1;LRP2,missense_variant,p.R390Q,ENST00000650252,,c.1169G>A,MODERATE,,tolerated(0.46),possibly_damaging(0.627),-1 12272/15657 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 95 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 70 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRP2,missense_variant,NMD_transcript_variant,p.D1013N,ENST00000649153.1,c.3037G>A,MODERATE,;LRP2,missense_variant,NMD_transcript_variant,p.R390Q,ENST00000650252.1,c.1169G>A,MODERATE,;LRP2,missense_variant,p.R4046Q,ENST00000649046.1,c.12137G>A,MODERATE,YES +KLHL41 10324 BI GRCh38 2 169509985 169509985 + synonymous_variant Silent SNP G G A rs373592757 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 88 16 c.207G>A p.Ala69= p.A69= ENST00000284669.2 NM_006063.3 69 gcG/gcA 1/6 P1 A A protein_coding YES CCDS2234.1 207/1821 GAGGCGAAAAA PROSITE_profiles:PS50097;CDD:cd18341;PANTHER:PTHR24412;PANTHER:PTHR24412:SF146;PIRSF:PIRSF037037;Pfam:PF00651;Gene3D:3.30.710.10;SMART:SM00225;Superfamily:SSF54695 ENSP00000284669 0.000227 0.0 1/6 rs373592757 ENST00000284669 Transcript 1.0 ENSG00000239474 HGNC:16905 LOW NM_006063.3 0.000227 AA synonymous_variant 1.0 Unknown O60662.170 KLHL41 HGNC 1 1.0 UPI0000000DC5 O60662-1 SNV KLHL41,synonymous_variant,p.A69=,ENST00000284669,NM_006063.3,c.207G>A,LOW,YES,,,1;AC093899.2,intron_variant,,ENST00000513963,,c.925-4589G>A,MODIFIER,YES,,,1;BBS5,downstream_gene_variant,,ENST00000295240,NM_152384.3,,MODIFIER,YES,,,1;BBS5,downstream_gene_variant,,ENST00000392663,,,MODIFIER,,,,1;KLHL41,upstream_gene_variant,,ENST00000463400,,,MODIFIER,,,,1;KLHL41,upstream_gene_variant,,ENST00000480330,,,MODIFIER,,,,1;BBS5,downstream_gene_variant,,ENST00000472667,,,MODIFIER,,,,1 284/2460 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.681e-05 6.207e-05 8.992e-05 0.0 0.0 0.0 8.034e-05 0.0001677 0.0 4.078579877386801e-05 7.336040289374068e-05 0.0 6.659560312982649e-05 0.0 0.0 0.0 oth 0.0009980039903894 0.0 0.0 0.0009980039903894 0.0 0 106 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 105 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KLHL41,synonymous_variant,p.A69=,ENST00000284669.2,c.207G>A,LOW,YES;ENSG00000251569,intron_variant,,ENST00000513963.1,c.925-4589G>A,MODIFIER,YES +MYO3B 140469 BI GRCh38 2 170515003 170515003 + synonymous_variant Silent SNP C C T rs750438385 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 7 c.3453C>T p.Ser1151= p.S1151= ENST00000408978.9 NM_138995.5 1151 agC/agT 29/35 P1 T S protein_coding YES CCDS42773.1 3453/4026 TGCAGCGAGCC MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000386213 29/35 rs750438385 ENST00000408978 Transcript ENSG00000071909 HGNC:15576 LOW NM_138995.5 3.276e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q8WXR4.162 MYO3B HGNC 1 1.0 UPI000020907B Q8WXR4-1 SNV MYO3B,synonymous_variant,p.S1151=,ENST00000408978,NM_138995.5,c.3453C>T,LOW,YES,,,1;MYO3B,synonymous_variant,p.S1124=,ENST00000409044,NM_001083615.4,c.3372C>T,LOW,,,,1;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,,n.2681C>T,MODIFIER,,,,1;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,,n.3596C>T,MODIFIER,,,,1;MYO3B,synonymous_variant,p.S1124=,ENST00000317935,,c.3372C>T,LOW,,,,1;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,,n.3596C>T,MODIFIER,,,,1 3594/6213 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.014e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.276e-05 6.761049917258788e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002090299967676 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 31 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYO3B,non_coding_transcript_exon_variant,,ENST00000602629.1,n.2681C>T,MODIFIER,;MYO3B,synonymous_variant,p.S1151=,ENST00000408978.9,c.3453C>T,LOW,YES;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940.6,n.3596C>T,MODIFIER,;MYO3B,synonymous_variant,p.S1124=,ENST00000409044.7,c.3372C>T,LOW,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642.6,n.3596C>T,MODIFIER,;MYO3B,synonymous_variant,NMD_transcript_variant,p.S1124=,ENST00000317935.10,c.3372C>T,LOW, +SLC25A12 8604 BI GRCh38 2 171785376 171785376 + synonymous_variant Silent SNP C C T rs369901246 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 17 c.1935G>A p.Thr645= p.T645= ENST00000422440.7 NM_003705.5 645 acG/acA 18/18 P1 T T protein_coding YES CCDS33327.1 1935/2037 GCAAACGTGGC PANTHER:PTHR45678:SF7;PANTHER:PTHR45678 ENSP00000388658 0.000227 0.0 18/18 rs369901246 ENST00000422440 Transcript 1.0 ENSG00000115840 HGNC:10982 LOW NM_003705.5 0.000227 AA synonymous_variant 1.0 Unknown O75746.191 SLC25A12 HGNC -1 1.0 UPI0000070D4E O75746-1 SNV SLC25A12,synonymous_variant,p.T645=,ENST00000422440,NM_003705.5,c.1935G>A,LOW,YES,,,-1;SLC25A12,3_prime_UTR_variant,,ENST00000263812,,c.*1555G>A,MODIFIER,,,,-1;SLC25A12,non_coding_transcript_exon_variant,,ENST00000472070,,n.1345G>A,MODIFIER,,,,-1 1965/3936 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.953e-06 0.000123 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.379569898243062e-05 9.726209827931598e-05 0.0 0.0 0.0 0.0 0.0 afr 9.726209827931598e-05 0.0 1.5430699932039715e-05 0.0 0.0 0 95 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 79 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC25A12,non_coding_transcript_exon_variant,,ENST00000472070.1,n.1345G>A,MODIFIER,;SLC25A12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000263812.8,c.*1555G>A,MODIFIER,;SLC25A12,synonymous_variant,p.T645=,ENST00000422440.7,c.1935G>A,LOW,YES +DLX2 1746 BI GRCh38 2 172100920 172100920 + missense_variant Missense_Mutation SNP G G A rs1414617008 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 6 c.610C>T p.Arg204Trp p.R204W ENST00000234198.9 NM_004405.4 204 Cgg/Tgg 3/3 P1 A R/W protein_coding YES CCDS2248.1 610/987 GGACCGGCGGT COSM1325760 Prints:PR00031;Prints:PR00024;PROSITE_patterns:PS00027;PANTHER:PTHR24327:SF23;PANTHER:PTHR24327;PROSITE_profiles:PS50071;Superfamily:SSF46689;SMART:SM00389;Pfam:PF00046;Gene3D:1.10.10.60;CDD:cd00086 ENSP00000234198 3/3 rs1414617008;COSV52233002 ENST00000234198 Transcript ENSG00000115844 HGNC:2915 MODERATE NM_004405.4 9.106e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q07687.169 DLX2 HGNC -1 Q53QU7.135;X5D7D8.44 1.0 UPI00001294AC Q07687-1 SNV DLX2,missense_variant,p.R204W,ENST00000234198,NM_004405.4,c.610C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;DLX2,3_prime_UTR_variant,,ENST00000466293,,c.*473C>T,MODIFIER,,,,-1;DLX2-DT,upstream_gene_variant,,ENST00000448117,,,MODIFIER,YES,,,1 972/2454 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.068e-06 0.0 0.0 0.0 0.0 0.0 9.106e-06 0.0 0.0 0 46 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 49 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DLX2,3_prime_UTR_variant,,ENST00000466293.2,c.*473C>T,MODIFIER,;DLX2,missense_variant,p.R204W,ENST00000234198.9,c.610C>T,MODERATE,YES +TTN 7273 BI GRCh38 2 178566447 178566447 + missense_variant Missense_Mutation SNP C C T rs538960023 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 80 30 c.74762G>A p.Arg24921Gln p.R24921Q ENST00000591111.5 24921 cGa/cAa 276/313 0.0002 0.0 0.0 0.0 0.0 0.001 T R/Q protein_coding 74762/103053 likely_benign AGACTCGTATT Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR13817;PANTHER:PTHR13817:SF10;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000465570 276/313 rs538960023 ENST00000591111 Transcript 1.0 ENSG00000155657 HGNC:12403 MODERATE 0.001 SAS missense_variant 1 probably_damaging(0.996) Unknown Q8WZ42.192 TTN HGNC -1 5.0 UPI00025287CD Q8WZ42-1 SNV TTN,missense_variant,p.R26562Q,ENST00000589042,NM_001267550.2,c.79685G>A,MODERATE,YES,,probably_damaging(0.996),-1;TTN,missense_variant,p.R24921Q,ENST00000591111,,c.74762G>A,MODERATE,,,probably_damaging(0.996),-1;TTN,missense_variant,p.R23994Q,ENST00000342992,NM_133378.4&NM_001256850.1,c.71981G>A,MODERATE,,,probably_damaging(0.992),-1;TTN,missense_variant,p.R17497Q,ENST00000460472,NM_003319.4,c.52490G>A,MODERATE,,,probably_damaging(0.998),-1;TTN,missense_variant,p.R17689Q,ENST00000342175,NM_133437.4,c.53066G>A,MODERATE,,,,-1;TTN,missense_variant,p.R17622Q,ENST00000359218,NM_133432.3,c.52865G>A,MODERATE,,,probably_damaging(0.998),-1;TTN-AS1,intron_variant,,ENST00000419746,,n.2044-16125C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000438095,,n.195-4853C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000456053,,n.414-4853C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000585451,,n.198+42811C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586452,,n.75-4853C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586707,,n.346-17266C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586831,,n.215-16125C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590773,,n.597+28756C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590807,,n.75-17077C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590932,,n.615+24086C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000591332,,n.442+30619C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592600,,n.346-18126C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592630,,n.433+28756C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592689,,n.462+24086C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592750,,n.346-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625480,,n.50-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625536,,n.22-24692C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626117,,n.75-24692C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626138,,n.50-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626954,,n.75-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000627564,,n.378-4853C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628296,,n.50-24692C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628826,,n.49+37634C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000630096,,n.552-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000653807,,n.220-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000657023,,n.119-31149C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000659121,,n.417-31149C>T,MODIFIER,YES,,,1 74987/104301 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.636e-05 0.0 0.0 0.0 0.0 0.0 1.779e-05 0.0 0.0003922 3.382310023880564e-05 2.432730070722755e-05 0.0 0.0 0.0 0.0 9.414419764652848e-05 nfe 3.088230005232617e-05 0.0 3.088230005232617e-05 0.0 0.0002085940068354 0 129 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 110 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TTN-AS1,intron_variant,,ENST00000590932.5,n.615+24086C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000438095.1,n.195-4853C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000627564.2,n.378-4853C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625536.2,n.22-24692C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628826.2,n.49+37634C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626138.2,n.50-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625480.2,n.50-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628296.2,n.50-24692C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626954.2,n.75-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592689.5,n.462+24086C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626117.2,n.75-24692C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590807.5,n.75-17077C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586452.5,n.75-4853C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586831.5,n.215-16125C>T,MODIFIER,;TTN,missense_variant,p.R23994Q,ENST00000342992.11,c.71981G>A,MODERATE,;TTN,missense_variant,p.R26534Q,ENST00000425332.3,c.79601G>A,MODERATE,;TTN,missense_variant,p.R24921Q,ENST00000591111.5,c.74762G>A,MODERATE,;TTN,missense_variant,p.R26562Q,ENST00000589042.5,c.79685G>A,MODERATE,YES;TTN,missense_variant,p.R26424Q,ENST00000715174.1,c.79271G>A,MODERATE,;TTN,missense_variant,p.R17689Q,ENST00000342175.12,c.53066G>A,MODERATE,;TTN,missense_variant,p.R17497Q,ENST00000460472.6,c.52490G>A,MODERATE,;TTN,missense_variant,p.R26470Q,ENST00000436599.2,c.79409G>A,MODERATE,;TTN,missense_variant,p.R17622Q,ENST00000359218.11,c.52865G>A,MODERATE,;TTN,missense_variant,p.R26510Q,ENST00000446966.2,c.79529G>A,MODERATE,;TTN,missense_variant,p.R26376Q,ENST00000426232.6,c.79127G>A,MODERATE,;TTN,missense_variant,p.R26562Q,ENST00000412264.2,c.79685G>A,MODERATE,;TTN-AS1,intron_variant,,ENST00000657023.1,n.119-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000585451.5,n.198+42811C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000653807.1,n.220-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000591332.5,n.442+30619C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592630.5,n.433+28756C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592600.6,n.346-18126C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592750.5,n.346-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586707.6,n.346-17266C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590773.6,n.597+28756C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000456053.5,n.414-4853C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000659121.1,n.417-31149C>T,MODIFIER,YES;TTN-AS1,intron_variant,,ENST00000702938.1,n.431-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000630096.2,n.552-31149C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000419746.5,n.2044-16125C>T,MODIFIER, +TTN 7273 BI GRCh38 2 178770077 178770077 + missense_variant Missense_Mutation SNP G G A rs1335787072 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 40 c.8624C>T p.Ala2875Val p.A2875V ENST00000591111.5 2875 gCa/gTa 36/313 A A/V protein_coding 8624/103053 GTTTTGCTTTG Gene3D:2.60.40.10;PDB-ENSP_mappings:5jdd.A;PDB-ENSP_mappings:5jde.A;PDB-ENSP_mappings:5jde.B;Pfam:PF07679;PANTHER:PTHR13817;PANTHER:PTHR13817:SF10;SMART:SM00409;Superfamily:SSF48726 ENSP00000465570 36/313 rs1335787072 ENST00000591111 Transcript 1.0 ENSG00000155657 HGNC:12403 MODERATE missense_variant probably_damaging(0.997) Unknown Q8WZ42.192 TTN HGNC -1 5.0 UPI00025287CD Q8WZ42-1 SNV TTN,missense_variant,p.A2875V,ENST00000589042,NM_001267550.2,c.8624C>T,MODERATE,YES,,probably_damaging(0.997),-1;TTN,missense_variant,p.A2875V,ENST00000591111,,c.8624C>T,MODERATE,,,probably_damaging(0.997),-1;TTN,missense_variant,p.A2875V,ENST00000342992,NM_133378.4&NM_001256850.1,c.8624C>T,MODERATE,,,probably_damaging(0.998),-1;TTN,missense_variant,p.A2829V,ENST00000460472,NM_003319.4,c.8486C>T,MODERATE,,,probably_damaging(0.998),-1;TTN,missense_variant,p.A2829V,ENST00000342175,NM_133437.4,c.8486C>T,MODERATE,,,,-1;TTN,missense_variant,p.A2829V,ENST00000359218,NM_133432.3,c.8486C>T,MODERATE,,,probably_damaging(0.998),-1;TTN,missense_variant,p.A2875V,ENST00000360870,NM_133379.5,c.8624C>T,MODERATE,,deleterious(0.03),probably_damaging(0.998),-1;TTN,upstream_gene_variant,,ENST00000634225,,,MODIFIER,,,,-1;TTN-AS1,intron_variant,,ENST00000585451,,n.457-3198G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590773,,n.1908-3198G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000610005,,n.562-3198G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000653807,,n.1628-3198G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000657023,,n.1134-3198G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000659121,,n.1593-3198G>A,MODIFIER,YES,,,1;TTN-AS1,upstream_gene_variant,,ENST00000584485,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000629094,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000657818,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000663178,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000664776,,,MODIFIER,,,,1 8849/104301 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 111 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 78 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TTN-AS1,intron_variant,,ENST00000610005.1,n.562-3198G>A,MODIFIER,;TTN,missense_variant,p.A2829V,ENST00000634225.2,c.8486C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000360870.10,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000342992.11,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000425332.3,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000591111.5,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000589042.5,c.8624C>T,MODERATE,YES;TTN,missense_variant,p.A2737V,ENST00000715174.1,c.8210C>T,MODERATE,;TTN,missense_variant,p.A2829V,ENST00000342175.12,c.8486C>T,MODERATE,;TTN,missense_variant,p.A2829V,ENST00000460472.6,c.8486C>T,MODERATE,;TTN,missense_variant,p.A2783V,ENST00000436599.2,c.8348C>T,MODERATE,;TTN,missense_variant,p.A2829V,ENST00000359218.11,c.8486C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000446966.2,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000426232.6,c.8624C>T,MODERATE,;TTN,missense_variant,p.A2875V,ENST00000412264.2,c.8624C>T,MODERATE,;TTN-AS1,intron_variant,,ENST00000657023.1,n.1134-3198G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000585451.5,n.457-3198G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000653807.1,n.1628-3198G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590773.6,n.1908-3198G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000659121.1,n.1593-3198G>A,MODIFIER,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 18 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +PLCL1 5334 BI GRCh38 2 198084033 198084033 + synonymous_variant Silent SNP G G A rs750066298 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 35 c.516G>A p.Thr172= p.T172= ENST00000428675.6 NM_006226.4 172 acG/acA 2/6 P1 A T protein_coding YES CCDS2326.2 516/3288 AACACGGAAAC COSM4551038;COSM4551039 Gene3D:2.30.29.30;Pfam:PF16457;PROSITE_profiles:PS50003;PANTHER:PTHR10336;PANTHER:PTHR10336:SF102;SMART:SM00233;Superfamily:SSF50729;CDD:cd13364 ENSP00000402861 2/6 rs750066298;COSV70821920 ENST00000428675 Transcript ENSG00000115896 HGNC:9063 LOW NM_006226.4 2.892e-05 gnomAD_AMR synonymous_variant 0;1 1.0 Unknown 0;1 Q15111.162 PLCL1 HGNC 1 1.0 UPI000165BCF5 Q15111-1 SNV PLCL1,synonymous_variant,p.T172=,ENST00000428675,NM_006226.4,c.516G>A,LOW,YES,,,1;PLCL1,synonymous_variant,p.T95=,ENST00000437704,,c.285G>A,LOW,,,,1;PLCL1,synonymous_variant,p.T98=,ENST00000487695,,c.294G>A,LOW,,,,1;PLCL1,3_prime_UTR_variant,,ENST00000435320,,c.*288G>A,MODIFIER,,,,1 1023/6696 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-06 0.0 2.892e-05 0.0 0.0 0.0 0.0 0.0 0.0 2.028010021604132e-05 0.0 0.0 0.000198886002181 0.0 0.0 0.0 amr 0.000198886002181 0.0 0.0 0.0 0.0 0 83 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 70 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLCL1,synonymous_variant,p.T98=,ENST00000487695.6,c.294G>A,LOW,;PLCL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000435320.1,c.*288G>A,MODIFIER,;PLCL1,synonymous_variant,p.T172=,ENST00000428675.6,c.516G>A,LOW,YES +PLEKHM3 389072 BI GRCh38 2 207931086 207931086 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 15 c.1726G>A p.Val576Met p.V576M ENST00000427836.8 NM_001080475.3 576 Gtg/Atg 5/8 P1 T V/M protein_coding YES CCDS42808.1 1726/2286 GTACACGTACT Pfam:PF13901;PANTHER:PTHR12326;PANTHER:PTHR12326:SF10;SMART:SM01175 ENSP00000417003 5/8 ENST00000427836 Transcript ENSG00000178385 HGNC:34006 MODERATE NM_001080475.3 missense_variant 1.0 probably_damaging(0.997) Unknown deleterious(0) Q6ZWE6.126 PLEKHM3 HGNC -1 5.0 UPI0000DBEE58 Q6ZWE6-1 SNV PLEKHM3,missense_variant,p.V576M,ENST00000427836,NM_001080475.3,c.1726G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;PLEKHM3,missense_variant,p.V576M,ENST00000457206,,c.1726G>A,MODERATE,,deleterious(0),probably_damaging(0.966),-1;PLEKHM3,missense_variant,p.V328M,ENST00000447645,,c.982G>A,MODERATE,,deleterious(0),probably_damaging(0.989),-1 2183/9774 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLEKHM3,missense_variant,p.V576M,ENST00000457206.1,c.1726G>A,MODERATE,;PLEKHM3,missense_variant,p.R327H,ENST00000447645.5,c.980G>A,MODERATE,;PLEKHM3,missense_variant,p.V576M,ENST00000427836.8,c.1726G>A,MODERATE,YES +PLCD4 84812 BI GRCh38 2 218618797 218618797 + missense_variant Missense_Mutation SNP C C T rs776903135 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 4 6 c.400C>T p.Arg134Cys p.R134C ENST00000417849.5 134 Cgc/Tgc 4/17 P4 T R/C protein_coding CCDS46516.1 400/2289 AGGAGCGCCTG Gene3D:2.30.29.30;PROSITE_profiles:PS50222;PANTHER:PTHR10336;PANTHER:PTHR10336:SF31;Superfamily:SSF47473 ENSP00000396942 4/17 rs776903135;COSV101335818 ENST00000417849 Transcript ENSG00000115556 HGNC:9062 MODERATE 0.0001661 gnomAD_AFR missense_variant 0;1 possibly_damaging(0.724) Unknown deleterious(0) 0;1 Q9BRC7.165 PLCD4 HGNC 1 5.0 UPI0000044279 Q9BRC7-1 SNV PLCD4,missense_variant,p.R134C,ENST00000432688,,c.400C>T,MODERATE,YES,deleterious(0),benign(0.029),1;PLCD4,missense_variant,p.R134C,ENST00000450993,NM_032726.4,c.400C>T,MODERATE,,deleterious(0),possibly_damaging(0.724),1;PLCD4,missense_variant,p.R134C,ENST00000417849,,c.400C>T,MODERATE,,deleterious(0),possibly_damaging(0.724),1;PLCD4,downstream_gene_variant,,ENST00000415854,,,MODIFIER,,,,1;PLCD4,3_prime_UTR_variant,,ENST00000444453,,c.*87C>T,MODIFIER,,,,1;PLCD4,3_prime_UTR_variant,,ENST00000446503,,c.*87C>T,MODIFIER,,,,1;PLCD4,non_coding_transcript_exon_variant,,ENST00000473443,,n.485C>T,MODIFIER,,,,1;PLCD4,non_coding_transcript_exon_variant,,ENST00000483685,,n.649C>T,MODIFIER,,,,1;PLCD4,non_coding_transcript_exon_variant,,ENST00000469493,,n.605C>T,MODIFIER,,,,1;PLCD4,non_coding_transcript_exon_variant,,ENST00000465713,,n.426C>T,MODIFIER,,,,1;PLCD4,upstream_gene_variant,,ENST00000459791,,,MODIFIER,,,,1 585/2738 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.434e-05 0.0001661 3.458e-05 0.0 0.0 0.0 2.229e-05 0.0 0.0 5.40883993380703e-05 0.0001945239928318 0.0 0.0 0.0 0.0 0.0 afr 0.0001945239928318 0.0 0.0 0.0 0.0 0 12 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLCD4,missense_variant,p.R134C,ENST00000432688.5,c.400C>T,MODERATE,;PLCD4,non_coding_transcript_exon_variant,,ENST00000465713.5,n.426C>T,MODIFIER,;PLCD4,missense_variant,p.R134C,ENST00000417849.5,c.400C>T,MODERATE,;PLCD4,non_coding_transcript_exon_variant,,ENST00000473443.5,n.485C>T,MODIFIER,;PLCD4,non_coding_transcript_exon_variant,,ENST00000469493.5,n.605C>T,MODIFIER,;PLCD4,missense_variant,p.R134C,ENST00000450993.7,c.400C>T,MODERATE,YES;PLCD4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000444453.5,c.*87C>T,MODIFIER,;PLCD4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000446503.5,c.*87C>T,MODIFIER,;PLCD4,non_coding_transcript_exon_variant,,ENST00000483685.5,n.649C>T,MODIFIER, +STK11IP 114790 BI GRCh38 2 219608632 219608632 + synonymous_variant Silent SNP C C T rs773472469 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 10 c.1653C>T p.Gly551= p.G551= ENST00000456909.6 NM_052902.4 551 ggC/ggT 15/25 P1 T G protein_coding YES CCDS46521.2 1653/3267 GAGGGCGTACG PANTHER:PTHR15454;PANTHER:PTHR15454:SF32 ENSP00000389383 15/25 rs773472469 ENST00000456909 Transcript ENSG00000144589 HGNC:19184 LOW NM_052902.4 3.286e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q8N1F8.141 STK11IP HGNC 1 1.0 UPI000013E286 SNV STK11IP,synonymous_variant,p.G551=,ENST00000456909,NM_052902.4,c.1653C>T,LOW,YES,,,1;STK11IP,upstream_gene_variant,,ENST00000483319,,,MODIFIER,,,,1;STK11IP,downstream_gene_variant,,ENST00000459692,,,MODIFIER,,,,1;STK11IP,non_coding_transcript_exon_variant,,ENST00000475396,,n.1634C>T,MODIFIER,,,,1;STK11IP,non_coding_transcript_exon_variant,,ENST00000473899,,n.83C>T,MODIFIER,,,,1;STK11IP,upstream_gene_variant,,ENST00000413891,,,MODIFIER,,,,1;STK11IP,downstream_gene_variant,,ENST00000465230,,,MODIFIER,,,,1;STK11IP,downstream_gene_variant,,ENST00000466648,,,MODIFIER,,,,1;STK11IP,upstream_gene_variant,,ENST00000495941,,,MODIFIER,,,,1 1746/3618 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.21e-05 0.0 0.0 0.0 0.0 0.0 1.783e-05 0.0 3.286e-05 6.761510121577885e-06 2.4316699636983685e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS STK11IP,non_coding_transcript_exon_variant,,ENST00000473899.1,n.83C>T,MODIFIER,;STK11IP,non_coding_transcript_exon_variant,,ENST00000475396.5,n.1634C>T,MODIFIER,;STK11IP,synonymous_variant,p.G551=,ENST00000456909.6,c.1653C>T,LOW,YES +DOCK10 55619 BI GRCh38 2 224823579 224823579 + synonymous_variant Silent SNP G G A rs369199175 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 8 c.3105C>T p.Ser1035= p.S1035= ENST00000258390.12 NM_014689.3 1035 tcC/tcT 28/56 A S protein_coding CCDS46528.1 3105/6561 TGGTCGGATAG COSM476996 PANTHER:PTHR23317;PANTHER:PTHR23317:SF71 ENSP00000258390 0.0002637 0.0 28/56 rs369199175 ENST00000258390 Transcript ENSG00000135905 HGNC:23479 LOW NM_014689.3 0.0002637 AA synonymous_variant Unknown Q96BY6.166 DOCK10 HGNC -1 5.0 UPI000021D2A7 Q96BY6-1 SNV DOCK10,synonymous_variant,p.S1029=,ENST00000409592,NM_001290263.2,c.3087C>T,LOW,,,,-1;DOCK10,synonymous_variant,p.S1035=,ENST00000258390,NM_014689.3,c.3105C>T,LOW,,,,-1;DOCK10,synonymous_variant,p.S1048=,ENST00000645028,NM_001363762.1,c.3144C>T,LOW,YES,,,-1;DOCK10,3_prime_UTR_variant,,ENST00000644695,,c.*2647C>T,MODIFIER,,,,-1 3199/7286 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.068e-05 0.0001325 3.127e-05 0.0 0.0001142 0.0 0.0 0.0 0.0 2.705410042835865e-05 7.301760342670605e-05 0.0 6.632180156884715e-05 0.0 0.0 0.0 afr 7.301760342670605e-05 0.0 0.0 0.0 0.0 0 43 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DOCK10,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698070.1,c.*211C>T,MODIFIER,;DOCK10,synonymous_variant,p.S1048=,ENST00000645028.1,c.3144C>T,LOW,;DOCK10,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644695.1,c.*2647C>T,MODIFIER,;DOCK10,synonymous_variant,p.S1029=,ENST00000409592.7,c.3087C>T,LOW,;DOCK10,synonymous_variant,p.S1035=,ENST00000258390.12,c.3105C>T,LOW,YES +HTR2B 3357 BI GRCh38 2 231108732 231108732 + missense_variant Missense_Mutation SNP G G A rs180891719 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 20 c.1231C>T p.Arg411Cys p.R411C ENST00000258400.4 NM_001320758.2 411 Cgc/Tgc 4/4 0.0002 0.0 0.0 0.001 0.0 0.0 P1 A R/C protein_coding YES CCDS2483.1 1231/1446 GGAGCGTTTTC Gene3D:1.20.1070.10;Prints:PR00651;PANTHER:PTHR24247;PANTHER:PTHR24247:SF31 ENSP00000258400 4/4 rs180891719 ENST00000258400 Transcript ENSG00000135914 HGNC:5294 MODERATE NM_000867.5 0.001 EAS missense_variant 1.0 benign(0) Unknown tolerated(0.25) P41595.191 HTR2B HGNC -1 1.0 UPI0000001C05 SNV HTR2B,missense_variant,p.R411C,ENST00000258400,NM_001320758.2&NM_000867.5,c.1231C>T,MODERATE,YES,tolerated(0.25),benign(0),-1;PSMD1,intron_variant,,ENST00000308696,NM_002807.4,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000373635,NM_001191037.1,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000409643,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000619128,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000676740,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677158,,c.1475+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677180,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677230,,c.1883+21551G>A,MODIFIER,YES,,,1;PSMD1,intron_variant,,ENST00000677259,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678679,,c.1818+23618G>A,MODIFIER,,,,1;PSMD1,non_coding_transcript_exon_variant,,ENST00000488354,,n.269G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000431051,,c.*1566+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000447633,,n.361+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000676506,,n.2045+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000676739,,n.2060+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000676818,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677000,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677195,,n.1342+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677233,,n.2060+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000677724,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678112,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678140,,c.*1505+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678241,,c.*717+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678460,,c.1818+23618G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000678632,,n.2060+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000679034,,c.1883+21551G>A,MODIFIER,,,,1;PSMD1,intron_variant,,ENST00000679095,,c.1883+21551G>A,MODIFIER,,,,1 1668/2170 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001155 0.0 0.0003181 0.0 0.0001088 0.0 0.0001323 0.0 3.266e-05 8.118199912132695e-05 2.4345099518541247e-05 0.0 0.0001989919983316 0.0 0.000201613001991 0.0 amr 0.0001989919983316 0.0 9.260119986720385e-05 0.0004960320075042 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HTR2B,missense_variant,p.R411C,ENST00000258400.4,c.1231C>T,MODERATE,YES;PSMD1,non_coding_transcript_exon_variant,,ENST00000488354.1,n.269G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000447633.1,n.361+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677195.1,n.1342+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677158.1,c.1475+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000373635.9,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000678140.1,c.*1505+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000431051.6,c.*1566+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000308696.11,c.1883+21551G>A,MODIFIER,YES;PSMD1,intron_variant,,ENST00000676506.1,n.2045+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000409643.6,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000678112.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000676740.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000676739.1,n.2060+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677233.1,n.2060+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000678460.1,c.1818+23618G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000619128.5,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000678679.1,c.1818+23618G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000677724.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000678241.1,c.*717+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000678632.1,n.2060+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000677000.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000679095.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000679034.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677230.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,NMD_transcript_variant,,ENST00000676818.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677259.1,c.1883+21551G>A,MODIFIER,;PSMD1,intron_variant,,ENST00000677180.1,c.1883+21551G>A,MODIFIER, +AGAP1 116987 BI GRCh38 2 235750488 235750488 + missense_variant,splice_region_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 18 c.673G>A p.Val225Ile p.V225I ENST00000304032.13 NM_001037131.3 225 Gtt/Att 6/18 A1 A V/I protein_coding CCDS33408.1 673/2574 AGGACGGTAAA Gene3D:3.40.50.300;Pfam:PF00071;PROSITE_profiles:PS51419;PANTHER:PTHR45819;PANTHER:PTHR45819:SF1;SMART:SM00173;SMART:SM00175;Superfamily:SSF52540;CDD:cd04103 ENSP00000307634 6/18 COSV58323024 ENST00000304032 Transcript ENSG00000157985 HGNC:16922 MODERATE NM_001037131.3 missense_variant 1 possibly_damaging(0.864) Unknown tolerated(0.07) 1 Q9UPQ3.197 AGAP1 HGNC 1 5.0 UPI00005E1AE1 Q9UPQ3-1 SNV AGAP1,missense_variant,p.V225I,ENST00000304032,NM_001037131.3,c.673G>A,MODERATE,,tolerated(0.07),possibly_damaging(0.864),1;AGAP1,missense_variant,p.V171I,ENST00000428334,,c.511G>A,MODERATE,,tolerated(0.07),possibly_damaging(0.864),1;AGAP1,missense_variant,p.V171I,ENST00000614409,,c.511G>A,MODERATE,,tolerated(0.12),benign(0.062),1;AGAP1,missense_variant,p.V490I,ENST00000409538,,c.1468G>A,MODERATE,YES,tolerated(0.09),benign(0.062),1;AGAP1,missense_variant,p.V225I,ENST00000336665,NM_014914.5,c.673G>A,MODERATE,,tolerated(0.13),possibly_damaging(0.53),1;AGAP1,missense_variant,p.V225I,ENST00000409457,NM_001244888.2,c.673G>A,MODERATE,,tolerated(0.07),benign(0.028),1;AGAP1,missense_variant,p.V171I,ENST00000619456,,c.511G>A,MODERATE,,tolerated(0.07),benign(0.028),1;AGAP1,splice_region_variant,,ENST00000635100,,c.*332G>A,LOW,,,,1 1317/10889 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 85 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 80 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AGAP1,missense_variant,splice_region_variant,p.V490I,ENST00000409538.5,c.1468G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V225I,ENST00000448025.6,c.673G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V225I,ENST00000418654.2,c.673G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V229I,ENST00000635100.2,c.685G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V229I,ENST00000699337.1,c.685G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V225I,ENST00000336665.9,c.673G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V225I,ENST00000409457.5,c.673G>A,MODERATE,;AGAP1,missense_variant,splice_region_variant,p.V225I,ENST00000304032.13,c.673G>A,MODERATE,YES +RNPEPL1 57140 BI GRCh38 2 240574547 240574547 + missense_variant Missense_Mutation SNP C C T rs757698209 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 10 c.1207C>T p.Arg403Cys p.R403C ENST00000270357.10 NM_018226.6 403 Cgc/Tgc 6/11 P1 T R/C protein_coding YES 1207/2178 CCTTCCGCCTG Gene3D:1.10.390.10;Pfam:PF01433;PANTHER:PTHR45726;PANTHER:PTHR45726:SF2;Superfamily:SSF55486;CDD:cd09599 ENSP00000270357 6/11 rs757698209 ENST00000270357 Transcript ENSG00000142327 HGNC:10079 MODERATE NM_018226.6 3.289e-05 gnomAD_SAS missense_variant 1.0 probably_damaging(0.988) Unknown deleterious(0.03) Q9HAU8.164 RNPEPL1 HGNC 1 1.0 UPI000004CF45 SNV RNPEPL1,missense_variant,p.R403C,ENST00000270357,NM_018226.6,c.1207C>T,MODERATE,YES,deleterious(0.03),probably_damaging(0.988),1;RNPEPL1,5_prime_UTR_variant,,ENST00000451363,,c.-24C>T,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000437406,,,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000464550,,,MODIFIER,,,,1;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000481757,,n.457C>T,MODIFIER,,,,1;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000486058,,n.1320C>T,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000460884,,,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000471657,,,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000493398,,,MODIFIER,,,,1;RNPEPL1,upstream_gene_variant,,ENST00000498042,,,MODIFIER,,,,1 1310/5761 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.06e-06 0.0 0.0 0.0 0.0 0.0 8.933e-06 0.0 3.289e-05 6.760500127711566e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435900422744453e-05 0.0 0.0 0 16 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RNPEPL1,non_coding_transcript_exon_variant,,ENST00000481757.5,n.457C>T,MODIFIER,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000486058.5,n.1320C>T,MODIFIER,;RNPEPL1,missense_variant,p.R403C,ENST00000270357.10,c.1207C>T,MODERATE,YES;RNPEPL1,5_prime_UTR_variant,,ENST00000451363.5,c.-24C>T,MODIFIER, +MAB21L4 79919 BI GRCh38 2 240890073 240890073 + missense_variant Missense_Mutation SNP C C T rs757923540 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 4 c.826G>A p.Asp276Asn p.D276N ENST00000388934.5 NM_001085437.3 276 Gac/Aac 3/5 P3 T D/N protein_coding YES CCDS42839.1 826/1344 CCGGTCGAGGA Gene3D:1.10.1410.40;Pfam:PF03281;PANTHER:PTHR10656;PANTHER:PTHR10656:SF7;SMART:SM01265 ENSP00000373586 3/5 rs757923540 ENST00000388934 Transcript ENSG00000172478 HGNC:26216 MODERATE NM_001085437.3 8.867e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.97) Unknown tolerated(0.09) Q08AI8.100 MAB21L4 HGNC -1 2.0 UPI000049DF42 Q08AI8-1 SNV MAB21L4,missense_variant,p.D276N,ENST00000388934,NM_001085437.3,c.826G>A,MODERATE,YES,tolerated(0.09),probably_damaging(0.97),-1;MAB21L4,missense_variant,p.D127N,ENST00000307486,NM_001282921.2,c.379G>A,MODERATE,,tolerated(0.08),probably_damaging(1),-1;MAB21L4,missense_variant,p.D108N,ENST00000402775,NM_024861.4,c.322G>A,MODERATE,,tolerated(0.08),probably_damaging(0.922),-1 985/2525 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.019e-06 0.0 0.0 0.0 0.0 0.0 8.867e-06 0.0 0.0 1.3520800166588742e-05 4.863809954258613e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863809954258613e-05 0.0 0.0 0.0 0.0 0 58 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAB21L4,missense_variant,p.D127N,ENST00000307486.12,c.379G>A,MODERATE,;MAB21L4,missense_variant,p.D108N,ENST00000402775.6,c.322G>A,MODERATE,;MAB21L4,missense_variant,p.D276N,ENST00000388934.5,c.826G>A,MODERATE,YES +HDLBP 3069 BI GRCh38 2 241239775 241239775 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 5 c.2437C>T p.Arg813Cys p.R813C ENST00000391975.5 NM_001320967.3 813 Cgc/Tgc 19/28 P1 A R/C protein_coding YES CCDS2547.1 2437/3807 GTGGCGGTGGT COSM4808548;COSM4808549 Gene3D:3.30.1370.10;Pfam:PF00013;PROSITE_profiles:PS50084;PANTHER:PTHR10627;PANTHER:PTHR10627:SF34;SMART:SM00322;Superfamily:SSF54791;CDD:cd02394 ENSP00000375836 19/28 COSV60498645 ENST00000391975 Transcript ENSG00000115677 HGNC:4857 MODERATE missense_variant 1 1.0 possibly_damaging(0.55) Unknown deleterious(0) 1 HDLBP HGNC -1 A0A024R4E5.54 1.0 UPI0000000C28 SNV HDLBP,missense_variant,p.R813C,ENST00000391975,NM_001320967.2&NM_203346.5,c.2437C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.55),-1;HDLBP,missense_variant,p.R813C,ENST00000310931,NM_005336.5&NM_001320966.2,c.2437C>T,MODERATE,,deleterious(0),possibly_damaging(0.55),-1;HDLBP,missense_variant,p.R780C,ENST00000427183,NM_001243900.2,c.2338C>T,MODERATE,,deleterious(0),probably_damaging(0.987),-1;HDLBP,missense_variant,p.R813C,ENST00000391976,NM_001320965.2,c.2437C>T,MODERATE,,deleterious(0),possibly_damaging(0.55),-1;HDLBP,missense_variant,p.R622C,ENST00000373292,,c.1864C>T,MODERATE,,deleterious(0),possibly_damaging(0.766),-1;HDLBP,missense_variant,p.R215C,ENST00000427487,,c.643C>T,MODERATE,,deleterious(0),probably_damaging(0.977),-1;HDLBP,downstream_gene_variant,,ENST00000452931,,,MODIFIER,,,,-1;HDLBP,upstream_gene_variant,,ENST00000470482,,,MODIFIER,,,,-1;HDLBP,downstream_gene_variant,,ENST00000471294,,,MODIFIER,,,,-1;HDLBP,upstream_gene_variant,,ENST00000483086,,,MODIFIER,,,,-1;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169,,n.2022C>T,MODIFIER,,,,-1;HDLBP,non_coding_transcript_exon_variant,,ENST00000479169,,n.349C>T,MODIFIER,,,,-1;HDLBP,downstream_gene_variant,,ENST00000459788,,,MODIFIER,,,,-1;HDLBP,upstream_gene_variant,,ENST00000479894,,,MODIFIER,,,,-1 2665/6372 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 42 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HDLBP,synonymous_variant,p.T214=,ENST00000427487.5,c.642C>T,LOW,;HDLBP,non_coding_transcript_exon_variant,,ENST00000479169.5,n.349C>T,MODIFIER,;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169.5,n.2022C>T,MODIFIER,;HDLBP,missense_variant,p.P621L,ENST00000373292.8,c.1862C>T,MODERATE,;HDLBP,missense_variant,p.R813C,ENST00000391976.6,c.2437C>T,MODERATE,;HDLBP,missense_variant,p.R813C,ENST00000310931.10,c.2437C>T,MODERATE,YES;HDLBP,missense_variant,p.R780C,ENST00000427183.6,c.2338C>T,MODERATE,;HDLBP,missense_variant,p.R813C,ENST00000391975.5,c.2437C>T,MODERATE, +MTMR14 64419 BI GRCh38 3 9701907 9701907 + synonymous_variant Silent SNP C C T rs777595702 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 1 23 c.1887C>T p.Ile629= p.I629= ENST00000296003.9 NM_001077525.3 629 atC/atT 19/19 P4 T I protein_coding YES CCDS43043.1 1887/1953 GCCATCGGGGG PANTHER:PTHR13524 ENSP00000296003 19/19 rs777595702 ENST00000296003 Transcript 1.0 ENSG00000163719 HGNC:26190 LOW NM_001077525.3 1.794e-05 gnomAD_NFE synonymous_variant 1.0 Unknown Q8NCE2.139 MTMR14 HGNC 1 1.0 UPI000007423D Q8NCE2-1 SNV MTMR14,synonymous_variant,p.I629=,ENST00000296003,NM_001077525.3,c.1887C>T,LOW,YES,,,1;MTMR14,synonymous_variant,p.I577=,ENST00000353332,NM_001077526.3,c.1731C>T,LOW,,,,1;MTMR14,synonymous_variant,p.I517=,ENST00000351233,NM_022485.5,c.1551C>T,LOW,,,,1;MTMR14,synonymous_variant,p.I271=,ENST00000420925,,c.813C>T,LOW,,,,1;CPNE9,upstream_gene_variant,,ENST00000383831,NM_001308388.2,,MODIFIER,,,,1;CPNE9,upstream_gene_variant,,ENST00000383832,NM_153635.3,,MODIFIER,YES,,,1;CPNE9,upstream_gene_variant,,ENST00000613455,,,MODIFIER,,,,1;MTMR14,3_prime_UTR_variant,,ENST00000414996,,c.*1064C>T,MODIFIER,,,,1;MTMR14,3_prime_UTR_variant,,ENST00000447144,,c.*680C>T,MODIFIER,,,,1;MTMR14,non_coding_transcript_exon_variant,,ENST00000606184,,n.2481C>T,MODIFIER,,,,1;CPNE9,upstream_gene_variant,,ENST00000491802,,,MODIFIER,,,,1;AC022382.2,intron_variant,,ENST00000670966,,n.185-6382G>A,MODIFIER,YES,,,-1 1966/2452 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.072e-06 0.0 0.0 0.0 0.0 0.0 1.794e-05 0.0 0.0 6.757119990652427e-06 2.4304899852722883e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 81 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 24 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MTMR14,non_coding_transcript_exon_variant,,ENST00000606184.1,n.2481C>T,MODIFIER,;ENSG00000287878,intron_variant,,ENST00000670966.1,n.185-6382G>A,MODIFIER,YES;MTMR14,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000414996.1,c.*1064C>T,MODIFIER,;MTMR14,synonymous_variant,p.I517=,ENST00000351233.9,c.1551C>T,LOW,;MTMR14,synonymous_variant,p.I629=,ENST00000296003.9,c.1887C>T,LOW,YES;MTMR14,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000447144.5,c.*680C>T,MODIFIER,;MTMR14,synonymous_variant,p.I271=,ENST00000420925.5,c.813C>T,LOW,;MTMR14,synonymous_variant,p.I577=,ENST00000353332.9,c.1731C>T,LOW, +TADA3 10474 BI GRCh38 3 9789751 9789751 + synonymous_variant Silent SNP G G A rs760618790 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 53 9 c.420C>T p.Ile140= p.I140= ENST00000301964.7 NM_006354.5 140 atC/atT 3/9 P1 A I protein_coding YES CCDS2583.1 420/1299 ACGTCGATAGG COSM3598403 PANTHER:PTHR13556 ENSP00000307684 3/9 rs760618790;COSV55029673 ENST00000301964 Transcript ENSG00000171148 HGNC:19422 LOW 5.782e-05 gnomAD_AMR synonymous_variant 0;1 1.0 Unknown 0;1 O75528.169 TADA3 HGNC -1 1.0 UPI000006F454 O75528-1 SNV TADA3,synonymous_variant,p.I140=,ENST00000343450,NM_133480.2,c.420C>T,LOW,,,,-1;TADA3,synonymous_variant,p.I140=,ENST00000301964,NM_006354.3,c.420C>T,LOW,YES,,,-1;TADA3,synonymous_variant,p.I140=,ENST00000440161,NM_001278270.1,c.420C>T,LOW,,,,-1;ARPC4-TTLL3,upstream_gene_variant,,ENST00000397256,NM_001198793.1,,MODIFIER,YES,,,1;ARPC4,upstream_gene_variant,,ENST00000397261,NM_005718.4,,MODIFIER,,,,1;OGG1,downstream_gene_variant,,ENST00000426518,,,MODIFIER,,,,1;ARPC4,upstream_gene_variant,,ENST00000433034,NM_001198780.2,,MODIFIER,YES,,,1;TADA3,downstream_gene_variant,,ENST00000439043,,,MODIFIER,,,,-1;ARPC4,upstream_gene_variant,,ENST00000485273,,,MODIFIER,,,,1;ARPC4,upstream_gene_variant,,ENST00000498623,NM_001024959.2&NM_001024960.2,,MODIFIER,,,,1;TADA3,non_coding_transcript_exon_variant,,ENST00000492635,,n.528C>T,MODIFIER,,,,-1;ARPC4,upstream_gene_variant,,ENST00000417500,,,MODIFIER,,,,1;ARPC4-TTLL3,upstream_gene_variant,,ENST00000418163,,,MODIFIER,,,,1;ARPC4-TTLL3,upstream_gene_variant,,ENST00000424442,,,MODIFIER,,,,1;ARPC4,upstream_gene_variant,,ENST00000440787,,,MODIFIER,,,,1;ARPC4,upstream_gene_variant,,ENST00000467289,,,MODIFIER,,,,1;ARPC4,upstream_gene_variant,,ENST00000479956,,,MODIFIER,,,,1;TADA3,upstream_gene_variant,,ENST00000492103,,,MODIFIER,,,,-1 979/2355 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.193e-05 0.0 5.782e-05 0.0 0.0 0.0 8.79e-06 0.0 0.0 6.759859843441518e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 120 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TADA3,non_coding_transcript_exon_variant,,ENST00000492635.1,n.528C>T,MODIFIER,;TADA3,synonymous_variant,p.I140=,ENST00000343450.2,c.420C>T,LOW,;TADA3,synonymous_variant,p.I140=,ENST00000440161.5,c.420C>T,LOW,;TADA3,synonymous_variant,p.I140=,ENST00000301964.7,c.420C>T,LOW,YES +NUP210 23225 BI GRCh38 3 13328829 13328829 + missense_variant Missense_Mutation SNP C C T rs769147767 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 26 c.4228G>A p.Asp1410Asn p.D1410N ENST00000254508.7 NM_024923.4 1410 Gac/Aac 31/40 P1 T D/N protein_coding YES CCDS33704.1 4228/5664 GTTGTCGTGGA PANTHER:PTHR23019;PANTHER:PTHR23019:SF2 ENSP00000254508 31/40 rs769147767;COSV54406568 ENST00000254508 Transcript ENSG00000132182 HGNC:30052 MODERATE NM_024923.4 5.437e-05 gnomAD_EAS missense_variant 0;1 1.0 possibly_damaging(0.852) Unknown tolerated(0.47) 0;1 Q8TEM1.152 NUP210 HGNC -1 2.0 UPI00001600AF Q8TEM1-1 SNV NUP210,missense_variant,p.D1410N,ENST00000254508,NM_024923.4,c.4228G>A,MODERATE,YES,tolerated(0.47),possibly_damaging(0.852),-1 4324/7206 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.954e-06 0.0 0.0 0.0 5.437e-05 0.0 8.792e-06 0.0 0.0 1.3519000276573934e-05 0.0 0.0 6.625150126637891e-05 0.0 0.0 0.0 0.0 1.5433499356731772e-05 0.0 0.0 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NUP210,non_coding_transcript_exon_variant,,ENST00000695491.1,n.2230G>A,MODIFIER,;NUP210,missense_variant,NMD_transcript_variant,p.D516N,ENST00000695490.1,c.1546G>A,MODERATE,;NUP210,missense_variant,p.D1410N,ENST00000254508.7,c.4228G>A,MODERATE,YES +SLC22A14 9389 BI GRCh38 3 38313803 38313803 + missense_variant Missense_Mutation SNP G G A rs760758304 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 1 39 c.1240G>A p.Val414Met p.V414M ENST00000273173.4 NM_004803.4 414 Gtg/Atg 7/10 P1 A V/M protein_coding YES CCDS2677.1 1240/1785 GACACGTGGTC COSM2986170 Transmembrane_helices:TMhelix;PROSITE_profiles:PS50850;CDD:cd17374;PANTHER:PTHR24064:SF48;PANTHER:PTHR24064;Pfam:PF00083;Gene3D:1.20.1250.20;Superfamily:SSF103473 ENSP00000273173 7/10 rs760758304;COSV56196780 ENST00000273173 Transcript ENSG00000144671 HGNC:8495 MODERATE 9.799e-05 gnomAD_SAS missense_variant 0;1 1.0 benign(0.223) Unknown tolerated(0.25) 0;1 Q9Y267.137 SLC22A14 HGNC 1 1.0 UPI00001AE9A8 SNV SLC22A14,missense_variant,p.V414M,ENST00000273173,NM_004803.4,c.1240G>A,MODERATE,YES,tolerated(0.25),benign(0.223),1;SLC22A14,missense_variant,p.V414M,ENST00000448498,NM_001320033.1,c.1240G>A,MODERATE,,tolerated(0.25),benign(0.223),1 1331/2202 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.784e-05 0.0 5.782e-05 0.0 0.0 0.0 1.758e-05 0.0 9.799e-05 1.352520030195592e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086520155193284e-05 0.0 3.086520155193284e-05 0.0 0.0 0 107 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC22A14,missense_variant,p.V414M,ENST00000273173.4,c.1240G>A,MODERATE,;SLC22A14,missense_variant,p.V414M,ENST00000448498.6,c.1240G>A,MODERATE,YES +CACNA1D 776 BI GRCh38 3 53735502 53735502 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs145327253 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 1 8 c.2750C>T p.Thr917Met p.T917M ENST00000350061.11 NM_001128840.3 917 aCg/aTg 20/48 A2 T T/M protein_coding CCDS46848.1 2750/6486 GAACACGGTAA Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR45628;PANTHER:PTHR45628:SF11;Superfamily:SSF81324 ENSP00000288133 0.000227 0.0 20/48 rs145327253 ENST00000350061 Transcript 1.0 ENSG00000157388 HGNC:1391 MODERATE NM_001128840.3 0.0003077 gnomAD_AFR missense_variant benign(0.172) Unknown tolerated(0.23) Q01668.202 CACNA1D HGNC 1 1.0 UPI000013DEF4 Q01668-1 SNV CACNA1D,missense_variant,p.T937M,ENST00000288139,NM_000720.4,c.2810C>T,MODERATE,YES,tolerated(0.23),possibly_damaging(0.536),1;CACNA1D,missense_variant,p.T917M,ENST00000350061,NM_001128840.3,c.2750C>T,MODERATE,,tolerated(0.23),benign(0.172),1;CACNA1D,missense_variant,p.T917M,ENST00000422281,NM_001128839.3,c.2750C>T,MODERATE,,tolerated(0.23),benign(0.335),1;CACNA1D,missense_variant,p.T917M,ENST00000636938,,c.2750C>T,MODERATE,,tolerated_low_confidence(0.11),benign(0.294),1;CACNA1D,missense_variant,p.T941M,ENST00000637424,,c.2822C>T,MODERATE,,tolerated(0.24),benign(0.294),1;CACNA1D,missense_variant,p.T917M,ENST00000636570,,c.2750C>T,MODERATE,,tolerated(0.23),benign(0.36),1;CACNA1D,missense_variant,p.T928M,ENST00000640483,,c.2783C>T,MODERATE,,tolerated_low_confidence(0.11),benign(0.251),1;CACNA1D,missense_variant,p.T610M,ENST00000481478,,c.1829C>T,MODERATE,,tolerated(0.24),benign(0.172),1;CACNA1D,missense_variant,p.T684M,ENST00000636627,,c.2051C>T,MODERATE,,tolerated_low_confidence(0.12),benign(0.294),1;CACNA1D,missense_variant,p.T162M,ENST00000637714,,c.485C>T,MODERATE,,deleterious_low_confidence(0.04),benign(0.083),1;CACNA1D,splice_region_variant,,ENST00000636138,,n.319C>T,LOW,,,,1;CACNA1D,splice_region_variant,,ENST00000637078,,n.462C>T,LOW,,,,1 3306/9369 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.786e-05 0.0003077 0.0 0.0 0.0 0.0 8.797e-06 0.0 3.266e-05 6.757400115020573e-05 0.00019441099721 0.0 0.0 0.0 0.0 0.0 afr 0.00019441099721 0.0 0.0 0.000494070991408 0.0002084199950331 0 37 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 9 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CACNA1D,non_coding_transcript_exon_variant,,ENST00000637078.1,n.462C>T,MODIFIER,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636138.1,n.319C>T,MODIFIER,;CACNA1D,synonymous_variant,splice_region_variant,p.H161=,ENST00000637714.1,c.483C>T,LOW,;CACNA1D,missense_variant,splice_region_variant,p.T928M,ENST00000640483.1,c.2783C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T917M,ENST00000422281.7,c.2750C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T917M,ENST00000636570.1,c.2750C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T917M,ENST00000636938.1,c.2750C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T917M,ENST00000350061.11,c.2750C>T,MODERATE,YES;CACNA1D,missense_variant,splice_region_variant,p.T937M,ENST00000481478.2,c.2810C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T937M,ENST00000288139.11,c.2810C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T937M,ENST00000636627.2,c.2810C>T,MODERATE,;CACNA1D,missense_variant,splice_region_variant,p.T941M,ENST00000637424.1,c.2822C>T,MODERATE, +IL17RD 54756 BI GRCh38 3 57097802 57097802 + missense_variant Missense_Mutation SNP C C T rs1486656267 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 7 c.1901G>A p.Arg634Gln p.R634Q ENST00000296318.12 NM_017563.5 634 cGg/cAg 12/13 P1 T R/Q protein_coding YES CCDS2880.2 1901/2220 CAGGCCGGGCC PANTHER:PTHR15583:SF14;PANTHER:PTHR15583 ENSP00000296318 12/13 rs1486656267 ENST00000296318 Transcript 1.0 ENSG00000144730 HGNC:17616 MODERATE NM_017563.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated_low_confidence(0.85) Q8NFM7.145 IL17RD HGNC -1 1.0 UPI0000047CC3 Q8NFM7-1 SNV IL17RD,missense_variant,p.R634Q,ENST00000296318,NM_017563.5,c.1901G>A,MODERATE,YES,tolerated_low_confidence(0.85),benign(0),-1;IL17RD,missense_variant,p.R490Q,ENST00000320057,NM_001318864.1,c.1469G>A,MODERATE,,tolerated_low_confidence(0.82),benign(0),-1;IL17RD,missense_variant,p.R490Q,ENST00000463523,,c.1469G>A,MODERATE,,tolerated_low_confidence(0.82),benign(0),-1;IL17RD,non_coding_transcript_exon_variant,,ENST00000469841,,n.1838G>A,MODIFIER,,,,-1 1968/8698 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 13 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IL17RD,non_coding_transcript_exon_variant,,ENST00000469841.5,n.1838G>A,MODIFIER,;IL17RD,missense_variant,p.R490Q,ENST00000463523.5,c.1469G>A,MODERATE,;IL17RD,missense_variant,p.R490Q,ENST00000320057.9,c.1469G>A,MODERATE,;IL17RD,missense_variant,p.R634Q,ENST00000296318.12,c.1901G>A,MODERATE,YES +ROBO1 6091 BI GRCh38 3 78651745 78651745 + synonymous_variant Silent SNP C C T rs374375350 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 0 10 c.2799G>A p.Ala933= p.A933= ENST00000464233.6 NM_002941.4 933 gcG/gcA 19/31 0.0002 0.0 0.0 0.0 0.001 0.0 A2 T A protein_coding YES CCDS54611.1 2799/4956 ATACCCGCGTA COSM5059962;COSM5059963;COSM5059964;COSM5059965 PANTHER:PTHR12231;PANTHER:PTHR12231:SF243 ENSP00000420321 0.0 0.0001215 19/31 rs374375350 ENST00000464233 Transcript 1.0 ENSG00000169855 HGNC:10249 LOW NM_002941.4 0.001 EUR synonymous_variant 1.0 Unknown Q9Y6N7.185 ROBO1 HGNC -1 5.0 UPI00000713D9 Q9Y6N7-1 SNV ROBO1,synonymous_variant,p.A813=,ENST00000436010,,c.2439G>A,LOW,,,,-1;ROBO1,synonymous_variant,p.A897=,ENST00000618833,,c.2691G>A,LOW,,,,-1;ROBO1,synonymous_variant,p.A816=,ENST00000618846,,c.2448G>A,LOW,,,,-1;ROBO1,synonymous_variant,p.A933=,ENST00000464233,NM_002941.4,c.2799G>A,LOW,YES,,,-1;ROBO1,synonymous_variant,p.A897=,ENST00000495273,NM_133631.3,c.2691G>A,LOW,,,,-1;ROBO1,synonymous_variant,p.A897=,ENST00000467549,NM_001145845.1,c.2691G>A,LOW,,,,-1;ROBO1,non_coding_transcript_exon_variant,,ENST00000498428,,n.1696G>A,MODIFIER,,,,-1 3096/6927 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.48e-05 0.0 0.0 0.0 0.0 0.0 5.463e-05 0.0 0.0 1.3535100151784718e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0872801289660856e-05 0.0 3.0872801289660856e-05 0.0 0.0 0 17 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ROBO1,non_coding_transcript_exon_variant,,ENST00000498428.5,n.1696G>A,MODIFIER,;ROBO1,synonymous_variant,p.A897=,ENST00000467549.5,c.2691G>A,LOW,;ROBO1,synonymous_variant,p.A897=,ENST00000495273.5,c.2691G>A,LOW,;ROBO1,synonymous_variant,p.A816=,ENST00000618846.4,c.2448G>A,LOW,;ROBO1,synonymous_variant,p.A813=,ENST00000436010.6,c.2439G>A,LOW,;ROBO1,synonymous_variant,p.A933=,ENST00000464233.6,c.2799G>A,LOW,YES +ADCY5 111 BI GRCh38 3 123330936 123330936 + synonymous_variant Silent SNP G G A rs552930549 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 1 14 c.1599C>T p.His533= p.H533= ENST00000462833.6 NM_183357.3 533 caC/caT 5/21 0.0006 0.0008 0.0014 0.0 0.001 0.0 P1 A H protein_coding YES CCDS3022.1 1599/3786 TGGGCGTGGTC PROSITE_profiles:PS50125;CDD:cd07556;PANTHER:PTHR45627;PANTHER:PTHR45627:SF7;Pfam:PF00211;PIRSF:PIRSF039050;Gene3D:3.30.70.1230;SMART:SM00044;Superfamily:SSF55073 ENSP00000419361 5/21 rs552930549 ENST00000462833 Transcript 1.0 ENSG00000173175 HGNC:236 LOW NM_183357.3 0.0014 AMR synonymous_variant 1.0 Unknown O95622.178 ADCY5 HGNC -1 A0A384P5Q5.10 1.0 UPI000015E262 O95622-1 SNV ADCY5,synonymous_variant,p.H533=,ENST00000462833,NM_183357.3&NM_001378259.1,c.1599C>T,LOW,YES,,,-1;ADCY5,synonymous_variant,p.H166=,ENST00000491190,,c.498C>T,LOW,,,,-1;ADCY5,synonymous_variant,p.H183=,ENST00000309879,NM_001199642.1,c.549C>T,LOW,,,,-1;ADCY5,synonymous_variant,p.H92=,ENST00000466617,,c.276C>T,LOW,,,,-1;ADCY5,downstream_gene_variant,,ENST00000483566,,,MODIFIER,,,,-1;ADCY5,downstream_gene_variant,,ENST00000476455,,,MODIFIER,,,,-1 2144/6643 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.96e-06 0.0 2.895e-05 0.0 0.0 0.0 8.8e-06 0.0 0.0 4.7307501517934725e-05 4.862160130869597e-05 0.0 0.0001986749994102 0.0 0.0 0.0 amr 0.0001986749994102 0.0 3.085749995079823e-05 0.0 0.0 0 22 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 15 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ADCY5,synonymous_variant,p.H183=,ENST00000309879.9,c.549C>T,LOW,;ADCY5,synonymous_variant,p.H533=,ENST00000699718.1,c.1599C>T,LOW,;ADCY5,synonymous_variant,p.H92=,ENST00000699716.1,c.276C>T,LOW,;ADCY5,synonymous_variant,p.H188=,ENST00000470367.2,c.564C>T,LOW,;ADCY5,synonymous_variant,p.H166=,ENST00000491190.5,c.498C>T,LOW,;ADCY5,synonymous_variant,p.H92=,ENST00000483566.2,c.276C>T,LOW,;ADCY5,synonymous_variant,p.H92=,ENST00000699715.1,c.276C>T,LOW,;ADCY5,synonymous_variant,p.H92=,ENST00000466617.6,c.276C>T,LOW,;ADCY5,synonymous_variant,p.H92=,ENST00000699714.1,c.276C>T,LOW,;ADCY5,synonymous_variant,p.H533=,ENST00000462833.6,c.1599C>T,LOW,YES +PRR23E 285311 BI GRCh38 3 127197038 127197038 + missense_variant Missense_Mutation SNP C C T rs371883407 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 67 c.353C>T p.Pro118Leu p.P118L ENST00000624688.2 NM_001007534.2 118 cCg/cTg 2/2 P1 T P/L protein_coding YES 353/729 AAGTCCGTATC PANTHER:PTHR31813;PANTHER:PTHR31813:SF17 ENSP00000493276 0.0 0.0001213 2/2 rs371883407 ENST00000624688 Transcript ENSG00000214324 HGNC:32481 MODERATE NM_001007534.2 0.0005229 gnomAD_FIN missense_variant 1.0 benign(0) Unknown tolerated(0.23) Q8N813.91 C3orf56 HGNC 1 1.0 UPI000006D9A8 SNV C3orf56,missense_variant,p.P118L,ENST00000624688,NM_001007534.2,c.353C>T,MODERATE,YES,tolerated(0.23),benign(0),1;AC112482.2,intron_variant,,ENST00000654542,,n.84+21352G>A,MODIFIER,YES,,,-1 593/1740 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001815 6.611e-05 0.0 0.0 0.0 0.0005229 0.0003063 0.0003455 0.0 0.0001352609979221 7.298559648916125e-05 0.0 0.0 0.0 0.0 0.000659755023662 fin 0.000659755023662 0.0 0.0001543690013932 0.0 0.0 0 228 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 94 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PRR23E,missense_variant,p.P118L,ENST00000624688.2,c.353C>T,MODERATE,YES;ENSG00000287784,intron_variant,,ENST00000654542.1,n.84+21352G>A,MODIFIER,YES +SLITRK3 22865 BI GRCh38 3 165188477 165188477 + missense_variant Missense_Mutation SNP G G A rs1490316717 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 20 c.2354C>T p.Pro785Leu p.P785L ENST00000241274.3 NM_014926.4 785 cCg/cTg 2/2 P1 A P/L protein_coding CCDS3197.1 2354/2934 TTCCCGGTGGT COSM76519 PANTHER:PTHR45773;PANTHER:PTHR45773:SF6 ENSP00000241274 2/2 rs1490316717;COSV53852040 ENST00000241274 Transcript ENSG00000121871 HGNC:23501 MODERATE 2.892e-05 gnomAD_AMR missense_variant 0;1 benign(0) Unknown tolerated(0.26) 0;1 O94933.155 SLITRK3 HGNC -1 1.0 UPI000004F259 SNV SLITRK3,missense_variant,p.P785L,ENST00000475390,NM_001318811.1&NM_001318810.2,c.2354C>T,MODERATE,YES,tolerated(0.26),benign(0),-1;SLITRK3,missense_variant,p.P785L,ENST00000241274,NM_014926.4,c.2354C>T,MODERATE,,tolerated(0.26),benign(0),-1;SLITRK3,downstream_gene_variant,,ENST00000497724,,,MODIFIER,,,,-1 2636/4391 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.984e-06 0.0 2.892e-05 0.0 0.0 0.0 0.0 0.0 0.0 2.031089934462216e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0887098546372727e-05 0.0 3.0887098546372727e-05 0.0004950499860569 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLITRK3,missense_variant,p.P785L,ENST00000241274.3,c.2354C>T,MODERATE,;SLITRK3,missense_variant,p.P785L,ENST00000475390.2,c.2354C>T,MODERATE,YES +MUC4 4585 BI GRCh38 3 195747259 195747259 + missense_variant Missense_Mutation SNP C C T rs769504147 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 10 c.16156G>A p.Gly5386Arg p.G5386R ENST00000463781.8 NM_018406.7 5386 Ggg/Agg 25/25 P4 T G/R protein_coding YES CCDS54700.1 16156/16239 CGTCCCGACCC COSM3591637;COSM3591638 PANTHER:PTHR13802;PANTHER:PTHR13802:SF53;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000417498 25/25 rs769504147;COSV57778525 ENST00000463781 Transcript 1.0 ENSG00000145113 HGNC:7514 MODERATE NM_018406.7 2.891e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.289) Unknown deleterious_low_confidence(0.03) 0;1 MUC4 HGNC -1 E9PDY6.64 5.0 UPI0001B3CB30 SNV MUC4,missense_variant,p.G5386R,ENST00000463781,NM_018406.7,c.16156G>A,MODERATE,YES,deleterious_low_confidence(0.03),benign(0.289),-1;MUC4,missense_variant,p.G5334R,ENST00000475231,,c.16000G>A,MODERATE,,deleterious_low_confidence(0.04),benign(0.289),-1;MUC4,missense_variant,p.G1150R,ENST00000346145,NM_004532.6,c.3448G>A,MODERATE,,deleterious_low_confidence(0.04),possibly_damaging(0.482),-1;MUC4,missense_variant,p.G1099R,ENST00000349607,NM_138297.5,c.3295G>A,MODERATE,,deleterious_low_confidence(0.04),possibly_damaging(0.482),-1;MUC4,3_prime_UTR_variant,,ENST00000478156,,c.*783G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000466475,,c.*2877G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000477756,,c.*2595G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000477086,,c.*2877G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000480843,,c.*2595G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000462323,,c.*2595G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000470451,,c.*2561G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000479406,,c.*2509G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000448861,,c.*2956G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000308466,,c.*2788G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000339251,,c.*2849G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000415455,,c.*2788G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000392407,,c.*2717G>A,MODIFIER,,,,-1;MUC4,non_coding_transcript_exon_variant,,ENST00000464234,,n.1592G>A,MODIFIER,,,,-1;MUC4,downstream_gene_variant,,ENST00000467235,,,MODIFIER,,,,-1;MUC4,downstream_gene_variant,,ENST00000469992,,,MODIFIER,,,,-1 16268/16756 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.982e-06 0.0 2.891e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 106 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 43 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MUC4,non_coding_transcript_exon_variant,,ENST00000464234.5,n.1592G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000480843.5,c.*2595G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000470451.5,c.*2561G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000477756.5,c.*2595G>A,MODIFIER,;MUC4,missense_variant,p.G5334R,ENST00000475231.5,c.16000G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000466475.5,c.*2877G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000462323.5,c.*2595G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000479406.5,c.*2509G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000477086.5,c.*2877G>A,MODIFIER,;MUC4,missense_variant,p.G5386R,ENST00000463781.8,c.16156G>A,MODERATE,YES;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000448861.5,c.*2956G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000478156.5,c.*783G>A,MODIFIER,;MUC4,missense_variant,p.G1150R,ENST00000346145.8,c.3448G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000415455.5,c.*2788G>A,MODIFIER,;MUC4,missense_variant,p.G1099R,ENST00000349607.8,c.3295G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000392407.6,c.*2717G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000339251.9,c.*2849G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000308466.12,c.*2788G>A,MODIFIER, +PDE6B 5158 BI GRCh38 4 653963 653963 + missense_variant Missense_Mutation SNP G G A rs199768318 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 6 c.823G>A p.Val275Met p.V275M ENST00000496514.6 NM_000283.4 275 Gtg/Atg 4/22 P3 A V/M protein_coding YES CCDS33932.1 823/2565 ACTCCGTGGGC COSM4424550 Gene3D:3.30.450.40;Pfam:PF01590;PANTHER:PTHR11347;PANTHER:PTHR11347:SF73;SMART:SM00065;Superfamily:SSF55781 ENSP00000420295 4/22 rs199768318;COSV55325135 ENST00000496514 Transcript 1.0 ENSG00000133256 HGNC:8786 MODERATE NM_000283.4 0.0001632 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.991) Unknown deleterious(0) 0;1 P35913.200 PDE6B HGNC 1 1.0 UPI0000DBEE72 P35913-1 SNV PDE6B,missense_variant,p.V275M,ENST00000496514,NM_000283.4,c.823G>A,MODERATE,YES,deleterious(0),probably_damaging(0.991),1;PDE6B,missense_variant,p.V275M,ENST00000255622,NM_001145291.2,c.823G>A,MODERATE,,deleterious(0),probably_damaging(0.985),1;PDE6B,5_prime_UTR_variant,,ENST00000429163,NM_001379246.1&NM_001379247.1&NM_001145292.2&NM_001350154.3&NM_001350155.3,c.-15G>A,MODIFIER,,,,1;PDE6B,5_prime_UTR_variant,,ENST00000488061,,c.-15G>A,MODIFIER,,,,1;PDE6B,5_prime_UTR_variant,,ENST00000487902,,c.-15G>A,MODIFIER,,,,1;PDE6B,5_prime_UTR_variant,,ENST00000465426,,c.-15G>A,MODIFIER,,,,1;PDE6B,non_coding_transcript_exon_variant,,ENST00000476034,,n.393G>A,MODIFIER,,,,1;PDE6B,non_coding_transcript_exon_variant,,ENST00000467152,,n.221G>A,MODIFIER,,,,1;PDE6B,non_coding_transcript_exon_variant,,ENST00000474251,,n.274G>A,MODIFIER,,,,1;PDE6B-AS1,non_coding_transcript_exon_variant,,ENST00000468356,,n.1290C>T,MODIFIER,YES,,,-1;PDE6B-AS1,non_coding_transcript_exon_variant,,ENST00000489312,,n.405C>T,MODIFIER,,,,-1;PDE6B-AS1,upstream_gene_variant,,ENST00000598370,,,MODIFIER,,,,-1;PDE6B-AS1,upstream_gene_variant,,ENST00000599030,,,MODIFIER,,,,-1 877/3294 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.788e-05 0.0 5.782e-05 0.0 0.0001632 0.0 1.764e-05 0.0 0.0 1.3518299965653569e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086420110776089e-05 0.0 3.086420110776089e-05 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PDE6B-AS1,non_coding_transcript_exon_variant,,ENST00000489312.1,n.405C>T,MODIFIER,;PDE6B,non_coding_transcript_exon_variant,,ENST00000467152.1,n.221G>A,MODIFIER,;PDE6B,5_prime_UTR_variant,,ENST00000429163.6,c.-15G>A,MODIFIER,;PDE6B,5_prime_UTR_variant,,ENST00000488061.5,c.-15G>A,MODIFIER,;PDE6B-AS1,non_coding_transcript_exon_variant,,ENST00000468356.3,n.1290C>T,MODIFIER,YES;PDE6B,non_coding_transcript_exon_variant,,ENST00000476034.5,n.393G>A,MODIFIER,;PDE6B,5_prime_UTR_variant,,ENST00000487902.5,c.-15G>A,MODIFIER,;PDE6B,non_coding_transcript_exon_variant,,ENST00000474251.5,n.274G>A,MODIFIER,;PDE6B,5_prime_UTR_variant,,ENST00000465426.5,c.-15G>A,MODIFIER,;PDE6B,missense_variant,p.V275M,ENST00000255622.10,c.823G>A,MODERATE,;PDE6B,missense_variant,p.V275M,ENST00000496514.6,c.823G>A,MODERATE,YES +DGKQ 1609 BI GRCh38 4 961562 961562 + missense_variant Missense_Mutation SNP C C T rs756724535 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 2 8 c.2479G>A p.Asp827Asn p.D827N ENST00000273814.8 NM_001347.4 827 Gac/Aac 21/23 P1 T D/N protein_coding YES CCDS3342.1 2479/2829 CAGGTCGGCCC COSM4138558 PANTHER:PTHR11255;PANTHER:PTHR11255:SF34;Gene3D:2.60.200.40;Pfam:PF00609;SMART:SM00045;Superfamily:SSF111331 ENSP00000273814 21/23 rs756724535;COSV53277554 ENST00000273814 Transcript ENSG00000145214 HGNC:2856 MODERATE NM_001347.4 7.035e-05 gnomAD_AFR missense_variant 0;1 1.0 probably_damaging(0.999) Unknown tolerated(0.61) 0;1 P52824.163 DGKQ HGNC -1 A0A140VKC1.24 1.0 UPI00001AE9B4 SNV DGKQ,missense_variant,p.D827N,ENST00000273814,NM_001347.4,c.2479G>A,MODERATE,YES,tolerated(0.61),probably_damaging(0.999),-1;DGKQ,missense_variant,p.D761N,ENST00000509465,,c.2281G>A,MODERATE,,tolerated(0.66),possibly_damaging(0.534),-1;DGKQ,missense_variant,p.D42N,ENST00000515182,,c.124G>A,MODERATE,,tolerated(0.61),benign(0.167),-1;TMEM175,downstream_gene_variant,,ENST00000264771,NM_032326.4,,MODIFIER,YES,,,1;TMEM175,downstream_gene_variant,,ENST00000508204,NM_001297423.2&NM_001297424.2&NM_001297425.2,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000510493,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000515492,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000515740,NM_001297428.2,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000622959,NM_001297426.1&NM_001297427.2,,MODIFIER,,,,1;DGKQ,downstream_gene_variant,,ENST00000502309,,,MODIFIER,,,,-1;TMEM175,downstream_gene_variant,,ENST00000438836,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000452360,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000513952,,,MODIFIER,,,,1 2566/4649 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.306e-06 7.035e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 11 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DGKQ,missense_variant,p.D42N,ENST00000515182.1,c.124G>A,MODERATE,;DGKQ,synonymous_variant,p.P760=,ENST00000509465.5,c.2280G>A,LOW,;DGKQ,missense_variant,p.D827N,ENST00000273814.8,c.2479G>A,MODERATE,YES +DGKQ 1609 BI GRCh38 4 961742 961742 + missense_variant Missense_Mutation SNP C C T rs143203696 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 9 c.2408G>A p.Arg803Gln p.R803Q ENST00000273814.8 NM_001347.4 803 cGg/cAg 20/23 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 T R/Q protein_coding YES CCDS3342.1 2408/2829 CCTGCCGCTCC PANTHER:PTHR11255;PANTHER:PTHR11255:SF34;Gene3D:2.60.200.40;Pfam:PF00609;SMART:SM00045;Superfamily:SSF111331 ENSP00000273814 0.0009079 0.0 20/23 rs143203696 ENST00000273814 Transcript ENSG00000145214 HGNC:2856 MODERATE NM_001347.4 0.0009079 AA missense_variant 1.0 benign(0) Unknown tolerated(0.88) P52824.163 DGKQ HGNC -1 A0A140VKC1.24 1.0 UPI00001AE9B4 SNV DGKQ,missense_variant,p.R803Q,ENST00000273814,NM_001347.4,c.2408G>A,MODERATE,YES,tolerated(0.88),benign(0),-1;DGKQ,missense_variant,p.R737Q,ENST00000509465,,c.2210G>A,MODERATE,,tolerated(0.76),benign(0.001),-1;DGKQ,intron_variant,,ENST00000515182,,c.108-164G>A,MODIFIER,,,,-1;TMEM175,downstream_gene_variant,,ENST00000264771,NM_032326.4,,MODIFIER,YES,,,1;TMEM175,downstream_gene_variant,,ENST00000508204,NM_001297423.2&NM_001297424.2&NM_001297425.2,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000510493,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000515492,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000515740,NM_001297428.2,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000622959,NM_001297426.1&NM_001297427.2,,MODIFIER,,,,1;DGKQ,downstream_gene_variant,,ENST00000502309,,,MODIFIER,,,,-1;TMEM175,downstream_gene_variant,,ENST00000438836,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000452360,,,MODIFIER,,,,1;TMEM175,downstream_gene_variant,,ENST00000513952,,,MODIFIER,,,,1 2495/4649 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.799e-05 0.0008655 0.0 0.0 5.442e-05 0.0 8.865e-06 0.0 3.267e-05 0.0001555460039526 0.0005108990008011 0.0 6.625150126637891e-05 0.0 0.0 0.0 afr 0.0005108990008011 0.0 0.0 0.0004960320075042 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DGKQ,intron_variant,,ENST00000515182.1,c.108-164G>A,MODIFIER,;DGKQ,missense_variant,p.G737S,ENST00000509465.5,c.2209G>A,MODERATE,;DGKQ,missense_variant,p.R803Q,ENST00000273814.8,c.2408G>A,MODERATE,YES +TNIP2 79155 BI GRCh38 4 2744727 2744727 + synonymous_variant Silent SNP C C T rs755915638 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 14 c.876G>A p.Ala292= p.A292= ENST00000315423.12 NM_024309.4 292 gcG/gcA 4/6 P1 T A protein_coding YES CCDS3362.1 876/1290 TCCAACGCAGC COSM4124273 Gene3D:1.20.5.990;PDB-ENSP_mappings:5h07.C;PDB-ENSP_mappings:5h07.D;Coiled-coils_(Ncoils):Coil;PANTHER:PTHR31882;PANTHER:PTHR31882:SF10 ENSP00000321203 4/6 rs755915638;COSV59569405 ENST00000315423 Transcript ENSG00000168884 HGNC:19118 LOW NM_024309.4 6.136e-05 gnomAD_FIN synonymous_variant 0;1 1.0 Unknown 0;1 Q8NFZ5.137 TNIP2 HGNC -1 1.0 UPI00000702D2 Q8NFZ5-1 SNV TNIP2,synonymous_variant,p.A185=,ENST00000510267,NM_001161527.2,c.555G>A,LOW,,,,-1;TNIP2,synonymous_variant,p.A292=,ENST00000315423,NM_024309.4,c.876G>A,LOW,YES,,,-1;TNIP2,intron_variant,,ENST00000503235,NM_001292016.2,c.658-221G>A,MODIFIER,,,,-1;TNIP2,non_coding_transcript_exon_variant,,ENST00000505186,,n.439G>A,MODIFIER,,,,-1;TNIP2,non_coding_transcript_exon_variant,,ENST00000502256,,n.137G>A,MODIFIER,,,,-1;TNIP2,downstream_gene_variant,,ENST00000507686,,,MODIFIER,,,,-1;TNIP2,downstream_gene_variant,,ENST00000511352,,,MODIFIER,,,,-1 923/1946 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.223e-05 0.0 0.0 0.0 0.0 6.136e-05 1.766e-05 0.0 0.0 1.3512800251191948e-05 0.0 0.0 0.0 0.0003028470091521 0.0 0.0 0.0 1.5427800462930463e-05 0.0 0.0 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNIP2,non_coding_transcript_exon_variant,,ENST00000505186.1,n.439G>A,MODIFIER,;TNIP2,non_coding_transcript_exon_variant,,ENST00000502256.1,n.137G>A,MODIFIER,;TNIP2,intron_variant,,ENST00000503235.1,c.658-221G>A,MODIFIER,;TNIP2,synonymous_variant,p.A292=,ENST00000315423.12,c.876G>A,LOW,YES;TNIP2,synonymous_variant,p.A185=,ENST00000510267.5,c.555G>A,LOW, +HTT 3064 BI GRCh38 4 3121326 3121326 + synonymous_variant Silent SNP C C T rs759711755 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 18 c.1167C>T p.Pro389= p.P389= ENST00000355072.11 NM_002111.8 389 ccC/ccT 9/67 P1 T P protein_coding YES CCDS43206.1 1167/9429 CCACCCGAGCT PDB-ENSP_mappings:6ez8.A;PDB-ENSP_mappings:6rmh.A;PANTHER:PTHR10170;Superfamily:SSF48371 ENSP00000347184 9/67 rs759711755 ENST00000355072 Transcript 1.0 ENSG00000197386 HGNC:4851 LOW 6.457e-05 gnomAD_AFR synonymous_variant 1.0 Unknown P42858.207 HTT HGNC 1 1.0 UPI000013D567 SNV HTT,synonymous_variant,p.P389=,ENST00000355072,NM_002111.8,c.1167C>T,LOW,YES,,,1;HTT,non_coding_transcript_exon_variant,,ENST00000506137,,n.395C>T,MODIFIER,,,,1;HTT,upstream_gene_variant,,ENST00000512909,,,MODIFIER,,,,1 1312/13475 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.014e-06 6.457e-05 0.0 0.0 0.0 4.638e-05 0.0 0.0 0.0 2.028010021604132e-05 0.0 0.0 0.0 0.0 0.0 0.0 oth 0.0009881419828161 0.0 1.5430699932039715e-05 0.0009881419828161 0.0 0 54 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HTT,non_coding_transcript_exon_variant,,ENST00000506137.1,n.395C>T,MODIFIER,;HTT,synonymous_variant,p.P389=,ENST00000355072.11,c.1167C>T,LOW,YES;HTT,non_coding_transcript_exon_variant,,ENST00000680291.1,n.1312C>T,MODIFIER,;HTT,synonymous_variant,NMD_transcript_variant,p.P303=,ENST00000680360.1,c.909C>T,LOW,;HTT,synonymous_variant,p.P303=,ENST00000681528.1,c.909C>T,LOW,;HTT,synonymous_variant,NMD_transcript_variant,p.P303=,ENST00000680239.1,c.909C>T,LOW,;HTT,synonymous_variant,p.P303=,ENST00000680956.1,c.909C>T,LOW, +PDGFRA 5156 BI GRCh38 4 54280424 54280424 + synonymous_variant Silent SNP C C T rs149659832 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 24 c.2265C>T p.Ser755= p.S755= ENST00000257290.10 NM_001347828.2 755 tcC/tcT 16/23 P1 T S protein_coding YES CCDS3495.1 2265/3270 likely_benign TATTCCGACAT Gene3D:1.10.510.10;PDB-ENSP_mappings:5grn.A;PDB-ENSP_mappings:5k5x.A;PDB-ENSP_mappings:6a32.A;PDB-ENSP_mappings:6joi.A;PDB-ENSP_mappings:6joj.A;PDB-ENSP_mappings:6jok.A;PDB-ENSP_mappings:6jol.A;Pfam:PF07714;PIRSF:PIRSF000615;PIRSF:PIRSF500950;PROSITE_profiles:PS50011;PANTHER:PTHR24416;PANTHER:PTHR24416:SF52;SMART:SM00219;SMART:SM00220;Superfamily:SSF56112;CDD:cd05105 ENSP00000257290 0.0004539 0.0001163 16/23 rs149659832;COSV99957457 ENST00000257290 Transcript 1.0 ENSG00000134853 HGNC:8803 LOW NM_006206.6 0.0004539 AA synonymous_variant 1;1 1.0 Unknown 0;1 P16234.225 PDGFRA HGNC 1 1.0 UPI0000131793 P16234-1 SNV PDGFRA,synonymous_variant,p.S755=,ENST00000257290,NM_001347828.2&NM_006206.6&NM_001347829.2&NM_001347830.1,c.2265C>T,LOW,YES,,,1;AC058822.1,synonymous_variant,p.S515=,ENST00000507166,,c.1545C>T,LOW,YES,,,1;PDGFRA,3_prime_UTR_variant,,ENST00000509490,NM_001347827.2,c.*186C>T,MODIFIER,,,,1;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092,,n.2083C>T,MODIFIER,,,,1;PDGFRA,non_coding_transcript_exon_variant,,ENST00000507536,,n.691C>T,MODIFIER,,,,1;PDGFRA,downstream_gene_variant,,ENST00000461294,,,MODIFIER,,,,1 2400/6378 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001155 0.0004306 0.0001446 0.0 0.0 0.0 0.000141 0.0 3.268e-05 0.0001622429990675 0.0002188399957958 0.0 0.000198886002181 0.0 0.0 0.0 afr 0.0002188399957958 0.0 0.0001851679990068 0.0 0.0 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 57 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PDGFRA,non_coding_transcript_exon_variant,,ENST00000507536.1,n.691C>T,MODIFIER,;PDGFRA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000509490.5,c.*186C>T,MODIFIER,;PDGFRA,synonymous_variant,p.S755=,ENST00000257290.10,c.2265C>T,LOW,YES;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092.5,n.2083C>T,MODIFIER,;ENSG00000282278,synonymous_variant,p.S515=,ENST00000507166.5,c.1545C>T,LOW,YES +FRAS1 80144 BI GRCh38 4 78413023 78413023 + missense_variant Missense_Mutation SNP G G A rs771270397 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 6 c.4363G>A p.Ala1455Thr p.A1455T ENST00000512123.4 NM_025074.7 1455 Gcg/Acg 32/74 P1 A A/T protein_coding YES CCDS54771.1 4363/12039 ACATCGCGATC Pfam:PF16184;PANTHER:PTHR45739;PANTHER:PTHR45739:SF1 ENSP00000422834 32/74 rs771270397 ENST00000512123 Transcript 1.0 ENSG00000138759 HGNC:19185 MODERATE NM_025074.7 5.953e-05 gnomAD_AMR missense_variant 1.0 possibly_damaging(0.743) Unknown tolerated(0.33) Q86XX4.163 FRAS1 HGNC 1 5.0 UPI000021D4C2 Q86XX4-2 SNV FRAS1,missense_variant,p.A1455T,ENST00000512123,NM_025074.7,c.4363G>A,MODERATE,YES,tolerated(0.33),possibly_damaging(0.743),1;FRAS1,missense_variant,p.A1455T,ENST00000325942,NM_001166133.1,c.4363G>A,MODERATE,,deleterious(0.01),probably_damaging(0.946),1 5050/15871 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.631e-05 0.0 5.953e-05 0.0 0.0 0.0 8.952e-06 0.0 3.356e-05 2.029909956036136e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086610013269819e-05 0.0 3.086610013269819e-05 0.0 0.0002089430054184 0 15 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FRAS1,missense_variant,p.A1455T,ENST00000325942.11,c.4363G>A,MODERATE,;FRAS1,missense_variant,p.A1455T,ENST00000682513.1,c.4363G>A,MODERATE,;FRAS1,missense_variant,p.A1455T,ENST00000684159.1,c.4363G>A,MODERATE,;FRAS1,missense_variant,p.A1455T,ENST00000512123.4,c.4363G>A,MODERATE,YES +UNC5C 8633 BI GRCh38 4 95242577 95242577 + synonymous_variant Silent SNP C C T rs760640387 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 13 8 c.960G>A p.Thr320= p.T320= ENST00000453304.6 NM_003728.4 320 acG/acA 7/16 P1 T T protein_coding YES CCDS3643.1 960/2796 CATGGCGTCCA COSM1059098 PROSITE_profiles:PS50092;PANTHER:PTHR12582:SF7;PANTHER:PTHR12582;Gene3D:2.20.100.10;Pfam:PF00090;SMART:SM00209;Superfamily:SSF82895 ENSP00000406022 7/16 rs760640387;COSV71661177 ENST00000453304 Transcript ENSG00000182168 HGNC:12569 LOW NM_003728.4 0.0002683 gnomAD_AMR synonymous_variant 0;1 1.0 Unknown 0;1 O95185.166 UNC5C HGNC -1 1.0 UPI000004E6A5 O95185-1 SNV UNC5C,synonymous_variant,p.T320=,ENST00000453304,NM_003728.4,c.960G>A,LOW,YES,,,-1;UNC5C,synonymous_variant,p.T279=,ENST00000610318,,c.837G>A,LOW,,,,-1;UNC5C,synonymous_variant,p.T320=,ENST00000513796,,c.960G>A,LOW,,,,-1;UNC5C,synonymous_variant,p.T320=,ENST00000506749,,c.960G>A,LOW,,,,-1 1076/9642 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 9.356e-05 0.0 0.0002683 0.0 0.0001203 0.0 9.494e-05 0.0001902 0.0 0.000101388002804 2.4314300389960408e-05 0.0 0.0001325210032518 0.0 0.0 0.0 nfe 0.0001851510023698 0.0 0.0001851510023698 0.0 0.0 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS UNC5C,synonymous_variant,p.T320=,ENST00000506749.5,c.960G>A,LOW,;UNC5C,synonymous_variant,p.T320=,ENST00000513796.5,c.960G>A,LOW,;UNC5C,synonymous_variant,p.T320=,ENST00000453304.6,c.960G>A,LOW,YES +EGF 1950 BI GRCh38 4 109960990 109960990 + splice_donor_variant Splice_Site SNP G G A rs764061176 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 84 9 c.1189+1G>A p.X397_splice p.X397_splice ENST00000265171.10 NM_001963.6 397 P1 A protein_coding YES CCDS3689.1 TCATCGTAAGT ENSP00000265171 rs764061176 ENST00000265171 Transcript NonExonic 1.0 ENSG00000138798 HGNC:3229 HIGH 7/23 NM_001963.6 0.0001632 gnomAD_OTH splice_donor_variant 1.0 Unknown P01133.220 EGF HGNC 1 1.0 UPI000013D5C8 P01133-1 SNV EGF,splice_donor_variant,p.X397_splice,ENST00000265171,NM_001963.6,c.1189+1G>A,HIGH,YES,,,1;EGF,splice_donor_variant,p.X397_splice,ENST00000503392,NM_001178130.3,c.1189+1G>A,HIGH,,,,1;EGF,splice_donor_variant,p.X355_splice,ENST00000509793,NM_001178131.3,c.1063+1G>A,HIGH,,,,1;EGF,splice_donor_variant,p.X355_splice,ENST00000652245,NM_001357021.2,c.1063+1G>A,HIGH,,,,1;EGF,splice_donor_variant,,ENST00000504633,,n.427+1G>A,HIGH,,,,1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.99e-05 0.0 2.896e-05 0.0 0.0001088 0.0 0.0 0.0001632 3.267e-05 6.762239991076058e-06 2.4330900487257168e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 87 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 93 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EGF,splice_donor_variant,,ENST00000504633.1,n.427+1G>A,HIGH,;EGF,splice_donor_variant,p.X397_splice,ENST00000503392.1,c.1189+1G>A,HIGH,;EGF,splice_donor_variant,p.X355_splice,ENST00000652245.1,c.1063+1G>A,HIGH,;EGF,splice_donor_variant,p.X355_splice,ENST00000509793.5,c.1063+1G>A,HIGH,;EGF,splice_donor_variant,p.X397_splice,ENST00000265171.10,c.1189+1G>A,HIGH,YES +FAM241A 132720 BI GRCh38 4 112186823 112186823 + missense_variant Missense_Mutation SNP G G A rs866555738 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 124 31 c.284G>A p.Arg95Gln p.R95Q ENST00000309733.6 NM_152400.3 95 cGa/cAa 2/2 P1 A R/Q protein_coding YES CCDS3695.1 284/399 AGAACGAATAG COSM3599169 Pfam:PF15378;PANTHER:PTHR33690;PANTHER:PTHR33690:SF1 ENSP00000310182 2/2 rs866555738;COSV59036448 ENST00000309733 Transcript ENSG00000174749 HGNC:26813 MODERATE NM_152400.3 1.76e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0.019) Unknown tolerated(0.14) 0;1 Q8N8J7.107 FAM241A HGNC 1 1.0 UPI000013EF13 SNV FAM241A,missense_variant,p.R95Q,ENST00000309733,NM_152400.3,c.284G>A,MODERATE,YES,tolerated(0.14),benign(0.019),1 411/8844 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.956e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 6.764530098735122e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433099179062992e-05 0.0 0.0 0 172 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 155 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FAM241A,missense_variant,p.R95Q,ENST00000309733.6,c.284G>A,MODERATE,YES +ANKRD50 57182 BI GRCh38 4 124671391 124671391 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 49 32 c.1886C>T p.Ala629Val p.A629V ENST00000504087.6 NM_020337.3 629 gCa/gTa 4/5 P1 A A/V protein_coding YES CCDS34060.1 1886/4290 GTAGTGCAGAA Gene3D:1.25.40.20;Pfam:PF12796;PROSITE_profiles:PS50088;PROSITE_profiles:PS50297;PANTHER:PTHR24123;PANTHER:PTHR24123:SF65;SMART:SM00248;Superfamily:SSF48403 ENSP00000425658 4/5 ENST00000504087 Transcript ENSG00000151458 HGNC:29223 MODERATE NM_020337.3 missense_variant 1.0 possibly_damaging(0.525) Unknown tolerated(1) Q9ULJ7.156 ANKRD50 HGNC -1 2.0 UPI00002377E8 Q9ULJ7-1 SNV ANKRD50,missense_variant,p.A629V,ENST00000504087,NM_020337.3,c.1886C>T,MODERATE,YES,tolerated(1),possibly_damaging(0.525),-1;ANKRD50,missense_variant,p.A450V,ENST00000515641,NM_001167882.2,c.1349C>T,MODERATE,,tolerated(1),possibly_damaging(0.525),-1 2924/8798 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 81 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ANKRD50,missense_variant,p.A450V,ENST00000515641.1,c.1349C>T,MODERATE,;ANKRD50,missense_variant,p.A629V,ENST00000504087.6,c.1886C>T,MODERATE,YES +ELMOD2 255520 BI GRCh38 4 140540191 140540191 + synonymous_variant Silent SNP G G A rs1041416616 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 4 c.423G>A p.Thr141= p.T141= ENST00000323570.8 NM_153702.4 141 acG/acA 6/9 P1 A T protein_coding YES CCDS3752.1 423/882 CCCACGAAGAA COSM1051456 Pfam:PF04727;PROSITE_profiles:PS51335;PANTHER:PTHR12771;PANTHER:PTHR12771:SF47 ENSP00000326342 6/9 rs1041416616;COSV60270867 ENST00000323570 Transcript ENSG00000179387 HGNC:28111 LOW NM_153702.4 1.759e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q8IZ81.116 ELMOD2 HGNC 1 1.0 UPI0000074163 SNV ELMOD2,synonymous_variant,p.T141=,ENST00000323570,NM_153702.4,c.423G>A,LOW,YES,,,1;ELMOD2,synonymous_variant,p.T141=,ENST00000502397,,c.423G>A,LOW,,,,1;ELMOD2,synonymous_variant,p.T64=,ENST00000513606,,c.192G>A,LOW,,,,1;ELMOD2,non_coding_transcript_exon_variant,,ENST00000512057,,n.568G>A,MODIFIER,,,,1;ELMOD2,upstream_gene_variant,,ENST00000502290,,,MODIFIER,,,,1 545/4399 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.956e-06 0.0 0.0 0.0 0.0 0.0 1.759e-05 0.0 0.0 2.0285100617911667e-05 4.864759830525145e-05 0.0 0.0 0.0 0.0 0.0 afr 4.864759830525145e-05 0.0 1.543160033179447e-05 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ELMOD2,non_coding_transcript_exon_variant,,ENST00000512057.1,n.568G>A,MODIFIER,;ELMOD2,synonymous_variant,p.T64=,ENST00000513606.1,c.192G>A,LOW,;ELMOD2,synonymous_variant,p.T141=,ENST00000502397.5,c.423G>A,LOW,;ELMOD2,synonymous_variant,p.T141=,ENST00000323570.8,c.423G>A,LOW,YES +OTUD4 54726 BI GRCh38 4 145137510 145137510 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 98 23 c.3265C>T p.Arg1089Ter p.R1089* ENST00000447906.8 NM_001366057.1 1089 Cga/Tga 21/21 P1 A R/* protein_coding YES 3265/3345 ATTTCGATGGT Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000395487 21/21 ENST00000447906 Transcript ENSG00000164164 HGNC:24949 HIGH NM_001366057.1 stop_gained 1.0 Unknown Q01804.162 OTUD4 HGNC -1 5.0 UPI0000E825C1 Q01804-1 SNV OTUD4,stop_gained,p.R1089*,ENST00000447906,NM_001366057.1,c.3265C>T,HIGH,YES,,,-1;OTUD4,stop_gained,p.R1024*,ENST00000454497,NM_001102653.1,c.3070C>T,HIGH,,,,-1;OTUD4,intron_variant,,ENST00000455611,,n.2028+2441C>T,MODIFIER,,,,-1 3881/7741 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 109 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 121 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS OTUD4,stop_gained,p.R1089*,ENST00000447906.8,c.3265C>T,HIGH,YES;OTUD4,stop_gained,p.R1024*,ENST00000454497.6,c.3070C>T,HIGH,;OTUD4,intron_variant,,ENST00000455611.6,n.2028+2441C>T,MODIFIER, +FBXW7 55294 BI GRCh38 4 152326214 152326214 + missense_variant Missense_Mutation SNP C C T rs866987936 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 6 c.1436G>A p.Arg479Gln p.R479Q ENST00000281708.10 NM_001349798.2 479 cGa/cAa 12/14 T R/Q protein_coding CCDS3777.1 1436/2124 likely_pathogenic CATCTCGAGAA COSM1154291;COSM22974;COSM447498;COSM447499;COSM94297 Gene3D:2.130.10.10;PDB-ENSP_mappings:2ovp.B;PDB-ENSP_mappings:2ovq.B;PDB-ENSP_mappings:2ovr.B;PDB-ENSP_mappings:5v4b.B;Pfam:PF00400;Prints:PR00320;PROSITE_patterns:PS00678;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR44129;PANTHER:PTHR44129:SF9;SMART:SM00320;Superfamily:SSF50978;CDD:cd00200 ENSP00000281708 12/14 rs866987936;COSV55890822;COSV55894913;COSV55899054 ENST00000281708 Transcript 1.0 ENSG00000109670 HGNC:16712 MODERATE NM_001349798.2 missense_variant 1;1;1;1 26619011 probably_damaging(1) Unknown deleterious(0.03) 0;1;1;1 Q969H0.184 FBXW7 HGNC -1 1.0 UPI000007007E Q969H0-1 SNV FBXW7,missense_variant,p.R479Q,ENST00000603548,NM_033632.3,c.1436G>A,MODERATE,YES,deleterious(0.03),probably_damaging(1),-1;FBXW7,missense_variant,p.R479Q,ENST00000281708,NM_001349798.2,c.1436G>A,MODERATE,,deleterious(0.03),probably_damaging(1),-1;FBXW7,missense_variant,p.R399Q,ENST00000393956,NM_018315.5,c.1196G>A,MODERATE,,deleterious(0.03),probably_damaging(1),-1;FBXW7,missense_variant,p.R361Q,ENST00000296555,NM_001013415.2,c.1082G>A,MODERATE,,deleterious(0.04),probably_damaging(1),-1;FBXW7,missense_variant,p.R479Q,ENST00000603841,,c.1436G>A,MODERATE,,deleterious(0.03),probably_damaging(1),-1;FBXW7,non_coding_transcript_exon_variant,,ENST00000647183,,n.985G>A,MODIFIER,,,,-1;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821,,n.884G>A,MODIFIER,,,,-1;FBXW7,downstream_gene_variant,,ENST00000604069,,,MODIFIER,,,,-1;FBXW7,upstream_gene_variant,,ENST00000604316,,,MODIFIER,,,,-1 2614/5639 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FBXW7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703555.1,c.*412G>A,MODIFIER,;FBXW7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703554.1,c.*1083G>A,MODIFIER,;FBXW7,missense_variant,p.R479Q,ENST00000703553.1,c.1436G>A,MODERATE,;FBXW7,missense_variant,p.R312Q,ENST00000703552.1,c.935G>A,MODERATE,;FBXW7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703551.1,c.*129G>A,MODIFIER,;FBXW7,non_coding_transcript_exon_variant,,ENST00000603821.1,n.884G>A,MODIFIER,;FBXW7,missense_variant,p.R479Q,ENST00000603841.1,c.1436G>A,MODERATE,;FBXW7,non_coding_transcript_exon_variant,,ENST00000647183.1,n.985G>A,MODIFIER,;FBXW7,missense_variant,p.R399Q,ENST00000393956.9,c.1196G>A,MODERATE,;FBXW7,missense_variant,p.R361Q,ENST00000296555.11,c.1082G>A,MODERATE,;FBXW7,missense_variant,p.R479Q,ENST00000603548.6,c.1436G>A,MODERATE,;FBXW7,missense_variant,p.R479Q,ENST00000281708.10,c.1436G>A,MODERATE,YES +LRP2BP 55805 BI GRCh38 4 185374341 185374341 + stop_gained Nonsense_Mutation SNP G G A rs201973995 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 40 27 c.451C>T p.Arg151Ter p.R151* ENST00000328559.11 NM_001385602.1 151 Cga/Tga 4/8 0.0004 0.0015 0.0 0.0 0.0 0.0 P1 A R/* protein_coding YES CCDS3840.1 451/1044 TGATCGTTTAA Gene3D:1.25.40.10;Pfam:PF08238;PANTHER:PTHR44554;SMART:SM00671;Superfamily:SSF81901 ENSP00000332681 0.0004539 0.0 4/8 rs201973995 ENST00000328559 Transcript ENSG00000109771 HGNC:25434 HIGH 0.0015 AFR stop_gained 1.0 Unknown Q9P2M1.130 LRP2BP HGNC -1 1.0 UPI00001BB2BB Q9P2M1-1 SNV LRP2BP,stop_gained,p.R151*,ENST00000328559,NM_018409.3,c.451C>T,HIGH,YES,,,-1;LRP2BP,stop_gained,p.R125*,ENST00000510776,NM_001377442.1&NM_001377443.1&NM_001377441.1,c.373C>T,HIGH,,,,-1;LRP2BP,stop_gained,p.R151*,ENST00000505916,NM_001377440.1,c.451C>T,HIGH,,,,-1;LRP2BP,stop_gained,p.R151*,ENST00000511404,,c.451C>T,HIGH,,,,-1;SNX25,downstream_gene_variant,,ENST00000504959,,,MODIFIER,,,,1;AC112722.1,intron_variant,,ENST00000514884,,n.242+3276G>A,MODIFIER,YES,,,1 1263/5157 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.763e-05 0.0004307 0.0 0.0 0.0 0.0 8.798e-05 0.0 0.0 5.413380131358281e-05 0.0001948370045283 0.0 0.0 0.0 0.0 0.0 afr 0.0001948370045283 0.0 0.0 0.0 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 67 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRP2BP,stop_gained,p.R151*,ENST00000511404.1,c.451C>T,HIGH,;LRP2BP-AS1,intron_variant,,ENST00000514884.1,n.242+3276G>A,MODIFIER,YES;LRP2BP,stop_gained,p.R125*,ENST00000510776.5,c.373C>T,HIGH,;LRP2BP,stop_gained,p.R151*,ENST00000328559.11,c.451C>T,HIGH,;LRP2BP,stop_gained,p.R151*,ENST00000505916.6,c.451C>T,HIGH,YES +SLC9A3 6550 BI GRCh38 5 476341 476341 + missense_variant Missense_Mutation SNP G G A rs150973602 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 61 42 c.1928C>T p.Thr643Met p.T643M ENST00000264938.8 NM_004174.4 643 aCg/aTg 13/17 A2 A T/M protein_coding CCDS3855.1 1928/2505 CCTCCGTGGGC PANTHER:PTHR10110;PANTHER:PTHR10110:SF90;TIGRFAM:TIGR00840 ENSP00000264938 0.000227 0.0 13/17 rs150973602 ENST00000264938 Transcript 1.0 ENSG00000066230 HGNC:11073 MODERATE NM_004174.4 0.000227 AA missense_variant benign(0.266) Unknown deleterious(0.01) P48764.169 SLC9A3 HGNC -1 1.0 UPI000013D597 P48764-1 SNV SLC9A3,missense_variant,p.T643M,ENST00000264938,NM_004174.4,c.1928C>T,MODERATE,,deleterious(0.01),benign(0.266),-1;SLC9A3,missense_variant,p.T643M,ENST00000644203,,c.1928C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.781),-1;SLC9A3,missense_variant,p.T634M,ENST00000514375,NM_001284351.3,c.1901C>T,MODERATE,,deleterious(0.01),benign(0.326),-1;EXOC3,downstream_gene_variant,,ENST00000509294,,,MODIFIER,,,,1;EXOC3,downstream_gene_variant,,ENST00000503889,,,MODIFIER,,,,1;SLC9A3,downstream_gene_variant,,ENST00000507407,,,MODIFIER,,,,-1;EXOC3,downstream_gene_variant,,ENST00000515601,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000534918,,,MODIFIER,YES,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000606074,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000606107,,,MODIFIER,,,,1;SLC9A3-AS1,non_coding_transcript_exon_variant,,ENST00000607286,,n.457G>A,MODIFIER,,,,1;SLC9A3-AS1,non_coding_transcript_exon_variant,,ENST00000606319,,n.328G>A,MODIFIER,,,,1;PP7080,upstream_gene_variant,,ENST00000342584,,,MODIFIER,YES,,,-1;PP7080,upstream_gene_variant,,ENST00000502511,,,MODIFIER,,,,-1;PP7080,upstream_gene_variant,,ENST00000510604,,,MODIFIER,,,,-1;PP7080,upstream_gene_variant,,ENST00000510714,,,MODIFIER,,,,-1;SLC9A3-AS1,upstream_gene_variant,,ENST00000606288,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000607005,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000655313,,,MODIFIER,,,,1;SLC9A3-AS1,downstream_gene_variant,,ENST00000658086,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000658225,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000667376,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000667998,,,MODIFIER,,,,1;SLC9A3-AS1,upstream_gene_variant,,ENST00000668009,,,MODIFIER,,,,1 2055/5555 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.606e-05 6.186e-05 2.895e-05 0.0 0.0 0.0 8.956e-06 0.0001643 0.0 1.3517899787984788e-05 4.863809954258613e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863809954258613e-05 0.0 0.0 0.0 0.0 0 123 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 103 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC9A3-AS1,non_coding_transcript_exon_variant,,ENST00000606319.1,n.328G>A,MODIFIER,;SLC9A3,missense_variant,p.T634M,ENST00000514375.1,c.1901C>T,MODERATE,;SLC9A3-AS1,non_coding_transcript_exon_variant,,ENST00000607286.5,n.457G>A,MODIFIER,YES;SLC9A3,missense_variant,p.T643M,ENST00000644203.1,c.1928C>T,MODERATE,;SLC9A3,missense_variant,p.T643M,ENST00000264938.8,c.1928C>T,MODERATE,YES +LPCAT1 79888 BI GRCh38 5 1501569 1501569 + missense_variant Missense_Mutation SNP C C T rs1307070775 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 12 c.170G>A p.Arg57Gln p.R57Q ENST00000283415.4 NM_024830.5 57 cGg/cAg 2/14 P1 T R/Q protein_coding YES CCDS3864.1 170/1605 GGAGCCGGACC COSM1619857 PANTHER:PTHR23063;PANTHER:PTHR23063:SF40;Transmembrane_helices:TMhelix ENSP00000283415 2/14 rs1307070775;COSV52035447 ENST00000283415 Transcript ENSG00000153395 HGNC:25718 MODERATE NM_024830.5 4.632e-05 gnomAD_FIN missense_variant 0;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1 Q8NF37.148 LPCAT1 HGNC -1 1.0 UPI000004771C SNV LPCAT1,missense_variant,p.R57Q,ENST00000283415,NM_024830.5,c.170G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;LPCAT1,non_coding_transcript_exon_variant,,ENST00000514484,,n.200G>A,MODIFIER,,,,-1;LPCAT1,missense_variant,p.R57Q,ENST00000475622,,c.170G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1 286/3945 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.99e-06 0.0 0.0 0.0 0.0 4.632e-05 0.0 0.0 0.0 0 73 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LPCAT1,non_coding_transcript_exon_variant,,ENST00000514484.6,n.200G>A,MODIFIER,;LPCAT1,missense_variant,p.R57Q,ENST00000283415.4,c.170G>A,MODERATE,YES;LPCAT1,missense_variant,NMD_transcript_variant,p.R57Q,ENST00000475622.5,c.170G>A,MODERATE, +TRIO 7204 BI GRCh38 5 14508240 14508240 + missense_variant Missense_Mutation SNP C C T rs1321773037 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 5 c.9112C>T p.Arg3038Cys p.R3038C ENST00000344204.9 NM_007118.4 3038 Cgt/Tgt 57/57 P1 T R/C protein_coding YES CCDS3883.1 9112/9294 CCAAGCGTCCC Gene3D:1.10.510.10;Pfam:PF00069;PROSITE_profiles:PS50011;PANTHER:PTHR22826;PANTHER:PTHR22826:SF104;SMART:SM00220;Superfamily:SSF56112;CDD:cd14113 ENSP00000339299 57/57 rs1321773037 ENST00000344204 Transcript 1.0 ENSG00000038382 HGNC:12303 MODERATE NM_007118.4 1.76e-05 gnomAD_NFE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) O75962.209 TRIO HGNC 1 1.0 UPI000034ECE6 O75962-1 SNV TRIO,missense_variant,p.R3038C,ENST00000344204,NM_007118.4,c.9112C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;TRIO,missense_variant,p.R537C,ENST00000344135,,c.1609C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;TRIO,intron_variant,,ENST00000513206,,c.7610+5583C>T,MODIFIER,,,,1;TRIO,intron_variant,,ENST00000620511,,c.706-1169C>T,MODIFIER,,,,1;TRIO,3_prime_UTR_variant,,ENST00000512070,,c.*1475C>T,MODIFIER,,,,1;TRIO,non_coding_transcript_exon_variant,,ENST00000508717,,n.766C>T,MODIFIER,,,,1;TRIO,downstream_gene_variant,,ENST00000508283,,,MODIFIER,,,,1 9496/11460 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.959e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 6.758580184396124e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 38 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TRIO,non_coding_transcript_exon_variant,,ENST00000508717.1,n.766C>T,MODIFIER,;TRIO,non_coding_transcript_exon_variant,,ENST00000344135.5,n.2102C>T,MODIFIER,;TRIO,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698542.1,c.*1630C>T,MODIFIER,;TRIO,intron_variant,,ENST00000513206.5,c.7610+5583C>T,MODIFIER,;TRIO,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000512070.6,c.*1475C>T,MODIFIER,;TRIO,missense_variant,p.R3038C,ENST00000344204.9,c.9112C>T,MODERATE,YES +CDH18 1016 BI GRCh38 5 19721362 19721362 + missense_variant Missense_Mutation SNP C C T rs750768779 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 102 11 c.628G>A p.Val210Ile p.V210I ENST00000274170.8 210 Gtc/Atc 3/11 P1 T V/I protein_coding CCDS3889.1 628/2373 GTCGACGGAGA COSM182561;COSM3854517 Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24027;PANTHER:PTHR24027:SF106;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000274170 3/11 rs750768779;COSV56917098 ENST00000274170 Transcript ENSG00000145526 HGNC:1757 MODERATE 4.629e-05 gnomAD_FIN missense_variant 0;1 probably_damaging(0.958) Unknown tolerated(0.1) 0;1 Q13634.161 CDH18 HGNC -1 1.0 UPI0000126DBD Q13634-1 SNV CDH18,missense_variant,p.V210I,ENST00000382275,NM_001349559.2&NM_004934.5&NM_001349563.2,c.628G>A,MODERATE,YES,tolerated(0.1),probably_damaging(0.958),-1;CDH18,missense_variant,p.V210I,ENST00000507958,NM_001349562.2&NM_001349556.2&NM_001291956.3&NM_001349558.2,c.628G>A,MODERATE,,tolerated(0.1),probably_damaging(0.958),-1;CDH18,missense_variant,p.V210I,ENST00000274170,,c.628G>A,MODERATE,,tolerated(0.1),probably_damaging(0.958),-1;CDH18,missense_variant,p.V210I,ENST00000506372,NM_001349560.2&NM_001291957.2,c.628G>A,MODERATE,,tolerated(0.08),benign(0.287),-1;CDH18,missense_variant,p.V210I,ENST00000502796,NM_001349561.2&NM_001167667.3,c.628G>A,MODERATE,,tolerated(0.09),benign(0.179),-1;CDH18,missense_variant,p.V210I,ENST00000511273,,c.628G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.548),-1;CDH18,missense_variant,p.V156I,ENST00000515257,,c.466G>A,MODERATE,,tolerated(0.09),probably_damaging(0.985),-1;CDH18,downstream_gene_variant,,ENST00000508350,,,MODIFIER,,,,-1 886/2809 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.595e-05 0.0 2.903e-05 0.0 0.0 4.629e-05 1.764e-05 0.0 0.0 1.3526299881050363e-05 0.0 0.0 6.63305982016027e-05 0.0 0.0 0.0 0.0 1.5432100553880446e-05 0.0 0.0 0 120 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 114 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CDH18,missense_variant,p.V210I,ENST00000511273.1,c.628G>A,MODERATE,;CDH18,missense_variant,p.V156I,ENST00000515257.6,c.466G>A,MODERATE,;CDH18,missense_variant,p.V210I,ENST00000502796.5,c.628G>A,MODERATE,;CDH18,missense_variant,p.V210I,ENST00000506372.5,c.628G>A,MODERATE,;CDH18,missense_variant,p.V210I,ENST00000507958.5,c.628G>A,MODERATE,;CDH18,missense_variant,p.V210I,ENST00000274170.8,c.628G>A,MODERATE,;CDH18,missense_variant,p.V210I,ENST00000382275.6,c.628G>A,MODERATE,YES +PDZD2 23037 BI GRCh38 5 32090571 32090571 + missense_variant Missense_Mutation SNP G G A rs761908408 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 40 7 c.7123G>A p.Gly2375Ser p.G2375S ENST00000438447.2 NM_178140.4 2375 Ggc/Agc 20/25 P1 A G/S protein_coding YES CCDS34137.1 7123/8520 CTTCCGGCAGC COSM1734246 PANTHER:PTHR11324;PANTHER:PTHR11324:SF16;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000402033 20/25 rs761908408;COSV56858806 ENST00000438447 Transcript ENSG00000133401 HGNC:18486 MODERATE NM_178140.4 9.932e-05 gnomAD_ASJ missense_variant 0;1 1.0 probably_damaging(0.999) Unknown tolerated(0.17) 0;1 O15018.150 PDZD2 HGNC 1 A0A024RE15.42 1.0 UPI000069648B O15018-1 SNV PDZD2,missense_variant,p.G2375S,ENST00000438447,NM_178140.4,c.7123G>A,MODERATE,YES,tolerated(0.17),probably_damaging(0.999),1 7790/11984 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.195e-05 6.179e-05 0.0 9.932e-05 0.0 0.0 0.0 0.0 3.267e-05 4.059540151502006e-05 9.737099753692746e-05 0.0 0.0 0.0 0.0004050220013596 0.0 eas 0.0004050220013596 0.0 0.0 0.0 0.0 0 45 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 47 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PDZD2,missense_variant,p.G2375S,ENST00000438447.2,c.7123G>A,MODERATE,YES +ITGA2 3673 BI GRCh38 5 53062848 53062848 + synonymous_variant Silent SNP C C T rs371281604 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 29 c.1521C>T p.Asp507= p.D507= ENST00000296585.10 NM_002203.4 507 gaC/gaT 13/30 P1 T D protein_coding YES CCDS3957.1 1521/3546 ACAGACGTGCT Gene3D:2.130.10.130;PROSITE_profiles:PS51470;PANTHER:PTHR23220;PANTHER:PTHR23220:SF23;SMART:SM00191;Superfamily:SSF69318 ENSP00000296585 0.0 0.0001163 13/30 rs371281604 ENST00000296585 Transcript 1.0 ENSG00000164171 HGNC:6137 LOW NM_002203.4 0.0001163 EA synonymous_variant 1.0 Unknown P17301.221 ITGA2 HGNC 1 1.0 UPI0000169C36 SNV ITGA2,synonymous_variant,p.D507=,ENST00000296585,NM_002203.4,c.1521C>T,LOW,YES,,,1;ITGA2,synonymous_variant,p.D507=,ENST00000509960,,c.1521C>T,LOW,,,,1;ITGA2,synonymous_variant,p.D507=,ENST00000510722,,c.1521C>T,LOW,,,,1;ITGA2,synonymous_variant,p.D507=,ENST00000509814,,c.1521C>T,LOW,,,,1;ITGA2,3_prime_UTR_variant,,ENST00000503810,,c.*865C>T,MODIFIER,,,,1;ITGA2,3_prime_UTR_variant,,ENST00000513685,,c.*1235C>T,MODIFIER,,,,1 1638/7843 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.187e-05 6.161e-05 2.901e-05 0.0 0.0 0.0 7.955e-05 0.0 6.534e-05 6.12619987805374e-05 4.901480133412406e-05 0.0 0.0 0.0 0.0 0.0 nfe 0.0001084329996956 0.0 0.0001084329996956 0.0 0.0 0 108 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 58 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ITGA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000513685.5,c.*1235C>T,MODIFIER,;ITGA2,synonymous_variant,NMD_transcript_variant,p.D507=,ENST00000509814.5,c.1521C>T,LOW,;ITGA2,synonymous_variant,NMD_transcript_variant,p.D507=,ENST00000510722.1,c.1521C>T,LOW,;ITGA2,synonymous_variant,NMD_transcript_variant,p.D507=,ENST00000509960.5,c.1521C>T,LOW,;ITGA2,synonymous_variant,p.D507=,ENST00000296585.10,c.1521C>T,LOW,YES;ITGA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000503810.6,c.*865C>T,MODIFIER, +ESM1 11082 BI GRCh38 5 54985236 54985257 + frameshift_variant Frame_Shift_Del DEL TTCACCAAAAGGATCCTCCCCA TTCACCAAAAGGATCCTCCCCA - novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 117 11 c.261_282del p.Glu94AspfsTer30 p.E94Dfs*30 ENST00000381405.5 NM_007036.5 87 aaTGGGGAGGATCCTTTTGGTGAA/aa 1/3 P2 - NGEDPFGE/X protein_coding YES CCDS3963.1 261-282/555 AAACTCTTCACCAAAAGGATCCTCCCCATTAGA PROSITE_profiles:PS51323;PANTHER:PTHR15428;Gene3D:3.30.60.30;SMART:SM00121;Superfamily:SSF57184 ENSP00000370812 1/3 ENST00000381405 Transcript ENSG00000164283 HGNC:3466 HIGH NM_007036.5 frameshift_variant 1.0 Unknown Q9NQ30.148 ESM1 HGNC -1 1.0 UPI000012A1BA Q9NQ30-1 deletion ESM1,frameshift_variant,p.N87Kfs*37,ENST00000381405,NM_007036.5,c.261_282del,HIGH,YES,,,-1;ESM1,frameshift_variant,p.N87Kfs*19,ENST00000381403,NM_001135604.2,c.261_282del,HIGH,,,,-1;ESM1,coding_sequence_variant,,ENST00000601836,,,MODIFIER,,,,-1;ESM1,intron_variant,,ENST00000598310,,n.230-5822_230-5801del,MODIFIER,,,,-1 337-358/2096 mutect2;pindel ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 138 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 128 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ESM1,intron_variant,,ENST00000598310.5,n.230-5822_230-5801del,MODIFIER,;ESM1,frameshift_variant,p.E94Dfs*12,ENST00000381403.4,c.261_282del,HIGH,;ESM1,frameshift_variant,p.E94Dfs*30,ENST00000381405.5,c.261_282del,HIGH,YES +CDC20B 166979 BI GRCh38 5 55124901 55124901 + missense_variant Missense_Mutation SNP C C T rs1338716023 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 72 9 c.1117G>A p.Gly373Ser p.G373S ENST00000381375.7 NM_001170402.1 373 Ggc/Agc 9/12 P4 T G/S protein_coding YES CCDS54852.1 1117/1560 GCAGCCGCTGG PROSITE_profiles:PS50294;PROSITE_profiles:PS50082;PANTHER:PTHR19918:SF4;PANTHER:PTHR19918;Gene3D:2.130.10.10;Pfam:PF00400;SMART:SM00320;Superfamily:SSF50978 ENSP00000370781 9/12 rs1338716023 ENST00000381375 Transcript ENSG00000164287 HGNC:24222 MODERATE NM_001170402.1 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q86Y33.139 CDC20B HGNC -1 1.0 UPI0000D61625 Q86Y33-1 SNV CDC20B,missense_variant,p.G373S,ENST00000381375,NM_001170402.1,c.1117G>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;CDC20B,missense_variant,p.G373S,ENST00000296733,NM_152623.2,c.1117G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;CDC20B,missense_variant,p.G373S,ENST00000322374,NM_001145734.2,c.1117G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;CDC20B,3_prime_UTR_variant,,ENST00000513180,,c.*84G>A,MODIFIER,,,,-1 1294/2984 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.760959877283312e-06 2.4326200218638405e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 85 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 81 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CDC20B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000513180.5,c.*84G>A,MODIFIER,;CDC20B,missense_variant,p.G373S,ENST00000322374.10,c.1117G>A,MODERATE,;CDC20B,missense_variant,p.G373S,ENST00000296733.5,c.1117G>A,MODERATE,;CDC20B,missense_variant,p.G373S,ENST00000381375.7,c.1117G>A,MODERATE,YES +SKIC3 9652 BI GRCh38 5 95523274 95523274 + missense_variant Missense_Mutation SNP G G A rs143193581 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 100 81 c.1685C>T p.Thr562Met p.T562M ENST00000358746.7 NM_014639.4 562 aCg/aTg 18/43 P1 A T/M protein_coding CCDS4072.1 1685/4695 TTGCCGTTCCA Gene3D:1.25.40.10;PROSITE_profiles:PS50293;PANTHER:PTHR15704;PANTHER:PTHR15704:SF7;Superfamily:SSF81901 ENSP00000351596 0.0004539 0.0 18/43 rs143193581 ENST00000358746 Transcript 1.0 ENSG00000198677 HGNC:23639 MODERATE NM_014639.4 0.0004539 AA missense_variant possibly_damaging(0.564) Unknown deleterious(0.04) Q6PGP7.148 TTC37 HGNC -1 1.0 UPI00000709BD SNV TTC37,missense_variant,p.T562M,ENST00000649566,,c.1685C>T,MODERATE,YES,deleterious(0.04),possibly_damaging(0.564),-1;TTC37,missense_variant,p.T562M,ENST00000358746,NM_014639.4,c.1685C>T,MODERATE,,deleterious(0.04),possibly_damaging(0.564),-1;TTC37,missense_variant,p.T514M,ENST00000514952,,c.1541C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.733),-1;RNU6-308P,downstream_gene_variant,,ENST00000390957,,,MODIFIER,YES,,,1;TTC37,downstream_gene_variant,,ENST00000504421,,,MODIFIER,,,,-1;TTC37,synonymous_variant,p.N124=,ENST00000505578,,c.372C>T,LOW,,,,-1;TTC37,3_prime_UTR_variant,,ENST00000513232,,c.*400C>T,MODIFIER,,,,-1;TTC37,upstream_gene_variant,,ENST00000507805,,,MODIFIER,,,,-1 1954/5677 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.36e-05 0.0002462 0.0 0.0 5.437e-05 0.0 5.286e-05 0.0 0.0003266 6.08750015089754e-05 0.0001217320022988 0.0 0.0 0.0 0.0 0.0 sas 0.0004173619963694 0.0 3.086520155193284e-05 0.0 0.0004173619963694 0 219 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 181 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SKIC3,missense_variant,p.T514M,ENST00000514952.5,c.1541C>T,MODERATE,;SKIC3,synonymous_variant,NMD_transcript_variant,p.N124=,ENST00000505578.5,c.372C>T,LOW,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698494.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698493.1,n.1975C>T,MODIFIER,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698492.1,c.*400C>T,MODIFIER,;SKIC3,missense_variant,p.T562M,ENST00000698490.1,c.1685C>T,MODERATE,;SKIC3,missense_variant,p.T562M,ENST00000358746.7,c.1685C>T,MODERATE,YES;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698476.1,c.1685C>T,MODERATE,;SKIC3,missense_variant,p.T562M,ENST00000698479.1,c.1685C>T,MODERATE,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698488.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698486.1,n.1975C>T,MODIFIER,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698472.1,c.*400C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698475.1,n.1975C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698482.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698484.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698489.1,n.5760C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698481.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698474.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698480.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698478.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698477.1,c.1685C>T,MODERATE,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698469.1,c.*1032C>T,MODIFIER,;SKIC3,missense_variant,p.T562M,ENST00000698487.1,c.1685C>T,MODERATE,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698470.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698473.1,n.1975C>T,MODIFIER,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000513232.2,c.*400C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000506007.2,n.1975C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698483.1,n.1975C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698468.1,n.2176C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698471.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698485.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698452.1,n.2176C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698451.1,n.1105C>T,MODIFIER,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698455.1,c.*1661C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T574M,ENST00000698458.1,c.1721C>T,MODERATE,;SKIC3,missense_variant,p.T559M,ENST00000698454.1,c.1676C>T,MODERATE,;SKIC3,missense_variant,p.T562M,ENST00000649566.1,c.1685C>T,MODERATE,;SKIC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698456.1,c.*543C>T,MODIFIER,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698450.1,n.1069C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698460.1,c.1685C>T,MODERATE,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698459.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698461.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,p.T562M,ENST00000698457.1,c.1685C>T,MODERATE,;SKIC3,non_coding_transcript_exon_variant,,ENST00000698462.1,n.1975C>T,MODIFIER,;SKIC3,missense_variant,NMD_transcript_variant,p.T562M,ENST00000698453.1,c.1685C>T,MODERATE, +ERAP2 64167 BI GRCh38 5 96883830 96883830 + missense_variant Missense_Mutation SNP G G A rs73150323 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 17 c.614G>A p.Arg205His p.R205H ENST00000437043.8 NM_001130140.2 205 cGc/cAc 3/19 0.0004 0.0015 0.0 0.0 0.0 0.0 P1 A R/H protein_coding YES CCDS4086.1 614/2883 GGCACGCATGG PDB-ENSP_mappings:3se6.A;PDB-ENSP_mappings:3se6.B;PDB-ENSP_mappings:4e36.A;PDB-ENSP_mappings:4e36.B;PDB-ENSP_mappings:4jbs.A;PDB-ENSP_mappings:4jbs.B;PDB-ENSP_mappings:5ab0.A;PDB-ENSP_mappings:5ab0.C;PDB-ENSP_mappings:5ab2.A;PDB-ENSP_mappings:5ab2.B;PDB-ENSP_mappings:5cu5.A;PDB-ENSP_mappings:5cu5.B;PDB-ENSP_mappings:5j6s.A;PDB-ENSP_mappings:5j6s.B;PDB-ENSP_mappings:5k1v.A;PDB-ENSP_mappings:5k1v.B;PDB-ENSP_mappings:6ea4.A;PDB-ENSP_mappings:6ea4.B;CDD:cd09601;PANTHER:PTHR11533;PANTHER:PTHR11533:SF239;Gene3D:2.60.40.1730;Pfam:PF17900;Superfamily:SSF63737;Prints:PR00756 ENSP00000400376 0.0009079 0.0 3/19 rs73150323 ENST00000437043 Transcript ENSG00000164308 HGNC:29499 MODERATE NM_022350.5 0.0015 AFR missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q6P179.141 ERAP2 HGNC 1 1.0 UPI0000036336 Q6P179-1 SNV ERAP2,missense_variant,p.R205H,ENST00000437043,NM_001130140.2&NM_022350.5,c.614G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;ERAP2,missense_variant,p.R205H,ENST00000379904,NM_001329229.1,c.614G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;ERAP2,missense_variant,p.R205H,ENST00000510373,,c.614G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ERAP2,missense_variant,p.R205H,ENST00000510309,NM_001329233.1,c.614G>A,MODERATE,,deleterious(0),probably_damaging(0.996),1;ERAP2,downstream_gene_variant,,ENST00000507346,,,MODIFIER,,,,1;ERAP2,missense_variant,p.R205H,ENST00000513084,,c.614G>A,MODERATE,,deleterious(0),probably_damaging(0.996),1;AC009126.1,intron_variant,,ENST00000501338,,n.1689-10452C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000655392,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000656950,,n.835-10452C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000659319,,n.835-10452C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000660209,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000660988,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000663822,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000665421,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000665723,,n.819-10158C>T,MODIFIER,,,,-1;AC009126.1,intron_variant,,ENST00000669694,,n.835-10452C>T,MODIFIER,YES,,,-1 764/5131 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.394e-05 0.0007399 0.0001166 0.0 0.0 4.623e-05 0.0 0.000164 9.876e-05 0.0002637520083226 0.0007786269998177 0.0 0.0002652519906405 0.0 0.0 0.0 oth 0.0009900990407913 0.0 1.5432100553880446e-05 0.0009900990407913 0.0 0 59 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ERAP2,missense_variant,p.R205H,ENST00000510309.1,c.614G>A,MODERATE,;ERAP2,missense_variant,p.R205H,ENST00000379904.8,c.614G>A,MODERATE,;ERAP2,missense_variant,p.R205H,ENST00000714228.1,c.614G>A,MODERATE,;ERAP2,missense_variant,NMD_transcript_variant,p.R205H,ENST00000513084.5,c.614G>A,MODERATE,;ERAP2,missense_variant,p.R205H,ENST00000437043.8,c.614G>A,MODERATE,YES;ERAP2,missense_variant,p.R205H,ENST00000508077.2,c.614G>A,MODERATE,;ERAP2,missense_variant,p.R205H,ENST00000510373.6,c.614G>A,MODERATE,;ENSG00000247121,intron_variant,,ENST00000669694.1,n.835-10452C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000665421.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000663822.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000660988.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000655392.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000659319.1,n.835-10452C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000656950.1,n.835-10452C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000660209.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000665723.1,n.819-10158C>T,MODIFIER,;ENSG00000247121,intron_variant,,ENST00000501338.5,n.1689-10452C>T,MODIFIER,YES +PCDHB7 56129 BI GRCh38 5 141174828 141174828 + missense_variant Missense_Mutation SNP G G A rs782528648 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 123 34 c.1993G>A p.Gly665Ser p.G665S ENST00000231137.6 NM_018940.4 665 Ggc/Agc 1/1 P1 A G/S protein_coding YES CCDS4249.1 1993/2382 TGGACGGCTTC COSM1434239 SMART:SM00112;PROSITE_profiles:PS50268;PANTHER:PTHR24028:SF69;PANTHER:PTHR24028 ENSP00000231137 1/1 rs782528648;COSV50799178;COSV99177125 ENST00000231137 Transcript ENSG00000113212 HGNC:8692 MODERATE NM_018940.4 6.541e-05 gnomAD_SAS missense_variant 0;1;1 probably_damaging(1) Unknown deleterious_low_confidence(0.01) 0;1;1 Q9Y5E2.157 PCDHB7 HGNC 1 UPI00001273E3 SNV PCDHB7,missense_variant,p.G665S,ENST00000231137,NM_018940.4,c.1993G>A,MODERATE,YES,deleterious_low_confidence(0.01),probably_damaging(1),1;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.5,,MODIFIER,YES,,,1;AC244517.11,intron_variant,,ENST00000624192,,n.73-37645C>T,MODIFIER,,,,-1;AC244517.8,upstream_gene_variant,,ENST00000623995,,,MODIFIER,YES,,,1;AC244517.2,upstream_gene_variant,,ENST00000624802,,,MODIFIER,,,,-1;AC244517.2,upstream_gene_variant,,ENST00000625128,,,MODIFIER,,,,-1 2185/3740 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.041e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.541e-05 6.7554801717051305e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002080730046145 0 225 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 157 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PCDHB7,missense_variant,p.G665S,ENST00000231137.6,c.1993G>A,MODERATE,YES;ENSG00000280029,intron_variant,,ENST00000624192.1,n.73-37645C>T,MODIFIER,YES +PCDHGA6 56109 BI GRCh38 5 141375181 141375181 + synonymous_variant Silent SNP C C T rs868598149 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 60 4 c.1098C>T p.Ile366= p.I366= ENST00000517434.3 NM_018919.3 366 atC/atT 1/4 P1 T I protein_coding YES CCDS54926.1 1098/2799 GTAATCGCCCT Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF107;Superfamily:SSF49313;CDD:cd11304 ENSP00000429601 1/4 rs868598149 ENST00000517434 Transcript ENSG00000253731 HGNC:8704 LOW NM_018919.3 synonymous_variant 1.0 Unknown Q9Y5G7.146 PCDHGA6 HGNC 1 1.0 UPI00000715C8 Q9Y5G7-1 SNV PCDHGA6,synonymous_variant,p.I366=,ENST00000610583,NM_032086.1,c.1098C>T,LOW,,,,1;PCDHGA6,synonymous_variant,p.I366=,ENST00000517434,NM_018919.3,c.1098C>T,LOW,YES,,,1;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.4,c.2424+28724C>T,MODIFIER,YES,,,1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.4,c.2424+33786C>T,MODIFIER,YES,,,1;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2,c.2421+42076C>T,MODIFIER,YES,,,1;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2,c.2421+8430C>T,MODIFIER,YES,,,1;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2,c.2421+12625C>T,MODIFIER,YES,,,1;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2,c.2409+22512C>T,MODIFIER,YES,,,1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.4,c.2514+17560C>T,MODIFIER,YES,,,1;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.5,c.2415+2372C>T,MODIFIER,YES,,,1;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.3,,MODIFIER,,,,1;PCDHGA3,intron_variant,,ENST00000612467,,c.*2003+28724C>T,MODIFIER,,,,1 1291/4794 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 64 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 64 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PCDHGA6,synonymous_variant,p.I366=,ENST00000610583.1,c.1098C>T,LOW,;PCDHGA6,synonymous_variant,p.I366=,ENST00000517434.3,c.1098C>T,LOW,YES;PCDHGB3,intron_variant,,ENST00000576222.2,c.2415+2372C>T,MODIFIER,YES;PCDHGA5,intron_variant,,ENST00000518069.2,c.2421+8430C>T,MODIFIER,YES;PCDHGB2,intron_variant,,ENST00000522605.2,c.2421+12625C>T,MODIFIER,YES;PCDHGA4,intron_variant,,ENST00000571252.3,c.2514+17560C>T,MODIFIER,YES;PCDHGB1,intron_variant,,ENST00000523390.2,c.2409+22512C>T,MODIFIER,YES;PCDHGA3,intron_variant,NMD_transcript_variant,,ENST00000612467.1,c.*2003+28724C>T,MODIFIER,;PCDHGA3,intron_variant,,ENST00000253812.8,c.2424+28724C>T,MODIFIER,YES;PCDHGA2,intron_variant,,ENST00000394576.3,c.2424+33786C>T,MODIFIER,YES;PCDHGA1,intron_variant,,ENST00000517417.3,c.2421+42076C>T,MODIFIER,YES +RBM22 55696 BI GRCh38 5 150695650 150695650 + missense_variant Missense_Mutation SNP C C T TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 72 44 c.602G>A p.Arg201His p.R201H ENST00000199814.9 NM_018047.3 201 cGt/cAt 7/11 P1 T R/H protein_coding YES CCDS34278.1 602/1263 AATAACGGTCT PDB-ENSP_mappings:5mqf.P;PDB-ENSP_mappings:5xjc.O;PDB-ENSP_mappings:5yzg.O;PDB-ENSP_mappings:5z56.O;PDB-ENSP_mappings:5z57.O;PDB-ENSP_mappings:6ff4.P;PDB-ENSP_mappings:6ff7.P;PDB-ENSP_mappings:6icz.O;PDB-ENSP_mappings:6id0.O;PDB-ENSP_mappings:6id1.O;PDB-ENSP_mappings:6qdv.M;PANTHER:PTHR14089:SF7;PANTHER:PTHR14089 ENSP00000199814 7/11 COSV52271021 ENST00000199814 Transcript ENSG00000086589 HGNC:25503 MODERATE NM_018047.3 missense_variant 1 1.0 probably_damaging(0.999) Unknown deleterious(0) 1 Q9NW64.174 RBM22 HGNC -1 1.0 UPI00000223D3 Q9NW64-1 SNV RBM22,missense_variant,p.R201H,ENST00000199814,NM_018047.3,c.602G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;RBM22,missense_variant,p.R152H,ENST00000447771,,c.455G>A,MODERATE,,deleterious(0),possibly_damaging(0.861),-1;RBM22,downstream_gene_variant,,ENST00000518917,,,MODIFIER,,,,-1;RBM22,downstream_gene_variant,,ENST00000521464,,,MODIFIER,,,,-1;RBM22,non_coding_transcript_exon_variant,,ENST00000522469,,n.663G>A,MODIFIER,,,,-1;RBM22,upstream_gene_variant,,ENST00000520132,,,MODIFIER,,,,-1;RBM22,downstream_gene_variant,,ENST00000521248,,,MODIFIER,,,,-1;RBM22,downstream_gene_variant,,ENST00000521594,,,MODIFIER,,,,-1 679/2299 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 134 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 116 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RBM22,non_coding_transcript_exon_variant,,ENST00000522469.5,n.663G>A,MODIFIER,;RBM22,missense_variant,p.R152H,ENST00000447771.6,c.455G>A,MODERATE,;RBM22,missense_variant,p.R201H,ENST00000199814.9,c.602G>A,MODERATE,YES +FAT2 2196 BI GRCh38 5 151512321 151512321 + missense_variant Missense_Mutation SNP C C T rs756607776 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 4 c.11749G>A p.Val3917Met p.V3917M ENST00000261800.6 NM_001447.3 3917 Gtg/Atg 21/24 P1 T V/M protein_coding YES CCDS4317.1 11749/13050 GACCACGACAG COSM3852889 Gene3D:2.60.120.200;Pfam:PF02210;PROSITE_profiles:PS50025;PANTHER:PTHR24026;PANTHER:PTHR24026:SF37;SMART:SM00282;Superfamily:SSF49899;CDD:cd00110 ENSP00000261800 20/23 rs756607776;COSV55816219 ENST00000261800 Transcript 1.0 ENSG00000086570 HGNC:3596 MODERATE 0.0001156 gnomAD_AMR missense_variant 0;1 1.0 benign(0.024) Unknown tolerated(0.28) 0;1 Q9NYQ8.181 FAT2 HGNC -1 1.0 UPI0000055B22 SNV FAT2,missense_variant,p.V3917M,ENST00000261800,NM_001447.2,c.11749G>A,MODERATE,YES,tolerated(0.28),benign(0.024),-1;FAT2,missense_variant,p.V690M,ENST00000520200,,c.2068G>A,MODERATE,,tolerated(0.17),benign(0.003),-1;AC011337.1,non_coding_transcript_exon_variant,,ENST00000606930,,n.2869C>T,MODIFIER,YES,,,1 11762/14534 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.785e-05 0.0 0.0001156 0.0 0.0001087 0.0 0.0 0.0 3.266e-05 1.3518299965653569e-05 0.0 0.0 6.622519867960364e-05 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 56 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000271795,non_coding_transcript_exon_variant,,ENST00000606930.1,n.2869C>T,MODIFIER,YES;FAT2,missense_variant,p.R689H,ENST00000520200.5,c.2066G>A,MODERATE,;FAT2,missense_variant,p.V3917M,ENST00000261800.6,c.11749G>A,MODERATE,YES +LARP1 23367 BI GRCh38 5 154793676 154793676 + missense_variant Missense_Mutation SNP G G A rs779864945 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 48 45 c.821G>A p.Arg274His p.R274H ENST00000518297.6 NM_033551.3 274 cGc/cAc 5/19 A2 A R/H protein_coding YES 821/3291 CACTCGCCCAC MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR22792:SF51;PANTHER:PTHR22792 ENSP00000428589 5/19 rs779864945 ENST00000518297 Transcript ENSG00000155506 HGNC:29531 MODERATE NM_033551.3 8.673e-05 gnomAD_AMR missense_variant 1.0 probably_damaging(0.959) Unknown deleterious(0.01) LARP1 HGNC 1 A0A0B4J210.44 5.0 UPI00004EA898 SNV LARP1,missense_variant,p.R274H,ENST00000518297,NM_033551.3&NM_001367718.1,c.821G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.959),1;LARP1,missense_variant,p.R197H,ENST00000336314,NM_001367714.1&NM_001367713.1&NM_001367716.1&NM_001367715.1&NM_015315.5&NM_001367717.1&NM_001367719.1,c.590G>A,MODERATE,,deleterious(0.01),probably_damaging(0.991),1;LARP1,missense_variant,p.R69H,ENST00000524248,,c.206G>A,MODERATE,,tolerated(0.12),probably_damaging(0.959),1;LARP1,missense_variant,p.R49H,ENST00000523163,,c.146G>A,MODERATE,,deleterious(0.02),probably_damaging(0.999),1;LARP1,missense_variant,p.R69H,ENST00000519931,,c.206G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.959),1;LARP1,missense_variant,p.R36H,ENST00000518194,,c.107G>A,MODERATE,,tolerated(0.07),probably_damaging(0.999),1;LARP1,downstream_gene_variant,,ENST00000517616,,,MODIFIER,,,,1;LARP1,upstream_gene_variant,,ENST00000518742,,,MODIFIER,,,,1;LARP1,3_prime_UTR_variant,,ENST00000521577,,c.*289G>A,MODIFIER,,,,1;LARP1,upstream_gene_variant,,ENST00000518595,,,MODIFIER,,,,1 1202/7181 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0 8.673e-05 0.0 5.437e-05 0.0 8.795e-06 0.0 0.0 6.762969860574231e-06 0.0 0.0 0.0 0.0 0.000202020004508 0.0 0.0 0.0 0.0 0.0 0 137 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 96 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LARP1,synonymous_variant,p.S35=,ENST00000518194.1,c.105G>A,LOW,;LARP1,missense_variant,p.R49H,ENST00000523163.5,c.146G>A,MODERATE,;LARP1,missense_variant,p.R69H,ENST00000685946.1,c.206G>A,MODERATE,;LARP1,missense_variant,p.R69H,ENST00000524248.5,c.206G>A,MODERATE,;LARP1,missense_variant,p.R69H,ENST00000519931.5,c.206G>A,MODERATE,;LARP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000521577.1,c.*289G>A,MODIFIER,;LARP1,missense_variant,p.R274H,ENST00000518297.6,c.821G>A,MODERATE,YES;LARP1,missense_variant,p.R69H,ENST00000690816.1,c.206G>A,MODERATE,;LARP1,missense_variant,p.R197H,ENST00000336314.9,c.590G>A,MODERATE,;LARP1,missense_variant,p.R69H,ENST00000687700.1,c.206G>A,MODERATE, +FGFR4 2264 BI GRCh38 5 177093430 177093430 + missense_variant Missense_Mutation SNP G G A rs55879131 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 49 16 c.1276G>A p.Gly426Ser p.G426S ENST00000292408.9 NM_213647.3 426 Ggc/Agc 10/18 0.0002 0.0 0.0 0.0 0.001 0.0 P4 A G/S protein_coding YES CCDS4410.1 1276/2409 CTTCCGGCAAG Low_complexity_(Seg):seg;PIRSF:PIRSF000628;PANTHER:PTHR24416:SF343;PANTHER:PTHR24416 ENSP00000292408 0.0 0.0001163 10/18 rs55879131 ENST00000292408 Transcript 1.0 ENSG00000160867 HGNC:3691 MODERATE NM_213647.3 0.001 EUR missense_variant 1.0 benign(0.015) Unknown tolerated(0.66) P22455.220 FGFR4 HGNC 1 1.0 UPI000012A72D P22455-1 SNV FGFR4,missense_variant,p.G426S,ENST00000292408,NM_213647.3&NM_002011.5&NM_001354984.2,c.1276G>A,MODERATE,YES,tolerated(0.66),benign(0.015),1;FGFR4,missense_variant,p.G426S,ENST00000502906,,c.1276G>A,MODERATE,,tolerated(0.66),benign(0.015),1;FGFR4,missense_variant,p.G386S,ENST00000393637,NM_022963.3,c.1156G>A,MODERATE,,tolerated(0.43),benign(0.103),1;FGFR4,missense_variant,p.G58S,ENST00000511076,,c.172G>A,MODERATE,,tolerated(0.46),benign(0.072),1;FGFR4,synonymous_variant,p.P374=,ENST00000393648,NM_001291980.2,c.1122G>A,LOW,,,,1;FGFR4,downstream_gene_variant,,ENST00000503708,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000510911,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000513166,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000514472,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000507708,,,MODIFIER,,,,1;FGFR4,non_coding_transcript_exon_variant,,ENST00000508139,,n.654G>A,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000426612,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000430285,,,MODIFIER,,,,1;FGFR4,upstream_gene_variant,,ENST00000483872,,,MODIFIER,,,,1;FGFR4,downstream_gene_variant,,ENST00000509511,,,MODIFIER,,,,1;FGFR4,upstream_gene_variant,,ENST00000513423,,,MODIFIER,,,,1 1492/3093 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.975e-05 0.0 8.675e-05 0.0 0.0 0.0 7.051e-05 0.0003259 6.533e-05 6.082230174797587e-05 2.4310800654347983e-05 0.0 6.622519867960364e-05 0.0 0.0 0.0 nfe 7.715570245636627e-05 0.0 7.715570245636627e-05 0.000494070991408 0.0002082470018649 0 90 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 66 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FGFR4,missense_variant,p.R57Q,ENST00000511076.1,c.170G>A,MODERATE,;FGFR4,non_coding_transcript_exon_variant,,ENST00000508139.1,n.654G>A,MODIFIER,;FGFR4,missense_variant,p.G386S,ENST00000393637.5,c.1156G>A,MODERATE,;FGFR4,missense_variant,p.G426S,ENST00000292408.9,c.1276G>A,MODERATE,YES;FGFR4,missense_variant,p.G426S,ENST00000502906.5,c.1276G>A,MODERATE,;FGFR4,synonymous_variant,p.P374=,ENST00000393648.6,c.1122G>A,LOW, +NSD1 64324 BI GRCh38 5 177210573 177210573 + missense_variant Missense_Mutation SNP C C T rs774810620 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 22 c.2174C>T p.Thr725Met p.T725M ENST00000439151.7 NM_022455.5 725 aCg/aTg 5/23 P4 T T/M protein_coding YES CCDS4412.1 2174/8091 CGAGACGTCTC PANTHER:PTHR22884;PANTHER:PTHR22884:SF312 ENSP00000395929 5/23 rs774810620;COSV61780019 ENST00000439151 Transcript 1.0 ENSG00000165671 HGNC:14234 MODERATE NM_022455.5 6.152e-05 gnomAD_AFR missense_variant 0;1 1.0 benign(0.003) Unknown tolerated_low_confidence(0.28) 0;1 Q96L73.187 NSD1 HGNC 1 1.0 UPI000006F9C6 Q96L73-1 SNV NSD1,missense_variant,p.T725M,ENST00000439151,NM_022455.5,c.2174C>T,MODERATE,YES,tolerated_low_confidence(0.28),benign(0.003),1;NSD1,missense_variant,p.T456M,ENST00000354179,NM_172349.2,c.1367C>T,MODERATE,,tolerated_low_confidence(0.28),benign(0.01),1;NSD1,missense_variant,p.T456M,ENST00000347982,NM_001365684.1,c.1367C>T,MODERATE,,tolerated_low_confidence(0.28),benign(0.01),1;NSD1,downstream_gene_variant,,ENST00000508896,,,MODIFIER,,,,1;NSD1,upstream_gene_variant,,ENST00000375350,,,MODIFIER,,,,1;NSD1,downstream_gene_variant,,ENST00000638627,,,MODIFIER,,,,1;NSD1,downstream_gene_variant,,ENST00000644863,,,MODIFIER,,,,1 2371/13042 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.386e-05 6.152e-05 0.0 0.0 5.438e-05 4.62e-05 1.759e-05 0.0 3.266e-05 2.7056999897467904e-05 7.299629942281172e-05 0.0 0.0 0.0 0.0 0.0 afr 7.299629942281172e-05 0.0 1.5433099179062992e-05 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 43 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NSD1,non_coding_transcript_exon_variant,,ENST00000688613.1,n.1571C>T,MODIFIER,;NSD1,non_coding_transcript_exon_variant,,ENST00000685206.1,n.1757C>T,MODIFIER,;NSD1,missense_variant,p.T622M,ENST00000687453.1,c.1865C>T,MODERATE,;NSD1,missense_variant,p.T434M,ENST00000347982.9,c.1301C>T,MODERATE,;NSD1,missense_variant,p.T434M,ENST00000689345.1,c.1301C>T,MODERATE,;NSD1,intron_variant,,ENST00000510954.6,n.612+6281C>T,MODIFIER,;NSD1,missense_variant,p.T725M,ENST00000439151.7,c.2174C>T,MODERATE,YES;NSD1,missense_variant,NMD_transcript_variant,p.T725M,ENST00000689326.1,c.2174C>T,MODERATE,;NSD1,missense_variant,p.T434M,ENST00000686993.1,c.1301C>T,MODERATE,;NSD1,missense_variant,p.T434M,ENST00000354179.9,c.1301C>T,MODERATE,;NSD1,non_coding_transcript_exon_variant,,ENST00000689549.1,n.2321C>T,MODIFIER,;NSD1,missense_variant,p.T434M,ENST00000508896.7,c.1301C>T,MODERATE, +FAM193B 54540 BI GRCh38 5 177531323 177531323 + intron_variant Intron SNP C C T rs763954713 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 11 8 c.1275+1120G>A ENST00000514747.6 NM_001190946.3 P1 T protein_coding YES CCDS54954.1 CCTGGCGCTGT ENSP00000422131 rs763954713 ENST00000514747 Transcript ENSG00000146067 HGNC:25524 MODIFIER 5/8 NM_001190946.3 0.000172 gnomAD_OTH intron_variant 1.0 Unknown Q96PV7.119 FAM193B HGNC -1 5.0 UPI0001D3BB6A Q96PV7-3 SNV FAM193B,missense_variant,p.A98T,ENST00000524677,NM_001366498.1&NM_001366499.1,c.292G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),-1;FAM193B,intron_variant,,ENST00000514747,NM_001190946.3&NM_001366500.1,c.1275+1120G>A,MODIFIER,YES,,,-1;FAM193B,intron_variant,,ENST00000508298,,n.470+1120G>A,MODIFIER,,,,-1;FAM193B,downstream_gene_variant,,ENST00000506064,,,MODIFIER,,,,-1;FAM193B,3_prime_UTR_variant,,ENST00000506955,,c.*2464G>A,MODIFIER,,,,-1;FAM193B,3_prime_UTR_variant,,ENST00000510479,,c.*761G>A,MODIFIER,,,,-1;FAM193B,3_prime_UTR_variant,,ENST00000510163,,c.*285G>A,MODIFIER,,,,-1;FAM193B,non_coding_transcript_exon_variant,,ENST00000513502,,n.512G>A,MODIFIER,,,,-1;FAM193B,downstream_gene_variant,,ENST00000515394,,,MODIFIER,,,,-1 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.265e-05 0.0 0.0 0.0 0.0 0.0 1.866e-05 0.000172 0.0 2.0327099264250137e-05 2.438669980620034e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.088989979005419e-05 0.0 3.088989979005419e-05 0.0 0.0 0 12 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 19 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FAM193B,intron_variant,,ENST00000508298.5,n.470+1120G>A,MODIFIER,;FAM193B,non_coding_transcript_exon_variant,,ENST00000513502.1,n.512G>A,MODIFIER,;FAM193B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000510163.5,c.*285G>A,MODIFIER,;FAM193B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000506955.5,c.*2464G>A,MODIFIER,;FAM193B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000510479.5,c.*761G>A,MODIFIER,;FAM193B,intron_variant,,ENST00000514747.6,c.1275+1120G>A,MODIFIER,YES;FAM193B,missense_variant,p.A492T,ENST00000524677.6,c.1474G>A,MODERATE, +ELOVL2 54898 BI GRCh38 6 10989828 10989828 + missense_variant Missense_Mutation SNP C C T rs202019761 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 26 7 c.640G>A p.Val214Met p.V214M ENST00000354666.4 NM_017770.4 214 Gtg/Atg 7/8 P1 T V/M protein_coding YES CCDS4518.1 640/891 GAGCACGAACT COSM1439750 Pfam:PF01151;PANTHER:PTHR11157;PANTHER:PTHR11157:SF16;HAMAP:MF_03202;Transmembrane_helices:TMhelix ENSP00000346693 7/8 rs202019761;COSV61156962 ENST00000354666 Transcript ENSG00000197977 HGNC:14416 MODERATE NM_017770.4 0.0002176 gnomAD_EAS missense_variant 0;1 1.0 possibly_damaging(0.656) Unknown tolerated(0.16) 0;1 Q9NXB9.144 ELOVL2 HGNC -1 A0A024QZV3.39 1.0 UPI0000051C66 SNV ELOVL2,missense_variant,p.V214M,ENST00000354666,NM_017770.4,c.640G>A,MODERATE,YES,tolerated(0.16),possibly_damaging(0.656),-1 715/3988 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.377e-05 0.0001847 2.892e-05 0.0 0.0002176 0.0 1.76e-05 0.0 3.267e-05 2.0291399778216143e-05 2.432730070722755e-05 0.0 0.0 0.0 0.0002021020045503 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 33 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ELOVL2,missense_variant,p.V214M,ENST00000354666.4,c.640G>A,MODERATE,YES +NCR3 259197 BI GRCh38 6 31589875 31589875 + stop_gained Nonsense_Mutation SNP G G A rs748321504 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 36 c.295C>T p.Arg99Ter p.R99* ENST00000340027.10 NM_147130.3 99 Cga/Tga 2/4 P4 A R/* protein_coding YES CCDS34397.1 295/606 GCCTCGCACGT COSM4706018;COSM4706019;COSM4706020 PDB-ENSP_mappings:3noi.A;PDB-ENSP_mappings:3noi.B;PDB-ENSP_mappings:3pv6.B;PROSITE_profiles:PS50835;CDD:cd00096;PANTHER:PTHR47904;Pfam:PF07686;Gene3D:2.60.40.10;SMART:SM00409;Superfamily:SSF48726 ENSP00000342156 2/4 rs748321504;COSV53000507;COSV99278988 ENST00000340027 Transcript 1.0 ENSG00000204475 HGNC:19077 HIGH NM_147130.3 3.292e-05 gnomAD_SAS stop_gained 0;1;1 1.0 Unknown 0;1;1 O14931.169 NCR3 HGNC -1 1.0 UPI0000073DEE O14931-1 SNV NCR3,stop_gained,p.R99*,ENST00000376073,NM_001145466.2,c.295C>T,HIGH,,,,-1;NCR3,stop_gained,p.R99*,ENST00000340027,NM_147130.3,c.295C>T,HIGH,YES,,,-1;NCR3,stop_gained,p.R99*,ENST00000376072,NM_001145467.2,c.295C>T,HIGH,,,,-1;NCR3,stop_gained,p.R74*,ENST00000376071,,c.220C>T,HIGH,,,,-1;LST1,downstream_gene_variant,,ENST00000211921,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000303757,NM_205840.2,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000339530,NM_205837.3,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376086,NM_001166538.1,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376089,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376090,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376092,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376093,NM_007161.3,,MODIFIER,YES,,,1;LST1,downstream_gene_variant,,ENST00000376096,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376099,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000376110,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000396101,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000396112,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000418507,NM_205838.3,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000433492,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000438075,NM_205839.3,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000464044,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000490742,,,MODIFIER,,,,1;NCR3,non_coding_transcript_exon_variant,,ENST00000491161,,n.355C>T,MODIFIER,,,,-1;NCR3,non_coding_transcript_exon_variant,,ENST00000495600,,n.47C>T,MODIFIER,,,,-1;LST1,downstream_gene_variant,,ENST00000419073,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000460834,,,MODIFIER,,,,1;LST1,downstream_gene_variant,,ENST00000464526,,,MODIFIER,,,,1 580/1063 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.216e-05 0.0 0.0 0.0 0.0 0.0 1.806e-05 0.0 3.292e-05 3.3787000575102866e-05 2.4299000870087184e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.171320274006575e-05 0.0 6.171320274006575e-05 0.0 0.0 0 93 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 79 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NCR3,stop_gained,p.R74*,ENST00000376071.4,c.220C>T,HIGH,;NCR3,stop_gained,p.R99*,ENST00000376072.7,c.295C>T,HIGH,;NCR3,non_coding_transcript_exon_variant,,ENST00000491161.1,n.355C>T,MODIFIER,;NCR3,non_coding_transcript_exon_variant,,ENST00000495600.5,n.47C>T,MODIFIER,;NCR3,stop_gained,p.R99*,ENST00000376073.8,c.295C>T,HIGH,;NCR3,stop_gained,p.R99*,ENST00000340027.10,c.295C>T,HIGH,YES +PRRC2A 7916 BI GRCh38 6 31625594 31625594 + missense_variant Missense_Mutation SNP G G A rs1258585778 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 16 c.742G>A p.Gly248Arg p.G248R ENST00000376007.8 NM_080686.3 248 Gga/Aga 7/31 P1 A G/R protein_coding CCDS4708.1 742/6474 ACCGCGGAATG PANTHER:PTHR14038;PANTHER:PTHR14038:SF5;Low_complexity_(Seg):seg ENSP00000365175 7/31 rs1258585778 ENST00000376007 Transcript ENSG00000204469 HGNC:13918 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant probably_damaging(0.989) Unknown deleterious(0.01) P48634.174 PRRC2A HGNC 1 A0A1U9X974.17 1.0 UPI000020E56F P48634-1 SNV PRRC2A,missense_variant,p.G248R,ENST00000376033,NM_004638.4,c.742G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.989),1;PRRC2A,missense_variant,p.G248R,ENST00000376007,NM_080686.3,c.742G>A,MODERATE,,deleterious(0.01),probably_damaging(0.989),1;SNORA38,downstream_gene_variant,,ENST00000363946,,,MODIFIER,YES,,,1;PRRC2A,non_coding_transcript_exon_variant,,ENST00000469577,,n.587G>A,MODIFIER,,,,1;PRRC2A,downstream_gene_variant,,ENST00000464079,,,MODIFIER,,,,1;PRRC2A,upstream_gene_variant,,ENST00000464890,,,MODIFIER,,,,1;PRRC2A,upstream_gene_variant,,ENST00000483470,,,MODIFIER,,,,1 944/6861 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.762969860574231e-06 2.4332099201274104e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PRRC2A,non_coding_transcript_exon_variant,,ENST00000469577.5,n.587G>A,MODIFIER,;PRRC2A,missense_variant,p.G248R,ENST00000376007.8,c.742G>A,MODERATE,;PRRC2A,missense_variant,p.G248R,ENST00000376033.3,c.742G>A,MODERATE,YES +LY6G6C 80740 BI GRCh38 6 31720137 31720137 + missense_variant Missense_Mutation SNP C C T rs761749993 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 15 c.119G>A p.Arg40His p.R40H ENST00000375819.3 NM_025261.3 40 cGc/cAc 2/3 P1 T R/H protein_coding YES CCDS4714.1 119/378 CCAGGCGGCAG PANTHER:PTHR32149;Superfamily:SSF57302 ENSP00000364978 2/3 rs761749993 ENST00000375819 Transcript ENSG00000204421 HGNC:13936 MODERATE NM_025261.3 6.595e-05 gnomAD_AFR missense_variant 1.0 benign(0.003) Unknown tolerated(0.08) O95867.149 LY6G6C HGNC -1 A0A1U9X7Z1.19 1.0 UPI0000048F36 SNV LY6G6C,missense_variant,p.R40H,ENST00000375819,NM_025261.3,c.119G>A,MODERATE,YES,tolerated(0.08),benign(0.003),-1;LY6G6C,5_prime_UTR_variant,,ENST00000495859,,c.-50G>A,MODIFIER,,,,-1;MPIG6B,upstream_gene_variant,,ENST00000375804,NM_138274.2,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000375805,NM_138273.2,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000375809,NM_025260.4,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000375810,NM_138277.2,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000375814,NM_138275.2,,MODIFIER,,,,1;LY6G6D,downstream_gene_variant,,ENST00000375824,,,MODIFIER,YES,,,1;LY6G6D,downstream_gene_variant,,ENST00000375825,NM_021246.2,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000480039,,,MODIFIER,,,,1;LY6G6F-LY6G6D,downstream_gene_variant,,ENST00000503322,NM_001353334.2,,MODIFIER,YES,,,1;MPIG6B,upstream_gene_variant,,ENST00000649779,NM_138272.3,,MODIFIER,YES,,,1;MPIG6B,intron_variant,,ENST00000460663,,n.90+1454C>T,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000466312,,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000471545,,,MODIFIER,,,,1;LY6G6D,downstream_gene_variant,,ENST00000479334,,,MODIFIER,,,,1;MPIG6B,upstream_gene_variant,,ENST00000485548,,,MODIFIER,,,,1 186/893 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.243e-05 6.595e-05 5.807e-05 0.0 0.0 4.626e-05 3.61e-05 0.0 0.0 2.0273300833650865e-05 4.8626301577314734e-05 0.0 0.0 0.0 0.0 0.0 afr 4.8626301577314734e-05 0.0 1.542830068501644e-05 0.0 0.0 0 73 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LY6G6C,missense_variant,p.R40H,ENST00000375819.3,c.119G>A,MODERATE,YES;LY6G6C,5_prime_UTR_variant,,ENST00000495859.1,c.-50G>A,MODIFIER,;MPIG6B,intron_variant,,ENST00000460663.5,n.90+1454C>T,MODIFIER, +TNXB 7148 BI GRCh38 6 32049283 32049283 + synonymous_variant Silent SNP G G A rs1239982151 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 5 c.9744C>T p.Thr3248= p.T3248= ENST00000644971.2 NM_019105.8 3248 acC/acT 28/44 P1 A T protein_coding YES 10485/13476 CCCACGGTGGA COSM1443480;COSM333044 Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR46708;PANTHER:PTHR46708:SF3;Superfamily:SSF49265;CDD:cd00063 ENSP00000497649 29/45 rs1239982151;COSV64478180 ENST00000647633 Transcript 1.0 ENSG00000168477 HGNC:11976 LOW synonymous_variant 0;1 1.0 Unknown 0;1 TNXB HGNC -1 A0A3B3ISX9.10 UPI000E6F2261 SNV TNXB,synonymous_variant,p.T3495=,ENST00000647633,,c.10485C>T,LOW,YES,,,-1;TNXB,synonymous_variant,p.T3248=,ENST00000375244,,c.9744C>T,LOW,,,,-1;TNXB,synonymous_variant,p.T3248=,ENST00000644971,NM_019105.8&NM_001365276.2,c.9744C>T,LOW,,,,-1;TNXB,synonymous_variant,p.T966=,ENST00000611016,,c.2898C>T,LOW,,,,-1;TNXB,upstream_gene_variant,,ENST00000451343,NM_032470.3,,MODIFIER,,,,-1;TNXB,upstream_gene_variant,,ENST00000490077,,,MODIFIER,,,,-1 10645/13831 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.7599498834169935e-06 2.431910070299637e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNXB,synonymous_variant,p.T3248=,ENST00000375244.7,c.9744C>T,LOW,;TNXB,synonymous_variant,p.T3495=,ENST00000647633.1,c.10485C>T,LOW,;TNXB,synonymous_variant,p.T3248=,ENST00000644971.2,c.9744C>T,LOW,YES +RPL10A 4736 BI GRCh38 6 35470194 35470194 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 4 c.326C>T p.Ala109Val p.A109V ENST00000322203.7 NM_007104.5 109 gCg/gTg 5/6 P1 T A/V protein_coding YES CCDS4806.1 326/654 TGATGCGTTTT PDB-ENSP_mappings:4ug0.Lz;PDB-ENSP_mappings:4v6x.Cz;PDB-ENSP_mappings:5aj0.Au;PDB-ENSP_mappings:5lks.Lz;PDB-ENSP_mappings:5t2c.l;PDB-ENSP_mappings:6ek0.Lz;PDB-ENSP_mappings:6ip5.2l;PDB-ENSP_mappings:6olg.Au;PDB-ENSP_mappings:6qzp.Lz;CDD:cd00403;PANTHER:PTHR23105;PANTHER:PTHR23105:SF107;PIRSF:PIRSF002155;Pfam:PF00687;Gene3D:3.30.190.20;Gene3D:3.40.50.790;Superfamily:SSF56808 ENSP00000363018 5/6 ENST00000322203 Transcript ENSG00000198755 HGNC:10299 MODERATE NM_007104.5 missense_variant 1.0 benign(0.045) Unknown tolerated(0.08) P62906.163 RPL10A HGNC 1 1.0 UPI0000025FC8 SNV RPL10A,missense_variant,p.A109V,ENST00000322203,NM_007104.5,c.326C>T,MODERATE,YES,tolerated(0.08),benign(0.045),1;FANCE,downstream_gene_variant,,ENST00000229769,NM_021922.3,,MODIFIER,YES,,,1;TEAD3,downstream_gene_variant,,ENST00000338863,NM_003214.4,,MODIFIER,YES,,,-1;TEAD3,downstream_gene_variant,,ENST00000639578,,,MODIFIER,,,,-1;MIR7111,upstream_gene_variant,,ENST00000619751,,,MODIFIER,YES,,,1;RPL10A,non_coding_transcript_exon_variant,,ENST00000467020,,n.706C>T,MODIFIER,,,,1;RPL10A,non_coding_transcript_exon_variant,,ENST00000464112,,n.700C>T,MODIFIER,,,,1;RPL10A,non_coding_transcript_exon_variant,,ENST00000478340,,n.599C>T,MODIFIER,,,,1;RPL10A,non_coding_transcript_exon_variant,,ENST00000490335,,n.414C>T,MODIFIER,,,,1;TEAD3,downstream_gene_variant,,ENST00000402886,,,MODIFIER,,,,-1;FANCE,downstream_gene_variant,,ENST00000648059,,,MODIFIER,,,,1 360/718 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RPL10A,non_coding_transcript_exon_variant,,ENST00000464112.5,n.700C>T,MODIFIER,;RPL10A,non_coding_transcript_exon_variant,,ENST00000478340.2,n.599C>T,MODIFIER,;RPL10A,non_coding_transcript_exon_variant,,ENST00000490335.4,n.414C>T,MODIFIER,;RPL10A,non_coding_transcript_exon_variant,,ENST00000467020.5,n.706C>T,MODIFIER,;RPL10A,missense_variant,p.A109V,ENST00000322203.7,c.326C>T,MODERATE,YES +CLPSL2 389383 BI GRCh38 6 35777538 35777538 + missense_variant Missense_Mutation SNP T T G novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 8 c.164T>G p.Phe55Cys p.F55C ENST00000403376.4 NM_207409.4 55 tTc/tGc 2/3 P1 G F/C protein_coding CCDS4810.2 164/303 AGCCTTCTGTG PROSITE_profiles:PS51342;PANTHER:PTHR10041:SF3;PANTHER:PTHR10041;Pfam:PF15083;Gene3D:2.10.80.10 ENSP00000385898 2/3 ENST00000403376 Transcript ENSG00000196748 HGNC:21250 MODERATE NM_207409.4 missense_variant probably_damaging(0.98) Unknown deleterious(0) Q6UWE3.107 CLPSL2 HGNC 1 1.0 UPI00015A355C Q6UWE3-1 SNV CLPSL2,missense_variant,p.F55C,ENST00000360454,NM_001286550.2,c.164T>G,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.98),1;CLPSL2,missense_variant,p.F55C,ENST00000403376,NM_207409.4,c.164T>G,MODERATE,,deleterious(0),probably_damaging(0.98),1;CLPSL1,upstream_gene_variant,,ENST00000373861,NM_001010886.5,,MODIFIER,YES,,,1;CLPSL2,non_coding_transcript_exon_variant,,ENST00000481904,,n.291T>G,MODIFIER,,,,1;CLPSL2,intron_variant,,ENST00000467122,,n.115+734T>G,MODIFIER,,,,1 185/426 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 45 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CLPSL2,intron_variant,,ENST00000467122.1,n.115+734T>G,MODIFIER,;CLPSL2,missense_variant,p.F55C,ENST00000360454.6,c.164T>G,MODERATE,;CLPSL2,missense_variant,p.F55C,ENST00000403376.4,c.164T>G,MODERATE,YES;CLPSL2,non_coding_transcript_exon_variant,,ENST00000481904.5,n.291T>G,MODIFIER, +GLP1R 2740 BI GRCh38 6 39085922 39085922 + missense_variant Missense_Mutation SNP G G A rs368940624 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 90 87 c.1241G>A p.Arg414Gln p.R414Q ENST00000373256.5 NM_002062.5 414 cGg/cAg 13/13 P1 A R/Q protein_coding YES CCDS4839.1 1241/1392 ATTTCGGAAGA COSM5748897 Gene3D:1.20.1070.10;PDB-ENSP_mappings:5nx2.A;PDB-ENSP_mappings:5vew.A;PDB-ENSP_mappings:5vew.B;PDB-ENSP_mappings:5vex.A;PDB-ENSP_mappings:5vex.B;PDB-ENSP_mappings:6b3j.R;PDB-ENSP_mappings:6kjv.A;PDB-ENSP_mappings:6kjv.B;PDB-ENSP_mappings:6kk1.A;PDB-ENSP_mappings:6kk1.B;PDB-ENSP_mappings:6kk7.A;PDB-ENSP_mappings:6kk7.B;PDB-ENSP_mappings:6ln2.A;PDB-ENSP_mappings:6orv.RP;PANTHER:PTHR45620;PANTHER:PTHR45620:SF25;Superfamily:SSF81321;CDD:cd15268 ENSP00000362353 0.0 0.0001163 13/13 rs368940624 ENST00000373256 Transcript ENSG00000112164 HGNC:4324 MODERATE NM_002062.5 0.0001163 EA missense_variant 1.0 benign(0.018) Unknown tolerated(0.43) P43220.191 GLP1R HGNC 1 1.0 UPI0000061F20 SNV GLP1R,missense_variant,p.R414Q,ENST00000373256,NM_002062.5,c.1241G>A,MODERATE,YES,tolerated(0.43),benign(0.018),1 1301/6682 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.033e-06 0.0 0.0 0.0 0.0 0.0 1.796e-05 0.0 0.0 3.382900104043074e-05 4.869970143772662e-05 0.0 0.0 0.0 0.0 0.0 afr 4.869970143772662e-05 0.0 4.6302000555442646e-05 0.0 0.0 0 198 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 178 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GLP1R,missense_variant,p.R414Q,ENST00000373256.5,c.1241G>A,MODERATE,YES +UNC5CL 222643 BI GRCh38 6 41033109 41033109 + missense_variant Missense_Mutation SNP C C T rs773255844 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 7 7 c.724G>A p.Glu242Lys p.E242K ENST00000244565.8 NM_173561.3 242 Gaa/Aaa 4/9 P1 T E/K protein_coding YES CCDS4847.1 724/1557 GGCTTCGCGCC COSM3873935 PANTHER:PTHR12582;PANTHER:PTHR12582:SF41;Gene3D:2.60.220.30 ENSP00000244565 4/9 rs773255844;COSV55112234;COSV99770864 ENST00000244565 Transcript ENSG00000124602 HGNC:21203 MODERATE NM_173561.3 0.0004395 gnomAD_AMR missense_variant 0;1;1 1.0 benign(0.003) Unknown tolerated(0.85) 0;1;1 Q8IV45.135 UNC5CL HGNC -1 H8YHX0.53 1.0 UPI00001609DB SNV UNC5CL,missense_variant,p.E242K,ENST00000244565,NM_173561.3,c.724G>A,MODERATE,YES,tolerated(0.85),benign(0.003),-1;UNC5CL,missense_variant,p.E242K,ENST00000373164,,c.724G>A,MODERATE,,tolerated(0.85),benign(0.003),-1;UNC5CL,upstream_gene_variant,,ENST00000470102,,,MODIFIER,,,,-1;OARD1,downstream_gene_variant,,ENST00000482853,,,MODIFIER,,,,-1 845/3156 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.945e-05 6.462e-05 0.0004395 0.0 0.0 0.0 2.7e-05 0.0 9.934e-05 1.351549963146681e-05 2.4301300072693263e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002082470018649 0 14 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 14 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS UNC5CL,missense_variant,p.E242K,ENST00000373164.1,c.724G>A,MODERATE,;UNC5CL,intron_variant,NMD_transcript_variant,,ENST00000714028.1,c.687-352G>A,MODIFIER,;UNC5CL,missense_variant,p.E242K,ENST00000244565.8,c.724G>A,MODERATE,YES +CUL7 9820 BI GRCh38 6 43043102 43043102 + missense_variant Missense_Mutation SNP C C T rs757432567 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 45 13 c.3434G>A p.Arg1145His p.R1145H ENST00000265348.9 NM_001374874.1 1145 cGc/cAc 18/26 P4 T R/H protein_coding CCDS4881.1 3434/5097 AACAGCGCGTC PANTHER:PTHR22771;PANTHER:PTHR22771:SF3;Pfam:PF00888 ENSP00000265348 18/26 rs757432567 ENST00000265348 Transcript 1.0 ENSG00000044090 HGNC:21024 MODERATE NM_014780.5 1.76e-05 gnomAD_NFE missense_variant benign(0.117) Unknown tolerated(0.07) Q14999.193 CUL7 HGNC -1 1.0 UPI000013D603 Q14999-1 SNV CUL7,missense_variant,p.R1177H,ENST00000674100,NM_001374872.1,c.3530G>A,MODERATE,,tolerated(0.07),benign(0.034),-1;CUL7,missense_variant,p.R1229H,ENST00000535468,,c.3686G>A,MODERATE,YES,tolerated(0.07),benign(0.034),-1;CUL7,missense_variant,p.R1177H,ENST00000674134,NM_001168370.2,c.3530G>A,MODERATE,,tolerated(0.07),benign(0.034),-1;CUL7,missense_variant,p.R1145H,ENST00000265348,NM_001374874.1&NM_014780.5&NM_001374873.1,c.3434G>A,MODERATE,,tolerated(0.07),benign(0.117),-1;CUL7,downstream_gene_variant,,ENST00000478630,,,MODIFIER,,,,-1;CUL7,missense_variant,p.R643H,ENST00000674112,,c.1928G>A,MODERATE,,tolerated(0.06),benign(0.04),-1;CUL7,missense_variant,p.R462H,ENST00000673725,,c.1385G>A,MODERATE,,tolerated(0.08),benign(0.037),-1;KLC4,5_prime_UTR_variant,,ENST00000467906,,c.-959C>T,MODIFIER,,,,1;CUL7,non_coding_transcript_exon_variant,,ENST00000673753,,n.4273G>A,MODIFIER,,,,-1 3672/5406 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.96e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 2.7045300157624297e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629199975170195e-05 0.0 4.629199975170195e-05 0.0 0.0002083330036839 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KLC4,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000467906.5,c.-959C>T,MODIFIER,;CUL7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000687225.1,c.*1731G>A,MODIFIER,;CUL7,non_coding_transcript_exon_variant,,ENST00000673753.1,n.4273G>A,MODIFIER,;CUL7,synonymous_variant,NMD_transcript_variant,p.A461=,ENST00000673725.1,c.1383G>A,LOW,;CUL7,non_coding_transcript_exon_variant,,ENST00000688302.1,n.3717G>A,MODIFIER,;CUL7,non_coding_transcript_exon_variant,,ENST00000686442.1,n.3995G>A,MODIFIER,;CUL7,missense_variant,p.R1177H,ENST00000674100.1,c.3530G>A,MODERATE,;CUL7,non_coding_transcript_exon_variant,,ENST00000478630.2,n.1505G>A,MODIFIER,;CUL7,missense_variant,NMD_transcript_variant,p.R1145H,ENST00000674112.2,c.3434G>A,MODERATE,;CUL7,missense_variant,p.R1177H,ENST00000674134.1,c.3530G>A,MODERATE,;CUL7,missense_variant,p.R1145H,ENST00000690231.1,c.3434G>A,MODERATE,;CUL7,non_coding_transcript_exon_variant,,ENST00000689256.1,n.4011G>A,MODIFIER,;CUL7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000685042.1,c.*90G>A,MODIFIER,;CUL7,missense_variant,p.R1145H,ENST00000265348.9,c.3434G>A,MODERATE,YES +TTBK1 84630 BI GRCh38 6 43283941 43283941 + synonymous_variant Silent SNP G G A rs376415608 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 8 c.3201G>A p.Ser1067= p.S1067= ENST00000259750.9 NM_032538.3 1067 tcG/tcA 14/15 P1 A S protein_coding YES CCDS34455.1 3201/3966 GGCTCGGAGCC MobiDB_lite:mobidb-lite ENSP00000259750 0.0009195 0.0 14/15 rs376415608 ENST00000259750 Transcript ENSG00000146216 HGNC:19140 LOW NM_032538.3 0.0009195 AA synonymous_variant 1.0 Unknown Q5TCY1.139 TTBK1 HGNC 1 1.0 UPI000041512B Q5TCY1-1 SNV TTBK1,synonymous_variant,p.S1067=,ENST00000259750,NM_032538.3,c.3201G>A,LOW,YES,,,1 3483/7130 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.451e-05 0.0005755 0.0 0.0 0.0 0.0 1.804e-05 0.0 0.0 0.0002163099998142 0.0007050809799693 0.0 0.0001987279974855 0.0 0.0 0.0 afr 0.0007050809799693 0.0 0.0 0.0 0.0 0 32 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 20 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TTBK1,synonymous_variant,p.S1067=,ENST00000259750.9,c.3201G>A,LOW,YES +PLA2G7 7941 BI GRCh38 6 46710550 46710550 + missense_variant Missense_Mutation SNP G G C novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 4 c.772C>G p.Leu258Val p.L258V ENST00000274793.12 NM_005084.4 258 Ctg/Gtg 8/12 P1 C L/V protein_coding YES CCDS4917.1 772/1326 CTTCAGTTGTT Gene3D:3.40.50.1820;PDB-ENSP_mappings:3d59.A;PDB-ENSP_mappings:3d59.B;PDB-ENSP_mappings:3d5e.A;PDB-ENSP_mappings:3d5e.B;PDB-ENSP_mappings:3f96.A;PDB-ENSP_mappings:3f96.B;PDB-ENSP_mappings:3f97.A;PDB-ENSP_mappings:3f97.B;PDB-ENSP_mappings:3f98.A;PDB-ENSP_mappings:3f98.B;PDB-ENSP_mappings:3f98.C;PDB-ENSP_mappings:3f9c.A;PDB-ENSP_mappings:3f9c.B;PDB-ENSP_mappings:5i8p.A;PDB-ENSP_mappings:5i8p.B;PDB-ENSP_mappings:5i9i.A;PDB-ENSP_mappings:5i9i.B;PDB-ENSP_mappings:5jad.A;PDB-ENSP_mappings:5jah.A;PDB-ENSP_mappings:5jal.A;PDB-ENSP_mappings:5jan.A;PDB-ENSP_mappings:5jao.A;PDB-ENSP_mappings:5jap.A;PDB-ENSP_mappings:5jar.A;PDB-ENSP_mappings:5jas.A;PDB-ENSP_mappings:5jat.A;PDB-ENSP_mappings:5jau.A;PDB-ENSP_mappings:5lp1.A;PDB-ENSP_mappings:5lyy.A;PDB-ENSP_mappings:5lz2.A;PDB-ENSP_mappings:5lz4.A;PDB-ENSP_mappings:5lz5.A;PDB-ENSP_mappings:5lz7.A;PDB-ENSP_mappings:5lz8.A;PDB-ENSP_mappings:5lz9.A;PDB-ENSP_mappings:5ye7.A;PDB-ENSP_mappings:5ye7.B;PDB-ENSP_mappings:5ye8.A;PDB-ENSP_mappings:5ye8.B;PDB-ENSP_mappings:5ye9.A;PDB-ENSP_mappings:5ye9.B;PDB-ENSP_mappings:5yea.A;PDB-ENSP_mappings:5yea.B;Pfam:PF03403;PIRSF:PIRSF018169;PANTHER:PTHR10272;PANTHER:PTHR10272:SF12;Superfamily:SSF53474 ENSP00000274793 8/12 ENST00000274793 Transcript 1.0 ENSG00000146070 HGNC:9040 MODERATE NM_005084.4 missense_variant 1.0 probably_damaging(0.951) Unknown deleterious(0.02) Q13093.183 PLA2G7 HGNC -1 1.0 UPI000002FED1 SNV PLA2G7,missense_variant,p.L258V,ENST00000274793,NM_005084.4,c.772C>G,MODERATE,YES,deleterious(0.02),probably_damaging(0.951),-1;PLA2G7,missense_variant,p.L258V,ENST00000537365,NM_001168357.1,c.772C>G,MODERATE,,deleterious(0.02),probably_damaging(0.951),-1 1002/1915 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 58 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLA2G7,missense_variant,p.L258V,ENST00000537365.1,c.772C>G,MODERATE,;PLA2G7,missense_variant,p.L258V,ENST00000274793.12,c.772C>G,MODERATE,YES +FUT9 10690 BI GRCh38 6 96203487 96203487 + missense_variant Missense_Mutation SNP G G A rs765684352 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 11 c.332G>A p.Arg111Gln p.R111Q ENST00000302103.6 NM_006581.4 111 cGa/cAa 3/3 P1 A R/Q protein_coding YES CCDS5033.1 332/1080 TCACCGAGACA COSM1082692 PANTHER:PTHR11929:SF201;PANTHER:PTHR11929;Pfam:PF17039;Superfamily:SSF53756 ENSP00000302599 3/3 rs765684352;COSV56142633;COSV56148853 ENST00000302103 Transcript ENSG00000172461 HGNC:4020 MODERATE NM_006581.4 2.911e-05 gnomAD_AMR missense_variant 0;1;1 1.0 probably_damaging(0.99) Unknown deleterious(0.01) 0;1;1 Q9Y231.149 FUT9 HGNC 1 1.0 UPI000013E792 SNV FUT9,missense_variant,p.R111Q,ENST00000302103,NM_006581.4,c.332G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.99),1;UFL1-AS1,intron_variant,,ENST00000658843,,n.298-472C>T,MODIFIER,YES,,,-1;UFL1-AS1,intron_variant,,ENST00000662501,,n.394-472C>T,MODIFIER,,,,-1 668/12793 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.209e-05 0.0 2.911e-05 0.0 0.0 0.0 1.785e-05 0.0 0.0 0 58 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 39 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS UFL1-AS1,intron_variant,,ENST00000662501.1,n.394-472C>T,MODIFIER,;UFL1-AS1,intron_variant,,ENST00000658843.2,n.302-472C>T,MODIFIER,YES;FUT9,missense_variant,p.R111Q,ENST00000302103.6,c.332G>A,MODERATE,YES +ASCC3 10973 BI GRCh38 6 100627948 100627948 + missense_variant Missense_Mutation SNP C C T rs1051651433 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 7 c.4415G>A p.Arg1472Gln p.R1472Q ENST00000369162.7 NM_006828.4 1472 cGa/cAa 28/42 P1 T R/Q protein_coding YES CCDS5046.1 4415/6609 TTGTTCGAGAT PROSITE_profiles:PS51192;CDD:cd18022;PANTHER:PTHR24075;PANTHER:PTHR24075:SF6;Gene3D:3.40.50.300;Pfam:PF00270;PIRSF:PIRSF039073;SMART:SM00382;SMART:SM00487;Superfamily:SSF52540 ENSP00000358159 28/42 rs1051651433;COSV64978721 ENST00000369162 Transcript 1.0 ENSG00000112249 HGNC:18697 MODERATE NM_006828.4 3.267e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q8N3C0.172 ASCC3 HGNC -1 5.0 UPI000014145A Q8N3C0-1 SNV ASCC3,missense_variant,p.R1472Q,ENST00000369162,NM_006828.4,c.4415G>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1 4725/8111 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.983e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.267e-05 3.388540062587708e-05 0.0 0.0 0.0001332620013272 0.0 0.0 0.0 oth 0.0009950250387191 0.0 1.5446899851667695e-05 0.0009950250387191 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ASCC3,missense_variant,p.R1472Q,ENST00000369162.7,c.4415G>A,MODERATE,YES +BEND3 57673 BI GRCh38 6 107069150 107069150 + missense_variant Missense_Mutation SNP G G A rs1554231348 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 7 c.2041C>T p.Arg681Trp p.R681W ENST00000369042.6 NM_001367314.1 681 Cgg/Tgg 4/4 P1 A R/W protein_coding CCDS34507.1 2041/2487 CTCCCGGAACC COSM5935079 PANTHER:PTHR28665;Low_complexity_(Seg):seg ENSP00000358038 4/4 rs1554231348;COSV64682505 ENST00000369042 Transcript ENSG00000178409 HGNC:23040 MODERATE NM_001367314.1 6.537e-05 gnomAD_SAS missense_variant 0;1 possibly_damaging(0.727) Unknown deleterious(0) 0;1 Q5T5X7.122 BEND3 HGNC -1 5.0 UPI00001D80D7 SNV BEND3,missense_variant,p.R681W,ENST00000429433,NM_001080450.2,c.2041C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.727),-1;BEND3,missense_variant,p.R681W,ENST00000369042,NM_001367314.1,c.2041C>T,MODERATE,,deleterious(0),possibly_damaging(0.727),-1 2478/6446 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.618e-05 0.0 0.0 0.0 0.0 4.624e-05 8.992e-06 0.0 6.537e-05 0 43 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 39 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BEND3,missense_variant,p.R681W,ENST00000429433.3,c.2041C>T,MODERATE,;BEND3,missense_variant,p.R681W,ENST00000369042.6,c.2041C>T,MODERATE,YES +FOXO3 2309 BI GRCh38 6 108664358 108664358 + missense_variant Missense_Mutation SNP G G A rs535867091 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 11 c.1525G>A p.Val509Met p.V509M ENST00000343882.10 NM_201559.3 509 Gtg/Atg 3/4 0.0016 0.0061 0.0 0.0 0.0 0.0 P1 A V/M protein_coding YES CCDS5068.1 1525/2022 GGAACGTGATG Pfam:PF16675;PANTHER:PTHR45767;PANTHER:PTHR45767:SF4 ENSP00000339527 3/4 rs535867091;COSV59630425 ENST00000343882 Transcript 1.0 ENSG00000118689 HGNC:3821 MODERATE 0.0061 AFR missense_variant 0;1 1.0 benign(0.227) Unknown tolerated(0.14) 0;1 O43524.216 FOXO3 HGNC 1 1.0 UPI000012ADEA O43524-1 SNV FOXO3,missense_variant,p.V509M,ENST00000343882,NM_201559.3,c.1525G>A,MODERATE,YES,tolerated(0.14),benign(0.227),1;FOXO3,missense_variant,p.V509M,ENST00000406360,NM_001455.4,c.1525G>A,MODERATE,,tolerated(0.14),benign(0.227),1;FOXO3,missense_variant,p.V289M,ENST00000540898,,c.865G>A,MODERATE,,tolerated(0.28),benign(0.227),1 1829/7308 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.609e-05 0.0004506 0.0 0.0 0.0 0.0 0.0 0.0 6.537e-05 8.133280061883852e-05 0.0002927969908341 0.0 0.0 0.0 0.0 0.0 afr 0.0002927969908341 0.0 0.0 0.0 0.0 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FOXO3,missense_variant,p.V289M,ENST00000540898.1,c.865G>A,MODERATE,;FOXO3,missense_variant,p.V509M,ENST00000406360.2,c.1525G>A,MODERATE,YES;FOXO3,missense_variant,p.V509M,ENST00000343882.10,c.1525G>A,MODERATE, +MFSD4B 91749 BI GRCh38 6 111262351 111262351 + intron_variant Intron SNP G G A rs200995803 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 136 62 c.27+2624G>A ENST00000368847.5 A protein_coding GGGTCGTGCCT ENSP00000357840 rs200995803;COSV64348666 ENST00000368847 Transcript ENSG00000173214 HGNC:21053 MODIFIER 1/1 6.534e-05 gnomAD_SAS intron_variant 0;1 Unknown 0;1 MFSD4B HGNC 1 A0A5K1VW69.2 1.0 UPI001235ACBD SNV MFSD4B,missense_variant,p.R41H,ENST00000671876,NM_153369.4,c.122G>A,MODERATE,,deleterious(0),probably_damaging(1),1;MFSD4B,missense_variant,p.R41H,ENST00000672554,,c.122G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.804),1;MFSD4B,missense_variant,p.R41H,ENST00000673024,,c.122G>A,MODERATE,,deleterious(0),possibly_damaging(0.804),1;MFSD4B,5_prime_UTR_variant,,ENST00000672303,,c.-53G>A,MODIFIER,,,,1;MFSD4B,intron_variant,,ENST00000368847,,c.27+2624G>A,MODIFIER,,,,1;MFSD4B,missense_variant,p.R41H,ENST00000671883,,c.122G>A,MODERATE,,deleterious(0),probably_damaging(1),1;MFSD4B,missense_variant,p.R41H,ENST00000672750,,c.122G>A,MODERATE,,deleterious(0),probably_damaging(1),1;MFSD4B,missense_variant,p.R41H,ENST00000672191,,c.122G>A,MODERATE,,deleterious(0),probably_damaging(1),1;AL360227.1,upstream_gene_variant,,ENST00000425364,,,MODIFIER,YES,,,-1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.954e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.534e-05 6.759500138286967e-06 2.431910070299637e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 199 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 198 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MFSD4B,missense_variant,NMD_transcript_variant,p.R41H,ENST00000671883.1,c.122G>A,MODERATE,;MFSD4B,missense_variant,p.R41H,ENST00000673024.1,c.122G>A,MODERATE,;MFSD4B,missense_variant,p.R41H,ENST00000672554.1,c.122G>A,MODERATE,;MFSD4B,intron_variant,,ENST00000368847.5,c.27+2624G>A,MODIFIER,;MFSD4B,missense_variant,NMD_transcript_variant,p.R41H,ENST00000672191.1,c.122G>A,MODERATE,;MFSD4B,missense_variant,p.R41H,ENST00000671876.2,c.122G>A,MODERATE,YES;MFSD4B,missense_variant,NMD_transcript_variant,p.R41H,ENST00000672750.1,c.122G>A,MODERATE,;MFSD4B,5_prime_UTR_variant,,ENST00000672303.1,c.-53G>A,MODIFIER, +MAN1A1 4121 BI GRCh38 6 119188411 119188411 + synonymous_variant Silent SNP G G A rs1227429309 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 82 13 c.1713C>T p.Ala571= p.A571= ENST00000368468.4 NM_005907.4 571 gcC/gcT 11/13 P1 A A protein_coding YES CCDS5122.1 1713/1962 TCTACGGCTTC PANTHER:PTHR11742:SF31;PANTHER:PTHR11742;Gene3D:1.50.10.10;Pfam:PF01532;Superfamily:SSF48225 ENSP00000357453 11/13 rs1227429309 ENST00000368468 Transcript ENSG00000111885 HGNC:6821 LOW NM_005907.4 synonymous_variant 1.0 Unknown P33908.181 MAN1A1 HGNC -1 2.0 UPI000013D632 P33908-1 SNV MAN1A1,synonymous_variant,p.A571=,ENST00000368468,NM_005907.4,c.1713C>T,LOW,YES,,,-1 2155/5018 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.764530098735122e-06 0.0 0.0 0.0 0.0 0.0 9.451799996895716e-05 0.0 0.0 0.0 0.0 0 100 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 95 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAN1A1,synonymous_variant,p.A571=,ENST00000368468.4,c.1713C>T,LOW,YES +GJA1 2697 BI GRCh38 6 121447580 121447580 + missense_variant Missense_Mutation SNP G G A rs367628979 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 7 c.733G>A p.Asp245Asn p.D245N ENST00000282561.4 NM_000165.5 245 Gac/Aac 2/2 P1 A D/N protein_coding YES CCDS5123.1 733/1149 AGAGCGACCCT PDB-ENSP_mappings:2ll2.A;PANTHER:PTHR11984;PANTHER:PTHR11984:SF33 ENSP00000282561 0.0 0.0001163 2/2 rs367628979;COSV56999590 ENST00000282561 Transcript 1.0 ENSG00000152661 HGNC:4274 MODERATE NM_000165.5 0.0001163 EA missense_variant 0;1 1.0 benign(0.003) Unknown tolerated(0.63) 0;1 P17302.240 GJA1 HGNC 1 A0A654IBU3.1 1.0 UPI000013DCEC SNV GJA1,missense_variant,p.D245N,ENST00000282561,NM_000165.5,c.733G>A,MODERATE,YES,tolerated(0.63),benign(0.003),1;GJA1,missense_variant,p.D245N,ENST00000649003,,c.733G>A,MODERATE,,tolerated(0.63),benign(0.003),1;GJA1,missense_variant,p.D245N,ENST00000650427,,c.733G>A,MODERATE,,tolerated(0.63),benign(0.003),1;GJA1,missense_variant,p.D245N,ENST00000647564,,c.733G>A,MODERATE,,tolerated(0.63),benign(0.003),1 936/3083 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GJA1,missense_variant,p.D245N,ENST00000647564.1,c.733G>A,MODERATE,;GJA1,missense_variant,p.D245N,ENST00000650427.1,c.733G>A,MODERATE,;GJA1,missense_variant,p.D245N,ENST00000282561.4,c.733G>A,MODERATE,YES;GJA1,missense_variant,p.D245N,ENST00000649003.1,c.733G>A,MODERATE, +SLC18B1 116843 BI GRCh38 6 132773014 132773014 + missense_variant Missense_Mutation SNP G G A rs573567211 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 7 c.1064C>T p.Pro355Leu p.P355L ENST00000275227.9 NM_052831.3 355 cCg/cTg 10/14 0.0002 0.0008 0.0 0.0 0.0 0.0 P2 A P/L protein_coding YES CCDS5163.1 1064/1371 TTTCCGGGAAA PROSITE_profiles:PS50850;CDD:cd17385;PANTHER:PTHR23506;PANTHER:PTHR23506:SF26;Gene3D:1.20.1250.20;Pfam:PF07690;Superfamily:SSF103473 ENSP00000275227 10/14 rs573567211;COSV99259120 ENST00000275227 Transcript ENSG00000146409 HGNC:21573 MODERATE NM_052831.3 0.0008 AFR missense_variant 0;1 1.0 possibly_damaging(0.781) Unknown tolerated(0.08) 0;1 Q6NT16.133 SLC18B1 HGNC -1 1.0 UPI000013DA50 SNV SLC18B1,missense_variant,p.P355L,ENST00000275227,NM_052831.3,c.1064C>T,MODERATE,YES,tolerated(0.08),possibly_damaging(0.781),-1;SLC18B1,missense_variant,p.P308L,ENST00000650278,,c.923C>T,MODERATE,,tolerated(0.1),possibly_damaging(0.781),-1;SLC18B1,missense_variant,p.P282L,ENST00000647932,,c.845C>T,MODERATE,,tolerated(0.1),possibly_damaging(0.781),-1;SLC18B1,downstream_gene_variant,,ENST00000367918,,,MODIFIER,,,,-1;SLC18B1,missense_variant,p.P308L,ENST00000650298,,c.923C>T,MODERATE,,deleterious(0.02),benign(0.019),-1;SLC18B1,3_prime_UTR_variant,,ENST00000650136,,c.*917C>T,MODIFIER,,,,-1 1245/2452 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.983e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0001633 0.0 4.7357498260680586e-05 0.0 0.0 0.0 0.0 0.0002021020045503 0.0 nfe 7.716529944445938e-05 0.0 7.716529944445938e-05 0.0 0.0002086809981847 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC18B1,missense_variant,NMD_transcript_variant,p.P308L,ENST00000650298.1,c.923C>T,MODERATE,;SLC18B1,missense_variant,p.P282L,ENST00000647932.1,c.845C>T,MODERATE,;SLC18B1,missense_variant,p.P308L,ENST00000650278.1,c.923C>T,MODERATE,;SLC18B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000650136.1,c.*917C>T,MODIFIER,;SLC18B1,missense_variant,p.P355L,ENST00000275227.9,c.1064C>T,MODERATE,YES +AHI1 54806 BI GRCh38 6 135457660 135457660 + stop_gained Nonsense_Mutation SNP G G A rs201391050 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 51 43 c.985C>T p.Arg329Ter p.R329* ENST00000265602.11 NM_001134831.2 329 Cga/Tga 9/29 P1 A R/* protein_coding YES CCDS47483.1 985/3591 pathogenic ATCTCGGCTTG PANTHER:PTHR44499 ENSP00000265602 9/29 rs201391050;CM080032 ENST00000265602 Transcript 1.0 ENSG00000135541 HGNC:21575 HIGH NM_001134831.2 8.853e-06 gnomAD_NFE stop_gained 1;1 1.0 21937992 Unknown Q8N157.162 AHI1 HGNC -1 1.0 UPI00000701FB Q8N157-1 SNV AHI1,stop_gained,p.R329*,ENST00000265602,NM_001134831.2&NM_001350503.1&NM_001350504.1,c.985C>T,HIGH,YES,,,-1;AHI1,stop_gained,p.R329*,ENST00000367800,NM_001134830.1,c.985C>T,HIGH,,,,-1;AHI1,stop_gained,p.R329*,ENST00000457866,NM_017651.4,c.985C>T,HIGH,,,,-1;AHI1,stop_gained,p.R329*,ENST00000327035,NM_001134832.1,c.985C>T,HIGH,,,,-1;AHI1,stop_gained,p.R329*,ENST00000531788,,c.985C>T,HIGH,,,,-1 1344/6063 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.013e-06 0.0 0.0 0.0 0.0 0.0 8.853e-06 0.0 0.0 1.353859988739714e-05 0.0 0.0 0.0 0.0 0.000201938993996 0.0 0.0 1.543829966976773e-05 0.0 0.0 0 85 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 94 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AHI1,intron_variant,NMD_transcript_variant,,ENST00000681477.1,c.932-1734C>T,MODIFIER,;AHI1,stop_gained,p.R329*,ENST00000327035.10,c.985C>T,HIGH,;AHI1,non_coding_transcript_exon_variant,,ENST00000681945.1,n.1489C>T,MODIFIER,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000531788.5,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680184.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680278.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680656.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R13*,ENST00000367799.7,c.37C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679622.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000681670.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000681756.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000679450.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000681301.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000681488.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679943.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679434.1,c.985C>T,HIGH,;AHI1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000679589.1,c.*1013C>T,MODIFIER,;AHI1,stop_gained,p.R329*,ENST00000681340.1,c.985C>T,HIGH,;AHI1,intron_variant,NMD_transcript_variant,,ENST00000681860.1,c.931+5465C>T,MODIFIER,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680119.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679742.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000457866.6,c.985C>T,HIGH,;AHI1,non_coding_transcript_exon_variant,,ENST00000680561.1,n.3728C>T,MODIFIER,;AHI1,stop_gained,p.R329*,ENST00000679925.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680840.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000681828.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000681718.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679668.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000679672.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000367800.8,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000265602.11,c.985C>T,HIGH,YES;AHI1,stop_gained,p.R329*,ENST00000681365.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680965.1,c.985C>T,HIGH,;AHI1,non_coding_transcript_exon_variant,,ENST00000681332.1,n.1502C>T,MODIFIER,;AHI1,stop_gained,p.R329*,ENST00000681841.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000681522.1,c.985C>T,HIGH,;AHI1,stop_gained,p.R329*,ENST00000681022.1,c.985C>T,HIGH,;AHI1,stop_gained,NMD_transcript_variant,p.R329*,ENST00000680826.1,c.985C>T,HIGH, +MAP3K5 4217 BI GRCh38 6 136567725 136567725 + missense_variant Missense_Mutation SNP C C T rs766760055 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 5 c.3667G>A p.Val1223Met p.V1223M ENST00000359015.5 NM_005923.4 1223 Gtg/Atg 26/30 P1 T V/M protein_coding YES CCDS5179.1 3667/4125 GCTCACGCCTG COSM3015423 Low_complexity_(Seg):seg;PANTHER:PTHR11584:SF332;PANTHER:PTHR11584 ENSP00000351908 26/30 rs766760055;COSV62886601 ENST00000359015 Transcript ENSG00000197442 HGNC:6857 MODERATE NM_005923.4 0.0001632 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.994) Unknown tolerated(0.26) 0;1 Q99683.210 MAP3K5 HGNC -1 1.0 UPI000012EAD5 Q99683-1 SNV MAP3K5,missense_variant,p.V1223M,ENST00000359015,NM_005923.4,c.3667G>A,MODERATE,YES,tolerated(0.26),probably_damaging(0.994),-1 3987/5157 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.186e-05 0.0 0.0 0.0 0.0001632 0.0 3.522e-05 0.0 3.267e-05 6.760779797332361e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 40 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAP3K5,missense_variant,p.V1332M,ENST00000698928.1,c.3994G>A,MODERATE,;MAP3K5,missense_variant,p.V1223M,ENST00000359015.5,c.3667G>A,MODERATE,YES +UTRN 7402 BI GRCh38 6 144493451 144493451 + missense_variant Missense_Mutation SNP G G A rs771082025 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 9 19 c.4588G>A p.Ala1530Thr p.A1530T ENST00000367545.8 NM_007124.2 1530 Gca/Aca 32/74 P1 A A/T protein_coding YES CCDS34547.1 4588/10302 TGGGCGCACAG PIRSF:PIRSF002341;PANTHER:PTHR12268;PANTHER:PTHR12268:SF15;SMART:SM00150;Superfamily:SSF46966 ENSP00000356515 32/74 rs771082025;COSV100839462 ENST00000367545 Transcript ENSG00000152818 HGNC:12635 MODERATE 3.269e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1 P46939.204 UTRN HGNC 1 5.0 UPI00003673F1 P46939-1 SNV UTRN,missense_variant,p.A1530T,ENST00000367545,NM_007124.2,c.4588G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),1 4588/12339 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.979e-06 0.0 0.0 0.0 0.0 0.0 8.835e-06 0.0 3.269e-05 1.3525899703381585e-05 2.4330900487257168e-05 0.0 6.632180156884715e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 41 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS UTRN,missense_variant,p.A1530T,ENST00000367545.8,c.4588G>A,MODERATE,YES +ESR1 2099 BI GRCh38 6 152011743 152011743 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 57 52 c.1184C>T p.Ser395Phe p.S395F ENST00000206249.8 NM_001291230.2 395 tCc/tTc 5/8 P1 T S/F protein_coding CCDS5234.1 1184/1788 GCGCTCCATGG 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SP_mappings:5t97.A;PDB-ENSP_mappings:5t97.B;PDB-ENSP_mappings:5tld.A;PDB-ENSP_mappings:5tld.B;PDB-ENSP_mappings:5tlf.A;PDB-ENSP_mappings:5tlf.B;PDB-ENSP_mappings:5tlg.A;PDB-ENSP_mappings:5tlg.B;PDB-ENSP_mappings:5tll.A;PDB-ENSP_mappings:5tll.B;PDB-ENSP_mappings:5tlm.A;PDB-ENSP_mappings:5tlm.B;PDB-ENSP_mappings:5tlo.A;PDB-ENSP_mappings:5tlo.B;PDB-ENSP_mappings:5tlp.A;PDB-ENSP_mappings:5tlp.B;PDB-ENSP_mappings:5tlt.A;PDB-ENSP_mappings:5tlt.B;PDB-ENSP_mappings:5tlu.A;PDB-ENSP_mappings:5tlu.B;PDB-ENSP_mappings:5tlv.A;PDB-ENSP_mappings:5tlv.B;PDB-ENSP_mappings:5tlx.A;PDB-ENSP_mappings:5tlx.B;PDB-ENSP_mappings:5tly.A;PDB-ENSP_mappings:5tly.B;PDB-ENSP_mappings:5tm1.A;PDB-ENSP_mappings:5tm1.B;PDB-ENSP_mappings:5tm2.A;PDB-ENSP_mappings:5tm2.B;PDB-ENSP_mappings:5tm3.A;PDB-ENSP_mappings:5tm3.B;PDB-ENSP_mappings:5tm4.A;PDB-ENSP_mappings:5tm4.B;PDB-ENSP_mappings:5tm5.A;PDB-ENSP_mappings:5tm5.B;PDB-ENSP_mappings:5tm6.A;PDB-ENSP_mappings:5tm6.B;PDB-ENSP_mappings:5tm7.A;PDB-ENSP_mappings:5tm7.B;PDB-ENSP_mappings:5tm8.A;PDB-ENSP_mappings:5tm8.B;PDB-ENSP_mappings:5tm9.A;PDB-ENSP_mappings:5tm9.B;PDB-ENSP_mappings:5tml.A;PDB-ENSP_mappings:5tml.B;PDB-ENSP_mappings:5tmm.A;PDB-ENSP_mappings:5tmm.B;PDB-ENSP_mappings:5tmo.A;PDB-ENSP_mappings:5tmo.B;PDB-ENSP_mappings:5tmq.A;PDB-ENSP_mappings:5tmq.B;PDB-ENSP_mappings:5tmr.A;PDB-ENSP_mappings:5tmr.B;PDB-ENSP_mappings:5tms.A;PDB-ENSP_mappings:5tms.B;PDB-ENSP_mappings:5tmt.A;PDB-ENSP_mappings:5tmt.B;PDB-ENSP_mappings:5tmu.A;PDB-ENSP_mappings:5tmu.B;PDB-ENSP_mappings:5tmv.A;PDB-ENSP_mappings:5tmv.B;PDB-ENSP_mappings:5tmw.A;PDB-ENSP_mappings:5tmw.B;PDB-ENSP_mappings:5tmz.A;PDB-ENSP_mappings:5tmz.B;PDB-ENSP_mappings:5tn1.A;PDB-ENSP_mappings:5tn1.B;PDB-ENSP_mappings:5tn3.A;PDB-ENSP_mappings:5tn3.B;PDB-ENSP_mappings:5tn4.A;PDB-ENSP_mappings:5tn4.B;PDB-ENSP_mappings:5tn5.A;PDB-ENSP_mappings:5tn5.B;PDB-ENSP_mappings:5tn6.A;PDB-ENSP_mappings:5tn6.B;PDB-ENSP_mappings:5tn7.A;PDB-ENSP_mappings:5tn7.B;PDB-ENSP_mappings:5tn8.A;PDB-ENSP_mappings:5tn8.B;PDB-ENSP_mappings:5tn9.A;PDB-ENSP_mappings:5tn9.B;PDB-ENSP_mappings:5tn9.C;PDB-ENSP_mappings:5tn9.D;PDB-ENSP_mappings:5tnb.A;PDB-ENSP_mappings:5tnb.B;PDB-ENSP_mappings:5tnb.C;PDB-ENSP_mappings:5tnb.D;PDB-ENSP_mappings:5u2b.A;PDB-ENSP_mappings:5u2b.B;PDB-ENSP_mappings:5u2b.C;PDB-ENSP_mappings:5u2b.D;PDB-ENSP_mappings:5u2b.E;PDB-ENSP_mappings:5u2b.F;PDB-ENSP_mappings:5u2d.A;PDB-ENSP_mappings:5u2d.B;PDB-ENSP_mappings:5ufw.A;PDB-ENSP_mappings:5ufw.B;PDB-ENSP_mappings:5ufx.A;PDB-ENSP_mappings:5ufx.B;PDB-ENSP_mappings:5w9c.A;PDB-ENSP_mappings:5w9c.B;PDB-ENSP_mappings:5w9c.C;PDB-ENSP_mappings:5w9c.D;PDB-ENSP_mappings:5w9d.A;PDB-ENSP_mappings:5w9d.B;PDB-ENSP_mappings:5wgd.A;PDB-ENSP_mappings:5wgd.B;PDB-ENSP_mappings:5wgq.A;PDB-ENSP_mappings:5wgq.B;PDB-ENSP_mappings:6b0f.A;PDB-ENSP_mappings:6b0f.B;PDB-ENSP_mappings:6c42.A;PDB-ENSP_mappings:6c42.B;PDB-ENSP_mappings:6cbz.A;PDB-ENSP_mappings:6cbz.B;PDB-ENSP_mappings:6chw.A;PDB-ENSP_mappings:6chz.A;PDB-ENSP_mappings:6czn.A;PDB-ENSP_mappings:6czn.B;PDB-ENSP_mappings:6d0f.A;PDB-ENSP_mappings:6d0f.B;PDB-ENSP_mappings:6df6.A;PDB-ENSP_mappings:6df6.B;PDB-ENSP_mappings:6df6.C;PDB-ENSP_mappings:6df6.D;PDB-ENSP_mappings:6dfn.A;PDB-ENSP_mappings:6dfn.B;PDB-ENSP_mappings:6dfn.C;PDB-ENSP_mappings:6dfn.D;PDB-ENSP_mappings:6iar.A;PDB-ENSP_mappings:6owc.A;PDB-ENSP_mappings:6owc.B;PDB-ENSP_mappings:6pet.A;PDB-ENSP_mappings:6pet.B;PDB-ENSP_mappings:6pet.C;PDB-ENSP_mappings:6pet.D;PDB-ENSP_mappings:6pfm.A;PDB-ENSP_mappings:6pfm.D;PDB-ENSP_mappings:6pit.A;PDB-ENSP_mappings:6pit.B;PDB-ENSP_mappings:6psj.A;PDB-ENSP_mappings:6psj.B;PDB-ENSP_mappings:6sbo.A;PDB-ENSP_mappings:6sbo.B;PDB-ENSP_mappings:6sq0.A;PDB-ENSP_mappings:6sq0.B;PDB-ENSP_mappings:6suo.A;PDB-ENSP_mappings:6suo.B;PDB-ENSP_mappings:6v87.A;PDB-ENSP_mappings:6v87.B;PDB-ENSP_mappings:6v8t.A;PDB-ENSP_mappings:6v8t.B;PDB-ENSP_mappings:6vgh.A;PDB-ENSP_mappings:6vgh.B;PDB-ENSP_mappings:6vig.A;PDB-ENSP_mappings:6vig.B;PDB-ENSP_mappings:6vig.C;PDB-ENSP_mappings:6vig.D;PDB-ENSP_mappings:6vj1.A;PDB-ENSP_mappings:6vj1.B;PDB-ENSP_mappings:6vj1.D;PDB-ENSP_mappings:6vj1.E;PDB-ENSP_mappings:6vjd.A;PDB-ENSP_mappings:6vjd.B;PDB-ENSP_mappings:6vjd.C;PDB-ENSP_mappings:6vjd.D;PDB-ENSP_mappings:6vmu.A;PDB-ENSP_mappings:6vmu.B;PDB-ENSP_mappings:6vmu.C;PDB-ENSP_mappings:6vmu.D;PDB-ENSP_mappings:6vnn.A;PDB-ENSP_mappings:6vnn.B;PDB-ENSP_mappings:6vnn.C;PDB-ENSP_mappings:6vnn.D;PDB-ENSP_mappings:6vpk.A;PDB-ENSP_mappings:6vpk.B;PDB-ENSP_mappings:6vpk.C;PDB-ENSP_mappings:6vpk.D;PDB-ENSP_mappings:6vvp.A;PDB-ENSP_mappings:6vvp.B;PDB-ENSP_mappings:6vvp.C;PDB-ENSP_mappings:6vvp.D;Pfam:PF00104;PIRSF:PIRSF002527;PIRSF:PIRSF500101;PROSITE_profiles:PS51843;PANTHER:PTHR24084;PANTHER:PTHR24084:SF3;SMART:SM00430;Superfamily:SSF48508;CDD:cd06949 ENSP00000206249 5/8 ENST00000206249 Transcript 1.0 ENSG00000091831 HGNC:3467 MODERATE NM_000125.4 missense_variant probably_damaging(0.999) Unknown deleterious(0) P03372.271 ESR1 HGNC 1 G4XH65.73 1.0 UPI000004A328 P03372-1 SNV ESR1,missense_variant,p.S395F,ENST00000440973,NM_001122742.1,c.1184C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;ESR1,missense_variant,p.S395F,ENST00000443427,NM_001122740.1,c.1184C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ESR1,missense_variant,p.S395F,ENST00000206249,NM_001291230.1&NM_001122741.1&NM_001291241.1&NM_000125.4,c.1184C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ESR1,missense_variant,p.S222F,ENST00000427531,NM_001328100.2,c.665C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ESR1,missense_variant,p.S395F,ENST00000338799,,c.1184C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ESR1,missense_variant,p.S68F,ENST00000415488,,c.203C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ESR1,intron_variant,,ENST00000406599,,c.453-49248C>T,MODIFIER,,,,1;ESR1,intron_variant,,ENST00000456483,,c.*111-49248C>T,MODIFIER,,,,1;ESR1,intron_variant,,ENST00000638569,,c.42+67494C>T,MODIFIER,,,,1;ESR1,non_coding_transcript_exon_variant,,ENST00000641399,,n.512C>T,MODIFIER,,,,1 1415/6327 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 115 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 109 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ESR1,non_coding_transcript_exon_variant,,ENST00000641399.1,n.512C>T,MODIFIER,;ESR1,missense_variant,p.S68F,ENST00000415488.1,c.203C>T,MODERATE,;ESR1,missense_variant,p.S222F,ENST00000427531.6,c.665C>T,MODERATE,;ESR1,missense_variant,p.S395F,ENST00000206249.8,c.1184C>T,MODERATE,YES;ESR1,intron_variant,,ENST00000456483.3,c.*111-49248C>T,MODIFIER,;ESR1,intron_variant,,ENST00000406599.5,c.453-49248C>T,MODIFIER,;ESR1,missense_variant,p.S395F,ENST00000443427.5,c.1184C>T,MODERATE,;ESR1,missense_variant,p.S395F,ENST00000338799.9,c.1184C>T,MODERATE,;ESR1,missense_variant,p.S395F,ENST00000440973.5,c.1184C>T,MODERATE, +SYTL3 100500851 BI GRCh38 6 158760651 158760651 + synonymous_variant Silent SNP C C T rs746313196 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 69 23 c.1320C>T p.Tyr440= p.Y440= ENST00000611299.5 440/610 P1 T Y protein_coding YES CCDS56458.1 1320/1833 AAATACGAAGA COSM1179205 PANTHER:PTHR45716:SF1;PANTHER:PTHR45716;Gene3D:2.60.40.150 ENSP00000483936 15/18 rs746313196;COSV51916175 ENST00000611299 Transcript ENSG00000164674 HGNC:15587 LOW 0.0002613 gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 Q4VX76.130 SYTL3 HGNC 1 5.0 UPI000015FE68 Q4VX76-1 SNV SYTL3,synonymous_variant,p.Y440=,ENST00000611299,NM_001242394.1&NM_001318745.1,c.1320C>T,LOW,YES,,,1;SYTL3,synonymous_variant,p.Y372=,ENST00000367081,NM_001242395.1&NM_001009991.3,c.1116C>T,LOW,,,,1;SYTL3,synonymous_variant,p.Y440=,ENST00000360448,NM_001242384.1,c.1320C>T,LOW,,,,1;MIR3918,downstream_gene_variant,,ENST00000581555,,,MODIFIER,YES,,,-1 2111/2896 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.17e-05 0.0 0.0 9.923e-05 0.0 0.0 3.517e-05 0.0 0.0002613 4.733890091301873e-05 2.4324999685632065e-05 0.0 6.628660048590973e-05 0.0 0.0004038769984617 9.428629709873348e-05 eas 0.0004038769984617 0.0 1.5435400200658478e-05 0.0 0.0002086809981847 0 93 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 92 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SYTL3,synonymous_variant,p.Y440=,ENST00000611299.5,c.1320C>T,LOW,YES;SYTL3,synonymous_variant,p.Y440=,ENST00000360448.8,c.1320C>T,LOW,;SYTL3,synonymous_variant,p.Y372=,ENST00000367081.7,c.1116C>T,LOW, +FNDC1 84624 BI GRCh38 6 159225606 159225606 + missense_variant Missense_Mutation SNP G G A rs544765580 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 84 50 c.956G>A p.Arg319His p.R319H ENST00000297267.14 NM_032532.3 319 cGt/cAt 8/23 P1 A R/H protein_coding YES CCDS47512.1 956/5685 CAGGCGTGTGC COSM3023123 Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR23197;PANTHER:PTHR23197:SF8;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000297267 8/23 rs544765580;COSV51936499 ENST00000297267 Transcript ENSG00000164694 HGNC:21184 MODERATE NM_032532.3 0.0001937 gnomAD_AFR missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q4ZHG4.128 FNDC1 HGNC 1 1.0 UPI0000579B80 Q4ZHG4-1 SNV FNDC1,missense_variant,p.R319H,ENST00000297267,NM_032532.3,c.956G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;FNDC1,missense_variant,p.R278H,ENST00000329629,,c.833G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;FNDC1,non_coding_transcript_exon_variant,,ENST00000480856,,n.591G>A,MODIFIER,,,,1 1153/6548 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.407e-05 0.0001937 5.792e-05 0.0 0.0 0.0 8.849e-06 0.0 0.0 2.028319977398496e-05 4.864759830525145e-05 0.0 6.626910180784762e-05 0.0 0.0 0.0 afr 4.864759830525145e-05 0.0 0.0 0.0 0.0 0 155 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 134 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FNDC1,non_coding_transcript_exon_variant,,ENST00000480856.1,n.591G>A,MODIFIER,;FNDC1,synonymous_variant,p.A277=,ENST00000329629.8,c.831G>A,LOW,;FNDC1,missense_variant,p.R319H,ENST00000297267.14,c.956G>A,MODERATE,YES +THBS2 7058 BI GRCh38 6 169248881 169248881 + missense_variant Missense_Mutation SNP C C T rs749837715 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 7 c.145G>A p.Asp49Asn p.D49N ENST00000366787.7 49 Gac/Aac 4/23 P2 T D/N protein_coding CCDS34574.1 145/3519 GGGGTCGGGCC COSM343721 Gene3D:2.60.120.200;PANTHER:PTHR10199;PANTHER:PTHR10199:SF10;SMART:SM00210;Superfamily:SSF49899 ENSP00000355751 4/23 rs749837715;COSV64682587 ENST00000366787 Transcript 1.0 ENSG00000186340 HGNC:11786 MODERATE 6.158e-05 gnomAD_AFR missense_variant 0;1 benign(0.001) Unknown tolerated(0.09) 0;1 P35442.198 THBS2 HGNC -1 1.0 UPI0000231C7F SNV THBS2,missense_variant,p.D49N,ENST00000366787,,c.145G>A,MODERATE,,tolerated(0.09),benign(0.001),-1;THBS2,missense_variant,p.D49N,ENST00000617924,NM_003247.5&NM_001381942.1,c.145G>A,MODERATE,,tolerated(0.09),benign(0.001),-1;THBS2,missense_variant,p.D49N,ENST00000649844,,c.145G>A,MODERATE,YES,tolerated(0.09),benign(0.027),-1;THBS2,missense_variant,p.D49N,ENST00000676498,,c.145G>A,MODERATE,,tolerated(0.09),benign(0.001),-1;THBS2,missense_variant,p.D49N,ENST00000676628,NM_001381939.1,c.145G>A,MODERATE,,tolerated_low_confidence(0.08),benign(0.09),-1;THBS2,missense_variant,p.D49N,ENST00000676760,,c.145G>A,MODERATE,,tolerated(0.09),benign(0.001),-1;THBS2,missense_variant,p.D49N,ENST00000676869,,c.145G>A,MODERATE,,tolerated(0.07),benign(0.143),-1;THBS2,missense_variant,p.D49N,ENST00000435791,,c.145G>A,MODERATE,,tolerated(0.14),benign(0.001),-1;THBS2,non_coding_transcript_exon_variant,,ENST00000677398,NM_001381940.1,n.372G>A,MODIFIER,,,,-1;THBS2,upstream_gene_variant,,ENST00000472733,,,MODIFIER,,,,-1;THBS2,missense_variant,p.D49N,ENST00000677429,,c.145G>A,MODERATE,,tolerated(0.11),benign(0.377),-1;BX322234.1,downstream_gene_variant,,ENST00000660724,,,MODIFIER,YES,,,1 395/5811 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.001e-06 6.158e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.353110019408632e-05 2.4338000002899207e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 42 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 31 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS THBS2,missense_variant,p.D49N,ENST00000435791.1,c.145G>A,MODERATE,;THBS2,non_coding_transcript_exon_variant,,ENST00000677398.1,n.372G>A,MODIFIER,;THBS2,missense_variant,p.D49N,ENST00000676869.1,c.145G>A,MODERATE,;THBS2,missense_variant,NMD_transcript_variant,p.D49N,ENST00000677429.1,c.145G>A,MODERATE,;THBS2,missense_variant,p.D49N,ENST00000676498.1,c.145G>A,MODERATE,;THBS2,missense_variant,p.D49N,ENST00000676760.1,c.145G>A,MODERATE,;THBS2,missense_variant,p.D49N,ENST00000649844.1,c.145G>A,MODERATE,;THBS2,missense_variant,p.D49N,ENST00000676628.1,c.145G>A,MODERATE,;THBS2,missense_variant,p.D49N,ENST00000617924.6,c.145G>A,MODERATE,YES;THBS2,missense_variant,p.D49N,ENST00000366787.7,c.145G>A,MODERATE, +WDR27 253769 BI GRCh38 6 169668046 169668046 + missense_variant Missense_Mutation SNP G G A rs376971037 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 7 c.596C>T p.Ala199Val p.A199V ENST00000448612.6 NM_182552.5 199 gCg/gTg 5/26 P4 A A/V protein_coding YES CCDS47520.2 596/2688 CCACCGCAGTC Superfamily:SSF50998;SMART:SM00320;Gene3D:2.130.10.10;Pfam:PF00400;PANTHER:PTHR44525;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294 ENSP00000416289 0.0 0.0001191 5/26 rs376971037 ENST00000448612 Transcript ENSG00000184465 HGNC:21248 MODERATE NM_182552.5 0.0001191 EA missense_variant 1.0 probably_damaging(0.963) Unknown deleterious(0.01) A2RRH5.107 WDR27 HGNC -1 1.0 UPI00015E06AF A2RRH5-4 SNV WDR27,missense_variant,p.A199V,ENST00000448612,NM_182552.5,c.596C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.963),-1;WDR27,3_prime_UTR_variant,,ENST00000650296,,c.*653C>T,MODIFIER,,,,-1;WDR27,intron_variant,,ENST00000423258,NM_001202550.1&NM_001350623.2,c.332-2490C>T,MODIFIER,,,,-1;WDR27,intron_variant,,ENST00000647873,NM_001350625.1&NM_001350624.1,c.457-859C>T,MODIFIER,,,,-1;AL031315.1,intron_variant,,ENST00000648086,,c.331+4209C>T,MODIFIER,YES,,,-1;WDR27,downstream_gene_variant,,ENST00000474018,,,MODIFIER,,,,-1;AL031315.1,intron_variant,,ENST00000650382,,n.108+33505C>T,MODIFIER,,,,-1;WDR27,upstream_gene_variant,,ENST00000467418,,,MODIFIER,,,,-1;WDR27,upstream_gene_variant,,ENST00000486490,,,MODIFIER,,,,-1;WDR27,upstream_gene_variant,,ENST00000546525,,,MODIFIER,,,,-1;WDR27,missense_variant,p.A199V,ENST00000649303,,c.596C>T,MODERATE,,deleterious(0.01),probably_damaging(0.986),-1;WDR27,3_prime_UTR_variant,,ENST00000647889,,c.*649C>T,MODIFIER,,,,-1;WDR27,3_prime_UTR_variant,,ENST00000647790,,c.*653C>T,MODIFIER,,,,-1;WDR27,non_coding_transcript_exon_variant,,ENST00000496752,,n.175C>T,MODIFIER,,,,-1;WDR27,intron_variant,,ENST00000648017,,c.457-2490C>T,MODIFIER,,,,-1;WDR27,intron_variant,,ENST00000648472,,c.332-3760C>T,MODIFIER,,,,-1;WDR27,upstream_gene_variant,,ENST00000476322,,,MODIFIER,,,,-1;WDR27,downstream_gene_variant,,ENST00000546953,,,MODIFIER,,,,-1;WDR27,downstream_gene_variant,,ENST00000649806,,,MODIFIER,,,,-1 1082/3554 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.614e-05 0.0 2.899e-05 0.0 0.0 0.0 6.201e-05 0.0 3.269e-05 4.054930104757659e-05 2.4308399588335305e-05 0.0 0.0 0.0 0.0 0.0 nfe 7.714620005572215e-05 0.0 7.714620005572215e-05 0.0 0.0 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS WDR27,3_prime_UTR_variant,,ENST00000650296.1,c.*653C>T,MODIFIER,;WDR27,non_coding_transcript_exon_variant,,ENST00000496752.1,n.175C>T,MODIFIER,;WDR27,intron_variant,NMD_transcript_variant,,ENST00000648017.1,c.457-2490C>T,MODIFIER,;WDR27,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647889.1,c.*649C>T,MODIFIER,;WDR27,missense_variant,NMD_transcript_variant,p.A199V,ENST00000649303.1,c.596C>T,MODERATE,;WDR27,intron_variant,,ENST00000647873.1,c.457-859C>T,MODIFIER,;WDR27,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647790.1,c.*653C>T,MODIFIER,;WDR27,intron_variant,,ENST00000423258.5,c.332-2490C>T,MODIFIER,;WDR27,intron_variant,NMD_transcript_variant,,ENST00000648472.1,c.332-3760C>T,MODIFIER,;WDR27,missense_variant,p.A199V,ENST00000448612.6,c.596C>T,MODERATE,YES;ENSG00000285733,intron_variant,,ENST00000650382.1,n.108+33505C>T,MODIFIER,;ENSG00000285733,intron_variant,,ENST00000648086.1,c.331+4209C>T,MODIFIER,YES +RADIL 55698 BI GRCh38 7 4877871 4877871 + missense_variant Missense_Mutation SNP C C T rs369472639 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 18 12 c.269G>A p.Arg90His p.R90H ENST00000399583.4 NM_018059.5 90 cGt/cAt 2/15 P1 T R/H protein_coding YES CCDS43544.1 269/3228 GCTCACGGGCG COSM3788285 PDB-ENSP_mappings:3ec8.A;PROSITE_profiles:PS50200;CDD:cd17116;PANTHER:PTHR16027:SF3;PANTHER:PTHR16027;Pfam:PF00788;Gene3D:3.10.20.90;SMART:SM00314;Superfamily:SSF54236 ENSP00000382492 0.0002496 0.0 2/15 rs369472639 ENST00000399583 Transcript ENSG00000157927 HGNC:22226 MODERATE NM_018059.5 0.0002496 AA missense_variant 1.0 benign(0.011) Unknown tolerated(0.21) Q96JH8.150 RADIL HGNC -1 5.0 UPI0000E0A787 Q96JH8-4 SNV RADIL,missense_variant,p.R90H,ENST00000399583,NM_018059.5,c.269G>A,MODERATE,YES,tolerated(0.21),benign(0.011),-1;RADIL,missense_variant,p.R90H,ENST00000457174,,c.269G>A,MODERATE,,tolerated(0.16),benign(0.011),-1;RADIL,missense_variant,p.R90H,ENST00000445392,,c.269G>A,MODERATE,,tolerated(0.27),benign(0.034),-1 454/5736 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.079e-05 0.0001339 2.908e-05 0.0 0.0 0.0 1.801e-05 0.0 0.0 6.75803967169486e-05 0.0001944389950949 0.0 0.0 0.0 0.0 0.0 afr 0.0001944389950949 0.0 3.085939897573553e-05 0.0 0.0 0 41 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 31 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RADIL,missense_variant,p.R90H,ENST00000457174.1,c.269G>A,MODERATE,;RADIL,missense_variant,NMD_transcript_variant,p.R90H,ENST00000445392.5,c.269G>A,MODERATE,;RADIL,missense_variant,p.R90H,ENST00000399583.4,c.269G>A,MODERATE,YES +RADIL 55698 BI GRCh38 7 4877998 4877998 + missense_variant Missense_Mutation SNP C C T rs200059500 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 6 c.142G>A p.Ala48Thr p.A48T ENST00000399583.4 NM_018059.5 48 Gcc/Acc 2/15 P1 T A/T protein_coding YES CCDS43544.1 142/3228 GCTGGCGCCCA COSM5550001 PANTHER:PTHR16027:SF3;PANTHER:PTHR16027;Gene3D:3.10.20.90 ENSP00000382492 0.0004955 0.0 2/15 rs200059500 ENST00000399583 Transcript ENSG00000157927 HGNC:22226 MODERATE NM_018059.5 0.0004955 AA missense_variant 1.0 benign(0.003) Unknown tolerated(0.23) Q96JH8.150 RADIL HGNC -1 5.0 UPI0000E0A787 Q96JH8-4 SNV RADIL,missense_variant,p.A48T,ENST00000399583,NM_018059.5,c.142G>A,MODERATE,YES,tolerated(0.23),benign(0.003),-1;RADIL,missense_variant,p.A48T,ENST00000457174,,c.142G>A,MODERATE,,tolerated(0.25),benign(0.003),-1;RADIL,missense_variant,p.A48T,ENST00000445392,,c.142G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.526),-1 327/5736 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.29e-05 6.729e-05 2.933e-05 0.0 0.0 0.0 5.462e-05 0.0 0.0 4.778480069944635e-05 4.9268401198787615e-05 0.0 0.0 0.0 0.0002061859995592 0.0 nfe 6.220649811439216e-05 0.0 6.220649811439216e-05 0.0 0.0 0 12 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RADIL,missense_variant,p.A48T,ENST00000457174.1,c.142G>A,MODERATE,;RADIL,missense_variant,NMD_transcript_variant,p.A48T,ENST00000445392.5,c.142G>A,MODERATE,;RADIL,missense_variant,p.A48T,ENST00000399583.4,c.142G>A,MODERATE,YES +FBXL18 80028 BI GRCh38 7 5501130 5501130 + missense_variant Missense_Mutation SNP G G A rs752384431 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 18 18 c.1139C>T p.Ala380Val p.A380V ENST00000382368.8 NM_001363441.2 380 gCg/gTg 3/5 P1 A A/V protein_coding YES CCDS43546.1 1139/2157 AGGACGCCACC COSM3929127;COSM3929128;COSM3929129 PANTHER:PTHR16134;PANTHER:PTHR16134:SF19;Gene3D:3.80.10.10;Superfamily:SSF52047 ENSP00000371805 3/5 rs752384431;COSV66665273;COSV66665695 ENST00000382368 Transcript ENSG00000155034 HGNC:21874 MODERATE NM_024963.6 5.514e-05 gnomAD_NFE missense_variant 0;1;1 1.0 benign(0) Unknown tolerated(0.31) 0;1;1 Q96ME1.151 FBXL18 HGNC -1 A0A024R857.43 5.0 UPI000020EA59 Q96ME1-4 SNV FBXL18,missense_variant,p.A380V,ENST00000382368,NM_001363441.2&NM_024963.6&NM_001321213.2&NM_001363442.2,c.1139C>T,MODERATE,YES,tolerated(0.31),benign(0),-1;FBXL18,missense_variant,p.A264V,ENST00000458142,,c.791C>T,MODERATE,,,benign(0.018),-1;FBXL18,intron_variant,,ENST00000453700,,c.1086+53C>T,MODIFIER,,,,-1;FBXL18,upstream_gene_variant,,ENST00000620087,NM_001367781.1&NM_001367780.1,,MODIFIER,,,,-1;FBXL18,missense_variant,p.A380V,ENST00000415009,,c.1139C>T,MODERATE,,tolerated(0.3),benign(0),-1 1274/8270 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.469e-05 0.0 0.0 0.0 0.0 0.0 5.514e-05 0.0 0.0 2.703509926504921e-05 4.861920024268329e-05 0.0 0.0 0.0 0.0 0.0 afr 4.861920024268329e-05 0.0 3.086130163865164e-05 0.0 0.0 0 43 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FBXL18,missense_variant,p.R264C,ENST00000458142.1,c.790C>T,MODERATE,;FBXL18,missense_variant,p.A380V,ENST00000382368.8,c.1139C>T,MODERATE,YES;FBXL18,missense_variant,NMD_transcript_variant,p.A380V,ENST00000415009.5,c.1139C>T,MODERATE, +CYTH3 9265 BI GRCh38 7 6165544 6165544 + splice_donor_variant Splice_Site SNP C C T rs764184600 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 30 c.972+1G>A p.X324_splice p.X324_splice ENST00000350796.8 325 P1 T protein_coding YES GCTTACGGGTT COSM1091139;COSM4875326 ENSP00000379967 rs764184600;COSV60363506 ENST00000396741 Transcript NonExonic ENSG00000008256 HGNC:9504 HIGH 11/12 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS splice_donor_variant 0;1 1.0 Unknown 0;1 O43739.177 CYTH3 HGNC -1 5.0 UPI0000128C2A O43739-1 SNV CYTH3,splice_donor_variant,p.X324_splice,ENST00000350796,NM_004227.4&NM_001367580.1&NM_001367581.1,c.972+1G>A,HIGH,,,,-1;CYTH3,splice_donor_variant,p.X325_splice,ENST00000396741,,c.975+1G>A,HIGH,YES,,,-1;USP42,downstream_gene_variant,,ENST00000306177,NM_032172.3&NM_001365764.1,,MODIFIER,YES,,,1;CYTH3,intron_variant,,ENST00000465320,,n.145-117G>A,MODIFIER,,,,-1;CYTH3,downstream_gene_variant,,ENST00000461891,,,MODIFIER,,,,-1;CYTH3,downstream_gene_variant,,ENST00000488964,,,MODIFIER,,,,-1;CYTH3,downstream_gene_variant,,ENST00000495176,,,MODIFIER,,,,-1;USP42,downstream_gene_variant,,ENST00000521713,,,MODIFIER,,,,1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.76023000778514e-06 2.4313199901371263e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CYTH3,intron_variant,,ENST00000465320.1,n.145-117G>A,MODIFIER,;CYTH3,splice_donor_variant,p.X324_splice,ENST00000350796.8,c.972+1G>A,HIGH,YES +BZW2 28969 BI GRCh38 7 16681313 16681313 + missense_variant Missense_Mutation SNP C C T rs371407289 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 5 c.248C>T p.Thr83Met p.T83M ENST00000258761.8 NM_001159767.2 83 aCg/aTg 4/12 P1 T T/M protein_coding CCDS5362.1 248/1260 AGGAACGCGCA PANTHER:PTHR14208;PANTHER:PTHR14208:SF7 ENSP00000258761 0.000227 0.0 4/12 rs371407289 ENST00000258761 Transcript ENSG00000136261 HGNC:18808 MODERATE NM_014038.3 0.0004307 gnomAD_AFR missense_variant possibly_damaging(0.568) Unknown deleterious(0) Q9Y6E2.150 BZW2 HGNC 1 A0A024RA42.47 1.0 UPI000003B445 Q9Y6E2-1 SNV BZW2,missense_variant,p.T83M,ENST00000433922,NM_001159767.1,c.248C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000258761,NM_014038.3&NM_001362717.2,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000630952,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.891),1;BZW2,missense_variant,p.T7M,ENST00000405202,,c.20C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000415365,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000446596,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000438834,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,missense_variant,p.T83M,ENST00000430000,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.568),1;BZW2,5_prime_UTR_variant,,ENST00000452975,,c.-190C>T,MODIFIER,,,,1;BZW2,non_coding_transcript_exon_variant,,ENST00000432311,,n.400C>T,MODIFIER,,,,1;BZW2,missense_variant,p.T83M,ENST00000436868,,c.248C>T,MODERATE,,deleterious(0.01),probably_damaging(0.923),1;BZW2,missense_variant,p.T83M,ENST00000437745,,c.248C>T,MODERATE,,deleterious(0),possibly_damaging(0.891),1;BZW2,non_coding_transcript_exon_variant,,ENST00000480517,,n.294C>T,MODIFIER,,,,1 363/1804 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.186e-05 0.0004307 0.0 0.0 0.0 0.0 8.81e-06 0.0 0.0 5.41082008567173e-05 0.0001216960008605 0.0 0.0 0.0 0.0 0.0 afr 0.0001216960008605 0.0 3.086229844484478e-05 0.0004945599939674 0.0 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BZW2,missense_variant,p.T83M,ENST00000430000.1,c.248C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000438834.5,c.248C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000446596.5,c.248C>T,MODERATE,;BZW2,non_coding_transcript_exon_variant,,ENST00000480517.5,n.294C>T,MODIFIER,;BZW2,missense_variant,p.T7M,ENST00000405202.5,c.20C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000258761.8,c.248C>T,MODERATE,YES;BZW2,missense_variant,NMD_transcript_variant,p.T83M,ENST00000436868.5,c.248C>T,MODERATE,;BZW2,non_coding_transcript_exon_variant,,ENST00000432311.5,n.400C>T,MODIFIER,;BZW2,missense_variant,NMD_transcript_variant,p.T83M,ENST00000437745.5,c.248C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000433922.6,c.248C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000630952.2,c.248C>T,MODERATE,;BZW2,missense_variant,p.T83M,ENST00000415365.5,c.248C>T,MODERATE, +TNS3 64759 BI GRCh38 7 47293777 47293777 + missense_variant Missense_Mutation SNP G G A rs375611617 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 26 c.3728C>T p.Pro1243Leu p.P1243L ENST00000311160.14 NM_022748.12 1243 cCg/cTg 25/31 P1 A P/L protein_coding YES CCDS5506.2 3728/4338 CCTTCGGGGTA COSM4735203 PROSITE_profiles:PS50001;CDD:cd09927;PANTHER:PTHR45734;PANTHER:PTHR45734:SF5;Gene3D:3.30.505.10;Pfam:PF00017;SMART:SM00252;Superfamily:SSF55550 ENSP00000312143 0.00026 0.0 25/31 rs375611617 ENST00000311160 Transcript ENSG00000136205 HGNC:21616 MODERATE NM_022748.12 0.00026 AA missense_variant 1.0 possibly_damaging(0.717) Unknown deleterious(0.01) Q68CZ2.141 TNS3 HGNC -1 1.0 UPI00001AE9DA Q68CZ2-1 SNV TNS3,missense_variant,p.P1243L,ENST00000311160,NM_022748.12,c.3728C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.717),-1 4053/7585 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.603e-05 6.457e-05 0.0 0.0 0.0 0.0 1.765e-05 0.0 3.268e-05 0 66 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 57 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNS3,missense_variant,p.P346L,ENST00000705473.1,c.1037C>T,MODERATE,;TNS3,missense_variant,p.P346L,ENST00000705472.1,c.1037C>T,MODERATE,;TNS3,missense_variant,p.P800L,ENST00000705474.1,c.2399C>T,MODERATE,;TNS3,missense_variant,p.P1357L,ENST00000705350.1,c.4070C>T,MODERATE,;TNS3,missense_variant,p.P1243L,ENST00000311160.14,c.3728C>T,MODERATE,YES;TNS3,missense_variant,p.P1346L,ENST00000457718.6,c.4037C>T,MODERATE,;TNS3,missense_variant,p.P1332L,ENST00000450444.6,c.3995C>T,MODERATE, +TNS3 64759 BI GRCh38 7 47368654 47368654 + synonymous_variant Silent SNP C C T rs374818505 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 129 29 c.1992G>A p.Ala664= p.A664= ENST00000311160.14 NM_022748.12 664 gcG/gcA 17/31 P1 T A protein_coding YES CCDS5506.2 1992/4338 TTGAACGCTTT PANTHER:PTHR45734;PANTHER:PTHR45734:SF5 ENSP00000312143 0.0002407 0.0 17/31 rs374818505 ENST00000311160 Transcript ENSG00000136205 HGNC:21616 LOW NM_022748.12 0.0002407 AA synonymous_variant 1.0 Unknown Q68CZ2.141 TNS3 HGNC -1 1.0 UPI00001AE9DA Q68CZ2-1 SNV TNS3,synonymous_variant,p.A664=,ENST00000311160,NM_022748.12,c.1992G>A,LOW,YES,,,-1;TNS3,synonymous_variant,p.A767=,ENST00000457718,,c.2301G>A,LOW,,,,-1;TNS3,downstream_gene_variant,,ENST00000450444,,,MODIFIER,,,,-1;TNS3,downstream_gene_variant,,ENST00000469470,,,MODIFIER,,,,-1 2317/7585 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.267e-05 6.49e-05 0.0 0.0 0.0 0.0 1.857e-05 0.0 0.0 1.3521000255423132e-05 2.4317900169990025e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 177 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 158 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNS3,synonymous_variant,p.A221=,ENST00000705474.1,c.663G>A,LOW,;TNS3,synonymous_variant,p.A778=,ENST00000705350.1,c.2334G>A,LOW,;TNS3,synonymous_variant,p.A664=,ENST00000311160.14,c.1992G>A,LOW,YES;TNS3,synonymous_variant,p.A767=,ENST00000457718.6,c.2301G>A,LOW,;TNS3,synonymous_variant,p.A753=,ENST00000450444.6,c.2259G>A,LOW, +TNS3 64759 BI GRCh38 7 47369008 47369008 + synonymous_variant Silent SNP G G A rs375420968 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 12 c.1638C>T p.Asp546= p.D546= ENST00000311160.14 NM_022748.12 546 gaC/gaT 17/31 0.0002 0.0 0.0 0.0 0.001 0.0 P1 A D protein_coding YES CCDS5506.2 1638/4338 GGGCCGTCCAT COSM1090119 PANTHER:PTHR45734;PANTHER:PTHR45734:SF5 ENSP00000312143 0.0002453 0.0001193 17/31 rs375420968 ENST00000311160 Transcript ENSG00000136205 HGNC:21616 LOW NM_022748.12 0.001 EUR synonymous_variant 1.0 Unknown Q68CZ2.141 TNS3 HGNC -1 1.0 UPI00001AE9DA Q68CZ2-1 SNV TNS3,synonymous_variant,p.D546=,ENST00000311160,NM_022748.12,c.1638C>T,LOW,YES,,,-1;TNS3,synonymous_variant,p.D649=,ENST00000457718,,c.1947C>T,LOW,,,,-1;TNS3,downstream_gene_variant,,ENST00000450444,,,MODIFIER,,,,-1;TNS3,downstream_gene_variant,,ENST00000469470,,,MODIFIER,,,,-1 1963/7585 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.63e-05 0.0001941 0.0 0.0 5.565e-05 0.0003251 5.317e-05 0.0 6.536e-05 8.108549809549004e-05 4.8609799705445766e-05 0.0 0.0 0.0 0.0 0.000282219989458 fin 0.000282219989458 0.0 0.0001079950015991 0.0 0.0 0 65 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 49 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNS3,synonymous_variant,p.D103=,ENST00000705474.1,c.309C>T,LOW,;TNS3,synonymous_variant,p.D660=,ENST00000705350.1,c.1980C>T,LOW,;TNS3,synonymous_variant,p.D546=,ENST00000311160.14,c.1638C>T,LOW,YES;TNS3,synonymous_variant,p.D649=,ENST00000457718.6,c.1947C>T,LOW,;TNS3,synonymous_variant,p.D635=,ENST00000450444.6,c.1905C>T,LOW, +TBL2 26608 BI GRCh38 7 73573956 73573956 + missense_variant Missense_Mutation SNP C C T rs373074498 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 44 33 c.428G>A p.Arg143His p.R143H ENST00000305632.11 NM_001362661.2 143 cGc/cAc 3/7 P3 T R/H protein_coding YES CCDS5551.1 428/1344 TGAAGCGCACC PROSITE_profiles:PS50294;PANTHER:PTHR44321;Gene3D:2.130.10.10;Superfamily:SSF50978 ENSP00000307260 0.0004539 0.0 3/7 rs373074498 ENST00000305632 Transcript 1.0 ENSG00000106638 HGNC:11586 MODERATE NM_012453.4 0.0004539 AA missense_variant 1.0 probably_damaging(0.951) Unknown deleterious(0.01) Q9Y4P3.162 TBL2 HGNC -1 A0A384MDS4.10 1.0 UPI0000048EF4 SNV TBL2,missense_variant,p.R143H,ENST00000305632,NM_001362661.2&NM_012453.4&NM_001362662.2&NM_001362660.2,c.428G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.951),-1;TBL2,missense_variant,p.R143H,ENST00000610724,,c.428G>A,MODERATE,,deleterious(0.01),probably_damaging(0.927),-1;TBL2,missense_variant,p.R107H,ENST00000432538,NM_001362663.2,c.320G>A,MODERATE,,deleterious(0.02),probably_damaging(0.951),-1;TBL2,missense_variant,p.R48H,ENST00000479892,,c.143G>A,MODERATE,,deleterious(0.02),probably_damaging(0.951),-1;TBL2,splice_region_variant,,ENST00000476136,,n.428+5G>A,LOW,,,,-1;TBL2,non_coding_transcript_exon_variant,,ENST00000459913,,n.595G>A,MODIFIER,,,,-1;TBL2,non_coding_transcript_exon_variant,,ENST00000452475,,n.513G>A,MODIFIER,,,,-1;TBL2,non_coding_transcript_exon_variant,,ENST00000465279,,n.673G>A,MODIFIER,,,,-1;TBL2,downstream_gene_variant,,ENST00000468669,,,MODIFIER,,,,-1;TBL2,splice_region_variant,,ENST00000450285,,c.423+5G>A,LOW,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000424598,,c.*345G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000417008,,c.*165G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000433464,,c.*37G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000426966,,c.*361G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000435792,,c.*554G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000437521,,c.*361G>A,MODIFIER,,,,-1;TBL2,3_prime_UTR_variant,,ENST00000452125,,c.*169G>A,MODIFIER,,,,-1;TBL2,non_coding_transcript_exon_variant,,ENST00000469518,,n.506G>A,MODIFIER,,,,-1;TBL2,non_coding_transcript_exon_variant,,ENST00000496056,,n.455G>A,MODIFIER,,,,-1;TBL2,downstream_gene_variant,,ENST00000458466,,,MODIFIER,,,,-1;TBL2,upstream_gene_variant,,ENST00000488915,,,MODIFIER,,,,-1;TBL2,upstream_gene_variant,,ENST00000495885,,,MODIFIER,,,,-1 458/4344 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.394e-05 0.0001231 2.892e-05 0.0 0.0 0.0 1.766e-05 0.0001632 0.0 2.027789923886303e-05 4.861449997406453e-05 0.0 0.0 0.0 0.0002015320060309 0.0 afr 4.861449997406453e-05 0.0 0.0 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 78 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TBL2,non_coding_transcript_exon_variant,,ENST00000469518.1,n.506G>A,MODIFIER,;TBL2,non_coding_transcript_exon_variant,,ENST00000496056.5,n.455G>A,MODIFIER,;TBL2,non_coding_transcript_exon_variant,,ENST00000465279.5,n.673G>A,MODIFIER,;TBL2,missense_variant,p.R48H,ENST00000479892.5,c.143G>A,MODERATE,;TBL2,splice_region_variant,intron_variant,,ENST00000476136.5,n.428+5G>A,LOW,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000452125.5,c.*169G>A,MODIFIER,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000435792.5,c.*554G>A,MODIFIER,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000437521.5,c.*361G>A,MODIFIER,;TBL2,non_coding_transcript_exon_variant,,ENST00000452475.5,n.513G>A,MODIFIER,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000426966.5,c.*361G>A,MODIFIER,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000433464.5,c.*37G>A,MODIFIER,;TBL2,missense_variant,p.R107H,ENST00000432538.5,c.320G>A,MODERATE,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000417008.5,c.*165G>A,MODIFIER,;TBL2,non_coding_transcript_exon_variant,,ENST00000459913.5,n.595G>A,MODIFIER,;TBL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000424598.5,c.*345G>A,MODIFIER,;TBL2,splice_region_variant,intron_variant,NMD_transcript_variant,,ENST00000450285.5,c.423+5G>A,LOW,;TBL2,missense_variant,p.R143H,ENST00000305632.11,c.428G>A,MODERATE,YES +GTF2IRD2 84163 BI GRCh38 7 74797159 74797159 + missense_variant Missense_Mutation SNP G G A rs782092217 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 22 c.2353C>T p.Arg785Trp p.R785W ENST00000451013.7 NM_001388083.1 785 Cgg/Tgg 16/16 A R/W protein_coding CCDS5576.1 2353/2850 CGCCCGGATCA PANTHER:PTHR47831;Superfamily:SSF53098 ENSP00000406723 16/16 COSV100736416;COSV100736448 ENST00000451013 Transcript ENSG00000196275 HGNC:30775 MODERATE missense_variant 1;1 probably_damaging(0.91) Unknown deleterious(0) 1;1 Q86UP8.132 GTF2IRD2 HGNC -1 1.0 UPI00033350AC Q86UP8-1 SNV GTF2IRD2,missense_variant,p.R947W,ENST00000651129,NM_001368300.1,c.2839C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.886),-1;GTF2IRD2,missense_variant,p.R785W,ENST00000451013,NM_173537.4,c.2353C>T,MODERATE,,deleterious(0),probably_damaging(0.91),-1;GTF2IRD2,downstream_gene_variant,,ENST00000625377,,,MODIFIER,,,,-1;GTF2IRD2,downstream_gene_variant,,ENST00000610955,,,MODIFIER,,,,-1 2543/3558 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 142 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GTF2IRD2,missense_variant,p.R947W,ENST00000651129.1,c.2839C>T,MODERATE,;GTF2IRD2,missense_variant,p.R785W,ENST00000451013.7,c.2353C>T,MODERATE,YES;ENSG00000289346,missense_variant,p.R785W,ENST00000625377.3,c.2353C>T,MODERATE,YES +CACNA2D1 781 BI GRCh38 7 82005772 82005772 + missense_variant Missense_Mutation SNP C C T rs758561622 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 22 c.1508G>A p.Arg503His p.R503H ENST00000356860.8 NM_001366867.1 503 cGt/cAt 17/39 P1 T R/H protein_coding YES 1508/3312 TAAAACGTGGT CDD:cd18774;PANTHER:PTHR10166;PANTHER:PTHR10166:SF6;Gene3D:3.30.450.20 ENSP00000348589 17/39 rs758561622;COSV62382055 ENST00000356253 Transcript 1.0 ENSG00000153956 HGNC:1399 MODERATE 0.0006074 gnomAD_AMR missense_variant 0;1 benign(0.013) Unknown deleterious(0.05) 0;1 P54289.193 CACNA2D1 HGNC -1 5.0 UPI0001B9E74B P54289-1 SNV CACNA2D1,missense_variant,p.R503H,ENST00000356860,NM_000722.4,c.1508G>A,MODERATE,,deleterious(0.05),benign(0.02),-1;CACNA2D1,missense_variant,p.R503H,ENST00000356253,NM_001366867.1,c.1508G>A,MODERATE,YES,deleterious(0.05),benign(0.013),-1;CACNA2D1,missense_variant,p.R7H,ENST00000443883,,c.20G>A,MODERATE,,deleterious(0.04),possibly_damaging(0.801),-1;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000464354,,n.524G>A,MODIFIER,,,,-1;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000466806,,n.244G>A,MODIFIER,,,,-1;CACNA2D1,downstream_gene_variant,,ENST00000475237,,,MODIFIER,,,,-1;CACNA2D1-AS1,upstream_gene_variant,,ENST00000439234,,,MODIFIER,YES,,,1;CACNA2D1-AS1,upstream_gene_variant,,ENST00000454066,,,MODIFIER,,,,1 1764/3858 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 9.558e-05 0.0 0.0006074 0.0 0.0 0.0 1.763e-05 0.0 3.268e-05 1.3546599802793937e-05 0.0 0.0 0.0001329259976046 0.0 0.0 0.0 amr 0.0001329259976046 0.0 0.0 0.0 0.0 0 72 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CACNA2D1,non_coding_transcript_exon_variant,,ENST00000464354.5,n.524G>A,MODIFIER,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000466806.5,n.244G>A,MODIFIER,;CACNA2D1,missense_variant,p.R475H,ENST00000705962.1,c.1424G>A,MODERATE,;CACNA2D1,synonymous_variant,p.T430=,ENST00000705961.1,c.1290G>A,LOW,;CACNA2D1,missense_variant,p.R503H,ENST00000443883.2,c.1508G>A,MODERATE,;CACNA2D1,missense_variant,p.R503H,ENST00000356860.8,c.1508G>A,MODERATE,YES +ELAPOR2 222223 BI GRCh38 7 86897555 86897555 + missense_variant Missense_Mutation SNP G G A rs760928278 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 11 c.2636C>T p.Thr879Met p.T879M ENST00000450689.7 NM_001142749.3 879 aCg/aTg 19/22 P4 A T/M protein_coding YES CCDS47632.1 2636/3090 GCTCCGTACAC COSM245241 PANTHER:PTHR22727;PANTHER:PTHR22727:SF3 ENSP00000413445 19/22 rs760928278;COSV51892954 ENST00000450689 Transcript ENSG00000164659 HGNC:21945 MODERATE NM_001142749.3 9.801e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.944) Unknown deleterious(0) 0;1 A8MWY0.105 ELAPOR2 HGNC -1 5.0 UPI000173AA00 A8MWY0-1 SNV ELAPOR2,missense_variant,p.T879M,ENST00000450689,NM_001142749.3,c.2636C>T,MODERATE,YES,deleterious(0),probably_damaging(0.944),-1;ELAPOR2,missense_variant,p.T808M,ENST00000444627,,c.2423C>T,MODERATE,,deleterious(0),possibly_damaging(0.59),-1;ELAPOR2,missense_variant,p.T712M,ENST00000416314,NM_001291991.1&NM_001291990.1&NM_152748.4,c.2135C>T,MODERATE,,deleterious(0),possibly_damaging(0.855),-1;ELAPOR2,missense_variant,p.T840M,ENST00000423294,,c.2519C>T,MODERATE,,deleterious(0),benign(0.094),-1;ELAPOR2,3_prime_UTR_variant,,ENST00000394714,,c.*1908C>T,MODIFIER,,,,-1;ELAPOR2,upstream_gene_variant,,ENST00000480216,,,MODIFIER,,,,-1 2777/6796 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.79e-05 0.0 0.0 0.0 0.0 0.0 3.526e-05 0.0 9.801e-05 4.059699858771637e-05 2.435220085317269e-05 0.0 0.0 0.0 0.0 0.0 nfe 7.717720291111618e-05 0.0 7.717720291111618e-05 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 47 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ELAPOR2,synonymous_variant,p.Y839=,ENST00000423294.5,c.2517C>T,LOW,;ELAPOR2,missense_variant,p.T712M,ENST00000416314.5,c.2135C>T,MODERATE,;ELAPOR2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000394714.6,c.*1908C>T,MODIFIER,;ELAPOR2,missense_variant,p.T808M,ENST00000444627.5,c.2423C>T,MODERATE,;ELAPOR2,missense_variant,p.T879M,ENST00000450689.7,c.2636C>T,MODERATE,YES +PTCD1 26024 BI GRCh38 7 99424909 99424909 + synonymous_variant Silent SNP C C T TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 8 c.1623G>A p.Ala541= p.A541= ENST00000292478.9 NM_015545.4 541 gcG/gcA 6/8 P1 T A protein_coding YES CCDS34691.1 1623/2103 AACAGCGCCTT Gene3D:1.25.40.10;PROSITE_profiles:PS51375;PANTHER:PTHR24014;PANTHER:PTHR24014:SF6 ENSP00000292478 6/8 COSV99464024 ENST00000292478 Transcript ENSG00000106246 HGNC:22198 LOW NM_015545.4 synonymous_variant 1 1.0 Unknown 1 O75127.141 PTCD1 HGNC -1 A4D273.104 1.0 UPI0000223FFA SNV PTCD1,synonymous_variant,p.A541=,ENST00000292478,NM_015545.4,c.1623G>A,LOW,YES,,,-1;ATP5MF-PTCD1,synonymous_variant,p.A590=,ENST00000413834,NM_001198879.2,c.1770G>A,LOW,YES,,,-1;PTCD1,downstream_gene_variant,,ENST00000485746,,,MODIFIER,,,,-1 1756/5464 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.7566697907750495e-06 2.4296599804074503e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 35 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ATP5MF-PTCD1,synonymous_variant,p.A590=,ENST00000413834.5,c.1770G>A,LOW,YES;PTCD1,synonymous_variant,p.A541=,ENST00000292478.9,c.1623G>A,LOW,YES +PVRIG 79037 BI GRCh38 7 100220121 100220121 + synonymous_variant Silent SNP G G A rs1397982881 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 5 c.126G>A p.Pro42= p.P42= ENST00000317271.3 NM_024070.3 42 ccG/ccA 3/6 P1 A P protein_coding YES CCDS5690.1 126/981 ACCCCGGAGGT PANTHER:PTHR39220 ENSP00000316675 3/6 rs1397982881 ENST00000317271 Transcript ENSG00000213413 HGNC:32190 LOW 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q6DKI7.114 PVRIG HGNC 1 1.0 UPI000013FFF0 SNV PVRIG,synonymous_variant,p.P42=,ENST00000317271,NM_024070.3,c.126G>A,LOW,YES,,,1;CASTOR3,intron_variant,,ENST00000328453,,n.887+2476C>T,MODIFIER,YES,,,-1;CASTOR3,intron_variant,,ENST00000414739,,n.895+2476C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000435519,,n.895+2476C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000437485,,n.129+3449C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000440058,,n.191+3449C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000454084,,n.739+2476C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000543273,,n.889+2476C>T,MODIFIER,,,,-1;CASTOR3,intron_variant,,ENST00000649671,,n.775+3449C>T,MODIFIER,,,,-1;CASTOR3,upstream_gene_variant,,ENST00000445230,,,MODIFIER,,,,-1;PVRIG,downstream_gene_variant,,ENST00000471803,,,MODIFIER,,,,1;CASTOR3,downstream_gene_variant,,ENST00000538588,,,MODIFIER,,,,-1;STAG3,3_prime_UTR_variant,,ENST00000451963,,c.*1363G>A,MODIFIER,,,,1;CASTOR3,downstream_gene_variant,,ENST00000647868,,,MODIFIER,,,,-1 489/1583 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.3519000276573934e-05 2.4314300389960408e-05 0.0 0.0 0.0 0.0002016939979512 0.0 0.0 0.0 0.0 0.0 0 8 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 8 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PVRIG,synonymous_variant,p.P22=,ENST00000699088.1,c.66G>A,LOW,YES;PVRIG,synonymous_variant,p.P42=,ENST00000317271.3,c.126G>A,LOW,;CASTOR3P,intron_variant,,ENST00000702747.1,n.399+3761C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000701477.1,n.648+2476C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000700967.1,n.641+2476C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000414739.3,n.895+2476C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000435519.6,n.895+2476C>T,MODIFIER,;ENSG00000292277,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000710637.1,c.*1363G>A,MODIFIER,YES;CASTOR3P,intron_variant,,ENST00000454084.5,n.739+2476C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000437485.5,n.129+3449C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000440058.5,n.191+3449C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000328453.9,n.887+2476C>T,MODIFIER,;CASTOR3P,intron_variant,,ENST00000649671.1,n.775+3449C>T,MODIFIER,YES;CASTOR3P,intron_variant,,ENST00000543273.5,n.889+2476C>T,MODIFIER, +MUC3A 4584 BI GRCh38 7 100959264 100959264 + synonymous_variant Silent SNP G G A rs79067082 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 35 c.7485G>A p.Ser2495= p.S2495= ENST00000379458.9 NM_005960.2 2495 tcG/tcA 2/12 0.0004 0.0 0.0 0.002 0.0 0.0 P4 A S protein_coding YES CCDS78262.1 7485/9972 CCTTCGTCTGT PANTHER:PTHR24041;PANTHER:PTHR24041:SF22;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000368771 2/12 rs79067082;COSV60210457 ENST00000379458 Transcript ENSG00000169894 HGNC:7513 LOW NM_005960.2 0.002 EAS synonymous_variant 0;1 Unknown 0;1 Q02505.146 MUC3A HGNC 1 5.0 UPI000455B941 Q02505-1 SNV MUC3A,synonymous_variant,p.S2495=,ENST00000379458,NM_005960.2,c.7485G>A,LOW,YES,,,1;MUC3A,synonymous_variant,p.S2495=,ENST00000483366,,c.7485G>A,LOW,,,,1;MUC3A,synonymous_variant,p.S434=,ENST00000414964,,c.1302G>A,LOW,,,,1;AC254629.1,downstream_gene_variant,,ENST00000610769,,,MODIFIER,,,,-1;AC254629.1,downstream_gene_variant,,ENST00000618276,,,MODIFIER,YES,,,-1 7576/11248 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0004482 0.001522 3.36e-05 0.0001231 0.0002715 0.0002518 0.0006285 0.0004148 0.0001646 0 66 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 47 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MUC3A,missense_variant,NMD_transcript_variant,p.V434I,ENST00000414964.5,c.1300G>A,MODERATE,;MUC3A,synonymous_variant,p.S2495=,ENST00000483366.5,c.7485G>A,LOW,;MUC3A,synonymous_variant,p.S2495=,ENST00000379458.9,c.7485G>A,LOW,YES +TRIM56 81844 BI GRCh38 7 101087775 101087775 + missense_variant Missense_Mutation SNP G G A rs1401771086 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 5 c.463G>A p.Gly155Arg p.G155R ENST00000306085.11 NM_030961.3 155 Ggg/Agg 3/3 P1 A G/R protein_coding YES CCDS43625.1 463/2268 GGGCCGGGTGG PANTHER:PTHR25462:SF209;PANTHER:PTHR25462;Gene3D:3.30.40.200 ENSP00000305161 3/3 rs1401771086;COSV100047644 ENST00000306085 Transcript ENSG00000169871 HGNC:19028 MODERATE NM_030961.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.921) Unknown deleterious(0) 0;1 Q9BRZ2.159 TRIM56 HGNC 1 1.0 UPI0000171C4A Q9BRZ2-1 SNV TRIM56,missense_variant,p.G155R,ENST00000306085,NM_030961.3,c.463G>A,MODERATE,YES,deleterious(0),probably_damaging(0.921),1;TRIM56,missense_variant,p.G155R,ENST00000412507,,c.463G>A,MODERATE,,deleterious(0),probably_damaging(0.921),1;TRIM56,downstream_gene_variant,,ENST00000467847,,,MODIFIER,,,,1;TRIM56,upstream_gene_variant,,ENST00000487252,,,MODIFIER,,,,1 718/10910 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 18 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 17 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TRIM56,missense_variant,p.G155R,ENST00000412507.1,c.463G>A,MODERATE,;TRIM56,missense_variant,p.G155R,ENST00000306085.11,c.463G>A,MODERATE,YES +MYL10 93408 BI GRCh38 7 101616294 101616294 + synonymous_variant Silent SNP C C T rs567400190 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 4 c.459G>A p.Thr153= p.T153= ENST00000223167.5 NM_138403.5 153 acG/acA 6/8 0.0002 0.0 0.0 0.001 0.0 0.0 T T protein_coding YES CCDS34713.1 459/681 GGGTCCGTGCC PANTHER:PTHR23049:SF36;PANTHER:PTHR23049;Gene3D:1.10.238.10;Superfamily:SSF47473 ENSP00000223167 6/8 rs567400190;COSV56209057 ENST00000223167 Transcript ENSG00000106436 HGNC:29825 LOW NM_138403.5 0.001 EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q9BUA6.143 MYL10 HGNC -1 1.0 UPI00001BBFAD SNV MYL10,synonymous_variant,p.T153=,ENST00000223167,NM_138403.5,c.459G>A,LOW,YES,,,-1;MYL10,synonymous_variant,p.T94=,ENST00000642629,,c.282G>A,LOW,,,,-1 637/1004 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.767e-05 0.0 0.0002315 9.929e-05 0.000272 9.244e-05 8.802e-06 0.0 0.0 2.704419966903515e-05 0.0 0.0 6.621640204684809e-05 0.0 0.0004045309906359 9.43039995036088e-05 eas 0.0004045309906359 0.0 0.0 0.0 0.0 0 37 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 18 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYL10,synonymous_variant,p.T94=,ENST00000642629.2,c.282G>A,LOW,;MYL10,synonymous_variant,p.T74=,ENST00000706943.1,c.222G>A,LOW,;MYL10,synonymous_variant,p.T153=,ENST00000223167.5,c.459G>A,LOW,YES +FOXP2 93986 BI GRCh38 7 114664354 114664354 + missense_variant Missense_Mutation SNP G G A rs745987986 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 21 c.1921G>A p.Val641Ile p.V641I ENST00000350908.9 NM_014491.4 641 Gtc/Atc 16/17 P4 A V/I protein_coding CCDS5760.1 1921/2148 AGGCCGTCCAC COSM3411501;COSM3411502 PANTHER:PTHR45796:SF8;PANTHER:PTHR45796 ENSP00000265436 16/17 rs745987986;COSV63484878 ENST00000350908 Transcript 1.0 ENSG00000128573 HGNC:13875 MODERATE NM_014491.4 5.451e-05 gnomAD_EAS missense_variant 0;1 benign(0) Unknown tolerated(0.94) 0;1 O15409.195 FOXP2 HGNC 1 1.0 UPI000012ADEC O15409-1 SNV FOXP2,missense_variant,p.V641I,ENST00000350908,NM_014491.4&NM_001172766.3,c.1921G>A,MODERATE,,tolerated(0.94),benign(0),1;FOXP2,missense_variant,p.V666I,ENST00000408937,NM_148898.4,c.1996G>A,MODERATE,YES,tolerated(0.92),benign(0.001),1;FOXP2,missense_variant,p.V658I,ENST00000403559,NM_148900.3,c.1972G>A,MODERATE,,tolerated(0.93),benign(0),1;FOXP2,missense_variant,p.V456I,ENST00000393491,,c.1366G>A,MODERATE,,tolerated(0.72),benign(0.038),1;FOXP2,missense_variant,p.V638I,ENST00000635534,,c.1912G>A,MODERATE,,tolerated(0.87),benign(0.001),1;FOXP2,missense_variant,p.V624I,ENST00000634411,,c.1870G>A,MODERATE,,tolerated(0.84),benign(0.001),1;FOXP2,missense_variant,p.V641I,ENST00000393494,,c.1921G>A,MODERATE,,tolerated(0.94),benign(0),1;FOXP2,missense_variant,p.V620I,ENST00000393498,,c.1858G>A,MODERATE,,tolerated(0.89),benign(0.001),1;FOXP2,missense_variant,p.V642I,ENST00000635638,,c.1924G>A,MODERATE,,tolerated(0.94),benign(0.001),1;FOXP2,downstream_gene_variant,,ENST00000634623,,,MODIFIER,,,,1;FOXP2,non_coding_transcript_exon_variant,,ENST00000634664,,n.396G>A,MODIFIER,,,,1;FOXP2,3_prime_UTR_variant,,ENST00000441290,,c.*1921G>A,MODIFIER,,,,1;FOXP2,3_prime_UTR_variant,,ENST00000412402,,c.*1639G>A,MODIFIER,,,,1;FOXP2,3_prime_UTR_variant,,ENST00000635109,,c.*1718G>A,MODIFIER,,,,1;FOXP2,3_prime_UTR_variant,,ENST00000393489,,c.*1715G>A,MODIFIER,,,,1 2477/6543 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.198e-05 0.0 0.0 0.0 5.451e-05 4.624e-05 0.0 0.0 3.267e-05 6.761330041626934e-06 0.0 0.0 6.634819874307141e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FOXP2,non_coding_transcript_exon_variant,,ENST00000634664.1,n.396G>A,MODIFIER,;FOXP2,missense_variant,p.R273H,ENST00000703618.1,c.818G>A,MODERATE,;FOXP2,missense_variant,p.V456I,ENST00000703617.1,c.1366G>A,MODERATE,;FOXP2,missense_variant,p.V638I,ENST00000635534.1,c.1912G>A,MODERATE,;FOXP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000393489.8,c.*1715G>A,MODIFIER,;FOXP2,missense_variant,p.V658I,ENST00000403559.9,c.1972G>A,MODERATE,;FOXP2,missense_variant,p.V620I,ENST00000393498.6,c.1858G>A,MODERATE,;FOXP2,missense_variant,p.V666I,ENST00000408937.7,c.1996G>A,MODERATE,;FOXP2,missense_variant,p.V641I,ENST00000350908.9,c.1921G>A,MODERATE,YES;FOXP2,missense_variant,p.V641I,ENST00000393494.6,c.1921G>A,MODERATE,;FOXP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000635109.1,c.*1718G>A,MODIFIER,;FOXP2,missense_variant,p.V624I,ENST00000634411.1,c.1870G>A,MODERATE,;FOXP2,missense_variant,p.V642I,ENST00000635638.1,c.1924G>A,MODERATE,;FOXP2,missense_variant,p.V683I,ENST00000703616.1,c.2047G>A,MODERATE,;FOXP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000441290.6,c.*1921G>A,MODIFIER,;FOXP2,missense_variant,p.V658I,ENST00000703613.1,c.1972G>A,MODERATE,;FOXP2,missense_variant,p.V641I,ENST00000703614.1,c.1921G>A,MODERATE,;FOXP2,missense_variant,p.V638I,ENST00000703612.1,c.1912G>A,MODERATE,;FOXP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000412402.5,c.*1639G>A,MODIFIER, +CTTNBP2 83992 BI GRCh38 7 117734992 117734992 + missense_variant Missense_Mutation SNP C C T rs200782612 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 8 c.3797G>A p.Arg1266His p.R1266H ENST00000160373.8 NM_033427.3 1266 cGc/cAc 16/23 P1 T R/H protein_coding YES CCDS5774.1 3797/4992 CCCAGCGGAAA COSM1312598 PANTHER:PTHR24166;PANTHER:PTHR24166:SF27 ENSP00000160373 16/23 rs200782612;COSV50392485 ENST00000160373 Transcript ENSG00000077063 HGNC:15679 MODERATE NM_033427.3 6.535e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.964) Unknown deleterious(0) 0;1 Q8WZ74.136 CTTNBP2 HGNC -1 Q20BG9.128 1.0 UPI000006E94A SNV CTTNBP2,missense_variant,p.R1266H,ENST00000160373,NM_033427.3&NM_001363349.1,c.3797G>A,MODERATE,YES,deleterious(0),probably_damaging(0.964),-1;CTTNBP2,missense_variant,p.R754H,ENST00000446636,NM_001363351.1&NM_001363350.1,c.2261G>A,MODERATE,,deleterious(0.01),probably_damaging(0.962),-1;CTTNBP2,downstream_gene_variant,,ENST00000435233,,,MODIFIER,,,,-1;CTTNBP2,3_prime_UTR_variant,,ENST00000441556,,c.*1711G>A,MODIFIER,,,,-1 3823/5904 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.584e-05 0.0 5.784e-05 0.0 0.0 0.0 4.406e-05 0.0 6.535e-05 6.757939900126075e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 38 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CTTNBP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000441556.5,c.*1711G>A,MODIFIER,;CTTNBP2,synonymous_variant,p.P753=,ENST00000446636.5,c.2259G>A,LOW,;CTTNBP2,missense_variant,p.R1266H,ENST00000160373.8,c.3797G>A,MODERATE,YES +SLC13A1 6561 BI GRCh38 7 123147268 123147268 + missense_variant Missense_Mutation SNP C C T rs774399049 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 9 c.703G>A p.Val235Met p.V235M ENST00000194130.7 NM_022444.4 235 Gtg/Atg 7/15 P1 T V/M protein_coding YES CCDS5786.1 703/1788 TGTCACGTGGC CDD:cd01115;PANTHER:PTHR10283:SF65;PANTHER:PTHR10283;Pfam:PF00939 ENSP00000194130 7/15 rs774399049;CM142587 ENST00000194130 Transcript ENSG00000081800 HGNC:10916 MODERATE NM_022444.4 3.533e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0) Unknown tolerated(1) Q9BZW2.146 SLC13A1 HGNC -1 A4D0X1.101 1.0 UPI0000049F9D SNV SLC13A1,missense_variant,p.V235M,ENST00000194130,NM_022444.4&NM_001324400.1,c.703G>A,MODERATE,YES,tolerated(1),benign(0),-1;SLC13A1,3_prime_UTR_variant,,ENST00000539873,,c.*370G>A,MODIFIER,,,,-1;SLC13A1,3_prime_UTR_variant,,ENST00000427975,,c.*646G>A,MODIFIER,,,,-1;SLC13A1,3_prime_UTR_variant,,ENST00000439260,,c.*1081G>A,MODIFIER,,,,-1 726/3798 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.597e-05 0.0 0.0 0.0 0.0 0.0 3.533e-05 0.0 0.0 1.352480012428714e-05 4.865469963988289e-05 0.0 0.0 0.0 0.0 0.0 afr 4.865469963988289e-05 0.0 0.0 0.0 0.0 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC13A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000439260.5,c.*1081G>A,MODIFIER,;SLC13A1,3_prime_UTR_variant,,ENST00000539873.1,c.*370G>A,MODIFIER,;SLC13A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000427975.5,c.*646G>A,MODIFIER,;SLC13A1,missense_variant,p.V235M,ENST00000194130.7,c.703G>A,MODERATE,YES +MEST 4232 BI GRCh38 7 130498185 130498185 + missense_variant Missense_Mutation SNP C C T rs782149861 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 54 11 c.386C>T p.Ala129Val p.A129V ENST00000223215.10 NM_001253900.1 129 gCg/gTg 5/12 A1 T A/V protein_coding YES CCDS5822.1 386/1008 GGAAGCGCTTT PANTHER:PTHR43139;PANTHER:PTHR43139:SF43;Gene3D:3.40.50.1820;Pfam:PF00561;Superfamily:SSF53474 ENSP00000223215 5/12 rs782149861 ENST00000223215 Transcript ENSG00000106484 HGNC:7028 MODERATE NM_002402.4 8.799e-06 gnomAD_NFE missense_variant 1.0 benign(0.007) Unknown tolerated(0.11) Q5EB52.132 MEST HGNC 1 A0A024R768.43 1.0 UPI000006DE62 Q5EB52-1 SNV MEST,missense_variant,p.A129V,ENST00000223215,NM_001253900.1&NM_002402.4,c.386C>T,MODERATE,YES,tolerated(0.11),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000427521,NM_001253902.1,c.359C>T,MODERATE,,tolerated(0.16),benign(0.003),1;MEST,missense_variant,p.A120V,ENST00000341441,NM_177524.2,c.359C>T,MODERATE,,tolerated(0.15),benign(0.007),1;MEST,missense_variant,p.A119V,ENST00000437945,,c.356C>T,MODERATE,,tolerated(0.1),benign(0.003),1;MEST,missense_variant,p.A120V,ENST00000393187,NM_177525.2,c.359C>T,MODERATE,,tolerated(0.15),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000462132,,c.359C>T,MODERATE,,tolerated(0.15),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000416162,NM_001253901.1,c.359C>T,MODERATE,,tolerated(0.16),benign(0.003),1;MEST,missense_variant,p.A120V,ENST00000378576,,c.359C>T,MODERATE,,tolerated(0.16),benign(0.003),1;MEST,missense_variant,p.A120V,ENST00000421001,,c.359C>T,MODERATE,,tolerated(0.18),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000437637,,c.359C>T,MODERATE,,tolerated(0.14),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000433159,,c.359C>T,MODERATE,,tolerated(0.12),benign(0.007),1;MEST,missense_variant,p.A120V,ENST00000458161,,c.359C>T,MODERATE,,tolerated(0.17),benign(0.007),1;MEST,downstream_gene_variant,,ENST00000399874,,,MODIFIER,,,,1;MEST,upstream_gene_variant,,ENST00000463263,,,MODIFIER,,,,1;MIR335,downstream_gene_variant,,ENST00000362173,,,MODIFIER,YES,,,1;MEST,non_coding_transcript_exon_variant,,ENST00000475188,,n.384C>T,MODIFIER,,,,1;MEST,upstream_gene_variant,,ENST00000488093,,,MODIFIER,,,,1;MEST,upstream_gene_variant,,ENST00000494868,,,MODIFIER,,,,1;AC007938.2,non_coding_transcript_exon_variant,,ENST00000604666,,n.243G>A,MODIFIER,YES,,,-1 615/2646 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.978e-06 0.0 0.0 0.0 0.0 0.0 8.799e-06 0.0 0.0 6.7614200816024095e-06 2.4329699954250827e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 91 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 65 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MEST,non_coding_transcript_exon_variant,,ENST00000475188.1,n.384C>T,MODIFIER,;ENSG00000270823,non_coding_transcript_exon_variant,,ENST00000604666.1,n.243G>A,MODIFIER,YES;MEST,missense_variant,p.A120V,ENST00000458161.2,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000437637.6,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000462132.6,c.359C>T,MODERATE,;MEST,missense_variant,p.A119V,ENST00000437945.6,c.356C>T,MODERATE,;MEST,missense_variant,p.A129V,ENST00000223215.10,c.386C>T,MODERATE,YES;MEST,missense_variant,p.A120V,ENST00000421001.5,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000393187.5,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000433159.5,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000378576.9,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000427521.6,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000416162.7,c.359C>T,MODERATE,;MEST,missense_variant,p.A120V,ENST00000341441.9,c.359C>T,MODERATE, +OR2A14 135941 BI GRCh38 7 144129903 144129903 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 71 43 c.791G>A p.Arg264His p.R264H ENST00000408899.2 NM_001001659.2 264 cGc/cAc 1/1 P1 A R/H protein_coding CCDS43672.1 791/933 GTCCCGCCATC PROSITE_profiles:PS50262;CDD:cd15420;PANTHER:PTHR26453:SF27;PANTHER:PTHR26453;Gene3D:1.20.1070.10;Pfam:PF13853;Superfamily:SSF81321 ENSP00000386137 1/1 COSV101376449;COSV101376499 ENST00000408899 Transcript ENSG00000221938 HGNC:15084 MODERATE missense_variant 1;1 benign(0.009) Unknown tolerated(0.18) 1;1 Q96R47.142 OR2A14 HGNC 1 A0A126GVB0.29 UPI0000061E6E SNV OR2A14,missense_variant,p.R264H,ENST00000641068,,c.791G>A,MODERATE,YES,tolerated(0.18),benign(0.009),1;OR2A14,missense_variant,p.R264H,ENST00000408899,NM_001001659.2,c.791G>A,MODERATE,,tolerated(0.18),benign(0.009),1 846/1012 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 188 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 114 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS OR2A14,missense_variant,p.R264H,ENST00000408899.2,c.791G>A,MODERATE,;OR2A14,missense_variant,p.R264H,ENST00000641068.1,c.791G>A,MODERATE,YES +ZNF425 155054 BI GRCh38 7 149105242 149105242 + missense_variant Missense_Mutation SNP C C T rs147910083 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 18 c.629G>A p.Arg210Gln p.R210Q ENST00000378061.7 NM_001001661.3 210 cGg/cAg 4/4 0.0004 0.0 0.0 0.0 0.002 0.0 P1 T R/Q protein_coding YES CCDS34773.1 629/2259 GGCTCCGTTTG PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24393;PANTHER:PTHR24393:SF73;SMART:SM00355;Superfamily:SSF57667 ENSP00000367300 0.000227 0.0 4/4 rs147910083 ENST00000378061 Transcript ENSG00000204947 HGNC:20690 MODERATE NM_001001661.3 0.002 EUR missense_variant 1.0 possibly_damaging(0.516) Unknown deleterious(0.05) Q6IV72.139 ZNF425 HGNC -1 A0A090N7U3.40 1.0 UPI00001B64B9 SNV ZNF425,missense_variant,p.R210Q,ENST00000378061,NM_001001661.3,c.629G>A,MODERATE,YES,deleterious(0.05),possibly_damaging(0.516),-1;ZNF425,downstream_gene_variant,,ENST00000483014,,,MODIFIER,,,,-1;ZNF425,downstream_gene_variant,,ENST00000495685,,,MODIFIER,,,,-1 740/3198 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.000179 0.0001232 0.000665 0.0 0.0 0.0 0.0001758 0.0 0.0 0.0001284699974348 4.863339927396737e-05 0.0 0.0001990180026041 0.0 0.0 0.0 nfe 0.0002006480062846 0.0 0.0002006480062846 0.0004950499860569 0.0 0 78 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 61 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF425,missense_variant,p.R210Q,ENST00000378061.7,c.629G>A,MODERATE,YES +SLC4A2 6522 BI GRCh38 7 151071750 151071750 + synonymous_variant Silent SNP C C T rs776758339 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 50 13 c.2253C>T p.Gly751= p.G751= ENST00000413384.7 NM_003040.4 751 ggC/ggT 15/23 P4 T G protein_coding CCDS5917.1 2253/3726 CAGGGCGTGGT PANTHER:PTHR11453:SF14;PANTHER:PTHR11453;Pfam:PF00955;TIGRFAM:TIGR00834 ENSP00000405600 15/23 rs776758339;COSV99879545 ENST00000413384 Transcript ENSG00000164889 HGNC:11028 LOW NM_003040.4 6.158e-05 gnomAD_AFR synonymous_variant 0;1 Unknown 0;1 P04920.208 SLC4A2 HGNC 1 1.0 UPI000013EFE9 P04920-1 SNV SLC4A2,synonymous_variant,p.G751=,ENST00000485713,NM_001199692.2,c.2253C>T,LOW,YES,,,1;SLC4A2,synonymous_variant,p.G737=,ENST00000461735,NM_001199694.2,c.2211C>T,LOW,,,,1;SLC4A2,synonymous_variant,p.G751=,ENST00000413384,NM_003040.4,c.2253C>T,LOW,,,,1;SLC4A2,synonymous_variant,p.G742=,ENST00000392826,NM_001199693.1,c.2226C>T,LOW,,,,1;FASTK,downstream_gene_variant,,ENST00000297532,NM_006712.5,,MODIFIER,YES,,,-1;FASTK,downstream_gene_variant,,ENST00000353841,NM_033015.3,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000482571,NM_001258461.1,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000540185,,,MODIFIER,,,,-1;SLC4A2,non_coding_transcript_exon_variant,,ENST00000482697,,n.22C>T,MODIFIER,,,,1;FASTK,downstream_gene_variant,,ENST00000489884,,,MODIFIER,,,,-1;SLC4A2,synonymous_variant,p.G751=,ENST00000677246,,c.2253C>T,LOW,,,,1;SLC4A2,non_coding_transcript_exon_variant,,ENST00000493040,,n.274C>T,MODIFIER,,,,1;SLC4A2,non_coding_transcript_exon_variant,,ENST00000460010,,n.86C>T,MODIFIER,,,,1;FASTK,downstream_gene_variant,,ENST00000460980,,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000465272,,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000466855,,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000467237,,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000469237,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000469355,,,MODIFIER,,,,1;SLC4A2,upstream_gene_variant,,ENST00000469467,,,MODIFIER,,,,1;SLC4A2,upstream_gene_variant,,ENST00000472204,,,MODIFIER,,,,1;SLC4A2,downstream_gene_variant,,ENST00000480107,,,MODIFIER,,,,1;FASTK,downstream_gene_variant,,ENST00000482806,,,MODIFIER,,,,-1;FASTK,downstream_gene_variant,,ENST00000483953,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000494298,,,MODIFIER,,,,1;AC010973.2,downstream_gene_variant,,ENST00000485974,,,MODIFIER,YES,,,-1 2490/4119 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.996e-06 6.158e-05 0.0 0.0 0.0 0.0 8.837e-06 0.0 0.0 6.768279945390532e-06 2.435930036881473e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 89 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 63 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC4A2,non_coding_transcript_exon_variant,,ENST00000482697.1,n.22C>T,MODIFIER,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000460010.1,n.86C>T,MODIFIER,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000493040.5,n.274C>T,MODIFIER,;SLC4A2,synonymous_variant,p.G737=,ENST00000461735.1,c.2211C>T,LOW,;SLC4A2,synonymous_variant,p.G742=,ENST00000392826.6,c.2226C>T,LOW,;SLC4A2,synonymous_variant,NMD_transcript_variant,p.G751=,ENST00000677246.1,c.2253C>T,LOW,;SLC4A2,synonymous_variant,p.G751=,ENST00000413384.7,c.2253C>T,LOW,YES;SLC4A2,synonymous_variant,p.G751=,ENST00000485713.5,c.2253C>T,LOW, +CSMD1 64478 BI GRCh38 8 3406061 3406061 + synonymous_variant Silent SNP G G A rs1471534448 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 14 c.2232C>T p.Asn744= p.N744= ENST00000635120.2 NM_033225.6 744 aaC/aaT 15/70 A2 A N protein_coding YES 2235/10698 ACCACGTTCCC Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR45656;PANTHER:PTHR45656:SF3;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000430733 16/71 rs1471534448 ENST00000520002 Transcript ENSG00000183117 HGNC:14026 LOW 5.569e-05 gnomAD_EAS synonymous_variant 1.0 Unknown CSMD1 HGNC -1 E5RIG2.77 5.0 UPI00015D46BB SNV CSMD1,synonymous_variant,p.N744=,ENST00000635120,NM_033225.6,c.2232C>T,LOW,,,,-1;CSMD1,synonymous_variant,p.N606=,ENST00000537824,,c.1818C>T,LOW,,,,-1;CSMD1,synonymous_variant,p.N225=,ENST00000335551,,c.675C>T,LOW,,,,-1;CSMD1,synonymous_variant,p.N745=,ENST00000520002,,c.2235C>T,LOW,YES,,,-1;CSMD1,synonymous_variant,p.N745=,ENST00000602557,,c.2235C>T,LOW,,,,-1;CSMD1,synonymous_variant,p.N745=,ENST00000400186,,c.2235C>T,LOW,,,,-1;CSMD1,synonymous_variant,p.N745=,ENST00000602723,,c.2235C>T,LOW,,,,-1;AC026991.2,upstream_gene_variant,,ENST00000647677,,,MODIFIER,YES,,,1 2791/11740 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.018e-06 0.0 0.0 0.0 5.569e-05 0.0 0.0 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CSMD1,synonymous_variant,p.N745=,ENST00000602557.5,c.2235C>T,LOW,;CSMD1,synonymous_variant,p.N745=,ENST00000602723.5,c.2235C>T,LOW,;CSMD1,synonymous_variant,p.N745=,ENST00000400186.7,c.2235C>T,LOW,;CSMD1,synonymous_variant,p.N745=,ENST00000520002.5,c.2235C>T,LOW,;CSMD1,synonymous_variant,p.N744=,ENST00000635120.2,c.2232C>T,LOW,YES;CSMD1,missense_variant,p.R225C,ENST00000335551.11,c.673C>T,MODERATE, +PRAG1 157285 BI GRCh38 8 8318203 8318203 + missense_variant Missense_Mutation SNP G G A rs746332662 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 17 c.4172C>T p.Ala1391Val p.A1391V ENST00000615670.5 NM_001080826.3 1391 gCg/gTg 6/6 P1 A A/V protein_coding CCDS43706.1 4172/4221 GCTCCGCAGAC PDB-ENSP_mappings:5ve6.A;PANTHER:PTHR22972;PANTHER:PTHR22972:SF3 ENSP00000479068 5/5 rs746332662 ENST00000622241 Transcript ENSG00000275342 HGNC:25438 MODERATE missense_variant probably_damaging(0.997) Unknown deleterious(0) Q86YV5.146 PRAG1 HGNC -1 2.0 UPI0003EAF98F SNV PRAG1,missense_variant,p.A1391V,ENST00000615670,NM_001080826.3,c.4172C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;PRAG1,missense_variant,p.A1391V,ENST00000622241,NM_001369759.1,c.4172C>T,MODERATE,,deleterious(0),probably_damaging(0.997),-1 4172/4639 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 33 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PRAG1,missense_variant,p.A1391V,ENST00000615670.5,c.4172C>T,MODERATE,YES +XPO7 23039 BI GRCh38 8 21981843 21981843 + missense_variant Missense_Mutation SNP G G A rs774932634 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 56 51 c.1070G>A p.Arg357Gln p.R357Q ENST00000252512.14 NM_001100161.2 357 cGa/cAa 10/28 P4 A R/Q protein_coding CCDS47818.1 1070/3264 CATCCGATTGA PANTHER:PTHR12596;PANTHER:PTHR12596:SF11;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000252512 10/28 rs774932634 ENST00000252512 Transcript ENSG00000130227 HGNC:14108 MODERATE NM_015024.5 0.0001653 gnomAD_OTH missense_variant benign(0.003) Unknown tolerated(0.79) Q9UIA9.173 XPO7 HGNC 1 1.0 UPI0000134559 SNV XPO7,missense_variant,p.R357Q,ENST00000252512,NM_001100161.2&NM_015024.5&NM_001362802.2,c.1070G>A,MODERATE,,tolerated(0.79),benign(0.003),1;XPO7,missense_variant,p.R358Q,ENST00000433566,,c.1073G>A,MODERATE,YES,tolerated(0.79),benign(0.003),1 1179/4870 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.025e-06 0.0 0.0 0.0 0.0 0.0 8.851e-06 0.0001653 0.0 0 131 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 107 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS XPO7,missense_variant,p.R358Q,ENST00000433566.8,c.1073G>A,MODERATE,;XPO7,missense_variant,p.R357Q,ENST00000252512.14,c.1070G>A,MODERATE,YES +CHMP7 91782 BI GRCh38 8 23249355 23249355 + missense_variant Missense_Mutation SNP G G A rs1346755630 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 18 c.445G>A p.Val149Ile p.V149I ENST00000313219.8 NM_001363183.2 149 Gtc/Atc 2/10 P1 A V/I protein_coding CCDS6040.1 445/1362 AGGAGGTCCTT PANTHER:PTHR22761;PANTHER:PTHR22761:SF21;Low_complexity_(Seg):seg ENSP00000324491 2/10 rs1346755630 ENST00000313219 Transcript ENSG00000147457 HGNC:28439 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant benign(0.201) Unknown tolerated(0.46) Q8WUX9.147 CHMP7 HGNC 1 1.0 UPI0000049FB7 Q8WUX9-1 SNV CHMP7,missense_variant,p.V149I,ENST00000397677,NM_152272.5,c.445G>A,MODERATE,YES,tolerated(0.46),benign(0.201),1;CHMP7,missense_variant,p.V149I,ENST00000313219,NM_001363183.2&NM_001317899.2,c.445G>A,MODERATE,,tolerated(0.46),benign(0.201),1;CHMP7,intron_variant,,ENST00000519984,,c.510+1158G>A,MODIFIER,,,,1;CHMP7,missense_variant,p.V149I,ENST00000519414,,c.445G>A,MODERATE,,tolerated(0.44),benign(0.201),1;CHMP7,3_prime_UTR_variant,,ENST00000517325,,c.*35G>A,MODIFIER,,,,1;CHMP7,intron_variant,,ENST00000519503,,c.299+2361G>A,MODIFIER,,,,1;CHMP7,intron_variant,,ENST00000519529,,n.336+2361G>A,MODIFIER,,,,1 1050/3367 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 45 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CHMP7,intron_variant,NMD_transcript_variant,,ENST00000519503.5,c.299+2361G>A,MODIFIER,;CHMP7,intron_variant,,ENST00000519529.1,n.336+2361G>A,MODIFIER,;CHMP7,intron_variant,,ENST00000519984.1,c.510+1158G>A,MODIFIER,;CHMP7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000517325.5,c.*35G>A,MODIFIER,;CHMP7,missense_variant,NMD_transcript_variant,p.V149I,ENST00000519414.5,c.445G>A,MODERATE,;CHMP7,missense_variant,p.V149I,ENST00000313219.8,c.445G>A,MODERATE,;CHMP7,missense_variant,p.V149I,ENST00000397677.6,c.445G>A,MODERATE,YES +GTF2E2 2961 BI GRCh38 8 30653556 30653556 + stop_gained Nonsense_Mutation SNP G G A rs763006801 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 17 c.43C>T p.Arg15Ter p.R15* ENST00000355904.9 NM_002095.6 15 Cga/Tga 2/8 P1 A R/* protein_coding YES CCDS6078.1 43/876 AGCTCGTTTTT PDB-ENSP_mappings:5iy6.R;PDB-ENSP_mappings:5iy7.R;PDB-ENSP_mappings:5iy8.R;PDB-ENSP_mappings:5iy9.R;PDB-ENSP_mappings:5iya.R;PDB-ENSP_mappings:5iyb.R;PDB-ENSP_mappings:5iyc.R;PDB-ENSP_mappings:5iyd.R;PDB-ENSP_mappings:6o9l.R;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR12716;PANTHER:PTHR12716:SF8;PIRSF:PIRSF016398 ENSP00000348168 2/8 rs763006801 ENST00000355904 Transcript 1.0 ENSG00000197265 HGNC:4651 HIGH NM_002095.6 3.275e-05 gnomAD_SAS stop_gained 1.0 Unknown P29084.192 GTF2E2 HGNC -1 1.0 UPI00001367F4 SNV GTF2E2,stop_gained,p.R15*,ENST00000355904,NM_002095.6,c.43C>T,HIGH,YES,,,-1;GTF2E2,stop_gained,p.R15*,ENST00000518599,NM_001348353.1,c.43C>T,HIGH,,,,-1;GTF2E2,stop_gained,p.R15*,ENST00000518445,,c.43C>T,HIGH,,,,-1;GTF2E2,stop_gained,p.R15*,ENST00000523499,,c.43C>T,HIGH,,,,-1 311/1747 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.968e-06 0.0 0.0 0.0 0.0 0.0 8.803e-06 0.0 3.275e-05 0 58 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GTF2E2,stop_gained,p.R15*,ENST00000518445.1,c.43C>T,HIGH,;GTF2E2,stop_gained,p.R15*,ENST00000518599.5,c.43C>T,HIGH,;GTF2E2,stop_gained,NMD_transcript_variant,p.R15*,ENST00000523499.5,c.43C>T,HIGH,;GTF2E2,stop_gained,p.R15*,ENST00000355904.9,c.43C>T,HIGH,YES +GSR 2936 BI GRCh38 8 30684166 30684166 + missense_variant Missense_Mutation SNP C C T rs138721223 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 55 38 c.1075G>A p.Val359Ile p.V359I ENST00000221130.11 NM_000637.5 359 Gta/Ata 10/13 0.0004 0.0015 0.0 0.0 0.0 0.0 P1 T V/I protein_coding YES CCDS34877.1 1075/1569 GTCTACGATGA COSM1099117 PDB-ENSP_mappings:1bwc.A;PDB-ENSP_mappings:1dnc.A;PDB-ENSP_mappings:1gra.A;PDB-ENSP_mappings:1grb.A;PDB-ENSP_mappings:1gre.A;PDB-ENSP_mappings:1grf.A;PDB-ENSP_mappings:1grg.A;PDB-ENSP_mappings:1grh.A;PDB-ENSP_mappings:1grt.A;PDB-ENSP_mappings:1gsn.A;PDB-ENSP_mappings:1k4q.A;PDB-ENSP_mappings:1xan.A;PDB-ENSP_mappings:2aaq.A;PDB-ENSP_mappings:2gh5.A;PDB-ENSP_mappings:2gh5.B;PDB-ENSP_mappings:2grt.A;PDB-ENSP_mappings:3djg.X;PDB-ENSP_mappings:3djj.A;PDB-ENSP_mappings:3dk4.A;PDB-ENSP_mappings:3dk8.A;PDB-ENSP_mappings:3dk9.A;PDB-ENSP_mappings:3grs.A;PDB-ENSP_mappings:3grt.A;PDB-ENSP_mappings:3sqp.A;PDB-ENSP_mappings:3sqp.B;PDB-ENSP_mappings:4gr1.A;PDB-ENSP_mappings:4grt.A;PDB-ENSP_mappings:5grt.A;PANTHER:PTHR42737;PANTHER:PTHR42737:SF2;Gene3D:3.50.50.60;TIGRFAM:TIGR01421;Pfam:PF07992;PIRSF:PIRSF000350;Superfamily:SSF51905;Prints:PR00368 ENSP00000221130 0.000227 0.0 10/13 rs138721223 ENST00000221130 Transcript 1.0 ENSG00000104687 HGNC:4623 MODERATE NM_000637.5 0.0015 AFR missense_variant 1.0 probably_damaging(0.995) Unknown deleterious(0) P00390.243 GSR HGNC -1 V9HW90.58 1.0 UPI000012BBFF P00390-1 SNV GSR,missense_variant,p.V359I,ENST00000221130,NM_000637.5,c.1075G>A,MODERATE,YES,deleterious(0),probably_damaging(0.995),-1;GSR,missense_variant,p.V330I,ENST00000546342,NM_001195102.2,c.988G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;GSR,missense_variant,p.V306I,ENST00000541648,NM_001195103.2,c.916G>A,MODERATE,,deleterious(0.01),probably_damaging(0.993),-1;GSR,missense_variant,p.V277I,ENST00000537535,NM_001195104.2,c.829G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.574),-1;GSR,non_coding_transcript_exon_variant,,ENST00000643525,,n.1054G>A,MODIFIER,,,,-1;GSR,3_prime_UTR_variant,,ENST00000643653,,c.*789G>A,MODIFIER,,,,-1;GSR,3_prime_UTR_variant,,ENST00000523295,,c.*308G>A,MODIFIER,,,,-1 1086/3034 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.386e-05 0.0003076 2.891e-05 0.0 0.0 0.0 0.0 0.0 0.0 3.381300120963715e-05 0.0001216370001202 0.0 0.0 0.0 0.0 0.0 afr 0.0001216370001202 0.0 0.0 0.0 0.0 0 119 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 93 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GSR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000523295.5,c.*308G>A,MODIFIER,;GSR,missense_variant,p.V277I,ENST00000537535.5,c.829G>A,MODERATE,;GSR,missense_variant,p.V330I,ENST00000546342.5,c.988G>A,MODERATE,;GSR,missense_variant,p.V306I,ENST00000541648.5,c.916G>A,MODERATE,;GSR,non_coding_transcript_exon_variant,,ENST00000643525.1,n.1054G>A,MODIFIER,;GSR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643653.1,c.*789G>A,MODIFIER,;GSR,missense_variant,p.V359I,ENST00000221130.11,c.1075G>A,MODERATE,YES +ADGRA2 25960 BI GRCh38 8 37841117 37841117 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 111 11 c.2779G>A p.Ala927Thr p.A927T ENST00000412232.3 NM_032777.10 927 Gcc/Acc 19/19 P1 A A/T protein_coding YES CCDS6097.2 2779/4017 TTGGCGCCTTC Pfam:PF00002;PROSITE_profiles:PS50261;PANTHER:PTHR45930;PANTHER:PTHR45930:SF1;CDD:cd15998 ENSP00000406367 19/19 COSV55103335 ENST00000412232 Transcript ENSG00000020181 HGNC:17849 MODERATE NM_032777.10 missense_variant 1 1.0 probably_damaging(0.919) Unknown deleterious(0) 1 Q96PE1.171 ADGRA2 HGNC 1 1.0 UPI00004AE50D Q96PE1-1 SNV ADGRA2,missense_variant,p.A927T,ENST00000412232,NM_032777.10,c.2779G>A,MODERATE,YES,deleterious(0),probably_damaging(0.919),1;ADGRA2,missense_variant,p.A710T,ENST00000315215,,c.2128G>A,MODERATE,,deleterious(0.01),probably_damaging(0.962),1;BRF2,downstream_gene_variant,,ENST00000220659,NM_018310.4,,MODIFIER,YES,,,-1;BRF2,downstream_gene_variant,,ENST00000520601,,,MODIFIER,,,,-1 3165/6944 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 136 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 122 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ADGRA2,missense_variant,p.A710T,ENST00000315215.11,c.2128G>A,MODERATE,;ADGRA2,missense_variant,p.A927T,ENST00000412232.3,c.2779G>A,MODERATE,YES +DDHD2 23259 BI GRCh38 8 38238156 38238156 + missense_variant Missense_Mutation SNP G G A rs1201437383 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 40 c.569G>A p.Arg190Gln p.R190Q ENST00000397166.7 NM_001362914.2 190 cGa/cAa 5/18 P1 A R/Q protein_coding YES CCDS34883.1 569/2136 GGGTCGACCAA PANTHER:PTHR23509;PANTHER:PTHR23509:SF7 ENSP00000380352 5/18 rs1201437383 ENST00000397166 Transcript 1.0 ENSG00000085788 HGNC:29106 MODERATE NM_015214.3 1.76e-05 gnomAD_NFE missense_variant 1.0 benign(0.125) Unknown deleterious(0.04) O94830.142 DDHD2 HGNC 1 2.0 UPI0000160E07 O94830-1 SNV DDHD2,missense_variant,p.R190Q,ENST00000397166,NM_001362913.1&NM_015214.3&NM_001362912.2&NM_001362911.2&NM_001362914.1,c.569G>A,MODERATE,YES,deleterious(0.04),benign(0.125),1;DDHD2,missense_variant,p.R190Q,ENST00000520272,NM_001164232.1,c.569G>A,MODERATE,,deleterious(0.04),benign(0.125),1;DDHD2,missense_variant,p.R190Q,ENST00000532222,NM_001164234.1,c.569G>A,MODERATE,,deleterious(0.04),probably_damaging(0.994),1;DDHD2,downstream_gene_variant,,ENST00000527834,,,MODIFIER,,,,1;DDHD2,downstream_gene_variant,,ENST00000528358,,,MODIFIER,,,,1;DDHD2,downstream_gene_variant,,ENST00000529642,,,MODIFIER,,,,1;DDHD2,upstream_gene_variant,,ENST00000532106,,,MODIFIER,,,,1;DDHD2,downstream_gene_variant,,ENST00000533100,,,MODIFIER,,,,1;DDHD2,downstream_gene_variant,,ENST00000526370,,,MODIFIER,,,,1;DDHD2,upstream_gene_variant,,ENST00000528888,,,MODIFIER,,,,1;DDHD2,3_prime_UTR_variant,,ENST00000526237,,c.*126G>A,MODIFIER,,,,1;DDHD2,non_coding_transcript_exon_variant,,ENST00000519857,,n.766G>A,MODIFIER,,,,1;DDHD2,intron_variant,,ENST00000527415,,c.411+529G>A,MODIFIER,,,,1;DDHD2,upstream_gene_variant,,ENST00000531344,,,MODIFIER,,,,1 852/4682 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.959e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 6.758220024494221e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 102 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 77 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DDHD2,intron_variant,NMD_transcript_variant,,ENST00000527415.5,c.411+529G>A,MODIFIER,;DDHD2,missense_variant,p.R190Q,ENST00000520272.6,c.569G>A,MODERATE,;DDHD2,missense_variant,p.R190Q,ENST00000532222.5,c.569G>A,MODERATE,;DDHD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000526237.5,c.*126G>A,MODIFIER,;DDHD2,non_coding_transcript_exon_variant,,ENST00000519857.5,n.766G>A,MODIFIER,;DDHD2,missense_variant,p.R190Q,ENST00000397166.7,c.569G>A,MODERATE,YES +PRKDC 5591 BI GRCh38 8 47936500 47936500 + synonymous_variant Silent SNP G G A rs1287171364 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 12 c.1131C>T p.Asn377= p.N377= ENST00000314191.7 NM_006904.7 377 aaC/aaT 12/86 P1 A N protein_coding YES CCDS75735.1 1131/12387 TTTGCGTTTAT COSM5745004 PDB-ENSP_mappings:5luq.A;PDB-ENSP_mappings:5luq.B;PDB-ENSP_mappings:5w1r.A;PDB-ENSP_mappings:5y3r.C;PANTHER:PTHR11139:SF68;PANTHER:PTHR11139;Superfamily:SSF48371 ENSP00000313420 12/86 rs1287171364;COSV58046196 ENST00000314191 Transcript 1.0 ENSG00000253729 HGNC:9413 LOW NM_006904.7 1.77e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 P78527.218 PRKDC HGNC -1 1.0 UPI0000013593 P78527-1 SNV PRKDC,synonymous_variant,p.N377=,ENST00000314191,NM_006904.7,c.1131C>T,LOW,YES,,,-1;PRKDC,synonymous_variant,p.N377=,ENST00000338368,NM_001081640.2,c.1131C>T,LOW,,,,-1;PRKDC,non_coding_transcript_exon_variant,,ENST00000535375,,n.418C>T,MODIFIER,,,,-1;AC021236.1,upstream_gene_variant,,ENST00000658178,,,MODIFIER,YES,,,1 1141/13459 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.025e-06 0.0 0.0 0.0 0.0 0.0 1.77e-05 0.0 0.0 2.704819962673355e-05 7.297140109585598e-05 0.0 0.0 0.0 0.0 0.0 afr 7.297140109585598e-05 0.0 1.5429699487867765e-05 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PRKDC,non_coding_transcript_exon_variant,,ENST00000535375.1,n.418C>T,MODIFIER,;PRKDC,non_coding_transcript_exon_variant,,ENST00000697591.1,n.1172C>T,MODIFIER,;PRKDC,synonymous_variant,p.N377=,ENST00000338368.7,c.1131C>T,LOW,;PRKDC,synonymous_variant,p.N377=,ENST00000314191.7,c.1131C>T,LOW,YES +SBSPON 157869 BI GRCh38 8 73081144 73081144 + missense_variant Missense_Mutation SNP C C T rs757345283 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 45 17 c.284G>A p.Arg95His p.R95H ENST00000297354.7 NM_153225.4 95 cGt/cAt 2/5 P1 T R/H protein_coding YES CCDS43747.2 284/795 GCACACGGGTT COSM5419461 PROSITE_profiles:PS50092;PANTHER:PTHR20920:SF2;PANTHER:PTHR20920;Pfam:PF19028;Gene3D:2.20.100.10;SMART:SM00209;Superfamily:SSF82895 ENSP00000297354 2/5 rs757345283;COSV52078369 ENST00000297354 Transcript ENSG00000164764 HGNC:30362 MODERATE NM_153225.4 0.0001317 gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.832) Unknown deleterious(0) 0;1 Q8IVN8.122 SBSPON HGNC -1 1.0 UPI0000D47CF3 SNV SBSPON,missense_variant,p.R95H,ENST00000297354,NM_153225.4,c.284G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.832),-1;SBSPON,non_coding_transcript_exon_variant,,ENST00000519697,,n.652G>A,MODIFIER,,,,-1;AC100823.1,downstream_gene_variant,,ENST00000442274,,,MODIFIER,YES,,,-1 389/3698 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.421e-05 6.478e-05 0.0 0.0 0.0 0.0 8.893e-06 0.0 0.0001317 4.05509999836795e-05 2.4308399588335305e-05 0.0 0.0 0.0 0.0006048390059731 0.0 eas 0.0006048390059731 0.0 1.542919926578179e-05 0.0 0.0002086809981847 0 108 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SBSPON,non_coding_transcript_exon_variant,,ENST00000519697.1,n.652G>A,MODIFIER,;SBSPON,missense_variant,p.R95H,ENST00000297354.7,c.284G>A,MODERATE,YES +GRHL2 79977 BI GRCh38 8 101558661 101558661 + missense_variant Missense_Mutation SNP G G A rs772933548 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 39 13 c.527G>A p.Arg176Gln p.R176Q ENST00000646743.1 NM_024915.4 176 cGg/cAg 4/16 P1 A R/Q protein_coding YES CCDS34931.1 527/1878 TCCCCGGGGAG PANTHER:PTHR11037;PANTHER:PTHR11037:SF17 ENSP00000495564 4/16 rs772933548;COSV104381766 ENST00000646743 Transcript 1.0 ENSG00000083307 HGNC:2799 MODERATE NM_024915.4 5.783e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.029) Unknown tolerated(0.44) 0;1 Q6ISB3.139 GRHL2 HGNC 1 UPI000013CD16 Q6ISB3-1 SNV GRHL2,missense_variant,p.R176Q,ENST00000646743,NM_024915.4,c.527G>A,MODERATE,YES,tolerated(0.44),benign(0.029),1;GRHL2,missense_variant,p.R160Q,ENST00000395927,NM_001330593.2,c.479G>A,MODERATE,,tolerated(0.45),benign(0.029),1;AP001207.1,downstream_gene_variant,,ENST00000524051,,,MODIFIER,YES,,,-1 858/5232 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.785e-05 0.0 5.783e-05 0.0 0.0 0.0 4.4e-05 0.0 0.0 1.3527999726647977e-05 0.0 0.0 0.0 0.0 0.000202020004508 0.0 0.0 1.5433099179062992e-05 0.0 0.0 0 76 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GRHL2,missense_variant,p.R160Q,ENST00000395927.1,c.479G>A,MODERATE,;GRHL2,missense_variant,p.R176Q,ENST00000646743.1,c.527G>A,MODERATE,YES +CCN4 8840 BI GRCh38 8 133213057 133213057 + missense_variant Missense_Mutation SNP C C T rs1854120495 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 5 c.263C>T p.Thr88Met p.T88M ENST00000250160.11 NM_003882.4 88 aCg/aTg 2/5 P1 T T/M protein_coding YES CCDS6371.1 263/1104 CTGCACGGAGG PROSITE_profiles:PS51323;PANTHER:PTHR11348:SF4;PANTHER:PTHR11348;Pfam:PF00219;PIRSF:PIRSF036495;SMART:SM00121;Superfamily:SSF57184 ENSP00000250160 2/5 COSV51531488 ENST00000250160 Transcript ENSG00000104415 HGNC:12769 MODERATE NM_003882.4 missense_variant 1 1.0 probably_damaging(0.963) Unknown deleterious(0) 1 O95388.172 CCN4 HGNC 1 1.0 UPI00000359FE O95388-1 SNV CCN4,missense_variant,p.T88M,ENST00000250160,NM_003882.4,c.263C>T,MODERATE,YES,deleterious(0),probably_damaging(0.963),1;CCN4,missense_variant,p.T88M,ENST00000220856,NM_080838.3,c.263C>T,MODERATE,,deleterious(0.02),probably_damaging(0.938),1;CCN4,missense_variant,p.T88M,ENST00000517423,NM_001204869.2,c.263C>T,MODERATE,,deleterious(0),probably_damaging(0.989),1;CCN4,intron_variant,,ENST00000519433,NM_001204870.2,c.70-14354C>T,MODIFIER,,,,1;CCN4,intron_variant,,ENST00000377862,,c.70-12333C>T,MODIFIER,,,,1 369/5190 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 71 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 43 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CCN4,missense_variant,p.T88M,ENST00000220856.6,c.263C>T,MODERATE,;CCN4,missense_variant,p.T88M,ENST00000517423.5,c.263C>T,MODERATE,;CCN4,intron_variant,,ENST00000519433.1,c.70-14354C>T,MODIFIER,;CCN4,intron_variant,NMD_transcript_variant,,ENST00000377862.6,c.70-12333C>T,MODIFIER,;CCN4,missense_variant,p.T88M,ENST00000250160.11,c.263C>T,MODERATE,YES +SLC45A4 57210 BI GRCh38 8 141217154 141217154 + synonymous_variant Silent SNP G G A rs1049181128 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 15 c.1665C>T p.Asn555= p.N555= ENST00000517878.6 NM_001286646.2 555 aaC/aaT 6/9 A N protein_coding YES CCDS75795.1 1665/2427 CCGGCGTTGTA COSM5659297;COSM5659298 Gene3D:1.20.1250.20;PANTHER:PTHR19432;PANTHER:PTHR19432:SF7;Superfamily:SSF103473;CDD:cd17313 ENSP00000428137 6/9 rs1049181128;COSV50140615 ENST00000517878 Transcript ENSG00000022567 HGNC:29196 LOW NM_001286646.2 synonymous_variant 0;1 1.0 Unknown 0;1 SLC45A4 HGNC -1 E7EV90.62 1.0 UPI0001E8F5C7 SNV SLC45A4,synonymous_variant,p.N504=,ENST00000519067,NM_001286648.1,c.1512C>T,LOW,,,,-1;SLC45A4,synonymous_variant,p.N555=,ENST00000517878,NM_001286646.2,c.1665C>T,LOW,YES,,,-1;SLC45A4,synonymous_variant,p.N504=,ENST00000024061,NM_001080431.2,c.1512C>T,LOW,,,,-1;SLC45A4,downstream_gene_variant,,ENST00000519986,,,MODIFIER,,,,-1;SLC45A4,downstream_gene_variant,,ENST00000520137,,,MODIFIER,,,,-1 2258/7418 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.758859854016919e-06 2.4314300389960408e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 65 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 42 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC45A4,synonymous_variant,p.N504=,ENST00000024061.7,c.1512C>T,LOW,;SLC45A4,synonymous_variant,p.N555=,ENST00000517878.6,c.1665C>T,LOW,YES;SLC45A4,synonymous_variant,p.N504=,ENST00000519067.5,c.1512C>T,LOW, +EPPK1 83481 BI GRCh38 8 143871042 143871042 + missense_variant Missense_Mutation SNP C C T rs746589906 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 75 8 c.2212G>A p.Val738Met p.V738M ENST00000615648.2 NM_031308.4 738 Gtg/Atg 2/2 A2 T V/M protein_coding YES CCDS75800.1 2212/15267 GGGCACGCGGT Gene3D:3.90.1290.10;Pfam:PF00681;PANTHER:PTHR23169;PANTHER:PTHR23169:SF21;SMART:SM00250;Superfamily:SSF75399 ENSP00000484472 2/2 rs746589906 ENST00000615648 Transcript ENSG00000261150 HGNC:15577 MODERATE NM_031308.4 0.0001113 gnomAD_EAS missense_variant 1.0 possibly_damaging(0.812) Unknown deleterious(0) P58107.161 EPPK1 HGNC -1 5.0 UPI0002065B93 SNV EPPK1,missense_variant,p.V738M,ENST00000615648,NM_031308.4,c.2212G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.812),-1;EPPK1,missense_variant,p.V713M,ENST00000568225,,c.2137G>A,MODERATE,,deleterious(0),possibly_damaging(0.812),-1 2287/16005 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.013e-05 6.514e-05 0.0 0.0 0.0001113 0.0 8.902e-06 0.0 3.269e-05 0 100 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 84 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EPPK1,missense_variant,p.V713M,ENST00000568225.2,c.2137G>A,MODERATE,;EPPK1,missense_variant,p.V738M,ENST00000615648.2,c.2212G>A,MODERATE,YES +PLEC 5339 BI GRCh38 8 143916620 143916620 + missense_variant Missense_Mutation SNP C C T rs782439392 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 21 c.13612G>A p.Asp4538Asn p.D4538N ENST00000322810.8 NM_201380.4 4538 Gac/Aac 32/32 P1 T D/N protein_coding YES CCDS43772.1 13612/14055 uncertain_significance CGTGTCGGGCT PDB-ENSP_mappings:2n03.A;Gene3D:3.90.1290.10;Pfam:PF00681;PANTHER:PTHR23169;PANTHER:PTHR23169:SF20;SMART:SM00250;Superfamily:SSF75399 ENSP00000323856 32/32 rs782439392 ENST00000322810 Transcript 1.0 ENSG00000178209 HGNC:9069 MODERATE 0.0002833 gnomAD_EAS missense_variant 1 1.0 benign(0.435) Unknown tolerated(0.12) Q15149.229 PLEC HGNC -1 1.0 UPI0000233FCD Q15149-1 SNV PLEC,missense_variant,p.D4538N,ENST00000322810,NM_201380.4,c.13612G>A,MODERATE,YES,tolerated(0.12),benign(0.435),-1;PLEC,missense_variant,p.D4401N,ENST00000345136,NM_201384.3,c.13201G>A,MODERATE,,tolerated(0.14),benign(0.213),-1;PLEC,missense_variant,p.D4428N,ENST00000436759,NM_000445.5,c.13282G>A,MODERATE,,tolerated(0.15),benign(0.213),-1;PLEC,missense_variant,p.D4379N,ENST00000354958,NM_201379.3,c.13135G>A,MODERATE,,tolerated(0.14),benign(0.213),-1;PLEC,missense_variant,p.D4401N,ENST00000354589,NM_201382.4,c.13201G>A,MODERATE,,tolerated(0.15),benign(0.308),-1;PLEC,missense_variant,p.D4405N,ENST00000357649,NM_201383.3,c.13213G>A,MODERATE,,tolerated(0.16),benign(0.213),-1;PLEC,missense_variant,p.D4387N,ENST00000356346,NM_201378.4,c.13159G>A,MODERATE,,tolerated(0.15),benign(0.213),-1;PLEC,missense_variant,p.D4369N,ENST00000398774,NM_201381.3,c.13105G>A,MODERATE,,tolerated(0.14),benign(0.213),-1;PLEC,missense_variant,p.D4424N,ENST00000527096,,c.13270G>A,MODERATE,,tolerated(0.16),benign(0.308),-1;PLEC,missense_variant,p.D3301N,ENST00000527303,,c.9901G>A,MODERATE,,tolerated(0.32),possibly_damaging(0.573),-1 13782/15249 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.942e-05 0.0 2.917e-05 0.0 0.0002833 0.0 9.498e-06 0.0 0.0 4.055859972140752e-05 4.862160130869597e-05 0.0 0.0 0.0 0.0006055710255168 0.0 eas 0.0006055710255168 0.0 1.543260077596642e-05 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLEC,missense_variant,p.D4445N,ENST00000528025.6,c.13333G>A,MODERATE,;PLEC,missense_variant,p.D4424N,ENST00000527096.5,c.13270G>A,MODERATE,;PLEC,missense_variant,p.D4418N,ENST00000685198.1,c.13252G>A,MODERATE,;PLEC,missense_variant,p.D4378N,ENST00000693060.1,c.13132G>A,MODERATE,;PLEC,missense_variant,p.D4307N,ENST00000687971.1,c.12919G>A,MODERATE,;PLEC,missense_variant,p.D4401N,ENST00000354589.7,c.13201G>A,MODERATE,;PLEC,missense_variant,p.D4387N,ENST00000356346.7,c.13159G>A,MODERATE,;PLEC,missense_variant,p.D4401N,ENST00000345136.8,c.13201G>A,MODERATE,YES;PLEC,missense_variant,p.D3301N,ENST00000527303.2,c.9901G>A,MODERATE,;PLEC,missense_variant,p.D4405N,ENST00000357649.6,c.13213G>A,MODERATE,;PLEC,missense_variant,p.D4538N,ENST00000322810.8,c.13612G>A,MODERATE,;PLEC,missense_variant,p.D4379N,ENST00000354958.6,c.13135G>A,MODERATE,;PLEC,missense_variant,p.D4369N,ENST00000398774.6,c.13105G>A,MODERATE,;PLEC,missense_variant,p.D4428N,ENST00000436759.6,c.13282G>A,MODERATE, +DCAF12 25853 BI GRCh38 9 34093295 34093295 + stop_gained Nonsense_Mutation SNP G G A rs1276644935 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 24 c.1015C>T p.Arg339Ter p.R339* ENST00000361264.9 NM_015397.4 339 Cga/Tga 7/9 P1 A R/* protein_coding YES CCDS6549.1 1015/1362 GCCTCGCTCCC COSM1108405 Gene3D:2.130.10.10;PANTHER:PTHR19860;PANTHER:PTHR19860:SF10;SMART:SM00320;Superfamily:SSF50978 ENSP00000355114 7/9 rs1276644935;COSV63513894 ENST00000361264 Transcript ENSG00000198876 HGNC:19911 HIGH NM_015397.4 stop_gained 0;1 1.0 Unknown 0;1 Q5T6F0.134 DCAF12 HGNC -1 1.0 UPI00000372E8 SNV DCAF12,stop_gained,p.R339*,ENST00000361264,NM_015397.4,c.1015C>T,HIGH,YES,,,-1;DCAF12,non_coding_transcript_exon_variant,,ENST00000466402,,n.485C>T,MODIFIER,,,,-1;AL354989.1,intron_variant,,ENST00000448245,,n.259-2554G>A,MODIFIER,YES,,,1 1282/3592 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.760779797332361e-06 0.0 0.0 0.0 0.0 0.0 9.4232898845803e-05 0.0 0.0 0.0 0.0 0 70 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 60 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DCAF12,non_coding_transcript_exon_variant,,ENST00000466402.1,n.485C>T,MODIFIER,;DCAF12,stop_gained,p.R339*,ENST00000361264.9,c.1015C>T,HIGH,YES;ENSG00000228352,intron_variant,,ENST00000448245.1,n.259-2554G>A,MODIFIER,YES +DAPK1 1612 BI GRCh38 9 87605063 87605063 + missense_variant Missense_Mutation SNP C C T rs753510016 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 9 c.172C>T p.Arg58Cys p.R58C ENST00000358077.9 NM_001288731.2 58 Cgc/Tgc 3/26 P1 T R/C protein_coding CCDS43842.1 172/4293 TGAGCCGCGAG COSM304407;COSM304408 PDB-ENSP_mappings:1ig1.A;PDB-ENSP_mappings:1jkk.A;PDB-ENSP_mappings:1jkl.A;PDB-ENSP_mappings:1jks.A;PDB-ENSP_mappings:1jkt.A;PDB-ENSP_mappings:1jkt.B;PDB-ENSP_mappings:1p4f.A;PDB-ENSP_mappings:1wvw.A;PDB-ENSP_mappings:1wvx.A;PDB-ENSP_mappings:1wvy.A;PDB-ENSP_mappings:2w4j.A;PDB-ENSP_mappings:2w4k.A;PDB-ENSP_mappings:2x0g.A;PDB-ENSP_mappings:2xuu.A;PDB-ENSP_mappings:2xzs.A;PDB-ENSP_mappings:2xzs.B;PDB-ENSP_mappings:2y0a.A;PDB-ENSP_mappings:2y4p.A;PDB-ENSP_mappings:2y4p.B;PDB-ENSP_mappings:2y4p.C;PDB-ENSP_mappings:2y4p.D;PDB-ENSP_mappings:2yak.A;PDB-ENSP_mappings:3dfc.B;PDB-ENSP_mappings:3dgk.A;PDB-ENSP_mappings:3eh9.A;PDB-ENSP_mappings:3eha.A;PDB-ENSP_mappings:3f5g.A;PDB-ENSP_mappings:3f5u.A;PDB-ENSP_mappings:3gu4.A;PDB-ENSP_mappings:3gu5.A;PDB-ENSP_mappings:3gu6.A;PDB-ENSP_mappings:3gu7.A;PDB-ENSP_mappings:3gu8.A;PDB-ENSP_mappings:3gub.A;PDB-ENSP_mappings:3zxt.A;PDB-ENSP_mappings:3zxt.B;PDB-ENSP_mappings:3zxt.C;PDB-ENSP_mappings:3zxt.D;PDB-ENSP_mappings:4b4l.A;PDB-ENSP_mappings:4pf4.A;PDB-ENSP_mappings:4tl0.A;PDB-ENSP_mappings:4txc.A;PDB-ENSP_mappings:4uv0.A;PDB-ENSP_mappings:4yo4.A;PDB-ENSP_mappings:4ypd.A;PDB-ENSP_mappings:5aut.A;PDB-ENSP_mappings:5auu.A;PDB-ENSP_mappings:5auv.A;PDB-ENSP_mappings:5auw.A;PDB-ENSP_mappings:5aux.A;PDB-ENSP_mappings:5auy.A;PDB-ENSP_mappings:5auz.A;PDB-ENSP_mappings:5av0.A;PDB-ENSP_mappings:5av1.A;PDB-ENSP_mappings:5av2.A;PDB-ENSP_mappings:5av3.A;PDB-ENSP_mappings:5av4.A;PDB-ENSP_mappings:6aar.A;PDB-ENSP_mappings:6fha.A;PDB-ENSP_mappings:6fhb.A;PDB-ENSP_mappings:6in4.A;PDB-ENSP_mappings:6qmo.A;PDB-ENSP_mappings:6qn4.A;CDD:cd14194;Pfam:PF00069;Gene3D:3.30.200.20;SMART:SM00220;Superfamily:SSF56112;PROSITE_profiles:PS50011;PANTHER:PTHR24342;PANTHER:PTHR24342:SF17 ENSP00000350785 3/26 rs753510016;COSV63789576 ENST00000358077 Transcript ENSG00000196730 HGNC:2674 MODERATE 6.535e-05 gnomAD_SAS missense_variant 0;1 possibly_damaging(0.902) Unknown deleterious(0) 0;1 P53355.214 DAPK1 HGNC 1 1.0 UPI0000210C2F P53355-1 SNV DAPK1,missense_variant,p.R58C,ENST00000408954,NM_004938.4,c.172C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.902),1;DAPK1,missense_variant,p.R58C,ENST00000469640,,c.172C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DAPK1,missense_variant,p.R58C,ENST00000622514,NM_001288729.1,c.172C>T,MODERATE,,deleterious(0),possibly_damaging(0.902),1;DAPK1,missense_variant,p.R58C,ENST00000472284,NM_001288730.2,c.172C>T,MODERATE,,deleterious(0),possibly_damaging(0.902),1;DAPK1,missense_variant,p.R58C,ENST00000358077,NM_001288731.2,c.172C>T,MODERATE,,deleterious(0),possibly_damaging(0.902),1;DAPK1,missense_variant,p.R58C,ENST00000491893,,c.172C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DAPK1,non_coding_transcript_exon_variant,,ENST00000496522,,n.382C>T,MODIFIER,,,,1;DAPK1,non_coding_transcript_exon_variant,,ENST00000472344,,n.306C>T,MODIFIER,,,,1;DAPK1,missense_variant,p.R58C,ENST00000489291,,c.172C>T,MODERATE,,deleterious(0),probably_damaging(0.966),1;DAPK1,non_coding_transcript_exon_variant,,ENST00000469067,,n.652C>T,MODIFIER,,,,1 355/5743 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.601e-05 6.396e-05 0.0 0.0 0.0 0.0 8.823e-06 0.0 6.535e-05 1.3519499589165209e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086229844484478e-05 0.0 3.086229844484478e-05 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DAPK1,missense_variant,NMD_transcript_variant,p.R58C,ENST00000489291.5,c.172C>T,MODERATE,;DAPK1,missense_variant,p.R58C,ENST00000491893.5,c.172C>T,MODERATE,;DAPK1,non_coding_transcript_exon_variant,,ENST00000472344.1,n.306C>T,MODIFIER,;DAPK1,missense_variant,p.R58C,ENST00000622514.4,c.172C>T,MODERATE,;DAPK1,non_coding_transcript_exon_variant,,ENST00000496522.5,n.382C>T,MODIFIER,;DAPK1,missense_variant,p.R58C,ENST00000408954.8,c.172C>T,MODERATE,YES;DAPK1,non_coding_transcript_exon_variant,,ENST00000469067.5,n.652C>T,MODIFIER,;DAPK1,missense_variant,p.R58C,ENST00000469640.6,c.172C>T,MODERATE,;DAPK1,missense_variant,p.R58C,ENST00000472284.5,c.172C>T,MODERATE,;DAPK1,missense_variant,p.R58C,ENST00000358077.9,c.172C>T,MODERATE, +ZNF367 195828 BI GRCh38 9 96394864 96394864 + missense_variant Missense_Mutation SNP C C T TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 21 c.650G>A p.Arg217His p.R217H ENST00000375256.5 NM_153695.4 217 cGt/cAt 3/5 P1 T R/H protein_coding YES CCDS6718.1 650/1053 GAAGACGCTGA COSM5486762 Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR23235;PANTHER:PTHR23235:SF51;SMART:SM00355;Superfamily:SSF57667 ENSP00000364405 3/5 COSV64547857 ENST00000375256 Transcript ENSG00000165244 HGNC:18320 MODERATE NM_153695.4 missense_variant 1 1.0 probably_damaging(0.999) Unknown deleterious(0) 1 Q7RTV3.137 ZNF367 HGNC -1 1.0 UPI000013E47A Q7RTV3-1 SNV ZNF367,missense_variant,p.R217H,ENST00000375256,NM_153695.4,c.650G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1 988/3687 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 82 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 57 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF367,missense_variant,p.R217H,ENST00000375256.5,c.650G>A,MODERATE,YES +FKTN 2218 BI GRCh38 9 105604290 105604290 + missense_variant Missense_Mutation SNP G G A rs200686690 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 40 50 c.445G>A p.Gly149Arg p.G149R ENST00000223528.6 NM_006731.2 149 Ggg/Agg 5/10 0.0006 0.0 0.0 0.0 0.0 0.0031 P1 A G/R protein_coding CCDS6766.1 445/1386 uncertain_significance TAGACGGGATA PANTHER:PTHR15407:SF28;PANTHER:PTHR15407 ENSP00000223528 5/10 rs200686690 ENST00000223528 Transcript 1.0 ENSG00000106692 HGNC:3622 MODERATE 0.0031 SAS missense_variant 1 benign(0.255) Unknown deleterious(0.05) O75072.161 FKTN HGNC 1 1.0 UPI000012A5A6 O75072-1 SNV FKTN,missense_variant,p.G149R,ENST00000357998,NM_001351502.2&NM_001351497.2&NM_001351499.2&NM_001351496.2&NM_001351500.2&NM_001079802.2,c.445G>A,MODERATE,YES,deleterious(0.05),benign(0.255),1;FKTN,missense_variant,p.G149R,ENST00000223528,NM_006731.2&NM_001351501.2&NM_001351498.2,c.445G>A,MODERATE,,deleterious(0.05),benign(0.255),1;FKTN,missense_variant,p.G149R,ENST00000675668,,c.445G>A,MODERATE,,deleterious(0.03),benign(0.17),1;FKTN,missense_variant,p.G149R,ENST00000676310,,c.445G>A,MODERATE,,deleterious(0.04),benign(0.17),1;FKTN,missense_variant,p.G149R,ENST00000674633,,c.445G>A,MODERATE,,deleterious(0.05),benign(0.046),1;FKTN,missense_variant,p.G149R,ENST00000448551,NM_001198963.2,c.445G>A,MODERATE,,deleterious(0.04),benign(0.107),1;FKTN,missense_variant,p.G149R,ENST00000675695,,c.445G>A,MODERATE,,deleterious(0.04),benign(0.198),1;FKTN,missense_variant,p.G149R,ENST00000674563,,c.445G>A,MODERATE,,deleterious(0.03),benign(0.216),1;FKTN,missense_variant,p.G149R,ENST00000642177,,c.445G>A,MODERATE,,deleterious(0.03),benign(0.216),1;FKTN,3_prime_UTR_variant,,ENST00000675736,,c.*53G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000602526,,c.*483G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000675232,,c.*580G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000676192,,c.*365G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000602661,,c.*53G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000675443,,c.*53G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000642952,,c.*443G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000642537,,c.*307G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000645933,,c.*443G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000642644,,c.*568G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000676371,,c.*252G>A,MODIFIER,,,,1;FKTN,3_prime_UTR_variant,,ENST00000374705,,c.*372G>A,MODIFIER,,,,1;FKTN,non_coding_transcript_exon_variant,,ENST00000676011,,n.1612G>A,MODIFIER,,,,1 569/7364 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.592e-05 6.152e-05 0.0 0.0 0.0 0.0 8.805e-06 0.0 6.533e-05 2.7052999939769503e-05 2.4328499421244487e-05 0.0 0.0 0.0 0.0 0.0 sas 0.000626043009106 0.0 0.0 0.0 0.000626043009106 0 76 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 90 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FKTN,non_coding_transcript_exon_variant,,ENST00000676011.1,n.1612G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642952.1,c.*443G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000374705.5,c.*372G>A,MODIFIER,;FKTN,missense_variant,p.G149R,ENST00000676310.1,c.445G>A,MODERATE,;FKTN,missense_variant,NMD_transcript_variant,p.G149R,ENST00000642177.1,c.445G>A,MODERATE,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642537.1,c.*307G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676371.1,c.*252G>A,MODIFIER,;FKTN,missense_variant,p.G149R,ENST00000674633.1,c.445G>A,MODERATE,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642644.1,c.*568G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645933.1,c.*443G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000602526.1,c.*483G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676192.1,c.*365G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675232.1,c.*580G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675736.1,c.*53G>A,MODIFIER,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000602661.6,c.*53G>A,MODIFIER,;FKTN,missense_variant,NMD_transcript_variant,p.G149R,ENST00000674563.1,c.445G>A,MODERATE,;FKTN,missense_variant,p.G149R,ENST00000448551.6,c.445G>A,MODERATE,;FKTN,missense_variant,p.G149R,ENST00000357998.10,c.445G>A,MODERATE,YES;FKTN,missense_variant,p.G149R,ENST00000675668.1,c.445G>A,MODERATE,;FKTN,missense_variant,p.G149R,ENST00000223528.6,c.445G>A,MODERATE,;FKTN,missense_variant,NMD_transcript_variant,p.G149R,ENST00000675695.1,c.445G>A,MODERATE,;FKTN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675443.1,c.*53G>A,MODIFIER, +RAD23B 5887 BI GRCh38 9 107322086 107322086 + missense_variant Missense_Mutation SNP C C T rs372514872 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 9 c.785C>T p.Thr262Met p.T262M ENST00000358015.8 NM_002874.5 262 aCg/aTg 7/10 P1 T T/M protein_coding YES CCDS6769.1 785/1230 AACTACGACAG Low_complexity_(Seg):seg;PANTHER:PTHR10621;PANTHER:PTHR10621:SF13;TIGRFAM:TIGR00601;MobiDB_lite:mobidb-lite ENSP00000350708 0.0 0.0001163 7/10 rs372514872 ENST00000358015 Transcript ENSG00000119318 HGNC:9813 MODERATE NM_002874.5 0.0001163 EA missense_variant 1.0 possibly_damaging(0.661) Unknown tolerated(0.17) P54727.197 RAD23B HGNC 1 1.0 UPI0000132F6C P54727-1 SNV RAD23B,missense_variant,p.T262M,ENST00000358015,NM_002874.5&NM_001244713.1,c.785C>T,MODERATE,YES,tolerated(0.17),possibly_damaging(0.661),1;RAD23B,missense_variant,p.T190M,ENST00000416373,NM_001244724.1,c.569C>T,MODERATE,,tolerated(0.08),possibly_damaging(0.661),1;RAD23B,intron_variant,,ENST00000457811,,c.290+3207C>T,MODIFIER,,,,1 1136/4114 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.02e-05 0.0 0.0 0.0 0.0 4.626e-05 3.547e-05 0.0 0.0 2.7045300157624297e-05 0.0 0.0010964899556711 0.0 0.0 0.0 0.0 nfe 4.62948992208112e-05 0.0 4.62948992208112e-05 0.0 0.0 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 71 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RAD23B,intron_variant,,ENST00000457811.1,c.290+3207C>T,MODIFIER,;RAD23B,missense_variant,p.T190M,ENST00000416373.6,c.569C>T,MODERATE,;RAD23B,missense_variant,p.T262M,ENST00000358015.8,c.785C>T,MODERATE,YES +KIAA1958 158405 BI GRCh38 9 112659400 112659400 + synonymous_variant Silent SNP C C T rs773442119 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 12 c.1482C>T p.Val494= p.V494= ENST00000337530.11 NM_133465.4 494 gtC/gtT 4/4 A1 T V protein_coding CCDS35108.1 1482/2151 GGTGTCGGCTT PANTHER:PTHR46963 ENSP00000336940 4/4 rs773442119 ENST00000337530 Transcript ENSG00000165185 HGNC:23427 LOW NM_133465.4 0.0003697 gnomAD_FIN synonymous_variant Unknown Q8N8K9.127 KIAA1958 HGNC 1 1.0 UPI000007327E Q8N8K9-1 SNV KIAA1958,synonymous_variant,p.V494=,ENST00000337530,NM_133465.4&NM_001287038.2,c.1482C>T,LOW,,,,1;KIAA1958,synonymous_variant,p.V522=,ENST00000536272,NM_001287036.1,c.1566C>T,LOW,YES,,,1 1798/11795 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.753e-05 0.0 0.0 0.0 5.441e-05 0.0003697 0.0001144 0.0 0.0 4.055639874422923e-05 2.4310800654347983e-05 0.0 0.0 0.0 0.0 0.0001881820062408 fin 0.0001881820062408 0.0 4.629629984265193e-05 0.0 0.0 0 47 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KIAA1958,synonymous_variant,p.V522=,ENST00000536272.5,c.1566C>T,LOW,;KIAA1958,synonymous_variant,p.V494=,ENST00000337530.11,c.1482C>T,LOW,YES +OR5C1 392391 BI GRCh38 9 122789588 122789588 + missense_variant Missense_Mutation SNP C C T rs772591814 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 20 c.656C>T p.Thr219Met p.T219M ENST00000373680.3 NM_001001923.1 219 aCg/aTg 1/1 P1 T T/M protein_coding YES CCDS35131.1 656/963 TATCACGGTGT Transmembrane_helices:TMhelix;PROSITE_profiles:PS50262;CDD:cd15945;PANTHER:PTHR26452:SF119;PANTHER:PTHR26452;Gene3D:1.20.1070.10;Pfam:PF13853;Superfamily:SSF81321 ENSP00000362784 1/1 rs772591814 ENST00000373680 Transcript ENSG00000148215 HGNC:8331 MODERATE 0.0001962 gnomAD_SAS missense_variant 1.0 benign(0.224) Unknown deleterious(0.02) Q8NGR4.139 OR5C1 HGNC 1 A0A126GW42.28 UPI0000061E7B SNV OR5C1,missense_variant,p.T219M,ENST00000373680,NM_001001923.1,c.656C>T,MODERATE,YES,deleterious(0.02),benign(0.224),1 656/963 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.188e-05 0.0 0.0 0.0 5.44e-05 0.0 0.0 0.0001636 0.0001962 1.3514600141206756e-05 0.0 0.0 0.0 0.0 0.0 0.0 sas 0.0004166669968981 0.0 0.0 0.0 0.0004166669968981 0 59 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 54 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS OR5C1,missense_variant,p.T219M,ENST00000373680.3,c.656C>T,MODERATE,YES +LRRC8A 56262 BI GRCh38 9 128908072 128908072 + missense_variant Missense_Mutation SNP C C T rs771228754 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 50 40 c.908C>T p.Thr303Met p.T303M ENST00000259324.5 NM_001127244.2 303 aCg/aTg 3/4 P1 T T/M protein_coding YES CCDS35155.1 908/2433 CCTGACGGGCT COSM5875632 PDB-ENSP_mappings:5zsu.A;PDB-ENSP_mappings:5zsu.B;PDB-ENSP_mappings:5zsu.C;PDB-ENSP_mappings:5zsu.D;PDB-ENSP_mappings:5zsu.E;PDB-ENSP_mappings:5zsu.F;PDB-ENSP_mappings:6djb.A;PDB-ENSP_mappings:6djb.B;PDB-ENSP_mappings:6djb.C;PDB-ENSP_mappings:6djb.D;PDB-ENSP_mappings:6djb.E;PDB-ENSP_mappings:6djb.F;Pfam:PF12534;PANTHER:PTHR45752;PANTHER:PTHR45752:SF23 ENSP00000259324 3/4 rs771228754;COSV52187071 ENST00000259324 Transcript 1.0 ENSG00000136802 HGNC:19027 MODERATE 0.0001735 gnomAD_AMR missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q8IWT6.169 LRRC8A HGNC 1 A0A024R892.49 2.0 UPI000004EF9E SNV LRRC8A,missense_variant,p.T303M,ENST00000259324,NM_001127244.1,c.908C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;LRRC8A,missense_variant,p.T303M,ENST00000372600,NM_019594.4,c.908C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;LRRC8A,missense_variant,p.T303M,ENST00000372599,NM_001127245.2,c.908C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;LRRC8A,upstream_gene_variant,,ENST00000492784,,,MODIFIER,,,,1 1431/4619 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.184e-05 0.0 0.0001735 0.0 0.0 0.0 8.798e-06 0.0 3.266e-05 4.733250170829706e-05 4.864050060859881e-05 0.0 0.0001326439960394 0.0 0.000201938993996 0.0 amr 0.0001326439960394 0.0 3.086130163865164e-05 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 90 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRRC8A,missense_variant,p.T303M,ENST00000259324.5,c.908C>T,MODERATE,;LRRC8A,missense_variant,p.T303M,ENST00000372599.7,c.908C>T,MODERATE,;LRRC8A,missense_variant,p.T303M,ENST00000372600.9,c.908C>T,MODERATE,YES +LRRC8A 56262 BI GRCh38 9 128908310 128908310 + synonymous_variant Silent SNP C C T rs776535684 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 23 c.1146C>T p.Tyr382= p.Y382= ENST00000259324.5 NM_001127244.2 382 taC/taT 3/4 P1 T Y protein_coding YES CCDS35155.1 1146/2433 CAATACGACCC PDB-ENSP_mappings:5zsu.A;PDB-ENSP_mappings:5zsu.B;PDB-ENSP_mappings:5zsu.C;PDB-ENSP_mappings:5zsu.D;PDB-ENSP_mappings:5zsu.E;PDB-ENSP_mappings:5zsu.F;PDB-ENSP_mappings:6djb.A;PDB-ENSP_mappings:6djb.B;PDB-ENSP_mappings:6djb.C;PDB-ENSP_mappings:6djb.D;PDB-ENSP_mappings:6djb.E;PDB-ENSP_mappings:6djb.F;PANTHER:PTHR45752;PANTHER:PTHR45752:SF23 ENSP00000259324 3/4 rs776535684 ENST00000259324 Transcript 1.0 ENSG00000136802 HGNC:19027 LOW 0.0001846 gnomAD_AFR synonymous_variant 1.0 Unknown Q8IWT6.169 LRRC8A HGNC 1 A0A024R892.49 2.0 UPI000004EF9E SNV LRRC8A,synonymous_variant,p.Y382=,ENST00000259324,NM_001127244.1,c.1146C>T,LOW,YES,,,1;LRRC8A,synonymous_variant,p.Y382=,ENST00000372600,NM_019594.4,c.1146C>T,LOW,,,,1;LRRC8A,synonymous_variant,p.Y382=,ENST00000372599,NM_001127245.2,c.1146C>T,LOW,,,,1;LRRC8A,upstream_gene_variant,,ENST00000492784,,,MODIFIER,,,,1 1669/4619 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0001846 0.0 0.0 0.0 0.0 8.794e-06 0.0 0.0 2.0276800569263287e-05 4.862869900534861e-05 0.0 6.629539711866528e-05 0.0 0.0 0.0 afr 4.862869900534861e-05 0.0 0.0 0.0 0.0 0 68 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 65 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRRC8A,synonymous_variant,p.Y382=,ENST00000259324.5,c.1146C>T,LOW,;LRRC8A,synonymous_variant,p.Y382=,ENST00000372599.7,c.1146C>T,LOW,;LRRC8A,synonymous_variant,p.Y382=,ENST00000372600.9,c.1146C>T,LOW,YES +COL5A1 1289 BI GRCh38 9 134820206 134820206 + missense_variant Missense_Mutation SNP G G A rs1489565447 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 7 c.4537G>A p.Gly1513Ser p.G1513S ENST00000371817.8 NM_000093.5 1513 Ggt/Agt 58/66 P3 A G/S protein_coding YES CCDS6982.1 4537/5517 CCTCCGGTCCT Pfam:PF01391;Pfam:PF01391;PANTHER:PTHR24023;PANTHER:PTHR24023:SF387;MobiDB_lite:mobidb-lite ENSP00000360882 58/66 rs1489565447;COSV100879461 ENST00000371817 Transcript 1.0 ENSG00000130635 HGNC:2209 MODERATE NM_000093.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 P20908.216 COL5A1 HGNC 1 A0A024R8E5.45 1.0 UPI0000210EE3 P20908-1 SNV COL5A1,missense_variant,p.G1513S,ENST00000371817,NM_000093.5,c.4537G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;COL5A1,missense_variant,p.G1513S,ENST00000618395,NM_001278074.1,c.4537G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;COL5A1,upstream_gene_variant,,ENST00000371820,,,MODIFIER,,,,1;COL5A1,upstream_gene_variant,,ENST00000460264,,,MODIFIER,,,,1;COL5A1,upstream_gene_variant,,ENST00000465877,,,MODIFIER,,,,1 4922/8442 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COL5A1,missense_variant,p.G1513S,ENST00000371817.8,c.4537G>A,MODERATE,YES;COL5A1,missense_variant,p.G1513S,ENST00000371820.4,c.4537G>A,MODERATE, +KCNT1 57582 BI GRCh38 9 135759775 135759775 + synonymous_variant Silent SNP C C T rs747685419 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 19 c.894C>T p.Tyr298= p.Y298= ENST00000488444.6 298 taC/taT 11/31 T Y protein_coding 894/3693 likely_benign GGCTACGGTGA Gene3D:1.10.287.70;Pfam:PF07885;PANTHER:PTHR10027;PANTHER:PTHR10027:SF14;Superfamily:SSF81324;Transmembrane_helices:TMhelix ENSP00000419007 11/31 rs747685419 ENST00000488444 Transcript 1.0 ENSG00000107147 HGNC:18865 LOW 6.175e-05 gnomAD_AFR synonymous_variant 1 Unknown Q5JUK3.148 KCNT1 HGNC 1 5.0 UPI000058E393 Q5JUK3-1 SNV KCNT1,synonymous_variant,p.Y317=,ENST00000371757,NM_020822.3,c.951C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y272=,ENST00000628528,NM_001272003.2,c.816C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y284=,ENST00000263604,,c.852C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y264=,ENST00000674572,,c.792C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y236=,ENST00000676421,,c.708C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y233=,ENST00000675399,,c.699C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y233=,ENST00000675090,,c.699C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y298=,ENST00000631073,,c.894C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y317=,ENST00000487664,,c.951C>T,LOW,YES,,,1;KCNT1,synonymous_variant,p.Y278=,ENST00000486577,,c.834C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y298=,ENST00000490355,,c.894C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y298=,ENST00000488444,,c.894C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y298=,ENST00000491806,,c.894C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y264=,ENST00000630792,,c.792C>T,LOW,,,,1;KCNT1,synonymous_variant,p.Y264=,ENST00000473941,,c.792C>T,LOW,,,,1;KCNT1,3_prime_UTR_variant,,ENST00000460750,,c.*561C>T,MODIFIER,,,,1;KCNT1,non_coding_transcript_exon_variant,,ENST00000490363,,n.770C>T,MODIFIER,,,,1 897/3696 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.795e-05 6.175e-05 2.896e-05 0.0 5.446e-05 0.0 2.654e-05 0.0 3.268e-05 2.027190021181013e-05 2.4303699319716543e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.086130163865164e-05 0.0 3.086130163865164e-05 0.0 0.0 0 42 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KCNT1,non_coding_transcript_exon_variant,,ENST00000490363.3,n.770C>T,MODIFIER,;KCNT1,synonymous_variant,p.Y236=,ENST00000676421.1,c.708C>T,LOW,;KCNT1,synonymous_variant,p.Y233=,ENST00000675399.1,c.699C>T,LOW,;KCNT1,synonymous_variant,p.Y233=,ENST00000675090.1,c.699C>T,LOW,;KCNT1,synonymous_variant,p.Y298=,ENST00000490355.6,c.894C>T,LOW,;KCNT1,synonymous_variant,p.Y298=,ENST00000488444.6,c.894C>T,LOW,;KCNT1,synonymous_variant,p.Y298=,ENST00000631073.2,c.894C>T,LOW,;KCNT1,synonymous_variant,p.Y298=,ENST00000491806.6,c.894C>T,LOW,;KCNT1,synonymous_variant,p.Y284=,ENST00000263604.5,c.852C>T,LOW,;KCNT1,synonymous_variant,p.Y264=,ENST00000630792.2,c.792C>T,LOW,;KCNT1,synonymous_variant,p.Y278=,ENST00000486577.6,c.834C>T,LOW,;KCNT1,synonymous_variant,p.Y264=,ENST00000473941.5,c.792C>T,LOW,;KCNT1,synonymous_variant,p.Y264=,ENST00000674572.1,c.792C>T,LOW,;KCNT1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000460750.5,c.*561C>T,MODIFIER,;KCNT1,synonymous_variant,p.Y272=,ENST00000628528.2,c.816C>T,LOW,;KCNT1,synonymous_variant,p.Y317=,ENST00000487664.5,c.951C>T,LOW,;KCNT1,synonymous_variant,p.Y317=,ENST00000371757.7,c.951C>T,LOW,YES +CAMSAP1 157922 BI GRCh38 9 135821233 135821233 + missense_variant Missense_Mutation SNP C C T rs749209361 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 39 36 c.3428G>A p.Arg1143Gln p.R1143Q ENST00000389532.9 NM_015447.4 1143 cGg/cAg 11/17 P4 T R/Q protein_coding CCDS35176.2 3428/4809 GCGTCCGAGGG PANTHER:PTHR21595;PANTHER:PTHR21595:SF3;MobiDB_lite:mobidb-lite ENSP00000374183 11/17 rs749209361 ENST00000389532 Transcript ENSG00000130559 HGNC:19946 MODERATE NM_015447.4 0.0001091 gnomAD_EAS missense_variant benign(0.057) Unknown tolerated(0.38) Q5T5Y3.132 CAMSAP1 HGNC -1 A0A384NY94.8 5.0 UPI0000EDA283 Q5T5Y3-1 SNV CAMSAP1,missense_variant,p.R1143Q,ENST00000389532,NM_015447.4,c.3428G>A,MODERATE,,tolerated(0.38),benign(0.057),-1;CAMSAP1,missense_variant,p.R865Q,ENST00000312405,,c.2594G>A,MODERATE,,tolerated(0.24),benign(0.057),-1;CAMSAP1,missense_variant,p.R1154Q,ENST00000409386,,c.3461G>A,MODERATE,YES,tolerated(0.38),benign(0.117),-1;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,,n.2490G>A,MODIFIER,,,,-1;CAMSAP1,upstream_gene_variant,,ENST00000493088,,,MODIFIER,,,,-1;CAMSAP1,upstream_gene_variant,,ENST00000482664,,,MODIFIER,,,,-1;CAMSAP1,upstream_gene_variant,,ENST00000487868,,,MODIFIER,,,,-1 3815/8018 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.037e-05 0.0 5.794e-05 0.0 0.0001091 0.0 0.0 0.0 3.27e-05 2.0276000213925727e-05 4.861449997406453e-05 0.0 0.0 0.0 0.0 0.0 afr 4.861449997406453e-05 0.0 1.5430699932039715e-05 0.0 0.0 0 78 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 75 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CAMSAP1,missense_variant,p.R1154Q,ENST00000409386.3,c.3461G>A,MODERATE,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991.5,n.2490G>A,MODIFIER,;CAMSAP1,missense_variant,p.R865Q,ENST00000312405.10,c.2594G>A,MODERATE,;CAMSAP1,missense_variant,p.R1143Q,ENST00000389532.9,c.3428G>A,MODERATE,YES +SEC16A 9919 BI GRCh38 9 136476551 136476551 + synonymous_variant Silent SNP G G A rs761577334 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 8 c.1065C>T p.Ala355= p.A355= ENST00000290037.10 NM_001276418.2 355 gcC/gcT 2/29 P3 A A protein_coding YES CCDS55351.1 1065/7074 GACCCGGCCCC PANTHER:PTHR13402;PANTHER:PTHR13402:SF13 ENSP00000325827 1/30 rs761577334 ENST00000313050 Transcript ENSG00000148396 HGNC:29006 LOW 5.578e-05 gnomAD_EAS synonymous_variant 1.0 Unknown O15027.174 SEC16A HGNC -1 2.0 UPI0000F0888B O15027-1 SNV SEC16A,synonymous_variant,p.A355=,ENST00000290037,NM_001276418.1,c.1065C>T,LOW,,,,-1;SEC16A,synonymous_variant,p.A355=,ENST00000313050,NM_014866.2,c.1065C>T,LOW,YES,,,-1;SEC16A,synonymous_variant,p.A177=,ENST00000371706,,c.531C>T,LOW,,,,-1;SEC16A,synonymous_variant,p.A177=,ENST00000431893,,c.531C>T,LOW,,,,-1 1139/8806 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.219e-05 0.0 2.914e-05 0.0 5.578e-05 0.0 8.991e-06 0.0 0.0 1.3517899787984788e-05 2.4311999368364923e-05 0.0 6.625150126637891e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 23 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SEC16A,synonymous_variant,p.A177=,ENST00000431893.3,c.531C>T,LOW,;SEC16A,synonymous_variant,p.A355=,ENST00000690691.1,c.1065C>T,LOW,;SEC16A,synonymous_variant,p.A355=,ENST00000684901.1,c.1065C>T,LOW,YES;SEC16A,missense_variant,p.R189W,ENST00000371706.8,c.565C>T,MODERATE,;SEC16A,synonymous_variant,p.A355=,ENST00000313050.11,c.1065C>T,LOW,;SEC16A,synonymous_variant,p.A355=,ENST00000290037.10,c.1065C>T,LOW, +KIAA1217 56243 BI GRCh38 10 24521895 24521895 + missense_variant Missense_Mutation SNP C C T rs751142962 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 19 c.2422C>T p.Arg808Cys p.R808C ENST00000376454.8 NM_019590.5 808 Cgc/Tgc 12/21 P3 T R/C protein_coding YES CCDS31165.1 2422/5832 GTGTGCGCAGC PANTHER:PTHR22741;PANTHER:PTHR22741:SF11 ENSP00000365637 12/21 rs751142962;COSV56824384 ENST00000376454 Transcript ENSG00000120549 HGNC:25428 MODERATE NM_019590.5 0.0004896 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.998) Unknown deleterious(0) 0;1 Q5T5P2.136 KIAA1217 HGNC 1 1.0 UPI000013EC2A Q5T5P2-1 SNV KIAA1217,missense_variant,p.R808C,ENST00000376454,NM_019590.5,c.2422C>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;KIAA1217,missense_variant,p.R491C,ENST00000376451,,c.1471C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;KIAA1217,missense_variant,p.R728C,ENST00000376462,NM_001098500.3,c.2182C>T,MODERATE,,deleterious(0),probably_damaging(0.992),1;KIAA1217,missense_variant,p.R773C,ENST00000376452,NM_001282767.1,c.2317C>T,MODERATE,,deleterious(0),probably_damaging(0.987),1;KIAA1217,missense_variant,p.R773C,ENST00000458595,NM_001282768.1,c.2317C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;KIAA1217,missense_variant,p.R728C,ENST00000430453,,c.2182C>T,MODERATE,,deleterious(0),probably_damaging(0.992),1;KIAA1217,missense_variant,p.R491C,ENST00000396445,,c.1471C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;KIAA1217,missense_variant,p.R491C,ENST00000307544,NM_001282769.2,c.1471C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;KIAA1217,missense_variant,p.R773C,ENST00000376456,,c.2317C>T,MODERATE,,deleterious(0),probably_damaging(0.987),1;KIAA1217,missense_variant,p.R491C,ENST00000396446,NM_001321681.2&NM_001282770.2,c.1471C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;KIAA1217,missense_variant,p.R623C,ENST00000438429,,c.1867C>T,MODERATE,,deleterious(0),probably_damaging(0.987),1 2478/7407 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.39e-05 6.156e-05 0.0 0.0 0.0004896 9.619e-05 1.761e-05 0.0 6.533e-05 3.3820298995124176e-05 7.299979915842414e-05 0.0 6.628660048590973e-05 0.0 0.0 0.0 afr 7.299979915842414e-05 0.0 0.0 0.0004945599939674 0.0 0 37 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KIAA1217,missense_variant,p.R491C,ENST00000376451.4,c.1471C>T,MODERATE,;KIAA1217,missense_variant,p.R491C,ENST00000396445.5,c.1471C>T,MODERATE,;KIAA1217,missense_variant,p.R491C,ENST00000396446.5,c.1471C>T,MODERATE,;KIAA1217,missense_variant,p.R491C,ENST00000307544.10,c.1471C>T,MODERATE,;KIAA1217,missense_variant,p.R729C,ENST00000696626.1,c.2185C>T,MODERATE,;KIAA1217,missense_variant,p.R623C,ENST00000438429.5,c.1867C>T,MODERATE,;KIAA1217,missense_variant,p.R808C,ENST00000376454.8,c.2422C>T,MODERATE,YES;KIAA1217,missense_variant,p.R773C,ENST00000376456.8,c.2317C>T,MODERATE,;KIAA1217,missense_variant,p.R728C,ENST00000430453.6,c.2182C>T,MODERATE,;KIAA1217,missense_variant,p.R773C,ENST00000376452.7,c.2317C>T,MODERATE,;KIAA1217,missense_variant,p.R773C,ENST00000458595.5,c.2317C>T,MODERATE,;KIAA1217,missense_variant,p.R728C,ENST00000376462.5,c.2182C>T,MODERATE, +JCAD 57608 BI GRCh38 10 30029627 30029627 + missense_variant Missense_Mutation SNP C C T rs772929418 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 146 15 c.521G>A p.Arg174Gln p.R174Q ENST00000375377.2 NM_001350021.2 174 cGa/cAa 3/4 P1 T R/Q protein_coding YES CCDS41500.1 521/4080 ACATTCGCAAT COSM3437171 PANTHER:PTHR34757;Pfam:PF15351 ENSP00000364526 3/4 rs772929418;COSV64757781 ENST00000375377 Transcript ENSG00000165757 HGNC:29283 MODERATE NM_020848.4 6.457e-05 gnomAD_AFR missense_variant 0;1 1.0 possibly_damaging(0.786) Unknown deleterious(0.02) 0;1 Q9P266.119 JCAD HGNC -1 5.0 UPI00001D8117 SNV JCAD,missense_variant,p.R174Q,ENST00000375377,NM_001350021.2&NM_001350022.2&NM_020848.4&NM_001350001.2,c.521G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.786),-1 685/9324 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.015e-06 6.457e-05 0.0 0.0 0.0 0.0 8.829e-06 0.0 0.0 3.379339977982454e-05 7.292530062841251e-05 0.0 0.0 0.0 0.0 0.0 afr 7.292530062841251e-05 0.0 3.085660137003288e-05 0.0 0.0 0 182 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 161 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS JCAD,missense_variant,p.R174Q,ENST00000375377.2,c.521G>A,MODERATE,YES +PARD3 56288 BI GRCh38 10 34359197 34359197 + stop_gained Nonsense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 72 32 c.2017C>T p.Arg673Ter p.R673* ENST00000374789.8 NM_019619.4 673 Cga/Tga 14/25 P4 A R/* protein_coding YES CCDS7178.1 2017/4071 TCCTCGTTTAT Gene3D:2.30.42.10;PANTHER:PTHR16484;PANTHER:PTHR16484:SF10;SMART:SM00228;Superfamily:SSF50156;CDD:cd00992 ENSP00000363921 14/25 COSV60757657 ENST00000374789 Transcript ENSG00000148498 HGNC:16051 HIGH stop_gained 1 1.0 Unknown 1 Q8TEW0.189 PARD3 HGNC -1 1.0 UPI0000073A9F Q8TEW0-1 SNV PARD3,stop_gained,p.R673*,ENST00000374789,NM_019619.4,c.2017C>T,HIGH,YES,,,-1;PARD3,stop_gained,p.R673*,ENST00000374788,NM_001184785.2,c.2017C>T,HIGH,,,,-1;PARD3,stop_gained,p.R660*,ENST00000545693,NM_001184786.1,c.1978C>T,HIGH,,,,-1;PARD3,stop_gained,p.R673*,ENST00000346874,NM_001184787.2,c.2017C>T,HIGH,,,,-1;PARD3,stop_gained,p.R660*,ENST00000350537,NM_001184789.2&NM_001184788.2,c.1978C>T,HIGH,,,,-1;PARD3,stop_gained,p.R616*,ENST00000374790,,c.1846C>T,HIGH,,,,-1;PARD3,stop_gained,p.R616*,ENST00000545260,NM_001184790.1,c.1846C>T,HIGH,,,,-1;PARD3,stop_gained,p.R616*,ENST00000374794,NM_001184791.2,c.1846C>T,HIGH,,,,-1;PARD3,stop_gained,p.R673*,ENST00000340077,NM_001184792.1,c.2017C>T,HIGH,,,,-1;PARD3,stop_gained,p.R673*,ENST00000374773,NM_001184793.2,c.2017C>T,HIGH,,,,-1;PARD3,stop_gained,p.R660*,ENST00000374776,NM_001184794.2,c.1978C>T,HIGH,,,,-1;PARD3,stop_gained,p.R390*,ENST00000544292,,c.1168C>T,HIGH,,,,-1;PARD3,stop_gained,p.R111*,ENST00000374768,,c.331C>T,HIGH,,,,-1;PARD3,non_coding_transcript_exon_variant,,ENST00000651752,,n.346C>T,MODIFIER,,,,-1 2318/5980 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 145 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 105 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PARD3,non_coding_transcript_exon_variant,,ENST00000651752.1,n.346C>T,MODIFIER,;PARD3,stop_gained,p.R111*,ENST00000374768.1,c.331C>T,HIGH,;PARD3,stop_gained,p.R390*,ENST00000544292.5,c.1168C>T,HIGH,;PARD3,stop_gained,p.R673*,ENST00000374773.6,c.2017C>T,HIGH,;PARD3,stop_gained,p.R673*,ENST00000340077.9,c.2017C>T,HIGH,;PARD3,stop_gained,p.R660*,ENST00000374776.6,c.1978C>T,HIGH,;PARD3,stop_gained,p.R616*,ENST00000374794.8,c.1846C>T,HIGH,;PARD3,stop_gained,p.R673*,ENST00000374788.8,c.2017C>T,HIGH,YES;PARD3,stop_gained,p.R616*,ENST00000374790.8,c.1846C>T,HIGH,;PARD3,stop_gained,p.R673*,ENST00000374789.8,c.2017C>T,HIGH,;PARD3,stop_gained,p.R673*,ENST00000346874.9,c.2017C>T,HIGH,;PARD3,stop_gained,p.R660*,ENST00000350537.9,c.1978C>T,HIGH,;PARD3,stop_gained,p.R646*,ENST00000696673.1,c.1936C>T,HIGH,;PARD3,stop_gained,p.R660*,ENST00000545693.5,c.1978C>T,HIGH,;PARD3,stop_gained,p.R616*,ENST00000545260.5,c.1846C>T,HIGH, +RET 5979 BI GRCh38 10 43102534 43102534 + missense_variant Missense_Mutation SNP G G A rs759229505 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 4 c.530G>A p.Arg177Gln p.R177Q ENST00000355710.8 NM_020975.6 177 cGg/cAg 3/20 A2 A R/Q protein_coding YES CCDS7200.1 530/3345 uncertain_significance CATTCGGGAGA COSM5359844;COSM5359845 PDB-ENSP_mappings:2x2u.A;PDB-ENSP_mappings:4ux8.A;PDB-ENSP_mappings:4ux8.B;PDB-ENSP_mappings:6gl7.E;PDB-ENSP_mappings:6gl7.F;PDB-ENSP_mappings:6q2j.E;PDB-ENSP_mappings:6q2j.F;PDB-ENSP_mappings:6q2n.E;PDB-ENSP_mappings:6q2n.F;PDB-ENSP_mappings:6q2o.E;PDB-ENSP_mappings:6q2o.F;PDB-ENSP_mappings:6q2r.E;PDB-ENSP_mappings:6q2r.F;PDB-ENSP_mappings:6q2r.Y;PDB-ENSP_mappings:6q2r.Z;PDB-ENSP_mappings:6q2s.E;PDB-ENSP_mappings:6q2s.F;CDD:cd11304;Pfam:PF00028;Gene3D:2.60.40.60;PIRSF:PIRSF000631;Superfamily:SSF49313;PROSITE_profiles:PS50268;PANTHER:PTHR24416;PANTHER:PTHR24416:SF485 ENSP00000347942 3/20 rs759229505;COSV60704547 ENST00000355710 Transcript 1.0 ENSG00000165731 HGNC:9967 MODERATE NM_020975.6 6.157e-05 gnomAD_NFE missense_variant 1;1 1.0 possibly_damaging(0.903) Unknown tolerated(0.2) 0;1 P07949.256 RET HGNC 1 A0A024R7T2.57 5.0 UPI00001336E1 P07949-1 SNV RET,missense_variant,p.R177Q,ENST00000355710,NM_020975.6,c.530G>A,MODERATE,YES,tolerated(0.2),possibly_damaging(0.903),1;RET,missense_variant,p.R177Q,ENST00000615310,,c.530G>A,MODERATE,,tolerated(0.07),probably_damaging(0.986),1;RET,missense_variant,p.R177Q,ENST00000340058,NM_020630.5&NM_001355216.1,c.530G>A,MODERATE,,tolerated(0.21),possibly_damaging(0.843),1;RET,missense_variant,p.R102Q,ENST00000640619,,c.305G>A,MODERATE,,tolerated_low_confidence(0.06),probably_damaging(0.916),1;RET,3_prime_UTR_variant,,ENST00000638465,,c.*129G>A,MODIFIER,,,,1;RET,intron_variant,,ENST00000498820,,c.74-9565G>A,MODIFIER,,,,1;RET,missense_variant,p.R177Q,ENST00000671844,,c.530G>A,MODERATE,,tolerated(0.08),possibly_damaging(0.672),1;RET,intron_variant,,ENST00000672389,,c.74-8673G>A,MODIFIER,,,,1;RET,upstream_gene_variant,,ENST00000479913,,,MODIFIER,,,,1 720/5617 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.58e-05 0.0 5.782e-05 0.0 0.0 0.0 6.157e-05 0.0 0.0 6.761510121577885e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5432100553880446e-05 0.0 0.0 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RET,missense_variant,p.R177Q,ENST00000615310.5,c.530G>A,MODERATE,;RET,intron_variant,,ENST00000498820.5,c.74-9565G>A,MODIFIER,;RET,3_prime_UTR_variant,,ENST00000638465.2,c.*129G>A,MODIFIER,;RET,missense_variant,p.R177Q,ENST00000355710.8,c.530G>A,MODERATE,YES;RET,3_prime_UTR_variant,,ENST00000683278.2,c.*129G>A,MODIFIER,;RET,intron_variant,NMD_transcript_variant,,ENST00000672389.1,c.74-8673G>A,MODIFIER,;RET,missense_variant,p.R177Q,ENST00000684216.2,c.530G>A,MODERATE,;RET,missense_variant,p.R134Q,ENST00000640619.2,c.401G>A,MODERATE,;RET,missense_variant,p.R177Q,ENST00000340058.6,c.530G>A,MODERATE,;RET,missense_variant,p.R134Q,ENST00000713926.1,c.401G>A,MODERATE,;RET,missense_variant,NMD_transcript_variant,p.R177Q,ENST00000671844.1,c.530G>A,MODERATE, +ZNF503 84858 BI GRCh38 10 75398847 75398847 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 8 4 c.1843G>A p.Ala615Thr p.A615T ENST00000372524.5 NM_032772.6 615 Gcc/Acc 2/2 P1 T A/T protein_coding YES CCDS7350.1 1843/1941 GGGGGCGCCAG PANTHER:PTHR12522;PANTHER:PTHR12522:SF3;Low_complexity_(Seg):seg ENSP00000361602 2/2 ENST00000372524 Transcript ENSG00000165655 HGNC:23589 MODERATE NM_032772.6 missense_variant 1.0 benign(0.318) Unknown tolerated(0.06) Q96F45.146 ZNF503 HGNC -1 1.0 UPI000004A951 Q96F45-1 SNV ZNF503,missense_variant,p.A615T,ENST00000372524,NM_032772.6,c.1843G>A,MODERATE,YES,tolerated(0.06),benign(0.318),-1;AC010997.3,intron_variant,,ENST00000418818,,n.142+2258G>A,MODIFIER,YES,,,-1;ZNF503-AS2,upstream_gene_variant,,ENST00000425916,,,MODIFIER,YES,,,1;ZNF503-AS2,upstream_gene_variant,,ENST00000466942,,,MODIFIER,,,,1;ZNF503-AS2,upstream_gene_variant,,ENST00000486015,,,MODIFIER,,,,1;ZNF503-AS2,upstream_gene_variant,,ENST00000491557,,,MODIFIER,,,,1 2188/3205 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 9 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 14 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF503,missense_variant,p.A615T,ENST00000372524.5,c.1843G>A,MODERATE,YES;ENSG00000270087,intron_variant,,ENST00000418818.6,n.142+2258G>A,MODIFIER,YES +KCNMA1 3778 BI GRCh38 10 76891570 76891570 + synonymous_variant Silent SNP G G A rs372103668 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 13 c.3297C>T p.Arg1099= p.R1099= ENST00000286628.14 NM_001161352.2 1099 cgC/cgT 26/28 A2 A R protein_coding CCDS60569.1 3297/3711 GCCACGCGGCA PDB-ENSP_mappings:3mt5.A;PDB-ENSP_mappings:3naf.A;PDB-ENSP_mappings:6v22.A;PDB-ENSP_mappings:6v22.B;PDB-ENSP_mappings:6v22.C;PDB-ENSP_mappings:6v22.D;PDB-ENSP_mappings:6v35.A;PDB-ENSP_mappings:6v35.B;PDB-ENSP_mappings:6v35.C;PDB-ENSP_mappings:6v35.D;PDB-ENSP_mappings:6v38.A;PDB-ENSP_mappings:6v38.B;PDB-ENSP_mappings:6v38.C;PDB-ENSP_mappings:6v38.D;PDB-ENSP_mappings:6v3g.A;PDB-ENSP_mappings:6v3g.B;PDB-ENSP_mappings:6v3g.C;PDB-ENSP_mappings:6v3g.D;PANTHER:PTHR10027;PANTHER:PTHR10027:SF28 ENSP00000286628 0.0 0.0001163 26/28 rs372103668 ENST00000286628 Transcript 1.0 ENSG00000156113 HGNC:6284 LOW NM_001161352.2 0.0001163 EA synonymous_variant Unknown Q12791.197 KCNMA1 HGNC -1 1.0 UPI00003519E7 Q12791-1 SNV KCNMA1,synonymous_variant,p.R1071=,ENST00000639913,,c.3213C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1044=,ENST00000638991,NM_001322829.2,c.3132C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000639601,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R906=,ENST00000604624,,c.2718C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000639486,NM_001322832.2,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1006=,ENST00000639205,,c.3018C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1099=,ENST00000286628,NM_001161352.2,c.3297C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000286627,NM_002247.4,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1070=,ENST00000640969,,c.3210C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R934=,ENST00000354353,,c.2802C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1044=,ENST00000640141,NM_001322836.2,c.3132C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R903=,ENST00000406533,,c.2709C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1071=,ENST00000639406,NM_001271519.2,c.3213C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1106=,ENST00000640523,,c.3318C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R883=,ENST00000638754,,c.2649C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1072=,ENST00000372443,NM_001322835.2&NM_001322837.2,c.3216C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1006=,ENST00000639498,,c.3018C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1103=,ENST00000638848,,c.3309C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1075=,ENST00000638223,NM_001322830.2,c.3225C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000639090,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1045=,ENST00000639489,NM_001014797.3,c.3135C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R995=,ENST00000639344,,c.2985C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1070=,ENST00000434208,,c.3210C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1099=,ENST00000404771,,c.3297C>T,LOW,YES,,,-1;KCNMA1,synonymous_variant,p.R1099=,ENST00000457953,,c.3297C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1102=,ENST00000639591,,c.3306C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1048=,ENST00000640605,,c.3144C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1045=,ENST00000638606,,c.3135C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1045=,ENST00000640182,,c.3135C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1044=,ENST00000372440,,c.3132C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1044=,ENST00000638351,,c.3132C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000638203,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000638306,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1046=,ENST00000372421,,c.3138C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1006=,ENST00000372408,,c.3018C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R438=,ENST00000639716,,c.1314C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1043=,ENST00000372437,,c.3129C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1103=,ENST00000638759,,c.3309C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1102=,ENST00000638575,,c.3306C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1085=,ENST00000638514,,c.3255C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1099=,ENST00000639544,,c.3297C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1034=,ENST00000638895,,c.3102C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000640834,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1082=,ENST00000626620,NM_001161353.2,c.3246C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1009=,ENST00000639823,,c.3027C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1051=,ENST00000639370,,c.3153C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1003=,ENST00000372403,,c.3009C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1041=,ENST00000640029,,c.3123C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1038=,ENST00000640934,,c.3114C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1049=,ENST00000640773,,c.3147C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R1005=,ENST00000404857,NM_001322838.1,c.3015C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R975=,ENST00000638283,,c.2925C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R991=,ENST00000640807,NM_001271518.2,c.2973C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R982=,ENST00000638252,,c.2946C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R925=,ENST00000640626,,c.2775C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R830=,ENST00000639730,,c.2490C>T,LOW,,,,-1;KCNMA1,synonymous_variant,p.R852=,ENST00000640353,,c.2556C>T,LOW,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639069,,n.2840C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639851,,n.3347C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000640570,,n.2827C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000638999,,n.2308C>T,MODIFIER,,,,-1;KCNMA1,upstream_gene_variant,,ENST00000468471,,,MODIFIER,,,,-1;KCNMA1,upstream_gene_variant,,ENST00000638512,,,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000638751,,c.*2254C>T,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000639968,,c.*2141C>T,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000639483,,c.*1819C>T,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000639995,,c.*1027C>T,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000640093,,c.*1946C>T,MODIFIER,,,,-1;KCNMA1,3_prime_UTR_variant,,ENST00000639691,,c.*2002C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000638632,,n.7486C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639657,,n.3206C>T,MODIFIER,,,,-1;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639321,,n.2044C>T,MODIFIER,,,,-1;KCNMA1-AS1,non_coding_transcript_exon_variant,,ENST00000609102,,n.386G>A,MODIFIER,,,,1;KCNMA1-AS1,intron_variant,,ENST00000426234,,n.69+3289G>A,MODIFIER,,,,1;KCNMA1-AS1,intron_variant,,ENST00000429850,,n.238+3289G>A,MODIFIER,YES,,,1;KCNMA1-AS1,intron_variant,,ENST00000458661,,n.206+3289G>A,MODIFIER,,,,1;KCNMA1-AS1,intron_variant,,ENST00000595702,,n.455+1802G>A,MODIFIER,,,,1 3463/6261 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.597e-05 0.0 0.0 9.956e-05 0.0 0.0 1.766e-05 0.0 3.267e-05 1.35235995912808e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0002088549954351 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KCNMA1-AS1,intron_variant,,ENST00000426234.5,n.69+3289G>A,MODIFIER,;KCNMA1-AS1,intron_variant,,ENST00000458661.6,n.206+3289G>A,MODIFIER,YES;KCNMA1-AS1,non_coding_transcript_exon_variant,,ENST00000609102.5,n.386G>A,MODIFIER,;KCNMA1-AS1,intron_variant,,ENST00000595702.1,n.455+1802G>A,MODIFIER,;KCNMA1-AS1,intron_variant,,ENST00000429850.2,n.238+3289G>A,MODIFIER,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639321.1,n.2044C>T,MODIFIER,;KCNMA1,missense_variant,p.R852C,ENST00000640353.1,c.2554C>T,MODERATE,;KCNMA1,missense_variant,p.R1049C,ENST00000640773.1,c.3145C>T,MODERATE,;KCNMA1,synonymous_variant,p.R1085=,ENST00000638514.1,c.3255C>T,LOW,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000638999.1,n.2308C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1103=,ENST00000638759.1,c.3309C>T,LOW,;KCNMA1,synonymous_variant,p.R1082=,ENST00000626620.3,c.3246C>T,LOW,;KCNMA1,synonymous_variant,p.R1102=,ENST00000638575.1,c.3306C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000640834.1,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1009=,ENST00000639823.1,c.3027C>T,LOW,;KCNMA1,synonymous_variant,p.R1071=,ENST00000639406.1,c.3213C>T,LOW,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000638751.1,c.*2254C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1070=,ENST00000640969.1,c.3210C>T,LOW,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000638632.1,n.7486C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R883=,ENST00000638754.1,c.2649C>T,LOW,;KCNMA1,synonymous_variant,p.R1044=,ENST00000640141.1,c.3132C>T,LOW,;KCNMA1,synonymous_variant,p.R438=,ENST00000639716.1,c.1314C>T,LOW,;KCNMA1,missense_variant,p.A830V,ENST00000639730.1,c.2489C>T,MODERATE,;KCNMA1,missense_variant,p.R1051C,ENST00000639370.1,c.3151C>T,MODERATE,;KCNMA1,synonymous_variant,p.R975=,ENST00000638283.1,c.2925C>T,LOW,;KCNMA1,synonymous_variant,p.R1099=,ENST00000286628.14,c.3297C>T,LOW,YES;KCNMA1,synonymous_variant,p.R934=,ENST00000354353.9,c.2802C>T,LOW,;KCNMA1,synonymous_variant,p.R903=,ENST00000406533.7,c.2709C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000286627.10,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1070=,ENST00000434208.6,c.3210C>T,LOW,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000640093.1,c.*1946C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1099=,ENST00000639544.1,c.3297C>T,LOW,;KCNMA1,synonymous_variant,p.R1005=,ENST00000404857.6,c.3015C>T,LOW,;KCNMA1,synonymous_variant,p.R982=,ENST00000638252.1,c.2946C>T,LOW,;KCNMA1,synonymous_variant,p.R991=,ENST00000640807.1,c.2973C>T,LOW,;KCNMA1,synonymous_variant,p.R1038=,ENST00000640934.1,c.3114C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000640029.1,c.3123C>T,LOW,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639851.1,n.3347C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1003=,ENST00000372403.9,c.3009C>T,LOW,;KCNMA1,synonymous_variant,p.R925=,ENST00000640626.1,c.2775C>T,LOW,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639968.1,c.*2141C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1044=,ENST00000372440.6,c.3132C>T,LOW,;KCNMA1,synonymous_variant,p.R1045=,ENST00000640182.1,c.3135C>T,LOW,;KCNMA1,missense_variant,p.R1034C,ENST00000638895.1,c.3100C>T,MODERATE,;KCNMA1,synonymous_variant,p.R1099=,ENST00000457953.6,c.3297C>T,LOW,;KCNMA1,synonymous_variant,p.R1045=,ENST00000638606.1,c.3135C>T,LOW,;KCNMA1,synonymous_variant,p.R1044=,ENST00000638351.1,c.3132C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000638203.1,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1048=,ENST00000640605.1,c.3144C>T,LOW,;KCNMA1,synonymous_variant,p.R1102=,ENST00000639591.1,c.3306C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000638306.1,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1099=,ENST00000404771.8,c.3297C>T,LOW,;KCNMA1,synonymous_variant,p.R1043=,ENST00000372437.6,c.3129C>T,LOW,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000640570.1,n.2827C>T,MODIFIER,;KCNMA1,missense_variant,p.A1046V,ENST00000372421.10,c.3137C>T,MODERATE,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639691.1,c.*2002C>T,MODIFIER,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639483.1,c.*1819C>T,MODIFIER,;KCNMA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639995.1,c.*1027C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1006=,ENST00000372408.7,c.3018C>T,LOW,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639657.1,n.3206C>T,MODIFIER,;KCNMA1,non_coding_transcript_exon_variant,,ENST00000639069.1,n.2840C>T,MODIFIER,;KCNMA1,synonymous_variant,p.R1041=,ENST00000639090.1,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1045=,ENST00000639489.1,c.3135C>T,LOW,;KCNMA1,synonymous_variant,p.R1103=,ENST00000638848.1,c.3309C>T,LOW,;KCNMA1,missense_variant,p.A995V,ENST00000639344.1,c.2984C>T,MODERATE,;KCNMA1,synonymous_variant,p.R1075=,ENST00000638223.1,c.3225C>T,LOW,;KCNMA1,synonymous_variant,p.R1072=,ENST00000372443.6,c.3216C>T,LOW,;KCNMA1,synonymous_variant,p.R1106=,ENST00000640523.1,c.3318C>T,LOW,;KCNMA1,synonymous_variant,p.R1006=,ENST00000639498.1,c.3018C>T,LOW,;KCNMA1,synonymous_variant,p.R1006=,ENST00000639205.1,c.3018C>T,LOW,;KCNMA1,synonymous_variant,p.R1041=,ENST00000639486.1,c.3123C>T,LOW,;KCNMA1,missense_variant,p.A947V,ENST00000707137.1,c.2840C>T,MODERATE,;KCNMA1,synonymous_variant,p.R1041=,ENST00000639601.1,c.3123C>T,LOW,;KCNMA1,synonymous_variant,p.R1044=,ENST00000638991.1,c.3132C>T,LOW,;KCNMA1,synonymous_variant,p.R1071=,ENST00000639913.1,c.3213C>T,LOW,;KCNMA1,synonymous_variant,p.R906=,ENST00000604624.6,c.2718C>T,LOW, +MYOF 26509 BI GRCh38 10 93359880 93359880 + stop_gained Nonsense_Mutation SNP G G A rs775643885 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 74 20 c.3073C>T p.Arg1025Ter p.R1025* ENST00000359263.9 NM_013451.4 1025 Cga/Tga 29/54 P4 A R/* protein_coding YES CCDS41551.1 3073/6186 TTTTCGGACCA PDB-ENSP_mappings:2k2o.A;PANTHER:PTHR12546;PANTHER:PTHR12546:SF55;SMART:SM00694;Low_complexity_(Seg):seg ENSP00000352208 29/54 rs775643885 ENST00000359263 Transcript ENSG00000138119 HGNC:3656 HIGH NM_013451.4 8.83e-06 gnomAD_NFE stop_gained 1.0 Unknown Q9NZM1.183 MYOF HGNC -1 1.0 UPI000012FBA1 Q9NZM1-1 SNV MYOF,stop_gained,p.R1025*,ENST00000359263,NM_013451.4,c.3073C>T,HIGH,YES,,,-1;MYOF,stop_gained,p.R1012*,ENST00000358334,NM_133337.3,c.3034C>T,HIGH,,,,-1;MYOF,stop_gained,p.R400*,ENST00000463743,,c.1198C>T,HIGH,,,,-1 3213/6860 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.007e-06 0.0 0.0 0.0 0.0 0.0 8.83e-06 0.0 0.0 0 111 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 94 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYOF,stop_gained,p.R1012*,ENST00000358334.9,c.3034C>T,HIGH,;MYOF,synonymous_variant,NMD_transcript_variant,p.S399=,ENST00000463743.5,c.1197C>T,LOW,;MYOF,stop_gained,p.R1025*,ENST00000359263.9,c.3073C>T,HIGH,YES +PI4K2A 55361 BI GRCh38 10 97656397 97656397 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 11 c.749G>A p.Arg250His p.R250H ENST00000370631.4 NM_018425.3 250 cGc/cAc 3/9 P1 A R/H protein_coding YES CCDS7469.1 749/1440 TAACCGCATCG PDB-ENSP_mappings:4hnd.A;PDB-ENSP_mappings:4hnd.B;PDB-ENSP_mappings:4hne.A;PDB-ENSP_mappings:4hne.B;PDB-ENSP_mappings:4pla.A;PDB-ENSP_mappings:4yc4.A;PDB-ENSP_mappings:5eut.A;PDB-ENSP_mappings:5i0n.A;Pfam:PF00454;PANTHER:PTHR12865;PANTHER:PTHR12865:SF7 ENSP00000359665 3/9 ENST00000370631 Transcript ENSG00000155252 HGNC:30031 MODERATE missense_variant 1.0 possibly_damaging(0.48) Unknown deleterious(0.01) Q9BTU6.158 PI4K2A HGNC 1 1.0 UPI0000071D95 SNV PI4K2A,missense_variant,p.R250H,ENST00000370631,NM_018425.3,c.749G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.48),1;AL355315.1,missense_variant,p.R220H,ENST00000370649,,c.659G>A,MODERATE,YES,deleterious_low_confidence(0.03),probably_damaging(0.993),1 806/4189 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PI4K2A,missense_variant,p.R250H,ENST00000370631.4,c.749G>A,MODERATE,YES;ENSG00000249967,missense_variant,p.R220H,ENST00000370649.3,c.659G>A,MODERATE,YES +SLC25A28 81894 BI GRCh38 10 99611134 99611134 + synonymous_variant Silent SNP G G A rs1193525175 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 45 11 c.810C>T p.Cys270= p.C270= ENST00000370495.6 NM_031212.4 270 tgC/tgT 4/4 P1 A C protein_coding YES CCDS41559.1 810/1095 CCTGCGCAAGC Low_complexity_(Seg):seg;PROSITE_profiles:PS50920;PANTHER:PTHR45758:SF1;PANTHER:PTHR45758;Gene3D:1.50.40.10;Pfam:PF00153;Superfamily:SSF103506 ENSP00000359526 4/4 rs1193525175;COSV100979652 ENST00000370495 Transcript ENSG00000155287 HGNC:23472 LOW NM_031212.4 8.829e-06 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q96A46.155 SLC25A28 HGNC -1 1.0 UPI000006F639 Q96A46-1 SNV SLC25A28,synonymous_variant,p.C270=,ENST00000370495,NM_031212.4,c.810C>T,LOW,YES,,,-1;SLC25A28,synonymous_variant,p.C131=,ENST00000434701,,c.393C>T,LOW,,,,-1;SLC25A28,non_coding_transcript_exon_variant,,ENST00000496035,,n.596C>T,MODIFIER,,,,-1;SLC25A28,downstream_gene_variant,,ENST00000479722,,,MODIFIER,,,,-1 914/1526 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.007e-06 0.0 0.0 0.0 0.0 0.0 8.829e-06 0.0 0.0 2.028259950748179e-05 7.29749008314684e-05 0.0 0.0 0.0 0.0 0.0 afr 7.29749008314684e-05 0.0 0.0 0.0 0.0 0 54 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 57 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC25A28,non_coding_transcript_exon_variant,,ENST00000700253.1,n.1927C>T,MODIFIER,;SLC25A28,non_coding_transcript_exon_variant,,ENST00000700252.1,n.1860C>T,MODIFIER,;SLC25A28,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000700249.1,c.*493C>T,MODIFIER,;SLC25A28,synonymous_variant,p.C171=,ENST00000496035.2,c.513C>T,LOW,;SLC25A28,synonymous_variant,p.C171=,ENST00000700251.1,c.513C>T,LOW,;SLC25A28,synonymous_variant,p.C196=,ENST00000700250.1,c.588C>T,LOW,;SLC25A28,synonymous_variant,p.C171=,ENST00000700248.1,c.513C>T,LOW,;SLC25A28,synonymous_variant,p.C131=,ENST00000434701.5,c.393C>T,LOW,;SLC25A28,synonymous_variant,p.C270=,ENST00000370495.6,c.810C>T,LOW,YES;SLC25A28,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000700247.1,c.*493C>T,MODIFIER, +CYP17A1 1586 BI GRCh38 10 102832610 102832610 + missense_variant Missense_Mutation SNP C C T rs61754278 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 60 23 c.1040G>A p.Arg347His p.R347H ENST00000369887.4 NM_000102.4 347 cGt/cAt 6/8 P3 T R/H protein_coding CCDS7541.1 1040/1527 pathogenic GGTTACGGTCA PDB-ENSP_mappings:3ruk.A;PDB-ENSP_mappings:3ruk.B;PDB-ENSP_mappings:3ruk.C;PDB-ENSP_mappings:3ruk.D;PDB-ENSP_mappings:3swz.A;PDB-ENSP_mappings:3swz.B;PDB-ENSP_mappings:3swz.C;PDB-ENSP_mappings:3swz.D;PDB-ENSP_mappings:4nkv.A;PDB-ENSP_mappings:4nkv.B;PDB-ENSP_mappings:4nkv.C;PDB-ENSP_mappings:4nkv.D;PDB-ENSP_mappings:4nkw.A;PDB-ENSP_mappings:4nkw.B;PDB-ENSP_mappings:4nkw.C;PDB-ENSP_mappings:4nkw.D;PDB-ENSP_mappings:4nkx.A;PDB-ENSP_mappings:4nkx.B;PDB-ENSP_mappings:4nkx.C;PDB-ENSP_mappings:4nkx.D;PDB-ENSP_mappings:4nky.A;PDB-ENSP_mappings:4nky.B;PDB-ENSP_mappings:4nky.C;PDB-ENSP_mappings:4nky.D;PDB-ENSP_mappings:4nkz.A;PDB-ENSP_mappings:4nkz.B;PDB-ENSP_mappings:4nkz.C;PDB-ENSP_mappings:4nkz.D;PDB-ENSP_mappings:5irq.A;PDB-ENSP_mappings:5irq.B;PDB-ENSP_mappings:5irq.C;PDB-ENSP_mappings:5irq.D;PDB-ENSP_mappings:5irv.A;PDB-ENSP_mappings:5irv.B;PDB-ENSP_mappings:5irv.C;PDB-ENSP_mappings:5irv.D;PDB-ENSP_mappings:5uys.A;PDB-ENSP_mappings:5uys.B;PDB-ENSP_mappings:5uys.C;PDB-ENSP_mappings:5uys.D;PDB-ENSP_mappings:6chi.A;PDB-ENSP_mappings:6chi.B;PDB-ENSP_mappings:6chi.C;PDB-ENSP_mappings:6chi.D;PDB-ENSP_mappings:6cir.A;PDB-ENSP_mappings:6cir.B;PDB-ENSP_mappings:6cir.C;PDB-ENSP_mappings:6cir.D;PDB-ENSP_mappings:6ciz.A;PDB-ENSP_mappings:6ciz.B;PDB-ENSP_mappings:6ciz.C;PDB-ENSP_mappings:6ciz.D;PANTHER:PTHR24289:SF1;PANTHER:PTHR24289;Gene3D:1.10.630.10;Pfam:PF00067;Superfamily:SSF48264 ENSP00000358903 6/8 rs61754278;CM960476;COSV64004824 ENST00000369887 Transcript 1.0 ENSG00000148795 HGNC:2593 MODERATE NM_000102.4 6.155e-05 gnomAD_AFR missense_variant 1;1;1 9326943;11549685;12466376 probably_damaging(0.989) Unknown deleterious(0) 0;0;1 P05093.216 CYP17A1 HGNC -1 Q1HB44.126 1.0 UPI0000128309 SNV CYP17A1,missense_variant,p.R347H,ENST00000369887,NM_000102.4,c.1040G>A,MODERATE,,deleterious(0),probably_damaging(0.989),-1;CYP17A1,missense_variant,p.R318H,ENST00000638971,,c.953G>A,MODERATE,,deleterious(0),probably_damaging(0.987),-1;CYP17A1,missense_variant,p.R347H,ENST00000639393,,c.1040G>A,MODERATE,YES,deleterious(0),probably_damaging(0.981),-1;CYP17A1,missense_variant,p.R246H,ENST00000638190,,c.737G>A,MODERATE,,deleterious(0.01),probably_damaging(0.975),-1;CYP17A1,missense_variant,p.R195H,ENST00000638272,,c.584G>A,MODERATE,,deleterious(0),probably_damaging(0.993),-1;CYP17A1,non_coding_transcript_exon_variant,,ENST00000640633,,n.802G>A,MODIFIER,,,,-1;WBP1L,upstream_gene_variant,,ENST00000369884,,,MODIFIER,,,,1;CYP17A1,downstream_gene_variant,,ENST00000489268,,,MODIFIER,,,,-1;WBP1L,3_prime_UTR_variant,,ENST00000647664,,c.*1641C>T,MODIFIER,,,,1;CYP17A1,upstream_gene_variant,,ENST00000469683,,,MODIFIER,,,,-1 1092/1750 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 6.155e-05 0.0 0.0 0.0 0.0 1.759e-05 0.0 3.267e-05 1.351589980913559e-05 4.861449997406453e-05 0.0 0.0 0.0 0.0 0.0 afr 4.861449997406453e-05 0.0 0.0 0.0 0.0 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 83 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CYP17A1,missense_variant,p.R347H,ENST00000639393.1,c.1040G>A,MODERATE,;CYP17A1,missense_variant,p.R195H,ENST00000638272.1,c.584G>A,MODERATE,;CYP17A1,non_coding_transcript_exon_variant,,ENST00000640633.1,n.802G>A,MODIFIER,;CYP17A1,missense_variant,p.R246H,ENST00000638190.1,c.737G>A,MODERATE,;CYP17A1,missense_variant,p.R318H,ENST00000638971.1,c.953G>A,MODERATE,;CYP17A1,missense_variant,p.R347H,ENST00000369887.4,c.1040G>A,MODERATE,YES;WBP1L,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647664.1,c.*1641C>T,MODIFIER, +CFAP43 80217 BI GRCh38 10 104212155 104212155 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs371285570 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 12 c.587C>T p.Ser196Leu p.S196L ENST00000357060.8 NM_025145.7 196 tCg/tTg 5/38 P4 A S/L protein_coding YES CCDS31281.1 587/4998 TCACCGACCTG PANTHER:PTHR14885:SF1;PANTHER:PTHR14885;Gene3D:2.130.10.10;Superfamily:SSF50978 ENSP00000349568 0.0 0.0002326 5/38 rs371285570 ENST00000357060 Transcript 1.0 ENSG00000197748 HGNC:26684 MODERATE NM_025145.7 0.000362 gnomAD_SAS missense_variant 1.0 benign(0.003) Unknown tolerated(0.2) Q8NDM7.132 CFAP43 HGNC -1 1.0 UPI0000D60FC7 Q8NDM7-1 SNV CFAP43,missense_variant,p.S196L,ENST00000357060,NM_025145.7,c.587C>T,MODERATE,YES,tolerated(0.2),benign(0.003),-1;CFAP43,missense_variant,p.S196L,ENST00000278064,,c.587C>T,MODERATE,,tolerated(0.2),benign(0.005),-1;CFAP43,missense_variant,p.S196L,ENST00000369720,,c.587C>T,MODERATE,,tolerated(0.36),benign(0.001),-1;CFAP43,missense_variant,p.S196L,ENST00000369719,,c.587C>T,MODERATE,,tolerated(0.15),benign(0.001),-1 705/5367 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.396e-05 6.162e-05 0.0 0.0 0.0 0.0 7.945e-05 0.0 0.000362 4.735169932246208e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 9.257539932150394e-05 0.0 9.257539932150394e-05 0.000494070991408 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 55 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CFAP43,missense_variant,splice_region_variant,p.S196L,ENST00000369719.2,c.587C>T,MODERATE,;CFAP43,missense_variant,splice_region_variant,p.S196L,ENST00000369720.6,c.587C>T,MODERATE,;CFAP43,missense_variant,splice_region_variant,p.S196L,ENST00000278064.7,c.587C>T,MODERATE,;CFAP43,missense_variant,splice_region_variant,p.S196L,ENST00000357060.8,c.587C>T,MODERATE,YES +VWA2 340706 BI GRCh38 10 114289066 114289066 + missense_variant Missense_Mutation SNP G G A rs768137633 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 15 c.1699G>A p.Val567Met p.V567M ENST00000392982.8 NM_001272046.2 567 Gtg/Atg 12/14 P1 A V/M protein_coding YES CCDS7589.2 1699/2268 CTGACGTGACA COSM2054031;COSM4173962 Pfam:PF00092;Gene3D:3.40.50.410;SMART:SM00327;Superfamily:SSF53300;PROSITE_profiles:PS50234;PANTHER:PTHR24020;PANTHER:PTHR24020:SF37 ENSP00000376708 12/14 rs768137633;COSV53911265 ENST00000392982 Transcript ENSG00000165816 HGNC:24709 MODERATE NM_001272046.2 9.799e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0.02) 0;1 Q5GFL6.131 VWA2 HGNC 1 1.0 UPI00004C7AA3 Q5GFL6-1 SNV VWA2,missense_variant,p.V567M,ENST00000392982,NM_001272046.2&NM_001320804.1,c.1699G>A,MODERATE,YES,deleterious(0.02),probably_damaging(1),1;VWA2,missense_variant,p.V263M,ENST00000603594,,c.787G>A,MODERATE,,deleterious(0.02),probably_damaging(0.965),1;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,,n.1949G>A,MODIFIER,,,,1 2025/5846 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0 2.891e-05 0.0 5.437e-05 0.0 0.0 0.0 9.799e-05 6.75903993396787e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002082470018649 0 32 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 31 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS VWA2,missense_variant,p.V263M,ENST00000603594.2,c.787G>A,MODERATE,;VWA2,non_coding_transcript_exon_variant,,ENST00000298715.8,n.1949G>A,MODIFIER,;VWA2,missense_variant,p.V567M,ENST00000392982.8,c.1699G>A,MODERATE,YES +INPP5F 22876 BI GRCh38 10 119792015 119792015 + synonymous_variant Silent SNP C C T rs375176930 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 59 33 c.591C>T p.Asp197= p.D197= ENST00000650623.2 NM_014937.4 197 gaC/gaT 5/20 P1 T D protein_coding YES CCDS7616.1 591/3399 AGGGACGGTCG PROSITE_profiles:PS50275;PANTHER:PTHR45662;PANTHER:PTHR45662:SF8;Pfam:PF02383 ENSP00000497527 0.0 0.0001163 5/20 rs375176930 ENST00000650623 Transcript ENSG00000198825 HGNC:17054 LOW NM_014937.4 0.0001629 gnomAD_OTH synonymous_variant 1.0 Unknown Q9Y2H2.138 INPP5F HGNC 1 UPI000006FBCA Q9Y2H2-1 SNV INPP5F,synonymous_variant,p.D101=,ENST00000649454,,c.303C>T,LOW,,,,1;INPP5F,synonymous_variant,p.D197=,ENST00000650623,NM_014937.4,c.591C>T,LOW,YES,,,1;INPP5F,synonymous_variant,p.D197=,ENST00000649251,,c.591C>T,LOW,,,,1;INPP5F,synonymous_variant,p.D154=,ENST00000648262,,c.462C>T,LOW,,,,1;INPP5F,synonymous_variant,p.D101=,ENST00000647699,,c.303C>T,LOW,,,,1;INPP5F,synonymous_variant,p.D101=,ENST00000649957,,c.303C>T,LOW,,,,1;INPP5F,synonymous_variant,p.D197=,ENST00000369081,NM_001243195.1,c.591C>T,LOW,,,,1;PHACTR2P1,downstream_gene_variant,,ENST00000636592,,,MODIFIER,,,,-1;INPP5F,synonymous_variant,p.D197=,ENST00000649742,,c.591C>T,LOW,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000650305,,c.*792C>T,MODIFIER,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000648621,,c.*587C>T,MODIFIER,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000649297,,c.*487C>T,MODIFIER,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000647933,,c.*493C>T,MODIFIER,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000648515,,c.*610C>T,MODIFIER,,,,1;INPP5F,3_prime_UTR_variant,,ENST00000648661,,c.*142C>T,MODIFIER,,,,1 804/4979 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.784e-05 0.0 0.0 0.0 0.0 4.62e-05 3.516e-05 0.0001629 3.266e-05 1.3519899766833989e-05 2.4321399905602448e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 98 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 92 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS INPP5F,synonymous_variant,p.D101=,ENST00000647699.1,c.303C>T,LOW,;INPP5F,synonymous_variant,p.D101=,ENST00000649957.1,c.303C>T,LOW,;INPP5F,synonymous_variant,p.D101=,ENST00000649454.1,c.303C>T,LOW,;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000648515.1,c.*610C>T,MODIFIER,;INPP5F,synonymous_variant,p.D154=,ENST00000648262.1,c.462C>T,LOW,;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000648661.1,c.*142C>T,MODIFIER,;INPP5F,synonymous_variant,p.D197=,ENST00000369081.3,c.591C>T,LOW,;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000650305.1,c.*792C>T,MODIFIER,;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647933.1,c.*493C>T,MODIFIER,;INPP5F,synonymous_variant,NMD_transcript_variant,p.D197=,ENST00000649742.1,c.591C>T,LOW,;INPP5F,synonymous_variant,p.D197=,ENST00000649251.1,c.591C>T,LOW,;INPP5F,synonymous_variant,p.D197=,ENST00000650623.2,c.591C>T,LOW,YES;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000648621.1,c.*587C>T,MODIFIER,;INPP5F,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000649297.1,c.*487C>T,MODIFIER, +MUC2 4583 BI GRCh38 11 1101903 1101903 + missense_variant Missense_Mutation SNP G G A rs750954497 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 5 c.826G>A p.Gly276Ser p.G276S ENST00000674892.1 276 Ggc/Agc 4/20 A2 A G/S protein_coding 826/2958 CCGACGGCTGC SMART:SM00216;PANTHER:PTHR11339;PANTHER:PTHR11339:SF261 ENSP00000501871 4/20 rs750954497 cds_start_NF ENST00000674892 Transcript ENSG00000198788 HGNC:7512 MODERATE 0.0001182 gnomAD_AMR missense_variant unknown(0) Unknown tolerated(0.31) MUC2 HGNC 1 SNV MUC2,missense_variant,p.G276S,ENST00000674892,,c.826G>A,MODERATE,,tolerated(0.31),unknown(0),1;MUC2,non_coding_transcript_exon_variant,,ENST00000361558,NM_002457.4,n.10379G>A,MODIFIER,,,,1 826/3111 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.553e-05 0.0 0.0001182 0.0 5.697e-05 0.0 9.346e-06 0.0 0.0 1.3519000276573934e-05 2.4323799152625725e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 17 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 26 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MUC2,missense_variant,p.G276S,ENST00000674892.1,c.826G>A,MODERATE,;MUC2,non_coding_transcript_exon_variant,,ENST00000361558.7,n.10379G>A,MODIFIER, +TNNT3 7140 BI GRCh38 11 1929136 1929136 + synonymous_variant Silent SNP C C T rs752603163 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 59 16 c.132C>T p.Asp44= p.D44= ENST00000397301.5 NM_001367846.1 44 gaC/gaT 8/17 A2 T D protein_coding YES 132/810 likely_benign GAGGACGCGGA COSM5628877 PANTHER:PTHR11521;PANTHER:PTHR11521:SF4;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000380468 8/17 rs752603163;COSV53488587 ENST00000397301 Transcript 1.0 ENSG00000130595 HGNC:11950 LOW 0.0001157 gnomAD_AMR synonymous_variant 1;1 1.0 Unknown 0;1 P45378.166 TNNT3 HGNC 1 5.0 UPI0000ED9058 P45378-1 SNV TNNT3,synonymous_variant,p.D33=,ENST00000278317,NM_006757.4,c.99C>T,LOW,,,,1;TNNT3,synonymous_variant,p.D44=,ENST00000397301,NM_001367846.1,c.132C>T,LOW,YES,,,1;TNNT3,intron_variant,,ENST00000344578,NM_001367850.1,c.68-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000381557,,c.65-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000381558,NM_001297646.2&NM_001042782.3,c.83-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000381563,NM_001363561.2&NM_001367848.1&NM_001367847.1,c.116-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000381579,NM_001042780.3,c.83-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000381589,NM_001042781.3&NM_001367845.1,c.101-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000397304,NM_001367849.1,c.50-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000446240,,c.50-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000453458,,c.50-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000641119,NM_001367843.1&NM_001367842.1,c.101-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000641225,NM_001367851.1&NM_001367852.1,c.-98-674C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000641787,NM_001367844.1,c.83-674C>T,MODIFIER,,,,1;TNNT3,non_coding_transcript_exon_variant,,ENST00000492075,,n.316C>T,MODIFIER,,,,1;TNNT3,intron_variant,,ENST00000639560,,n.217-674C>T,MODIFIER,,,,1;TNNT3,upstream_gene_variant,,ENST00000493234,,,MODIFIER,,,,1 140/818 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.787e-05 0.0 0.0001157 0.0 0.0001088 0.0 5.29e-05 0.0 0.0 2.027409936999902e-05 0.0 0.0 0.0001324680051766 0.0 0.0 0.0 amr 0.0001324680051766 0.0 0.0 0.0004945599939674 0.0 0 123 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 75 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TNNT3,intron_variant,,ENST00000639560.1,n.217-674C>T,MODIFIER,;TNNT3,non_coding_transcript_exon_variant,,ENST00000492075.5,n.316C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000397304.6,c.50-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000446240.1,c.50-674C>T,MODIFIER,;TNNT3,synonymous_variant,p.D44=,ENST00000397301.5,c.132C>T,LOW,;TNNT3,intron_variant,,ENST00000706488.1,c.101-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000641119.1,c.101-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000641787.1,c.83-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000641225.1,c.-98-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000381558.6,c.83-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000344578.8,c.68-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000381563.8,c.116-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000453458.5,c.50-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000381579.7,c.83-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000381589.7,c.101-674C>T,MODIFIER,;TNNT3,intron_variant,,ENST00000381557.6,c.65-674C>T,MODIFIER,;TNNT3,synonymous_variant,p.D33=,ENST00000278317.11,c.99C>T,LOW,YES +PPFIBP2 8495 BI GRCh38 11 7630931 7630931 + missense_variant Missense_Mutation SNP C C T rs201945661 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 52 23 c.971C>T p.Ser324Leu p.S324L ENST00000299492.9 NM_001351862.2 324 tCg/tTg 11/24 0.0002 0.0 0.0 0.001 0.0 0.0 P3 T S/L protein_coding YES CCDS31419.1 971/2631 GCCTTCGGAGA PANTHER:PTHR12587;PANTHER:PTHR12587:SF18 ENSP00000299492 11/24 rs201945661 ENST00000299492 Transcript ENSG00000166387 HGNC:9250 MODERATE NM_003621.5 0.001142 gnomAD_EAS missense_variant 1.0 benign(0.003) Unknown deleterious(0.01) Q8ND30.159 PPFIBP2 HGNC 1 1.0 UPI00001C1EF8 Q8ND30-1 SNV PPFIBP2,missense_variant,p.S324L,ENST00000299492,NM_001351862.2&NM_001351856.2&NM_001351855.2&NM_001351853.2&NM_003621.5&NM_001351854.2&NM_001351857.2&NM_001351859.2&NM_001351861.2&NM_001351858.2&NM_001351860.2,c.971C>T,MODERATE,YES,deleterious(0.01),benign(0.003),1;PPFIBP2,missense_variant,p.S166L,ENST00000533792,,c.497C>T,MODERATE,,tolerated(0.07),benign(0.003),1;PPFIBP2,missense_variant,p.S181L,ENST00000530181,NM_001256569.2,c.542C>T,MODERATE,,tolerated(0.06),benign(0.053),1;PPFIBP2,missense_variant,p.S212L,ENST00000528883,NM_001256568.2,c.635C>T,MODERATE,,tolerated(0.07),benign(0),1;PPFIBP2,missense_variant,p.S4L,ENST00000534409,,c.11C>T,MODERATE,,deleterious(0),benign(0.289),1;PPFIBP2,downstream_gene_variant,,ENST00000529575,,,MODIFIER,,,,1;PPFIBP2,upstream_gene_variant,,ENST00000530081,,,MODIFIER,,,,1;PPFIBP2,intron_variant,,ENST00000529021,,n.317-24483C>T,MODIFIER,,,,1;PPFIBP2,intron_variant,,ENST00000532926,,n.1097+20509C>T,MODIFIER,,,,1;PPFIBP2,upstream_gene_variant,,ENST00000530582,,,MODIFIER,,,,1;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000532416,,n.226C>T,MODIFIER,,,,1;PPFIBP2,upstream_gene_variant,,ENST00000532381,,,MODIFIER,,,,1 1130/3328 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001074 0.0 0.0 0.0 0.001142 4.624e-05 2.639e-05 0.000163 3.267e-05 2.7043099180446006e-05 0.0 0.0 0.0 0.0 0.0008051529875956 0.0 eas 0.0008051529875956 0.0 0.0 0.0 0.0 0 105 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 75 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPFIBP2,synonymous_variant,p.F3=,ENST00000534409.5,c.9C>T,LOW,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000532416.1,n.226C>T,MODIFIER,;PPFIBP2,missense_variant,p.S181L,ENST00000530181.5,c.542C>T,MODERATE,;PPFIBP2,missense_variant,p.S212L,ENST00000528883.5,c.635C>T,MODERATE,;PPFIBP2,intron_variant,,ENST00000529021.1,n.317-24483C>T,MODIFIER,;PPFIBP2,missense_variant,p.S247L,ENST00000684215.1,c.740C>T,MODERATE,;PPFIBP2,intron_variant,,ENST00000532926.5,n.1097+20509C>T,MODIFIER,;PPFIBP2,missense_variant,p.S166L,ENST00000533792.5,c.497C>T,MODERATE,;PPFIBP2,missense_variant,p.S324L,ENST00000299492.9,c.971C>T,MODERATE,YES;PPFIBP2,missense_variant,p.S324L,ENST00000684123.1,c.971C>T,MODERATE, +IRAG1 10335 BI GRCh38 11 10626510 10626510 + missense_variant Missense_Mutation SNP C C T rs565811419 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 9 c.824G>A p.Arg275His p.R275H ENST00000423302.7 NM_130385.4 275 cGt/cAt 9/21 P4 T R/H protein_coding YES CCDS55746.1 824/2739 GAGGACGAGGA PANTHER:PTHR15352;PANTHER:PTHR15352:SF2;MobiDB_lite:mobidb-lite ENSP00000412130 9/21 rs565811419 ENST00000423302 Transcript ENSG00000072952 HGNC:7237 MODERATE 0.000112 gnomAD_EAS missense_variant 1.0 benign(0.033) Unknown tolerated(0.11) Q9Y6F6.129 IRAG1 HGNC -1 2.0 UPI0001F78343 Q9Y6F6-7 SNV IRAG1,missense_variant,p.R275H,ENST00000423302,NM_130385.4,c.824G>A,MODERATE,YES,tolerated(0.11),benign(0.033),-1;IRAG1,missense_variant,p.R267H,ENST00000531107,NM_001098579.3,c.800G>A,MODERATE,,tolerated(0.11),benign(0.007),-1;IRAG1,missense_variant,p.R184H,ENST00000527509,NM_001100163.3,c.551G>A,MODERATE,,tolerated(0.12),benign(0.01),-1;IRAG1,5_prime_UTR_variant,,ENST00000547195,NM_001206881.2,c.-122G>A,MODIFIER,,,,-1;IRAG1,5_prime_UTR_variant,,ENST00000424001,,c.-122G>A,MODIFIER,,,,-1;IRAG1,5_prime_UTR_variant,,ENST00000558540,NM_001100167.3,c.-122G>A,MODIFIER,,,,-1;IRAG1,5_prime_UTR_variant,,ENST00000534266,,c.-122G>A,MODIFIER,,,,-1;IRAG1,intron_variant,,ENST00000541483,NM_001206880.2,c.750+1206G>A,MODIFIER,,,,-1;IRAG1,downstream_gene_variant,,ENST00000532037,,,MODIFIER,,,,-1;IRAG1,3_prime_UTR_variant,,ENST00000529448,,c.*349G>A,MODIFIER,,,,-1;IRAG1,intron_variant,,ENST00000526414,,c.597+1206G>A,MODIFIER,,,,-1;IRAG1,intron_variant,,ENST00000533631,,c.*34+1206G>A,MODIFIER,,,,-1 974/6126 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.437e-05 6.537e-05 0.0 0.0 0.000112 0.0 1.803e-05 0.0 3.294e-05 2.028259950748179e-05 2.4320199372596107e-05 0.0 0.0 0.0 0.0 9.43039995036088e-05 0.0 1.5432100553880446e-05 0.0 0.0 0 18 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 15 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IRAG1,intron_variant,NMD_transcript_variant,,ENST00000533631.1,c.*34+1206G>A,MODIFIER,;IRAG1,intron_variant,NMD_transcript_variant,,ENST00000526414.5,c.597+1206G>A,MODIFIER,;IRAG1,5_prime_UTR_variant,,ENST00000534266.6,c.-122G>A,MODIFIER,;IRAG1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000529448.5,c.*349G>A,MODIFIER,;IRAG1,missense_variant,p.R267H,ENST00000531107.5,c.800G>A,MODERATE,;IRAG1,intron_variant,,ENST00000541483.5,c.750+1206G>A,MODIFIER,;IRAG1,5_prime_UTR_variant,,ENST00000558540.5,c.-122G>A,MODIFIER,;IRAG1,missense_variant,p.R275H,ENST00000423302.7,c.824G>A,MODERATE,YES;IRAG1,5_prime_UTR_variant,,ENST00000547195.5,c.-122G>A,MODIFIER,;IRAG1,5_prime_UTR_variant,,ENST00000424001.5,c.-122G>A,MODIFIER, +MRGPRX2 117194 BI GRCh38 11 19056304 19056304 + synonymous_variant Silent SNP C C T rs771220636 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 99 21 c.99G>A p.Pro33= p.P33= ENST00000329773.3 NM_054030.4 33 ccG/ccA 2/2 P1 T P protein_coding YES CCDS7847.1 99/993 AAGACCGGGAT CDD:cd15106;PANTHER:PTHR11334:SF29;PANTHER:PTHR11334;Gene3D:1.20.1070.10;Superfamily:SSF81321;Prints:PR00237 ENSP00000333800 2/2 rs771220636 ENST00000329773 Transcript ENSG00000183695 HGNC:17983 LOW NM_054030.4 0.0001307 gnomAD_SAS synonymous_variant 1.0 Unknown Q96LB1.143 MRGPRX2 HGNC -1 1.0 UPI0000038C81 SNV MRGPRX2,synonymous_variant,p.P33=,ENST00000329773,NM_054030.4&NM_001303615.1,c.99G>A,LOW,YES,,,-1 223/2072 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0 0.0 0.0 0.0 0.0 8.796e-06 0.0 0.0001307 0 116 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 121 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MRGPRX2,synonymous_variant,p.P33=,ENST00000329773.3,c.99G>A,LOW,YES +SLC6A5 9152 BI GRCh38 11 20654742 20654742 + synonymous_variant Silent SNP G G A rs373204248 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 26 c.2268G>A p.Pro756= p.P756= ENST00000525748.6 NM_004211.5 756 ccG/ccA 16/16 0.0004 0.0008 0.0 0.001 0.0 0.0 P1 A P protein_coding YES CCDS7854.1 2268/2394 likely_benign CAGCCGGACTG CDD:cd11499;PANTHER:PTHR11616;PANTHER:PTHR11616:SF158 ENSP00000434364 0.000227 0.0 16/16 rs373204248 ENST00000525748 Transcript 1.0 ENSG00000165970 HGNC:11051 LOW NM_004211.5 0.001 EAS synonymous_variant 1 1.0 Unknown Q9Y345.172 SLC6A5 HGNC 1 1.0 UPI00004564A5 SNV SLC6A5,synonymous_variant,p.P756=,ENST00000525748,NM_004211.5&NM_001318369.2,c.2268G>A,LOW,YES,,,1;SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440,,n.799G>A,MODIFIER,,,,1;SLC6A5,3_prime_UTR_variant,,ENST00000298923,,c.*1565G>A,MODIFIER,,,,1 2333/6876 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.181e-05 0.0001845 0.0 0.0 5.437e-05 4.62e-05 2.637e-05 0.0 0.0 4.733119931188412e-05 0.000145900005009 0.0 0.0 0.0 0.0002021020045503 0.0 afr 0.000145900005009 0.0 0.0 0.0 0.0 0 69 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440.1,n.799G>A,MODIFIER,;SLC6A5,synonymous_variant,p.P756=,ENST00000525748.6,c.2268G>A,LOW,YES;SLC6A5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000298923.11,c.*1565G>A,MODIFIER, +BBOX1 8424 BI GRCh38 11 27127319 27127319 + missense_variant Missense_Mutation SNP C C T rs764375198 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 50 16 c.1030C>T p.Arg344Cys p.R344C ENST00000263182.8 NM_003986.3 344 Cgc/Tgc 9/9 P1 T R/C protein_coding YES CCDS7862.1 1030/1164 ACTGGCGCTTA COSM3687244 PDB-ENSP_mappings:3ms5.A;PDB-ENSP_mappings:3n6w.A;PDB-ENSP_mappings:3o2g.A;PDB-ENSP_mappings:4bg1.A;PDB-ENSP_mappings:4bgk.A;PDB-ENSP_mappings:4bgm.A;PDB-ENSP_mappings:4bhf.A;PDB-ENSP_mappings:4bhg.A;PDB-ENSP_mappings:4bhi.A;PDB-ENSP_mappings:4c5w.A;PDB-ENSP_mappings:4c8r.A;PDB-ENSP_mappings:4c8r.B;PDB-ENSP_mappings:4c8r.C;PDB-ENSP_mappings:4c8r.D;PDB-ENSP_mappings:4c8r.E;PDB-ENSP_mappings:4c8r.F;PDB-ENSP_mappings:4cwd.A;CDD:cd00250;PANTHER:PTHR10696:SF33;PANTHER:PTHR10696;Gene3D:3.60.130.10;TIGRFAM:TIGR02409;Pfam:PF02668;Superfamily:SSF51197 ENSP00000263182 9/9 rs764375198;COSV54192621 ENST00000263182 Transcript ENSG00000129151 HGNC:964 MODERATE NM_003986.3 8.798e-06 gnomAD_NFE missense_variant 0;1 probably_damaging(1) Unknown deleterious(0) 0;1 O75936.171 BBOX1 HGNC 1 5.0 UPI0000126A4C SNV BBOX1,missense_variant,p.R344C,ENST00000263182,NM_003986.3&NM_001376260.1&NM_001376258.1&NM_001376259.1,c.1030C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;BBOX1,missense_variant,p.R344C,ENST00000529202,,c.1030C>T,MODERATE,,deleterious(0),probably_damaging(1),1;BBOX1,missense_variant,p.R344C,ENST00000528583,,c.1030C>T,MODERATE,,deleterious(0),probably_damaging(1),1;BBOX1,missense_variant,p.R344C,ENST00000525090,NM_001376261.1,c.1030C>T,MODERATE,,deleterious(0),probably_damaging(1),1;BBOX1-AS1,intron_variant,,ENST00000525302,,n.334+23731G>A,MODIFIER,,,,-1;BBOX1-AS1,intron_variant,,ENST00000526061,,n.344+23731G>A,MODIFIER,,,,-1;BBOX1-AS1,intron_variant,,ENST00000530430,,n.667+23731G>A,MODIFIER,YES,,,-1 1545/2035 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-06 0.0 0.0 0.0 0.0 0.0 8.798e-06 0.0 0.0 6.762420071027009e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 76 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 66 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BBOX1-AS1,intron_variant,,ENST00000530430.1,n.667+23731G>A,MODIFIER,;BBOX1-AS1,intron_variant,,ENST00000525302.5,n.334+23731G>A,MODIFIER,;BBOX1,missense_variant,p.R344C,ENST00000525090.1,c.1030C>T,MODERATE,;BBOX1-AS1,intron_variant,,ENST00000526061.5,n.344+23731G>A,MODIFIER,YES;BBOX1,missense_variant,p.R344C,ENST00000528583.5,c.1030C>T,MODERATE,;BBOX1,missense_variant,p.R344C,ENST00000263182.8,c.1030C>T,MODERATE,YES;BBOX1,missense_variant,p.R344C,ENST00000529202.5,c.1030C>T,MODERATE, +CLP1 10978 BI GRCh38 11 57660774 57660774 + missense_variant Missense_Mutation SNP C C T rs777290319 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 61 9 c.616C>T p.Arg206Cys p.R206C ENST00000525602.1 206 Cgt/Tgt 3/3 P1 T R/C protein_coding CCDS7964.1 616/1278 CATCTCGTTTA COSM1718427 Gene3D:3.40.50.300;HAMAP:MF_03035;Pfam:PF16575;PANTHER:PTHR12755;PANTHER:PTHR12755:SF6;Superfamily:SSF52540 ENSP00000436066 3/3 rs777290319;COSV57053898 ENST00000525602 Transcript 1.0 ENSG00000172409 HGNC:16999 MODERATE 3.651e-05 gnomAD_SAS missense_variant 0;1 benign(0.013) Unknown tolerated(0.06) 0;1 Q92989.160 CLP1 HGNC 1 1.0 UPI000012754A Q92989-1 SNV CLP1,missense_variant,p.R206C,ENST00000533682,NM_006831.3,c.616C>T,MODERATE,,tolerated(0.06),benign(0.013),1;CLP1,missense_variant,p.R217C,ENST00000529430,,c.649C>T,MODERATE,YES,tolerated(0.06),benign(0.022),1;CLP1,missense_variant,p.R142C,ENST00000302731,NM_001142597.1,c.424C>T,MODERATE,,tolerated(0.08),benign(0),1;CLP1,missense_variant,p.R206C,ENST00000525602,,c.616C>T,MODERATE,,tolerated(0.06),benign(0.013),1;CLP1,downstream_gene_variant,,ENST00000529773,,,MODIFIER,,,,1;CLP1,downstream_gene_variant,,ENST00000533905,,,MODIFIER,,,,1 730/1392 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.48e-06 0.0 3.103e-05 0.0 0.0 0.0 0.0 0.0 3.651e-05 1.351730043097632e-05 2.4311999368364923e-05 0.0 0.0 0.0 0.0002013689954765 0.0 0.0 0.0 0.0 0.0 0 72 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 70 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CLP1,missense_variant,p.R142C,ENST00000302731.4,c.424C>T,MODERATE,;CLP1,missense_variant,p.R206C,ENST00000533682.2,c.616C>T,MODERATE,YES;CLP1,missense_variant,p.R206C,ENST00000525602.1,c.616C>T,MODERATE,;CLP1,intron_variant,,ENST00000529773.2,c.607-10C>T,MODIFIER,;CLP1,missense_variant,p.R217C,ENST00000529430.1,c.649C>T,MODERATE,;CLP1,missense_variant,p.R206C,ENST00000681650.1,c.616C>T,MODERATE, +MS4A15 219995 BI GRCh38 11 60763748 60763748 + synonymous_variant Silent SNP C C T rs372949576 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 46 22 c.15C>T p.Pro5= p.P5= ENST00000405633.4 NM_001098835.2 5 ccC/ccT 2/7 P1 T P protein_coding YES CCDS44617.1 15/723 GCTCCCGCCAG COSM3397951 ENSP00000386022 0.0 0.0001194 2/7 rs372949576 ENST00000405633 Transcript ENSG00000166961 HGNC:28573 LOW NM_001098835.2 0.0001194 EA synonymous_variant 1.0 Unknown Q8N5U1.114 MS4A15 HGNC 1 1.0 UPI00001FA81E Q8N5U1-1 SNV MS4A15,synonymous_variant,p.P5=,ENST00000405633,NM_001098835.2,c.15C>T,LOW,YES,,,1;MS4A15,synonymous_variant,p.P5=,ENST00000528170,NM_001278242.2,c.15C>T,LOW,,,,1;MS4A15,intron_variant,,ENST00000337911,NM_152717.3,c.-20-3819C>T,MODIFIER,,,,1;MS4A15,synonymous_variant,p.P5=,ENST00000429322,,c.15C>T,LOW,,,,1 235/1961 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.204e-05 0.0 0.0 0.0 0.0 0.0 2.657e-05 0.0 0.0 6.757759820175124e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5427800462930463e-05 0.0 0.0 0 93 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MS4A15,synonymous_variant,NMD_transcript_variant,p.P5=,ENST00000429322.6,c.15C>T,LOW,;MS4A15,intron_variant,,ENST00000337911.8,c.-20-3819C>T,MODIFIER,;MS4A15,synonymous_variant,p.P5=,ENST00000528170.5,c.15C>T,LOW,;MS4A15,synonymous_variant,p.P5=,ENST00000405633.4,c.15C>T,LOW,YES +TKFC 26007 BI GRCh38 11 61339326 61339326 + missense_variant Missense_Mutation SNP G G A rs750037556 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 77 31 c.377G>A p.Arg126Gln p.R126Q ENST00000394900.8 NM_001351978.2 126 cGg/cAg 5/18 P1 A R/Q protein_coding YES CCDS8003.1 377/1728 GGCCCGGGCTG PROSITE_profiles:PS51481;PANTHER:PTHR28629:SF4;PANTHER:PTHR28629;Pfam:PF02733;TIGRFAM:TIGR02361;Gene3D:3.40.50.10440;Superfamily:SSF82549 ENSP00000378360 5/18 rs750037556 ENST00000394900 Transcript 1.0 ENSG00000149476 HGNC:24552 MODERATE NM_015533.4 6.185e-05 gnomAD_NFE missense_variant 1.0 benign(0.109) Unknown tolerated(0.05) Q3LXA3.136 TKFC HGNC 1 A0A140VJH7.21 1.0 UPI00000718B9 Q3LXA3-1 SNV TKFC,missense_variant,p.R126Q,ENST00000394900,NM_001351978.1&NM_001351977.2&NM_001351976.2&NM_015533.4,c.377G>A,MODERATE,YES,tolerated(0.05),benign(0.109),1;TKFC,missense_variant,p.R125Q,ENST00000529479,NM_001351980.2&NM_001351979.2,c.374G>A,MODERATE,,tolerated(0.06),benign(0.012),1;TKFC,missense_variant,p.R126Q,ENST00000532173,,c.377G>A,MODERATE,,tolerated(0.09),benign(0.109),1;TKFC,downstream_gene_variant,,ENST00000524968,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000534084,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000525170,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000529620,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000530057,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000530456,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000533393,,,MODIFIER,,,,1;TKFC,non_coding_transcript_exon_variant,,ENST00000529092,,n.132G>A,MODIFIER,,,,1;DDB1,intron_variant,,ENST00000540166,,c.-166+3042C>T,MODIFIER,,,,-1;TKFC,upstream_gene_variant,,ENST00000524953,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000528061,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000529121,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000533853,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000534134,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000534370,,,MODIFIER,,,,1 588/4678 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.192e-05 0.0 2.893e-05 0.0 0.0 0.0 6.185e-05 0.0 0.0 2.703320024011191e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.173030124045908e-05 0.0 6.173030124045908e-05 0.0 0.0 0 92 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 109 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TKFC,non_coding_transcript_exon_variant,,ENST00000529092.1,n.132G>A,MODIFIER,;TKFC,missense_variant,p.R125Q,ENST00000529479.5,c.374G>A,MODERATE,;TKFC,missense_variant,p.R126Q,ENST00000394900.8,c.377G>A,MODERATE,YES;TKFC,missense_variant,p.R126Q,ENST00000532173.6,c.377G>A,MODERATE,;DDB1,intron_variant,NMD_transcript_variant,,ENST00000540166.5,c.-166+3042C>T,MODIFIER, +CHRM1 1128 BI GRCh38 11 62910764 62910764 + missense_variant Missense_Mutation SNP C C T TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 3 c.337G>A p.Val113Ile p.V113I ENST00000306960.4 NM_000738.3 113 Gtc/Atc 2/2 P1 T V/I protein_coding YES CCDS8040.1 337/1383 CATGACGGAGG PDB-ENSP_mappings:5cxv.A;PDB-ENSP_mappings:6oij.R;Transmembrane_helices:TMhelix;PROSITE_profiles:PS50262;CDD:cd17790;PANTHER:PTHR24248:SF155;PANTHER:PTHR24248;PROSITE_patterns:PS00237;Pfam:PF00001;Gene3D:1.20.1070.10;Superfamily:SSF81321;Prints:PR00243;Prints:PR00237 ENSP00000306490 2/2 COSV61006143 ENST00000306960 Transcript ENSG00000168539 HGNC:1950 MODERATE NM_000738.3 missense_variant 1 1.0 possibly_damaging(0.844) Unknown deleterious(0) 1 P11229.204 CHRM1 HGNC -1 Q53XZ3.140 1.0 UPI00001252AB P11229-1 SNV CHRM1,missense_variant,p.V113I,ENST00000306960,NM_000738.3,c.337G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.844),-1;CHRM1,missense_variant,p.V113I,ENST00000543973,,c.337G>A,MODERATE,,deleterious(0),possibly_damaging(0.844),-1;CHRM1,missense_variant,p.V113I,ENST00000536524,,c.337G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.844),-1;AP000438.1,non_coding_transcript_exon_variant,,ENST00000543624,,n.232C>T,MODIFIER,YES,,,1 561/2646 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 18 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CHRM1,missense_variant,p.V113I,ENST00000536524.1,c.337G>A,MODERATE,;CHRM1,missense_variant,p.V113I,ENST00000543973.1,c.337G>A,MODERATE,;ENSG00000257002,non_coding_transcript_exon_variant,,ENST00000543624.1,n.232C>T,MODIFIER,YES;CHRM1,missense_variant,p.V113I,ENST00000306960.4,c.337G>A,MODERATE,YES +PLAAT5 117245 BI GRCh38 11 63490316 63490316 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 151 42 c.196G>A p.Ala66Thr p.A66T ENST00000301790.4 NM_054108.4 66 Gca/Aca 2/6 A2 T A/T protein_coding YES CCDS8044.1 196/840 CGCTGCGAATC PANTHER:PTHR13943;PANTHER:PTHR13943:SF2 ENSP00000301790 2/6 ENST00000301790 Transcript ENSG00000168004 HGNC:24978 MODERATE missense_variant 1.0 benign(0.033) Unknown tolerated_low_confidence(0.09) Q96KN8.123 PLAAT5 HGNC -1 1.0 UPI000013E758 Q96KN8-1 SNV PLAAT5,missense_variant,p.A56T,ENST00000540857,NM_001146729.2,c.166G>A,MODERATE,,tolerated_low_confidence(0.22),benign(0.037),-1;PLAAT5,missense_variant,p.A66T,ENST00000539221,NM_001146728.2,c.196G>A,MODERATE,,tolerated_low_confidence(0.1),benign(0.073),-1;PLAAT5,missense_variant,p.A66T,ENST00000301790,NM_054108.4,c.196G>A,MODERATE,YES,tolerated_low_confidence(0.09),benign(0.033),-1;PLAAT5,5_prime_UTR_variant,,ENST00000538712,,c.-459G>A,MODIFIER,,,,-1;PLAAT5,missense_variant,p.A25T,ENST00000536887,,c.73G>A,MODERATE,,tolerated_low_confidence(0.48),probably_damaging(0.992),-1;PLAAT5,intron_variant,,ENST00000394615,,c.79+571G>A,MODIFIER,,,,-1 356/1166 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 211 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 193 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLAAT5,5_prime_UTR_variant,,ENST00000538712.1,c.-459G>A,MODIFIER,;PLAAT5,intron_variant,NMD_transcript_variant,,ENST00000394615.2,c.79+571G>A,MODIFIER,;PLAAT5,missense_variant,p.A66T,ENST00000301790.4,c.196G>A,MODERATE,;PLAAT5,missense_variant,p.A66T,ENST00000539221.5,c.196G>A,MODERATE,;PLAAT5,missense_variant,p.A56T,ENST00000540857.6,c.166G>A,MODERATE,YES;PLAAT5,missense_variant,NMD_transcript_variant,p.R24H,ENST00000536887.5,c.71G>A,MODERATE, +MEN1 4221 BI GRCh38 11 64807649 64807649 + missense_variant Missense_Mutation SNP C C T rs878855197 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 16 c.686G>A p.Arg229His p.R229H ENST00000312049.11 NM_130799.2 229 cGc/cAc 4/10 T R/H protein_coding CCDS8083.1 701/1848 uncertain_significance CACAGCGCATG COSM2164488 PDB-ENSP_mappings:3u84.A;PDB-ENSP_mappings:3u84.B;PDB-ENSP_mappings:3u85.A;PDB-ENSP_mappings:3u86.A;PDB-ENSP_mappings:3u88.A;PDB-ENSP_mappings:3u88.B;PDB-ENSP_mappings:4gpq.A;PDB-ENSP_mappings:4gq3.A;PDB-ENSP_mappings:4gq4.A;PDB-ENSP_mappings:4gq6.A;PDB-ENSP_mappings:4i80.A;PDB-ENSP_mappings:4og3.A;PDB-ENSP_mappings:4og4.A;PDB-ENSP_mappings:4og5.A;PDB-ENSP_mappings:4og6.A;PDB-ENSP_mappings:4og7.A;PDB-ENSP_mappings:4og8.A;PDB-ENSP_mappings:4x5y.A;PDB-ENSP_mappings:4x5z.A;PDB-ENSP_mappings:5db0.A;PDB-ENSP_mappings:5db1.A;PDB-ENSP_mappings:5db2.A;PDB-ENSP_mappings:5db3.A;PDB-ENSP_mappings:5dd9.A;PDB-ENSP_mappings:5dda.A;PDB-ENSP_mappings:5ddb.A;PDB-ENSP_mappings:5ddc.A;PDB-ENSP_mappings:5ddd.A;PDB-ENSP_mappings:5dde.A;PDB-ENSP_mappings:5ddf.A;PDB-ENSP_mappings:6b41.A;PDB-ENSP_mappings:6bxh.A;PDB-ENSP_mappings:6bxy.A;PDB-ENSP_mappings:6by8.A;PDB-ENSP_mappings:6e1a.A;PDB-ENSP_mappings:6o5i.A;PDB-ENSP_mappings:6pkc.A;PDB-ENSP_mappings:6pkc.B;PDB-ENSP_mappings:6wnh.A;CDD:cd14456;PANTHER:PTHR12693;Pfam:PF05053 ENSP00000337088 4/10 rs878855197;CM004415;CM045305;COSV53640570 ENST00000337652 Transcript 1.0 ENSG00000133895 HGNC:7010 MODERATE 2.892e-05 gnomAD_AMR missense_variant 1;1;1;1 benign(0.095) Unknown tolerated(0.13) 0;0;0;1 O00255.201 MEN1 HGNC -1 5.0 UPI0000246DC0 O00255-1 SNV MEN1,missense_variant,p.R234H,ENST00000337652,NM_130803.2,c.701G>A,MODERATE,,tolerated(0.13),benign(0.095),-1;MEN1,missense_variant,p.R234H,ENST00000394374,NM_130802.2&NM_000244.3&NM_130801.2&NM_130800.2,c.701G>A,MODERATE,,tolerated(0.13),benign(0.095),-1;MEN1,missense_variant,p.R229H,ENST00000377326,,c.686G>A,MODERATE,,tolerated(0.13),benign(0.041),-1;MEN1,missense_variant,p.R234H,ENST00000394376,NM_130804.2,c.701G>A,MODERATE,,tolerated(0.13),benign(0.095),-1;MEN1,missense_variant,p.R229H,ENST00000315422,NM_001370261.1,c.686G>A,MODERATE,,tolerated(0.13),benign(0.041),-1;MEN1,missense_variant,p.R229H,ENST00000377316,,c.686G>A,MODERATE,,tolerated(0.33),possibly_damaging(0.703),-1;MEN1,missense_variant,p.R229H,ENST00000672304,NM_001370251.1,c.686G>A,MODERATE,YES,tolerated(0.27),benign(0.011),-1;MEN1,missense_variant,p.R229H,ENST00000312049,NM_130799.2,c.686G>A,MODERATE,,tolerated(0.13),benign(0.041),-1;MEN1,missense_variant,p.R229H,ENST00000450708,NM_001370260.1&NM_001370259.2,c.686G>A,MODERATE,,tolerated(0.13),benign(0.041),-1;MEN1,missense_variant,p.R234H,ENST00000377313,,c.701G>A,MODERATE,,tolerated(0.13),benign(0.095),-1;MEN1,missense_variant,p.R229H,ENST00000440873,,c.686G>A,MODERATE,,tolerated(0.13),benign(0.041),-1;MEN1,missense_variant,p.R194H,ENST00000377321,NM_001370263.1&NM_001370262.1,c.581G>A,MODERATE,,tolerated(0.13),possibly_damaging(0.579),-1;MEN1,missense_variant,p.R229H,ENST00000413626,,c.686G>A,MODERATE,,tolerated(0.36),possibly_damaging(0.703),-1;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.5,,MODIFIER,YES,,,-1;MAP4K2,upstream_gene_variant,,ENST00000377350,NM_001307990.2,,MODIFIER,,,,-1;MEN1,downstream_gene_variant,,ENST00000424912,,,MODIFIER,,,,-1;MEN1,downstream_gene_variant,,ENST00000429702,,,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000439069,,,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000468062,,,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000482314,,,MODIFIER,,,,-1;MEN1,missense_variant,p.R138H,ENST00000672079,,c.413G>A,MODERATE,,tolerated(0.28),benign(0.007),-1;MEN1,non_coding_transcript_exon_variant,,ENST00000478548,,n.726G>A,MODIFIER,,,,-1;MEN1,non_coding_transcript_exon_variant,,ENST00000671939,,n.963G>A,MODIFIER,,,,-1;MEN1,non_coding_transcript_exon_variant,,ENST00000671965,,n.346G>A,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000433890,,,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000435926,,,MODIFIER,,,,-1;MAP4K2,upstream_gene_variant,,ENST00000444560,,,MODIFIER,,,,-1 1205/3162 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.979e-06 0.0 2.892e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 82 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MEN1,non_coding_transcript_exon_variant,,ENST00000671965.2,n.346G>A,MODIFIER,;MEN1,non_coding_transcript_exon_variant,,ENST00000671939.2,n.648G>A,MODIFIER,;MEN1,missense_variant,p.R229H,ENST00000440873.6,c.686G>A,MODERATE,;MEN1,synonymous_variant,NMD_transcript_variant,p.A224=,ENST00000394374.8,c.672G>A,LOW,;MEN1,missense_variant,p.R229H,ENST00000672304.1,c.686G>A,MODERATE,;MEN1,non_coding_transcript_exon_variant,,ENST00000478548.3,n.718G>A,MODIFIER,;MEN1,missense_variant,p.R229H,ENST00000429702.6,c.686G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000312049.11,c.686G>A,MODERATE,;MEN1,missense_variant,p.R194H,ENST00000377321.5,c.581G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000377326.7,c.686G>A,MODERATE,;MEN1,missense_variant,NMD_transcript_variant,p.R229H,ENST00000672079.2,c.686G>A,MODERATE,;MEN1,missense_variant,p.R234H,ENST00000710881.1,c.701G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000450708.7,c.686G>A,MODERATE,YES;MEN1,missense_variant,p.R229H,ENST00000424912.2,c.686G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000413626.2,c.686G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000394376.7,c.686G>A,MODERATE,;MEN1,missense_variant,p.R234H,ENST00000377313.7,c.701G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000315422.9,c.686G>A,MODERATE,;MEN1,missense_variant,p.R229H,ENST00000377316.6,c.686G>A,MODERATE, +EHD1 10938 BI GRCh38 11 64855340 64855340 + synonymous_variant Silent SNP C C T rs144668933 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 9 c.1062G>A p.Pro354= p.P354= ENST00000320631.8 NM_006795.4 354 ccG/ccA 4/5 P1 T P protein_coding CCDS8084.1 1062/1605 AGGCTCGGGAA PANTHER:PTHR11216:SF127;PANTHER:PTHR11216;Gene3D:1.10.268.20;Pfam:PF18150 ENSP00000320516 0.0002272 0.0003491 4/5 rs144668933 ENST00000320631 Transcript ENSG00000110047 HGNC:3242 LOW NM_006795.4 0.0003491 EA synonymous_variant Unknown Q9H4M9.174 EHD1 HGNC -1 B2R5U3.114 1.0 UPI0000129E22 SNV EHD1,synonymous_variant,p.P354=,ENST00000320631,NM_006795.4,c.1062G>A,LOW,,,,-1;EHD1,synonymous_variant,p.P354=,ENST00000359393,NM_001282444.2,c.1062G>A,LOW,,,,-1;EHD1,synonymous_variant,p.P368=,ENST00000621096,NM_001282445.1,c.1104G>A,LOW,YES,,,-1;EHD1,synonymous_variant,p.P368=,ENST00000433803,,c.1104G>A,LOW,,,,-1;EHD1,synonymous_variant,p.P218=,ENST00000421510,,c.654G>A,LOW,,,,-1;EHD1,downstream_gene_variant,,ENST00000455148,,,MODIFIER,,,,-1;EHD1,upstream_gene_variant,,ENST00000488711,,,MODIFIER,,,,-1;EHD1,non_coding_transcript_exon_variant,,ENST00000484846,,n.1324G>A,MODIFIER,,,,-1;EHD1,non_coding_transcript_exon_variant,,ENST00000498472,,n.269G>A,MODIFIER,,,,-1;EHD1,downstream_gene_variant,,ENST00000466015,,,MODIFIER,,,,-1 1219/4453 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.382e-05 6.16e-05 2.894e-05 0.0 0.0001631 0.0 5.287e-05 0.0 0.0 0.0001013770015561 0.0001701919973129 0.0 0.0 0.0 0.0 0.0 afr 0.0001701919973129 0.0 0.0001234450028277 0.0 0.0 0 56 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EHD1,synonymous_variant,p.P368=,ENST00000433803.1,c.1104G>A,LOW,;EHD1,non_coding_transcript_exon_variant,,ENST00000498472.1,n.269G>A,MODIFIER,;EHD1,synonymous_variant,p.P218=,ENST00000421510.5,c.654G>A,LOW,;EHD1,synonymous_variant,p.P354=,ENST00000359393.6,c.1062G>A,LOW,;EHD1,non_coding_transcript_exon_variant,,ENST00000484846.1,n.1324G>A,MODIFIER,;EHD1,synonymous_variant,p.P368=,ENST00000621096.4,c.1104G>A,LOW,;EHD1,synonymous_variant,p.P354=,ENST00000320631.8,c.1062G>A,LOW,YES +EFEMP2 30008 BI GRCh38 11 65870560 65870560 + missense_variant Missense_Mutation SNP G G A rs573771187 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 5 10 c.466C>T p.Arg156Cys p.R156C ENST00000307998.11 NM_016938.5 156 Cgc/Tgc 5/11 0.0004 0.0015 0.0 0.0 0.0 0.0 P1 A R/C protein_coding YES CCDS8116.1 466/1332 CTTGCGGTAAC CDD:cd00054;Pfam:PF07645;Gene3D:2.10.25.10;SMART:SM00181;SMART:SM00179;Superfamily:SSF57184;PROSITE_profiles:PS50026;PANTHER:PTHR24034:SF96;PANTHER:PTHR24034;PROSITE_patterns:PS01186 ENSP00000309953 5/11 rs573771187;COSV57259852 ENST00000307998 Transcript 1.0 ENSG00000172638 HGNC:3219 MODERATE NM_016938.5 0.0015 AFR missense_variant 0;1 1.0 probably_damaging(0.993) Unknown tolerated(0.18) 0;1 O95967.202 EFEMP2 HGNC -1 A0A024R5G1.55 1.0 UPI000013EC97 SNV EFEMP2,missense_variant,p.R156C,ENST00000307998,NM_016938.5,c.466C>T,MODERATE,YES,tolerated(0.18),probably_damaging(0.993),-1;EFEMP2,missense_variant,p.R156C,ENST00000528176,,c.466C>T,MODERATE,,tolerated(0.17),probably_damaging(0.995),-1;EFEMP2,missense_variant,p.R156C,ENST00000526624,,c.466C>T,MODERATE,,deleterious(0.04),probably_damaging(0.993),-1;EFEMP2,missense_variant,p.R156C,ENST00000527378,,c.466C>T,MODERATE,,deleterious(0.01),probably_damaging(0.993),-1;MUS81,downstream_gene_variant,,ENST00000308110,NM_001350283.2&NM_025128.5,,MODIFIER,YES,,,1;EFEMP2,upstream_gene_variant,,ENST00000526911,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000529742,,,MODIFIER,,,,1;EFEMP2,upstream_gene_variant,,ENST00000530806,,,MODIFIER,,,,-1;EFEMP2,upstream_gene_variant,,ENST00000531645,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000533035,,,MODIFIER,,,,1;MUS81,downstream_gene_variant,,ENST00000525006,,,MODIFIER,,,,1;EFEMP2,upstream_gene_variant,,ENST00000532648,,,MODIFIER,,,,-1;EFEMP2,missense_variant,p.R156C,ENST00000531972,,c.466C>T,MODERATE,,tolerated(0.18),probably_damaging(0.993),-1;EFEMP2,3_prime_UTR_variant,,ENST00000533347,,c.*278C>T,MODIFIER,,,,-1;EFEMP2,3_prime_UTR_variant,,ENST00000530850,,c.*278C>T,MODIFIER,,,,-1;EFEMP2,non_coding_transcript_exon_variant,,ENST00000531005,,n.1460C>T,MODIFIER,,,,-1;EFEMP2,non_coding_transcript_exon_variant,,ENST00000527969,,n.145C>T,MODIFIER,,,,-1;EFEMP2,upstream_gene_variant,,ENST00000524408,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000524647,,,MODIFIER,,,,1;EFEMP2,upstream_gene_variant,,ENST00000525392,,,MODIFIER,,,,-1;EFEMP2,upstream_gene_variant,,ENST00000526628,,,MODIFIER,,,,-1;EFEMP2,upstream_gene_variant,,ENST00000527277,,,MODIFIER,,,,-1;EFEMP2,upstream_gene_variant,,ENST00000528409,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000529786,,,MODIFIER,,,,1;EFEMP2,downstream_gene_variant,,ENST00000529870,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000530282,,,MODIFIER,,,,1;MUS81,downstream_gene_variant,,ENST00000530928,,,MODIFIER,,,,1;MUS81,downstream_gene_variant,,ENST00000531905,,,MODIFIER,,,,1;EFEMP2,upstream_gene_variant,,ENST00000532084,,,MODIFIER,,,,-1;MUS81,downstream_gene_variant,,ENST00000533519,,,MODIFIER,,,,1 591/1934 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.188e-05 0.0001233 0.0 0.0 5.44e-05 0.0 2.645e-05 0.0 6.534e-05 6.762969860574231e-06 2.4340399249922484e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 15 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS EFEMP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000530850.1,c.*278C>T,MODIFIER,;EFEMP2,missense_variant,p.R156C,ENST00000527378.1,c.466C>T,MODERATE,;EFEMP2,missense_variant,p.R156C,ENST00000526624.5,c.466C>T,MODERATE,;EFEMP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000533347.5,c.*278C>T,MODIFIER,;EFEMP2,non_coding_transcript_exon_variant,,ENST00000527969.1,n.145C>T,MODIFIER,;EFEMP2,non_coding_transcript_exon_variant,,ENST00000531005.5,n.1460C>T,MODIFIER,;EFEMP2,missense_variant,p.R156C,ENST00000528176.5,c.466C>T,MODERATE,;EFEMP2,missense_variant,NMD_transcript_variant,p.R156C,ENST00000531972.5,c.466C>T,MODERATE,;EFEMP2,missense_variant,p.R156C,ENST00000307998.11,c.466C>T,MODERATE,YES +PPFIA1 8500 BI GRCh38 11 70362369 70362369 + missense_variant Missense_Mutation SNP G G A rs750191381 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 4 c.2746G>A p.Asp916Asn p.D916N ENST00000253925.12 NM_003626.5 916 Gac/Aac 21/28 P1 A D/N protein_coding CCDS31627.1 2746/3609 TGTCCGACACA COSM388992 Gene3D:1.10.150.50;PROSITE_profiles:PS50105;PANTHER:PTHR12587;PANTHER:PTHR12587:SF15;SMART:SM00454;Superfamily:SSF47769;CDD:cd09562 ENSP00000253925 21/28 rs750191381;COSV54131213 ENST00000253925 Transcript ENSG00000131626 HGNC:9245 MODERATE NM_003626.5 5.782e-05 gnomAD_AMR missense_variant 0;1 probably_damaging(0.948) Unknown deleterious(0) 0;1 Q13136.182 PPFIA1 HGNC 1 1.0 UPI0000072426 Q13136-1 SNV PPFIA1,missense_variant,p.D908N,ENST00000644155,NM_001378006.1,c.2722G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.893),1;PPFIA1,missense_variant,p.D916N,ENST00000253925,NM_003626.5,c.2746G>A,MODERATE,,deleterious(0),probably_damaging(0.948),1;PPFIA1,missense_variant,p.D916N,ENST00000389547,NM_177423.3,c.2746G>A,MODERATE,,deleterious(0),probably_damaging(0.913),1;PPFIA1,missense_variant,p.D359N,ENST00000528750,,c.1075G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;PPFIA1,missense_variant,p.D123N,ENST00000638133,,c.367G>A,MODERATE,,deleterious_low_confidence(0.01),probably_damaging(0.932),1;PPFIA1,upstream_gene_variant,,ENST00000530548,,,MODIFIER,,,,1;PPFIA1,3_prime_UTR_variant,,ENST00000648755,,c.*2508G>A,MODIFIER,,,,1;PPFIA1,3_prime_UTR_variant,,ENST00000532504,,c.*1005G>A,MODIFIER,,,,1;PPFIA1,3_prime_UTR_variant,,ENST00000526262,,c.*1005G>A,MODIFIER,,,,1;PPFIA1,3_prime_UTR_variant,,ENST00000530390,,c.*635G>A,MODIFIER,,,,1;PPFIA1,non_coding_transcript_exon_variant,,ENST00000532793,,n.124G>A,MODIFIER,,,,1;PPFIA1,downstream_gene_variant,,ENST00000527612,,,MODIFIER,,,,1;AP002336.2,intron_variant,,ENST00000528607,,n.493+507C>T,MODIFIER,YES,,,-1;AP000487.2,upstream_gene_variant,,ENST00000324630,,,MODIFIER,YES,,,-1 2971/5240 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0 5.782e-05 0.0 5.438e-05 4.622e-05 0.0 0.0 0.0 3.379890040378086e-05 0.0 0.0 0.0003312570042908 0.0 0.0 0.0 amr 0.0003312570042908 0.0 0.0 0.0 0.0 0 66 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPFIA1,non_coding_transcript_exon_variant,,ENST00000532793.1,n.124G>A,MODIFIER,;PPFIA1,synonymous_variant,p.P122=,ENST00000638133.1,c.366G>A,LOW,;PPFIA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000530390.5,c.*635G>A,MODIFIER,;PPFIA1,synonymous_variant,p.P358=,ENST00000528750.1,c.1074G>A,LOW,;PPFIA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000526262.5,c.*1005G>A,MODIFIER,;ENSG00000254604,intron_variant,,ENST00000528607.1,n.493+507C>T,MODIFIER,YES;PPFIA1,synonymous_variant,p.P907=,ENST00000644155.1,c.2721G>A,LOW,;PPFIA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000648755.1,c.*2508G>A,MODIFIER,;PPFIA1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000532504.5,c.*1005G>A,MODIFIER,;PPFIA1,missense_variant,p.D916N,ENST00000389547.7,c.2746G>A,MODERATE,;PPFIA1,missense_variant,p.D916N,ENST00000253925.12,c.2746G>A,MODERATE,YES +P2RY2 5029 BI GRCh38 11 73234622 73234622 + missense_variant Missense_Mutation SNP G G A rs1292801922 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 44 6 c.463G>A p.Gly155Arg p.G155R ENST00000311131.6 155 Ggg/Agg 3/3 P1 A G/R protein_coding CCDS8219.1 463/1134 TGGCCGGGGCC COSM5487202 Low_complexity_(Seg):seg;Transmembrane_helices:TMhelix;PROSITE_profiles:PS50262;CDD:cd15373;PANTHER:PTHR24231;PANTHER:PTHR24231:SF17;Pfam:PF00001;Gene3D:1.20.1070.10;Superfamily:SSF81321;Prints:PR00237 ENSP00000310305 3/3 rs1292801922;COSV60776120 ENST00000311131 Transcript ENSG00000175591 HGNC:8541 MODERATE missense_variant 0;1 benign(0.333) Unknown deleterious(0.03) 0;1 P41231.186 P2RY2 HGNC 1 1.0 UPI000013F103 SNV P2RY2,missense_variant,p.G155R,ENST00000393597,NM_176072.3&NM_002564.4,c.463G>A,MODERATE,YES,deleterious(0.03),benign(0.333),1;P2RY2,missense_variant,p.G155R,ENST00000311131,,c.463G>A,MODERATE,,deleterious(0.03),benign(0.333),1;P2RY2,missense_variant,p.G155R,ENST00000393596,NM_176071.3,c.463G>A,MODERATE,,deleterious(0.03),benign(0.333),1;AP002761.4,upstream_gene_variant,,ENST00000565433,,,MODIFIER,YES,,,1 930/2660 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.757580194971524e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 50 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS P2RY2,missense_variant,p.G155R,ENST00000393596.2,c.463G>A,MODERATE,;P2RY2,missense_variant,p.G155R,ENST00000311131.6,c.463G>A,MODERATE,;P2RY2,missense_variant,p.G155R,ENST00000393597.7,c.463G>A,MODERATE,YES +ARHGEF17 9828 BI GRCh38 11 73310305 73310305 + missense_variant Missense_Mutation SNP G G A rs373537661 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 4 c.1667G>A p.Arg556His p.R556H ENST00000263674.4 NM_014786.4 556 cGc/cAc 1/21 P3 A R/H protein_coding YES CCDS8221.1 1667/6192 GGCCCGCCGCC MobiDB_lite:mobidb-lite;PANTHER:PTHR12877:SF15;PANTHER:PTHR12877 ENSP00000263674 0.0002273 0.0 1/21 rs373537661 ENST00000263674 Transcript ENSG00000110237 HGNC:21726 MODERATE NM_014786.4 0.0002273 AA missense_variant 1.0 benign(0.003) Unknown deleterious_low_confidence(0.04) Q96PE2.148 ARHGEF17 HGNC 1 1.0 UPI000004980B SNV ARHGEF17,missense_variant,p.R556H,ENST00000263674,NM_014786.4,c.1667G>A,MODERATE,YES,deleterious_low_confidence(0.04),benign(0.003),1;ARHGEF17,upstream_gene_variant,,ENST00000544519,,,MODIFIER,,,,1;AP002761.3,upstream_gene_variant,,ENST00000546324,,,MODIFIER,YES,,,-1 2030/8163 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.989e-06 6.188e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ARHGEF17,missense_variant,p.R556H,ENST00000263674.4,c.1667G>A,MODERATE,YES +KCNE3 10008 BI GRCh38 11 74457407 74457407 + missense_variant Missense_Mutation SNP G G A rs371666083 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 15 c.157C>T p.Arg53Cys p.R53C ENST00000310128.9 NM_005472.5 53 Cgt/Tgt 3/3 P1 A R/C protein_coding YES CCDS8232.1 157/312 ATCACGGCCAG PDB-ENSP_mappings:2ndj.A;PDB-ENSP_mappings:6v00.C;PDB-ENSP_mappings:6v00.F;PDB-ENSP_mappings:6v00.I;PDB-ENSP_mappings:6v00.L;PDB-ENSP_mappings:6v01.C;PDB-ENSP_mappings:6v01.F;PDB-ENSP_mappings:6v01.I;PDB-ENSP_mappings:6v01.L;PANTHER:PTHR15282;PANTHER:PTHR15282:SF6;Pfam:PF02060;Prints:PR01606 ENSP00000310557 0.0 0.0001165 3/3 rs371666083 ENST00000310128 Transcript 1.0 ENSG00000175538 HGNC:6243 MODERATE NM_005472.5 0.0001165 EA missense_variant 1.0 benign(0.013) Unknown deleterious(0) Q9Y6H6.160 KCNE3 HGNC -1 Q6IAE6.132 1.0 UPI000012F15C SNV KCNE3,missense_variant,p.R53C,ENST00000310128,NM_005472.5,c.157C>T,MODERATE,YES,deleterious(0),benign(0.013),-1;KCNE3,missense_variant,p.R53C,ENST00000525550,,c.157C>T,MODERATE,,deleterious(0),benign(0.013),-1;KCNE3,missense_variant,p.R53C,ENST00000532569,,c.157C>T,MODERATE,,deleterious(0),benign(0.013),-1;KCNE3,incomplete_terminal_codon_variant,p.*53=,ENST00000531854,,c.157C>T,LOW,,,,-1;KCNE3,downstream_gene_variant,,ENST00000526855,,,MODIFIER,,,,-1;KCNE3,downstream_gene_variant,,ENST00000529425,,,MODIFIER,,,,-1;AP001372.1,intron_variant,,ENST00000533008,,n.155-26770G>A,MODIFIER,,,,1;AP001372.3,downstream_gene_variant,,ENST00000530510,,,MODIFIER,YES,,,1 498/3064 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.992e-05 0.0 0.0 0.0 0.0 0.0 4.407e-05 0.0 0.0 2.0283699996070936e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629629984265193e-05 0.0 4.629629984265193e-05 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 31 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KCNE3,coding_sequence_variant,splice_region_variant,,ENST00000531854.5,c.157C>T,LOW,;KCNE3,missense_variant,p.R53C,ENST00000532569.5,c.157C>T,MODERATE,;KCNE3,missense_variant,p.R53C,ENST00000525550.1,c.157C>T,MODERATE,;KCNE3,missense_variant,p.R53C,ENST00000310128.9,c.157C>T,MODERATE,YES;ENSG00000254631,intron_variant,,ENST00000533008.1,n.155-26770G>A,MODIFIER,YES +SLCO2B1 11309 BI GRCh38 11 75196593 75196593 + missense_variant Missense_Mutation SNP G G A rs1009964902 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 17 c.1513G>A p.Asp505Asn p.D505N ENST00000289575.10 NM_007256.5 505 Gac/Aac 10/14 P4 A D/N protein_coding YES CCDS8235.1 1513/2130 TCTGCGACCCC PROSITE_profiles:PS51465;CDD:cd17460;PANTHER:PTHR11388:SF87;PANTHER:PTHR11388;TIGRFAM:TIGR00805;Pfam:PF03137;Superfamily:SSF103473 ENSP00000289575 10/14 rs1009964902;COSV99215093 ENST00000289575 Transcript ENSG00000137491 HGNC:10962 MODERATE NM_007256.5 missense_variant 0;1 1.0 benign(0.168) Unknown deleterious(0.04) 0;1 SLCO2B1 HGNC 1 A0A024R5I4.51 1.0 UPI000000D99A SNV SLCO2B1,missense_variant,p.D505N,ENST00000289575,NM_007256.5,c.1513G>A,MODERATE,YES,deleterious(0.04),benign(0.168),1;SLCO2B1,missense_variant,p.D278N,ENST00000454962,,c.832G>A,MODERATE,,tolerated(0.09),benign(0.249),1;SLCO2B1,missense_variant,p.D389N,ENST00000532236,,c.1165G>A,MODERATE,,tolerated(0.06),benign(0.254),1;SLCO2B1,missense_variant,p.D483N,ENST00000428359,NM_001145211.3,c.1447G>A,MODERATE,,deleterious(0.04),benign(0.169),1;SLCO2B1,missense_variant,p.D361N,ENST00000525650,NM_001145212.3,c.1081G>A,MODERATE,,tolerated(0.05),benign(0.168),1;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000531756,,n.1060G>A,MODIFIER,,,,1;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000530012,,n.340G>A,MODIFIER,,,,1;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000528108,,n.319G>A,MODIFIER,,,,1;SLCO2B1,upstream_gene_variant,,ENST00000530015,,,MODIFIER,,,,1 1788/4374 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 50 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLCO2B1,non_coding_transcript_exon_variant,,ENST00000528108.1,n.319G>A,MODIFIER,;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000530012.1,n.340G>A,MODIFIER,;SLCO2B1,missense_variant,p.D483N,ENST00000428359.6,c.1447G>A,MODERATE,;SLCO2B1,missense_variant,p.D278N,ENST00000454962.6,c.832G>A,MODERATE,;SLCO2B1,missense_variant,p.D361N,ENST00000525650.5,c.1081G>A,MODERATE,;SLCO2B1,missense_variant,p.D505N,ENST00000289575.10,c.1513G>A,MODERATE,YES;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000531756.5,n.1060G>A,MODIFIER,;SLCO2B1,missense_variant,p.D389N,ENST00000532236.5,c.1165G>A,MODERATE, +MYO7A 4647 BI GRCh38 11 77179069 77179069 + synonymous_variant Silent SNP C C T rs782329400 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 5 c.2307C>T p.Asn769= p.N769= ENST00000409709.9 NM_000260.4 769 aaC/aaT 20/49 T N protein_coding YES CCDS53683.1 2307/6648 AAGAACGCTGC PROSITE_profiles:PS50096;PANTHER:PTHR22692:SF19;PANTHER:PTHR22692;Pfam:PF00612;Gene3D:1.20.5.190;SMART:SM00015;Superfamily:SSF52540 ENSP00000386331 20/49 rs782329400;CD136753 ENST00000409709 Transcript 1.0 ENSG00000137474 HGNC:7606 LOW NM_000260.4 0.0001695 gnomAD_EAS synonymous_variant 0;1 1.0 Unknown Q13402.224 MYO7A HGNC 1 1.0 UPI00001FAFE6 Q13402-1 SNV MYO7A,synonymous_variant,p.N769=,ENST00000409709,NM_000260.4,c.2307C>T,LOW,YES,,,1;MYO7A,synonymous_variant,p.N769=,ENST00000458637,NM_001127180.2,c.2307C>T,LOW,,,,1;MYO7A,synonymous_variant,p.N758=,ENST00000409619,NM_001369365.1,c.2274C>T,LOW,,,,1;MYO7A,synonymous_variant,p.N769=,ENST00000620575,,c.2307C>T,LOW,,,,1;MYO7A,synonymous_variant,p.N124=,ENST00000409893,,c.372C>T,LOW,,,,1;MYO7A,upstream_gene_variant,,ENST00000458169,,,MODIFIER,,,,1;MYO7A,synonymous_variant,p.N50=,ENST00000670577,,c.150C>T,LOW,,,,1;MYO7A,upstream_gene_variant,,ENST00000481328,,,MODIFIER,,,,1 2597/7483 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.73e-05 0.0 2.94e-05 0.0 0.0001695 0.0 9.186e-06 0.0001689 0.0001023 3.3785199775593355e-05 0.0 0.0 6.625150126637891e-05 0.0 0.0002014500059885 0.0 nfe 4.6280598326120526e-05 0.0 4.6280598326120526e-05 0.0 0.0 0 15 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 8 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYO7A,missense_variant,NMD_transcript_variant,p.R50C,ENST00000670577.1,c.148C>T,MODERATE,;MYO7A,synonymous_variant,p.N124=,ENST00000409893.6,c.372C>T,LOW,;MYO7A,synonymous_variant,p.N758=,ENST00000409619.6,c.2274C>T,LOW,;MYO7A,synonymous_variant,p.N769=,ENST00000458637.6,c.2307C>T,LOW,;MYO7A,synonymous_variant,p.N769=,ENST00000409709.9,c.2307C>T,LOW,YES +YAP1 10413 BI GRCh38 11 102223694 102223694 + missense_variant Missense_Mutation SNP G G A rs1433803164 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 36 c.1105G>A p.Gly369Arg p.G369R ENST00000282441.10 NM_001130145.3 369 Ggg/Agg 7/9 P4 A G/R protein_coding CCDS44716.1 1105/1515 CTCCCGGGATG MobiDB_lite:mobidb-lite;PANTHER:PTHR17616:SF9;PANTHER:PTHR17616 ENSP00000282441 7/9 rs1433803164;COSV99176372 ENST00000282441 Transcript 1.0 ENSG00000137693 HGNC:16262 MODERATE NM_001130145.3 0.0001089 gnomAD_EAS missense_variant 0;1 probably_damaging(0.999) Unknown tolerated(0.06) 0;1 P46937.204 YAP1 HGNC 1 1.0 UPI00000746D8 P46937-1 SNV YAP1,missense_variant,p.G369R,ENST00000282441,NM_001130145.3,c.1105G>A,MODERATE,,tolerated(0.06),probably_damaging(0.999),1;YAP1,missense_variant,p.G373R,ENST00000615667,NM_001282101.1,c.1117G>A,MODERATE,YES,tolerated(0.07),possibly_damaging(0.524),1;YAP1,missense_variant,p.G357R,ENST00000537274,NM_001282100.1,c.1069G>A,MODERATE,,tolerated(0.06),probably_damaging(0.952),1;YAP1,missense_variant,p.G335R,ENST00000345877,NM_001282097.2&NM_001282099.1,c.1003G>A,MODERATE,,deleterious(0.05),benign(0.233),1;YAP1,missense_variant,p.G315R,ENST00000526343,NM_006106.5,c.943G>A,MODERATE,,tolerated(0.07),probably_damaging(0.999),1;YAP1,missense_variant,p.G191R,ENST00000524575,NM_001195045.2,c.571G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),1;YAP1,missense_variant,p.G353R,ENST00000531439,NM_001195044.2,c.1057G>A,MODERATE,,tolerated(0.07),probably_damaging(0.956),1;YAP1,missense_variant,p.G123R,ENST00000529029,,c.367G>A,MODERATE,,tolerated(0.05),benign(0.261),1;YAP1,missense_variant,p.G319R,ENST00000629586,NM_001282098.2,c.955G>A,MODERATE,,tolerated(0.06),probably_damaging(1),1;YAP1,upstream_gene_variant,,ENST00000528834,,,MODIFIER,,,,1 1507/5401 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.592e-05 0.0 0.0 0.0 0.0001089 0.0 1.76e-05 0.0 0.0 0 73 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 73 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS YAP1,synonymous_variant,p.P122=,ENST00000529029.1,c.366G>A,LOW,;YAP1,missense_variant,p.G191R,ENST00000524575.5,c.571G>A,MODERATE,;YAP1,missense_variant,p.G319R,ENST00000629586.2,c.955G>A,MODERATE,;YAP1,missense_variant,p.G353R,ENST00000531439.5,c.1057G>A,MODERATE,;YAP1,missense_variant,p.G373R,ENST00000615667.4,c.1117G>A,MODERATE,;YAP1,missense_variant,p.G315R,ENST00000526343.5,c.943G>A,MODERATE,;YAP1,missense_variant,p.G335R,ENST00000345877.6,c.1003G>A,MODERATE,;YAP1,missense_variant,p.G357R,ENST00000537274.5,c.1069G>A,MODERATE,;YAP1,missense_variant,p.G369R,ENST00000282441.10,c.1105G>A,MODERATE,YES +APOA4 337 BI GRCh38 11 116821060 116821060 + missense_variant Missense_Mutation SNP G G A rs113263292 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 11 c.998C>T p.Ala333Val p.A333V ENST00000357780.5 NM_000482.4 333 gCg/gTg 3/3 P1 A A/V protein_coding YES CCDS31681.1 998/1191 CCCCCGCATGG PANTHER:PTHR18976:SF1;PANTHER:PTHR18976;Pfam:PF01442;Gene3D:1.20.120.20;Superfamily:SSF58113 ENSP00000350425 3/3 rs113263292 ENST00000357780 Transcript ENSG00000110244 HGNC:602 MODERATE NM_000482.4 6.533e-05 gnomAD_SAS missense_variant 1.0 benign(0.078) Unknown tolerated(0.12) P06727.215 APOA4 HGNC -1 1.0 UPI00001AE660 SNV APOA4,missense_variant,p.A333V,ENST00000357780,NM_000482.4,c.998C>T,MODERATE,YES,tolerated(0.12),benign(0.078),-1;AP006216.3,non_coding_transcript_exon_variant,,ENST00000645414,,n.209G>A,MODIFIER,YES,,,1 1111/1471 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.784e-05 6.152e-05 0.0 0.0 0.0 0.0 3.516e-05 0.0 6.533e-05 2.027929986070376e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629199975170195e-05 0.0 4.629199975170195e-05 0.0 0.0 0 70 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 49 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS APOA4,missense_variant,p.A333V,ENST00000357780.5,c.998C>T,MODERATE,YES;ENSG00000285513,non_coding_transcript_exon_variant,,ENST00000645414.1,n.209G>A,MODIFIER,YES +PCSK7 9159 BI GRCh38 11 117219101 117219101 + missense_variant Missense_Mutation SNP C C T rs1407631588 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 6 c.1387G>A p.Gly463Ser p.G463S ENST00000320934.8 NM_004716.4 463 Ggt/Agt 11/17 P1 T G/S protein_coding YES CCDS8382.1 1387/2358 GAAACCGTGCT PROSITE_profiles:PS51892;PANTHER:PTHR42884:SF17;PANTHER:PTHR42884;Gene3D:3.40.50.200;Superfamily:SSF52743 ENSP00000325917 11/17 rs1407631588;COSV100309357;COSV100309381 ENST00000320934 Transcript ENSG00000160613 HGNC:8748 MODERATE NM_004716.4 2.894e-05 gnomAD_AMR missense_variant 0;1;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1;1 Q16549.192 PCSK7 HGNC -1 1.0 UPI0000070E4E SNV PCSK7,missense_variant,p.G463S,ENST00000320934,NM_004716.4,c.1387G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;PCSK7,missense_variant,p.G463S,ENST00000524507,,c.1387G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;PCSK7,missense_variant,p.G463S,ENST00000676339,,c.1387G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;PCSK7,missense_variant,p.G463S,ENST00000540028,,c.1387G>A,MODERATE,,deleterious(0),probably_damaging(0.991),-1;PCSK7,non_coding_transcript_exon_variant,,ENST00000533135,,n.65G>A,MODIFIER,,,,-1;PCSK7,non_coding_transcript_exon_variant,,ENST00000534529,,n.3417G>A,MODIFIER,,,,-1;PCSK7,non_coding_transcript_exon_variant,,ENST00000527037,,n.1038G>A,MODIFIER,,,,-1;PCSK7,downstream_gene_variant,,ENST00000528217,,,MODIFIER,,,,-1;PCSK7,upstream_gene_variant,,ENST00000528973,,,MODIFIER,,,,-1 1566/4197 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.028e-06 0.0 2.894e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 21 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PCSK7,non_coding_transcript_exon_variant,,ENST00000533135.1,n.65G>A,MODIFIER,;PCSK7,non_coding_transcript_exon_variant,,ENST00000527037.5,n.1038G>A,MODIFIER,;PCSK7,non_coding_transcript_exon_variant,,ENST00000534529.5,n.3417G>A,MODIFIER,;PCSK7,missense_variant,p.G463S,ENST00000524507.6,c.1387G>A,MODERATE,;PCSK7,missense_variant,p.G463S,ENST00000676339.1,c.1387G>A,MODERATE,;PCSK7,missense_variant,p.G463S,ENST00000320934.8,c.1387G>A,MODERATE,YES +DSCAML1 57453 BI GRCh38 11 117430983 117430983 + missense_variant Missense_Mutation SNP C C T rs1394687991 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 43 c.5425G>A p.Glu1809Lys p.E1809K ENST00000651296.2 NM_020693.4 1809 Gag/Aag 32/33 P1 T E/K protein_coding YES CCDS8384.1 5605/6342 CTCCTCGTAGG PANTHER:PTHR13817;PANTHER:PTHR13817:SF54 ENSP00000315465 32/33 rs1394687991;COSV58391648 ENST00000321322 Transcript ENSG00000177103 HGNC:14656 MODERATE 8.807e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1 DSCAML1 HGNC -1 A0A384DVL8.11 1.0 UPI00000726E2 SNV DSCAML1,missense_variant,p.E1869K,ENST00000321322,,c.5605G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;DSCAML1,missense_variant,p.E1809K,ENST00000651296,NM_020693.4,c.5425G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;DSCAML1,missense_variant,p.E1869K,ENST00000651172,,c.5605G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;DSCAML1,missense_variant,p.E1599K,ENST00000527706,,c.4795G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1 5607/6899 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-06 0.0 0.0 0.0 0.0 0.0 8.807e-06 0.0 0.0 6.763249984942377e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 103 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DSCAML1,missense_variant,p.E1869K,ENST00000651172.1,c.5605G>A,MODERATE,;DSCAML1,missense_variant,p.E1599K,ENST00000527706.5,c.4795G>A,MODERATE,;DSCAML1,missense_variant,p.E1869K,ENST00000321322.6,c.5605G>A,MODERATE,;DSCAML1,missense_variant,p.E1809K,ENST00000651296.2,c.5425G>A,MODERATE,YES +DSCAML1 57453 BI GRCh38 11 117780694 117780694 + missense_variant Missense_Mutation SNP C C T rs775200712 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 26 29 c.163G>A p.Ala55Thr p.A55T ENST00000651296.2 NM_020693.4 55 Gcg/Acg 2/33 P1 T A/T protein_coding YES CCDS8384.1 343/6342 GGCCGCGCTGG PROSITE_profiles:PS50835;CDD:cd00096;PANTHER:PTHR13817;PANTHER:PTHR13817:SF54;Gene3D:2.60.40.10;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726 ENSP00000315465 2/33 rs775200712;COSV100355237 ENST00000321322 Transcript ENSG00000177103 HGNC:14656 MODERATE 3.347e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.038) Unknown tolerated(0.16) 0;1 DSCAML1 HGNC -1 A0A384DVL8.11 1.0 UPI00000726E2 SNV DSCAML1,missense_variant,p.A115T,ENST00000321322,,c.343G>A,MODERATE,YES,tolerated(0.16),benign(0.038),-1;DSCAML1,missense_variant,p.A55T,ENST00000651296,NM_020693.4,c.163G>A,MODERATE,,tolerated(0.27),possibly_damaging(0.738),-1;DSCAML1,missense_variant,p.A115T,ENST00000651172,,c.343G>A,MODERATE,,tolerated(0.16),benign(0.038),-1;DSCAML1,5_prime_UTR_variant,,ENST00000525836,,c.-133G>A,MODIFIER,,,,-1;DSCAML1,intron_variant,,ENST00000527706,,c.102+61G>A,MODIFIER,,,,-1 345/6899 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.337e-06 0.0 3.347e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 68 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DSCAML1,5_prime_UTR_variant,,ENST00000525836.1,c.-133G>A,MODIFIER,;DSCAML1,missense_variant,p.A115T,ENST00000651172.1,c.343G>A,MODERATE,;DSCAML1,intron_variant,,ENST00000527706.5,c.102+61G>A,MODIFIER,;DSCAML1,missense_variant,p.A115T,ENST00000321322.6,c.343G>A,MODERATE,;DSCAML1,missense_variant,p.A55T,ENST00000651296.2,c.163G>A,MODERATE,YES +CBL 867 BI GRCh38 11 119273988 119273988 + synonymous_variant Silent SNP G G A rs146662327 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 12 c.711G>A p.Ser237= p.S237= ENST00000264033.6 NM_005188.4 237 tcG/tcA 4/16 P3 A S protein_coding YES CCDS8418.1 711/2721 ATTTCGGTTTT Gene3D:1.10.238.10;PDB-ENSP_mappings:1b47.A;PDB-ENSP_mappings:1b47.B;PDB-ENSP_mappings:1b47.C;PDB-ENSP_mappings:1fbv.A;PDB-ENSP_mappings:1yvh.A;PDB-ENSP_mappings:2cbl.A;PDB-ENSP_mappings:2y1m.A;PDB-ENSP_mappings:2y1m.B;PDB-ENSP_mappings:2y1m.C;PDB-ENSP_mappings:2y1m.D;PDB-ENSP_mappings:2y1m.E;PDB-ENSP_mappings:2y1m.F;PDB-ENSP_mappings:2y1n.A;PDB-ENSP_mappings:2y1n.C;PDB-ENSP_mappings:3bum.B;PDB-ENSP_mappings:3bun.B;PDB-ENSP_mappings:3buo.B;PDB-ENSP_mappings:3buo.D;PDB-ENSP_mappings:3buw.B;PDB-ENSP_mappings:3buw.D;PDB-ENSP_mappings:3bux.B;PDB-ENSP_mappings:3bux.D;PDB-ENSP_mappings:3ob1.B;PDB-ENSP_mappings:3ob2.B;PDB-ENSP_mappings:3plf.B;PDB-ENSP_mappings:3plf.D;PDB-ENSP_mappings:4a4b.A;PDB-ENSP_mappings:4a4c.A;PDB-ENSP_mappings:4gpl.B;PDB-ENSP_mappings:5hkw.A;PDB-ENSP_mappings:5hkw.B;PDB-ENSP_mappings:5hkw.C;PDB-ENSP_mappings:5hkx.A;PDB-ENSP_mappings:5hky.A;PDB-ENSP_mappings:5hkz.A;PDB-ENSP_mappings:5hl0.A;PDB-ENSP_mappings:5j3x.A;PDB-ENSP_mappings:5j3x.B;PDB-ENSP_mappings:5j3x.C;PDB-ENSP_mappings:5j3x.D;PDB-ENSP_mappings:5j3x.E;PDB-ENSP_mappings:5j3x.F;PDB-ENSP_mappings:5o76.A;PDB-ENSP_mappings:5o76.C;Pfam:PF02761;PROSITE_profiles:PS51506;PANTHER:PTHR23007;PANTHER:PTHR23007:SF5;Superfamily:SSF47473 ENSP00000264033 0.0002274 0.0 4/16 rs146662327 ENST00000264033 Transcript 1.0 ENSG00000110395 HGNC:1541 LOW NM_005188.4 0.0003076 gnomAD_AFR synonymous_variant 1.0 Unknown P22681.234 CBL HGNC 1 1.0 UPI000013D4A7 SNV CBL,synonymous_variant,p.S237=,ENST00000264033,NM_005188.4,c.711G>A,LOW,YES,,,1;CBL,synonymous_variant,p.S237=,ENST00000634840,,c.711G>A,LOW,,,,1;CBL,synonymous_variant,p.S237=,ENST00000634586,,c.711G>A,LOW,,,,1;CBL,synonymous_variant,p.S235=,ENST00000637974,,c.705G>A,LOW,,,,1 790/11168 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.977e-05 0.0003076 0.0 0.0 5.437e-05 0.0 2.638e-05 0.0 3.266e-05 6.0946698795305565e-05 9.7494397778064e-05 0.0 6.639219645876437e-05 0.0 0.0002017759979935 0.0 sas 0.0006255210028029 0.0 0.0 0.0 0.0006255210028029 0 83 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 46 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CBL,synonymous_variant,p.S235=,ENST00000637974.1,c.705G>A,LOW,;CBL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000700472.1,c.*163G>A,MODIFIER,;CBL,synonymous_variant,p.S237=,ENST00000264033.6,c.711G>A,LOW,YES;CBL,synonymous_variant,p.S237=,ENST00000634840.1,c.711G>A,LOW,;CBL,synonymous_variant,p.S237=,ENST00000634586.1,c.711G>A,LOW, +NECTIN1 5818 BI GRCh38 11 119664864 119664864 + synonymous_variant Silent SNP G G A rs141036439 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 4 c.1437C>T p.Asp479= p.D479= ENST00000264025.8 NM_002855.5 479 gaC/gaT 6/6 P1 A D protein_coding YES CCDS8426.1 1437/1554 TAGCCGTCCTG PANTHER:PTHR23277;PANTHER:PTHR23277:SF69;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000264025 6/6 rs141036439 ENST00000264025 Transcript 1.0 ENSG00000110400 HGNC:9706 LOW NM_002855.5 8.817e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q15223.192 NECTIN1 HGNC -1 1.0 UPI000004A2BE Q15223-1 SNV NECTIN1,synonymous_variant,p.D479=,ENST00000264025,NM_002855.5,c.1437C>T,LOW,YES,,,-1;NECTIN1,intron_variant,,ENST00000341398,NM_203285.2,c.1003+10295C>T,MODIFIER,,,,-1 2084/5956 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.987e-06 0.0 0.0 0.0 0.0 0.0 8.817e-06 0.0 0.0 2.7047899493481964e-05 0.0 0.0 0.0 0.0 0.0002017759979935 0.0 nfe 3.087369987042621e-05 0.0 3.087369987042621e-05 0.0 0.0002080730046145 0 34 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NECTIN1,synonymous_variant,p.D479=,ENST00000264025.8,c.1437C>T,LOW,YES;NECTIN1,intron_variant,,ENST00000341398.6,n.1003+10295C>T,MODIFIER,;NECTIN1,intron_variant,,ENST00000531468.2,c.1003+10295C>T,MODIFIER, +TECTA 7007 BI GRCh38 11 121130063 121130063 + synonymous_variant Silent SNP C C T rs750710717 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 11 c.2793C>T p.Asn931= p.N931= ENST00000264037.2 931 aaC/aaT 9/23 P1 T N protein_coding CCDS8434.1 2793/6468 GTGAACGTCAC Pfam:PF08742;PANTHER:PTHR46160;PANTHER:PTHR46160:SF3;SMART:SM00832 ENSP00000264037 9/23 rs750710717 ENST00000264037 Transcript 1.0 ENSG00000109927 HGNC:11720 LOW 0.0002603 gnomAD_AMR synonymous_variant Unknown O75443.172 TECTA HGNC 1 1.0 UPI000045659D SNV TECTA,synonymous_variant,p.N931=,ENST00000392793,NM_005422.4,c.2793C>T,LOW,YES,,,1;TECTA,synonymous_variant,p.N931=,ENST00000642222,NM_001378761.1,c.2793C>T,LOW,,,,1;TECTA,synonymous_variant,p.N931=,ENST00000264037,,c.2793C>T,LOW,,,,1;TECTA,synonymous_variant,p.N34=,ENST00000645008,,c.102C>T,LOW,,,,1 2793/6468 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-05 0.0 0.0002603 0.0 0.0 0.0 8.802e-06 0.0 0.0 2.0275800125091337e-05 2.4310800654347983e-05 0.0 6.624269735766575e-05 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TECTA,missense_variant,p.R34C,ENST00000645008.1,c.100C>T,MODERATE,;TECTA,synonymous_variant,p.N931=,ENST00000264037.2,c.2793C>T,LOW,;TECTA,synonymous_variant,p.N931=,ENST00000642222.1,c.2793C>T,LOW,;TECTA,synonymous_variant,p.N931=,ENST00000392793.6,c.2793C>T,LOW,YES +IGSF9B 22997 BI GRCh38 11 133936156 133936156 + missense_variant Missense_Mutation SNP C C T rs1235172280 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 5 c.718G>A p.Val240Ile p.V240I ENST00000321016.12 240 Gtc/Atc 6/19 T V/I protein_coding 718/4050 GTTGACGGTGA COSM4019497 Gene3D:2.60.40.10;Pfam:PF13927;PROSITE_profiles:PS50835;PANTHER:PTHR12231;PANTHER:PTHR12231:SF240;SMART:SM00060;SMART:SM00409;Superfamily:SSF48726 ENSP00000317980 6/19 rs1235172280;COSV58065092 ENST00000321016 Transcript ENSG00000080854 HGNC:32326 MODERATE 5.612e-05 gnomAD_EAS missense_variant 0;1 benign(0.067) Unknown deleterious(0) 0;1 Q9UPX0.150 IGSF9B HGNC -1 5.0 UPI0001545E3E Q9UPX0-1 SNV IGSF9B,missense_variant,p.V240I,ENST00000533871,NM_001277285.4,c.718G>A,MODERATE,YES,tolerated(0.05),probably_damaging(0.998),-1;IGSF9B,missense_variant,p.V240I,ENST00000321016,,c.718G>A,MODERATE,,deleterious(0),benign(0.067),-1;IGSF9B,downstream_gene_variant,,ENST00000533160,,,MODIFIER,,,,-1;IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648,,n.448G>A,MODIFIER,,,,-1 718/4050 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.165e-06 0.0 2.931e-05 0.0 5.612e-05 0.0 0.0 0.0 0.0 0 10 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648.2,n.448G>A,MODIFIER,;IGSF9B,missense_variant,p.V240I,ENST00000321016.12,c.718G>A,MODERATE,;IGSF9B,missense_variant,p.V240I,ENST00000533871.8,c.718G>A,MODERATE,YES +IGSF9B 22997 BI GRCh38 11 133937457 133937457 + missense_variant Missense_Mutation SNP G G A rs750817042 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 18 24 c.598C>T p.Arg200Trp p.R200W ENST00000321016.12 200 Cgg/Tgg 5/19 A R/W protein_coding 598/4050 CTCCCGACTGA COSM4761593 Gene3D:2.60.40.10;Pfam:PF13927;PROSITE_profiles:PS50835;PANTHER:PTHR12231;PANTHER:PTHR12231:SF240;SMART:SM00406;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096 ENSP00000317980 5/19 rs750817042;COSV58066675 ENST00000321016 Transcript ENSG00000080854 HGNC:32326 MODERATE 8.868e-06 gnomAD_NFE missense_variant 0;1 probably_damaging(0.995) Unknown deleterious(0) 0;1 Q9UPX0.150 IGSF9B HGNC -1 5.0 UPI0001545E3E Q9UPX0-1 SNV IGSF9B,missense_variant,p.R200W,ENST00000533871,NM_001277285.4,c.598C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;IGSF9B,missense_variant,p.R200W,ENST00000321016,,c.598C>T,MODERATE,,deleterious(0),probably_damaging(0.995),-1;IGSF9B,missense_variant,p.R190W,ENST00000533160,,c.568C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648,,n.328C>T,MODIFIER,,,,-1 598/4050 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.019e-06 0.0 0.0 0.0 0.0 0.0 8.868e-06 0.0 0.0 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 42 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IGSF9B,missense_variant,p.R190W,ENST00000533160.1,c.568C>T,MODERATE,;IGSF9B,non_coding_transcript_exon_variant,,ENST00000527648.2,n.328C>T,MODIFIER,;IGSF9B,missense_variant,p.R200W,ENST00000321016.12,c.598C>T,MODERATE,;IGSF9B,missense_variant,p.R200W,ENST00000533871.8,c.598C>T,MODERATE,YES +SLC6A12 6539 BI GRCh38 12 209980 209980 + missense_variant Missense_Mutation SNP C C T rs1044859657 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 8 c.7G>A p.Gly3Arg p.G3R ENST00000359674.8 NM_001122847.3 3 Ggg/Agg 3/16 P1 T G/R protein_coding CCDS8501.1 7/1845 CTTCCCGTCCA ENSP00000352702 3/16 rs1044859657 ENST00000359674 Transcript ENSG00000111181 HGNC:11045 MODERATE 8.804e-06 gnomAD_NFE missense_variant benign(0) Unknown tolerated_low_confidence(0.65) P48065.167 SLC6A12 HGNC -1 1.0 UPI000013C8DB SNV SLC6A12,missense_variant,p.G3R,ENST00000424061,NM_003044.5,c.7G>A,MODERATE,YES,tolerated_low_confidence(0.65),benign(0),-1;SLC6A12,missense_variant,p.G3R,ENST00000397296,,c.7G>A,MODERATE,,tolerated_low_confidence(0.65),benign(0),-1;SLC6A12,missense_variant,p.G3R,ENST00000359674,NM_001122848.3&NM_001122847.3,c.7G>A,MODERATE,,tolerated_low_confidence(0.65),benign(0),-1;SLC6A12,missense_variant,p.G3R,ENST00000536824,NM_001206931.2,c.7G>A,MODERATE,,tolerated_low_confidence(0.65),benign(0),-1;SLC6A12,missense_variant,p.G3R,ENST00000537793,,c.7G>A,MODERATE,,tolerated_low_confidence(0.62),benign(0),-1;SLC6A12,missense_variant,p.G3R,ENST00000535347,,c.7G>A,MODERATE,,tolerated_low_confidence(1),benign(0.001),-1;SLC6A12,non_coding_transcript_exon_variant,,ENST00000536116,,n.184G>A,MODIFIER,,,,-1;SLC6A12,downstream_gene_variant,,ENST00000538424,,,MODIFIER,,,,-1;SLC6A12,non_coding_transcript_exon_variant,,ENST00000537826,,n.283G>A,MODIFIER,,,,-1;SLC6A12-AS1,downstream_gene_variant,,ENST00000539568,,,MODIFIER,YES,,,1 336/3165 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-06 0.0 0.0 0.0 0.0 0.0 8.804e-06 0.0 0.0 6.759310053894296e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 24 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC6A12,non_coding_transcript_exon_variant,,ENST00000537826.1,n.283G>A,MODIFIER,;SLC6A12,missense_variant,p.G3R,ENST00000535347.5,c.7G>A,MODERATE,;SLC6A12,missense_variant,p.G3R,ENST00000537793.1,c.7G>A,MODERATE,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000536116.5,n.184G>A,MODIFIER,;SLC6A12,missense_variant,p.G3R,ENST00000536824.5,c.7G>A,MODERATE,;SLC6A12,missense_variant,p.G3R,ENST00000424061.6,c.7G>A,MODERATE,;SLC6A12,missense_variant,p.G3R,ENST00000684302.1,c.7G>A,MODERATE,YES;SLC6A12,missense_variant,p.G3R,ENST00000397296.6,c.7G>A,MODERATE,;SLC6A12,missense_variant,p.G3R,ENST00000359674.8,c.7G>A,MODERATE, +ERC1 23085 BI GRCh38 12 1027962 1027962 + missense_variant Missense_Mutation SNP G G A rs549963000 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 68 51 c.59G>A p.Arg20His p.R20H ENST00000360905.9 NM_178040.4 20 cGt/cAt 2/19 0.0002 0.0 0.0 0.0 0.0 0.001 A R/H protein_coding CCDS8508.1 59/3351 TGGGCGTTCAC PANTHER:PTHR18861;PANTHER:PTHR18861:SF1;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000354158 2/19 rs549963000 ENST00000360905 Transcript 1.0 ENSG00000082805 HGNC:17072 MODERATE NM_178040.4 0.001 SAS missense_variant probably_damaging(0.984) Unknown tolerated(0.05) Q8IUD2.181 ERC1 HGNC 1 1.0 UPI000007479C Q8IUD2-1 SNV ERC1,missense_variant,p.R20H,ENST00000360905,NM_178040.4,c.59G>A,MODERATE,,tolerated(0.05),probably_damaging(0.984),1;ERC1,missense_variant,p.R20H,ENST00000543086,NM_178039.4,c.59G>A,MODERATE,,tolerated(0.06),probably_damaging(0.994),1;ERC1,missense_variant,p.R20H,ENST00000589028,,c.59G>A,MODERATE,,tolerated(0.05),probably_damaging(0.984),1;ERC1,missense_variant,p.R20H,ENST00000397203,,c.59G>A,MODERATE,,tolerated(0.06),probably_damaging(0.994),1;ERC1,missense_variant,p.R20H,ENST00000355446,NM_001301248.1,c.59G>A,MODERATE,,tolerated(0.06),probably_damaging(0.997),1;ERC1,missense_variant,p.R20H,ENST00000546231,,c.59G>A,MODERATE,YES,tolerated(0.05),probably_damaging(0.997),1;ERC1,missense_variant,p.R20H,ENST00000611180,,c.59G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;ERC1,missense_variant,p.R20H,ENST00000589132,,c.59G>A,MODERATE,,deleterious(0),probably_damaging(0.984),1;ERC1,missense_variant,p.R20H,ENST00000545318,,c.59G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.984),1;ERC1,intron_variant,,ENST00000592048,,c.-18-377G>A,MODIFIER,,,,1;ERC1,downstream_gene_variant,,ENST00000587595,,,MODIFIER,,,,1;ERC1,missense_variant,p.R20H,ENST00000440394,,c.59G>A,MODERATE,,tolerated(0.08),probably_damaging(0.994),1;ERC1,missense_variant,p.R20H,ENST00000347735,,c.59G>A,MODERATE,,tolerated(0.08),probably_damaging(0.994),1;ERC1,missense_variant,p.R20H,ENST00000542302,,c.59G>A,MODERATE,,tolerated(0.08),probably_damaging(0.999),1;ERC1,missense_variant,p.R20H,ENST00000545948,,c.59G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1 315/9308 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.786e-05 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0001634 6.7600499278341886e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002086809981847 0 91 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 119 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ERC1,missense_variant,p.R20H,ENST00000355446.9,c.59G>A,MODERATE,;ERC1,missense_variant,p.R20H,ENST00000589132.1,c.59G>A,MODERATE,;ERC1,missense_variant,p.R20H,ENST00000589028.6,c.59G>A,MODERATE,;ERC1,missense_variant,NMD_transcript_variant,p.R20H,ENST00000545948.5,c.59G>A,MODERATE,;ERC1,missense_variant,NMD_transcript_variant,p.R20H,ENST00000440394.7,c.59G>A,MODERATE,;ERC1,intron_variant,,ENST00000592048.5,c.-18-377G>A,MODIFIER,;ERC1,non_coding_transcript_exon_variant,,ENST00000686476.1,n.450G>A,MODIFIER,;ERC1,non_coding_transcript_exon_variant,,ENST00000692909.1,n.450G>A,MODIFIER,;ERC1,non_coding_transcript_exon_variant,,ENST00000690222.1,n.450G>A,MODIFIER,;ERC1,non_coding_transcript_exon_variant,,ENST00000536573.7,n.450G>A,MODIFIER,;ERC1,missense_variant,p.R20H,ENST00000397203.7,c.59G>A,MODERATE,;ERC1,missense_variant,NMD_transcript_variant,p.R20H,ENST00000347735.10,c.59G>A,MODERATE,;ERC1,missense_variant,p.R20H,ENST00000546231.6,c.59G>A,MODERATE,;ERC1,missense_variant,p.R20H,ENST00000545318.3,c.59G>A,MODERATE,;ERC1,missense_variant,NMD_transcript_variant,p.R20H,ENST00000542302.6,c.59G>A,MODERATE,;ERC1,intron_variant,,ENST00000690948.1,n.259+36475G>A,MODIFIER,;ERC1,non_coding_transcript_exon_variant,,ENST00000691018.1,n.478G>A,MODIFIER,;ERC1,missense_variant,p.R20H,ENST00000360905.9,c.59G>A,MODERATE,YES;ERC1,missense_variant,p.R20H,ENST00000543086.7,c.59G>A,MODERATE,;ERC1,missense_variant,p.R20H,ENST00000611180.5,c.59G>A,MODERATE, +DCP1B 196513 BI GRCh38 12 1953069 1953069 + missense_variant Missense_Mutation SNP A A G novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 19 c.871T>C p.Cys291Arg p.C291R ENST00000280665.11 NM_152640.5 291 Tgt/Cgt 7/9 P1 G C/R protein_coding YES CCDS31727.1 871/1854 TGGACAGAGCT PANTHER:PTHR16290;PANTHER:PTHR16290:SF5 ENSP00000280665 7/9 ENST00000280665 Transcript ENSG00000151065 HGNC:24451 MODERATE NM_152640.5 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q8IZD4.148 DCP1B HGNC -1 1.0 UPI000013DC30 Q8IZD4-1 SNV DCP1B,missense_variant,p.C291R,ENST00000280665,NM_152640.5,c.871T>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;DCP1B,missense_variant,p.C165R,ENST00000540622,,c.493T>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;DCP1B,non_coding_transcript_exon_variant,,ENST00000541700,,n.656T>C,MODIFIER,,,,-1;DCP1B,non_coding_transcript_exon_variant,,ENST00000536665,,n.547T>C,MODIFIER,,,,-1;DCP1B,3_prime_UTR_variant,,ENST00000543381,,c.*637T>C,MODIFIER,,,,-1 897/2033 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 63 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 54 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DCP1B,non_coding_transcript_exon_variant,,ENST00000541700.5,n.656T>C,MODIFIER,;DCP1B,non_coding_transcript_exon_variant,,ENST00000536665.5,n.547T>C,MODIFIER,;DCP1B,missense_variant,p.C165R,ENST00000540622.1,c.493T>C,MODERATE,;DCP1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000543381.5,c.*637T>C,MODIFIER,;DCP1B,missense_variant,p.C291R,ENST00000280665.11,c.871T>C,MODERATE,YES +CACNA1C 775 BI GRCh38 12 2610625 2610625 + missense_variant Missense_Mutation SNP G G A rs747533547 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 7 c.3643G>A p.Val1215Met p.V1215M ENST00000399655.6 NM_000719.7 1215 Gtg/Atg 28/47 A V/M protein_coding YES 3643/6630 uncertain_significance GGTACGTGGTC COSM5840805;COSM5840806;COSM5840807;COSM5840808;COSM5840809;COSM5840810 Gene3D:1.20.120.350;PANTHER:PTHR45628;PANTHER:PTHR45628:SF11;Transmembrane_helices:TMhelix ENSP00000382542 28/48 rs747533547;COSV59700086 ENST00000399634 Transcript 1.0 ENSG00000151067 HGNC:1390 MODERATE 5.787e-05 gnomAD_AMR missense_variant 1;1 1.0 probably_damaging(0.987) Unknown tolerated(0.09) 0;1 CACNA1C HGNC 1 E9PDI6.70 5.0 UPI000155D4FC SNV CACNA1C,missense_variant,p.V1235M,ENST00000347598,NM_001129827.2&NM_199460.3,c.3703G>A,MODERATE,,tolerated(0.08),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000327702,NM_001129830.3,c.3643G>A,MODERATE,,tolerated(0.09),probably_damaging(0.996),1;CACNA1C,missense_variant,p.V1215M,ENST00000399603,NM_001167623.2,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.994),1;CACNA1C,missense_variant,p.V1215M,ENST00000399641,NM_001129840.2,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.998),1;CACNA1C,missense_variant,p.V1215M,ENST00000399655,NM_000719.7,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.737),1;CACNA1C,missense_variant,p.V1215M,ENST00000399634,NM_001167625.1,c.3643G>A,MODERATE,YES,tolerated(0.09),probably_damaging(0.987),1;CACNA1C,missense_variant,p.V1215M,ENST00000406454,,c.3643G>A,MODERATE,,tolerated(0.09),probably_damaging(0.994),1;CACNA1C,missense_variant,p.V1215M,ENST00000399617,NM_001167624.2,c.3643G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.845),1;CACNA1C,missense_variant,p.V1240M,ENST00000335762,,c.3718G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000344100,NM_001129829.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.997),1;CACNA1C,missense_variant,p.V1215M,ENST00000399638,NM_001129831.1,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.576),1;CACNA1C,missense_variant,p.V1235M,ENST00000399606,NM_001129832.1,c.3703G>A,MODERATE,,tolerated(0.08),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000399621,NM_001129834.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000399637,NM_001129835.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000402845,NM_001129833.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.998),1;CACNA1C,missense_variant,p.V1215M,ENST00000399629,NM_001129836.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000399591,NM_001129838.1&NM_001129846.1,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.814),1;CACNA1C,missense_variant,p.V1215M,ENST00000399595,NM_001129837.1,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.73),1;CACNA1C,missense_variant,p.V1215M,ENST00000399649,NM_001129839.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.999),1;CACNA1C,missense_variant,p.V1215M,ENST00000399597,NM_001129842.1&NM_001129844.1,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.737),1;CACNA1C,missense_variant,p.V1215M,ENST00000399601,NM_001129843.1,c.3643G>A,MODERATE,,tolerated(0.1),probably_damaging(0.998),1;CACNA1C,missense_variant,p.V1215M,ENST00000399644,NM_001129841.1,c.3643G>A,MODERATE,,tolerated(0.1),possibly_damaging(0.576),1;CACNA1C,non_coding_transcript_exon_variant,,ENST00000496818,,n.471G>A,MODIFIER,,,,1;CACNA1C,3_prime_UTR_variant,,ENST00000480911,,c.*2250G>A,MODIFIER,,,,1;CACNA1C,downstream_gene_variant,,ENST00000672806,,,MODIFIER,,,,1;CACNA1C-AS3,upstream_gene_variant,,ENST00000543559,,,MODIFIER,YES,,,-1 3643/7590 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.198e-05 0.0 5.787e-05 0.0 0.0 0.0 8.814e-06 0.0 0.0 0 49 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CACNA1C,non_coding_transcript_exon_variant,,ENST00000496818.3,n.471G>A,MODIFIER,;CACNA1C,missense_variant,p.V1215M,ENST00000399597.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1235M,ENST00000399606.5,c.3703G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399649.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1240M,ENST00000682336.1,c.3718G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399644.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399629.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000344100.7,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399637.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399601.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000402845.7,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399638.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000682686.1,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399595.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399591.5,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399621.5,c.3643G>A,MODERATE,;CACNA1C,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000480911.6,c.*2250G>A,MODIFIER,;CACNA1C,missense_variant,p.V1212M,ENST00000683482.1,c.3634G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399617.6,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000682835.1,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1240M,ENST00000335762.10,c.3718G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399641.6,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399655.6,c.3643G>A,MODERATE,YES;CACNA1C,missense_variant,p.V1215M,ENST00000327702.12,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399603.6,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000406454.8,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1215M,ENST00000399634.6,c.3643G>A,MODERATE,;CACNA1C,missense_variant,p.V1235M,ENST00000347598.9,c.3703G>A,MODERATE,;CACNA1C,missense_variant,p.V1270M,ENST00000683824.1,c.3808G>A,MODERATE,;CACNA1C,missense_variant,p.V1245M,ENST00000683956.1,c.3733G>A,MODERATE,;CACNA1C,missense_variant,p.V1245M,ENST00000683840.1,c.3733G>A,MODERATE,;CACNA1C,missense_variant,p.V1245M,ENST00000682462.1,c.3733G>A,MODERATE,;CACNA1C,missense_variant,p.V1245M,ENST00000683781.1,c.3733G>A,MODERATE,;CACNA1C,missense_variant,p.V1265M,ENST00000682544.1,c.3793G>A,MODERATE, +KCNA5 3741 BI GRCh38 12 5045137 5045137 + synonymous_variant Silent SNP G G A rs1174477337 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 65 8 c.990G>A p.Thr330= p.T330= ENST00000252321.5 NM_002234.4 330 acG/acA 1/1 P1 A T protein_coding YES CCDS8536.1 990/1842 ACCACGTGCGT Gene3D:1.20.120.350;Pfam:PF00520;Prints:PR00169;PANTHER:PTHR11537;PANTHER:PTHR11537:SF250;Superfamily:SSF81324 ENSP00000252321 1/1 rs1174477337;COSV52904835;COSV99363676 ENST00000252321 Transcript 1.0 ENSG00000130037 HGNC:6224 LOW NM_002234.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 0;1;1 1.0 Unknown 0;1;1 P22460.195 KCNA5 HGNC 1 UPI000013CD56 P22460-1 SNV KCNA5,synonymous_variant,p.T330=,ENST00000252321,NM_002234.4,c.990G>A,LOW,YES,,,1 1259/2910 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 93 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 73 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KCNA5,synonymous_variant,p.T330=,ENST00000252321.5,c.990G>A,LOW,YES +VWF 7450 BI GRCh38 12 6019473 6019473 + synonymous_variant Silent SNP G G A rs143009893 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 28 c.3945C>T p.Arg1315= p.R1315= ENST00000261405.10 NM_000552.5 1315 cgC/cgT 28/52 0.0002 0.0 0.0 0.001 0.0 0.0 P1 A R protein_coding YES CCDS8539.1 3945/8442 GCCACGCGGAC COSM1363502 PDB-ENSP_mappings:1auq.A;PDB-ENSP_mappings:1fns.A;PDB-ENSP_mappings:1ijb.A;PDB-ENSP_mappings:1ijk.A;PDB-ENSP_mappings:1m10.A;PDB-ENSP_mappings:1oak.A;PDB-ENSP_mappings:1sq0.A;PDB-ENSP_mappings:1u0n.A;PDB-ENSP_mappings:1uex.C;Gene3D:3.40.50.410;PDB-ENSP_mappings:3hxo.A;PDB-ENSP_mappings:3hxq.A;PDB-ENSP_mappings:4c29.A;PDB-ENSP_mappings:4c29.B;PDB-ENSP_mappings:4c2a.A;PDB-ENSP_mappings:4c2b.A;PDB-ENSP_mappings:4c2b.C;PDB-ENSP_mappings:4c2b.E;PDB-ENSP_mappings:4c2b.G;PDB-ENSP_mappings:5bv8.A;Pfam:PF00092;PIRSF:PIRSF002495;PROSITE_profiles:PS50234;PANTHER:PTHR11339;PANTHER:PTHR11339:SF361;SMART:SM00327;Superfamily:SSF53300;CDD:cd01450 ENSP00000261405 0.0 0.0001163 28/52 rs143009893 ENST00000261405 Transcript 1.0 ENSG00000110799 HGNC:12726 LOW NM_000552.5 0.001 EAS synonymous_variant 1.0 Unknown P04275.252 VWF HGNC -1 1.0 UPI00001AE7EE P04275-1 SNV VWF,synonymous_variant,p.R1315=,ENST00000261405,NM_000552.5,c.3945C>T,LOW,YES,,,-1;VWF,intron_variant,,ENST00000538635,,n.421-25539C>T,MODIFIER,,,,-1;VWF,downstream_gene_variant,,ENST00000539641,,,MODIFIER,,,,-1 4195/8830 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.367e-05 6.161e-05 0.0 0.0 0.0009247 0.0 2.647e-05 0.0 0.0 4.056140096508898e-05 0.0 0.0 0.0 0.0 0.0008080810075625 0.0 eas 0.0008080810075625 0.0 3.085850039497018e-05 0.0 0.0 0 69 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS VWF,intron_variant,,ENST00000538635.5,n.421-25539C>T,MODIFIER,;VWF,synonymous_variant,p.R1315=,ENST00000261405.10,c.3945C>T,LOW,YES +ATF7IP 55729 BI GRCh38 12 14497771 14497771 + missense_variant Missense_Mutation SNP G G A rs1180964456 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 21 c.3511G>A p.Val1171Ile p.V1171I ENST00000261168.9 NM_018179.5 1171 Gtt/Att 15/15 A2 A V/I protein_coding CCDS8663.1 3511/3813 CACGCGTTCAG Gene3D:2.60.40.10;Pfam:PF16794;PROSITE_profiles:PS50853;PANTHER:PTHR23210;PANTHER:PTHR23210:SF22;Superfamily:SSF49265 ENSP00000261168 15/15 rs1180964456 ENST00000261168 Transcript ENSG00000171681 HGNC:20092 MODERATE 8.83e-06 gnomAD_NFE missense_variant probably_damaging(0.987) Unknown deleterious_low_confidence(0.03) Q6VMQ6.155 ATF7IP HGNC 1 A0A024RAY1.45 5.0 UPI00001FB6B1 Q6VMQ6-1 SNV ATF7IP,missense_variant,p.V1171I,ENST00000261168,NM_018179.4,c.3511G>A,MODERATE,,deleterious_low_confidence(0.03),probably_damaging(0.987),1;ATF7IP,missense_variant,p.V1170I,ENST00000536444,NM_001286514.2,c.3508G>A,MODERATE,,,probably_damaging(0.987),1;ATF7IP,missense_variant,p.V1179I,ENST00000544627,NM_181352.2,c.3535G>A,MODERATE,YES,deleterious_low_confidence(0.03),probably_damaging(0.987),1;ATF7IP,missense_variant,p.V1171I,ENST00000540793,,c.3511G>A,MODERATE,,deleterious_low_confidence(0.03),probably_damaging(0.987),1 3714/8878 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.986e-06 0.0 0.0 0.0 0.0 0.0 8.83e-06 0.0 0.0 0 36 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ATF7IP,missense_variant,p.V1171I,ENST00000540793.5,c.3511G>A,MODERATE,;ATF7IP,missense_variant,p.V1179I,ENST00000544627.5,c.3535G>A,MODERATE,;ATF7IP,missense_variant,p.V1170I,ENST00000536444.5,c.3508G>A,MODERATE,;ATF7IP,missense_variant,p.V1171I,ENST00000261168.9,c.3511G>A,MODERATE,YES +TMTC1 83857 BI GRCh38 12 29518477 29518477 + synonymous_variant Silent SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 58 54 c.2019C>T p.Tyr673= p.Y673= ENST00000539277.6 NM_001193451.2 673 taC/taT 13/18 A Y protein_coding CCDS53772.1 2019/2649 CGCTTGTACCA Gene3D:1.25.40.10;Pfam:PF13424;PROSITE_profiles:PS50005;PROSITE_profiles:PS50293;PANTHER:PTHR44809;SMART:SM00028;Superfamily:SSF48452 ENSP00000442046 13/18 ENST00000539277 Transcript ENSG00000133687 HGNC:24099 LOW NM_001193451.2 synonymous_variant Unknown Q8IUR5.144 TMTC1 HGNC -1 1.0 UPI0001DD37FA Q8IUR5-5 SNV TMTC1,synonymous_variant,p.Y673=,ENST00000539277,NM_001193451.2,c.2019C>T,LOW,,,,-1;TMTC1,synonymous_variant,p.Y565=,ENST00000256062,NM_175861.3,c.1695C>T,LOW,,,,-1;TMTC1,synonymous_variant,p.Y735=,ENST00000551659,NM_001367875.2,c.2205C>T,LOW,YES,,,-1;TMTC1,synonymous_variant,p.Y697=,ENST00000552618,,c.2091C>T,LOW,,,,-1;TMTC1,splice_region_variant,,ENST00000552925,,n.364+4C>T,LOW,,,,-1;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,,n.1760C>T,MODIFIER,,,,-1;AC009320.1,upstream_gene_variant,,ENST00000549070,,,MODIFIER,YES,,,1 2210/8846 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.3519000276573934e-05 2.4321399905602448e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0004945599939674 0.0 0 118 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 112 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TMTC1,non_coding_transcript_exon_variant,,ENST00000319685.12,n.1760C>T,MODIFIER,;TMTC1,splice_region_variant,intron_variant,,ENST00000552925.5,n.364+4C>T,LOW,;TMTC1,synonymous_variant,p.Y697=,ENST00000552618.5,c.2091C>T,LOW,;TMTC1,synonymous_variant,p.Y565=,ENST00000256062.9,c.1695C>T,LOW,;TMTC1,synonymous_variant,p.Y735=,ENST00000551659.6,c.2205C>T,LOW,;TMTC1,synonymous_variant,p.Y673=,ENST00000539277.6,c.2019C>T,LOW,YES +BICD1 636 BI GRCh38 12 32327564 32327564 + missense_variant Missense_Mutation SNP G G A rs199625504 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 6 c.1109G>A p.Arg370Gln p.R370Q ENST00000652176.1 NM_001354186.2 370 cGg/cAg 5/10 A1 A R/Q protein_coding YES CCDS8726.1 1109/2928 GCACCGGCTCA Pfam:PF09730;PANTHER:PTHR31233;PANTHER:PTHR31233:SF3 ENSP00000498700 5/10 rs199625504 ENST00000652176 Transcript ENSG00000151746 HGNC:1049 MODERATE NM_001714.4 1.762e-05 gnomAD_NFE missense_variant 1.0 benign(0.007) Unknown tolerated(0.18) Q96G01.148 BICD1 HGNC 1 UPI00001AEA67 Q96G01-1 SNV BICD1,missense_variant,p.R370Q,ENST00000652176,NM_001354186.2&NM_001714.4&NM_001354187.2,c.1109G>A,MODERATE,YES,tolerated(0.18),benign(0.007),1;BICD1,missense_variant,p.R370Q,ENST00000548411,NM_001003398.3&NM_001354188.2,c.1109G>A,MODERATE,,tolerated(0.1),benign(0.308),1;BICD1,upstream_gene_variant,,ENST00000547680,,,MODIFIER,,,,1;BICD1,missense_variant,p.R370Q,ENST00000395758,NM_001363603.1,c.1109G>A,MODERATE,,tolerated(0.1),benign(0.435),1 1594/9419 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.965e-06 0.0 0.0 0.0 0.0 0.0 1.762e-05 0.0 0.0 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 17 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BICD1,missense_variant,NMD_transcript_variant,p.R370Q,ENST00000395758.3,c.1109G>A,MODERATE,;BICD1,missense_variant,p.R370Q,ENST00000548411.6,c.1109G>A,MODERATE,;BICD1,missense_variant,p.R370Q,ENST00000652176.1,c.1109G>A,MODERATE,YES +CNTN1 1272 BI GRCh38 12 41027930 41027930 + synonymous_variant Silent SNP C C T rs758326489 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 9 c.2784C>T p.Val928= p.V928= ENST00000347616.5 928 gtC/gtT 21/23 P1 T V protein_coding CCDS8737.1 2784/3057 CATGTCGTTGC Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR44170;PANTHER:PTHR44170:SF10;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000325660 21/23 rs758326489 ENST00000347616 Transcript 1.0 ENSG00000018236 HGNC:2171 LOW 5.437e-05 gnomAD_EAS synonymous_variant Unknown Q12860.190 CNTN1 HGNC 1 A0A024R104.54 1.0 UPI0000127EBA Q12860-1 SNV CNTN1,synonymous_variant,p.V928=,ENST00000551295,NM_001843.4,c.2784C>T,LOW,YES,,,1;CNTN1,synonymous_variant,p.V928=,ENST00000347616,,c.2784C>T,LOW,,,,1;CNTN1,synonymous_variant,p.V917=,ENST00000348761,NM_175038.2,c.2751C>T,LOW,,,,1;CNTN1,downstream_gene_variant,,ENST00000550305,,,MODIFIER,,,,1;CNTN1,upstream_gene_variant,,ENST00000548481,,,MODIFIER,,,,1 2863/5507 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0 2.893e-05 0.0 5.437e-05 0.0 1.759e-05 0.0 0.0 6.764440058759647e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433999578817748e-05 0.0 0.0 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CNTN1,synonymous_variant,p.V917=,ENST00000348761.2,c.2751C>T,LOW,;CNTN1,synonymous_variant,p.V928=,ENST00000347616.5,c.2784C>T,LOW,;CNTN1,synonymous_variant,p.V928=,ENST00000551295.7,c.2784C>T,LOW,YES +KMT2D 8085 BI GRCh38 12 49040001 49040001 + missense_variant Missense_Mutation SNP G G A rs760007799 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 3 c.7769C>T p.Ser2590Leu p.S2590L ENST00000301067.12 NM_003482.4 2590 tCg/tTg 32/55 P1 A S/L protein_coding YES CCDS44873.1 7769/16614 TGCCCGATGGG COSM5349807;COSM5349808 PANTHER:PTHR45888;PANTHER:PTHR45888:SF2;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000301067 32/55 rs760007799;COSV56421757 ENST00000301067 Transcript 1.0 ENSG00000167548 HGNC:7133 MODERATE NM_003482.4 0.0001313 gnomAD_SAS missense_variant 0;1 1.0 benign(0.001) Unknown deleterious(0.03) 0;1 O14686.191 KMT2D HGNC -1 5.0 UPI0000EE84D6 O14686-1 SNV KMT2D,missense_variant,p.S2590L,ENST00000301067,NM_003482.4,c.7769C>T,MODERATE,YES,deleterious(0.03),benign(0.001),-1;KMT2D,downstream_gene_variant,,ENST00000650290,,,MODIFIER,,,,-1;KMT2D,upstream_gene_variant,,ENST00000549743,,,MODIFIER,,,,-1;KMT2D,upstream_gene_variant,,ENST00000549799,,,MODIFIER,,,,-1;KMT2D,downstream_gene_variant,,ENST00000550356,,,MODIFIER,,,,-1 8988/20635 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.831e-05 0.0 0.0 0.0 0.0 0.0 2.682e-05 0.0 0.0001313 6.7584001044451725e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5431100109708495e-05 0.0 0.0 0 18 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 13 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KMT2D,synonymous_variant,p.I626=,ENST00000689944.1,c.1878C>T,LOW,;KMT2D,synonymous_variant,p.I596=,ENST00000689060.1,c.1788C>T,LOW,;KMT2D,missense_variant,NMD_transcript_variant,p.S481L,ENST00000689143.1,c.1442C>T,MODERATE,;KMT2D,missense_variant,p.S2593L,ENST00000685166.1,c.7778C>T,MODERATE,;KMT2D,missense_variant,p.S2589L,ENST00000692637.1,c.7766C>T,MODERATE,;KMT2D,missense_variant,p.S2590L,ENST00000301067.12,c.7769C>T,MODERATE,YES;KMT2D,missense_variant,p.S2590L,ENST00000683543.2,c.7769C>T,MODERATE, +ITGA5 3678 BI GRCh38 12 54405675 54405675 + synonymous_variant Silent SNP G G A rs1287637256 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 43 c.1005C>T p.Val335= p.V335= ENST00000293379.9 NM_002205.5 335 gtC/gtT 11/30 P1 A V protein_coding YES CCDS8880.1 1005/3150 CCATTGACGTC PDB-ENSP_mappings:3vi3.A;PDB-ENSP_mappings:3vi3.C;PDB-ENSP_mappings:3vi4.A;PDB-ENSP_mappings:3vi4.C;PDB-ENSP_mappings:4wjk.A;PDB-ENSP_mappings:4wk0.A;PDB-ENSP_mappings:4wk2.A;PDB-ENSP_mappings:4wk4.A;PROSITE_profiles:PS51470;PANTHER:PTHR23220:SF3;PANTHER:PTHR23220;Gene3D:2.130.10.130;Pfam:PF01839;SMART:SM00191;Superfamily:SSF69318;Prints:PR01185 ENSP00000293379 11/30 rs1287637256 ENST00000293379 Transcript ENSG00000161638 HGNC:6141 LOW NM_002205.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown P08648.222 ITGA5 HGNC -1 1.0 UPI000012D9F3 SNV ITGA5,synonymous_variant,p.V335=,ENST00000293379,NM_002205.5,c.1005C>T,LOW,YES,,,-1;ITGA5,3_prime_UTR_variant,,ENST00000435631,,c.*460C>T,MODIFIER,,,,-1;ITGA5,3_prime_UTR_variant,,ENST00000553071,,c.*460C>T,MODIFIER,,,,-1;ITGA5,non_coding_transcript_exon_variant,,ENST00000552564,,n.289C>T,MODIFIER,,,,-1;ITGA5,upstream_gene_variant,,ENST00000550141,,,MODIFIER,,,,-1;ITGA5,upstream_gene_variant,,ENST00000551564,,,MODIFIER,,,,-1;ITGA5,upstream_gene_variant,,ENST00000551861,,,MODIFIER,,,,-1;ITGA5,upstream_gene_variant,,ENST00000552387,,,MODIFIER,,,,-1;ITGA5,upstream_gene_variant,,ENST00000552583,,,MODIFIER,,,,-1;AC079313.2,intron_variant,,ENST00000550474,,n.48-22182G>A,MODIFIER,YES,,,1;AC079313.1,intron_variant,,ENST00000552785,,n.106-1722G>A,MODIFIER,YES,,,1 1073/4250 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 76 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ITGA5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000553071.1,c.*460C>T,MODIFIER,;ITGA5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000435631.6,c.*460C>T,MODIFIER,;ITGA5,non_coding_transcript_exon_variant,,ENST00000552564.5,n.289C>T,MODIFIER,;ITGA5,synonymous_variant,p.V335=,ENST00000293379.9,c.1005C>T,LOW,YES;GPR84-AS1,intron_variant,,ENST00000688443.2,n.126+14131G>A,MODIFIER,;GPR84-AS1,intron_variant,,ENST00000552785.1,n.106-1722G>A,MODIFIER,YES;GPR84-AS1,intron_variant,,ENST00000550474.5,n.48-22182G>A,MODIFIER,YES +AGAP2 116986 BI GRCh38 12 57731454 57731454 + missense_variant Missense_Mutation SNP C C T rs2140358838 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 27 c.2057G>A p.Arg686Gln p.R686Q ENST00000547588.6 NM_001122772.3 686 cGa/cAa 10/19 P3 T R/Q protein_coding YES CCDS44932.1 2057/3579 CACTTCGTTTT COSM4534178;COSM4534179 Gene3D:2.30.29.30;PROSITE_profiles:PS50003;PANTHER:PTHR45819;PANTHER:PTHR45819:SF3;SMART:SM00233;Superfamily:SSF50729;CDD:cd01250 ENSP00000449241 10/19 COSV57729592 ENST00000547588 Transcript ENSG00000135439 HGNC:16921 MODERATE missense_variant 1 1.0 probably_damaging(0.999) Unknown deleterious(0.01) 1 AGAP2 HGNC -1 F8VVT9.81 1.0 UPI00001AF80C SNV AGAP2,missense_variant,p.R350Q,ENST00000257897,NM_014770.4,c.1049G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;AGAP2,missense_variant,p.R550Q,ENST00000328568,,c.1649G>A,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;AGAP2,missense_variant,p.R686Q,ENST00000547588,NM_001122772.2,c.2057G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),-1;AGAP2,missense_variant,p.R42Q,ENST00000549129,,c.125G>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;AGAP2-AS1,downstream_gene_variant,,ENST00000542466,,,MODIFIER,YES,,,1 2057/3579 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.764889803889673e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0032894699834287 0.0 0.0 0.0 0 78 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AGAP2,missense_variant,p.R42Q,ENST00000549129.1,c.125G>A,MODERATE,;AGAP2,synonymous_variant,p.T549=,ENST00000328568.9,c.1647G>A,LOW,;AGAP2,missense_variant,p.R686Q,ENST00000547588.6,c.2057G>A,MODERATE,YES;AGAP2,missense_variant,p.R350Q,ENST00000257897.7,c.1049G>A,MODERATE, +MSRB3 253827 BI GRCh38 12 65463286 65463286 + synonymous_variant Silent SNP C C T rs370488628 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 52 7 c.543C>T p.Val181= p.V181= ENST00000355192.8 NM_198080.4 181 gtC/gtT 6/6 A2 T V protein_coding YES CCDS8973.1 543/579 likely_benign GGGGTCGCCAG PDB-ENSP_mappings:6q9v.A;PDB-ENSP_mappings:6q9v.B;MobiDB_lite:mobidb-lite;Gene3D:2.170.150.20 ENSP00000347324 6/6 rs370488628 ENST00000355192 Transcript 1.0 ENSG00000174099 HGNC:27375 LOW 6.533e-05 gnomAD_SAS synonymous_variant 1 1.0 Unknown Q8IXL7.144 MSRB3 HGNC 1 1.0 UPI0000051E32 Q8IXL7-1 SNV MSRB3,synonymous_variant,p.V174=,ENST00000646299,,c.522C>T,LOW,,,,1;MSRB3,synonymous_variant,p.V174=,ENST00000308259,NM_001193460.2&NM_001031679.3,c.522C>T,LOW,,,,1;MSRB3,synonymous_variant,p.V174=,ENST00000642404,,c.522C>T,LOW,,,,1;MSRB3,synonymous_variant,p.V181=,ENST00000355192,NM_198080.4,c.543C>T,LOW,YES,,,1;MSRB3,synonymous_variant,p.V174=,ENST00000614640,NM_001193461.1,c.522C>T,LOW,,,,1;MSRB3,synonymous_variant,p.V174=,ENST00000642411,,c.522C>T,LOW,,,,1;MSRB3,synonymous_variant,p.V174=,ENST00000535664,,c.522C>T,LOW,,,,1;MSRB3,intron_variant,,ENST00000446731,,c.265+9461C>T,MODIFIER,,,,1;MSRB3,intron_variant,,ENST00000541189,,c.436+9461C>T,MODIFIER,,,,1;MSRB3,intron_variant,,ENST00000647481,,c.195+9461C>T,MODIFIER,,,,1;MSRB3,downstream_gene_variant,,ENST00000535239,,,MODIFIER,,,,1;MSRB3,non_coding_transcript_exon_variant,,ENST00000535143,,n.361C>T,MODIFIER,,,,1;MSRB3,downstream_gene_variant,,ENST00000541897,,,MODIFIER,,,,1;AC025419.1,downstream_gene_variant,,ENST00000537250,,,MODIFIER,,,,-1 669/4290 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.182e-05 6.153e-05 2.891e-05 0.0 0.0 0.0 3.518e-05 0.0 6.533e-05 2.028860035352409e-05 4.867359893978573e-05 0.0 0.0 0.0 0.0 0.0 afr 4.867359893978573e-05 0.0 1.5429699487867765e-05 0.0 0.0 0 42 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MSRB3,non_coding_transcript_exon_variant,,ENST00000535143.1,n.361C>T,MODIFIER,;MSRB3,intron_variant,,ENST00000647481.1,c.195+9461C>T,MODIFIER,;MSRB3,intron_variant,,ENST00000446731.2,c.265+9461C>T,MODIFIER,;MSRB3,synonymous_variant,p.V174=,ENST00000642404.1,c.522C>T,LOW,;MSRB3,synonymous_variant,p.V174=,ENST00000646299.1,c.522C>T,LOW,;MSRB3,synonymous_variant,p.V174=,ENST00000614640.4,c.522C>T,LOW,;MSRB3,synonymous_variant,p.V174=,ENST00000642411.1,c.522C>T,LOW,;MSRB3,intron_variant,,ENST00000541189.5,c.436+9461C>T,MODIFIER,;MSRB3,synonymous_variant,p.V174=,ENST00000535664.5,c.522C>T,LOW,;MSRB3,synonymous_variant,p.V174=,ENST00000308259.10,c.522C>T,LOW,YES;MSRB3,synonymous_variant,p.V181=,ENST00000355192.8,c.543C>T,LOW, +TBC1D15 64786 BI GRCh38 12 71894789 71894789 + missense_variant Missense_Mutation SNP G G A rs1384304017 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 31 c.812G>A p.Arg271Gln p.R271Q ENST00000550746.5 NM_022771.6 271 cGa/cAa 8/18 A1 A R/Q protein_coding YES CCDS31858.1 812/2076 TCAACGACCAC PANTHER:PTHR22957;PANTHER:PTHR22957:SF300 ENSP00000448182 8/18 COSV100042203 ENST00000550746 Transcript ENSG00000121749 HGNC:25694 MODERATE missense_variant 1 1.0 possibly_damaging(0.652) Unknown deleterious(0.04) 1 Q8TC07.147 TBC1D15 HGNC 1 1.0 UPI000049DD7C Q8TC07-1 SNV TBC1D15,missense_variant,p.R271Q,ENST00000550746,NM_022771.5,c.812G>A,MODERATE,YES,deleterious(0.04),possibly_damaging(0.652),1;TBC1D15,missense_variant,p.R254Q,ENST00000485960,NM_001146213.2,c.761G>A,MODERATE,,deleterious(0.04),probably_damaging(0.918),1;TBC1D15,missense_variant,p.R262Q,ENST00000319106,NM_001146214.2,c.785G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.83),1;TBC1D15,missense_variant,p.R155Q,ENST00000491063,,c.464G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.86),1;TBC1D15,downstream_gene_variant,,ENST00000482439,,,MODIFIER,,,,1;TBC1D15,downstream_gene_variant,,ENST00000474468,,,MODIFIER,,,,1;TBC1D15,upstream_gene_variant,,ENST00000548679,,,MODIFIER,,,,1;TBC1D15,downstream_gene_variant,,ENST00000549402,,,MODIFIER,,,,1;TBC1D15,3_prime_UTR_variant,,ENST00000462788,,c.*175G>A,MODIFIER,,,,1;TBC1D15,downstream_gene_variant,,ENST00000468049,,,MODIFIER,,,,1;TBC1D15,downstream_gene_variant,,ENST00000472611,,,MODIFIER,,,,1;TBC1D15,upstream_gene_variant,,ENST00000479971,,,MODIFIER,,,,1;TBC1D15,upstream_gene_variant,,ENST00000483828,,,MODIFIER,,,,1 876/6184 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.772770120733185e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002086809981847 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 66 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TBC1D15,missense_variant,p.R262Q,ENST00000319106.12,c.785G>A,MODERATE,;TBC1D15,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000462788.6,c.*175G>A,MODIFIER,;TBC1D15,missense_variant,p.R254Q,ENST00000485960.7,c.761G>A,MODERATE,YES;TBC1D15,missense_variant,p.R155Q,ENST00000491063.5,c.464G>A,MODERATE,;TBC1D15,missense_variant,p.R271Q,ENST00000550746.5,c.812G>A,MODERATE, +E2F7 144455 BI GRCh38 12 77024071 77024071 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 72 25 c.2680C>T p.Arg894Ter p.R894* ENST00000322886.12 NM_203394.3 894 Cga/Tga 13/13 P2 A R/* protein_coding YES CCDS9016.1 2680/2736 GTTTCGTGACT MobiDB_lite:mobidb-lite;PANTHER:PTHR12081:SF25;PANTHER:PTHR12081 ENSP00000323246 13/13 ENST00000322886 Transcript ENSG00000165891 HGNC:23820 HIGH NM_203394.3 stop_gained 1.0 Unknown Q96AV8.138 E2F7 HGNC -1 1.0 UPI00001B64A1 Q96AV8-1 SNV E2F7,stop_gained,p.R894*,ENST00000322886,NM_203394.3,c.2680C>T,HIGH,YES,,,-1;E2F7,3_prime_UTR_variant,,ENST00000416496,,c.*68C>T,MODIFIER,,,,-1;E2F7,downstream_gene_variant,,ENST00000550669,,,MODIFIER,,,,-1 2905/5725 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 129 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 97 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS E2F7,stop_gained,p.R894*,ENST00000322886.12,c.2680C>T,HIGH,YES;E2F7,3_prime_UTR_variant,,ENST00000416496.6,c.*68C>T,MODIFIER, +TMTC3 160418 BI GRCh38 12 88172668 88172668 + synonymous_variant Silent SNP C C T rs376400054 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 68 23 c.1122C>T p.Ala374= p.A374= ENST00000266712.11 NM_181783.4 374 gcC/gcT 8/14 0.0002 0.0 0.0 0.001 0.0 0.0 P1 T A protein_coding YES CCDS9032.1 1122/2745 GTTGCCGAGCG COSM5342237 PANTHER:PTHR44395;PANTHER:PTHR44395:SF1 ENSP00000266712 0.0 0.0001163 8/14 rs376400054 ENST00000266712 Transcript 1.0 ENSG00000139324 HGNC:26899 LOW NM_181783.4 0.001 EAS synonymous_variant 1.0 Unknown Q6ZXV5.136 TMTC3 HGNC 1 1.0 UPI000004D255 Q6ZXV5-2 SNV TMTC3,synonymous_variant,p.A374=,ENST00000266712,NM_181783.4&NM_001366579.1&NM_001366574.1&NM_001366580.1&NM_001366583.1,c.1122C>T,LOW,YES,,,1;TMTC3,synonymous_variant,p.A374=,ENST00000547034,,c.1122C>T,LOW,,,,1 1331/7192 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.94e-05 0.0 0.0 0.0 5.838e-05 0.0 1.833e-05 0.0 0.0001394 1.3703699551115278e-05 0.0 0.0 0.0 0.0 0.0002030869945883 0.0 0.0 1.5519299267907627e-05 0.0 0.0 0 120 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 92 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TMTC3,synonymous_variant,p.A374=,ENST00000266712.11,c.1122C>T,LOW,YES;TMTC3,synonymous_variant,NMD_transcript_variant,p.A374=,ENST00000547034.5,c.1122C>T,LOW, +ULK1 8408 BI GRCh38 12 131911950 131911950 + synonymous_variant Silent SNP C C T rs756270836 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 13 17 c.957C>T p.Gly319= p.G319= ENST00000321867.6 NM_003565.4 319 ggC/ggT 13/28 P1 T G protein_coding YES CCDS9274.1 957/3153 CTGGGCGAGAT MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR24348;PANTHER:PTHR24348:SF19;PIRSF:PIRSF000580;Superfamily:SSF56112 ENSP00000324560 13/28 rs756270836 ENST00000321867 Transcript ENSG00000177169 HGNC:12558 LOW NM_003565.4 3.267e-05 gnomAD_SAS synonymous_variant 1.0 Unknown O75385.196 ULK1 HGNC 1 1.0 UPI00001FB0D9 SNV ULK1,synonymous_variant,p.G319=,ENST00000321867,NM_003565.4,c.957C>T,LOW,YES,,,1;ULK1,downstream_gene_variant,,ENST00000537421,,,MODIFIER,,,,1;ULK1,upstream_gene_variant,,ENST00000541761,,,MODIFIER,,,,1;ULK1,downstream_gene_variant,,ENST00000542313,,,MODIFIER,,,,1 1337/5322 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.014e-06 0.0 2.894e-05 0.0 0.0 0.0 0.0 0.0 3.267e-05 0 54 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ULK1,synonymous_variant,p.G319=,ENST00000321867.6,c.957C>T,LOW,YES +KL 9365 BI GRCh38 13 33063877 33063877 + synonymous_variant Silent SNP C C T rs758010223 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 107 31 c.2730C>T p.Cys910= p.C910= ENST00000380099.4 NM_004795.4 910 tgC/tgT 5/5 P1 T C protein_coding YES CCDS9347.1 2730/3039 CTTTGCGGATA PDB-ENSP_mappings:5w21.A;Superfamily:SSF51445;Pfam:PF00232;Gene3D:3.20.20.80;PANTHER:PTHR10353;PANTHER:PTHR10353:SF10 ENSP00000369442 5/5 rs758010223 ENST00000380099 Transcript 1.0 ENSG00000133116 HGNC:6344 LOW NM_004795.4 0.0003262 gnomAD_EAS synonymous_variant 1.0 Unknown Q9UEF7.163 KL HGNC 1 1.0 UPI000013CEBA Q9UEF7-1 SNV KL,synonymous_variant,p.C910=,ENST00000380099,NM_004795.4,c.2730C>T,LOW,YES,,,1;KL,non_coding_transcript_exon_variant,,ENST00000487852,,n.2788C>T,MODIFIER,,,,1 2748/5014 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.976e-05 0.0 2.891e-05 0.0 0.0003262 0.0 8.791e-06 0.0001629 3.266e-05 2.7052599762100726e-05 2.4332099201274104e-05 0.0 0.0 0.0 0.0002014500059885 0.0 nfe 3.086520155193284e-05 0.0 3.086520155193284e-05 0.0 0.0 0 183 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 138 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KL,non_coding_transcript_exon_variant,,ENST00000487852.1,n.2788C>T,MODIFIER,;KL,synonymous_variant,p.C910=,ENST00000380099.4,c.2730C>T,LOW,YES +ZC3H13 23091 BI GRCh38 13 46042217 46042217 + missense_variant Missense_Mutation SNP C C T rs199682940 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 84 9 c.286G>A p.Val96Met p.V96M ENST00000242848.8 NM_001330565.2 96 Gtg/Atg 4/19 P3 T V/M protein_coding CCDS81766.1 286/5007 GTCCACGTCTT PANTHER:PTHR13585;PANTHER:PTHR13585:SF19;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000242848 4/19 rs199682940;COSV104387464;COSV54459644 ENST00000242848 Transcript ENSG00000123200 HGNC:20368 MODERATE 9.927e-05 gnomAD_ASJ missense_variant 0;1;1 benign(0.13) Unknown deleterious_low_confidence(0.02) 0;1;1 Q5T200.138 ZC3H13 HGNC -1 5.0 UPI000046F8EB Q5T200-1 SNV ZC3H13,missense_variant,p.V96M,ENST00000679008,NM_001382214.1&NM_001382207.1&NM_001076788.2&NM_001382206.1&NM_001382208.1&NM_001330564.2&NM_001382211.1,c.286G>A,MODERATE,YES,deleterious_low_confidence(0.02),benign(0.255),-1;ZC3H13,missense_variant,p.V96M,ENST00000242848,NM_001330565.2&NM_001382212.1&NM_001382210.1&NM_001330567.2&NM_001382213.1&NM_001382209.1&NM_001330566.2,c.286G>A,MODERATE,,deleterious_low_confidence(0.02),benign(0.13),-1;ZC3H13,missense_variant,p.V96M,ENST00000282007,NM_015070.6,c.286G>A,MODERATE,,deleterious_low_confidence(0.02),benign(0.255),-1;ZC3H13,non_coding_transcript_exon_variant,,ENST00000428921,,n.635G>A,MODIFIER,,,,-1 635/8018 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0 0.0 9.927e-05 5.437e-05 0.0 8.798e-06 0.0 6.534e-05 0 81 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 93 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZC3H13,non_coding_transcript_exon_variant,,ENST00000428921.1,n.635G>A,MODIFIER,;ZC3H13,missense_variant,p.V96M,ENST00000282007.7,c.286G>A,MODERATE,;ZC3H13,missense_variant,p.V96M,ENST00000242848.8,c.286G>A,MODERATE,;ZC3H13,missense_variant,p.V96M,ENST00000679008.1,c.286G>A,MODERATE,YES +THSD1 55901 BI GRCh38 13 52378534 52378534 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 13 c.1436C>T p.Ser479Leu p.S479L ENST00000258613.5 NM_018676.4 479 tCg/tTg 5/5 P1 A S/L protein_coding YES CCDS9432.1 1436/2559 CATCCGAGAAG PANTHER:PTHR16311;Low_complexity_(Seg):seg ENSP00000258613 5/5 ENST00000258613 Transcript 1.0 ENSG00000136114 HGNC:17754 MODERATE NM_018676.4 missense_variant 1.0 benign(0.076) Unknown deleterious(0) Q9NS62.137 THSD1 HGNC -1 A0A024R064.52 1.0 UPI000007376D Q9NS62-1 SNV THSD1,missense_variant,p.S426L,ENST00000349258,NM_199263.3,c.1277C>T,MODERATE,,deleterious(0),benign(0.103),-1;THSD1,missense_variant,p.S426L,ENST00000648254,,c.1277C>T,MODERATE,,deleterious(0),benign(0.103),-1;THSD1,missense_variant,p.S479L,ENST00000258613,NM_018676.4,c.1436C>T,MODERATE,YES,deleterious(0),benign(0.076),-1 1659/3026 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS THSD1,missense_variant,p.S426L,ENST00000648254.1,c.1277C>T,MODERATE,;THSD1,missense_variant,p.S479L,ENST00000258613.5,c.1436C>T,MODERATE,YES;THSD1,missense_variant,p.S426L,ENST00000349258.8,c.1277C>T,MODERATE, +RNF113B 140432 BI GRCh38 13 98177204 98177204 + synonymous_variant Silent SNP G G A rs754829186 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 9 c.33C>T p.Ala11= p.A11= ENST00000267291.7 NM_178861.5 11 gcC/gcT 1/2 P1 A A protein_coding YES CCDS9486.1 33/969 TGGTCGGCCGT PANTHER:PTHR12930:SF1;PANTHER:PTHR12930 ENSP00000267291 1/2 rs754829186 ENST00000267291 Transcript ENSG00000139797 HGNC:17267 LOW NM_178861.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q8IZP6.142 RNF113B HGNC -1 1.0 UPI000006F203 SNV RNF113B,synonymous_variant,p.A11=,ENST00000267291,NM_178861.5,c.33C>T,LOW,YES,,,-1;FARP1,intron_variant,,ENST00000319562,NM_005766.4,c.-24+33712G>A,MODIFIER,,,,1;FARP1,intron_variant,,ENST00000376581,NM_001001715.4,c.-24+33712G>A,MODIFIER,,,,1;FARP1,intron_variant,,ENST00000595437,NM_001286839.2,c.-24+34427G>A,MODIFIER,,,,1;FARP1,intron_variant,,ENST00000596580,,c.-24+33712G>A,MODIFIER,,,,1;FARP1,intron_variant,,ENST00000627049,,c.-24+33712G>A,MODIFIER,YES,,,1;FARP1,upstream_gene_variant,,ENST00000598389,,,MODIFIER,,,,1;FARP1,intron_variant,,ENST00000600648,,n.420+17606G>A,MODIFIER,,,,1 66/1380 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 33 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 39 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RNF113B,synonymous_variant,p.A11=,ENST00000267291.7,c.33C>T,LOW,YES;FARP1,intron_variant,,ENST00000376581.9,c.-24+33712G>A,MODIFIER,;FARP1,intron_variant,,ENST00000596580.2,c.-24+33712G>A,MODIFIER,;FARP1,intron_variant,,ENST00000600648.1,n.420+17606G>A,MODIFIER,;FARP1,intron_variant,,ENST00000627049.2,c.-24+33712G>A,MODIFIER,;FARP1,intron_variant,,ENST00000319562.11,c.-24+33712G>A,MODIFIER,YES;FARP1,intron_variant,,ENST00000595437.5,c.-24+34427G>A,MODIFIER, +COL4A1 1282 BI GRCh38 13 110152429 110152429 + synonymous_variant Silent SNP C C T rs771624014 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 40 28 c.4833G>A p.Ala1611= p.A1611= ENST00000375820.10 NM_001845.6 1611 gcG/gcA 51/52 P1 T A protein_coding YES CCDS9511.1 4833/5010 AATGGCGCACT COSM945322;COSM945323 PDB-ENSP_mappings:1li1.A;PDB-ENSP_mappings:1li1.B;PDB-ENSP_mappings:1li1.D;PDB-ENSP_mappings:1li1.E;Gene3D:2.170.240.10;PDB-ENSP_mappings:5nax.A;PDB-ENSP_mappings:5nax.B;PDB-ENSP_mappings:5nax.D;PDB-ENSP_mappings:5nax.F;PDB-ENSP_mappings:5nay.A;PDB-ENSP_mappings:5nay.B;PDB-ENSP_mappings:5nay.C;PDB-ENSP_mappings:5nay.D;PDB-ENSP_mappings:5nay.E;PDB-ENSP_mappings:5nay.F;PDB-ENSP_mappings:6mpx.A;Pfam:PF01413;PROSITE_profiles:PS51403;PANTHER:PTHR24023;PANTHER:PTHR24023:SF854;SMART:SM00111;Superfamily:SSF56436 ENSP00000364979 51/52 rs771624014;COSV65431424 ENST00000375820 Transcript 1.0 ENSG00000187498 HGNC:2202 LOW NM_001845.6 3.267e-05 gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 P02462.213 COL4A1 HGNC -1 1.0 UPI000004981D P02462-1 SNV COL4A1,synonymous_variant,p.A1611=,ENST00000375820,NM_001845.6,c.4833G>A,LOW,YES,,,-1;COL4A1,synonymous_variant,p.A330=,ENST00000650424,,c.990G>A,LOW,,,,-1;COL4A1,non_coding_transcript_exon_variant,,ENST00000649720,,n.1001G>A,MODIFIER,,,,-1 4963/6540 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.955e-06 0.0 0.0 0.0 0.0 0.0 8.793e-06 0.0 3.267e-05 2.703909922274761e-05 7.292530062841251e-05 0.0 0.0 0.0 0.0 0.0 afr 7.292530062841251e-05 0.0 1.542919926578179e-05 0.0 0.0 0 110 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COL4A1,synonymous_variant,p.A1611=,ENST00000650424.2,c.4833G>A,LOW,;COL4A1,non_coding_transcript_exon_variant,,ENST00000649720.1,n.1001G>A,MODIFIER,;COL4A1,synonymous_variant,p.A1547=,ENST00000615732.3,c.4641G>A,LOW,;COL4A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000714331.1,c.*2429G>A,MODIFIER,;COL4A1,synonymous_variant,p.A1496=,ENST00000714330.1,c.4488G>A,LOW,;COL4A1,synonymous_variant,p.A1611=,ENST00000375820.10,c.4833G>A,LOW,YES;COL4A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000714329.1,c.*2429G>A,MODIFIER, +COL4A1 1282 BI GRCh38 13 110210038 110210038 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 18 c.557C>T p.Pro186Leu p.P186L ENST00000375820.10 NM_001845.6 186 cCa/cTa 10/52 P1 A P/L protein_coding YES CCDS9511.1 557/5010 CTGGTGGGCCC Pfam:PF01391;PANTHER:PTHR24023;PANTHER:PTHR24023:SF854;Low_complexity_(Seg):seg ENSP00000364979 10/52 ENST00000375820 Transcript 1.0 ENSG00000187498 HGNC:2202 MODERATE NM_001845.6 missense_variant 1.0 benign(0) Unknown tolerated(0.38) P02462.213 COL4A1 HGNC -1 1.0 UPI000004981D P02462-1 SNV COL4A1,missense_variant,p.P186L,ENST00000375820,NM_001845.6,c.557C>T,MODERATE,YES,tolerated(0.38),benign(0),-1;COL4A1,missense_variant,p.P186L,ENST00000543140,NM_001303110.2,c.557C>T,MODERATE,,tolerated(0.65),benign(0),-1;COL4A1,missense_variant,p.P146L,ENST00000647797,,c.437C>T,MODERATE,,tolerated(0.37),benign(0.023),-1;COL4A1,missense_variant,p.P122L,ENST00000615732,,c.365C>T,MODERATE,,tolerated(0.41),benign(0),-1;COL4A1,missense_variant,p.P146L,ENST00000648966,,c.437C>T,MODERATE,,tolerated(0.7),benign(0),-1;COL4A1,3_prime_UTR_variant,,ENST00000649484,,c.*76C>T,MODIFIER,,,,-1;COL4A1,non_coding_transcript_exon_variant,,ENST00000649738,,n.687C>T,MODIFIER,,,,-1;COL4A1,non_coding_transcript_exon_variant,,ENST00000648170,,n.1125C>T,MODIFIER,,,,-1;COL4A1,non_coding_transcript_exon_variant,,ENST00000647632,,n.190C>T,MODIFIER,,,,-1;COL4A1,downstream_gene_variant,,ENST00000650138,,,MODIFIER,,,,-1 687/6540 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COL4A1,3_prime_UTR_variant,,ENST00000649484.2,c.*76C>T,MODIFIER,;COL4A1,missense_variant,p.P186L,ENST00000648966.2,c.557C>T,MODERATE,;COL4A1,non_coding_transcript_exon_variant,,ENST00000648170.1,n.1125C>T,MODIFIER,;COL4A1,non_coding_transcript_exon_variant,,ENST00000647632.1,n.190C>T,MODIFIER,;COL4A1,missense_variant,p.P186L,ENST00000647797.2,c.557C>T,MODERATE,;COL4A1,missense_variant,p.P186L,ENST00000543140.6,c.557C>T,MODERATE,;COL4A1,non_coding_transcript_exon_variant,,ENST00000649738.1,n.687C>T,MODIFIER,;COL4A1,missense_variant,p.P186L,ENST00000650424.2,c.557C>T,MODERATE,;COL4A1,missense_variant,p.P122L,ENST00000615732.3,c.365C>T,MODERATE,;COL4A1,missense_variant,NMD_transcript_variant,p.P186L,ENST00000714331.1,c.557C>T,MODERATE,;COL4A1,missense_variant,p.P186L,ENST00000714330.1,c.557C>T,MODERATE,;COL4A1,missense_variant,p.P186L,ENST00000375820.10,c.557C>T,MODERATE,YES;COL4A1,missense_variant,NMD_transcript_variant,p.P186L,ENST00000714329.1,c.557C>T,MODERATE, +F7 2155 BI GRCh38 13 113118613 113118613 + missense_variant Missense_Mutation SNP G G A rs374305125 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 8 c.1006G>A p.Val336Met p.V336M ENST00000375581.3 NM_000131.4 336 Gtg/Atg 9/9 P4 A V/M protein_coding YES CCDS9528.1 1006/1401 uncertain_significance CCTTCGTGCGC COSM2264072 PDB-ENSP_mappings:1cvw.H;PDB-ENSP_mappings:1dan.H;PDB-ENSP_mappings:1dva.H;PDB-ENSP_mappings:1dva.I;PDB-ENSP_mappings:1fak.H;PDB-ENSP_mappings:1j9c.H;PDB-ENSP_mappings:1jbu.H;PDB-ENSP_mappings:1kli.H;PDB-ENSP_mappings:1klj.H;PDB-ENSP_mappings:1o5d.H;PDB-ENSP_mappings:1qfk.H;PDB-ENSP_mappings:1w0y.H;PDB-ENSP_mappings:1w2k.H;PDB-ENSP_mappings:1w7x.H;PDB-ENSP_mappings:1w8b.H;PDB-ENSP_mappings:1wqv.H;PDB-ENSP_mappings:1wss.H;PDB-ENSP_mappings:1wtg.H;PDB-ENSP_mappings:1wun.H;PDB-ENSP_mappings:1wv7.H;PDB-ENSP_mappings:1ygc.H;PDB-ENSP_mappings:1z6j.H;Gene3D:2.40.10.10;Gene3D:2.40.10.10;PDB-ENSP_mappings:2a2q.H;PDB-ENSP_mappings:2aei.H;PDB-ENSP_mappings:2aer.H;PDB-ENSP_mappings:2b7d.H;PDB-ENSP_mappings:2b8o.H;PDB-ENSP_mappings:2bz6.H;PDB-ENSP_mappings:2c4f.H;PDB-ENSP_mappings:2ec9.H;PDB-ENSP_mappings:2f9b.H;PDB-ENSP_mappings:2fir.H;PDB-ENSP_mappings:2flb.H;PDB-ENSP_mappings:2flr.H;PDB-ENSP_mappings:2puq.H;PDB-ENSP_mappings:2zp0.H;PDB-ENSP_mappings:2zwl.H;PDB-ENSP_mappings:2zzu.H;PDB-ENSP_mappings:3ela.H;PDB-ENSP_mappings:3th2.H;PDB-ENSP_mappings:3th3.H;PDB-ENSP_mappings:3th4.H;PDB-ENSP_mappings:4ibl.H;PDB-ENSP_mappings:4ish.H;PDB-ENSP_mappings:4isi.H;PDB-ENSP_mappings:4jyu.H;PDB-ENSP_mappings:4jyv.H;PDB-ENSP_mappings:4jzd.H;PDB-ENSP_mappings:4jze.H;PDB-ENSP_mappings:4jzf.H;PDB-ENSP_mappings:4na9.H;PDB-ENSP_mappings:4ng9.H;PDB-ENSP_mappings:4nga.H;PDB-ENSP_mappings:4x8s.H;PDB-ENSP_mappings:4x8t.H;PDB-ENSP_mappings:4x8u.H;PDB-ENSP_mappings:4x8v.H;PDB-ENSP_mappings:4ylq.H;PDB-ENSP_mappings:4yt6.H;PDB-ENSP_mappings:4yt7.H;PDB-ENSP_mappings:4z6a.H;PDB-ENSP_mappings:4zma.H;PDB-ENSP_mappings:4zxx.H;PDB-ENSP_mappings:4zxy.H;PDB-ENSP_mappings:5i46.H;PDB-ENSP_mappings:5l2y.H;PDB-ENSP_mappings:5l2z.H;PDB-ENSP_mappings:5l30.H;PDB-ENSP_mappings:5pa8.C;PDB-ENSP_mappings:5pa9.C;PDB-ENSP_mappings:5paa.C;PDB-ENSP_mappings:5pab.H;PDB-ENSP_mappings:5pac.B;PDB-ENSP_mappings:5pae.B;PDB-ENSP_mappings:5paf.B;PDB-ENSP_mappings:5pag.B;PDB-ENSP_mappings:5pai.B;PDB-ENSP_mappings:5paj.B;PDB-ENSP_mappings:5pak.C;PDB-ENSP_mappings:5pam.B;PDB-ENSP_mappings:5pan.B;PDB-ENSP_mappings:5pao.C;PDB-ENSP_mappings:5paq.B;PDB-ENSP_mappings:5par.C;PDB-ENSP_mappings:5pas.C;PDB-ENSP_mappings:5pat.B;PDB-ENSP_mappings:5pau.C;PDB-ENSP_mappings:5pav.C;PDB-ENSP_mappings:5paw.B;PDB-ENSP_mappings:5pax.C;PDB-ENSP_mappings:5pay.C;PDB-ENSP_mappings:5pb0.B;PDB-ENSP_mappings:5pb1.D;PDB-ENSP_mappings:5pb2.C;PDB-ENSP_mappings:5pb3.C;PDB-ENSP_mappings:5pb4.C;PDB-ENSP_mappings:5pb5.B;PDB-ENSP_mappings:5pb6.C;PDB-ENSP_mappings:5tqe.H;PDB-ENSP_mappings:5tqf.H;PDB-ENSP_mappings:5tqg.H;PDB-ENSP_mappings:5u6j.H;PDB-ENSP_mappings:6r2w.H;Pfam:PF00089;PIRSF:PIRSF001143;PROSITE_profiles:PS50240;PANTHER:PTHR24278;PANTHER:PTHR24278:SF26;SMART:SM00020;Superfamily:SSF50494;CDD:cd00190 ENSP00000364731 0.0002271 0.0 9/9 rs374305125;CD010610 ENST00000375581 Transcript 1.0 ENSG00000057593 HGNC:3544 MODERATE 0.0002271 AA missense_variant 1;1 1.0 possibly_damaging(0.86) Unknown tolerated(0.05) P08709.263 F7 HGNC 1 1.0 UPI000012A414 P08709-1 SNV F7,missense_variant,p.V336M,ENST00000375581,NM_000131.4,c.1006G>A,MODERATE,YES,tolerated(0.05),possibly_damaging(0.86),1;F7,missense_variant,p.V314M,ENST00000346342,NM_019616.4,c.940G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.832),1;F7,missense_variant,p.V252M,ENST00000541084,NM_001267554.1,c.754G>A,MODERATE,,deleterious(0.05),probably_damaging(0.91),1;F10,upstream_gene_variant,,ENST00000375551,NM_001312675.2,,MODIFIER,,,,1;F10,upstream_gene_variant,,ENST00000375559,NM_000504.4&NM_001312674.2,,MODIFIER,YES,,,1;F10,upstream_gene_variant,,ENST00000409306,,,MODIFIER,,,,1;F7,downstream_gene_variant,,ENST00000473085,,,MODIFIER,,,,1;F10,upstream_gene_variant,,ENST00000483537,,,MODIFIER,,,,1;F10,upstream_gene_variant,,ENST00000410083,,,MODIFIER,,,,1;F7,downstream_gene_variant,,ENST00000444337,,,MODIFIER,,,,1;F10,upstream_gene_variant,,ENST00000477269,,,MODIFIER,,,,1;F7,downstream_gene_variant,,ENST00000479674,,,MODIFIER,,,,1 1041/3109 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.602e-05 6.207e-05 0.0 0.0 0.0 4.627e-05 8.896e-06 0.0 3.269e-05 1.3519499589165209e-05 2.4321399905602448e-05 0.0 6.62339007249102e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 27 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS F7,missense_variant,p.V336M,ENST00000375581.3,c.1006G>A,MODERATE,;F7,missense_variant,p.V314M,ENST00000346342.8,c.940G>A,MODERATE,YES;F7,missense_variant,p.V252M,ENST00000541084.5,c.754G>A,MODERATE, +IL25 64806 BI GRCh38 14 23375833 23375833 + missense_variant Missense_Mutation SNP C C T rs767350854 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 33 c.487C>T p.Arg163Cys p.R163C ENST00000329715.2 NM_022789.3 163 Cgt/Tgt 2/2 P4 T R/C protein_coding YES CCDS9597.1 487/534 TGTACCGTGTT COSM4050024 Gene3D:2.10.90.10;Pfam:PF06083;Superfamily:SSF57501 ENSP00000328111 2/2 rs767350854;COSV59306867 ENST00000329715 Transcript ENSG00000166090 HGNC:13765 MODERATE 0.0003259 gnomAD_OTH missense_variant 0;1 1.0 possibly_damaging(0.825) Unknown deleterious(0) 0;1 Q9H293.145 IL25 HGNC 1 1.0 UPI0000038A0A Q9H293-1 SNV IL25,missense_variant,p.R163C,ENST00000329715,NM_022789.3,c.487C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.825),1;IL25,missense_variant,p.R147C,ENST00000397242,NM_172314.1,c.439C>T,MODERATE,,deleterious(0),possibly_damaging(0.742),1;CMTM5,upstream_gene_variant,,ENST00000339180,NM_001288746.2,,MODIFIER,YES,,,1;CMTM5,upstream_gene_variant,,ENST00000342473,NM_001288745.2,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000359320,NM_138460.3,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000382809,NM_001037288.2,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000397227,NM_001288744.2,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000555731,,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000649278,,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000553750,,,MODIFIER,,,,1;CMTM5,upstream_gene_variant,,ENST00000555487,,,MODIFIER,,,,1 745/1315 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.967e-05 0.0 0.0002313 0.0 0.0 0.0 4.398e-05 0.0003259 0.0 2.027409936999902e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629059912986122e-05 0.0 4.629059912986122e-05 0.0 0.0 0 92 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 67 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IL25,missense_variant,p.R163C,ENST00000329715.2,c.487C>T,MODERATE,;IL25,missense_variant,p.R147C,ENST00000397242.3,c.439C>T,MODERATE,YES +CPNE6 9362 BI GRCh38 14 24074745 24074745 + missense_variant Missense_Mutation SNP C C T rs755460754 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 8 5 c.622C>T p.Arg208Cys p.R208C ENST00000397016.6 NM_001385056.1 208 Cgc/Tgc 8/18 P1 T R/C protein_coding CCDS9607.1 622/1674 CGTTCCGCCTG PROSITE_profiles:PS50004;CDD:cd04047;PANTHER:PTHR10857:SF5;PANTHER:PTHR10857;Gene3D:2.60.40.150;Pfam:PF00168;SMART:SM00239;Superfamily:SSF49562 ENSP00000380211 8/18 rs755460754 ENST00000397016 Transcript ENSG00000100884 HGNC:2319 MODERATE 3.268e-05 gnomAD_SAS missense_variant probably_damaging(0.935) Unknown deleterious(0) O95741.171 CPNE6 HGNC 1 2.0 UPI000013C707 O95741-1 SNV CPNE6,missense_variant,p.R208C,ENST00000397016,NM_006032.4,c.622C>T,MODERATE,,deleterious(0),probably_damaging(0.935),1;CPNE6,missense_variant,p.R263C,ENST00000537691,NM_001280558.1,c.787C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.894),1;CPNE6,missense_variant,p.R208C,ENST00000558541,,c.622C>T,MODERATE,,deleterious(0),probably_damaging(0.935),1;CPNE6,missense_variant,p.R33C,ENST00000559207,,c.97C>T,MODERATE,,deleterious(0),probably_damaging(0.935),1;CPNE6,downstream_gene_variant,,ENST00000557889,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000558450,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000558859,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000559197,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000559778,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000560356,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000560761,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000560828,,,MODIFIER,,,,1;CPNE6,downstream_gene_variant,,ENST00000560884,,,MODIFIER,,,,1;NRL,downstream_gene_variant,,ENST00000561028,NM_001354768.3&NM_001354770.2&NM_006177.5,,MODIFIER,YES,,,-1;CPNE6,downstream_gene_variant,,ENST00000560092,,,MODIFIER,,,,1;CPNE6,3_prime_UTR_variant,,ENST00000558795,,c.*554C>T,MODIFIER,,,,1;CPNE6,non_coding_transcript_exon_variant,,ENST00000460657,,n.2391C>T,MODIFIER,,,,1;CPNE6,non_coding_transcript_exon_variant,,ENST00000558995,,n.1484C>T,MODIFIER,,,,1;CPNE6,upstream_gene_variant,,ENST00000557829,,,MODIFIER,,,,1;CPNE6,upstream_gene_variant,,ENST00000560845,,,MODIFIER,,,,1 933/2235 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.98e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.268e-05 2.0289500753278844e-05 7.302110316231847e-05 0.0 0.0 0.0 0.0 0.0 afr 7.302110316231847e-05 0.0 0.0 0.0 0.0 0 20 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 13 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CPNE6,non_coding_transcript_exon_variant,,ENST00000460657.1,n.2391C>T,MODIFIER,;CPNE6,missense_variant,p.R33C,ENST00000559207.1,c.97C>T,MODERATE,;CPNE6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000558795.1,c.*554C>T,MODIFIER,;CPNE6,missense_variant,p.R208C,ENST00000689861.1,c.622C>T,MODERATE,YES;CPNE6,missense_variant,p.R208C,ENST00000558541.5,c.622C>T,MODERATE,;CPNE6,non_coding_transcript_exon_variant,,ENST00000558995.5,n.1484C>T,MODIFIER,;CPNE6,missense_variant,p.R208C,ENST00000397016.6,c.622C>T,MODERATE,;CPNE6,missense_variant,p.R263C,ENST00000537691.5,c.787C>T,MODERATE, +REC8 9985 BI GRCh38 14 24172948 24172948 + missense_variant Missense_Mutation SNP G G A rs1475840583 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 9 c.175G>A p.Gly59Ser p.G59S ENST00000611366.5 NM_001048205.2 59 Ggc/Agc 3/19 P1 A G/S protein_coding CCDS41932.1 175/1644 AGCCCGGCCTG PANTHER:PTHR12585:SF27;PANTHER:PTHR12585;Pfam:PF04825 ENSP00000482439 3/19 rs1475840583 ENST00000611366 Transcript ENSG00000100918 HGNC:16879 MODERATE NM_001048205.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant possibly_damaging(0.626) Unknown tolerated(0.19) O95072.139 REC8 HGNC 1 1.0 UPI00000700FD O95072-1 SNV REC8,missense_variant,p.G59S,ENST00000620473,,c.175G>A,MODERATE,YES,tolerated(0.19),possibly_damaging(0.626),1;REC8,missense_variant,p.G59S,ENST00000611366,NM_001048205.2&NM_005132.3,c.175G>A,MODERATE,,tolerated(0.19),possibly_damaging(0.626),1;REC8,missense_variant,p.G59S,ENST00000557806,,c.175G>A,MODERATE,,deleterious(0.05),possibly_damaging(0.626),1;REC8,5_prime_UTR_variant,,ENST00000560501,,c.-153G>A,MODIFIER,,,,1;REC8,non_coding_transcript_exon_variant,,ENST00000619469,,n.593G>A,MODIFIER,,,,1;REC8,non_coding_transcript_exon_variant,,ENST00000619284,,n.83G>A,MODIFIER,,,,1;REC8,non_coding_transcript_exon_variant,,ENST00000560032,,n.446G>A,MODIFIER,,,,1;REC8,upstream_gene_variant,,ENST00000560823,,,MODIFIER,,,,1;REC8,upstream_gene_variant,,ENST00000619111,,,MODIFIER,,,,1 648/2276 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 37 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS REC8,non_coding_transcript_exon_variant,,ENST00000619284.5,n.83G>A,MODIFIER,;REC8,5_prime_UTR_variant,,ENST00000560501.1,c.-153G>A,MODIFIER,;REC8,non_coding_transcript_exon_variant,,ENST00000560032.1,n.446G>A,MODIFIER,;REC8,non_coding_transcript_exon_variant,,ENST00000619469.4,n.593G>A,MODIFIER,;REC8,missense_variant,p.G59S,ENST00000611366.5,c.175G>A,MODERATE,YES;REC8,missense_variant,p.G59S,ENST00000557806.5,c.175G>A,MODERATE,;REC8,missense_variant,p.G59S,ENST00000620473.4,c.175G>A,MODERATE, +KIAA0586 9786 BI GRCh38 14 58465939 58465939 + missense_variant Missense_Mutation SNP G G A rs750671663 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 8 c.2119G>A p.Asp707Asn p.D707N ENST00000619416.4 NM_001244190.2 707 Gat/Aat 16/32 P4 A D/N protein_coding CCDS58321.1 2119/4602 ATGGCGATCAG Pfam:PF15324;PANTHER:PTHR15721 ENSP00000478083 16/32 rs750671663 ENST00000619416 Transcript 1.0 ENSG00000100578 HGNC:19960 MODERATE 0.0004181 gnomAD_FIN missense_variant benign(0.187) Unknown deleterious(0.05) Q9BVV6.142 KIAA0586 HGNC 1 1.0 UPI000013D14E Q9BVV6-1 SNV KIAA0586,missense_variant,p.D722N,ENST00000652326,NM_001329944.2&NM_001329943.3&NM_001329946.2&NM_001329947.2,c.2164G>A,MODERATE,,deleterious(0.05),possibly_damaging(0.847),1;KIAA0586,missense_variant,p.D707N,ENST00000619416,NM_001244190.2,c.2119G>A,MODERATE,,deleterious(0.05),benign(0.187),1;KIAA0586,missense_variant,p.D722N,ENST00000650904,,c.2164G>A,MODERATE,,deleterious(0.05),benign(0.131),1;KIAA0586,missense_variant,p.D678N,ENST00000423743,NM_001244192.2,c.2032G>A,MODERATE,,deleterious(0.05),possibly_damaging(0.787),1;KIAA0586,missense_variant,p.D775N,ENST00000354386,NM_001244189.2,c.2323G>A,MODERATE,YES,tolerated(0.05),benign(0.187),1;KIAA0586,missense_variant,p.D646N,ENST00000261244,NM_014749.5,c.1936G>A,MODERATE,,tolerated(0.05),possibly_damaging(0.656),1;KIAA0586,missense_variant,p.D637N,ENST00000619722,NM_001244191.1&NM_001364701.2&NM_001329945.2&NM_001364700.1&NM_001244193.1,c.1909G>A,MODERATE,,tolerated(0.07),benign(0.187),1;KIAA0586,missense_variant,p.D90N,ENST00000652414,,c.268G>A,MODERATE,,tolerated(0.05),benign(0.284),1;KIAA0586,upstream_gene_variant,,ENST00000651852,,,MODIFIER,,,,1;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571,,n.1754G>A,MODIFIER,,,,1;KIAA0586,missense_variant,p.D305N,ENST00000651759,,c.913G>A,MODERATE,,tolerated(0.06),benign(0.106),1;KIAA0586,3_prime_UTR_variant,,ENST00000652732,,c.*1730G>A,MODIFIER,,,,1;KIAA0586,3_prime_UTR_variant,,ENST00000651937,,c.*245G>A,MODIFIER,,,,1;KIAA0586,non_coding_transcript_exon_variant,,ENST00000650845,,n.2710G>A,MODIFIER,,,,1;HSBP1P1,downstream_gene_variant,,ENST00000555205,,,MODIFIER,YES,,,1 2393/8233 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.24e-05 0.0 0.0 0.0 5.565e-05 0.0004181 6.207e-05 0.0001659 0.0 4.732350134872832e-05 0.0 0.0 0.0 0.0 0.0 0.0003772159980144 fin 0.0003772159980144 0.0 3.085850039497018e-05 0.0 0.0002086809981847 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 70 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KIAA0586,missense_variant,p.D90N,ENST00000652414.1,c.268G>A,MODERATE,;KIAA0586,missense_variant,NMD_transcript_variant,p.D305N,ENST00000651759.1,c.913G>A,MODERATE,;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571.6,n.1754G>A,MODIFIER,;KIAA0586,missense_variant,p.D646N,ENST00000261244.9,c.1936G>A,MODERATE,;KIAA0586,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000651937.1,c.*245G>A,MODIFIER,;KIAA0586,missense_variant,p.D722N,ENST00000652326.2,c.2164G>A,MODERATE,YES;KIAA0586,non_coding_transcript_exon_variant,,ENST00000650845.1,n.2710G>A,MODIFIER,;KIAA0586,missense_variant,p.D722N,ENST00000650904.1,c.2164G>A,MODERATE,;KIAA0586,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652732.1,c.*1730G>A,MODIFIER,;KIAA0586,missense_variant,p.D678N,ENST00000423743.7,c.2032G>A,MODERATE,;KIAA0586,missense_variant,p.D637N,ENST00000619722.5,c.1909G>A,MODERATE,;KIAA0586,missense_variant,p.D707N,ENST00000619416.4,c.2119G>A,MODERATE,;KIAA0586,missense_variant,p.D775N,ENST00000354386.10,c.2323G>A,MODERATE, +COX16 51241 BI GRCh38 14 70342681 70342681 + stop_gained Nonsense_Mutation SNP G G A rs761014452 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 15 c.118C>T p.Arg40Ter p.R40* ENST00000389912.7 NM_001204090.2 40 Cga/Tga 2/4 P1 A R/* protein_coding YES CCDS9802.1 118/321 ATATCGGATTT COSM4443265 Pfam:PF14138;PANTHER:PTHR17130 ENSP00000374562 2/4 rs761014452;COSV66303043 ENST00000389912 Transcript ENSG00000133983 HGNC:20213 HIGH NM_016468.7 0.0001091 gnomAD_EAS stop_gained 0;1 1.0 Unknown 0;1 Q9P0S2.138 COX16 HGNC -1 1.0 UPI000004A06F SNV COX16,stop_gained,p.R40*,ENST00000389912,NM_001204090.2&NM_016468.7,c.118C>T,HIGH,YES,,,-1;SYNJ2BP-COX16,stop_gained,p.R116*,ENST00000621525,NM_001202548.2,c.346C>T,HIGH,YES,,,-1;COX16,5_prime_UTR_variant,,ENST00000555276,,c.-24C>T,MODIFIER,,,,-1;SYNJ2BP-COX16,intron_variant,,ENST00000617124,NM_001202549.2&NM_001202547.2,c.298-13445C>T,MODIFIER,,,,-1;COX16,intron_variant,,ENST00000555601,,n.154-13445C>T,MODIFIER,,,,-1;COX16,intron_variant,,ENST00000557612,,n.183-13445C>T,MODIFIER,,,,-1;SYNJ2BP-COX16,intron_variant,,ENST00000617196,,n.418-13445C>T,MODIFIER,,,,-1;AL356804.1,non_coding_transcript_exon_variant,,ENST00000655620,,n.722G>A,MODIFIER,,,,1 214/1669 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.201e-05 0.0 0.0 0.0 0.0001091 0.0 5.3e-05 0.0 0.0 2.706539999053348e-05 2.435100032016635e-05 0.0 0.0 0.0 0.0 0.0 nfe 4.630920011550188e-05 0.0 4.630920011550188e-05 0.0 0.0 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS COX16,5_prime_UTR_variant,,ENST00000555276.5,c.-24C>T,MODIFIER,;SYNJ2BP-COX16,intron_variant,,ENST00000617124.4,c.298-13445C>T,MODIFIER,;SYNJ2BP-COX16,intron_variant,,ENST00000617196.4,n.418-13445C>T,MODIFIER,;COX16,intron_variant,,ENST00000555601.1,n.154-13445C>T,MODIFIER,;COX16,intron_variant,,ENST00000557612.5,n.183-13445C>T,MODIFIER,;SYNJ2BP-COX16,stop_gained,p.R116*,ENST00000621525.4,c.346C>T,HIGH,YES;COX16,stop_gained,p.R40*,ENST00000389912.7,c.118C>T,HIGH,YES;ENSG00000259033,non_coding_transcript_exon_variant,,ENST00000655620.1,n.722G>A,MODIFIER,YES +PTPN21 11099 BI GRCh38 14 88479009 88479009 + stop_gained Nonsense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 7 c.2422C>T p.Arg808Ter p.R808* ENST00000328736.7 808 Cga/Tga 12/18 P1 A R/* protein_coding CCDS9884.1 2422/3525 GGCTCGGTAGC PIRSF:PIRSF000934;PANTHER:PTHR45706;PANTHER:PTHR45706:SF3 ENSP00000330276 12/18 COSV100162404 ENST00000328736 Transcript ENSG00000070778 HGNC:9651 HIGH stop_gained 1 Unknown 1 Q16825.173 PTPN21 HGNC -1 1.0 UPI000013D15F SNV PTPN21,stop_gained,p.R808*,ENST00000556564,NM_007039.4,c.2422C>T,HIGH,YES,,,-1;PTPN21,stop_gained,p.R808*,ENST00000328736,,c.2422C>T,HIGH,,,,-1;PTPN21,3_prime_UTR_variant,,ENST00000536337,,c.*2359C>T,MODIFIER,,,,-1;PTPN21,non_coding_transcript_exon_variant,,ENST00000554270,,n.2535C>T,MODIFIER,,,,-1 2627/6089 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 65 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 43 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PTPN21,non_coding_transcript_exon_variant,,ENST00000554270.5,n.2535C>T,MODIFIER,;PTPN21,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000536337.5,c.*2359C>T,MODIFIER,;PTPN21,stop_gained,p.R808*,ENST00000328736.7,c.2422C>T,HIGH,;PTPN21,stop_gained,p.R808*,ENST00000556564.6,c.2422C>T,HIGH,YES +TTC8 123016 BI GRCh38 14 88871652 88871652 + missense_variant Missense_Mutation SNP C C T rs772733868 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 57 41 c.1153C>T p.Arg385Cys p.R385C ENST00000380656.7 NM_144596.4 385 Cgt/Tgt 12/15 T R/C protein_coding YES CCDS73674.1 1201/1596 TTGAACGTGCC Gene3D:1.25.40.10;PROSITE_profiles:PS50005;PROSITE_profiles:PS50293;PANTHER:PTHR44177;SMART:SM00028;Superfamily:SSF48452;Low_complexity_(Seg):seg ENSP00000337653 12/15 rs772733868 ENST00000338104 Transcript 1.0 ENSG00000165533 HGNC:20087 MODERATE 4.62e-05 gnomAD_FIN missense_variant 1.0 probably_damaging(0.993) Unknown deleterious(0) TTC8 HGNC 1 A0A0C4DGX9.47 1.0 UPI0000071182 SNV TTC8,missense_variant,p.R375C,ENST00000622513,NM_198309.3&NM_001366535.2,c.1123C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;TTC8,missense_variant,p.R401C,ENST00000338104,NM_001288781.1,c.1201C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),1;TTC8,missense_variant,p.R385C,ENST00000380656,NM_144596.4,c.1153C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;TTC8,missense_variant,p.R345C,ENST00000346301,NM_001288782.1&NM_198310.3,c.1033C>T,MODERATE,,deleterious(0),probably_damaging(0.969),1;TTC8,missense_variant,p.R335C,ENST00000554686,NM_001366536.2,c.1003C>T,MODERATE,,deleterious(0),probably_damaging(0.982),1;TTC8,missense_variant,p.R120C,ENST00000354441,NM_001288783.1,c.358C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;TTC8,3_prime_UTR_variant,,ENST00000555057,,c.*560C>T,MODIFIER,,,,1;TTC8,3_prime_UTR_variant,,ENST00000557580,,c.*425C>T,MODIFIER,,,,1 1253/2226 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.961e-06 0.0 0.0 0.0 0.0 4.62e-05 8.806e-06 0.0 0.0 6.762610155419679e-06 2.4328499421244487e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 108 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 98 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TTC8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000557580.3,c.*425C>T,MODIFIER,;TTC8,synonymous_variant,p.N334=,ENST00000554686.5,c.1002C>T,LOW,;TTC8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000555057.5,c.*560C>T,MODIFIER,;TTC8,missense_variant,p.R120C,ENST00000354441.10,c.358C>T,MODERATE,;TTC8,missense_variant,p.R345C,ENST00000346301.8,c.1033C>T,MODERATE,;TTC8,missense_variant,p.R401C,ENST00000338104.10,c.1201C>T,MODERATE,;TTC8,missense_variant,p.R385C,ENST00000380656.7,c.1153C>T,MODERATE,YES;TTC8,missense_variant,p.R375C,ENST00000622513.4,c.1123C>T,MODERATE, +SERPINA3 12 BI GRCh38 14 94614562 94614562 + stop_gained Nonsense_Mutation SNP C C T rs373526796 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 20 c.121C>T p.Arg41Ter p.R41* ENST00000393080.8 41 Cga/Tga 2/5 P1 T R/* protein_coding CCDS32150.1 121/1272 AAGACCGAGGG COSM1225273 PDB-ENSP_mappings:1qmn.A;PDB-ENSP_mappings:2ach.A;PDB-ENSP_mappings:3dlw.A;PDB-ENSP_mappings:5om2.A;PDB-ENSP_mappings:5om3.A;PDB-ENSP_mappings:5om5.A;PDB-ENSP_mappings:5om6.A;PDB-ENSP_mappings:5om6.C;PDB-ENSP_mappings:5om7.A;PDB-ENSP_mappings:5om8.A;PDB-ENSP_mappings:6ftp.A;PDB-ENSP_mappings:6hgd.A;PDB-ENSP_mappings:6hge.A;PDB-ENSP_mappings:6hge.B;PDB-ENSP_mappings:6hge.C;PDB-ENSP_mappings:6hge.D;PDB-ENSP_mappings:6hgf.A;PDB-ENSP_mappings:6hgg.A;PDB-ENSP_mappings:6hgh.A;PDB-ENSP_mappings:6hgi.A;PDB-ENSP_mappings:6hgj.A;PDB-ENSP_mappings:6hgk.A;PDB-ENSP_mappings:6hgl.A;PDB-ENSP_mappings:6hgm.A;PDB-ENSP_mappings:6hgn.A;PANTHER:PTHR11461;PANTHER:PTHR11461:SF145;Superfamily:SSF56574 ENSP00000376795 0.000227 0.0 2/5 rs373526796 ENST00000393080 Transcript 1.0 ENSG00000196136 HGNC:16 HIGH 0.000227 AA stop_gained Unknown P01011.234 SERPINA3 HGNC 1 A0A024R6P0.52 1.0 UPI000012509B P01011-1 SNV SERPINA3,stop_gained,p.R41*,ENST00000467132,,c.121C>T,HIGH,YES,,,1;SERPINA3,stop_gained,p.R41*,ENST00000393080,,c.121C>T,HIGH,,,,1;SERPINA3,stop_gained,p.R41*,ENST00000393078,NM_001085.5,c.121C>T,HIGH,,,,1;SERPINA3,stop_gained,p.R41*,ENST00000555820,,c.121C>T,HIGH,,,,1;SERPINA3,upstream_gene_variant,,ENST00000482740,,,MODIFIER,,,,1;SERPINA3,upstream_gene_variant,,ENST00000621603,,,MODIFIER,,,,1;SERPINA3,intron_variant,,ENST00000556388,,n.57+2115C>T,MODIFIER,,,,1;SERPINA3,downstream_gene_variant,,ENST00000485588,,,MODIFIER,,,,1;SERPINA3,stop_gained,p.R41*,ENST00000556968,,c.121C>T,HIGH,,,,1;AL049839.2,3_prime_UTR_variant,,ENST00000553947,,c.*947C>T,MODIFIER,YES,,,1 189/1581 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.98e-05 0.000123 5.783e-05 0.0 0.0001087 0.0 2.641e-05 0.0 3.266e-05 2.028400012932252e-05 0.0 0.0 0.0 0.0 0.0002024290006374 0.0 0.0 1.5432100553880446e-05 0.0 0.0002085940068354 0 87 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SERPINA3,stop_gained,NMD_transcript_variant,p.R41*,ENST00000556968.2,c.121C>T,HIGH,;SERPINA3,stop_gained,p.R41*,ENST00000467132.5,c.121C>T,HIGH,;SERPINA3,intron_variant,,ENST00000556388.1,n.57+2115C>T,MODIFIER,;SERPINA3,stop_gained,p.R41*,ENST00000393078.5,c.121C>T,HIGH,YES;SERPINA3,stop_gained,p.R41*,ENST00000555820.1,c.121C>T,HIGH,;SERPINA3,stop_gained,p.R41*,ENST00000393080.8,c.121C>T,HIGH,;ENSG00000273259,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000553947.1,c.*947C>T,MODIFIER,YES +IGHV3-16 28447 BI GRCh38 14 106165325 106165325 + synonymous_variant Silent SNP C C T rs1427833114 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 66 c.231G>A p.Thr77= p.T77= ENST00000390604.2 77 acG/acA 2/2 P1 T T IG_V_gene YES 231/351 TAGTGCGTCCT ENSP00000375013 2/2 rs1427833114 cds_end_NF ENST00000390604 Transcript ENSG00000211944 HGNC:5583 LOW 2.899e-05 gnomAD_AMR synonymous_variant 1.0 Unknown A0A0C4DH30.39 IGHV3-16 HGNC -1 UPI000011AADA SNV IGHV3-16,synonymous_variant,p.T77=,ENST00000390604,,c.231G>A,LOW,YES,,,-1;IGHVII-15-1,upstream_gene_variant,,ENST00000517931,,,MODIFIER,YES,,,-1 305/425 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.124e-06 0.0 2.899e-05 0.0 0.0 0.0 9.081e-06 0.0 0.0 2.7473999580251984e-05 4.9578600737731904e-05 0.0 0.0 0.0 0.0 0.0 afr 4.9578600737731904e-05 0.0 1.5513500329689123e-05 0.0005040320102125 0.0 0 104 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 69 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IGHV3-16,synonymous_variant,p.T77=,ENST00000390604.2,c.231G>A,LOW,YES +HERC2P3 283755 BI GRCh38 15 20457656 20457656 + non_coding_transcript_exon_variant RNA SNP C C T rs761042944 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 7 n.1334G>A ENST00000429257.5 10/26 T processed_transcript YES GGCAACGTTCT 3776.0 rs761042944 ENST00000426501 Transcript ENSG00000180229 HGNC:4871 MODIFIER 0.001443 gnomAD_EAS upstream_gene_variant 1.0 Unknown HERC2P3 HGNC -1 1.0 SNV HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453,,n.1287G>A,MODIFIER,,,,-1;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598,,n.1191G>A,MODIFIER,,,,-1;HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318,,n.1279G>A,MODIFIER,,,,-1;HERC2P3,downstream_gene_variant,,ENST00000412154,,,MODIFIER,,,,-1;HERC2P3,downstream_gene_variant,,ENST00000414804,,,MODIFIER,,,,-1;HERC2P3,upstream_gene_variant,,ENST00000426501,,,MODIFIER,YES,,,-1;HERC2P3,upstream_gene_variant,,ENST00000440441,,,MODIFIER,,,,-1;HERC2P3,upstream_gene_variant,,ENST00000440774,,,MODIFIER,,,,-1;HERC2P3,upstream_gene_variant,,ENST00000424611,,,MODIFIER,,,,-1;HERC2P3,downstream_gene_variant,,ENST00000429926,,,MODIFIER,,,,-1;HERC2P3,downstream_gene_variant,,ENST00000456027,,,MODIFIER,,,,-1;HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257,,n.1334G>A,MODIFIER,,,,-1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001315 0.0 0.0 0.0 0.001443 0.0 1.865e-05 0.0001736 6.983e-05 0 90 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HERC2P3,non_coding_transcript_exon_variant,,ENST00000429257.5,n.1334G>A,MODIFIER,YES;HERC2P3,non_coding_transcript_exon_variant,,ENST00000430598.5,n.1191G>A,MODIFIER,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000437318.5,n.1279G>A,MODIFIER,;HERC2P3,non_coding_transcript_exon_variant,,ENST00000428453.5,n.1287G>A,MODIFIER,YES +NOP10 55505 BI GRCh38 15 34342029 34342029 + missense_variant Missense_Mutation SNP C C T rs201604296 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 13 c.134G>A p.Arg45Gln p.R45Q ENST00000328848.6 NM_018648.4 45 cGa/cAa 2/2 P1 T R/Q protein_coding YES CCDS10037.1 134/195 TGATTCGGTGT Gene3D:2.20.28.40;Pfam:PF04135;PANTHER:PTHR13305;PANTHER:PTHR13305:SF0;Superfamily:SSF144210 ENSP00000332198 2/2 rs201604296;COSV60995433 ENST00000328848 Transcript 1.0 ENSG00000182117 HGNC:14378 MODERATE NM_018648.4 5.782e-05 gnomAD_AMR missense_variant 0;1 1.0 possibly_damaging(0.59) Unknown tolerated(0.06) 0;1 Q9NPE3.149 NOP10 HGNC -1 1.0 UPI0000022AEE SNV NOP10,missense_variant,p.R45Q,ENST00000328848,NM_018648.4,c.134G>A,MODERATE,YES,tolerated(0.06),possibly_damaging(0.59),-1;NOP10,missense_variant,p.E26K,ENST00000557912,,c.76G>A,MODERATE,,tolerated_low_confidence(0.64),benign(0.006),-1;NUTM1,upstream_gene_variant,,ENST00000333756,,,MODIFIER,,,,1;SLC12A6,upstream_gene_variant,,ENST00000354181,NM_001365088.1,,MODIFIER,YES,,,-1;SLC12A6,upstream_gene_variant,,ENST00000397702,NM_001042495.2,,MODIFIER,,,,-1;NUTM1,upstream_gene_variant,,ENST00000438749,NM_001284293.1,,MODIFIER,,,,1;SLC12A6,upstream_gene_variant,,ENST00000458406,NM_001042494.2,,MODIFIER,,,,-1;NUTM1,upstream_gene_variant,,ENST00000537011,NM_001284292.2,,MODIFIER,YES,,,1;SLC12A6,upstream_gene_variant,,ENST00000558589,NM_001042496.2,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000558667,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000559236,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000559484,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000561120,,,MODIFIER,,,,-1;NUTM1,upstream_gene_variant,,ENST00000614490,NM_175741.2,,MODIFIER,,,,1;SLC12A6,upstream_gene_variant,,ENST00000676379,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000559523,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000559664,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000561080,,,MODIFIER,,,,-1;SLC12A6,upstream_gene_variant,,ENST00000675289,,,MODIFIER,,,,-1 197/507 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.953e-06 0.0 5.782e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NOP10,missense_variant,p.R45Q,ENST00000328848.6,c.134G>A,MODERATE,YES;NOP10,non_coding_transcript_exon_variant,,ENST00000699939.1,n.281G>A,MODIFIER,;NOP10,missense_variant,p.R40Q,ENST00000699937.1,c.119G>A,MODERATE,;NOP10,missense_variant,p.R45Q,ENST00000699938.1,c.134G>A,MODERATE,;NOP10,missense_variant,p.E26K,ENST00000557912.2,c.76G>A,MODERATE,;NOP10,missense_variant,p.R53Q,ENST00000699935.1,c.158G>A,MODERATE,;NOP10,missense_variant,p.R23Q,ENST00000699936.1,c.68G>A,MODERATE,;NOP10,missense_variant,p.R46Q,ENST00000699926.1,c.137G>A,MODERATE,;NOP10,missense_variant,p.R45Q,ENST00000699934.1,c.134G>A,MODERATE, +IVD 3712 BI GRCh38 15 40410720 40410720 + missense_variant Missense_Mutation SNP G G A rs754570116 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 13 c.379G>A p.Gly127Ser p.G127S ENST00000487418.8 NM_001354600.3 127 Ggt/Agt 4/12 A1 A G/S protein_coding YES CCDS10057.2 388/1281 GTTACGGTGCC CDD:cd01156;PANTHER:PTHR43884;PANTHER:PTHR43884:SF10;Gene3D:1.10.540.10;Pfam:PF02771;Superfamily:SSF56645 ENSP00000499074 4/12 rs754570116 ENST00000651168 Transcript 1.0 ENSG00000128928 HGNC:6186 MODERATE 6.533e-05 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.903) Unknown deleterious(0) P26440.204 IVD HGNC 1 UPI0000D4AF3D P26440-1 SNV IVD,missense_variant,p.G130S,ENST00000651168,,c.388G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.903),1;IVD,missense_variant,p.G100S,ENST00000650656,,c.298G>A,MODERATE,,deleterious(0),probably_damaging(0.988),1;IVD,missense_variant,p.G127S,ENST00000487418,NM_001354600.3&NM_001354598.3&NM_001354601.3&NM_001354597.3&NM_001354599.3&NM_002225.5,c.379G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;IVD,missense_variant,p.G97S,ENST00000479013,NM_001159508.3,c.289G>A,MODERATE,,deleterious(0),probably_damaging(0.988),1;IVD,missense_variant,p.G47S,ENST00000473112,,c.139G>A,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.894),1;IVD,missense_variant,p.G111S,ENST00000558610,,c.331G>A,MODERATE,,deleterious(0),probably_damaging(0.982),1;IVD,missense_variant,p.G156S,ENST00000610693,,c.466G>A,MODERATE,,deleterious(0),probably_damaging(0.946),1;IVD,upstream_gene_variant,,ENST00000491554,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000497252,,,MODIFIER,,,,1;IVD,non_coding_transcript_exon_variant,,ENST00000484250,,n.2G>A,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000481262,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000497816,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000560660,,,MODIFIER,,,,1 722/4665 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 6.152e-05 0.0 0.0 0.0 0.0 8.792e-06 0.0 6.533e-05 2.7043099180446006e-05 7.297850243048742e-05 0.0 0.0 0.0 0.0 0.0 afr 7.297850243048742e-05 0.0 1.543019970995374e-05 0.0 0.0 0 49 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IVD,non_coding_transcript_exon_variant,,ENST00000484250.1,n.2G>A,MODIFIER,;IVD,synonymous_variant,p.T46=,ENST00000473112.6,c.138G>A,LOW,;IVD,missense_variant,p.G111S,ENST00000558610.5,c.331G>A,MODERATE,;IVD,missense_variant,p.G156S,ENST00000610693.5,c.466G>A,MODERATE,;IVD,missense_variant,p.G97S,ENST00000479013.7,c.289G>A,MODERATE,;IVD,missense_variant,p.G127S,ENST00000487418.8,c.379G>A,MODERATE,YES;IVD,missense_variant,p.G100S,ENST00000650656.1,c.298G>A,MODERATE,;IVD,missense_variant,p.G130S,ENST00000651168.1,c.388G>A,MODERATE, +TLN2 83660 BI GRCh38 15 62736932 62736932 + missense_variant Missense_Mutation SNP G G A rs750147149 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 24 c.3413G>A p.Arg1138His p.R1138H ENST00000561311.5 NM_015059.2 1138 cGt/cAt 28/58 P1 A R/H protein_coding YES CCDS32261.1 3413/7629 CGCCCGTGGAG Gene3D:1.20.1420.10;PANTHER:PTHR19981;PANTHER:PTHR19981:SF34;Superfamily:SSF47220 ENSP00000453508 28/58 rs750147149 ENST00000561311 Transcript ENSG00000171914 HGNC:15447 MODERATE 4.62e-05 gnomAD_FIN missense_variant 1.0 possibly_damaging(0.908) Unknown tolerated(0.21) Q9Y4G6.191 TLN2 HGNC 1 5.0 UPI00001FE5FC SNV TLN2,missense_variant,p.R1138H,ENST00000561311,NM_015059.2,c.3413G>A,MODERATE,YES,tolerated(0.21),possibly_damaging(0.908),1;TLN2,missense_variant,p.R163H,ENST00000636159,,c.488G>A,MODERATE,,tolerated(0.16),probably_damaging(0.997),1;TLN2,missense_variant,p.R52H,ENST00000494733,,c.155G>A,MODERATE,,tolerated(0.16),possibly_damaging(0.71),1;TLN2,non_coding_transcript_exon_variant,,ENST00000559908,,n.245G>A,MODIFIER,,,,1;TLN2,upstream_gene_variant,,ENST00000489129,,,MODIFIER,,,,1 3643/11880 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.983e-06 0.0 0.0 0.0 0.0 4.62e-05 0.0 0.0 0.0 0 52 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TLN2,non_coding_transcript_exon_variant,,ENST00000559908.1,n.245G>A,MODIFIER,;TLN2,missense_variant,p.R52H,ENST00000494733.5,c.155G>A,MODERATE,;TLN2,missense_variant,p.R1138H,ENST00000561311.5,c.3413G>A,MODERATE,;TLN2,missense_variant,p.R1138H,ENST00000636159.2,c.3413G>A,MODERATE,YES +IGDCC3 9543 BI GRCh38 15 65329794 65329794 + synonymous_variant Silent SNP G G A rs759891168 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 10 c.1929C>T p.Ile643= p.I643= ENST00000327987.9 NM_004884.4 643 atC/atT 12/14 P1 A I protein_coding YES CCDS10205.1 1929/2445 ATGCCGATGAC PANTHER:PTHR44170;PANTHER:PTHR44170:SF20;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000332773 12/14 rs759891168;COSV60078987 ENST00000327987 Transcript ENSG00000174498 HGNC:9700 LOW NM_004884.4 0.0001087 gnomAD_EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q8IVU1.142 IGDCC3 HGNC -1 1.0 UPI000019908F SNV IGDCC3,synonymous_variant,p.I643=,ENST00000327987,NM_004884.4,c.1929C>T,LOW,YES,,,-1;IGDCC3,synonymous_variant,p.I506=,ENST00000558354,,c.1518C>T,LOW,,,,-1;IGDCC3,downstream_gene_variant,,ENST00000559058,,,MODIFIER,,,,-1;IGDCC3,downstream_gene_variant,,ENST00000559231,,,MODIFIER,,,,-1 2143/4441 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.958e-06 0.0 0.0 0.0 0.0001087 0.0 0.0 0.0 0.0 0 33 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS IGDCC3,synonymous_variant,p.I506=,ENST00000558354.5,c.1518C>T,LOW,;IGDCC3,synonymous_variant,p.I643=,ENST00000327987.9,c.1929C>T,LOW,YES +HCN4 10021 BI GRCh38 15 73323555 73323555 + synonymous_variant Silent SNP C C T rs372747050 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 26 c.2538G>A p.Pro846= p.P846= ENST00000261917.4 NM_005477.3 846 ccG/ccA 8/8 P1 T P protein_coding YES CCDS10248.1 2538/3612 TGGGACGGGCT COSM1749303 PANTHER:PTHR45689;PANTHER:PTHR45689:SF4;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000261917 0.0002278 0.0 8/8 rs372747050 ENST00000261917 Transcript 1.0 ENSG00000138622 HGNC:16882 LOW NM_005477.3 0.0002278 AA synonymous_variant 1.0 Unknown Q9Y3Q4.175 HCN4 HGNC -1 1.0 UPI000003FFB5 SNV HCN4,synonymous_variant,p.P846=,ENST00000261917,NM_005477.3,c.2538G>A,LOW,YES,,,-1 3226/6922 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.514e-05 6.318e-05 0.0 0.0 0.0 0.0 0.0001015 0.0 3.275e-05 1.3520600077754352e-05 2.4320199372596107e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5433999578817748e-05 0.0 0.0 0 73 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 69 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HCN4,synonymous_variant,p.P846=,ENST00000261917.4,c.2538G>A,LOW,YES +AP3B2 8120 BI GRCh38 15 82677724 82677724 + missense_variant Missense_Mutation SNP C C T rs1362293215 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 13 c.1325G>A p.Arg442Gln p.R442Q ENST00000261722.8 442 cGa/cAa 12/26 A2 T R/Q protein_coding 1325/3267 GGACTCGGCCG PANTHER:PTHR11134;PANTHER:PTHR11134:SF11;Pfam:PF01602;PIRSF:PIRSF037096;Superfamily:SSF48371 ENSP00000261722 12/26 rs1362293215 ENST00000261722 Transcript 1.0 ENSG00000103723 HGNC:567 MODERATE 3.522e-05 gnomAD_SAS missense_variant possibly_damaging(0.457) Unknown tolerated(0.15) AP3B2 HGNC -1 A0A5F9UJV3.3 1.0 UPI00114897B5 SNV AP3B2,missense_variant,p.R442Q,ENST00000535359,NM_001278512.2,c.1325G>A,MODERATE,,tolerated(0.15),benign(0.009),-1;AP3B2,missense_variant,p.R442Q,ENST00000261722,,c.1325G>A,MODERATE,,tolerated(0.15),possibly_damaging(0.457),-1;AP3B2,missense_variant,p.R442Q,ENST00000652847,,c.1325G>A,MODERATE,YES,tolerated(0.13),possibly_damaging(0.611),-1;AP3B2,missense_variant,p.R442Q,ENST00000668990,NM_004644.5,c.1325G>A,MODERATE,,tolerated(0.13),benign(0.009),-1;AP3B2,missense_variant,p.R485Q,ENST00000642989,,c.1454G>A,MODERATE,,tolerated(0.11),benign(0.042),-1;AP3B2,missense_variant,p.R385Q,ENST00000669930,,c.1154G>A,MODERATE,,tolerated(0.11),possibly_damaging(0.611),-1;AP3B2,missense_variant,p.R442Q,ENST00000666973,,c.1325G>A,MODERATE,,tolerated(0.12),benign(0.373),-1;AP3B2,missense_variant,p.R410Q,ENST00000535348,NM_001278511.1,c.1229G>A,MODERATE,,tolerated(0.13),benign(0.044),-1;AP3B2,missense_variant,p.R78Q,ENST00000660624,,c.233G>A,MODERATE,,deleterious(0.01),benign(0.009),-1;AP3B2,missense_variant,p.R410Q,ENST00000664460,,c.1229G>A,MODERATE,,tolerated(0.19),benign(0.187),-1;AP3B2,missense_variant,p.R442Q,ENST00000666055,,c.1325G>A,MODERATE,,tolerated(0.31),benign(0.187),-1;AP3B2,missense_variant,p.R78Q,ENST00000666894,,c.233G>A,MODERATE,,tolerated(0.19),benign(0.122),-1;AP3B2,downstream_gene_variant,,ENST00000541693,,,MODIFIER,,,,-1;AP3B2,upstream_gene_variant,,ENST00000665513,,,MODIFIER,,,,-1;AP3B2,non_coding_transcript_exon_variant,,ENST00000537735,,n.1471G>A,MODIFIER,,,,-1;AP3B2,non_coding_transcript_exon_variant,,ENST00000663651,,n.1467G>A,MODIFIER,,,,-1;AP3B2,intron_variant,,ENST00000669880,,n.225-341G>A,MODIFIER,,,,-1;AP3B2,missense_variant,p.R185Q,ENST00000661532,,c.554G>A,MODERATE,,tolerated(0.13),benign(0.373),-1;AP3B2,missense_variant,p.R316Q,ENST00000668458,,c.947G>A,MODERATE,,tolerated(0.16),benign(0.373),-1;AP3B2,3_prime_UTR_variant,,ENST00000667758,,c.*1213G>A,MODIFIER,,,,-1;AP3B2,3_prime_UTR_variant,,ENST00000657321,,c.*949G>A,MODIFIER,,,,-1;AP3B2,3_prime_UTR_variant,,ENST00000668385,,c.*1123G>A,MODIFIER,,,,-1;AP3B2,non_coding_transcript_exon_variant,,ENST00000535385,,n.1828G>A,MODIFIER,,,,-1;AP3B2,non_coding_transcript_exon_variant,,ENST00000543938,,n.1528G>A,MODIFIER,,,,-1;AP3B2,downstream_gene_variant,,ENST00000559888,,,MODIFIER,,,,-1;AP3B2,upstream_gene_variant,,ENST00000659252,,,MODIFIER,,,,-1;AP3B2,downstream_gene_variant,,ENST00000666672,,,MODIFIER,,,,-1;CPEB1-AS1,intron_variant,,ENST00000560650,,n.1329-14287C>T,MODIFIER,,,,1 1538/3738 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.217e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.522e-05 0 10 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 19 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AP3B2,missense_variant,p.R78Q,ENST00000666894.1,c.233G>A,MODERATE,;AP3B2,missense_variant,p.R442Q,ENST00000666055.1,c.1325G>A,MODERATE,;AP3B2,intron_variant,,ENST00000669880.1,n.225-341G>A,MODIFIER,;AP3B2,missense_variant,p.R410Q,ENST00000664460.1,c.1229G>A,MODERATE,;AP3B2,missense_variant,NMD_transcript_variant,p.E316K,ENST00000668458.1,c.946G>A,MODERATE,;AP3B2,non_coding_transcript_exon_variant,,ENST00000535385.6,n.1828G>A,MODIFIER,;AP3B2,missense_variant,p.R410Q,ENST00000535348.5,c.1229G>A,MODERATE,;AP3B2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000668385.1,c.*1123G>A,MODIFIER,;AP3B2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000657321.1,c.*949G>A,MODIFIER,;AP3B2,missense_variant,p.R442Q,ENST00000666973.1,c.1325G>A,MODERATE,;AP3B2,synonymous_variant,NMD_transcript_variant,p.P184=,ENST00000661532.1,c.552G>A,LOW,;AP3B2,missense_variant,p.R385Q,ENST00000669930.1,c.1154G>A,MODERATE,;AP3B2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000667758.1,c.*1213G>A,MODIFIER,;AP3B2,missense_variant,p.R442Q,ENST00000261722.8,c.1325G>A,MODERATE,;AP3B2,non_coding_transcript_exon_variant,,ENST00000663651.1,n.1467G>A,MODIFIER,;AP3B2,missense_variant,p.R442Q,ENST00000652847.1,c.1325G>A,MODERATE,;AP3B2,non_coding_transcript_exon_variant,,ENST00000537735.2,n.1471G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000679950.1,n.1704G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000681452.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000679388.1,n.1264G>A,MODIFIER,;AP3B2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681327.1,c.*949G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000679531.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000681464.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000680946.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000680492.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000681044.1,n.1731G>A,MODIFIER,;AP3B2,non_coding_transcript_exon_variant,,ENST00000543938.6,n.1528G>A,MODIFIER,;AP3B2,missense_variant,p.R78Q,ENST00000660624.1,c.233G>A,MODERATE,;AP3B2,missense_variant,p.R485Q,ENST00000642989.2,c.1454G>A,MODERATE,;AP3B2,missense_variant,p.R442Q,ENST00000535359.6,c.1325G>A,MODERATE,YES;AP3B2,missense_variant,p.R442Q,ENST00000668990.2,c.1325G>A,MODERATE,;CPEB1-AS1,intron_variant,,ENST00000560650.1,n.1329-14287C>T,MODIFIER,YES +AKAP13 11214 BI GRCh38 15 85581231 85581231 + missense_variant Missense_Mutation SNP G G A rs753131765 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 18 c.3163G>A p.Asp1055Asn p.D1055N ENST00000394518.7 NM_007200.5 1055 Gat/Aat 7/37 A2 A D/N protein_coding CCDS32319.1 3163/8442 GGTCCGATGCT PANTHER:PTHR13944;PANTHER:PTHR13944:SF18 ENSP00000378026 7/37 rs753131765 ENST00000394518 Transcript ENSG00000170776 HGNC:371 MODERATE NM_007200.5 2.892e-05 gnomAD_AMR missense_variant benign(0) Unknown deleterious_low_confidence(0.02) Q12802.183 AKAP13 HGNC 1 1.0 UPI0000167BA0 Q12802-1 SNV AKAP13,missense_variant,p.D1055N,ENST00000394518,NM_007200.5,c.3163G>A,MODERATE,,deleterious_low_confidence(0.02),benign(0),1;AKAP13,missense_variant,p.D1055N,ENST00000361243,NM_006738.6,c.3163G>A,MODERATE,YES,deleterious_low_confidence(0.02),benign(0),1;AKAP13,missense_variant,p.D1055N,ENST00000559362,,c.3163G>A,MODERATE,,deleterious(0),benign(0),1;AKAP13,downstream_gene_variant,,ENST00000558166,,,MODIFIER,,,,1;AKAP13,downstream_gene_variant,,ENST00000558811,,,MODIFIER,,,,1;AKAP13,upstream_gene_variant,,ENST00000560340,,,MODIFIER,,,,1;AC087286.3,upstream_gene_variant,,ENST00000561409,,,MODIFIER,YES,,,-1 3370/13327 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.194e-05 0.0 2.892e-05 0.0 0.0 0.0 1.761e-05 0.0 0.0 1.35215996124316e-05 0.0 0.0 6.627779657719657e-05 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 60 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AKAP13,missense_variant,p.D1055N,ENST00000361243.6,c.3163G>A,MODERATE,;AKAP13,missense_variant,p.D1055N,ENST00000394518.7,c.3163G>A,MODERATE,YES;AKAP13,missense_variant,p.D1055N,ENST00000559362.5,c.3163G>A,MODERATE, +ENSG00000259655 106479400 BI GRCh38 15 99792083 99792083 + intron_variant Intron SNP C C T rs113961788 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 17 n.174-113C>T ENST00000557959.1 T misc_RNA YES CCCACCGGGCC 673.0 rs113961788 ENST00000462651 Transcript ENSG00000241588 HGNC:46500 MODIFIER 6.552e-05 gnomAD_SAS downstream_gene_variant Unknown RN7SL484P HGNC 1 SNV RN7SL484P,downstream_gene_variant,,ENST00000462651,,,MODIFIER,YES,,,1;DNM1P46,non_coding_transcript_exon_variant,,ENST00000341853,,n.1904G>A,MODIFIER,YES,,,-1;DNM1P46,non_coding_transcript_exon_variant,,ENST00000559110,,n.1834G>A,MODIFIER,,,,-1;DNM1P46,non_coding_transcript_exon_variant,,ENST00000561042,,n.1759G>A,MODIFIER,,,,-1;AC090825.2,intron_variant,,ENST00000557959,,n.174-113C>T,MODIFIER,YES,,,1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.169e-05 0.0 2.902e-05 0.0 5.535e-05 0.0 5.412e-05 0.0 6.552e-05 6.760410087736091e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433499356731772e-05 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 33 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000259655,intron_variant,,ENST00000557959.1,n.174-113C>T,MODIFIER,YES;ENSG00000290767,non_coding_transcript_exon_variant,,ENST00000559110.5,n.1834G>A,MODIFIER,;ENSG00000290767,non_coding_transcript_exon_variant,,ENST00000561042.5,n.1759G>A,MODIFIER,;ENSG00000290767,non_coding_transcript_exon_variant,,ENST00000341853.5,n.1904G>A,MODIFIER,YES +ALDH1A3 220 BI GRCh38 15 100900655 100900655 + missense_variant Missense_Mutation SNP G G A rs1596129599 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 7 c.964G>A p.Val322Met p.V322M ENST00000329841.10 NM_000693.4 322 Gtg/Atg 9/13 P1 A V/M protein_coding YES CCDS10389.1 964/1539 TGTTCGTGGAG PDB-ENSP_mappings:5fhz.A;PDB-ENSP_mappings:5fhz.B;PDB-ENSP_mappings:5fhz.C;PDB-ENSP_mappings:5fhz.D;PDB-ENSP_mappings:5fhz.E;PDB-ENSP_mappings:5fhz.F;PDB-ENSP_mappings:5fhz.G;PDB-ENSP_mappings:5fhz.H;PDB-ENSP_mappings:6s6w.A;PDB-ENSP_mappings:6s6w.B;CDD:cd07141;PANTHER:PTHR11699;PANTHER:PTHR11699:SF209;Gene3D:3.40.309.10;Pfam:PF00171;Gene3D:3.40.605.10;Superfamily:SSF53720 ENSP00000332256 9/13 CM163655 ENST00000329841 Transcript 1.0 ENSG00000184254 HGNC:409 MODERATE NM_000693.4 missense_variant 1 1.0 probably_damaging(0.999) Unknown deleterious(0.01) P47895.179 ALDH1A3 HGNC 1 A0A024RC95.52 1.0 UPI00001AFAF8 SNV ALDH1A3,missense_variant,p.V322M,ENST00000329841,NM_000693.4,c.964G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),1;ALDH1A3,missense_variant,p.V215M,ENST00000346623,NM_001293815.2,c.643G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ALDH1A3,non_coding_transcript_exon_variant,,ENST00000558869,,n.207G>A,MODIFIER,,,,1;ALDH1A3,downstream_gene_variant,,ENST00000558033,,,MODIFIER,,,,1;AC015712.2,intron_variant,,ENST00000560351,,n.481-4589C>T,MODIFIER,,,,-1;AC015712.2,intron_variant,,ENST00000656756,,n.589-4589C>T,MODIFIER,YES,,,-1;AC015712.2,intron_variant,,ENST00000659873,,n.610-4589C>T,MODIFIER,,,,-1 1041/3469 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 29 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ALDH1A3,non_coding_transcript_exon_variant,,ENST00000558869.1,n.207G>A,MODIFIER,;ALDH1A3-AS1,intron_variant,,ENST00000659873.1,n.610-4589C>T,MODIFIER,;ALDH1A3-AS1,intron_variant,,ENST00000560351.2,n.481-4589C>T,MODIFIER,;ALDH1A3-AS1,intron_variant,,ENST00000656756.1,n.589-4589C>T,MODIFIER,YES;ALDH1A3,missense_variant,p.V215M,ENST00000346623.6,c.643G>A,MODERATE,;ALDH1A3,missense_variant,p.V322M,ENST00000329841.10,c.964G>A,MODERATE,YES +SNRNP25 64285 BI GRCh38 16 55487 55487 + missense_variant Missense_Mutation SNP T T C rs1024654436 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 97 6 c.71T>C p.Ile24Thr p.I24T ENST00000293861.8 NM_022450.5 33/132 A2 C I/T protein_coding YES CCDS10396.1 98/399 CCAAATAGCCC PANTHER:PTHR14942;PANTHER:PTHR14942:SF0 ENSP00000372482 2/5 rs1024654436;COSV51955144 ENST00000383018 Transcript ENSG00000161981 HGNC:14161 MODERATE 9.923e-05 gnomAD_ASJ missense_variant 0;1 1.0 possibly_damaging(0.676) Unknown tolerated(0.05) 0;1 Q9BV90.139 SNRNP25 HGNC 1 1.0 UPI000006FC43 SNV SNRNP25,missense_variant,p.I24T,ENST00000293861,NM_024571.4,c.71T>C,MODERATE,,tolerated(0.05),possibly_damaging(0.676),1;SNRNP25,missense_variant,p.I33T,ENST00000383018,,c.98T>C,MODERATE,YES,tolerated(0.05),possibly_damaging(0.676),1;SNRNP25,missense_variant,p.I24T,ENST00000417493,,c.71T>C,MODERATE,,tolerated(0.05),possibly_damaging(0.564),1;RHBDF1,downstream_gene_variant,,ENST00000262316,NM_022450.5,,MODIFIER,YES,,,-1;POLR3K,upstream_gene_variant,,ENST00000293860,NM_016310.5,,MODIFIER,YES,,,-1;RHBDF1,downstream_gene_variant,,ENST00000448893,,,MODIFIER,,,,-1;SNRNP25,non_coding_transcript_exon_variant,,ENST00000493672,,n.189T>C,MODIFIER,,,,1;SNRNP25,missense_variant,p.I24T,ENST00000397876,,c.71T>C,MODERATE,,deleterious(0.04),possibly_damaging(0.897),1;SNRNP25,non_coding_transcript_exon_variant,,ENST00000466183,,n.528T>C,MODIFIER,,,,1;RHBDF1,downstream_gene_variant,,ENST00000428730,,,MODIFIER,,,,-1;POLR3K,upstream_gene_variant,,ENST00000481810,,,MODIFIER,,,,-1;SNRNP25,upstream_gene_variant,,ENST00000481947,,,MODIFIER,,,,1;RHBDF1,downstream_gene_variant,,ENST00000486045,,,MODIFIER,,,,-1;RHBDF1,downstream_gene_variant,,ENST00000493647,,,MODIFIER,,,,-1 259/1085 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.193e-05 0.0 2.891e-05 9.923e-05 0.0 0.0 8.791e-06 0.0 0.0 0 170 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 103 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SNRNP25,non_coding_transcript_exon_variant,,ENST00000466183.1,n.528T>C,MODIFIER,;SNRNP25,non_coding_transcript_exon_variant,,ENST00000493672.1,n.189T>C,MODIFIER,;SNRNP25,missense_variant,p.I24T,ENST00000417493.1,c.71T>C,MODERATE,;SNRNP25,missense_variant,NMD_transcript_variant,p.I24T,ENST00000397876.6,c.71T>C,MODERATE,;SNRNP25,missense_variant,p.I24T,ENST00000293861.8,c.71T>C,MODERATE,YES;SNRNP25,missense_variant,p.I61T,ENST00000710415.1,c.182T>C,MODERATE, +ABCA3 21 BI GRCh38 16 2297525 2297525 + synonymous_variant Silent SNP G G A rs765175808 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 8 c.2067C>T p.Asp689= p.D689= ENST00000301732.10 NM_001089.3 689 gaC/gaT 17/33 P2 A D protein_coding YES CCDS10466.1 2067/5115 GGCTCGTCCAG Gene3D:3.40.50.300;Pfam:PF00005;PROSITE_profiles:PS50893;PANTHER:PTHR19229;PANTHER:PTHR19229:SF98;SMART:SM00382;Superfamily:SSF52540;CDD:cd03263 ENSP00000301732 17/33 rs765175808 ENST00000301732 Transcript 1.0 ENSG00000167972 HGNC:33 LOW NM_001089.3 8.841e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q99758.174 ABCA3 HGNC -1 1.0 UPI0000001232 Q99758-1 SNV ABCA3,synonymous_variant,p.D689=,ENST00000301732,NM_001089.3,c.2067C>T,LOW,YES,,,-1;ABCA3,synonymous_variant,p.D631=,ENST00000382381,,c.1893C>T,LOW,,,,-1;ABCA3,non_coding_transcript_exon_variant,,ENST00000563623,,n.2630C>T,MODIFIER,,,,-1 2761/6602 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.99e-06 0.0 0.0 0.0 0.0 0.0 8.841e-06 0.0 0.0 0 42 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ABCA3,non_coding_transcript_exon_variant,,ENST00000563623.5,n.2630C>T,MODIFIER,;ABCA3,synonymous_variant,p.D631=,ENST00000382381.7,c.1893C>T,LOW,;ABCA3,synonymous_variant,p.D689=,ENST00000301732.10,c.2067C>T,LOW,YES +ADCY9 115 BI GRCh38 16 4114054 4114054 + synonymous_variant Silent SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 56 6 c.1389C>T p.Ile463= p.I463= ENST00000294016.8 NM_001116.4 463 atC/atT 2/11 P1 A I protein_coding YES CCDS32382.1 1389/4062 ATCTCGATGCA COSM3691001 Gene3D:3.30.70.1230;Pfam:PF00211;PROSITE_profiles:PS50125;PANTHER:PTHR45627;PANTHER:PTHR45627:SF8;SMART:SM00044;Superfamily:SSF55073;CDD:cd07302 ENSP00000294016 2/11 COSV53582610 ENST00000294016 Transcript ENSG00000162104 HGNC:240 LOW NM_001116.4 synonymous_variant 1 1.0 Unknown 1 O60503.176 ADCY9 HGNC -1 1.0 UPI000012887F SNV ADCY9,synonymous_variant,p.I463=,ENST00000294016,NM_001116.4,c.1389C>T,LOW,YES,,,-1;ADCY9,upstream_gene_variant,,ENST00000572288,,,MODIFIER,,,,-1;ADCY9,upstream_gene_variant,,ENST00000571467,,,MODIFIER,,,,-1 2185/7980 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 81 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ADCY9,synonymous_variant,p.I463=,ENST00000294016.8,c.1389C>T,LOW,YES +PPL 5493 BI GRCh38 16 4883600 4883600 + synonymous_variant Silent SNP G G A rs772773621 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 18 c.5055C>T p.Phe1685= p.F1685= ENST00000345988.7 NM_002705.5 1685 ttC/ttT 22/22 P3 A F protein_coding YES CCDS10526.1 5055/5271 TTCACGAACAT Gene3D:3.30.160.780;PDB-ENSP_mappings:4q28.A;PDB-ENSP_mappings:4q28.B;PDB-ENSP_mappings:4q28.C;PDB-ENSP_mappings:4q28.D;PANTHER:PTHR23169;PANTHER:PTHR23169:SF10;SMART:SM00250;Superfamily:SSF75399 ENSP00000340510 22/22 rs772773621 ENST00000345988 Transcript ENSG00000118898 HGNC:9273 LOW NM_002705.5 0.0001307 gnomAD_SAS synonymous_variant 1.0 Unknown O60437.180 PPL HGNC -1 1.0 UPI00001AE832 SNV PPL,synonymous_variant,p.F1685=,ENST00000345988,NM_002705.5,c.5055C>T,LOW,YES,,,-1;PPL,synonymous_variant,p.F1683=,ENST00000590782,,c.5049C>T,LOW,,,,-1;PPL,synonymous_variant,p.F1106=,ENST00000592772,,c.3318C>T,LOW,,,,-1;UBN1,downstream_gene_variant,,ENST00000262376,NM_001079514.3,,MODIFIER,YES,,,1;UBN1,downstream_gene_variant,,ENST00000396658,,,MODIFIER,,,,1;UBN1,downstream_gene_variant,,ENST00000590769,NM_001288656.1,,MODIFIER,,,,1;UBN1,downstream_gene_variant,,ENST00000589191,,,MODIFIER,,,,1 5158/6251 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.785e-05 0.0 0.0 0.0 0.0 0.0 2.639e-05 0.0 0.0001307 6.761229997209739e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5432100553880446e-05 0.0 0.0 0 46 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPL,synonymous_variant,p.F1106=,ENST00000592772.1,c.3318C>T,LOW,;PPL,synonymous_variant,p.F1683=,ENST00000590782.6,c.5049C>T,LOW,;PPL,synonymous_variant,p.F1685=,ENST00000345988.7,c.5055C>T,LOW,YES +PPL 5493 BI GRCh38 16 4899057 4899057 + missense_variant Missense_Mutation SNP C C T rs763239987 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 47 25 c.832G>A p.Asp278Asn p.D278N ENST00000345988.7 NM_002705.5 278 Gac/Aac 8/22 P3 T D/N protein_coding YES CCDS10526.1 832/5271 CTGGTCGCCCT Gene3D:1.20.58.1940;Coiled-coils_(Ncoils):Coil;PANTHER:PTHR23169;PANTHER:PTHR23169:SF10;SMART:SM00150;Superfamily:SSF46966 ENSP00000340510 8/22 rs763239987 ENST00000345988 Transcript ENSG00000118898 HGNC:9273 MODERATE NM_002705.5 0.0001846 gnomAD_AFR missense_variant 1.0 benign(0.013) Unknown tolerated(0.14) O60437.180 PPL HGNC -1 1.0 UPI00001AE832 SNV PPL,missense_variant,p.D278N,ENST00000345988,NM_002705.5,c.832G>A,MODERATE,YES,tolerated(0.14),benign(0.013),-1;PPL,missense_variant,p.D276N,ENST00000590782,,c.826G>A,MODERATE,,tolerated(0.14),benign(0.027),-1;PPL,intron_variant,,ENST00000592772,,c.252+3382G>A,MODIFIER,,,,-1 935/6251 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.981e-05 0.0001846 5.784e-05 0.0 0.0 0.0 4.396e-05 0.0 0.0 8.790080028120428e-05 0.0001946279953699 0.0 0.0001988069998333 0.0 0.0 0.0 amr 0.0001988069998333 0.0 1.5432100553880446e-05 0.0004960320075042 0.0 0 92 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPL,intron_variant,,ENST00000592772.1,c.252+3382G>A,MODIFIER,;PPL,missense_variant,p.D276N,ENST00000590782.6,c.826G>A,MODERATE,;PPL,missense_variant,p.D278N,ENST00000345988.7,c.832G>A,MODERATE,YES +CIITA 4261 BI GRCh38 16 10907288 10907288 + missense_variant Missense_Mutation SNP G G A rs141095229 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 7 c.1796G>A p.Arg599Gln p.R599Q ENST00000324288.14 NM_000246.4 599 cGg/cAg 11/20 P4 A R/Q protein_coding CCDS10544.1 1796/3393 CCTCCGGGACC PROSITE_profiles:PS50837;PANTHER:PTHR47189;Superfamily:SSF52540;Low_complexity_(Seg):seg ENSP00000316328 0.0 0.0001163 11/20 rs141095229 ENST00000324288 Transcript 1.0 ENSG00000179583 HGNC:7067 MODERATE 0.0001163 EA missense_variant benign(0.005) Unknown tolerated(0.36) CIITA HGNC 1 A0A0B4J1S1.43 1.0 UPI00015BB2D6 SNV CIITA,missense_variant,p.R599Q,ENST00000324288,NM_000246.3&NM_001379333.1&NM_001379331.1,c.1796G>A,MODERATE,,tolerated(0.36),benign(0.005),1;CIITA,missense_variant,p.R600Q,ENST00000618327,NM_001286402.1&NM_001379332.1&NM_001379330.1&NM_001379334.1,c.1799G>A,MODERATE,YES,tolerated(0.36),benign(0.005),1;CIITA,intron_variant,,ENST00000381835,NM_001286403.2,c.860-1695G>A,MODIFIER,,,,1;CIITA,intron_variant,,ENST00000618207,,c.1006+2476G>A,MODIFIER,,,,1;CIITA,intron_variant,,ENST00000537380,,n.1006+2476G>A,MODIFIER,,,,1;CIITA,non_coding_transcript_exon_variant,,ENST00000570546,,n.1917G>A,MODIFIER,,,,1;CIITA,non_coding_transcript_exon_variant,,ENST00000573309,,n.1767G>A,MODIFIER,,,,1;CIITA,downstream_gene_variant,,ENST00000571186,,,MODIFIER,,,,1 1929/16059 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.008e-05 0.0 0.0 0.0 0.0 0.0 4.461e-05 0.0 0.0 2.0293000488891263e-05 2.4338000002899207e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.087750155827962e-05 0.0 3.087750155827962e-05 0.0 0.0 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 22 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CIITA,non_coding_transcript_exon_variant,,ENST00000695879.1,n.1690G>A,MODIFIER,;CIITA,intron_variant,,ENST00000537380.1,n.1006+2476G>A,MODIFIER,;CIITA,non_coding_transcript_exon_variant,,ENST00000573309.5,n.1767G>A,MODIFIER,;CIITA,non_coding_transcript_exon_variant,,ENST00000570546.5,n.1917G>A,MODIFIER,;CIITA,intron_variant,,ENST00000381835.9,c.860-1695G>A,MODIFIER,;CIITA,missense_variant,p.R599Q,ENST00000324288.14,c.1796G>A,MODERATE,YES;CIITA,missense_variant,p.R600Q,ENST00000618327.4,c.1799G>A,MODERATE,;CIITA,intron_variant,NMD_transcript_variant,,ENST00000618207.4,c.1006+2476G>A,MODIFIER, +ZNF764 92595 BI GRCh38 16 30555532 30555532 + missense_variant Missense_Mutation SNP C C T rs772140866 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 4 6 c.889G>A p.Ala297Thr p.A297T ENST00000252797.6 NM_033410.4 297 Gcc/Acc 3/3 P4 T A/T protein_coding YES CCDS10683.1 889/1227 GTAGGCGAAGG Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF299;SMART:SM00355;Superfamily:SSF57667 ENSP00000252797 3/3 rs772140866 ENST00000252797 Transcript ENSG00000169951 HGNC:28200 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.613) Unknown tolerated(0.28) Q96H86.144 ZNF764 HGNC -1 A0A024QZB2.51 1.0 UPI000013CD86 Q96H86-1 SNV ZNF764,missense_variant,p.A296T,ENST00000395091,NM_001172679.2,c.886G>A,MODERATE,,tolerated(0.27),possibly_damaging(0.682),-1;ZNF764,missense_variant,p.A297T,ENST00000252797,NM_033410.4,c.889G>A,MODERATE,YES,tolerated(0.28),possibly_damaging(0.613),-1;ZNF764,downstream_gene_variant,,ENST00000568333,,,MODIFIER,,,,-1 970/2738 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.3544599823944736e-05 4.875200102105737e-05 0.0 0.0 0.0 0.0 0.0 afr 4.875200102105737e-05 0.0 0.0 0.0 0.0 0 13 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF764,missense_variant,p.A297T,ENST00000252797.6,c.889G>A,MODERATE,;ZNF764,missense_variant,p.A296T,ENST00000395091.3,c.886G>A,MODERATE,YES +ZNF629 23361 BI GRCh38 16 30781988 30781988 + synonymous_variant Silent SNP G G A rs1411967172 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 89 27 c.2340C>T p.Arg780= p.R780= ENST00000262525.6 NM_001080417.3 780 cgC/cgT 3/3 P1 A R protein_coding YES CCDS45463.1 2340/2610 GCCACGCGGTC COSM4744507 PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24376;PANTHER:PTHR24376:SF78;SMART:SM00355;Superfamily:SSF57667 ENSP00000262525 3/3 rs1411967172;COSV52698695 ENST00000262525 Transcript ENSG00000102870 HGNC:29008 LOW NM_001080417.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 Q9UEG4.150 ZNF629 HGNC -1 1.0 UPI00001C1FA5 SNV ZNF629,synonymous_variant,p.R780=,ENST00000262525,NM_001080417.3&NM_001345970.2,c.2340C>T,LOW,YES,,,-1 2551/6083 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 125 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 116 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF629,synonymous_variant,p.R780=,ENST00000262525.6,c.2340C>T,LOW,YES +ITGAX 3687 BI GRCh38 16 31363232 31363232 + missense_variant Missense_Mutation SNP C C T rs200458998 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 64 22 c.1568C>T p.Ala523Val p.A523V ENST00000268296.9 NM_000887.5 523 gCg/gTg 14/30 P4 T A/V protein_coding CCDS10711.1 1568/3492 TGGGGCGGCTC COSM3969547 Gene3D:2.130.10.130;PDB-ENSP_mappings:3k6s.A;PDB-ENSP_mappings:3k6s.C;PDB-ENSP_mappings:3k6s.E;PDB-ENSP_mappings:3k6s.G;PDB-ENSP_mappings:3k71.A;PDB-ENSP_mappings:3k71.C;PDB-ENSP_mappings:3k71.E;PDB-ENSP_mappings:3k71.G;PDB-ENSP_mappings:3k72.A;PDB-ENSP_mappings:3k72.C;PDB-ENSP_mappings:4neh.A;PDB-ENSP_mappings:4nen.A;PDB-ENSP_mappings:5es4.A;PDB-ENSP_mappings:5es4.C;PDB-ENSP_mappings:5es4.E;PDB-ENSP_mappings:5es4.G;Pfam:PF01839;Prints:PR01185;PROSITE_profiles:PS51470;PANTHER:PTHR23220;PANTHER:PTHR23220:SF124;SMART:SM00191;Superfamily:SSF69318 ENSP00000268296 14/30 rs200458998;COSV51650268 ENST00000268296 Transcript ENSG00000140678 HGNC:6152 MODERATE NM_000887.5 3.528e-05 gnomAD_NFE missense_variant 0;1 possibly_damaging(0.529) Unknown deleterious(0.01) 0;1 P20702.193 ITGAX HGNC 1 1.0 UPI00001C0366 SNV ITGAX,missense_variant,p.A523V,ENST00000268296,NM_000887.5,c.1568C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.529),1;ITGAX,missense_variant,p.A523V,ENST00000562522,NM_001286375.2,c.1568C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.935),1;ITGAX,downstream_gene_variant,,ENST00000562918,,,MODIFIER,,,,1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,,n.1589C>T,MODIFIER,,,,1;AC093520.2,upstream_gene_variant,,ENST00000561830,,,MODIFIER,YES,,,-1 1647/4663 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.994e-05 0.0 0.0 0.0 0.0 0.0 3.528e-05 0.0 3.268e-05 0 107 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 87 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ITGAX,non_coding_transcript_exon_variant,,ENST00000571644.1,n.1589C>T,MODIFIER,;ITGAX,missense_variant,p.A523V,ENST00000562522.2,c.1568C>T,MODERATE,;ITGAX,missense_variant,p.A523V,ENST00000268296.9,c.1568C>T,MODERATE,YES +ZNF423 23090 BI GRCh38 16 49635691 49635691 + missense_variant Missense_Mutation SNP C C T rs532940886 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 44 20 c.3485G>A p.Arg1162Gln p.R1162Q ENST00000563137.7 NM_001379286.1 1162 cGg/cAg 4/8 0.0002 0.0 0.0 0.001 0.0 0.0 A2 T R/Q protein_coding YES 3485/3879 CTTTCCGGGGC Gene3D:3.30.160.60;PANTHER:PTHR24408;PANTHER:PTHR24408:SF28;MobiDB_lite:mobidb-lite ENSP00000455588 4/8 rs532940886;COSV52188947 ENST00000563137 Transcript 1.0 ENSG00000102935 HGNC:16762 MODERATE NM_001379286.1 0.001 EAS missense_variant 0;1 1.0 benign(0.007) Unknown tolerated(0.64) 0;1 Q2M1K9.144 ZNF423 HGNC -1 5.0 UPI0007DC742E Q2M1K9-2 SNV ZNF423,missense_variant,p.R1162Q,ENST00000563137,NM_001379286.1,c.3485G>A,MODERATE,YES,tolerated(0.64),benign(0.007),-1;ZNF423,missense_variant,p.R1154Q,ENST00000561648,NM_015069.4,c.3461G>A,MODERATE,,tolerated(0.65),benign(0.018),-1;ZNF423,missense_variant,p.R1094Q,ENST00000562871,,c.3281G>A,MODERATE,,tolerated(0.62),benign(0.018),-1;ZNF423,missense_variant,p.R1037Q,ENST00000535559,NM_001330533.2,c.3110G>A,MODERATE,,tolerated(0.59),benign(0.018),-1;ZNF423,missense_variant,p.R1094Q,ENST00000562520,NM_001271620.2,c.3281G>A,MODERATE,,tolerated(0.62),benign(0.018),-1;ZNF423,missense_variant,p.R1037Q,ENST00000567169,,c.3110G>A,MODERATE,,tolerated(0.59),benign(0.018),-1 3823/7968 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.638e-05 0.0 0.0 0.0 0.0001165 0.0 3.866e-05 0.0 0.0 4.060969877173193e-05 2.4358199880225584e-05 0.0 6.628660048590973e-05 0.0 0.0002030040050158 0.0 nfe 4.631769843399525e-05 0.0 4.631769843399525e-05 0.0 0.0 0 91 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 64 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF423,missense_variant,p.R1094Q,ENST00000562520.1,c.3281G>A,MODERATE,;ZNF423,missense_variant,p.R1037Q,ENST00000567169.5,c.3110G>A,MODERATE,;ZNF423,missense_variant,p.R1037Q,ENST00000535559.5,c.3110G>A,MODERATE,;ZNF423,missense_variant,p.R1094Q,ENST00000562871.5,c.3281G>A,MODERATE,;ZNF423,missense_variant,p.R1162Q,ENST00000563137.7,c.3485G>A,MODERATE,YES;ZNF423,missense_variant,p.R1154Q,ENST00000561648.5,c.3461G>A,MODERATE, +ZNF423 23090 BI GRCh38 16 49638347 49638347 + missense_variant Missense_Mutation SNP C C T rs745876102 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 15 6 c.829G>A p.Glu277Lys p.E277K ENST00000563137.7 NM_001379286.1 277 Gag/Aag 4/8 A2 T E/K protein_coding YES 829/3879 GTCCTCGCAGT Gene3D:3.30.160.60;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24408;PANTHER:PTHR24408:SF28;SMART:SM00355 ENSP00000455588 4/8 rs745876102;COSV52179263 ENST00000563137 Transcript 1.0 ENSG00000102935 HGNC:16762 MODERATE NM_001379286.1 1.774e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0.336) Unknown tolerated(0.07) 0;1 Q2M1K9.144 ZNF423 HGNC -1 5.0 UPI0007DC742E Q2M1K9-2 SNV ZNF423,missense_variant,p.E277K,ENST00000563137,NM_001379286.1,c.829G>A,MODERATE,YES,tolerated(0.07),benign(0.336),-1;ZNF423,missense_variant,p.E269K,ENST00000561648,NM_015069.4,c.805G>A,MODERATE,,tolerated(0.07),probably_damaging(0.999),-1;ZNF423,missense_variant,p.E209K,ENST00000562871,,c.625G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1;ZNF423,missense_variant,p.E152K,ENST00000535559,NM_001330533.2,c.454G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1;ZNF423,missense_variant,p.E209K,ENST00000562520,NM_001271620.2,c.625G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1;ZNF423,missense_variant,p.E152K,ENST00000567169,,c.454G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1 1167/7968 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.988e-06 0.0 0.0 0.0 0.0 0.0 1.774e-05 0.0 0.0 0 23 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF423,missense_variant,p.E209K,ENST00000562520.1,c.625G>A,MODERATE,;ZNF423,missense_variant,p.E152K,ENST00000567169.5,c.454G>A,MODERATE,;ZNF423,missense_variant,p.E152K,ENST00000535559.5,c.454G>A,MODERATE,;ZNF423,missense_variant,p.E209K,ENST00000562871.5,c.625G>A,MODERATE,;ZNF423,missense_variant,p.E277K,ENST00000563137.7,c.829G>A,MODERATE,YES;ZNF423,missense_variant,p.E269K,ENST00000561648.5,c.805G>A,MODERATE, +TOX3 27324 BI GRCh38 16 52464133 52464133 + missense_variant Missense_Mutation SNP G G A rs768449574 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 55 20 c.209C>T p.Thr70Met p.T70M ENST00000219746.14 NM_001080430.4 70 aCg/aTg 3/7 P4 A T/M protein_coding YES CCDS54009.1 209/1731 GAGGCGTGATT PANTHER:PTHR45781;PANTHER:PTHR45781:SF3;Low_complexity_(Seg):seg ENSP00000219746 3/7 rs768449574 ENST00000219746 Transcript ENSG00000103460 HGNC:11972 MODERATE NM_001080430.4 3.488e-05 gnomAD_AMR missense_variant 1.0 probably_damaging(0.987) Unknown deleterious(0) O15405.145 TOX3 HGNC -1 2.0 UPI00001972E7 O15405-1 SNV TOX3,missense_variant,p.T70M,ENST00000219746,NM_001080430.4,c.209C>T,MODERATE,YES,deleterious(0),probably_damaging(0.987),-1;TOX3,missense_variant,p.T65M,ENST00000407228,NM_001146188.2,c.194C>T,MODERATE,,deleterious(0),probably_damaging(0.992),-1;TOX3,missense_variant,p.T34M,ENST00000563091,,c.101C>T,MODERATE,,deleterious(0),probably_damaging(0.987),-1;TOX3,3_prime_UTR_variant,,ENST00000568436,,c.*133C>T,MODIFIER,,,,-1 629/4959 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.429e-06 0.0 3.488e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 75 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TOX3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000568436.1,c.*133C>T,MODIFIER,;TOX3,missense_variant,p.T34M,ENST00000563091.1,c.101C>T,MODERATE,;TOX3,missense_variant,p.T65M,ENST00000407228.7,c.194C>T,MODERATE,;TOX3,missense_variant,p.T70M,ENST00000219746.14,c.209C>T,MODERATE,YES +DPEP2 64174 BI GRCh38 16 67992144 67992144 + missense_variant Missense_Mutation SNP C C T rs768027580 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 29 c.440G>A p.Arg147His p.R147H ENST00000393847.6 NM_022355.4 147 cGc/cAc 4/11 P1 T R/H protein_coding CCDS10857.1 440/1461 TGAGGCGCAGG PROSITE_profiles:PS51365;CDD:cd01301;PANTHER:PTHR10443:SF14;PANTHER:PTHR10443;Pfam:PF01244;Gene3D:3.20.20.140;Superfamily:SSF51556 ENSP00000377430 4/11 rs768027580;COSV99263083 ENST00000393847 Transcript ENSG00000167261 HGNC:23028 MODERATE NM_022355.4 5.782e-05 gnomAD_AMR missense_variant 0;1 benign(0.336) Unknown deleterious(0.04) 0;1 Q9H4A9.145 DPEP2 HGNC -1 1.0 UPI000007277C Q9H4A9-1 SNV DPEP2,missense_variant,p.R147H,ENST00000572888,NM_001324159.1&NM_001369657.1,c.440G>A,MODERATE,YES,deleterious(0.04),benign(0.336),-1;DPEP2,missense_variant,p.R147H,ENST00000393847,NM_022355.4,c.440G>A,MODERATE,,deleterious(0.04),benign(0.336),-1;DPEP2,missense_variant,p.R31H,ENST00000573808,,c.92G>A,MODERATE,,tolerated(0.07),benign(0.031),-1;DUS2,intron_variant,,ENST00000570709,,c.-19+4191C>T,MODIFIER,,,,1;DUS2,intron_variant,,ENST00000571081,,c.-99+4191C>T,MODIFIER,,,,1;DPEP2,intron_variant,,ENST00000575510,,c.39-960G>A,MODIFIER,,,,-1;DPEP2,downstream_gene_variant,,ENST00000572624,,,MODIFIER,,,,-1;DPEP2,downstream_gene_variant,,ENST00000574865,,,MODIFIER,,,,-1;DUS2,upstream_gene_variant,,ENST00000575677,,,MODIFIER,,,,1;DPEP2,missense_variant,p.R147H,ENST00000575203,,c.440G>A,MODERATE,,deleterious(0.05),probably_damaging(0.985),-1;DPEP2,non_coding_transcript_exon_variant,,ENST00000268795,,n.492G>A,MODIFIER,,,,-1;DPEP2,downstream_gene_variant,,ENST00000574316,,,MODIFIER,,,,-1 595/1728 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.785e-05 0.0 5.782e-05 0.0 0.0 0.0 4.398e-05 0.0 0.0 3.380890120752156e-05 2.432730070722755e-05 0.0 6.632180156884715e-05 0.0 0.0 0.0 nfe 4.62948992208112e-05 0.0 4.62948992208112e-05 0.0 0.0 0 74 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 54 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DPEP2,non_coding_transcript_exon_variant,,ENST00000268795.5,n.492G>A,MODIFIER,;DPEP2,missense_variant,p.R31H,ENST00000573808.1,c.92G>A,MODERATE,;DPEP2,intron_variant,,ENST00000575510.5,c.39-960G>A,MODIFIER,;DUS2,intron_variant,,ENST00000570709.6,c.-19+4191C>T,MODIFIER,;DUS2,intron_variant,,ENST00000571081.6,c.-99+4191C>T,MODIFIER,;DPEP2,missense_variant,p.R147H,ENST00000572888.5,c.440G>A,MODERATE,;DPEP2,missense_variant,NMD_transcript_variant,p.R147H,ENST00000575203.5,c.440G>A,MODERATE,;DPEP2,missense_variant,p.R147H,ENST00000393847.6,c.440G>A,MODERATE,YES +SMPD3 55512 BI GRCh38 16 68371449 68371449 + missense_variant Missense_Mutation SNP C C T rs200081668 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 3 12 c.733G>A p.Val245Met p.V245M ENST00000219334.10 NM_018667.4 245 Gtg/Atg 3/9 P1 T V/M protein_coding YES CCDS10867.1 733/1968 GCGCACGATGC COSM1128901 PDB-ENSP_mappings:5uvg.A;MobiDB_lite:mobidb-lite;PANTHER:PTHR16320:SF8;PANTHER:PTHR16320 ENSP00000219334 3/9 rs200081668;COSV54715870 ENST00000219334 Transcript ENSG00000103056 HGNC:14240 MODERATE NM_018667.4 0.0001775 gnomAD_OTH missense_variant 0;1 1.0 benign(0.395) Unknown tolerated(0.12) 0;1 Q9NY59.144 SMPD3 HGNC -1 1.0 UPI0000037769 Q9NY59-1 SNV SMPD3,missense_variant,p.V245M,ENST00000219334,NM_018667.4,c.733G>A,MODERATE,YES,tolerated(0.12),benign(0.395),-1;SMPD3,missense_variant,p.V245M,ENST00000563226,,c.733G>A,MODERATE,,tolerated(0.14),benign(0.395),-1;SMPD3,missense_variant,p.V245M,ENST00000568373,,c.733G>A,MODERATE,,tolerated(0.13),possibly_damaging(0.868),-1;SMPD3,downstream_gene_variant,,ENST00000561749,,,MODIFIER,,,,-1;SMPD3,upstream_gene_variant,,ENST00000574662,,,MODIFIER,,,,-1;SMPD3,intron_variant,,ENST00000566723,,n.406-357G>A,MODIFIER,,,,-1;SMPD3,upstream_gene_variant,,ENST00000563455,,,MODIFIER,,,,-1;SMPD3,upstream_gene_variant,,ENST00000566009,,,MODIFIER,,,,-1;SMPD3,upstream_gene_variant,,ENST00000566466,,,MODIFIER,,,,-1;AC099521.2,upstream_gene_variant,,ENST00000624251,,,MODIFIER,YES,,,-1;SMPD3,upstream_gene_variant,,ENST00000567223,,,MODIFIER,,,,-1;SMPD3,upstream_gene_variant,,ENST00000567811,,,MODIFIER,,,,-1 1157/5271 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.137e-05 6.794e-05 0.0 0.0 5.794e-05 0.0 2.893e-05 0.0001775 3.428e-05 6.082150139263831e-05 7.293240196304396e-05 0.0 0.0001323979959124 0.0 0.0 9.410880011273548e-05 amr 0.0001323979959124 0.0 3.086039941990748e-05 0.000494070991408 0.0 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 15 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SMPD3,intron_variant,,ENST00000566723.1,n.406-357G>A,MODIFIER,;SMPD3,missense_variant,p.V245M,ENST00000563226.1,c.733G>A,MODERATE,;SMPD3,missense_variant,p.V245M,ENST00000568373.5,c.733G>A,MODERATE,;SMPD3,missense_variant,p.V245M,ENST00000219334.10,c.733G>A,MODERATE,YES +ZFHX3 463 BI GRCh38 16 72959267 72959267 + synonymous_variant Silent SNP G G A rs183134469 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 31 c.879C>T p.Tyr293= p.Y293= ENST00000268489.10 NM_006885.4 293 taC/taT 2/10 0.0002 0.0 0.0 0.001 0.0 0.0 P1 A Y protein_coding CCDS10908.1 879/11112 CGGACGTACCC PANTHER:PTHR45891;PANTHER:PTHR45891:SF4;SMART:SM00355 ENSP00000268489 2/10 rs183134469;COSV51720547;COSV51737782 ENST00000268489 Transcript 1.0 ENSG00000140836 HGNC:777 LOW NM_006885.4 0.001 EAS synonymous_variant 0;1;1 Unknown 0;1;1 Q15911.195 ZFHX3 HGNC -1 1.0 UPI00001AE937 Q15911-1 SNV ZFHX3,synonymous_variant,p.Y293=,ENST00000641206,,c.879C>T,LOW,YES,,,-1;ZFHX3,synonymous_variant,p.Y293=,ENST00000268489,NM_006885.4,c.879C>T,LOW,,,,-1;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.2,c.-23-8302C>T,MODIFIER,,,,-1 1305/15817 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.169e-05 0.0 5.782e-05 0.0 0.0004349 0.0 2.637e-05 0.0 0.0 6.083469997975044e-05 0.0 0.0 0.0001324500044574 0.0 0.0006053270190022 9.421519644092768e-05 eas 0.0006053270190022 0.0 4.629340037354268e-05 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 60 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZFHX3,synonymous_variant,p.Y293=,ENST00000641206.2,c.879C>T,LOW,;ZFHX3,synonymous_variant,p.Y293=,ENST00000268489.10,c.879C>T,LOW,YES;ZFHX3,intron_variant,,ENST00000397992.5,c.-23-8302C>T,MODIFIER, +ZFHX3 463 BI GRCh38 16 72959756 72959756 + synonymous_variant Silent SNP G G A rs144573608 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 20 c.390C>T p.Ala130= p.A130= ENST00000268489.10 NM_006885.4 130 gcC/gcT 2/10 P1 A A protein_coding CCDS10908.1 390/11112 TCCCCGGCCAG PANTHER:PTHR45891;PANTHER:PTHR45891:SF4 ENSP00000268489 0.0002275 0.0001163 2/10 rs144573608 ENST00000268489 Transcript 1.0 ENSG00000140836 HGNC:777 LOW NM_006885.4 0.0002275 AA synonymous_variant Unknown Q15911.195 ZFHX3 HGNC -1 1.0 UPI00001AE937 Q15911-1 SNV ZFHX3,synonymous_variant,p.A130=,ENST00000641206,,c.390C>T,LOW,YES,,,-1;ZFHX3,synonymous_variant,p.A130=,ENST00000268489,NM_006885.4,c.390C>T,LOW,,,,-1;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.2,c.-23-8791C>T,MODIFIER,,,,-1 816/15817 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.225e-05 6.212e-05 0.0 0.0 0.0 0.0 5.375e-05 0.0 3.302e-05 2.703690006455872e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.172269786475226e-05 0.0 6.172269786475226e-05 0.0 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZFHX3,synonymous_variant,p.A130=,ENST00000641206.2,c.390C>T,LOW,;ZFHX3,synonymous_variant,p.A130=,ENST00000268489.10,c.390C>T,LOW,YES;ZFHX3,intron_variant,,ENST00000397992.5,c.-23-8791C>T,MODIFIER, +CLEC18B 497190 BI GRCh38 16 74418161 74418161 + synonymous_variant Silent SNP C C T rs779514803 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 11 c.354G>A p.Ala118= p.A118= ENST00000339953.9 NM_001011880.3 118 gcG/gcA 3/13 A2 T A protein_coding YES CCDS32484.1 354/1368 AAGGACGCCAA CDD:cd05380;Pfam:PF00188;Gene3D:3.40.33.10;SMART:SM00198;Superfamily:SSF55797;PANTHER:PTHR10334;PANTHER:PTHR10334:SF245 ENSP00000341051 3/13 rs779514803;COSV60579116 ENST00000339953 Transcript ENSG00000140839 HGNC:33849 LOW 0.000172 gnomAD_OTH synonymous_variant 0;1 1.0 Unknown 0;1 Q6UXF7.142 CLEC18B HGNC -1 1.0 UPI000025210E Q6UXF7-1 SNV CLEC18B,synonymous_variant,p.A118=,ENST00000617101,,c.354G>A,LOW,,,,-1;CLEC18B,synonymous_variant,p.A118=,ENST00000619275,,c.354G>A,LOW,,,,-1;CLEC18B,synonymous_variant,p.A118=,ENST00000339953,NM_001011880.2,c.354G>A,LOW,YES,,,-1;CLEC18B,synonymous_variant,p.A118=,ENST00000620745,,c.354G>A,LOW,,,,-1;CLEC18B,intron_variant,,ENST00000425714,,n.416+2340G>A,MODIFIER,,,,-1;AC009053.3,upstream_gene_variant,,ENST00000566506,,,MODIFIER,,,,1;AC009053.3,upstream_gene_variant,,ENST00000567148,,,MODIFIER,,,,1;AC009053.3,upstream_gene_variant,,ENST00000669286,,,MODIFIER,YES,,,1 476/1865 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.145e-05 0.0 0.0 0.0 0.0 0.0 3.727e-05 0.000172 0.0 2.218309964518994e-05 2.793299972836394e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.25818000419531e-05 0.0 3.25818000419531e-05 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CLEC18B,intron_variant,,ENST00000425714.2,n.416+2340G>A,MODIFIER,;CLEC18B,synonymous_variant,p.A118=,ENST00000682950.1,c.354G>A,LOW,YES;CLEC18B,synonymous_variant,p.A118=,ENST00000339953.9,c.354G>A,LOW, +ZFP1 162239 BI GRCh38 16 75170066 75170066 + missense_variant Missense_Mutation SNP C C T rs770638807 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 21 c.956C>T p.Thr319Met p.T319M ENST00000393430.6 319 aCg/aTg 4/4 P1 T T/M protein_coding CCDS10914.2 956/1224 TCACACGGGGG COSM4757621 Gene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377;PANTHER:PTHR24377:SF751;PANTHER:PTHR24377:SF751;Superfamily:SSF57667 ENSP00000377080 4/4 rs770638807;COSV60033043 ENST00000393430 Transcript ENSG00000184517 HGNC:23328 MODERATE 0.0001633 gnomAD_OTH missense_variant 0;1 probably_damaging(0.992) Unknown deleterious(0) 0;1 Q6P2D0.149 ZFP1 HGNC 1 1.0 UPI00001FFC12 Q6P2D0-1 SNV ZFP1,missense_variant,p.T319M,ENST00000570010,NM_001318469.2&NM_001318473.2&NM_153688.4&NM_001318474.2,c.956C>T,MODERATE,YES,deleterious(0),probably_damaging(0.992),1;ZFP1,missense_variant,p.T319M,ENST00000393430,,c.956C>T,MODERATE,,deleterious(0),probably_damaging(0.992),1;ZFP1,missense_variant,p.T286M,ENST00000332307,NM_001318471.2&NM_001318472.2,c.857C>T,MODERATE,,deleterious(0),probably_damaging(0.992),1;ZFP1,3_prime_UTR_variant,,ENST00000464850,NM_001318476.2,c.*742C>T,MODIFIER,,,,1;ZFP1,3_prime_UTR_variant,,ENST00000568079,,c.*742C>T,MODIFIER,,,,1;ZFP1,downstream_gene_variant,,ENST00000567481,NM_001318475.1,,MODIFIER,,,,1;ZFP1,downstream_gene_variant,,ENST00000563356,,,MODIFIER,,,,1 1080/3250 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.194e-05 0.0 2.893e-05 0.0 0.0 0.0 0.0 0.0001633 3.267e-05 1.353029983874876e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0867999157635495e-05 0.0 3.0867999157635495e-05 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZFP1,missense_variant,p.T319M,ENST00000393430.6,c.956C>T,MODERATE,;ZFP1,missense_variant,p.T286M,ENST00000332307.4,c.857C>T,MODERATE,;ZFP1,3_prime_UTR_variant,,ENST00000464850.5,c.*742C>T,MODIFIER,;ZFP1,missense_variant,p.T319M,ENST00000570010.6,c.956C>T,MODERATE,YES;ZFP1,3_prime_UTR_variant,,ENST00000568079.5,c.*742C>T,MODIFIER, +ADAD2 161931 BI GRCh38 16 84196270 84196270 + missense_variant Missense_Mutation SNP G G A rs754189973 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 57 11 c.1426G>A p.Glu476Lys p.E476K ENST00000315906.10 NM_001145400.2 476 Gaa/Aaa 8/10 P1 A E/K protein_coding CCDS45536.1 1426/1752 CTTCCGAACCC COSM1380181 PROSITE_profiles:PS50141;PANTHER:PTHR10910:SF106;PANTHER:PTHR10910;Pfam:PF02137;SMART:SM00552 ENSP00000325153 8/10 rs754189973;COSV51893826 ENST00000315906 Transcript ENSG00000140955 HGNC:30714 MODERATE NM_001145400.2 0.0003294 gnomAD_OTH missense_variant 0;1 benign(0.011) Unknown tolerated(0.14) 0;1 Q8NCV1.122 ADAD2 HGNC 1 1.0 UPI0000073CA5 Q8NCV1-1 SNV ADAD2,missense_variant,p.E558K,ENST00000268624,NM_139174.4,c.1672G>A,MODERATE,YES,tolerated(0.09),benign(0.009),1;ADAD2,missense_variant,p.E476K,ENST00000315906,NM_001145400.2,c.1426G>A,MODERATE,,tolerated(0.14),benign(0.011),1;ADAD2,downstream_gene_variant,,ENST00000567685,,,MODIFIER,,,,1;ADAD2,downstream_gene_variant,,ENST00000567413,,,MODIFIER,,,,1;ADAD2,non_coding_transcript_exon_variant,,ENST00000564430,,n.2040G>A,MODIFIER,,,,1;ADAD2,non_coding_transcript_exon_variant,,ENST00000566526,,n.2024G>A,MODIFIER,,,,1;ADAD2,upstream_gene_variant,,ENST00000563849,,,MODIFIER,,,,1;ADAD2,downstream_gene_variant,,ENST00000564169,,,MODIFIER,,,,1;ADAD2,downstream_gene_variant,,ENST00000569221,,,MODIFIER,,,,1;AC009123.1,intron_variant,,ENST00000536986,,n.172+612C>T,MODIFIER,YES,,,-1;AC009123.1,intron_variant,,ENST00000565643,,n.172+612C>T,MODIFIER,,,,-1;AC009123.1,intron_variant,,ENST00000569834,,n.171+612C>T,MODIFIER,,,,-1;AC009123.1,upstream_gene_variant,,ENST00000561900,,,MODIFIER,,,,-1 1500/2018 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.635e-05 0.0001291 2.899e-05 0.0 0.0 0.0 3.586e-05 0.0003294 0.0 4.7344601625809446e-05 4.863809954258613e-05 0.0 6.624269735766575e-05 0.0 0.0 0.0 oth 0.0009910799562931 0.0 3.089090023422614e-05 0.0009910799562931 0.0 0 92 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000250685,intron_variant,,ENST00000569834.1,n.171+612C>T,MODIFIER,;ADAD2,non_coding_transcript_exon_variant,,ENST00000564430.1,n.2040G>A,MODIFIER,;ADAD2,non_coding_transcript_exon_variant,,ENST00000566526.5,n.2024G>A,MODIFIER,;ENSG00000250685,intron_variant,,ENST00000565643.5,n.172+612C>T,MODIFIER,;ENSG00000250685,intron_variant,,ENST00000536986.5,n.172+612C>T,MODIFIER,YES;ADAD2,missense_variant,p.E476K,ENST00000315906.10,c.1426G>A,MODERATE,YES;ADAD2,missense_variant,p.E558K,ENST00000268624.7,c.1672G>A,MODERATE, +ATP2C2 9914 BI GRCh38 16 84448604 84448604 + synonymous_variant Silent SNP C C T rs577350687 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 21 c.1575C>T p.Asn525= p.N525= ENST00000262429.9 NM_014861.4 525 aaC/aaT 17/27 P1 T N protein_coding CCDS42207.1 1575/2841 AACAACGGGGG SFLD:SFLDS00003;SFLD:SFLDF00027;CDD:cd02085;TIGRFAM:TIGR01522;Gene3D:1.20.1110.10;Gene3D:3.40.1110.10;Gene3D:3.40.50.1000;Pfam:PF00702;Superfamily:SSF56784;Superfamily:SSF81660;Superfamily:SSF81665;PANTHER:PTHR42861:SF23;PANTHER:PTHR42861 ENSP00000262429 17/27 rs577350687;COSV52297070;COSV52302067 ENST00000262429 Transcript ENSG00000064270 HGNC:29103 LOW NM_014861.4 9.277e-05 gnomAD_FIN synonymous_variant 0;1;1 Unknown 0;1;1 O75185.174 ATP2C2 HGNC 1 1.0 UPI0000425C6A O75185-1 SNV ATP2C2,synonymous_variant,p.N525=,ENST00000416219,NM_001286527.2,c.1575C>T,LOW,YES,,,1;ATP2C2,synonymous_variant,p.N525=,ENST00000262429,NM_014861.4&NM_001291454.1,c.1575C>T,LOW,,,,1;ATP2C2,non_coding_transcript_exon_variant,,ENST00000420010,,n.1248C>T,MODIFIER,,,,1;ATP2C2,non_coding_transcript_exon_variant,,ENST00000565631,,n.2066C>T,MODIFIER,,,,1;ATP2C2,upstream_gene_variant,,ENST00000567892,,,MODIFIER,,,,1 1653/3374 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.406e-05 0.0 0.0 0.0 5.566e-05 9.277e-05 1.767e-05 0.0 3.27e-05 2.7043099180446006e-05 2.432730070722755e-05 0.0 0.0 0.0 0.0002013689954765 0.0 nfe 3.086610013269819e-05 0.0 3.086610013269819e-05 0.0 0.0 0 82 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ATP2C2,non_coding_transcript_exon_variant,,ENST00000420010.6,n.1248C>T,MODIFIER,;ATP2C2,non_coding_transcript_exon_variant,,ENST00000565631.5,n.2066C>T,MODIFIER,;ATP2C2,synonymous_variant,p.N525=,ENST00000262429.9,c.1575C>T,LOW,YES;ATP2C2,synonymous_variant,p.N525=,ENST00000416219.6,c.1575C>T,LOW, +JPH3 57338 BI GRCh38 16 87690283 87690283 + synonymous_variant Silent SNP C C T rs749538454 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 4 4 c.1923C>T p.Asp641= p.D641= ENST00000284262.3 NM_020655.4 641 gaC/gaT 4/5 P1 T D protein_coding YES CCDS10962.1 1923/2247 GGGGACGACCA COSM1380331 PIRSF:PIRSF037387;PANTHER:PTHR23085;PANTHER:PTHR23085:SF7 ENSP00000284262 4/5 rs749538454;COSV52465723 ENST00000284262 Transcript 1.0 ENSG00000154118 HGNC:14203 LOW NM_020655.4 3.149e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q8WXH2.165 JPH3 HGNC 1 1.0 UPI000012DAC4 Q8WXH2-1 SNV JPH3,synonymous_variant,p.D641=,ENST00000284262,NM_020655.4,c.1923C>T,LOW,YES,,,1;JPH3,non_coding_transcript_exon_variant,,ENST00000563609,,n.2217C>T,MODIFIER,,,,1;JPH3,non_coding_transcript_exon_variant,,ENST00000537256,,n.1637C>T,MODIFIER,,,,1;AC010536.1,downstream_gene_variant,,ENST00000538868,,,MODIFIER,YES,,,-1 2562/4382 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.379e-05 0.0 0.0 0.0 0.0 0.0 3.149e-05 0.0 0.0 0 16 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 8 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS JPH3,non_coding_transcript_exon_variant,,ENST00000563609.1,n.2217C>T,MODIFIER,;JPH3,synonymous_variant,p.D641=,ENST00000284262.3,c.1923C>T,LOW,YES;JPH3,non_coding_transcript_exon_variant,,ENST00000537256.5,n.1637C>T,MODIFIER, +SPG7 6687 BI GRCh38 16 89548085 89548085 + synonymous_variant Silent SNP C C T rs770394077 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 59 15 c.1614C>T p.Phe538= p.F538= ENST00000268704.7 538 ttC/ttT 12/17 A2 T F protein_coding 1614/2367 AACTTCGAGTA PANTHER:PTHR43655;PANTHER:PTHR43655:SF8;Pfam:PF17862;TIGRFAM:TIGR01241;Gene3D:1.10.8.60;Superfamily:SSF52540 ENSP00000268704 12/17 rs770394077 ENST00000268704 Transcript 1.0 ENSG00000197912 HGNC:11237 LOW 5.456e-05 gnomAD_EAS synonymous_variant Unknown SPG7 HGNC 1 A0A2U3TZH1.13 1.0 UPI000D1973D3 SNV SPG7,synonymous_variant,p.F409=,ENST00000647079,,c.1227C>T,LOW,,,,1;SPG7,synonymous_variant,p.F545=,ENST00000645063,NM_001363850.1,c.1635C>T,LOW,YES,,,1;SPG7,synonymous_variant,p.F501=,ENST00000646303,,c.1503C>T,LOW,,,,1;SPG7,synonymous_variant,p.F545=,ENST00000645818,NM_003119.4,c.1635C>T,LOW,,,,1;SPG7,synonymous_variant,p.F538=,ENST00000268704,,c.1614C>T,LOW,,,,1;SPG7,synonymous_variant,p.F545=,ENST00000644781,,c.1635C>T,LOW,,,,1;SPG7,synonymous_variant,p.F431=,ENST00000644671,,c.1293C>T,LOW,,,,1;SPG7,synonymous_variant,p.F417=,ENST00000647032,,c.1251C>T,LOW,,,,1;SPG7,synonymous_variant,p.F391=,ENST00000645897,,c.1173C>T,LOW,,,,1;SPG7,synonymous_variant,p.F229=,ENST00000646716,,c.687C>T,LOW,,,,1;SPG7,synonymous_variant,p.F165=,ENST00000646445,,c.495C>T,LOW,,,,1;SPG7,intron_variant,,ENST00000643649,,c.1552+1325C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000643496,,n.1452C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645842,,n.1480C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000643350,,n.692C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645742,,n.269C>T,MODIFIER,,,,1;SPG7,intron_variant,,ENST00000644556,,n.261-217C>T,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000565370,,,MODIFIER,,,,1;SPG7,synonymous_variant,p.F216=,ENST00000566682,,c.648C>T,LOW,,,,1;SPG7,synonymous_variant,p.F60=,ENST00000561911,,c.180C>T,LOW,,,,1;SPG7,synonymous_variant,p.F78=,ENST00000566221,,c.234C>T,LOW,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646930,,c.*1564C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000644901,,c.*2029C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000644498,,c.*1454C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000642334,,c.*1788C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000643954,,c.*1383C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000643668,,c.*1929C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646399,,c.*1454C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000643105,,c.*885C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646263,,c.*508C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000645042,,c.*409C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000569820,,c.*409C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646826,,c.*308C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646531,,c.*258C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000645354,,c.*1643C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000643724,,c.*683C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000644210,,c.*207C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000647227,,c.*1191C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000646589,,c.*763C>T,MODIFIER,,,,1;SPG7,3_prime_UTR_variant,,ENST00000645886,,c.*521C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000644748,,n.6193C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000643734,,n.4548C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000644225,,n.1652C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645977,,n.2753C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000644171,,n.2395C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000647302,,n.2285C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000643409,,n.2060C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645392,,n.1976C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000644464,,n.288C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000642226,,n.1484C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000647123,,n.1592C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000644930,,n.2761C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000646958,,n.2680C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000646005,,n.1393C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000647491,,n.1379C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000642984,,n.1231C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645952,,n.1500C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000646543,,n.2389C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000645944,,n.1409C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000642814,,n.1050C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000642427,,n.1035C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000646454,,n.896C>T,MODIFIER,,,,1;SPG7,non_coding_transcript_exon_variant,,ENST00000563218,,n.694C>T,MODIFIER,,,,1;SPG7,intron_variant,,ENST00000644751,,c.852-2409C>T,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000561702,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000561945,,,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000568205,,,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000569720,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000642263,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643345,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643370,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644044,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644061,,,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000644281,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645258,,,MODIFIER,,,,1;SPG7,upstream_gene_variant,,ENST00000647476,,,MODIFIER,,,,1 1622/3026 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.218e-05 0.0 0.0 0.0 5.456e-05 0.0 1.771e-05 0.0 0.0 1.3514199963537976e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085850039497018e-05 0.0 3.085850039497018e-05 0.0 0.0 0 80 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 74 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SPG7,synonymous_variant,NMD_transcript_variant,p.F60=,ENST00000561911.5,c.180C>T,LOW,;SPG7,non_coding_transcript_exon_variant,,ENST00000644464.1,n.288C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000563218.6,n.694C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000645742.1,n.269C>T,MODIFIER,;SPG7,missense_variant,NMD_transcript_variant,p.S78L,ENST00000566221.5,c.233C>T,MODERATE,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000569820.6,c.*409C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000646543.1,n.2389C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000645944.1,n.1409C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000645952.1,n.1500C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000647491.1,n.1379C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000642984.1,n.1231C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000642226.1,n.1484C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000646005.1,n.1393C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000643409.1,n.2060C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000647123.1,n.1592C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000647302.1,n.2285C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000644930.1,n.2761C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000645392.1,n.1976C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000643350.1,n.692C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000642814.1,n.1050C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000643734.1,n.4548C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000645842.1,n.1480C>T,MODIFIER,;SPG7,intron_variant,,ENST00000644556.1,n.261-217C>T,MODIFIER,;SPG7,synonymous_variant,NMD_transcript_variant,p.F216=,ENST00000566682.2,c.648C>T,LOW,;SPG7,non_coding_transcript_exon_variant,,ENST00000644171.1,n.2395C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000646454.1,n.896C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645886.1,c.*521C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000642427.1,n.1035C>T,MODIFIER,;SPG7,intron_variant,NMD_transcript_variant,,ENST00000644751.1,c.852-2409C>T,MODIFIER,;SPG7,missense_variant,p.S417L,ENST00000647032.1,c.1250C>T,MODERATE,;SPG7,non_coding_transcript_exon_variant,,ENST00000643496.1,n.1452C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000644748.1,n.6193C>T,MODIFIER,;SPG7,missense_variant,p.S431L,ENST00000644671.1,c.1292C>T,MODERATE,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646399.1,c.*1454C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643954.1,c.*1383C>T,MODIFIER,;SPG7,stop_gained,p.R165*,ENST00000646445.1,c.493C>T,HIGH,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647227.1,c.*1191C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642334.1,c.*1788C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645354.1,c.*1643C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643105.1,c.*885C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000646958.1,n.2680C>T,MODIFIER,;SPG7,synonymous_variant,p.F229=,ENST00000646716.1,c.687C>T,LOW,;SPG7,synonymous_variant,p.F538=,ENST00000268704.7,c.1614C>T,LOW,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646826.1,c.*308C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646589.1,c.*763C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644210.1,c.*207C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646531.1,c.*258C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646930.1,c.*1564C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643724.1,c.*683C>T,MODIFIER,;SPG7,synonymous_variant,p.F545=,ENST00000644781.1,c.1635C>T,LOW,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644901.1,c.*2029C>T,MODIFIER,;SPG7,synonymous_variant,p.F545=,ENST00000645818.2,c.1635C>T,LOW,YES;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645042.1,c.*409C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646263.1,c.*508C>T,MODIFIER,;SPG7,synonymous_variant,p.F545=,ENST00000645063.1,c.1635C>T,LOW,;SPG7,non_coding_transcript_exon_variant,,ENST00000645977.1,n.2753C>T,MODIFIER,;SPG7,non_coding_transcript_exon_variant,,ENST00000644225.1,n.1652C>T,MODIFIER,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643668.1,c.*1929C>T,MODIFIER,;SPG7,synonymous_variant,p.F391=,ENST00000645897.1,c.1173C>T,LOW,;SPG7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644498.1,c.*1454C>T,MODIFIER,;SPG7,intron_variant,,ENST00000643649.1,c.1552+1325C>T,MODIFIER,;SPG7,synonymous_variant,p.F501=,ENST00000646303.1,c.1503C>T,LOW,;SPG7,synonymous_variant,p.F409=,ENST00000647079.1,c.1227C>T,LOW, +PRPF8 10594 BI GRCh38 17 1656478 1656478 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 57 13 c.5707G>A p.Gly1903Arg p.G1903R ENST00000304992.11 NM_006445.4 1903 Ggg/Agg 36/43 P1 T G/R protein_coding CCDS11010.1 5707/7008 ATCCCCGAATT Gene3D:3.30.420.230;PDB-ENSP_mappings:3e9l.A;PDB-ENSP_mappings:3enb.A;PDB-ENSP_mappings:3enb.B;PDB-ENSP_mappings:3jcr.A;PDB-ENSP_mappings:3lru.A;PDB-ENSP_mappings:3lru.B;PDB-ENSP_mappings:4jk7.A;PDB-ENSP_mappings:4jk7.B;PDB-ENSP_mappings:4jk8.A;PDB-ENSP_mappings:4jk8.B;PDB-ENSP_mappings:4jk9.A;PDB-ENSP_mappings:4jk9.B;PDB-ENSP_mappings:4jka.A;PDB-ENSP_mappings:4jka.B;PDB-ENSP_mappings:4jkb.A;PDB-ENSP_mappings:4jkb.B;PDB-ENSP_mappings:4jkc.A;PDB-ENSP_mappings:4jkc.B;PDB-ENSP_mappings:4jkd.A;PDB-ENSP_mappings:4jkd.B;PDB-ENSP_mappings:4jke.A;PDB-ENSP_mappings:4jke.B;PDB-ENSP_mappings:4jkf.A;PDB-ENSP_mappings:4jkf.B;PDB-ENSP_mappings:4jkg.A;PDB-ENSP_mappings:4jkg.B;PDB-ENSP_mappings:4jkh.A;PDB-ENSP_mappings:4jkh.B;PDB-ENSP_mappings:5mqf.A;PDB-ENSP_mappings:5o9z.A;PDB-ENSP_mappings:5xjc.A;PDB-ENSP_mappings:5yzg.A;PDB-ENSP_mappings:5z56.A;PDB-ENSP_mappings:5z57.A;PDB-ENSP_mappings:5z58.A;PDB-ENSP_mappings:6ah0.A;PDB-ENSP_mappings:6ahd.A;PDB-ENSP_mappings:6ff4.A;PDB-ENSP_mappings:6ff7.A;PDB-ENSP_mappings:6icz.A;PDB-ENSP_mappings:6id0.A;PDB-ENSP_mappings:6id1.A;PDB-ENSP_mappings:6qdv.A;PDB-ENSP_mappings:6qw6.5A;PDB-ENSP_mappings:6qx9.5A;Pfam:PF12134;PANTHER:PTHR11140;PANTHER:PTHR11140:SF1;Superfamily:SSF53098;CDD:cd13838 ENSP00000304350 36/43 ENST00000304992 Transcript 1.0 ENSG00000174231 HGNC:17340 MODERATE NM_006445.4 missense_variant probably_damaging(0.999) Unknown tolerated(0.11) Q6P2Q9.178 PRPF8 HGNC -1 1.0 UPI000006F2DD SNV PRPF8,missense_variant,p.G1903R,ENST00000572621,,c.5707G>A,MODERATE,YES,tolerated(0.11),probably_damaging(0.999),-1;PRPF8,missense_variant,p.G1903R,ENST00000304992,NM_006445.4,c.5707G>A,MODERATE,,tolerated(0.11),probably_damaging(0.999),-1;PRPF8,downstream_gene_variant,,ENST00000573725,,,MODIFIER,,,,-1;PRPF8,upstream_gene_variant,,ENST00000575116,,,MODIFIER,,,,-1;PRPF8,downstream_gene_variant,,ENST00000572445,,,MODIFIER,,,,-1;PRPF8,upstream_gene_variant,,ENST00000572723,,,MODIFIER,,,,-1;PRPF8,downstream_gene_variant,,ENST00000573681,,,MODIFIER,,,,-1;PRPF8,upstream_gene_variant,,ENST00000576585,,,MODIFIER,,,,-1 5806/7280 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 77 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 71 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PRPF8,missense_variant,p.G1858R,ENST00000703541.1,c.5572G>A,MODERATE,;PRPF8,non_coding_transcript_exon_variant,,ENST00000703539.1,n.2021G>A,MODIFIER,;PRPF8,missense_variant,p.G1854R,ENST00000703540.1,c.5560G>A,MODERATE,;PRPF8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703538.1,c.*5430G>A,MODIFIER,;PRPF8,synonymous_variant,p.S485=,ENST00000703537.1,c.1455G>A,LOW,;PRPF8,missense_variant,p.G1843R,ENST00000573725.2,c.5527G>A,MODERATE,;PRPF8,missense_variant,p.G1903R,ENST00000572621.5,c.5707G>A,MODERATE,;PRPF8,missense_variant,p.G1903R,ENST00000304992.11,c.5707G>A,MODERATE,YES +FXR2 9513 BI GRCh38 17 7595872 7595872 + synonymous_variant Silent SNP G G A rs779325705 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 10 c.783C>T p.Thr261= p.T261= ENST00000250113.12 NM_004860.4 261 acC/acT 8/17 P1 A T protein_coding YES CCDS45604.1 783/2022 ATGGCGGTCAC Gene3D:3.30.1370.10;Pfam:PF00013;PROSITE_profiles:PS50084;PANTHER:PTHR10603;PANTHER:PTHR10603:SF3;SMART:SM00322;Superfamily:SSF54791;CDD:cd00105 ENSP00000250113 8/17 rs779325705 ENST00000250113 Transcript ENSG00000129245 HGNC:4024 LOW NM_004860.4 0.0001652 gnomAD_OTH synonymous_variant 1.0 Unknown P51116.184 FXR2 HGNC -1 1.0 UPI0000072727 SNV FXR2,synonymous_variant,p.T261=,ENST00000250113,NM_004860.4,c.783C>T,LOW,YES,,,-1;MPDU1,downstream_gene_variant,,ENST00000423172,,,MODIFIER,,,,1;MPDU1,downstream_gene_variant,,ENST00000584378,,,MODIFIER,,,,1;FXR2,upstream_gene_variant,,ENST00000573057,,,MODIFIER,,,,-1;FXR2,non_coding_transcript_exon_variant,,ENST00000574490,,n.609C>T,MODIFIER,,,,-1;FXR2,non_coding_transcript_exon_variant,,ENST00000573957,,n.151C>T,MODIFIER,,,,-1;FXR2,upstream_gene_variant,,ENST00000571079,,,MODIFIER,,,,-1 1148/2987 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.611e-05 6.458e-05 0.0 0.0 0.0 0.0 5.31e-05 0.0001652 3.268e-05 3.383450166438706e-05 7.304250175366178e-05 0.0 0.0 0.0 0.0 0.0 afr 7.304250175366178e-05 0.0 3.087369987042621e-05 0.0 0.0 0 57 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FXR2,non_coding_transcript_exon_variant,,ENST00000574490.1,n.609C>T,MODIFIER,;FXR2,non_coding_transcript_exon_variant,,ENST00000573957.1,n.151C>T,MODIFIER,;FXR2,synonymous_variant,p.T261=,ENST00000250113.12,c.783C>T,LOW,YES;FXR2,synonymous_variant,p.T334=,ENST00000704984.1,c.1002C>T,LOW, +DNAH2 146754 BI GRCh38 17 7792796 7792796 + missense_variant Missense_Mutation SNP G G A rs771140126 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 26 10 c.7285G>A p.Val2429Ile p.V2429I ENST00000389173.6 2429 Gtt/Att 46/85 P1 A V/I protein_coding CCDS32551.1 7285/13284 AGAGCGTTCTG Gene3D:3.40.50.300;Pfam:PF12775;PANTHER:PTHR10676;PANTHER:PTHR10676:SF183;SMART:SM00382;Superfamily:SSF52540;CDD:cd00009 ENSP00000373825 46/85 rs771140126;COSV66720969 ENST00000389173 Transcript ENSG00000183914 HGNC:2948 MODERATE 8.794e-06 gnomAD_NFE missense_variant 0;1 benign(0.304) Unknown tolerated(0.18) 0;1 Q9P225.136 DNAH2 HGNC 1 2.0 UPI00005B2F0D Q9P225-1 SNV DNAH2,missense_variant,p.V2429I,ENST00000572933,NM_020877.4,c.7285G>A,MODERATE,YES,tolerated(0.18),benign(0.304),1;DNAH2,missense_variant,p.V2429I,ENST00000389173,,c.7285G>A,MODERATE,,tolerated(0.18),benign(0.304),1 7299/13505 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.794e-06 0.0 0.0 6.758670224371599e-06 2.4310800654347983e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 59 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DNAH2,missense_variant,p.V2429I,ENST00000389173.6,c.7285G>A,MODERATE,;DNAH2,missense_variant,p.V2429I,ENST00000572933.6,c.7285G>A,MODERATE,YES +ARHGEF15 22899 BI GRCh38 17 8318575 8318575 + synonymous_variant Silent SNP C C T rs779827070 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 7 9 c.1785C>T p.Ile595= p.I595= ENST00000361926.8 NM_173728.4 595 atC/atT 11/16 P1 T I protein_coding YES CCDS11139.1 1785/2526 ATCATCGAGCG COSM3821101 Gene3D:1.20.900.10;Pfam:PF00621;PROSITE_profiles:PS50010;PANTHER:PTHR12845;PANTHER:PTHR12845:SF7;SMART:SM00325;Superfamily:SSF48065;CDD:cd00160 ENSP00000355026 11/16 rs779827070;COSV62724633;COSV62725454 ENST00000361926 Transcript ENSG00000198844 HGNC:15590 LOW NM_173728.4 0.0001737 gnomAD_AMR synonymous_variant 0;1;1 1.0 Unknown 0;1;1 O94989.155 ARHGEF15 HGNC 1 A0A0S2Z547.26 1.0 UPI000013D2C0 SNV ARHGEF15,synonymous_variant,p.I595=,ENST00000361926,NM_173728.4,c.1785C>T,LOW,YES,,,1;ARHGEF15,synonymous_variant,p.I595=,ENST00000421050,NM_025014.1,c.1785C>T,LOW,,,,1;ARHGEF15,synonymous_variant,p.I416=,ENST00000647883,,c.1248C>T,LOW,,,,1;ARHGEF15,upstream_gene_variant,,ENST00000582060,,,MODIFIER,,,,1;ARHGEF15,downstream_gene_variant,,ENST00000455564,,,MODIFIER,,,,1;ARHGEF15,downstream_gene_variant,,ENST00000578286,,,MODIFIER,,,,1;ARHGEF15,downstream_gene_variant,,ENST00000581809,,,MODIFIER,,,,1;AC135178.2,non_coding_transcript_exon_variant,,ENST00000458568,,n.138G>A,MODIFIER,YES,,,-1 1937/4196 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.181e-05 6.163e-05 0.0001737 0.0 0.0001631 0.0 1.763e-05 0.0001636 0.0 1.3521699656848796e-05 0.0 0.0 6.628660048590973e-05 0.0 0.0002014500059885 0.0 0.0 0.0 0.0 0.0 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ENSG00000226871,non_coding_transcript_exon_variant,,ENST00000458568.1,n.138G>A,MODIFIER,YES;ARHGEF15,synonymous_variant,p.I416=,ENST00000647883.1,c.1248C>T,LOW,;ARHGEF15,synonymous_variant,p.I595=,ENST00000421050.2,c.1785C>T,LOW,;ARHGEF15,synonymous_variant,p.I595=,ENST00000361926.8,c.1785C>T,LOW,YES +CFAP52 146845 BI GRCh38 17 9628802 9628802 + missense_variant Missense_Mutation SNP G G A rs780939657 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 46 13 c.1156G>A p.Gly386Ser p.G386S ENST00000352665.10 NM_145054.5 386 Ggc/Agc 9/14 P1 A G/S protein_coding YES CCDS11149.2 1156/1863 GGGACGGCAAA Gene3D:2.130.10.10;PROSITE_profiles:PS50294;PANTHER:PTHR13720;PANTHER:PTHR13720:SF14;SMART:SM00320;Superfamily:SSF50978 ENSP00000339449 9/14 rs780939657 ENST00000352665 Transcript 1.0 ENSG00000166596 HGNC:16053 MODERATE NM_145054.5 0.0002613 gnomAD_SAS missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q8N1V2.150 CFAP52 HGNC 1 1.0 UPI00001AECC1 Q8N1V2-1 SNV CFAP52,missense_variant,p.G386S,ENST00000352665,NM_145054.5,c.1156G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;CFAP52,missense_variant,p.G318S,ENST00000396219,NM_001080556.2,c.952G>A,MODERATE,,deleterious(0),probably_damaging(1),1;CFAP52,upstream_gene_variant,,ENST00000576714,,,MODIFIER,,,,1;CFAP52,3_prime_UTR_variant,,ENST00000576630,,c.*1217G>A,MODIFIER,,,,1 1210/2166 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.58e-05 6.152e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0002613 2.029360075539444e-05 4.8661800974514335e-05 0.0 0.0 0.0 0.0 0.0 afr 4.8661800974514335e-05 0.0 0.0 0.0 0.0002090299967676 0 77 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CFAP52,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000576630.5,c.*1217G>A,MODIFIER,;CFAP52,missense_variant,p.G386S,ENST00000352665.10,c.1156G>A,MODERATE,YES;CFAP52,missense_variant,p.G318S,ENST00000396219.7,c.952G>A,MODERATE, +MED9 55090 BI GRCh38 17 17491388 17491388 + missense_variant Missense_Mutation SNP G G A rs1342679748 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 30 25 c.334G>A p.Glu112Lys p.E112K ENST00000268711.4 NM_018019.3 112 Gaa/Aaa 2/2 P1 A E/K protein_coding YES CCDS11184.1 334/441 GCCCCGAACAG COSM976108 Pfam:PF07544;PANTHER:PTHR20844;Superfamily:SSF140718;Low_complexity_(Seg):seg ENSP00000268711 2/2 rs1342679748;COSV51957529 ENST00000268711 Transcript ENSG00000141026 HGNC:25487 MODERATE NM_018019.3 8.8e-06 gnomAD_NFE missense_variant 0;1 1.0 possibly_damaging(0.454) Unknown deleterious(0.01) 0;1 Q9NWA0.140 MED9 HGNC 1 1.0 UPI000006F39B SNV MED9,missense_variant,p.E112K,ENST00000268711,NM_018019.3,c.334G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.454),1;RASD1,downstream_gene_variant,,ENST00000225688,NM_016084.5,,MODIFIER,YES,,,-1;RASD1,downstream_gene_variant,,ENST00000579152,NM_001199989.2,,MODIFIER,,,,-1;MED9,downstream_gene_variant,,ENST00000624097,,,MODIFIER,,,,1;MED9,3_prime_UTR_variant,,ENST00000581315,,c.*219G>A,MODIFIER,,,,1 376/2209 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.8e-06 0.0 0.0 0 98 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 55 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MED9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000581315.1,c.*219G>A,MODIFIER,;MED9,missense_variant,p.E112K,ENST00000268711.4,c.334G>A,MODERATE,YES +MAP2K3 5606 BI GRCh38 17 21298480 21298480 + splice_donor_variant Splice_Site SNP G G A rs368105298 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 90 20 c.116+1G>A p.X39_splice p.X39_splice ENST00000342679.9 NM_145109.3 39 P1 A protein_coding YES CCDS11217.1 CCCACGTGAGT COSM3402664;COSM3402665 ENSP00000345083 0.000227 0.0 rs368105298;COSV57575118 ENST00000342679 Transcript NonExonic ENSG00000034152 HGNC:6843 HIGH 2/11 NM_145109.3 0.000227 AA splice_donor_variant 0;1 1.0 Unknown 0;1 P46734.205 MAP2K3 HGNC 1 Q6FI23.129 1.0 UPI000012F48C P46734-1 SNV MAP2K3,splice_donor_variant,p.X10_splice,ENST00000316920,NM_001316332.2,c.29+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,p.X39_splice,ENST00000342679,NM_145109.3,c.116+1G>A,HIGH,YES,,,1;MAP2K3,splice_donor_variant,p.X10_splice,ENST00000361818,NM_002756.4,c.29+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,p.X10_splice,ENST00000526076,,c.29+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,p.X10_splice,ENST00000613338,,c.29+1G>A,HIGH,,,,1;MAP2K3,downstream_gene_variant,,ENST00000529517,,,MODIFIER,,,,1;MAP2K3,downstream_gene_variant,,ENST00000627447,,,MODIFIER,,,,1;MAP2K3,splice_donor_variant,,ENST00000395491,,c.*100+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,,ENST00000479129,,c.*70+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,p.X39_splice,ENST00000496046,,c.116+1G>A,HIGH,,,,1;MAP2K3,splice_donor_variant,,ENST00000583508,,n.326+1G>A,HIGH,,,,1;MAP2K3,downstream_gene_variant,,ENST00000483928,,,MODIFIER,,,,1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.783e-05 0.0001845 0.0 0.0 5.437e-05 0.0 8.79e-06 0.0 6.533e-05 6.754839705536142e-05 0.0001700599968899 0.0 6.619890336878598e-05 0.0 0.0 0.0 afr 0.0001700599968899 0.0 1.5426900063175708e-05 0.0 0.0002080730046145 0 145 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 110 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAP2K3,splice_donor_variant,p.X10_splice,ENST00000316920.10,c.29+1G>A,HIGH,;MAP2K3,splice_donor_variant,p.X10_splice,ENST00000526076.6,c.29+1G>A,HIGH,;MAP2K3,splice_donor_variant,p.X10_splice,ENST00000361818.9,c.29+1G>A,HIGH,;MAP2K3,splice_donor_variant,NMD_transcript_variant,p.X39_splice,ENST00000496046.5,c.116+1G>A,HIGH,;MAP2K3,splice_donor_variant,p.X39_splice,ENST00000342679.9,c.116+1G>A,HIGH,YES;MAP2K3,splice_donor_variant,NMD_transcript_variant,,ENST00000479129.5,c.*70+1G>A,HIGH,;MAP2K3,splice_donor_variant,,ENST00000583508.1,n.326+1G>A,HIGH,;MAP2K3,splice_donor_variant,NMD_transcript_variant,,ENST00000395491.6,c.*100+1G>A,HIGH, +SPAG5 10615 BI GRCh38 17 28585864 28585864 + synonymous_variant,splice_region_variant Silent SNP C C T rs1318352378 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 100 24 c.1740G>A p.Ala580= p.A580= ENST00000321765.10 NM_006461.4 580 gcG/gcA 7/24 P1 T A protein_coding YES CCDS32594.1 1740/3582 CTTACCGCATC PANTHER:PTHR15347 ENSP00000323300 7/24 rs1318352378 ENST00000321765 Transcript ENSG00000076382 HGNC:13452 LOW NM_006461.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS splice_region_variant 1.0 Unknown Q96R06.156 SPAG5 HGNC -1 1.0 UPI0000073414 SNV SPAG5,splice_region_variant,p.A580=,ENST00000321765,NM_006461.4,c.1740G>A,LOW,YES,,,-1;SPAG5,splice_region_variant,p.A120=,ENST00000584206,,c.360G>A,LOW,,,,-1;AC005726.1,intron_variant,,ENST00000531839,,c.525-1612G>A,MODIFIER,YES,,,-1;SPAG5,splice_region_variant,p.A45=,ENST00000580083,,c.135G>A,LOW,,,,-1;AC005726.1,intron_variant,,ENST00000481916,,c.*1195+18187G>A,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000378976,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000577259,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000578230,,,MODIFIER,,,,-1 1819/3786 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 142 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 124 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SPAG5,missense_variant,splice_region_variant,p.R120Q,ENST00000584206.1,c.359G>A,MODERATE,;ENSG00000258472,intron_variant,,ENST00000531839.5,c.525-1612G>A,MODIFIER,YES;SPAG5,synonymous_variant,splice_region_variant,NMD_transcript_variant,p.A45=,ENST00000580083.6,c.135G>A,LOW,;SPAG5,synonymous_variant,splice_region_variant,p.A580=,ENST00000321765.10,c.1740G>A,LOW,YES;RSKR,intron_variant,NMD_transcript_variant,,ENST00000481916.6,c.*1195+18187G>A,MODIFIER, +NUFIP2 57532 BI GRCh38 17 29286299 29286299 + synonymous_variant Silent SNP G G A rs150088850 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 61 17 c.1695C>T p.Tyr565= p.Y565= ENST00000225388.9 NM_020772.3 565 taC/taT 2/4 P1 A Y protein_coding YES CCDS32600.1 1695/2088 AGCTCGTAAGC COSM560461 Pfam:PF15293;PANTHER:PTHR28333;PANTHER:PTHR28333:SF2 ENSP00000225388 0.0 0.0002326 2/4 rs150088850 ENST00000225388 Transcript ENSG00000108256 HGNC:17634 LOW NM_020772.3 0.0002326 EA synonymous_variant 1.0 Unknown Q7Z417.144 NUFIP2 HGNC -1 1.0 UPI00001B078D Q7Z417-1 SNV NUFIP2,synonymous_variant,p.Y565=,ENST00000225388,NM_020772.3,c.1695C>T,LOW,YES,,,-1;NUFIP2,intron_variant,,ENST00000579665,,c.277+7484C>T,MODIFIER,,,,-1 1784/10877 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.386e-05 0.0 2.891e-05 9.921e-05 0.0 0.0 1.758e-05 0.0 6.533e-05 2.028400012932252e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.62948992208112e-05 0.0 4.62948992208112e-05 0.0 0.0 0 79 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 78 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NUFIP2,intron_variant,,ENST00000579665.1,c.277+7484C>T,MODIFIER,;NUFIP2,synonymous_variant,p.Y565=,ENST00000225388.9,c.1695C>T,LOW,YES +GIT1 28964 BI GRCh38 17 29575139 29575139 + synonymous_variant Silent SNP G G A rs745617945 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 18 c.2013C>T p.Phe671= p.F671= ENST00000225394.8 NM_014030.4 671 ttC/ttT 19/20 A2 A F protein_coding CCDS11250.1 2013/2286 GGCACGAAGCT Gene3D:1.20.120.330;Pfam:PF12205;PANTHER:PTHR46097;PANTHER:PTHR46097:SF1 ENSP00000225394 19/20 rs745617945;COSV99838480 ENST00000225394 Transcript ENSG00000108262 HGNC:4272 LOW NM_014030.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 0;1 Unknown 0;1 Q9Y2X7.204 GIT1 HGNC -1 1.0 UPI000013C867 Q9Y2X7-1 SNV GIT1,synonymous_variant,p.F671=,ENST00000225394,NM_014030.4,c.2013C>T,LOW,,,,-1;GIT1,synonymous_variant,p.F680=,ENST00000394869,NM_001085454.2,c.2040C>T,LOW,YES,,,-1;GIT1,synonymous_variant,p.F657=,ENST00000581348,,c.1971C>T,LOW,,,,-1;GIT1,synonymous_variant,p.F671=,ENST00000579937,,c.2013C>T,LOW,,,,-1;GIT1,synonymous_variant,p.F134=,ENST00000578266,,c.402C>T,LOW,,,,-1;TP53I13,downstream_gene_variant,,ENST00000301057,NM_001346082.1&NM_001346077.1&NM_001346078.1&NM_138349.4&NM_001346081.2&NM_001346079.2,,MODIFIER,YES,,,1;TP53I13,downstream_gene_variant,,ENST00000378818,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000578749,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000580183,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000581411,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000582829,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000583940,,,MODIFIER,,,,1;GIT1,downstream_gene_variant,,ENST00000585148,,,MODIFIER,,,,-1;GIT1,3_prime_UTR_variant,,ENST00000578670,,c.*7C>T,MODIFIER,,,,-1;GIT1,non_coding_transcript_exon_variant,,ENST00000473217,,n.1962C>T,MODIFIER,,,,-1;GIT1,downstream_gene_variant,,ENST00000491377,,,MODIFIER,,,,-1;TP53I13,downstream_gene_variant,,ENST00000577934,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000579674,,,MODIFIER,,,,1;GIT1,downstream_gene_variant,,ENST00000581925,,,MODIFIER,,,,-1;GIT1,downstream_gene_variant,,ENST00000586574,,,MODIFIER,,,,-1;ABHD15-AS1,intron_variant,,ENST00000581474,,n.153+14440G>A,MODIFIER,YES,,,1;AC104564.3,downstream_gene_variant,,ENST00000579050,,,MODIFIER,YES,,,1 2283/3783 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 75 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GIT1,synonymous_variant,p.F134=,ENST00000578266.1,c.402C>T,LOW,;GIT1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000578670.5,c.*7C>T,MODIFIER,;GIT1,synonymous_variant,p.F671=,ENST00000579937.5,c.2013C>T,LOW,;GIT1,synonymous_variant,p.F657=,ENST00000581348.5,c.1971C>T,LOW,;GIT1,synonymous_variant,p.F680=,ENST00000394869.7,c.2040C>T,LOW,;GIT1,synonymous_variant,p.F671=,ENST00000225394.8,c.2013C>T,LOW,YES;GIT1,non_coding_transcript_exon_variant,,ENST00000473217.5,n.1962C>T,MODIFIER,;ABHD15-AS1,intron_variant,,ENST00000581474.1,n.153+14440G>A,MODIFIER,YES +GIT1 28964 BI GRCh38 17 29576343 29576343 + synonymous_variant Silent SNP G G A rs768836653 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 48 7 c.1488C>T p.Gly496= p.G496= ENST00000225394.8 NM_014030.4 496 ggC/ggT 14/20 A2 A G protein_coding CCDS11250.1 1488/2286 CTCCCGCCTGG PANTHER:PTHR46097;PANTHER:PTHR46097:SF1;MobiDB_lite:mobidb-lite ENSP00000225394 14/20 rs768836653 ENST00000225394 Transcript ENSG00000108262 HGNC:4272 LOW NM_014030.4 9.954e-05 gnomAD_ASJ synonymous_variant Unknown Q9Y2X7.204 GIT1 HGNC -1 1.0 UPI000013C867 Q9Y2X7-1 SNV GIT1,synonymous_variant,p.G496=,ENST00000225394,NM_014030.4,c.1488C>T,LOW,,,,-1;GIT1,synonymous_variant,p.G505=,ENST00000394869,NM_001085454.2,c.1515C>T,LOW,YES,,,-1;GIT1,synonymous_variant,p.G505=,ENST00000581348,,c.1515C>T,LOW,,,,-1;GIT1,synonymous_variant,p.G496=,ENST00000579937,,c.1488C>T,LOW,,,,-1;TP53I13,downstream_gene_variant,,ENST00000301057,NM_001346082.1&NM_001346077.1&NM_001346078.1&NM_138349.4&NM_001346081.2&NM_001346079.2,,MODIFIER,YES,,,1;TP53I13,downstream_gene_variant,,ENST00000378818,,,MODIFIER,,,,1;GIT1,upstream_gene_variant,,ENST00000578266,,,MODIFIER,,,,-1;TP53I13,downstream_gene_variant,,ENST00000578749,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000580183,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000581411,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000582829,,,MODIFIER,,,,1;TP53I13,downstream_gene_variant,,ENST00000583940,,,MODIFIER,,,,1;GIT1,downstream_gene_variant,,ENST00000585148,,,MODIFIER,,,,-1;GIT1,synonymous_variant,p.G31=,ENST00000578670,,c.93C>T,LOW,,,,-1;GIT1,non_coding_transcript_exon_variant,,ENST00000473217,,n.1278C>T,MODIFIER,,,,-1;GIT1,non_coding_transcript_exon_variant,,ENST00000491377,,n.441C>T,MODIFIER,,,,-1;TP53I13,downstream_gene_variant,,ENST00000577934,,,MODIFIER,,,,1;GIT1,downstream_gene_variant,,ENST00000579536,,,MODIFIER,,,,-1;TP53I13,downstream_gene_variant,,ENST00000579674,,,MODIFIER,,,,1;GIT1,downstream_gene_variant,,ENST00000581925,,,MODIFIER,,,,-1;GIT1,downstream_gene_variant,,ENST00000586574,,,MODIFIER,,,,-1;ABHD15-AS1,intron_variant,,ENST00000581474,,n.153+15644G>A,MODIFIER,YES,,,1 1758/3783 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.595e-05 0.0 0.0 9.954e-05 0.0 0.0 2.646e-05 0.0 0.0 1.3517899787984788e-05 2.4310800654347983e-05 0.0 0.0 0.0003028470091521 0.0 0.0 0.0 0.0 0.0 0.0 0 96 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 55 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GIT1,non_coding_transcript_exon_variant,,ENST00000491377.1,n.441C>T,MODIFIER,;GIT1,missense_variant,NMD_transcript_variant,p.A31V,ENST00000578670.5,c.92C>T,MODERATE,;GIT1,synonymous_variant,p.G496=,ENST00000579937.5,c.1488C>T,LOW,;GIT1,synonymous_variant,p.G505=,ENST00000581348.5,c.1515C>T,LOW,;GIT1,synonymous_variant,p.G505=,ENST00000394869.7,c.1515C>T,LOW,;GIT1,synonymous_variant,p.G496=,ENST00000225394.8,c.1488C>T,LOW,YES;GIT1,non_coding_transcript_exon_variant,,ENST00000473217.5,n.1278C>T,MODIFIER,;ABHD15-AS1,intron_variant,,ENST00000581474.1,n.153+15644G>A,MODIFIER,YES +CSF3 1440 BI GRCh38 17 40016854 40016854 + synonymous_variant Silent SNP C C T rs774912212 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 6 c.519C>T p.Phe173= p.F173= ENST00000225474.6 NM_000759.4 173 ttC/ttT 5/5 P4 T F protein_coding YES CCDS11357.1 519/624 benign GCCTTCGCCTC COSM1302754 Gene3D:1.20.1250.10;PDB-ENSP_mappings:1cd9.A;PDB-ENSP_mappings:1cd9.C;PDB-ENSP_mappings:1gnc.A;PDB-ENSP_mappings:1pgr.A;PDB-ENSP_mappings:1pgr.C;PDB-ENSP_mappings:1pgr.E;PDB-ENSP_mappings:1pgr.G;PDB-ENSP_mappings:1rhg.A;PDB-ENSP_mappings:1rhg.B;PDB-ENSP_mappings:1rhg.C;PDB-ENSP_mappings:2d9q.A;PDB-ENSP_mappings:5gw9.A;PDB-ENSP_mappings:5gw9.B;PDB-ENSP_mappings:5gw9.C;PDB-ENSP_mappings:5gw9.D;PDB-ENSP_mappings:5zo6.X;Pfam:PF16647;PIRSF:PIRSF001935;PANTHER:PTHR10511;PANTHER:PTHR10511:SF2;SMART:SM00126;Superfamily:SSF47266 ENSP00000225474 5/5 rs774912212;COSV56641658 ENST00000225474 Transcript ENSG00000108342 HGNC:2438 LOW 0.003559 gnomAD_AMR synonymous_variant 1;1 1.0 Unknown 0;1 P09919.210 CSF3 HGNC 1 1.0 UPI0000128525 P09919-1 SNV CSF3,synonymous_variant,p.F166=,ENST00000331769,,c.498C>T,LOW,,,,1;CSF3,synonymous_variant,p.F173=,ENST00000225474,NM_000759.4,c.519C>T,LOW,YES,,,1;CSF3,synonymous_variant,p.F170=,ENST00000394149,NM_172219.3,c.510C>T,LOW,,,,1;CSF3,synonymous_variant,p.F130=,ENST00000577675,,c.390C>T,LOW,,,,1;CSF3,synonymous_variant,p.F137=,ENST00000394148,NM_172220.3&NM_001178147.2,c.411C>T,LOW,,,,1;CSF3,synonymous_variant,p.F134=,ENST00000583218,,c.402C>T,LOW,,,,1;MED24,downstream_gene_variant,,ENST00000356271,NM_001267797.2,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000394126,,,MODIFIER,YES,,,-1;MED24,downstream_gene_variant,,ENST00000394127,NM_001079518.2,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000394128,NM_014815.4,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000422942,,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000501516,NM_001330211.2,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000614384,,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000470126,,,MODIFIER,,,,-1;CSF3,3_prime_UTR_variant,,ENST00000579852,,c.*181C>T,MODIFIER,,,,1;CSF3,non_coding_transcript_exon_variant,,ENST00000479880,,n.858C>T,MODIFIER,,,,1;MED24,downstream_gene_variant,,ENST00000491466,,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000535508,,,MODIFIER,,,,-1;MED24,downstream_gene_variant,,ENST00000579364,,,MODIFIER,,,,-1;CSF3,downstream_gene_variant,,ENST00000582798,,,MODIFIER,,,,1;AC090844.3,upstream_gene_variant,,ENST00000583462,,,MODIFIER,YES,,,-1;AC090844.3,upstream_gene_variant,,ENST00000584649,,,MODIFIER,,,,-1 550/1509 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0005017 0.0 0.003559 0.0 0.0 0.0 8.805e-06 0.0003263 0.0 4.730690125143156e-05 0.0 0.0 0.0003975089930463 0.0 0.0 0.0 amr 0.0003975089930463 0.0 0.0 0.0004945599939674 0.0 0 46 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CSF3,synonymous_variant,p.F130=,ENST00000577675.1,c.390C>T,LOW,;CSF3,synonymous_variant,p.F137=,ENST00000394148.7,c.411C>T,LOW,;CSF3,non_coding_transcript_exon_variant,,ENST00000479880.1,n.858C>T,MODIFIER,;CSF3,synonymous_variant,p.F166=,ENST00000331769.6,c.498C>T,LOW,;CSF3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000579852.1,c.*181C>T,MODIFIER,;CSF3,synonymous_variant,p.F173=,ENST00000225474.6,c.519C>T,LOW,;CSF3,synonymous_variant,p.F170=,ENST00000394149.8,c.510C>T,LOW,YES;CSF3,synonymous_variant,p.F134=,ENST00000583218.5,c.402C>T,LOW, +CASC3 22794 BI GRCh38 17 40164154 40164154 + missense_variant Missense_Mutation SNP C C T rs1447750347 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 5 4 c.1459C>T p.Arg487Trp p.R487W ENST00000264645.12 NM_007359.5 487 Cgg/Tgg 7/14 P1 T R/W protein_coding YES CCDS11362.1 1459/2112 AACCACGGGAA PDB-ENSP_mappings:5xjc.x;PDB-ENSP_mappings:5yzg.x;PDB-ENSP_mappings:6icz.x;PANTHER:PTHR13434 ENSP00000264645 7/14 rs1447750347 ENST00000264645 Transcript ENSG00000108349 HGNC:17040 MODERATE NM_007359.5 missense_variant 1.0 probably_damaging(0.99) Unknown deleterious_low_confidence(0) O15234.187 CASC3 HGNC 1 1.0 UPI000000DAAA SNV CASC3,missense_variant,p.R487W,ENST00000264645,NM_007359.5,c.1459C>T,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.99),1;CASC3,downstream_gene_variant,,ENST00000584997,,,MODIFIER,,,,1;MIR6866,downstream_gene_variant,,ENST00000638146,,,MODIFIER,YES,,,1;CASC3,missense_variant,p.R82W,ENST00000577605,,c.244C>T,MODERATE,,deleterious(0.01),probably_damaging(0.979),1;CASC3,3_prime_UTR_variant,,ENST00000474190,,c.*165C>T,MODIFIER,,,,1;CASC3,non_coding_transcript_exon_variant,,ENST00000418132,,n.1690C>T,MODIFIER,,,,1;CASC3,upstream_gene_variant,,ENST00000394114,,,MODIFIER,,,,1;CASC3,upstream_gene_variant,,ENST00000579238,,,MODIFIER,,,,1;CASC3,downstream_gene_variant,,ENST00000581849,,,MODIFIER,,,,1;CASC3,upstream_gene_variant,,ENST00000583902,,,MODIFIER,,,,1 1471/3890 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.761690201528836e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0004945599939674 0.0 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 9 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CASC3,synonymous_variant,NMD_transcript_variant,p.H81=,ENST00000577605.1,c.243C>T,LOW,;CASC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000474190.1,c.*165C>T,MODIFIER,;CASC3,missense_variant,p.R487W,ENST00000264645.12,c.1459C>T,MODERATE,YES;CASC3,non_coding_transcript_exon_variant,,ENST00000418132.7,n.1690C>T,MODIFIER, +KAT2A 2648 BI GRCh38 17 42119389 42119389 + missense_variant Missense_Mutation SNP C C T rs781796429 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 32 c.929G>A p.Arg310His p.R310H ENST00000225916.10 NM_021078.3 310 cGc/cAc 6/18 P1 T R/H protein_coding YES CCDS11417.1 929/2514 CGTAGCGGGGG COSM5443039 Pfam:PF06466;PIRSF:PIRSF003048;PANTHER:PTHR45750;PANTHER:PTHR45750:SF1 ENSP00000225916 6/18 rs781796429;COSV56790563 ENST00000225916 Transcript ENSG00000108773 HGNC:4201 MODERATE NM_021078.3 3.522e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0.076) Unknown tolerated(0.56) 0;1 Q92830.214 KAT2A HGNC -1 1.0 UPI000000D978 Q92830-1 SNV KAT2A,missense_variant,p.R310H,ENST00000225916,NM_021078.3&NM_001376227.1,c.929G>A,MODERATE,YES,tolerated(0.56),benign(0.076),-1;HSPB9,upstream_gene_variant,,ENST00000565659,NM_033194.3,,MODIFIER,YES,,,1;AC099811.2,downstream_gene_variant,,ENST00000592574,,,MODIFIER,YES,,,-1;KAT2A,missense_variant,p.R228H,ENST00000465682,,c.683G>A,MODERATE,,tolerated(0.74),benign(0.076),-1;AC099811.2,downstream_gene_variant,,ENST00000585562,,,MODIFIER,,,,-1;KAT2A,upstream_gene_variant,,ENST00000586972,,,MODIFIER,,,,-1;KAT2A,upstream_gene_variant,,ENST00000588759,,,MODIFIER,,,,-1;AC099811.2,downstream_gene_variant,,ENST00000592248,,,MODIFIER,,,,-1;KAT2A,upstream_gene_variant,,ENST00000592310,,,MODIFIER,,,,-1 992/3115 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.991e-05 0.0 2.897e-05 0.0 0.0 0.0 3.522e-05 0.0 0.0 0 105 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 67 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KAT2A,missense_variant,NMD_transcript_variant,p.R228H,ENST00000465682.5,c.683G>A,MODERATE,;KAT2A,missense_variant,p.R310H,ENST00000225916.10,c.929G>A,MODERATE,YES +HSD17B1 3292 BI GRCh38 17 42554479 42554479 + missense_variant Missense_Mutation SNP T T C novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 4 12 c.614T>C p.Leu205Pro p.L205P ENST00000585807.6 NM_000413.4 205 cTg/cCg 5/6 P4 C L/P protein_coding CCDS11428.1 614/987 GGTGCTGGACC PDB-ENSP_mappings:1a27.A;PDB-ENSP_mappings:1bhs.A;PDB-ENSP_mappings:1dht.A;PDB-ENSP_mappings:1equ.A;PDB-ENSP_mappings:1equ.B;PDB-ENSP_mappings:1fds.A;PDB-ENSP_mappings:1fdt.A;PDB-ENSP_mappings:1fdu.A;PDB-ENSP_mappings:1fdu.B;PDB-ENSP_mappings:1fdu.C;PDB-ENSP_mappings:1fdu.D;PDB-ENSP_mappings:1fdv.A;PDB-ENSP_mappings:1fdv.B;PDB-ENSP_mappings:1fdv.C;PDB-ENSP_mappings:1fdv.D;PDB-ENSP_mappings:1fdw.A;PDB-ENSP_mappings:1i5r.A;PDB-ENSP_mappings:1iol.A;PDB-ENSP_mappings:1jtv.A;PDB-ENSP_mappings:1qyv.A;PDB-ENSP_mappings:1qyw.A;PDB-ENSP_mappings:1qyx.A;Gene3D:3.40.50.720;PDB-ENSP_mappings:3dey.X;PDB-ENSP_mappings:3dhe.A;PDB-ENSP_mappings:3hb4.X;PDB-ENSP_mappings:3hb5.X;PDB-ENSP_mappings:3klm.X;PDB-ENSP_mappings:3klp.X;PDB-ENSP_mappings:3km0.A;PDB-ENSP_mappings:3km0.B;PDB-ENSP_mappings:6cgc.A;PDB-ENSP_mappings:6cgc.B;PDB-ENSP_mappings:6cge.A;PDB-ENSP_mappings:6cge.B;PDB-ENSP_mappings:6dtp.A;PDB-ENSP_mappings:6dtp.B;PDB-ENSP_mappings:6mnc.A;PDB-ENSP_mappings:6mnc.B;PDB-ENSP_mappings:6mne.A;PDB-ENSP_mappings:6mne.B;PIRSF:PIRSF000095;PANTHER:PTHR43391;PANTHER:PTHR43391:SF15;Superfamily:SSF51735;CDD:cd09806 ENSP00000466799 5/6 ENST00000585807 Transcript ENSG00000108786 HGNC:5210 MODERATE NM_000413.4 missense_variant benign(0.214) Unknown deleterious(0) P14061.210 HSD17B1 HGNC 1 1.0 UPI00001AE658 SNV HSD17B1,missense_variant,p.L205P,ENST00000585807,NM_000413.4,c.614T>C,MODERATE,,deleterious(0),benign(0.214),1;HSD17B1,missense_variant,p.L206P,ENST00000225929,NM_001330219.3,c.617T>C,MODERATE,YES,deleterious(0),probably_damaging(0.946),1;HSD17B1,3_prime_UTR_variant,,ENST00000590299,,c.*70T>C,MODIFIER,,,,1;HSD17B1,downstream_gene_variant,,ENST00000587280,,,MODIFIER,,,,1;HSD17B1,downstream_gene_variant,,ENST00000593215,,,MODIFIER,,,,1;AC067852.2,non_coding_transcript_exon_variant,,ENST00000590513,,n.270A>G,MODIFIER,YES,,,-1;AC067852.1,intron_variant,,ENST00000585572,,n.380-7140T>C,MODIFIER,YES,,,1 625/1274 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HSD17B1,missense_variant,p.L206P,ENST00000225929.5,c.617T>C,MODERATE,;HSD17B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000590299.5,c.*70T>C,MODIFIER,;HSD17B1,missense_variant,p.L205P,ENST00000585807.6,c.614T>C,MODERATE,YES;HSD17B1-AS1,non_coding_transcript_exon_variant,,ENST00000590513.3,n.363A>G,MODIFIER,YES;ENSG00000266929,intron_variant,,ENST00000585572.1,n.380-7140T>C,MODIFIER,YES +HDAC5 10014 BI GRCh38 17 44085024 44085024 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs2143119188 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 16 c.2182G>A p.Glu728Lys p.E728K ENST00000586802.5 728 Gag/Aag 15/27 P4 T E/K protein_coding CCDS45696.1 2182/3369 TACCTCGCACT Gene3D:3.40.800.20;Pfam:PF00850;PIRSF:PIRSF037911;PANTHER:PTHR45364;PANTHER:PTHR45364:SF2;Superfamily:SSF52768;CDD:cd10007 ENSP00000468004 15/27 COSV99870995 ENST00000586802 Transcript ENSG00000108840 HGNC:14068 MODERATE missense_variant 1 benign(0.26) Unknown deleterious(0.01) 1 Q9UQL6.207 HDAC5 HGNC -1 1.0 UPI0000201355 Q9UQL6-1 SNV HDAC5,missense_variant,p.E729K,ENST00000225983,NM_001015053.2,c.2185G>A,MODERATE,YES,deleterious(0.01),benign(0.169),-1;HDAC5,missense_variant,p.E728K,ENST00000586802,NM_005474.5&NM_001382393.1,c.2182G>A,MODERATE,,deleterious(0.01),benign(0.26),-1;HDAC5,intron_variant,,ENST00000336057,,c.2051-1170G>A,MODIFIER,,,,-1;HDAC5,downstream_gene_variant,,ENST00000588261,,,MODIFIER,,,,-1;HDAC5,splice_region_variant,,ENST00000592385,,n.1162G>A,LOW,,,,-1;HDAC5,splice_region_variant,,ENST00000593013,,n.332G>A,LOW,,,,-1;HDAC5,splice_region_variant,,ENST00000588419,,n.316G>A,LOW,,,,-1 2393/3662 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HDAC5,non_coding_transcript_exon_variant,,ENST00000588419.1,n.316G>A,MODIFIER,;HDAC5,non_coding_transcript_exon_variant,,ENST00000593013.5,n.332G>A,MODIFIER,;HDAC5,non_coding_transcript_exon_variant,,ENST00000592385.5,n.1162G>A,MODIFIER,;HDAC5,missense_variant,splice_region_variant,p.E728K,ENST00000586802.5,c.2182G>A,MODERATE,;HDAC5,intron_variant,,ENST00000336057.9,c.2051-1170G>A,MODIFIER,;HDAC5,missense_variant,splice_region_variant,p.E728K,ENST00000715273.1,c.2182G>A,MODERATE,;HDAC5,missense_variant,splice_region_variant,p.E728K,ENST00000682912.1,c.2182G>A,MODERATE,YES;HDAC5,missense_variant,splice_region_variant,p.E729K,ENST00000225983.10,c.2185G>A,MODERATE, +HDAC5 10014 BI GRCh38 17 44093715 44093715 + missense_variant Missense_Mutation SNP G G A rs746035403 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 3 c.214C>T p.Arg72Trp p.R72W ENST00000586802.5 72 Cgg/Tgg 4/27 P4 A R/W protein_coding CCDS45696.1 214/3369 CTCCCGCAGTG COSM4066861 Pfam:PF12203;PIRSF:PIRSF037911;PANTHER:PTHR45364;PANTHER:PTHR45364:SF2;CDD:cd10164 ENSP00000468004 4/27 rs746035403;COSV56817977 ENST00000586802 Transcript ENSG00000108840 HGNC:14068 MODERATE 0.0001056 gnomAD_ASJ missense_variant 0;1 probably_damaging(0.996) Unknown deleterious_low_confidence(0.03) 0;1 Q9UQL6.207 HDAC5 HGNC -1 1.0 UPI0000201355 Q9UQL6-1 SNV HDAC5,missense_variant,p.R73W,ENST00000225983,NM_001015053.2,c.217C>T,MODERATE,YES,deleterious_low_confidence(0.03),probably_damaging(0.994),-1;HDAC5,missense_variant,p.R72W,ENST00000336057,,c.214C>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1;HDAC5,missense_variant,p.R72W,ENST00000586802,NM_005474.5&NM_001382393.1,c.214C>T,MODERATE,,deleterious_low_confidence(0.03),probably_damaging(0.996),-1;HDAC5,missense_variant,p.R63W,ENST00000588703,,c.187C>T,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;HDAC5,downstream_gene_variant,,ENST00000587135,,,MODIFIER,,,,-1;HDAC5,upstream_gene_variant,,ENST00000588261,,,MODIFIER,,,,-1;HDAC5,downstream_gene_variant,,ENST00000591714,,,MODIFIER,,,,-1;HDAC5,upstream_gene_variant,,ENST00000587776,,,MODIFIER,,,,-1;HDAC5,upstream_gene_variant,,ENST00000592385,,,MODIFIER,,,,-1 425/3662 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.743e-05 0.0 0.0 0.0001056 0.0 0.0 2.935e-05 0.0 0.0 0 16 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 14 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HDAC5,missense_variant,p.R63W,ENST00000588703.5,c.187C>T,MODERATE,;HDAC5,missense_variant,p.R72W,ENST00000586802.5,c.214C>T,MODERATE,;HDAC5,missense_variant,p.R72W,ENST00000336057.9,c.214C>T,MODERATE,;HDAC5,missense_variant,p.R72W,ENST00000715273.1,c.214C>T,MODERATE,;HDAC5,missense_variant,p.R72W,ENST00000682912.1,c.214C>T,MODERATE,YES;HDAC5,missense_variant,p.R73W,ENST00000225983.10,c.217C>T,MODERATE, +FMNL1 752 BI GRCh38 17 45243247 45243247 + missense_variant Missense_Mutation SNP C C T rs1302823411 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 7 c.2140C>T p.Arg714Trp p.R714W ENST00000331495.8 NM_005892.4 714 Cgg/Tgg 17/27 P1 T R/W protein_coding YES CCDS11497.1 2140/3303 CCAACCGGGCC Gene3D:1.20.58.2220;Pfam:PF02181;PROSITE_profiles:PS51444;PANTHER:PTHR45857;PANTHER:PTHR45857:SF2;SMART:SM00498;Superfamily:SSF101447 ENSP00000329219 17/27 rs1302823411;COSV100055955 ENST00000331495 Transcript ENSG00000184922 HGNC:1212 MODERATE NM_005892.4 2.64e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 O95466.177 FMNL1 HGNC 1 1.0 UPI0000246EE9 O95466-1 SNV FMNL1,missense_variant,p.R714W,ENST00000331495,NM_005892.4,c.2140C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;FMNL1,missense_variant,p.R292W,ENST00000587489,,c.874C>T,MODERATE,,deleterious(0),probably_damaging(1),1;FMNL1,missense_variant,p.R369W,ENST00000328118,,c.1105C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;FMNL1,missense_variant,p.R44W,ENST00000586643,,c.130C>T,MODERATE,,deleterious(0),probably_damaging(1),1;FMNL1,upstream_gene_variant,,ENST00000586092,,,MODIFIER,,,,1;FMNL1,upstream_gene_variant,,ENST00000589911,,,MODIFIER,,,,1;AC008105.2,downstream_gene_variant,,ENST00000420431,,,MODIFIER,,,,-1;AC008105.2,downstream_gene_variant,,ENST00000589518,,,MODIFIER,,,,-1;AC008105.2,downstream_gene_variant,,ENST00000591361,,,MODIFIER,,,,-1;FMNL1,downstream_gene_variant,,ENST00000592006,,,MODIFIER,,,,1;FMNL1,non_coding_transcript_exon_variant,,ENST00000587856,,n.2709C>T,MODIFIER,,,,1;AC008105.2,downstream_gene_variant,,ENST00000642422,,,MODIFIER,YES,,,-1;AC008105.1,upstream_gene_variant,,ENST00000393507,,,MODIFIER,,,,-1;MAP3K14-AS1,upstream_gene_variant,,ENST00000585346,,,MODIFIER,,,,1;AC008105.1,upstream_gene_variant,,ENST00000587534,,,MODIFIER,YES,,,-1;MAP3K14-AS1,upstream_gene_variant,,ENST00000588504,,,MODIFIER,,,,1;MAP3K14-AS1,upstream_gene_variant,,ENST00000590100,,,MODIFIER,,,,1;MAP3K14-AS1,upstream_gene_variant,,ENST00000591263,,,MODIFIER,,,,1;MAP3K14-AS1,upstream_gene_variant,,ENST00000592422,,,MODIFIER,,,,1;MAP3K14-AS1,upstream_gene_variant,,ENST00000655903,,,MODIFIER,,,,1;MAP3K14-AS1,upstream_gene_variant,,ENST00000657572,,,MODIFIER,,,,1 2380/4003 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.194e-05 0.0 0.0 0.0 0.0 0.0 2.64e-05 0.0 0.0 0 85 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FMNL1,missense_variant,p.R44W,ENST00000586643.5,c.130C>T,MODERATE,;FMNL1,non_coding_transcript_exon_variant,,ENST00000587856.1,n.2709C>T,MODIFIER,;FMNL1,missense_variant,p.R714W,ENST00000331495.8,c.2140C>T,MODERATE,YES;FMNL1,missense_variant,p.R714W,ENST00000587489.6,c.2140C>T,MODERATE, +CDC27 996 BI GRCh38 17 47181601 47181601 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 7 c.64C>T p.Arg22Ter p.R22* ENST00000066544.8 NM_001353049.2 22 Cga/Tga 2/19 A1 A R/* protein_coding CCDS11509.1 64/2475 ATCTCGGTAAG Gene3D:1.25.40.10;PDB-ENSP_mappings:4rg6.A;PDB-ENSP_mappings:4rg6.B;PDB-ENSP_mappings:4rg7.A;PDB-ENSP_mappings:4rg7.B;PDB-ENSP_mappings:4rg9.A;PDB-ENSP_mappings:4rg9.B;PDB-ENSP_mappings:4ui9.F;PDB-ENSP_mappings:4ui9.H;PDB-ENSP_mappings:5a31.F;PDB-ENSP_mappings:5a31.H;PDB-ENSP_mappings:5g04.F;PDB-ENSP_mappings:5g04.H;PDB-ENSP_mappings:5g05.F;PDB-ENSP_mappings:5g05.H;PDB-ENSP_mappings:5khr.F;PDB-ENSP_mappings:5khr.H;PDB-ENSP_mappings:5khu.F;PDB-ENSP_mappings:5khu.H;PDB-ENSP_mappings:5l9t.F;PDB-ENSP_mappings:5l9t.H;PDB-ENSP_mappings:5l9u.F;PDB-ENSP_mappings:5l9u.H;PDB-ENSP_mappings:5lcw.F;PDB-ENSP_mappings:5lcw.H;PDB-ENSP_mappings:6q6g.J;PDB-ENSP_mappings:6q6g.P;PDB-ENSP_mappings:6q6h.J;PDB-ENSP_mappings:6q6h.P;PDB-ENSP_mappings:6tlj.F;PDB-ENSP_mappings:6tlj.H;PDB-ENSP_mappings:6tm5.F;PDB-ENSP_mappings:6tm5.H;Pfam:PF12895;PANTHER:PTHR12558;PANTHER:PTHR12558:SF13 ENSP00000066544 2/19 ENST00000066544 Transcript ENSG00000004897 HGNC:1728 HIGH NM_001256.6 stop_gained Unknown P30260.210 CDC27 HGNC -1 1.0 UPI000012722D P30260-1 SNV CDC27,stop_gained,p.R22*,ENST00000066544,NM_001353049.2&NM_001293091.3&NM_001353035.2&NM_001256.6,c.64C>T,HIGH,,,,-1;CDC27,stop_gained,p.R22*,ENST00000531206,NM_001353050.2&NM_001114091.4,c.64C>T,HIGH,YES,,,-1;CDC27,stop_gained,p.R22*,ENST00000527547,NM_001353051.2&NM_001353047.2&NM_001293089.3,c.64C>T,HIGH,,,,-1;CDC27,stop_gained,p.R22*,ENST00000575483,,c.64C>T,HIGH,,,,-1;CDC27,non_coding_transcript_exon_variant,,ENST00000528748,,n.228C>T,MODIFIER,,,,-1;CDC27,non_coding_transcript_exon_variant,,ENST00000532575,,n.199C>T,MODIFIER,,,,-1;CDC27,stop_gained,p.R22*,ENST00000533415,,c.64C>T,HIGH,,,,-1;CDC27,stop_gained,p.R22*,ENST00000526866,,c.64C>T,HIGH,,,,-1;CDC27,stop_gained,p.R3*,ENST00000573550,,c.7C>T,HIGH,,,,-1;CDC27,stop_gained,p.R22*,ENST00000532893,,c.64C>T,HIGH,,,,-1;CDC27,non_coding_transcript_exon_variant,,ENST00000525495,,n.153C>T,MODIFIER,,,,-1;CDC27,non_coding_transcript_exon_variant,,ENST00000528147,,n.144C>T,MODIFIER,,,,-1 187/5830 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 23 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 30 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CDC27,non_coding_transcript_exon_variant,,ENST00000528147.1,n.144C>T,MODIFIER,;CDC27,non_coding_transcript_exon_variant,,ENST00000532575.1,n.199C>T,MODIFIER,;CDC27,non_coding_transcript_exon_variant,,ENST00000528748.5,n.228C>T,MODIFIER,;CDC27,stop_gained,NMD_transcript_variant,p.R22*,ENST00000532893.5,c.64C>T,HIGH,;CDC27,stop_gained,p.R22*,ENST00000575483.5,c.64C>T,HIGH,;CDC27,missense_variant,NMD_transcript_variant,p.P2L,ENST00000573550.5,c.5C>T,MODERATE,;CDC27,non_coding_transcript_exon_variant,,ENST00000525495.6,n.153C>T,MODIFIER,;CDC27,stop_gained,NMD_transcript_variant,p.R22*,ENST00000526866.5,c.64C>T,HIGH,;CDC27,stop_gained,p.R22*,ENST00000527547.5,c.64C>T,HIGH,;CDC27,stop_gained,NMD_transcript_variant,p.R22*,ENST00000533415.5,c.64C>T,HIGH,;CDC27,stop_gained,p.R22*,ENST00000531206.5,c.64C>T,HIGH,;CDC27,stop_gained,p.R22*,ENST00000066544.8,c.64C>T,HIGH,YES +KPNB1 3837 BI GRCh38 17 47665103 47665103 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 21 5 c.944C>T p.Ala315Val p.A315V ENST00000290158.9 NM_002265.6 315 gCg/gTg 9/22 P1 T A/V protein_coding CCDS11513.1 944/2631 TTATGCGAAGG Gene3D:1.25.10.10;PDB-ENSP_mappings:1f59.A;PDB-ENSP_mappings:1f59.B;PDB-ENSP_mappings:1ibr.B;PDB-ENSP_mappings:1ibr.D;PDB-ENSP_mappings:1m5n.S;PDB-ENSP_mappings:1o6o.A;PDB-ENSP_mappings:1o6o.B;PDB-ENSP_mappings:1o6o.C;PDB-ENSP_mappings:1o6p.A;PDB-ENSP_mappings:1o6p.B;PDB-ENSP_mappings:1qgk.A;PDB-ENSP_mappings:1qgr.A;PDB-ENSP_mappings:2p8q.A;PDB-ENSP_mappings:2q5d.A;PDB-ENSP_mappings:2q5d.B;PDB-ENSP_mappings:2qna.A;PDB-ENSP_mappings:3lww.A;PDB-ENSP_mappings:3lww.C;PDB-ENSP_mappings:3w5k.A;PDB-ENSP_mappings:6n88.B;PDB-ENSP_mappings:6n89.A;PANTHER:PTHR10527;PANTHER:PTHR10527:SF1;Superfamily:SSF48371 ENSP00000290158 9/22 ENST00000290158 Transcript ENSG00000108424 HGNC:6400 MODERATE NM_002265.6 missense_variant benign(0.25) Unknown tolerated(0.07) Q14974.219 KPNB1 HGNC 1 1.0 UPI0000001C21 Q14974-1 SNV KPNB1,missense_variant,p.A315V,ENST00000583648,,c.944C>T,MODERATE,YES,tolerated(0.07),benign(0.25),1;KPNB1,missense_variant,p.A315V,ENST00000290158,NM_002265.6,c.944C>T,MODERATE,,tolerated(0.07),benign(0.25),1;KPNB1,missense_variant,p.A170V,ENST00000535458,,c.509C>T,MODERATE,,tolerated(0.05),benign(0.25),1;KPNB1,missense_variant,p.A170V,ENST00000540627,NM_001276453.2,c.509C>T,MODERATE,,tolerated(0.05),benign(0.25),1;KPNB1,intron_variant,,ENST00000582097,,c.439+1925C>T,MODIFIER,,,,1;KPNB1,upstream_gene_variant,,ENST00000583013,,,MODIFIER,,,,1;KPNB1,downstream_gene_variant,,ENST00000577918,,,MODIFIER,,,,1;KPNB1,non_coding_transcript_exon_variant,,ENST00000677036,,n.545C>T,MODIFIER,,,,1;KPNB1,upstream_gene_variant,,ENST00000677341,,,MODIFIER,,,,1 1270/6058 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 41 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 26 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KPNB1,non_coding_transcript_exon_variant,,ENST00000677036.1,n.545C>T,MODIFIER,;KPNB1,intron_variant,,ENST00000582097.5,c.439+1925C>T,MODIFIER,;KPNB1,missense_variant,p.A170V,ENST00000540627.5,c.509C>T,MODERATE,;KPNB1,missense_variant,p.A315V,ENST00000290158.9,c.944C>T,MODERATE,YES;KPNB1,missense_variant,p.A315V,ENST00000583648.6,c.944C>T,MODERATE,;KPNB1,missense_variant,p.A170V,ENST00000535458.6,c.509C>T,MODERATE, +GIP 2695 BI GRCh38 17 48964409 48964409 + missense_variant Missense_Mutation SNP G G A rs367741847 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 51 14 c.158C>T p.Ala53Val p.A53V ENST00000357424.2 NM_004123.3 53 gCg/gTg 3/6 P1 A A/V protein_coding YES CCDS11542.1 158/462 CTTCCGCGTAC PDB-ENSP_mappings:1t5q.A;PDB-ENSP_mappings:2b4n.A;PDB-ENSP_mappings:2l70.A;PDB-ENSP_mappings:2l71.A;PDB-ENSP_mappings:2obu.A;PDB-ENSP_mappings:2qkh.B;Pfam:PF00123;PROSITE_patterns:PS00260;PANTHER:PTHR15211;SMART:SM00070 ENSP00000350005 0.0 0.0001163 3/6 rs367741847 ENST00000357424 Transcript ENSG00000159224 HGNC:4270 MODERATE NM_004123.3 0.0001629 gnomAD_OTH missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) P09681.167 GIP HGNC -1 1.0 UPI000012B4C0 SNV GIP,missense_variant,p.A53V,ENST00000357424,NM_004123.3,c.158C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1 259/716 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.76e-05 6.152e-05 8.673e-05 0.0 0.0 0.0 0.0001055 0.0001629 0.0 6.764889985788614e-05 4.868310134042986e-05 0.0 0.000132836998091 0.0 0.0 0.0 amr 0.000132836998091 0.0 9.259550279239193e-05 0.0 0.0 0 83 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 65 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GIP,missense_variant,p.A53V,ENST00000357424.2,c.158C>T,MODERATE,YES +B4GALNT2 124872 BI GRCh38 17 49156586 49156586 + missense_variant Missense_Mutation SNP G G A rs776879040 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 40 c.661G>A p.Asp221Asn p.D221N ENST00000300404.2 NM_153446.3 221 Gat/Aat 5/11 A2 A D/N protein_coding YES CCDS11544.1 661/1701 GACCCGATGCC COSM3518880 PIRSF:PIRSF000474;PANTHER:PTHR15046;PANTHER:PTHR15046:SF2 ENSP00000300404 5/11 rs776879040;COSV55928297 ENST00000300404 Transcript ENSG00000167080 HGNC:24136 MODERATE 0.0001969 gnomAD_SAS missense_variant 0;1 1.0 benign(0.006) Unknown tolerated(0.35) 0;1 Q8NHY0.129 B4GALNT2 HGNC 1 1.0 UPI000013E655 Q8NHY0-1 SNV B4GALNT2,missense_variant,p.D161N,ENST00000393354,NM_001159387.2,c.481G>A,MODERATE,,tolerated(0.26),benign(0.003),1;B4GALNT2,missense_variant,p.D221N,ENST00000300404,NM_153446.3,c.661G>A,MODERATE,YES,tolerated(0.35),benign(0.006),1;B4GALNT2,missense_variant,p.D135N,ENST00000504681,NM_001159388.1,c.403G>A,MODERATE,,tolerated(0.33),benign(0.006),1 720/1906 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.791e-05 0.0 0.0 0.0 0.0 0.0 8.795e-06 0.0 0.0001969 1.3529100215237122e-05 0.0 0.0 0.0 0.0 0.000201613001991 0.0 0.0 0.0 0.0 0.0002087680040858 0 96 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS B4GALNT2,missense_variant,p.D221N,ENST00000300404.2,c.661G>A,MODERATE,;B4GALNT2,missense_variant,p.D161N,ENST00000393354.7,c.481G>A,MODERATE,YES;B4GALNT2,missense_variant,p.D135N,ENST00000504681.5,c.403G>A,MODERATE, +NGFR 4804 BI GRCh38 17 49512923 49512923 + missense_variant Missense_Mutation SNP G G A rs534528579 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 7 c.1198G>A p.Ala400Thr p.A400T ENST00000172229.8 NM_002507.4 400 Gcc/Acc 6/6 0.0002 0.0 0.0014 0.0 0.0 0.0 P1 A A/T protein_coding YES CCDS11549.1 1198/1284 TGGACGCCCTC COSM265824 Gene3D:1.10.533.10;PDB-ENSP_mappings:2n80.A;PDB-ENSP_mappings:2n83.A;PDB-ENSP_mappings:2n97.A;PDB-ENSP_mappings:2n97.B;PDB-ENSP_mappings:3ewv.E;Pfam:PF00531;PROSITE_profiles:PS50017;PANTHER:PTHR46605;PANTHER:PTHR46605:SF3;SMART:SM00005;Superfamily:SSF47986;CDD:cd08311;Low_complexity_(Seg):seg ENSP00000172229 6/6 rs534528579;COSV50803870 ENST00000172229 Transcript ENSG00000064300 HGNC:7809 MODERATE NM_002507.4 0.0014 AMR missense_variant 0;1 1.0 benign(0.139) Unknown tolerated(0.25) 0;1 P08138.213 NGFR HGNC 1 1.0 UPI0000049854 P08138-1 SNV NGFR,missense_variant,p.A400T,ENST00000172229,NM_002507.4,c.1198G>A,MODERATE,YES,tolerated(0.25),benign(0.139),1;NGFR,missense_variant,p.A306T,ENST00000504201,,c.916G>A,MODERATE,,tolerated(0.29),benign(0.139),1;MIR6165,downstream_gene_variant,,ENST00000614803,,,MODIFIER,YES,,,1;AC006487.1,intron_variant,,ENST00000514506,,n.247-1810C>T,MODIFIER,YES,,,-1 1323/3408 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.104e-06 0.0 0.0 0.0 0.0 0.0 9.184e-06 0.0 0.0 4.057729893247597e-05 0.0 0.0 0.0003976139996666 0.0 0.0 0.0 amr 0.0003976139996666 0.0 0.0 0.0 0.0 0 19 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 17 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NGFR-AS1,intron_variant,,ENST00000514506.1,n.247-1810C>T,MODIFIER,YES;NGFR,missense_variant,p.A306T,ENST00000504201.1,c.916G>A,MODERATE,;NGFR,missense_variant,p.A400T,ENST00000172229.8,c.1198G>A,MODERATE,YES +MYCBPAP 84073 BI GRCh38 17 50519667 50519667 + stop_gained Nonsense_Mutation SNP C C T rs1473578827 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 6 c.796C>T p.Arg266Ter p.R266* ENST00000323776.11 NM_032133.6 266 Cga/Tga 7/19 A2 T R/* protein_coding 796/2826 GGAGTCGACTG COSM981071;COSM981072 Pfam:PF14646;PANTHER:PTHR12276;PANTHER:PTHR12276:SF54 ENSP00000323184 7/19 rs1473578827;COSV60405372 ENST00000323776 Transcript ENSG00000136449 HGNC:19677 HIGH NM_032133.6 8.798e-06 gnomAD_NFE stop_gained 0;1 Unknown 0;1 Q8TBZ2.120 MYCBPAP HGNC 1 1.0 UPI0000200FF6 SNV MYCBPAP,stop_gained,p.R309*,ENST00000652471,,c.925C>T,HIGH,YES,,,1;MYCBPAP,stop_gained,p.R266*,ENST00000323776,NM_001366294.2&NM_032133.6,c.796C>T,HIGH,,,,1;MYCBPAP,stop_gained,p.R272*,ENST00000436259,,c.814C>T,HIGH,,,,1;MYCBPAP,downstream_gene_variant,,ENST00000452039,,,MODIFIER,,,,1;MYCBPAP,downstream_gene_variant,,ENST00000458692,,,MODIFIER,,,,1;MYCBPAP,upstream_gene_variant,,ENST00000488432,,,MODIFIER,,,,1;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000468821,,n.73C>T,MODIFIER,,,,1;MYCBPAP,downstream_gene_variant,,ENST00000576179,,,MODIFIER,,,,1;MYCBPAP,stop_gained,p.R266*,ENST00000437498,,c.796C>T,HIGH,,,,1;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,,n.1046C>T,MODIFIER,,,,1;MYCBPAP,upstream_gene_variant,,ENST00000459754,,,MODIFIER,,,,1 1032/3135 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.978e-06 0.0 0.0 0.0 0.0 0.0 8.798e-06 0.0 0.0 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 33 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYCBPAP,non_coding_transcript_exon_variant,,ENST00000468821.1,n.73C>T,MODIFIER,;MYCBPAP,stop_gained,NMD_transcript_variant,p.R266*,ENST00000437498.2,c.796C>T,HIGH,;MYCBPAP,stop_gained,p.R281*,ENST00000452039.7,c.841C>T,HIGH,;MYCBPAP,stop_gained,p.R266*,ENST00000323776.11,c.796C>T,HIGH,YES;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609.5,n.1046C>T,MODIFIER, +CUEDC1 404093 BI GRCh38 17 57872771 57872771 + missense_variant Missense_Mutation SNP G G A rs150759994 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 65 9 c.676C>T p.Arg226Cys p.R226C ENST00000360238.6 NM_001292025.2 226 Cgc/Tgc 5/11 P1 A R/C protein_coding CCDS11599.1 676/1161 CCAGCGGCTCT COSM981700 PANTHER:PTHR13467 ENSP00000353373 0.000227 0.0001163 5/11 rs150759994;COSV64226368 ENST00000360238 Transcript ENSG00000180891 HGNC:31350 MODERATE 0.0002461 gnomAD_AFR missense_variant 0;1 possibly_damaging(0.719) Unknown deleterious(0) 0;1 Q9NWM3.137 CUEDC1 HGNC -1 2.0 UPI0000073340 Q9NWM3-1 SNV CUEDC1,missense_variant,p.R226C,ENST00000577830,NM_001271875.2,c.676C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.719),-1;CUEDC1,missense_variant,p.R226C,ENST00000360238,NM_001292025.1,c.676C>T,MODERATE,,deleterious(0),possibly_damaging(0.719),-1;CUEDC1,missense_variant,p.R226C,ENST00000407144,,c.676C>T,MODERATE,,deleterious(0),possibly_damaging(0.719),-1;CUEDC1,missense_variant,p.R89C,ENST00000577840,,c.265C>T,MODERATE,,deleterious(0),possibly_damaging(0.719),-1;CUEDC1,downstream_gene_variant,,ENST00000577589,,,MODIFIER,,,,-1;CUEDC1,upstream_gene_variant,,ENST00000581898,,,MODIFIER,,,,-1;CUEDC1,upstream_gene_variant,,ENST00000578357,,,MODIFIER,,,,-1;CUEDC1,upstream_gene_variant,,ENST00000581391,,,MODIFIER,,,,-1;CUEDC1,upstream_gene_variant,,ENST00000584746,,,MODIFIER,,,,-1 1395/2193 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0002461 0.0 0.0 0.0 0.0 8.792e-06 0.0 0.0 1.3518800187739544e-05 4.862390051130205e-05 0.0 0.0 0.0 0.0 0.0 afr 4.862390051130205e-05 0.0 0.0 0.0 0.0 0 78 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 74 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CUEDC1,missense_variant,p.R89C,ENST00000577840.5,c.265C>T,MODERATE,;CUEDC1,missense_variant,p.R226C,ENST00000360238.6,c.676C>T,MODERATE,;CUEDC1,missense_variant,p.R226C,ENST00000407144.6,c.676C>T,MODERATE,;CUEDC1,missense_variant,p.R226C,ENST00000577830.6,c.676C>T,MODERATE,YES +RNF43 54894 BI GRCh38 17 58357950 58357950 + missense_variant Missense_Mutation SNP C C T rs759694077 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 22 c.1826G>A p.Arg609Gln p.R609Q ENST00000407977.7 NM_017763.6 609 cGg/cAg 9/10 P1 T R/Q protein_coding CCDS11607.1 1826/2352 AGAGCCGCCCC COSM1224019 PANTHER:PTHR16200;PANTHER:PTHR16200:SF2;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000385328 9/10 rs759694077;COSV68459662;COSV68459732 ENST00000407977 Transcript 1.0 ENSG00000108375 HGNC:18505 MODERATE NM_017763.6 0.0001321 gnomAD_SAS missense_variant 0;1;1 benign(0) Unknown tolerated_low_confidence(1) 0;1;1 Q68DV7.150 RNF43 HGNC -1 2.0 UPI000022A469 Q68DV7-1 SNV RNF43,missense_variant,p.R609Q,ENST00000584437,,c.1826G>A,MODERATE,YES,tolerated_low_confidence(1),benign(0),-1;RNF43,missense_variant,p.R609Q,ENST00000407977,NM_017763.6,c.1826G>A,MODERATE,,tolerated_low_confidence(1),benign(0),-1;RNF43,missense_variant,p.R609Q,ENST00000577716,NM_001305544.2,c.1826G>A,MODERATE,,tolerated_low_confidence(1),benign(0),-1;RNF43,missense_variant,p.R568Q,ENST00000583753,,c.1703G>A,MODERATE,,tolerated(1),benign(0),-1;RNF43,missense_variant,p.R482Q,ENST00000581868,,c.1445G>A,MODERATE,,tolerated_low_confidence(1),benign(0),-1;RNF43,missense_variant,p.R482Q,ENST00000577625,NM_001305545.1,c.1445G>A,MODERATE,,tolerated(1),benign(0),-1;SUPT4H1,upstream_gene_variant,,ENST00000580947,,,MODIFIER,,,,-1;AC004687.2,missense_variant,p.R609Q,ENST00000648873,,c.1826G>A,MODERATE,YES,tolerated_low_confidence(1),benign(0),-1;TSPOAP1-AS1,intron_variant,,ENST00000583841,,n.434+20271C>T,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000578025,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000579527,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000579859,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000580022,,,MODIFIER,YES,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000585236,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000667382,,,MODIFIER,,,,1 2729/4522 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.828e-05 0.0 2.938e-05 0.0 5.458e-05 0.0 8.928e-06 0.0 0.0001321 1.3519499589165209e-05 2.4317900169990025e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002083330036839 0 76 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 51 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RNF43,missense_variant,p.R482Q,ENST00000581868.1,c.1445G>A,MODERATE,;RNF43,missense_variant,p.R482Q,ENST00000577625.5,c.1445G>A,MODERATE,;RNF43,missense_variant,p.R609Q,ENST00000577716.5,c.1826G>A,MODERATE,;RNF43,missense_variant,p.R609Q,ENST00000407977.7,c.1826G>A,MODERATE,YES;RNF43,missense_variant,p.R609Q,ENST00000584437.5,c.1826G>A,MODERATE,;RNF43,missense_variant,p.R568Q,ENST00000583753.5,c.1703G>A,MODERATE,;ENSG00000285897,missense_variant,NMD_transcript_variant,p.R609Q,ENST00000648873.1,c.1826G>A,MODERATE,YES;TSPOAP1-AS1,intron_variant,,ENST00000583841.1,n.434+20271C>T,MODIFIER,YES +CYB561 1534 BI GRCh38 17 63437539 63437539 + synonymous_variant Silent SNP G G A rs768220809 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 13 10 c.9C>T p.Gly3= p.G3= ENST00000360793.8 NM_001915.4 3 ggC/ggT 2/6 P1 A G protein_coding CCDS11636.1 9/756 GCCCCGCCCTC ENSP00000354028 2/6 rs768220809 ENST00000360793 Transcript 1.0 ENSG00000008283 HGNC:2571 LOW NM_001915.4 0.0004943 gnomAD_EAS synonymous_variant Unknown P49447.175 CYB561 HGNC -1 1.0 UPI0000126C79 P49447-1 SNV CYB561,synonymous_variant,p.G3=,ENST00000584031,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000392976,NM_001017916.1,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000392975,NM_001017917.2,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000360793,NM_001915.4,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000581573,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000448884,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G70=,ENST00000542042,,c.210C>T,LOW,YES,,,-1;CYB561,synonymous_variant,p.G57=,ENST00000580691,,c.171C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000582297,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G10=,ENST00000582997,NM_001330421.2,c.30C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000584291,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G3=,ENST00000578072,,c.9C>T,LOW,,,,-1;CYB561,synonymous_variant,p.G39=,ENST00000580592,,c.117C>T,LOW,,,,-1;CYB561,intron_variant,,ENST00000582034,,c.-24-55C>T,MODIFIER,,,,-1;CYB561,upstream_gene_variant,,ENST00000585153,,,MODIFIER,,,,-1;CYB561,non_coding_transcript_exon_variant,,ENST00000578016,,n.118C>T,MODIFIER,,,,-1;CYB561,intron_variant,,ENST00000577989,,n.65-1387C>T,MODIFIER,,,,-1;CYB561,upstream_gene_variant,,ENST00000581163,,,MODIFIER,,,,-1;CYB561,non_coding_transcript_exon_variant,,ENST00000577368,,n.84C>T,MODIFIER,,,,-1;CYB561,non_coding_transcript_exon_variant,,ENST00000583478,,n.109C>T,MODIFIER,,,,-1;CYB561,upstream_gene_variant,,ENST00000582143,,,MODIFIER,,,,-1 84/2929 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.718e-05 0.0 0.0 0.0 0.0004943 0.0 0.0 0.0 0.0 3.3819000236690044e-05 0.0 0.0 0.0 0.0 0.0008093889919109 0.0 eas 0.0008093889919109 0.0 1.5436400644830428e-05 0.0 0.0 0 18 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 23 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CYB561,synonymous_variant,p.G39=,ENST00000580592.1,c.117C>T,LOW,;CYB561,non_coding_transcript_exon_variant,,ENST00000583478.1,n.109C>T,MODIFIER,;CYB561,synonymous_variant,p.G3=,ENST00000578072.1,c.9C>T,LOW,;CYB561,non_coding_transcript_exon_variant,,ENST00000578016.1,n.118C>T,MODIFIER,;CYB561,non_coding_transcript_exon_variant,,ENST00000577368.5,n.84C>T,MODIFIER,;CYB561,intron_variant,,ENST00000577989.5,n.65-1387C>T,MODIFIER,;CYB561,synonymous_variant,p.G3=,ENST00000584291.5,c.9C>T,LOW,;CYB561,synonymous_variant,p.G10=,ENST00000582997.5,c.30C>T,LOW,;CYB561,missense_variant,p.A57V,ENST00000580691.5,c.170C>T,MODERATE,;CYB561,synonymous_variant,p.G70=,ENST00000542042.5,c.210C>T,LOW,;CYB561,intron_variant,,ENST00000582034.5,c.-24-55C>T,MODIFIER,;CYB561,synonymous_variant,p.G3=,ENST00000448884.6,c.9C>T,LOW,;CYB561,synonymous_variant,p.G3=,ENST00000581573.5,c.9C>T,LOW,;CYB561,synonymous_variant,p.G3=,ENST00000582297.5,c.9C>T,LOW,;CYB561,synonymous_variant,p.G3=,ENST00000392976.5,c.9C>T,LOW,;CYB561,synonymous_variant,p.G3=,ENST00000584031.5,c.9C>T,LOW,;CYB561,synonymous_variant,p.G3=,ENST00000360793.8,c.9C>T,LOW,YES;CYB561,synonymous_variant,p.G3=,ENST00000392975.6,c.9C>T,LOW, +SCN4A 6329 BI GRCh38 17 63941137 63941137 + synonymous_variant Silent SNP G G A rs768902509 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 25 c.5145C>T p.Tyr1715= p.Y1715= ENST00000435607.3 NM_000334.4 1715 taC/taT 24/24 P1 A Y protein_coding YES CCDS45761.1 5145/5511 GGCTCGTAGGA Gene3D:1.10.238.10;PDB-ENSP_mappings:6agf.A;PDB-ENSP_mappings:6mba.A;PDB-ENSP_mappings:6mc9.A;PANTHER:PTHR10037;PANTHER:PTHR10037:SF223 ENSP00000396320 24/24 rs768902509 ENST00000435607 Transcript 1.0 ENSG00000007314 HGNC:10591 LOW NM_000334.4 8.852e-06 gnomAD_NFE synonymous_variant 1.0 Unknown P35499.204 SCN4A HGNC -1 1.0 UPI0000201254 SNV SCN4A,synonymous_variant,p.Y1715=,ENST00000435607,NM_000334.4,c.5145C>T,LOW,YES,,,-1 5222/7805 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.013e-06 0.0 0.0 0.0 0.0 0.0 8.852e-06 0.0 0.0 4.0580598579254e-05 0.0 0.0 6.629539711866528e-05 0.0 0.0 0.0 nfe 7.718909910181537e-05 0.0 7.718909910181537e-05 0.0 0.0 0 95 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 59 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SCN4A,synonymous_variant,p.Y1715=,ENST00000435607.3,c.5145C>T,LOW,YES +LLGL2 3993 BI GRCh38 17 75573209 75573209 + missense_variant Missense_Mutation SNP C C T rs370466207 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 55 13 c.2656C>T p.Arg886Cys p.R886C ENST00000392550.8 NM_001031803.2 886 Cgc/Tgc 20/26 P4 T R/C protein_coding YES CCDS32733.1 2656/3063 AGGTGCGCTAC PDB-ENSP_mappings:6n8p.A;PDB-ENSP_mappings:6n8q.A;PDB-ENSP_mappings:6n8r.A;PDB-ENSP_mappings:6n8s.A;PDB-ENSP_mappings:6n8s.D;PANTHER:PTHR10241;PANTHER:PTHR10241:SF20 ENSP00000376333 0.0 0.0001163 20/26 rs370466207 ENST00000392550 Transcript ENSG00000073350 HGNC:6629 MODERATE NM_001031803.2 0.0002181 gnomAD_EAS missense_variant 1.0 possibly_damaging(0.836) Unknown deleterious(0.01) Q6P1M3.152 LLGL2 HGNC 1 1.0 UPI00005905A8 Q6P1M3-1 SNV LLGL2,missense_variant,p.R886C,ENST00000392550,NM_001031803.2,c.2656C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.836),1;LLGL2,missense_variant,p.R886C,ENST00000167462,NM_004524.3,c.2656C>T,MODERATE,,deleterious(0.01),probably_damaging(0.921),1;LLGL2,missense_variant,p.R886C,ENST00000577200,,c.2656C>T,MODERATE,,deleterious(0.01),probably_damaging(0.999),1;LLGL2,3_prime_UTR_variant,,ENST00000578638,,c.*1388C>T,MODIFIER,,,,1;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227,,n.2833C>T,MODIFIER,,,,1;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500,,n.2176C>T,MODIFIER,,,,1;LLGL2,non_coding_transcript_exon_variant,,ENST00000579092,,n.722C>T,MODIFIER,,,,1;LLGL2,upstream_gene_variant,,ENST00000577211,,,MODIFIER,,,,1;LLGL2,upstream_gene_variant,,ENST00000578034,,,MODIFIER,,,,1;LLGL2,downstream_gene_variant,,ENST00000578719,,,MODIFIER,,,,1;LLGL2,upstream_gene_variant,,ENST00000582393,,,MODIFIER,,,,1;LLGL2,upstream_gene_variant,,ENST00000583514,,,MODIFIER,,,,1 2815/3553 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.205e-05 0.0 2.895e-05 0.0 0.0002181 0.0 2.671e-05 0.0 0.0 2.027549999183975e-05 2.4308399588335305e-05 0.0 0.0 0.0 0.0002013689954765 0.0 0.0 1.5431100109708495e-05 0.0 0.0 0 77 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 68 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LLGL2,non_coding_transcript_exon_variant,,ENST00000579092.1,n.722C>T,MODIFIER,;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500.5,n.2176C>T,MODIFIER,;LLGL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000578638.5,c.*1388C>T,MODIFIER,;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227.6,n.2833C>T,MODIFIER,;LLGL2,missense_variant,p.R886C,ENST00000577200.5,c.2656C>T,MODERATE,;LLGL2,missense_variant,p.R886C,ENST00000167462.9,c.2656C>T,MODERATE,;LLGL2,missense_variant,p.R886C,ENST00000392550.8,c.2656C>T,MODERATE,YES +CDK3 1018 BI GRCh38 17 76003290 76003290 + synonymous_variant Silent SNP C C T rs141477491 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 81 11 c.684C>T p.Pro228= p.P228= ENST00000425876.6 228 ccC/ccT 6/7 P1 T P protein_coding YES CCDS11736.1 684/918 TGGCCCGGGGT Gene3D:1.10.510.10;Pfam:PF00069;PROSITE_profiles:PS50011;PANTHER:PTHR24056;PANTHER:PTHR24056:SF379;SMART:SM00220;Superfamily:SSF56112;CDD:cd07860 ENSP00000410561 0.0 0.0001163 6/7 rs141477491 ENST00000425876 Transcript ENSG00000250506 HGNC:1772 LOW 0.0001163 EA synonymous_variant 1.0 Unknown Q00526.198 CDK3 HGNC 1 1.0 UPI0000113587 SNV CDK3,synonymous_variant,p.P228=,ENST00000425876,,c.684C>T,LOW,YES,,,1;CDK3,synonymous_variant,p.P228=,ENST00000448471,NM_001258.2,c.684C>T,LOW,,,,1;CDK3,synonymous_variant,p.P188=,ENST00000586261,,c.564C>T,LOW,,,,1;EVPL,downstream_gene_variant,,ENST00000301607,NM_001988.4,,MODIFIER,,,,-1;TEN1,downstream_gene_variant,,ENST00000397640,NM_001113324.3,,MODIFIER,YES,,,1;EVPL,downstream_gene_variant,,ENST00000586740,NM_001320747.2,,MODIFIER,YES,,,-1;TEN1,downstream_gene_variant,,ENST00000588202,,,MODIFIER,,,,1;EVPL,downstream_gene_variant,,ENST00000589231,,,MODIFIER,,,,-1;TEN1-CDK3,3_prime_UTR_variant,,ENST00000649294,,c.*825C>T,MODIFIER,YES,,,1;TEN1-CDK3,non_coding_transcript_exon_variant,,ENST00000567351,,n.3088C>T,MODIFIER,,,,1;TEN1-CDK3,non_coding_transcript_exon_variant,,ENST00000569284,,n.2477C>T,MODIFIER,,,,1;EVPL,downstream_gene_variant,,ENST00000587569,,,MODIFIER,,,,-1 772/1582 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0 0.0 0.0 0.0 4.62e-05 2.638e-05 0.0 0.0 1.3520800166588742e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085850039497018e-05 0.0 3.085850039497018e-05 0.0 0.0 0 110 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 92 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CDK3,synonymous_variant,p.P188=,ENST00000586261.2,c.564C>T,LOW,;CDK3,synonymous_variant,p.P228=,ENST00000425876.6,c.684C>T,LOW,;CDK3,synonymous_variant,p.P228=,ENST00000448471.3,c.684C>T,LOW,YES;TEN1-CDK3,non_coding_transcript_exon_variant,,ENST00000569284.1,n.2477C>T,MODIFIER,;TEN1-CDK3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000649294.1,c.*825C>T,MODIFIER,YES;TEN1-CDK3,non_coding_transcript_exon_variant,,ENST00000567351.5,n.3088C>T,MODIFIER, +CBX2 84733 BI GRCh38 17 79784065 79784065 + missense_variant Missense_Mutation SNP G G A rs61738483 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 7 c.622G>A p.Val208Ile p.V208I ENST00000310942.9 NM_005189.3 208 Gtt/Att 5/5 P1 A V/I protein_coding YES CCDS32757.1 622/1599 CCCCCGTTGCA PANTHER:PTHR46860;Low_complexity_(Seg):seg ENSP00000308750 5/5 rs61738483 ENST00000310942 Transcript 1.0 ENSG00000173894 HGNC:1552 MODERATE NM_005189.3 0.0001453 gnomAD_AMR missense_variant 1.0 benign(0.137) Unknown tolerated(0.31) Q14781.178 CBX2 HGNC 1 1.0 UPI000004C4E1 Q14781-1 SNV CBX2,missense_variant,p.V208I,ENST00000310942,NM_005189.3,c.622G>A,MODERATE,YES,tolerated(0.31),benign(0.137),1;CBX2,downstream_gene_variant,,ENST00000269399,NM_032647.3,,MODIFIER,,,,1;CBX2,downstream_gene_variant,,ENST00000571484,,,MODIFIER,,,,1 710/4628 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.684e-05 0.0 0.0001453 0.0 5.524e-05 0.0 2.748e-05 0.0 0.0 5.405840056482703e-05 2.4303699319716543e-05 0.0 0.0 0.0 0.0002014500059885 0.0 nfe 9.25839995034039e-05 0.0 9.25839995034039e-05 0.0 0.0 0 34 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CBX2,missense_variant,p.V208I,ENST00000310942.9,c.622G>A,MODERATE,YES +CEP131 22994 BI GRCh38 17 81219965 81219965 + missense_variant Missense_Mutation SNP C C T rs372370793 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 32 c.92G>A p.Arg31Gln p.R31Q ENST00000269392.8 NM_001319228.2 31 cGg/cAg 2/26 P4 T R/Q protein_coding YES CCDS82215.1 92/3252 GACGCCGGGAC PANTHER:PTHR31540;MobiDB_lite:mobidb-lite ENSP00000269392 0.000227 0.0 2/26 rs372370793 ENST00000269392 Transcript ENSG00000141577 HGNC:29511 MODERATE 0.000227 AA missense_variant 1.0 benign(0.011) Unknown tolerated(0.22) Q9UPN4.158 CEP131 HGNC -1 1.0 UPI00001C1FC8 Q9UPN4-1 SNV CEP131,missense_variant,p.R31Q,ENST00000269392,NM_001319228.2,c.92G>A,MODERATE,YES,tolerated(0.22),benign(0.011),-1;CEP131,missense_variant,p.R31Q,ENST00000450824,NM_014984.4,c.92G>A,MODERATE,,tolerated(0.21),benign(0.007),-1;CEP131,missense_variant,p.R31Q,ENST00000374782,NM_001009811.4,c.92G>A,MODERATE,,tolerated(0.22),benign(0.015),-1;CEP131,missense_variant,p.R31Q,ENST00000575907,NM_001319229.2,c.92G>A,MODERATE,,tolerated(0.22),benign(0.005),-1 340/3673 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.044e-06 0.0 0.0 0.0 0.0 0.0 8.866e-06 0.0 3.306e-05 1.3520800166588742e-05 2.4323799152625725e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 101 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 69 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CEP131,missense_variant,p.R31Q,ENST00000575907.5,c.92G>A,MODERATE,;CEP131,missense_variant,p.R31Q,ENST00000450824.7,c.92G>A,MODERATE,YES;CEP131,missense_variant,p.R31Q,ENST00000269392.8,c.92G>A,MODERATE,;CEP131,missense_variant,p.R31Q,ENST00000374782.7,c.92G>A,MODERATE, +OXLD1 339229 BI GRCh38 17 81665484 81665484 + missense_variant Missense_Mutation SNP C C T rs752069209 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 4 c.161G>A p.Arg54His p.R54H ENST00000374741.4 NM_001039842.3 54 cGc/cAc 2/2 P4 T R/H protein_coding YES CCDS32766.1 161/444 TTCTGCGCCCA PANTHER:PTHR21193 ENSP00000363873 2/2 rs752069209;COSV100235870 ENST00000374741 Transcript ENSG00000204237 HGNC:27901 MODERATE NM_001039842.3 3.557e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0) Unknown tolerated(0.35) 0;1 Q5BKU9.100 OXLD1 HGNC -1 1.0 UPI000022A58F SNV OXLD1,missense_variant,p.R54H,ENST00000374741,NM_001039842.3&NM_001304994.2,c.161G>A,MODERATE,YES,tolerated(0.35),benign(0),-1;OXLD1,3_prime_UTR_variant,,ENST00000571503,NM_001304995.2&NM_001304999.2,c.*123G>A,MODIFIER,,,,-1;CCDC137,upstream_gene_variant,,ENST00000329214,NM_199287.3,,MODIFIER,,,,1;PDE6G,upstream_gene_variant,,ENST00000571224,NM_001365724.1,,MODIFIER,,,,-1;CCDC137,upstream_gene_variant,,ENST00000574107,,,MODIFIER,YES,,,1;OXLD1,non_coding_transcript_exon_variant,,ENST00000573786,,n.250G>A,MODIFIER,,,,-1;PDE6G,upstream_gene_variant,,ENST00000574777,,,MODIFIER,,,,-1;OXLD1,3_prime_UTR_variant,,ENST00000571757,,c.*245G>A,MODIFIER,,,,-1;OXLD1,3_prime_UTR_variant,,ENST00000575992,,c.*254G>A,MODIFIER,,,,-1;OXLD1,3_prime_UTR_variant,,ENST00000571092,,c.*250G>A,MODIFIER,,,,-1;OXLD1,non_coding_transcript_exon_variant,,ENST00000575963,,n.1152G>A,MODIFIER,,,,-1;CCDC137,upstream_gene_variant,,ENST00000571916,,,MODIFIER,,,,1;CCDC137,upstream_gene_variant,,ENST00000574200,,,MODIFIER,,,,1;CCDC137,upstream_gene_variant,,ENST00000575223,,,MODIFIER,,,,1 189/637 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.602e-05 0.0 0.0 0.0 0.0 0.0 3.557e-05 0.0 0.0 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 38 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS OXLD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000571092.1,c.*250G>A,MODIFIER,;OXLD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000575992.1,c.*254G>A,MODIFIER,;OXLD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000571757.1,c.*245G>A,MODIFIER,;OXLD1,3_prime_UTR_variant,,ENST00000571503.1,c.*123G>A,MODIFIER,;OXLD1,non_coding_transcript_exon_variant,,ENST00000573786.1,n.250G>A,MODIFIER,;OXLD1,non_coding_transcript_exon_variant,,ENST00000575963.1,n.1152G>A,MODIFIER,;OXLD1,missense_variant,p.R54H,ENST00000374741.4,c.161G>A,MODERATE,YES +RAC3 5881 BI GRCh38 17 82032779 82032779 + missense_variant Missense_Mutation SNP C C T rs1379395211 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 54 13 c.176C>T p.Ala59Val p.A59V ENST00000306897.9 NM_001316307.2 59 gCg/gTg 3/6 P1 T A/V protein_coding YES CCDS11798.1 176/579 CACAGCGGGTC PDB-ENSP_mappings:2c2h.A;PDB-ENSP_mappings:2c2h.B;PDB-ENSP_mappings:2g0n.A;PDB-ENSP_mappings:2g0n.B;PDB-ENSP_mappings:2ic5.A;PDB-ENSP_mappings:2ic5.B;PDB-ENSP_mappings:2ov2.A;PDB-ENSP_mappings:2ov2.B;PDB-ENSP_mappings:2ov2.C;PDB-ENSP_mappings:2ov2.D;PDB-ENSP_mappings:2ov2.E;PDB-ENSP_mappings:2ov2.F;PDB-ENSP_mappings:2ov2.G;PDB-ENSP_mappings:2ov2.H;PDB-ENSP_mappings:2qme.A;Gene3D:3.40.50.300;PDB-ENSP_mappings:6tm1.A;Pfam:PF00071;Prints:PR00449;PROSITE_profiles:PS51420;PANTHER:PTHR24072;PANTHER:PTHR24072:SF297;SMART:SM00173;SMART:SM00174;SMART:SM00175;Superfamily:SSF52540;TIGRFAM:TIGR00231;CDD:cd01871 ENSP00000304283 3/6 rs1379395211 ENST00000306897 Transcript 1.0 ENSG00000169750 HGNC:9803 MODERATE NM_005052.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1 1.0 29276006 possibly_damaging(0.797) Unknown deleterious_low_confidence(0.02) P60763.163 RAC3 HGNC 1 1.0 UPI00000041DA SNV RAC3,missense_variant,p.A59V,ENST00000306897,NM_001316307.2&NM_005052.3,c.176C>T,MODERATE,YES,deleterious_low_confidence(0.02),possibly_damaging(0.797),1;RAC3,missense_variant,p.A15V,ENST00000580965,,c.44C>T,MODERATE,,deleterious_low_confidence(0.02),possibly_damaging(0.797),1;RAC3,missense_variant,p.A15V,ENST00000584341,,c.44C>T,MODERATE,,deleterious_low_confidence(0.02),possibly_damaging(0.797),1;LRRC45,downstream_gene_variant,,ENST00000306688,NM_144999.4,,MODIFIER,YES,,,1;DCXR,downstream_gene_variant,,ENST00000306869,NM_016286.4&NM_001195218.1,,MODIFIER,YES,,,-1;DCXR,downstream_gene_variant,,ENST00000577532,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000577712,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000579004,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000579155,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000581584,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000582900,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000577996,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000584318,,,MODIFIER,,,,-1;AC137723.1,downstream_gene_variant,,ENST00000623540,,,MODIFIER,YES,,,-1;DCXR,downstream_gene_variant,,ENST00000577286,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000578273,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000578885,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000579334,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000579821,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000579842,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000580320,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000580750,,,MODIFIER,,,,-1;LRRC45,downstream_gene_variant,,ENST00000581227,,,MODIFIER,,,,1;DCXR,downstream_gene_variant,,ENST00000582074,,,MODIFIER,,,,-1;LRRC45,downstream_gene_variant,,ENST00000582083,,,MODIFIER,,,,1;DCXR,downstream_gene_variant,,ENST00000582613,,,MODIFIER,,,,-1;LRRC45,downstream_gene_variant,,ENST00000583302,,,MODIFIER,,,,1;RAC3,upstream_gene_variant,,ENST00000585014,,,MODIFIER,,,,1;DCXR,downstream_gene_variant,,ENST00000585085,,,MODIFIER,,,,-1;DCXR,downstream_gene_variant,,ENST00000585164,,,MODIFIER,,,,-1 260/1038 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 86 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 67 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RAC3,missense_variant,p.A15V,ENST00000584341.1,c.44C>T,MODERATE,;RAC3,missense_variant,p.A15V,ENST00000580965.5,c.44C>T,MODERATE,;RAC3,missense_variant,p.A59V,ENST00000306897.9,c.176C>T,MODERATE,YES +LRRC30 339291 BI GRCh38 18 7231427 7231427 + missense_variant Missense_Mutation SNP G G A rs1400196214 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 27 8 c.289G>A p.Val97Met p.V97M ENST00000383467.3 NM_001105581.2 97 Gtg/Atg 1/1 P1 A V/M protein_coding YES CCDS42409.1 289/906 GGATCGTGGTC PROSITE_profiles:PS51450;PANTHER:PTHR27000:SF498;PANTHER:PTHR27000;Gene3D:3.80.10.10;SMART:SM00369;Superfamily:SSF52058 ENSP00000372959 1/1 COSV67301708 ENST00000383467 Transcript ENSG00000206422 HGNC:30219 MODERATE missense_variant 1 1.0 benign(0.286) Unknown deleterious(0.01) 1 A6NM36.104 LRRC30 HGNC 1 UPI00001D7ABB SNV LRRC30,missense_variant,p.V97M,ENST00000383467,NM_001105581.2,c.289G>A,MODERATE,YES,deleterious(0.01),benign(0.286),1 303/923 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 43 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRRC30,missense_variant,p.V97M,ENST00000383467.3,c.289G>A,MODERATE,YES +LAMA3 3909 BI GRCh38 18 23904054 23904054 + missense_variant Missense_Mutation SNP G G A rs201023601 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 92 8 c.6440G>A p.Arg2147Gln p.R2147Q ENST00000313654.14 NM_198129.4 2147 cGg/cAg 50/75 P1 A R/Q protein_coding YES CCDS42419.1 6440/10002 CGCGCGGTCCT Coiled-coils_(Ncoils):Coil;PANTHER:PTHR10574;PANTHER:PTHR10574:SF285 ENSP00000324532 50/75 rs201023601 ENST00000313654 Transcript 1.0 ENSG00000053747 HGNC:6483 MODERATE NM_198129.4 0.0007839 gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(1) Q16787.197 LAMA3 HGNC 1 1.0 UPI000035154D SNV LAMA3,missense_variant,p.R2147Q,ENST00000313654,NM_198129.4,c.6440G>A,MODERATE,YES,tolerated(1),benign(0),1;LAMA3,missense_variant,p.R2091Q,ENST00000399516,NM_001127717.4,c.6272G>A,MODERATE,,tolerated(1),benign(0),1;LAMA3,missense_variant,p.R1111Q,ENST00000649721,,c.3332G>A,MODERATE,,tolerated(0.17),benign(0),1;LAMA3,missense_variant,p.R538Q,ENST00000269217,NM_000227.6,c.1613G>A,MODERATE,,tolerated(1),benign(0),1;LAMA3,missense_variant,p.R482Q,ENST00000587184,NM_001127718.4,c.1445G>A,MODERATE,,tolerated(1),benign(0),1;LAMA3,missense_variant,p.R407Q,ENST00000586751,,c.1220G>A,MODERATE,,tolerated(1),benign(0.001),1;LAMA3,non_coding_transcript_exon_variant,,ENST00000588770,,n.1018G>A,MODIFIER,,,,1;LAMA3,downstream_gene_variant,,ENST00000586709,,,MODIFIER,,,,1 6671/10651 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001034 0.0 0.0 0.0 0.0 4.62e-05 0.0 0.000163 0.0007839 3.379700137884356e-05 0.0 0.0 0.0 0.0 0.000201613001991 9.417969704372808e-05 sas 0.0004166669968981 0.0 0.0 0.0004945599939674 0.0004166669968981 0 114 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 100 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LAMA3,non_coding_transcript_exon_variant,,ENST00000588770.5,n.1018G>A,MODIFIER,;LAMA3,synonymous_variant,p.A406=,ENST00000586751.5,c.1218G>A,LOW,;LAMA3,missense_variant,p.R482Q,ENST00000587184.5,c.1445G>A,MODERATE,;LAMA3,missense_variant,p.R538Q,ENST00000269217.11,c.1613G>A,MODERATE,;LAMA3,missense_variant,p.R1111Q,ENST00000649721.1,c.3332G>A,MODERATE,;LAMA3,missense_variant,p.R2091Q,ENST00000399516.7,c.6272G>A,MODERATE,;LAMA3,missense_variant,p.R2147Q,ENST00000313654.14,c.6440G>A,MODERATE,YES +ZNF521 25925 BI GRCh38 18 25227562 25227562 + missense_variant Missense_Mutation SNP G G A rs149969134 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 73 15 c.356C>T p.Pro119Leu p.P119L ENST00000361524.8 NM_015461.3 119 cCg/cTg 4/8 P1 A P/L protein_coding YES CCDS32806.1 356/3936 GACACGGGTAT Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_profiles:PS50157;PANTHER:PTHR24376;PANTHER:PTHR24376:SF84;SMART:SM00355;Superfamily:SSF57667 ENSP00000354794 0.0 0.0001163 4/8 rs149969134 ENST00000361524 Transcript 1.0 ENSG00000198795 HGNC:24605 MODERATE NM_015461.3 0.0001307 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.804) Unknown deleterious(0.01) Q96K83.153 ZNF521 HGNC -1 1.0 UPI000006F982 SNV ZNF521,missense_variant,p.P119L,ENST00000361524,NM_015461.3,c.356C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.804),-1;ZNF521,missense_variant,p.P119L,ENST00000538137,,c.356C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.804),-1;ZNF521,missense_variant,p.P119L,ENST00000577801,,c.356C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.804),-1;ZNF521,missense_variant,p.P119L,ENST00000580488,,c.356C>T,MODERATE,,deleterious(0),possibly_damaging(0.804),-1;ZNF521,5_prime_UTR_variant,,ENST00000584787,NM_001308225.2,c.-305C>T,MODIFIER,,,,-1;ZNF521,upstream_gene_variant,,ENST00000577775,,,MODIFIER,,,,-1;ZNF521,non_coding_transcript_exon_variant,,ENST00000577720,,n.196C>T,MODIFIER,,,,-1;ZNF521,non_coding_transcript_exon_variant,,ENST00000581869,,n.357C>T,MODIFIER,,,,-1;ZNF521,downstream_gene_variant,,ENST00000579111,,,MODIFIER,,,,-1;ZNF521,downstream_gene_variant,,ENST00000583005,,,MODIFIER,,,,-1;ZNF521,missense_variant,p.P119L,ENST00000399425,,c.356C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.704),-1;ZNF521,downstream_gene_variant,,ENST00000583398,,,MODIFIER,,,,-1 519/4887 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.777e-05 6.153e-05 5.783e-05 0.0 0.0 0.0 4.405e-05 0.0 0.0001307 2.0285899154259823e-05 2.432730070722755e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.086229844484478e-05 0.0 3.086229844484478e-05 0.0 0.0 0 96 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 88 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF521,missense_variant,p.P119L,ENST00000580488.1,c.356C>T,MODERATE,;ZNF521,non_coding_transcript_exon_variant,,ENST00000581869.1,n.357C>T,MODIFIER,;ZNF521,missense_variant,p.P119L,ENST00000577801.5,c.356C>T,MODERATE,;ZNF521,non_coding_transcript_exon_variant,,ENST00000577720.1,n.196C>T,MODIFIER,;ZNF521,missense_variant,p.P119L,ENST00000538137.6,c.356C>T,MODERATE,;ZNF521,missense_variant,NMD_transcript_variant,p.P119L,ENST00000399425.6,c.356C>T,MODERATE,;ZNF521,5_prime_UTR_variant,,ENST00000584787.5,c.-305C>T,MODIFIER,;ZNF521,missense_variant,p.P119L,ENST00000361524.8,c.356C>T,MODERATE,YES +ZCCHC2 54877 BI GRCh38 18 62575069 62575069 + synonymous_variant Silent SNP C C T rs780469141 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 4 c.2988C>T p.Asn996= p.N996= ENST00000269499.10 NM_017742.6 996 aaC/aaT 13/14 P4 T N protein_coding YES CCDS45880.1 2988/3537 ACGAACGCTAA PANTHER:PTHR46939 ENSP00000269499 13/14 rs780469141;COSV99502318 ENST00000269499 Transcript ENSG00000141664 HGNC:22916 LOW NM_017742.6 8.855e-06 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q9C0B9.146 ZCCHC2 HGNC 1 5.0 UPI00016D385A Q9C0B9-1 SNV ZCCHC2,synonymous_variant,p.N996=,ENST00000269499,NM_017742.6,c.2988C>T,LOW,YES,,,1;ZCCHC2,synonymous_variant,p.N675=,ENST00000586834,,c.2025C>T,LOW,,,,1;ZCCHC2,intron_variant,,ENST00000587612,,n.167-244C>T,MODIFIER,,,,1;ZCCHC2,synonymous_variant,p.N916=,ENST00000585873,,c.2748C>T,LOW,,,,1;ZCCHC2,non_coding_transcript_exon_variant,,ENST00000585949,,n.1730C>T,MODIFIER,,,,1;ZCCHC2,upstream_gene_variant,,ENST00000591145,,,MODIFIER,,,,1 3388/5937 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.014e-06 0.0 0.0 0.0 0.0 0.0 8.855e-06 0.0 0.0 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 20 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZCCHC2,intron_variant,,ENST00000587612.1,n.167-244C>T,MODIFIER,;ZCCHC2,non_coding_transcript_exon_variant,,ENST00000585949.1,n.1730C>T,MODIFIER,;ZCCHC2,synonymous_variant,p.N675=,ENST00000586834.1,c.2025C>T,LOW,;ZCCHC2,missense_variant,NMD_transcript_variant,p.R916C,ENST00000585873.5,c.2746C>T,MODERATE,;ZCCHC2,synonymous_variant,p.N996=,ENST00000269499.10,c.2988C>T,LOW,YES +CDH7 1005 BI GRCh38 18 65843882 65843882 + missense_variant Missense_Mutation SNP G G A rs1269949009 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 60 21 c.1052G>A p.Arg351His p.R351H ENST00000323011.7 NM_033646.4 351 cGc/cAc 7/12 P1 A R/H protein_coding CCDS11993.1 1052/2358 CCCTCGCTTTC Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24027;PANTHER:PTHR24027:SF91;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000319166 7/12 rs1269949009;COSV59898182 ENST00000323011 Transcript ENSG00000081138 HGNC:1766 MODERATE 1.91e-05 gnomAD_NFE missense_variant 0;1 possibly_damaging(0.815) Unknown tolerated(0.06) 0;1 Q9ULB5.156 CDH7 HGNC 1 1.0 UPI000013D269 SNV CDH7,missense_variant,p.R351H,ENST00000397968,NM_001362438.2&NM_004361.5,c.1052G>A,MODERATE,YES,tolerated(0.06),possibly_damaging(0.815),1;CDH7,missense_variant,p.R351H,ENST00000536984,NM_001317214.3,c.1052G>A,MODERATE,,tolerated(0.05),benign(0.094),1;CDH7,missense_variant,p.R351H,ENST00000323011,NM_033646.3,c.1052G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.815),1 1377/2728 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.622e-06 0.0 0.0 0.0 0.0 0.0 1.91e-05 0.0 0.0 0 79 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 81 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CDH7,missense_variant,p.R351H,ENST00000397968.4,c.1052G>A,MODERATE,YES;CDH7,missense_variant,p.R351H,ENST00000536984.6,c.1052G>A,MODERATE,;CDH7,missense_variant,p.R351H,ENST00000323011.7,c.1052G>A,MODERATE, +SALL3 27164 BI GRCh38 18 78994682 78994682 + synonymous_variant Silent SNP C C T rs755579014 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 17 c.2691C>T p.Ser897= p.S897= ENST00000537592.7 NM_171999.4 897 tcC/tcT 2/3 P1 T S protein_coding YES CCDS12013.1 2691/3903 CTGTCCGAGTC COSM3668145 PANTHER:PTHR23233;PANTHER:PTHR23233:SF46;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000441823 2/3 rs755579014;COSV101609935;COSV73306272 ENST00000537592 Transcript ENSG00000256463 HGNC:10527 LOW 5.672e-05 gnomAD_EAS synonymous_variant 0;1;1 1.0 Unknown 0;1;1 Q9BXA9.169 SALL3 HGNC 1 A0A384MEH2.9 5.0 UPI000013E5A7 Q9BXA9-1 SNV SALL3,synonymous_variant,p.S897=,ENST00000537592,NM_171999.3,c.2691C>T,LOW,YES,,,1;SALL3,synonymous_variant,p.S764=,ENST00000536229,,c.2292C>T,LOW,,,,1;SALL3,synonymous_variant,p.S897=,ENST00000575389,,c.2691C>T,LOW,,,,1;SALL3,synonymous_variant,p.S629=,ENST00000616649,,c.1887C>T,LOW,,,,1;SALL3,upstream_gene_variant,,ENST00000573324,,,MODIFIER,,,,1;SALL3,downstream_gene_variant,,ENST00000572928,,,MODIFIER,,,,1 2691/6555 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.338e-06 0.0 0.0 0.0 5.672e-05 0.0 0.0 0.0 0.0 0 27 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 27 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SALL3,synonymous_variant,p.S764=,ENST00000536229.7,c.2292C>T,LOW,;SALL3,synonymous_variant,p.S897=,ENST00000575389.6,c.2691C>T,LOW,;SALL3,synonymous_variant,p.S897=,ENST00000537592.7,c.2691C>T,LOW,YES +PWWP3A 84939 BI GRCh38 19 1360197 1360197 + synonymous_variant Silent SNP C C T rs769424395 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 8 c.276C>T p.Arg92= p.R92= ENST00000591337.7 NM_001369789.1 92 cgC/cgT 5/14 A2 T R protein_coding YES 279/2199 CTTCGCGTGGC PANTHER:PTHR31333;PANTHER:PTHR31333:SF4 ENSP00000487567 4/13 rs769424395 ENST00000627377 Transcript ENSG00000160953 HGNC:29641 LOW 3.377e-05 gnomAD_SAS synonymous_variant 1.0 Unknown PWWP3A HGNC 1 A0A0D9SGJ8.36 5.0 UPI000206507A SNV PWWP3A,synonymous_variant,p.R92=,ENST00000591806,NM_001369789.1&NM_001369793.1&NM_001382408.1&NM_001369790.1&NM_001382409.1&NM_032853.5&NM_001382410.1&NM_001369792.1,c.276C>T,LOW,,,,1;PWWP3A,synonymous_variant,p.R93=,ENST00000652273,,c.279C>T,LOW,,,,1;PWWP3A,synonymous_variant,p.R92=,ENST00000415183,NM_001369794.1,c.276C>T,LOW,,,,1;PWWP3A,synonymous_variant,p.R93=,ENST00000627377,,c.279C>T,LOW,YES,,,1;PWWP3A,synonymous_variant,p.R92=,ENST00000591337,,c.276C>T,LOW,,,,1;PWWP3A,downstream_gene_variant,,ENST00000592374,,,MODIFIER,,,,1;PWWP3A,3_prime_UTR_variant,,ENST00000587460,,c.*152C>T,MODIFIER,,,,1;PWWP3A,3_prime_UTR_variant,,ENST00000591433,NM_001369791.1,c.*152C>T,MODIFIER,,,,1;PWWP3A,3_prime_UTR_variant,,ENST00000588810,NM_001369796.1&NM_001369797.1,c.*145C>T,MODIFIER,,,,1;PWWP3A,non_coding_transcript_exon_variant,,ENST00000590695,,n.1856C>T,MODIFIER,,,,1;PWWP3A,upstream_gene_variant,,ENST00000586996,,,MODIFIER,,,,1;PWWP3A,downstream_gene_variant,,ENST00000590866,NM_001369795.1,,MODIFIER,,,,1 279/2235 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.073e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.377e-05 6.7597698034660425e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 63 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PWWP3A,synonymous_variant,p.R93=,ENST00000627377.1,c.279C>T,LOW,;PWWP3A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000587460.6,c.*152C>T,MODIFIER,;PWWP3A,synonymous_variant,p.R92=,ENST00000415183.7,c.276C>T,LOW,;PWWP3A,synonymous_variant,p.R93=,ENST00000652273.1,c.279C>T,LOW,;PWWP3A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000588810.6,c.*145C>T,MODIFIER,;PWWP3A,synonymous_variant,p.R92=,ENST00000591806.6,c.276C>T,LOW,;PWWP3A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000591433.6,c.*152C>T,MODIFIER,;PWWP3A,synonymous_variant,p.R92=,ENST00000591337.7,c.276C>T,LOW,YES;PWWP3A,non_coding_transcript_exon_variant,,ENST00000590695.2,n.1856C>T,MODIFIER, +REXO1 57455 BI GRCh38 19 1828398 1828398 + missense_variant Missense_Mutation SNP C C T rs202065048 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 3 c.391G>A p.Gly131Ser p.G131S ENST00000170168.9 NM_020695.4 131 Ggc/Agc 2/16 0.0006 0.0 0.0014 0.002 0.0 0.0 P2 T G/S protein_coding YES CCDS32866.1 391/3666 GGGGCCGCGGG MobiDB_lite:mobidb-lite ENSP00000170168 2/16 rs202065048 ENST00000170168 Transcript ENSG00000079313 HGNC:24616 MODERATE NM_020695.4 0.002 EAS missense_variant 1.0 benign(0) Unknown tolerated(0.38) Q8N1G1.143 REXO1 HGNC -1 1.0 UPI0000202F63 SNV REXO1,missense_variant,p.G131S,ENST00000170168,NM_020695.4,c.391G>A,MODERATE,YES,tolerated(0.38),benign(0),-1;REXO1,non_coding_transcript_exon_variant,,ENST00000587524,,n.640G>A,MODIFIER,,,,-1;AC012615.6,downstream_gene_variant,,ENST00000590823,,,MODIFIER,YES,,,1;AC012615.6,downstream_gene_variant,,ENST00000587741,,,MODIFIER,,,,1;AC012615.6,downstream_gene_variant,,ENST00000593201,,,MODIFIER,,,,1 516/4609 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 9.144e-05 7.467e-05 2.975e-05 0.0 0.001089 0.0 0.0 0.0 0.0 4.055969839100726e-05 2.4314300389960408e-05 0.0 6.62339007249102e-05 0.0 0.0006048390059731 0.0 eas 0.0006048390059731 0.0 1.5436900866916403e-05 0.0 0.0 0 20 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 18 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS REXO1,non_coding_transcript_exon_variant,,ENST00000587524.1,n.640G>A,MODIFIER,;REXO1,missense_variant,p.G131S,ENST00000170168.9,c.391G>A,MODERATE,YES +AP3D1 8943 BI GRCh38 19 2118738 2118738 + missense_variant Missense_Mutation SNP C C T rs369318068 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 7 c.1576G>A p.Val526Met p.V526M ENST00000345016.9 NM_003938.8 526 Gtg/Atg 15/30 0.0008 0.0008 0.0029 0.0 0.001 0.0 A2 T V/M protein_coding CCDS42459.1 1576/3462 GACCACGTTCT COSM6021753;COSM6021754;COSM6021755 PANTHER:PTHR22781;Pfam:PF01602;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000344055 0.0 0.0002327 15/30 rs369318068 ENST00000345016 Transcript 1.0 ENSG00000065000 HGNC:568 MODERATE 0.0029 AMR missense_variant benign(0.157) Unknown tolerated(0.12) O14617.194 AP3D1 HGNC -1 1.0 UPI0000125031 O14617-1 SNV AP3D1,missense_variant,p.V526M,ENST00000643116,NM_001374799.1&NM_001261826.3,c.1576G>A,MODERATE,YES,tolerated(0.15),benign(0.101),-1;AP3D1,missense_variant,p.V526M,ENST00000345016,NM_003938.8,c.1576G>A,MODERATE,,tolerated(0.12),benign(0.157),-1;AP3D1,missense_variant,p.V268M,ENST00000644728,,c.802G>A,MODERATE,,tolerated(0.24),benign(0.186),-1;AP3D1,downstream_gene_variant,,ENST00000643010,,,MODIFIER,,,,-1;AP3D1,non_coding_transcript_exon_variant,,ENST00000591631,,n.101G>A,MODIFIER,,,,-1;AP3D1,upstream_gene_variant,,ENST00000586177,,,MODIFIER,,,,-1;AP3D1,downstream_gene_variant,,ENST00000590683,,,MODIFIER,,,,-1;AP3D1,upstream_gene_variant,,ENST00000592488,,,MODIFIER,,,,-1 1799/4870 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.825e-05 0.000258 0.0001739 0.0 0.0 0.0 1.776e-05 0.0 0.0 9.459329885430634e-05 0.0002673279959708 0.0 0.0001324150071013 0.0 0.0 0.0 afr 0.0002673279959708 0.0 1.5427800462930463e-05 0.0 0.0 0 27 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 38 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS AP3D1,non_coding_transcript_exon_variant,,ENST00000591631.2,n.101G>A,MODIFIER,;AP3D1,non_coding_transcript_exon_variant,,ENST00000699945.1,n.1229G>A,MODIFIER,;AP3D1,non_coding_transcript_exon_variant,,ENST00000699944.1,n.1554G>A,MODIFIER,;AP3D1,missense_variant,p.V526M,ENST00000700387.1,c.1576G>A,MODERATE,;AP3D1,missense_variant,p.V526M,ENST00000643116.3,c.1576G>A,MODERATE,YES;AP3D1,missense_variant,p.V526M,ENST00000345016.9,c.1576G>A,MODERATE, +SF3A2 8175 BI GRCh38 19 2243427 2243427 + frameshift_variant Frame_Shift_Del DEL C C - novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 7 c.10del p.Gln4SerfsTer44 p.Q4Sfs*44 ENST00000221494.10 NM_007165.5 3 ttC/tt 2/9 P1 - F/X protein_coding YES CCDS12084.1 9/1395 GGACTTCCAGCA PDB-ENSP_mappings:5z56.v;PDB-ENSP_mappings:5z57.v;PDB-ENSP_mappings:5z58.v;PDB-ENSP_mappings:6ah0.v;PDB-ENSP_mappings:6ahd.v;PDB-ENSP_mappings:6ff4.7;PDB-ENSP_mappings:6ff7.7;PDB-ENSP_mappings:6qx9.A2;PANTHER:PTHR23205;MobiDB_lite:mobidb-lite ENSP00000221494 2/9 ENST00000221494 Transcript ENSG00000104897 HGNC:10766 1.0 HIGH NM_007165.5 frameshift_variant 1.0 Unknown Q15428.181 SF3A2 HGNC 1 1.0 UPI0000135468 deletion SF3A2,frameshift_variant,p.Q4Sfs*44,ENST00000221494,NM_007165.5,c.10del,HIGH,YES,,,1;SF3A2,frameshift_variant,p.Q4Sfs*44,ENST00000586396,,c.10del,HIGH,,,,1;SF3A2,non_coding_transcript_exon_variant,,ENST00000592314,,n.89del,MODIFIER,,,,1;SF3A2,non_coding_transcript_exon_variant,,ENST00000589118,,n.117del,MODIFIER,,,,1;SF3A2,non_coding_transcript_exon_variant,,ENST00000592839,,n.96del,MODIFIER,,,,1;SF3A2,non_coding_transcript_exon_variant,,ENST00000590034,,n.47del,MODIFIER,,,,1;SF3A2,upstream_gene_variant,,ENST00000587637,,,MODIFIER,,,,1 124/1619 mutect2;pindel;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 30 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 24 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SF3A2,non_coding_transcript_exon_variant,,ENST00000590034.2,n.46del,MODIFIER,;SF3A2,frameshift_variant,p.Q4Sfs*44,ENST00000586396.2,c.10del,HIGH,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592314.5,n.88del,MODIFIER,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592839.6,n.95del,MODIFIER,;SF3A2,non_coding_transcript_exon_variant,,ENST00000589118.5,n.116del,MODIFIER,;SF3A2,frameshift_variant,p.Q4Sfs*44,ENST00000221494.10,c.10del,HIGH,YES +TLE5 166 BI GRCh38 19 3061249 3061249 + synonymous_variant Silent SNP C C T rs1304356681 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 64 12 c.36G>A p.Ser12= p.S12= ENST00000327141.9 NM_198970.2 12 tcG/tcA 2/7 P1 T S protein_coding CCDS12102.1 36/594 AGGTGCGAGGA PANTHER:PTHR10814:SF31;PANTHER:PTHR10814;Pfam:PF03920 ENSP00000317537 2/7 rs1304356681 ENST00000327141 Transcript ENSG00000104964 HGNC:307 LOW NM_001130.6 6.155e-05 gnomAD_AFR synonymous_variant Unknown Q08117.186 TLE5 HGNC -1 1.0 UPI0000043C26 Q08117-1 SNV TLE5,synonymous_variant,p.S79=,ENST00000221561,NM_198969.1,c.237G>A,LOW,YES,,,-1;TLE5,synonymous_variant,p.S12=,ENST00000327141,NM_198970.2&NM_001130.6,c.36G>A,LOW,,,,-1;TLE5,synonymous_variant,p.S65=,ENST00000586742,,c.195G>A,LOW,,,,-1;TLE5,5_prime_UTR_variant,,ENST00000586839,,c.-133G>A,MODIFIER,,,,-1;TLE5,non_coding_transcript_exon_variant,,ENST00000592330,,n.26G>A,MODIFIER,,,,-1;TLE5,synonymous_variant,p.S12=,ENST00000585557,,c.36G>A,LOW,,,,-1;TLE5,non_coding_transcript_exon_variant,,ENST00000585782,,n.113G>A,MODIFIER,,,,-1;TLE5,non_coding_transcript_exon_variant,,ENST00000586003,,n.70G>A,MODIFIER,,,,-1;TLE5,upstream_gene_variant,,ENST00000587083,,,MODIFIER,,,,-1;TLE5,upstream_gene_variant,,ENST00000587393,,,MODIFIER,,,,-1;TLE5,upstream_gene_variant,,ENST00000592414,,,MODIFIER,,,,-1 331/1798 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.993e-06 6.155e-05 2.892e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 128 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 76 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TLE5,non_coding_transcript_exon_variant,,ENST00000586003.1,n.70G>A,MODIFIER,;TLE5,non_coding_transcript_exon_variant,,ENST00000585782.1,n.113G>A,MODIFIER,;TLE5,synonymous_variant,NMD_transcript_variant,p.S12=,ENST00000585557.1,c.36G>A,LOW,;TLE5,5_prime_UTR_variant,,ENST00000586839.1,c.-133G>A,MODIFIER,;TLE5,non_coding_transcript_exon_variant,,ENST00000592330.5,n.26G>A,MODIFIER,;TLE5,missense_variant,p.A65T,ENST00000586742.5,c.193G>A,MODERATE,;TLE5,synonymous_variant,p.S12=,ENST00000327141.9,c.36G>A,LOW,YES;TLE5,synonymous_variant,p.S79=,ENST00000221561.12,c.237G>A,LOW, +GNA11 2767 BI GRCh38 19 3115014 3115014 + missense_variant Missense_Mutation SNP C C T rs1555702147 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 49 39 c.547C>T p.Arg183Cys p.R183C ENST00000078429.9 NM_002067.5 183 Cgc/Tgc 4/7 P1 T R/C protein_coding YES CCDS12103.1 547/1080 likely_pathogenic GGGTCCGCGTG COSM21651 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Gene3D:1.10.400.10;Pfam:PF00503;SMART:SM00275;Superfamily:SSF47895;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 4/7 rs1555702147;COSV50017316 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.R183C,ENST00000078429,NM_002067.5,c.547C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;GNA11,missense_variant,p.R32C,ENST00000587636,,c.94C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.999),1;GNA11,missense_variant,p.R24C,ENST00000588401,,c.70C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;GNA11,upstream_gene_variant,,ENST00000586180,,,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,upstream_gene_variant,,ENST00000590534,,,MODIFIER,,,,1;GNA11,upstream_gene_variant,,ENST00000591301,,,MODIFIER,,,,1;AC005262.2,downstream_gene_variant,,ENST00000587701,,,MODIFIER,YES,,,-1 837/4190 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 131 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 88 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GNA11,missense_variant,p.P23L,ENST00000588401.1,c.68C>T,MODERATE,;GNA11,synonymous_variant,p.S31=,ENST00000587636.1,c.93C>T,LOW,;GNA11,missense_variant,p.R183C,ENST00000078429.9,c.547C>T,MODERATE,YES +S1PR4 8698 BI GRCh38 19 3179434 3179434 + synonymous_variant Silent SNP C C T rs760646337 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 131 50 c.642C>T p.Gly214= p.G214= ENST00000246115.5 NM_003775.4 214 ggC/ggT 1/1 P1 T G protein_coding YES CCDS12105.1 642/1155 GCCGGCGTCCT Gene3D:1.20.1070.10;Pfam:PF00001;PROSITE_profiles:PS50262;PANTHER:PTHR22750;PANTHER:PTHR22750:SF13;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15349 ENSP00000246115 1/1 rs760646337 ENST00000246115 Transcript ENSG00000125910 HGNC:3170 LOW NM_003775.4 9.801e-05 gnomAD_SAS synonymous_variant 1.0 Unknown O95977.161 S1PR4 HGNC 1 UPI0000050462 SNV S1PR4,synonymous_variant,p.G214=,ENST00000246115,NM_003775.4,c.642C>T,LOW,YES,,,1;S1PR4,non_coding_transcript_exon_variant,,ENST00000591346,,n.320C>T,MODIFIER,,,,1 666/1564 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.599e-05 0.0 2.893e-05 0.0 0.0 0.0 0.0 0.0 9.801e-05 6.757580194971524e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002081599959637 0 208 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 181 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS S1PR4,synonymous_variant,p.G214=,ENST00000246115.5,c.642C>T,LOW,YES;S1PR4,non_coding_transcript_exon_variant,,ENST00000591346.1,n.320C>T,MODIFIER, +MATK 4145 BI GRCh38 19 3778528 3778528 + missense_variant Missense_Mutation SNP C C T rs780442262 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 10 6 c.1265G>A p.Arg422Gln p.R422Q ENST00000310132.11 NM_139355.3 422 cGg/cAg 13/14 T R/Q protein_coding CCDS12114.1 1265/1524 GAGCCCGTCCA CDD:cd05083;Pfam:PF07714;Gene3D:1.10.510.10;SMART:SM00219;Superfamily:SSF56112;PROSITE_profiles:PS50011;PANTHER:PTHR24418:SF399;PANTHER:PTHR24418;Prints:PR00109 ENSP00000308734 13/14 rs780442262 ENST00000310132 Transcript ENSG00000007264 HGNC:6906 MODERATE NM_139355.3 0.0001065 gnomAD_NFE missense_variant probably_damaging(0.995) Unknown deleterious(0) P42679.203 MATK HGNC -1 F1T0G6.79 1.0 UPI0000000C50 P42679-1 SNV MATK,missense_variant,p.R422Q,ENST00000310132,NM_139355.3,c.1265G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;MATK,missense_variant,p.R423Q,ENST00000395045,NM_002378.4,c.1268G>A,MODERATE,YES,deleterious(0),probably_damaging(0.995),-1;MATK,missense_variant,p.R421Q,ENST00000585778,,c.1262G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;MATK,missense_variant,p.R381Q,ENST00000395040,NM_139354.3,c.1142G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;MATK,missense_variant,p.R423Q,ENST00000619596,,c.1268G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;MATK,downstream_gene_variant,,ENST00000587180,,,MODIFIER,,,,-1;MATK,downstream_gene_variant,,ENST00000588983,,,MODIFIER,,,,-1;MATK,downstream_gene_variant,,ENST00000590493,,,MODIFIER,,,,-1;AC005777.1,upstream_gene_variant,,ENST00000588332,,,MODIFIER,YES,,,-1 1629/2098 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.202e-05 6.207e-05 0.0 0.0 0.0 0.0 0.0001065 0.0 0.0 6.761510303476825e-05 0.0001215950032928 0.0 0.0 0.0 0.0 0.0 afr 0.0001215950032928 0.0 7.718669803580269e-05 0.0 0.0 0 23 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 16 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MATK,missense_variant,p.R421Q,ENST00000585778.5,c.1262G>A,MODERATE,;MATK,missense_variant,p.R423Q,ENST00000395045.6,c.1268G>A,MODERATE,;MATK,missense_variant,p.R422Q,ENST00000310132.11,c.1265G>A,MODERATE,YES;MATK,missense_variant,p.R381Q,ENST00000395040.6,c.1142G>A,MODERATE,;MATK,missense_variant,p.R423Q,ENST00000619596.4,c.1268G>A,MODERATE, +ZBTB7A 51341 BI GRCh38 19 4054869 4054869 + missense_variant Missense_Mutation SNP C C T rs1299968386 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 6 6 c.364G>A p.Val122Met p.V122M ENST00000322357.9 NM_015898.4 122 Gtg/Atg 2/3 P1 T V/M protein_coding YES CCDS12119.1 364/1755 GCACACGTGGC PDB-ENSP_mappings:2if5.A;PDB-ENSP_mappings:2nn2.A;PDB-ENSP_mappings:2nn2.B;Gene3D:3.30.710.10;Pfam:PF00651;PANTHER:PTHR46105;PANTHER:PTHR46105:SF6;SMART:SM00225;Superfamily:SSF54695;CDD:cd18326 ENSP00000323670 2/3 rs1299968386 ENST00000322357 Transcript ENSG00000178951 HGNC:18078 MODERATE NM_015898.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.984) Unknown deleterious(0) O95365.188 ZBTB7A HGNC -1 1.0 UPI000006E9D9 SNV ZBTB7A,missense_variant,p.V122M,ENST00000322357,NM_015898.4,c.364G>A,MODERATE,YES,deleterious(0),probably_damaging(0.984),-1;ZBTB7A,missense_variant,p.V122M,ENST00000601588,NM_001317990.2,c.364G>A,MODERATE,,deleterious(0),probably_damaging(0.984),-1 597/6437 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 12 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZBTB7A,missense_variant,p.V122M,ENST00000601588.1,c.364G>A,MODERATE,;ZBTB7A,missense_variant,p.V122M,ENST00000322357.9,c.364G>A,MODERATE,YES +HSD11B1L 374875 BI GRCh38 19 5687638 5687638 + missense_variant Missense_Mutation SNP G G A rs1214771188 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 8 4 c.638G>A p.Arg213Gln p.R213Q ENST00000423665.6 NM_198533.3 213 cGa/cAa 7/8 A R/Q protein_coding CCDS45931.1 638/948 CCTCCGAGATC Gene3D:3.40.50.720;PANTHER:PTHR44279;PANTHER:PTHR44279:SF3;Superfamily:SSF51735 ENSP00000407154 7/8 rs1214771188 ENST00000423665 Transcript ENSG00000167733 HGNC:30419 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant benign(0.019) Unknown tolerated(0.15) Q7Z5J1.125 HSD11B1L HGNC 1 1.0 UPI00001B2966 Q7Z5J1-1 SNV HSD11B1L,missense_variant,p.R213Q,ENST00000581521,,c.638G>A,MODERATE,,tolerated(0.11),benign(0.01),1;HSD11B1L,missense_variant,p.R213Q,ENST00000339423,NM_198706.3,c.638G>A,MODERATE,,tolerated(0.11),benign(0.01),1;HSD11B1L,missense_variant,p.R213Q,ENST00000581773,,c.638G>A,MODERATE,,tolerated(0.11),benign(0.01),1;HSD11B1L,missense_variant,p.R126Q,ENST00000342970,NM_198707.3,c.377G>A,MODERATE,,tolerated(0.1),benign(0.01),1;HSD11B1L,missense_variant,p.R260Q,ENST00000616276,NM_001267868.2,c.779G>A,MODERATE,YES,tolerated(0.13),benign(0.031),1;HSD11B1L,missense_variant,p.R132Q,ENST00000577917,NM_001267871.2,c.395G>A,MODERATE,,tolerated(0.35),benign(0.005),1;HSD11B1L,missense_variant,p.R79Q,ENST00000581893,NM_198708.3&NM_001267869.2,c.236G>A,MODERATE,,tolerated(0.07),benign(0.01),1;HSD11B1L,missense_variant,p.R213Q,ENST00000423665,NM_198533.3,c.638G>A,MODERATE,,tolerated(0.15),benign(0.019),1;HSD11B1L,missense_variant,p.R132Q,ENST00000301382,NM_198705.3,c.395G>A,MODERATE,,tolerated(0.1),benign(0.044),1;HSD11B1L,missense_variant,p.R79Q,ENST00000411793,NM_198704.3,c.236G>A,MODERATE,,tolerated(0.37),benign(0.019),1;HSD11B1L,missense_variant,p.R79Q,ENST00000583928,,c.236G>A,MODERATE,,tolerated(0.07),benign(0.01),1;HSD11B1L,missense_variant,p.R125Q,ENST00000578046,,c.374G>A,MODERATE,,tolerated(0.06),benign(0.013),1;HSD11B1L,synonymous_variant,p.P101=,ENST00000579559,NM_001267870.2,c.303G>A,LOW,,,,1;RPL36,intron_variant,,ENST00000577222,,c.-299-2393G>A,MODIFIER,YES,,,1;RPL36,intron_variant,,ENST00000579649,,c.-59-2695G>A,MODIFIER,,,,1;RPL36,upstream_gene_variant,,ENST00000347512,NM_015414.4&NM_033643.3,,MODIFIER,,,,1;LONP1,downstream_gene_variant,,ENST00000360614,NM_004793.4,,MODIFIER,YES,,,-1;RPL36,upstream_gene_variant,,ENST00000394580,,,MODIFIER,,,,1;HSD11B1L,downstream_gene_variant,,ENST00000422535,,,MODIFIER,,,,1;LONP1,downstream_gene_variant,,ENST00000540670,NM_001276480.1,,MODIFIER,,,,-1;HSD11B1L,downstream_gene_variant,,ENST00000577257,,,MODIFIER,,,,1;RPL36,upstream_gene_variant,,ENST00000579446,,,MODIFIER,,,,1;RPL36,upstream_gene_variant,,ENST00000582463,,,MODIFIER,,,,1;LONP1,downstream_gene_variant,,ENST00000585374,,,MODIFIER,,,,-1;LONP1,downstream_gene_variant,,ENST00000589473,,,MODIFIER,,,,-1;LONP1,downstream_gene_variant,,ENST00000590729,,,MODIFIER,,,,-1;LONP1,downstream_gene_variant,,ENST00000593119,NM_001276479.2,,MODIFIER,,,,-1;RPL36,intron_variant,,ENST00000582380,,n.246-2393G>A,MODIFIER,,,,1;HSD11B1L,downstream_gene_variant,,ENST00000577701,,,MODIFIER,,,,1;HSD11B1L,3_prime_UTR_variant,,ENST00000579562,,c.*298G>A,MODIFIER,,,,1;HSD11B1L,non_coding_transcript_exon_variant,,ENST00000578167,,n.841G>A,MODIFIER,,,,1;HSD11B1L,non_coding_transcript_exon_variant,,ENST00000577920,,n.838G>A,MODIFIER,,,,1;HSD11B1L,non_coding_transcript_exon_variant,,ENST00000581423,,n.274G>A,MODIFIER,,,,1;HSD11B1L,downstream_gene_variant,,ENST00000578832,,,MODIFIER,,,,1;HSD11B1L,downstream_gene_variant,,ENST00000582346,,,MODIFIER,,,,1;HSD11B1L,downstream_gene_variant,,ENST00000584904,,,MODIFIER,,,,1;LONP1,downstream_gene_variant,,ENST00000587552,,,MODIFIER,,,,-1;LONP1,downstream_gene_variant,,ENST00000590558,,,MODIFIER,,,,-1;RPL36,upstream_gene_variant,,ENST00000590786,,,MODIFIER,,,,1 888/1525 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 10 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HSD11B1L,non_coding_transcript_exon_variant,,ENST00000581423.1,n.274G>A,MODIFIER,;HSD11B1L,missense_variant,p.E125K,ENST00000578046.1,c.373G>A,MODERATE,;HSD11B1L,missense_variant,p.R260Q,ENST00000616276.4,c.779G>A,MODERATE,;RPL36,intron_variant,,ENST00000577222.5,c.-299-2393G>A,MODIFIER,;HSD11B1L,non_coding_transcript_exon_variant,,ENST00000577920.1,n.838G>A,MODIFIER,;HSD11B1L,synonymous_variant,p.P101=,ENST00000579559.1,c.303G>A,LOW,;HSD11B1L,missense_variant,p.R213Q,ENST00000581521.5,c.638G>A,MODERATE,;HSD11B1L,non_coding_transcript_exon_variant,,ENST00000578167.5,n.841G>A,MODIFIER,;HSD11B1L,missense_variant,p.R126Q,ENST00000342970.6,c.377G>A,MODERATE,;HSD11B1L,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000579562.5,c.*298G>A,MODIFIER,;HSD11B1L,missense_variant,p.R79Q,ENST00000583928.5,c.236G>A,MODERATE,;HSD11B1L,missense_variant,p.R213Q,ENST00000423665.6,c.638G>A,MODERATE,;RPL36,intron_variant,,ENST00000582380.6,n.246-2393G>A,MODIFIER,;HSD11B1L,missense_variant,p.R213Q,ENST00000339423.7,c.638G>A,MODERATE,YES;HSD11B1L,missense_variant,p.R213Q,ENST00000581773.5,c.638G>A,MODERATE,;HSD11B1L,missense_variant,p.R79Q,ENST00000411793.6,c.236G>A,MODERATE,;HSD11B1L,missense_variant,p.R132Q,ENST00000301382.8,c.395G>A,MODERATE,;HSD11B1L,missense_variant,p.R79Q,ENST00000581893.5,c.236G>A,MODERATE,;HSD11B1L,missense_variant,p.R132Q,ENST00000577917.5,c.395G>A,MODERATE,;RPL36,intron_variant,,ENST00000579649.5,c.-59-2695G>A,MODIFIER, +XAB2 56949 BI GRCh38 19 7620650 7620650 + missense_variant Missense_Mutation SNP G G A rs1467600531 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 4 c.1991C>T p.Ala664Val p.A664V ENST00000358368.5 NM_020196.3 664 gCg/gTg 15/19 P1 A A/V protein_coding YES CCDS32892.1 1991/2568 CACGCGCGTGC Gene3D:1.25.40.10;PDB-ENSP_mappings:5mqf.M;PDB-ENSP_mappings:5xjc.I;PDB-ENSP_mappings:5yzg.I;PDB-ENSP_mappings:5z56.I;PDB-ENSP_mappings:5z57.I;PDB-ENSP_mappings:6ff7.M;PDB-ENSP_mappings:6icz.I;PDB-ENSP_mappings:6id0.I;PDB-ENSP_mappings:6id1.I;PDB-ENSP_mappings:6qdv.T;PANTHER:PTHR11246;PANTHER:PTHR11246:SF5;Superfamily:SSF48452 ENSP00000351137 15/19 rs1467600531;COSV50367954 ENST00000358368 Transcript ENSG00000076924 HGNC:14089 MODERATE NM_020196.3 8.918e-06 gnomAD_NFE missense_variant 0;1 1.0 benign(0.026) Unknown tolerated(0.27) 0;1 Q9HCS7.189 XAB2 HGNC -1 1.0 UPI0000001BDE SNV XAB2,missense_variant,p.A664V,ENST00000358368,NM_020196.3,c.1991C>T,MODERATE,YES,tolerated(0.27),benign(0.026),-1;CAMSAP3,downstream_gene_variant,,ENST00000160298,NM_020902.2,,MODIFIER,,,,1;CAMSAP3,downstream_gene_variant,,ENST00000446248,NM_001080429.3,,MODIFIER,YES,,,1;MIR6792,downstream_gene_variant,,ENST00000614460,,,MODIFIER,YES,,,1;XAB2,non_coding_transcript_exon_variant,,ENST00000595288,,n.3719C>T,MODIFIER,,,,-1;XAB2,non_coding_transcript_exon_variant,,ENST00000600230,,n.374C>T,MODIFIER,,,,-1;CAMSAP3,downstream_gene_variant,,ENST00000593434,,,MODIFIER,,,,1;CAMSAP3,downstream_gene_variant,,ENST00000595692,,,MODIFIER,,,,1;XAB2,downstream_gene_variant,,ENST00000596134,,,MODIFIER,,,,-1 2009/2647 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.013e-06 0.0 0.0 0.0 0.0 0.0 8.918e-06 0.0 0.0 0 50 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 36 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS XAB2,non_coding_transcript_exon_variant,,ENST00000600230.1,n.374C>T,MODIFIER,;XAB2,non_coding_transcript_exon_variant,,ENST00000595288.5,n.3719C>T,MODIFIER,;XAB2,missense_variant,p.A664V,ENST00000358368.5,c.1991C>T,MODERATE,YES +MYO1F 4542 BI GRCh38 19 8536319 8536319 + missense_variant Missense_Mutation SNP G G A rs201138222 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 7 c.1976C>T p.Ala659Val p.A659V ENST00000644032.2 NM_001348355.2 659 gCg/gTg 19/28 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 A A/V protein_coding YES 1976/3297 TGACCGCCCGA COSM1286451 PROSITE_profiles:PS51456;CDD:cd01378;PANTHER:PTHR13140;PANTHER:PTHR13140:SF747;Pfam:PF00063;Gene3D:3.30.70.3240;SMART:SM00242;Superfamily:SSF52540 ENSP00000481682 20/29 rs201138222;COSV57796026 ENST00000613525 Transcript ENSG00000142347 HGNC:7600 MODERATE 0.0008 AFR missense_variant 0;1 1.0 benign(0.164) Unknown deleterious(0.02) 0;1 O00160.189 MYO1F HGNC -1 5.0 UPI00001678F0 SNV MYO1F,missense_variant,p.A659V,ENST00000613525,,c.1976C>T,MODERATE,YES,deleterious(0.02),benign(0.164),-1;MYO1F,missense_variant,p.A659V,ENST00000644032,NM_001348355.2&NM_012335.4,c.1976C>T,MODERATE,,deleterious(0.02),benign(0.164),-1;MYO1F,non_coding_transcript_exon_variant,,ENST00000598005,,n.459C>T,MODIFIER,,,,-1;MYO1F,non_coding_transcript_exon_variant,,ENST00000597222,,n.390C>T,MODIFIER,,,,-1;MYO1F,downstream_gene_variant,,ENST00000602136,,,MODIFIER,,,,-1 2244/4296 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.668e-05 6.501e-05 0.000116 0.0 5.588e-05 0.0 1.772e-05 0.0001657 0.0 2.712860077735968e-05 2.441409924358595e-05 0.0 0.0001331380044575 0.0 0.0 0.0 amr 0.0001331380044575 0.0 1.5443500160472468e-05 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYO1F,non_coding_transcript_exon_variant,,ENST00000598005.2,n.459C>T,MODIFIER,;MYO1F,non_coding_transcript_exon_variant,,ENST00000597222.2,n.390C>T,MODIFIER,;MYO1F,missense_variant,p.A659V,ENST00000644032.2,c.1976C>T,MODERATE,YES +KRI1 65095 BI GRCh38 19 10561226 10561226 + synonymous_variant Silent SNP G G A rs565439115 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 4 c.528C>T p.Gly176= p.G176= ENST00000312962.12 NM_023008.5 176 ggC/ggT 7/19 0.0002 0.0 0.0 0.0 0.0 0.001 P4 A G protein_coding 528/2112 CCAGCGCCGTC PANTHER:PTHR14490;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000320917 7/19 rs565439115;COSV100469798 ENST00000312962 Transcript ENSG00000129347 HGNC:25769 LOW NM_023008.5 0.001 SAS synonymous_variant 0;1 Unknown 0;1 Q8N9T8.131 KRI1 HGNC -1 1.0 UPI0000203328 SNV KRI1,synonymous_variant,p.G182=,ENST00000652042,,c.546C>T,LOW,YES,,,-1;KRI1,synonymous_variant,p.G176=,ENST00000312962,NM_023008.5,c.528C>T,LOW,,,,-1;KRI1,synonymous_variant,p.G64=,ENST00000432197,,c.192C>T,LOW,,,,-1;KRI1,synonymous_variant,p.G116=,ENST00000543682,,c.348C>T,LOW,,,,-1;KRI1,intron_variant,,ENST00000539027,,c.429+565C>T,MODIFIER,,,,-1;KRI1,non_coding_transcript_exon_variant,,ENST00000537964,,n.430C>T,MODIFIER,,,,-1;KRI1,upstream_gene_variant,,ENST00000618579,,,MODIFIER,,,,-1;KRI1,non_coding_transcript_exon_variant,,ENST00000536689,,n.1208C>T,MODIFIER,,,,-1;KRI1,non_coding_transcript_exon_variant,,ENST00000612875,,n.664C>T,MODIFIER,,,,-1;KRI1,non_coding_transcript_exon_variant,,ENST00000478863,,n.500C>T,MODIFIER,,,,-1;KRI1,non_coding_transcript_exon_variant,,ENST00000546063,,n.537C>T,MODIFIER,,,,-1;KRI1,upstream_gene_variant,,ENST00000536714,,,MODIFIER,,,,-1;KRI1,upstream_gene_variant,,ENST00000537363,,,MODIFIER,,,,-1;KRI1,upstream_gene_variant,,ENST00000537433,,,MODIFIER,,,,-1;KRI1,upstream_gene_variant,,ENST00000543842,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000544397,,,MODIFIER,,,,-1 539/2989 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.193e-05 6.152e-05 0.0 0.0 0.0 0.0 8.793e-06 0.0 3.266e-05 2.0294399291742596e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086320066358894e-05 0.0 3.086320066358894e-05 0.0 0.0002085940068354 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 42 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KRI1,non_coding_transcript_exon_variant,,ENST00000537964.5,n.430C>T,MODIFIER,;KRI1,non_coding_transcript_exon_variant,,ENST00000546063.5,n.537C>T,MODIFIER,;KRI1,synonymous_variant,p.G116=,ENST00000543682.3,c.348C>T,LOW,;KRI1,synonymous_variant,p.G64=,ENST00000432197.5,c.192C>T,LOW,;KRI1,intron_variant,,ENST00000539027.5,c.429+565C>T,MODIFIER,;KRI1,non_coding_transcript_exon_variant,,ENST00000612875.4,n.664C>T,MODIFIER,;KRI1,non_coding_transcript_exon_variant,,ENST00000478863.5,n.500C>T,MODIFIER,;KRI1,non_coding_transcript_exon_variant,,ENST00000536689.5,n.1208C>T,MODIFIER,;KRI1,synonymous_variant,p.G182=,ENST00000652042.1,c.546C>T,LOW,;KRI1,synonymous_variant,p.G176=,ENST00000312962.12,c.528C>T,LOW,YES +SMARCA4 6597 BI GRCh38 19 11021837 11021837 + missense_variant Missense_Mutation SNP C C T rs1238758086 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 5 13 c.2729C>T p.Thr910Met p.T910M ENST00000646693.2 NM_001128849.3 910 aCg/aTg 19/36 P4 T T/M protein_coding CCDS12253.1 2729/4944 other;uncertain_significance GCTGACGGGCA COSM1226753;COSM88025 PDB-ENSP_mappings:6lth.I;PDB-ENSP_mappings:6ltj.I;CDD:cd18062;Pfam:PF00176;Gene3D:3.40.50.10810;SMART:SM00487;Superfamily:SSF52540;PROSITE_profiles:PS51192;PANTHER:PTHR10799;PANTHER:PTHR10799:SF76 ENSP00000343896 19/35 rs1238758086;COSV60785486;COSV60802491 ENST00000344626 Transcript 1.0 ENSG00000127616 HGNC:11100 MODERATE NM_003072.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1;1;1 probably_damaging(0.998) Unknown deleterious(0) 0;1;1 P51532.227 SMARCA4 HGNC 1 A7E2E1.120 1.0 UPI000006F973 P51532-1 SNV SMARCA4,missense_variant,p.T910M,ENST00000644737,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T910M,ENST00000646693,NM_001128849.3,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;SMARCA4,missense_variant,p.T910M,ENST00000590574,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000642726,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;SMARCA4,missense_variant,p.T910M,ENST00000429416,NM_001128844.3,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000642628,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;SMARCA4,missense_variant,p.T910M,ENST00000643549,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T910M,ENST00000646510,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000646484,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000344626,NM_003072.5,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000643296,NM_001128845.2,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T910M,ENST00000647230,NM_001128847.4&NM_001374457.1,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T974M,ENST00000413806,,c.2921C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;SMARCA4,missense_variant,p.T910M,ENST00000450717,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;SMARCA4,missense_variant,p.T910M,ENST00000645460,NM_001128848.2,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000444061,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T868M,ENST00000591545,,c.2603C>T,MODERATE,,deleterious(0),probably_damaging(1),1;SMARCA4,missense_variant,p.T910M,ENST00000589677,NM_001128846.2,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T910M,ENST00000541122,,c.2729C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T715M,ENST00000643995,,c.2144C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T459M,ENST00000644963,,c.1376C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T429M,ENST00000643208,,c.1286C>T,MODERATE,,deleterious(0),probably_damaging(1),1;SMARCA4,missense_variant,p.T486M,ENST00000644065,,c.1457C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T405M,ENST00000642350,,c.1214C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;SMARCA4,missense_variant,p.T344M,ENST00000646746,,c.1031C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;SMARCA4,missense_variant,p.T362M,ENST00000643857,,c.1085C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;SMARCA4,missense_variant,p.T361M,ENST00000647268,,c.1082C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T359M,ENST00000646183,,c.1076C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;SMARCA4,missense_variant,p.T339M,ENST00000643534,,c.1016C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;SMARCA4,missense_variant,p.T31M,ENST00000642508,,c.92C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;SMARCA4,missense_variant,p.T188M,ENST00000646513,,c.563C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122,,n.311C>T,MODIFIER,,,,1;SMARCA4,missense_variant,p.T501M,ENST00000644327,,c.1502C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T406M,ENST00000645061,,c.1217C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;SMARCA4,missense_variant,p.T198M,ENST00000645648,,c.593C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;SMARCA4,missense_variant,p.T71M,ENST00000646236,,c.212C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;SMARCA4,3_prime_UTR_variant,,ENST00000644290,,c.*409C>T,MODIFIER,,,,1;SMARCA4,3_prime_UTR_variant,,ENST00000646593,,c.*409C>T,MODIFIER,,,,1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,,n.1257C>T,MODIFIER,,,,1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000644267,,n.1084C>T,MODIFIER,,,,1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,,n.801C>T,MODIFIER,,,,1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,,n.1060C>T,MODIFIER,,,,1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988,,n.378C>T,MODIFIER,,,,1 2905/5577 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 38 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 18 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SMARCA4,synonymous_variant,p.D30=,ENST00000642508.1,c.90C>T,LOW,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799.5,n.1257C>T,MODIFIER,;SMARCA4,missense_variant,NMD_transcript_variant,p.T71M,ENST00000646236.1,c.212C>T,MODERATE,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595.5,n.801C>T,MODIFIER,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988.5,n.378C>T,MODIFIER,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122.5,n.311C>T,MODIFIER,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604.6,n.1060C>T,MODIFIER,;SMARCA4,missense_variant,NMD_transcript_variant,p.T198M,ENST00000645648.1,c.593C>T,MODERATE,;SMARCA4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646593.1,c.*409C>T,MODIFIER,;SMARCA4,missense_variant,p.T188M,ENST00000646513.1,c.563C>T,MODERATE,;SMARCA4,synonymous_variant,p.D338=,ENST00000643534.1,c.1014C>T,LOW,;SMARCA4,synonymous_variant,p.D343=,ENST00000646746.1,c.1029C>T,LOW,;SMARCA4,missense_variant,p.R359W,ENST00000646183.1,c.1075C>T,MODERATE,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000644267.1,n.1084C>T,MODIFIER,;SMARCA4,missense_variant,p.R362W,ENST00000643857.1,c.1084C>T,MODERATE,;SMARCA4,missense_variant,p.T361M,ENST00000647268.1,c.1082C>T,MODERATE,;SMARCA4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644290.1,c.*409C>T,MODIFIER,;SMARCA4,missense_variant,p.T405M,ENST00000642350.1,c.1214C>T,MODERATE,;SMARCA4,missense_variant,NMD_transcript_variant,p.T406M,ENST00000645061.1,c.1217C>T,MODERATE,;SMARCA4,missense_variant,p.T429M,ENST00000643208.1,c.1286C>T,MODERATE,;SMARCA4,synonymous_variant,p.D458=,ENST00000644963.1,c.1374C>T,LOW,;SMARCA4,missense_variant,p.R486W,ENST00000644065.1,c.1456C>T,MODERATE,;SMARCA4,synonymous_variant,NMD_transcript_variant,p.D500=,ENST00000644327.1,c.1500C>T,LOW,;SMARCA4,missense_variant,p.R715W,ENST00000643995.1,c.2143C>T,MODERATE,;SMARCA4,missense_variant,p.R868W,ENST00000591545.6,c.2602C>T,MODERATE,;SMARCA4,missense_variant,p.T907M,ENST00000704345.1,c.2720C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000590574.6,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000444061.8,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000589677.5,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000541122.6,c.2729C>T,MODERATE,;SMARCA4,missense_variant,NMD_transcript_variant,p.T910M,ENST00000704344.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000645460.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000344626.10,c.2729C>T,MODERATE,YES;SMARCA4,missense_variant,p.T910M,ENST00000646693.2,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000429416.8,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000646510.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000711079.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000647230.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000643296.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000642628.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000643549.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000644737.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000646484.1,c.2729C>T,MODERATE,;SMARCA4,missense_variant,p.T910M,ENST00000642726.1,c.2729C>T,MODERATE, +MAN2B1 4125 BI GRCh38 19 12647467 12647467 + synonymous_variant Silent SNP G G A rs1403072896 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 70 16 c.2796C>T p.Ser932= p.S932= ENST00000456935.7 NM_000528.4 932 agC/agT 22/24 P4 A S protein_coding YES CCDS32919.1 2796/3036 GGGGCGCTCAG PANTHER:PTHR11607;PANTHER:PTHR11607:SF3;Gene3D:2.60.40.1360;Pfam:PF17677;Superfamily:SSF74650 ENSP00000395473 22/24 rs1403072896;COSV55474793 ENST00000456935 Transcript 1.0 ENSG00000104774 HGNC:6826 LOW NM_000528.4 3.266e-05 gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 O00754.205 MAN2B1 HGNC -1 1.0 UPI00000559EC O00754-1 SNV MAN2B1,synonymous_variant,p.S932=,ENST00000456935,NM_000528.4,c.2796C>T,LOW,YES,,,-1;MAN2B1,synonymous_variant,p.S931=,ENST00000221363,NM_001173498.1,c.2793C>T,LOW,,,,-1;MAN2B1,downstream_gene_variant,,ENST00000433513,,,MODIFIER,,,,-1;MAN2B1,upstream_gene_variant,,ENST00000480851,,,MODIFIER,,,,-1;MAN2B1,downstream_gene_variant,,ENST00000595880,,,MODIFIER,,,,-1;AC010422.3,synonymous_variant,p.S119=,ENST00000597692,,c.357C>T,LOW,YES,,,-1;MAN2B1,non_coding_transcript_exon_variant,,ENST00000466794,,n.3386C>T,MODIFIER,,,,-1;MAN2B1,non_coding_transcript_exon_variant,,ENST00000469423,,n.118C>T,MODIFIER,,,,-1;MAN2B1,non_coding_transcript_exon_variant,,ENST00000493218,,n.207C>T,MODIFIER,,,,-1;MAN2B1,downstream_gene_variant,,ENST00000593686,,,MODIFIER,,,,-1;MAN2B1,downstream_gene_variant,,ENST00000596591,,,MODIFIER,,,,-1;RPL10P16,upstream_gene_variant,,ENST00000325000,,,MODIFIER,YES,,,-1 2837/3185 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.98e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.266e-05 0 123 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 86 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAN2B1,non_coding_transcript_exon_variant,,ENST00000466794.5,n.3386C>T,MODIFIER,;MAN2B1,synonymous_variant,p.S931=,ENST00000221363.8,c.2793C>T,LOW,;MAN2B1,non_coding_transcript_exon_variant,,ENST00000493218.5,n.207C>T,MODIFIER,;MAN2B1,synonymous_variant,p.S932=,ENST00000456935.7,c.2796C>T,LOW,YES;MAN2B1,non_coding_transcript_exon_variant,,ENST00000469423.1,n.118C>T,MODIFIER,;ENSG00000269242,missense_variant,NMD_transcript_variant,p.R119C,ENST00000597692.1,c.355C>T,MODERATE,YES +DHPS 1725 BI GRCh38 19 12679863 12679863 + synonymous_variant Silent SNP C C T rs776689877 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 5 c.432G>A p.Ala144= p.A144= ENST00000210060.12 NM_001930.4 144 gcG/gcA 3/9 P2 T A protein_coding CCDS12276.1 432/1110 GTGGGCGCCAG PDB-ENSP_mappings:1dhs.A;PDB-ENSP_mappings:1rlz.A;PDB-ENSP_mappings:1roz.A;PDB-ENSP_mappings:1roz.B;PDB-ENSP_mappings:1rqd.A;PDB-ENSP_mappings:1rqd.B;Gene3D:3.40.910.10;PDB-ENSP_mappings:6p4v.A;PDB-ENSP_mappings:6p4v.B;PDB-ENSP_mappings:6pgr.A;PDB-ENSP_mappings:6pgr.B;PDB-ENSP_mappings:6xxh.A;PDB-ENSP_mappings:6xxh.B;PDB-ENSP_mappings:6xxi.A;PDB-ENSP_mappings:6xxi.B;PDB-ENSP_mappings:6xxj.A;PDB-ENSP_mappings:6xxj.B;PDB-ENSP_mappings:6xxk.A;PDB-ENSP_mappings:6xxk.B;PDB-ENSP_mappings:6xxl.A;PDB-ENSP_mappings:6xxl.B;PDB-ENSP_mappings:6xxm.A;PDB-ENSP_mappings:6xxm.B;Pfam:PF01916;PANTHER:PTHR11703;PANTHER:PTHR11703:SF0;Superfamily:SSF52467;TIGRFAM:TIGR00321 ENSP00000210060 3/9 rs776689877;COSV52951698 ENST00000210060 Transcript 1.0 ENSG00000095059 HGNC:2869 LOW NM_001930.4 4.621e-05 gnomAD_FIN synonymous_variant 0;1 Unknown 0;1 P49366.193 DHPS HGNC -1 A0A024R7D0.35 1.0 UPI00001293B4 P49366-1 SNV DHPS,synonymous_variant,p.A144=,ENST00000210060,NM_001930.4,c.432G>A,LOW,,,,-1;DHPS,synonymous_variant,p.A102=,ENST00000594424,NM_001206974.1,c.306G>A,LOW,,,,-1;DHPS,synonymous_variant,p.A143=,ENST00000614126,NM_001369691.1,c.429G>A,LOW,YES,,,-1;DHPS,synonymous_variant,p.A144=,ENST00000351660,NM_013406.2&NM_001369692.1,c.432G>A,LOW,,,,-1;DHPS,synonymous_variant,p.A21=,ENST00000597152,,c.63G>A,LOW,,,,-1;DHPS,synonymous_variant,p.A77=,ENST00000596162,,c.231G>A,LOW,,,,-1;WDR83,downstream_gene_variant,,ENST00000418543,NM_001099737.3&NM_032332.4,,MODIFIER,YES,,,1;WDR83,downstream_gene_variant,,ENST00000547797,,,MODIFIER,,,,1;DHPS,upstream_gene_variant,,ENST00000598246,NM_001369693.1,,MODIFIER,,,,-1;DHPS,upstream_gene_variant,,ENST00000600639,,,MODIFIER,,,,-1;DHPS,upstream_gene_variant,,ENST00000600864,,,MODIFIER,,,,-1;DHPS,non_coding_transcript_exon_variant,,ENST00000599481,,n.319G>A,MODIFIER,,,,-1;AC010422.8,missense_variant,p.A131T,ENST00000648033,,c.391G>A,MODERATE,YES,,unknown(0),-1;DHPS,missense_variant,p.A133T,ENST00000595912,,c.397G>A,MODERATE,,,unknown(0),-1;DHPS,missense_variant,p.A50T,ENST00000600451,,c.148G>A,MODERATE,,,unknown(0),-1;DHPS,synonymous_variant,p.A144=,ENST00000601537,,c.432G>A,LOW,,,,-1;DHPS,3_prime_UTR_variant,,ENST00000598850,,c.*132G>A,MODIFIER,,,,-1;DHPS,3_prime_UTR_variant,,ENST00000595100,,c.*44G>A,MODIFIER,,,,-1;DHPS,3_prime_UTR_variant,,ENST00000593423,,c.*44G>A,MODIFIER,,,,-1;DHPS,non_coding_transcript_exon_variant,,ENST00000595844,,n.120G>A,MODIFIER,,,,-1;DHPS,non_coding_transcript_exon_variant,,ENST00000596847,,n.168G>A,MODIFIER,,,,-1;DHPS,non_coding_transcript_exon_variant,,ENST00000593400,,n.52G>A,MODIFIER,,,,-1;DHPS,non_coding_transcript_exon_variant,,ENST00000593432,,n.315G>A,MODIFIER,,,,-1;DHPS,intron_variant,,ENST00000601639,,c.373-144G>A,MODIFIER,,,,-1;WDR83,downstream_gene_variant,,ENST00000425834,,,MODIFIER,,,,1;WDR83,downstream_gene_variant,,ENST00000546754,,,MODIFIER,,,,1;WDR83,downstream_gene_variant,,ENST00000548381,,,MODIFIER,,,,1;WDR83,downstream_gene_variant,,ENST00000552700,,,MODIFIER,,,,1;DHPS,downstream_gene_variant,,ENST00000593473,,,MODIFIER,,,,-1;DHPS,upstream_gene_variant,,ENST00000600510,,,MODIFIER,,,,-1;AC010422.2,downstream_gene_variant,,ENST00000593554,,,MODIFIER,YES,,,-1 546/1345 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.198e-05 0.0 0.0 0.0 0.0 4.621e-05 1.77e-05 0.0 0.0 2.7042000510846265e-05 2.4320199372596107e-05 0.0 0.000198833993636 0.0 0.0 0.0 amr 0.000198833993636 0.0 0.0 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DHPS,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000595100.1,c.*44G>A,MODIFIER,;DHPS,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000593423.5,c.*44G>A,MODIFIER,;DHPS,non_coding_transcript_exon_variant,,ENST00000599481.1,n.319G>A,MODIFIER,;DHPS,non_coding_transcript_exon_variant,,ENST00000593432.1,n.315G>A,MODIFIER,;DHPS,synonymous_variant,p.A77=,ENST00000596162.1,c.231G>A,LOW,;DHPS,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000598850.5,c.*132G>A,MODIFIER,;DHPS,synonymous_variant,p.A21=,ENST00000597152.5,c.63G>A,LOW,;DHPS,missense_variant,NMD_transcript_variant,p.R49H,ENST00000600451.5,c.146G>A,MODERATE,;DHPS,missense_variant,NMD_transcript_variant,p.A133T,ENST00000595912.5,c.397G>A,MODERATE,;DHPS,non_coding_transcript_exon_variant,,ENST00000596847.5,n.168G>A,MODIFIER,;DHPS,non_coding_transcript_exon_variant,,ENST00000593400.5,n.52G>A,MODIFIER,;DHPS,non_coding_transcript_exon_variant,,ENST00000595844.5,n.120G>A,MODIFIER,;DHPS,synonymous_variant,NMD_transcript_variant,p.A144=,ENST00000601537.5,c.432G>A,LOW,;DHPS,synonymous_variant,p.A102=,ENST00000594424.5,c.306G>A,LOW,;DHPS,intron_variant,NMD_transcript_variant,,ENST00000601639.5,c.373-144G>A,MODIFIER,;DHPS,synonymous_variant,p.A144=,ENST00000351660.9,c.432G>A,LOW,;DHPS,synonymous_variant,p.A144=,ENST00000210060.12,c.432G>A,LOW,YES;ENSG00000285589,missense_variant,NMD_transcript_variant,p.A131T,ENST00000648033.1,c.391G>A,MODERATE,YES +RNASEH2A 10535 BI GRCh38 19 12807497 12807497 + synonymous_variant Silent SNP C C T rs778120777 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 34 c.402C>T p.Asn134= p.N134= ENST00000221486.6 NM_006397.3 134 aaC/aaT 4/8 P1 T N protein_coding YES CCDS12282.1 402/900 uncertain_significance GTGAACGTCAC PDB-ENSP_mappings:3p56.A;PDB-ENSP_mappings:3p56.D;PDB-ENSP_mappings:3puf.A;PDB-ENSP_mappings:3puf.D;PDB-ENSP_mappings:3puf.G;PDB-ENSP_mappings:3puf.J;PDB-ENSP_mappings:3puf.M;PDB-ENSP_mappings:3puf.P;CDD:cd07181;PANTHER:PTHR10954;PANTHER:PTHR10954:SF7;TIGRFAM:TIGR00729;Gene3D:3.30.420.10;Pfam:PF01351;Superfamily:SSF53098 ENSP00000221486 4/8 rs778120777 ENST00000221486 Transcript 1.0 ENSG00000104889 HGNC:18518 LOW NM_006397.3 2.637e-05 gnomAD_NFE synonymous_variant 1 1.0 Unknown O75792.175 RNASEH2A HGNC 1 1.0 UPI00001343E6 SNV RNASEH2A,synonymous_variant,p.N134=,ENST00000221486,NM_006397.3,c.402C>T,LOW,YES,,,1;RNASEH2A,synonymous_variant,p.N133=,ENST00000590121,,c.399C>T,LOW,,,,1;THSD8,downstream_gene_variant,,ENST00000639810,,,MODIFIER,YES,,,1;HOOK2,intron_variant,,ENST00000589765,,n.41+17681G>A,MODIFIER,,,,-1;THSD8,downstream_gene_variant,,ENST00000643364,,,MODIFIER,,,,1;THSD8,3_prime_UTR_variant,,ENST00000639767,,c.*281C>T,MODIFIER,,,,1;RNASEH2A,3_prime_UTR_variant,,ENST00000646769,,c.*62C>T,MODIFIER,,,,1;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000593017,,n.688C>T,MODIFIER,,,,1;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000643757,,n.437C>T,MODIFIER,,,,1;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000590279,,n.817C>T,MODIFIER,,,,1 492/1164 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.193e-05 0.0 0.0 0.0 0.0 0.0 2.637e-05 0.0 0.0 6.761780241504312e-05 2.4324999685632065e-05 0.0 0.0 0.0 0.0 0.0 nfe 0.0001389020035276 0.0 0.0001389020035276 0.0 0.0 0 64 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 57 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RNASEH2A,non_coding_transcript_exon_variant,,ENST00000643757.1,n.437C>T,MODIFIER,;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000593017.2,n.688C>T,MODIFIER,;RNASEH2A,synonymous_variant,p.N133=,ENST00000590121.2,c.399C>T,LOW,;RNASEH2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646769.1,c.*62C>T,MODIFIER,;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000590279.2,n.817C>T,MODIFIER,;RNASEH2A,synonymous_variant,p.N134=,ENST00000221486.6,c.402C>T,LOW,YES;THSD8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000639767.2,c.*281C>T,MODIFIER,;HOOK2,intron_variant,,ENST00000589765.1,n.41+17681G>A,MODIFIER, +KLHL26 55295 BI GRCh38 19 18668080 18668080 + missense_variant Missense_Mutation SNP G G A rs148044384 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 20 c.683G>A p.Arg228His p.R228H ENST00000300976.9 NM_001345982.2 228 cGc/cAc 3/3 P1 A R/H protein_coding YES CCDS12384.1 683/1848 GTTCCGCGCGG COSM4075715 CDD:cd18465;PANTHER:PTHR45632:SF13;PANTHER:PTHR45632;Pfam:PF07707;PIRSF:PIRSF037037;Gene3D:1.25.40.420;SMART:SM00875 ENSP00000300976 0.000227 0.0 3/3 rs148044384 ENST00000300976 Transcript ENSG00000167487 HGNC:25623 MODERATE NM_018316.3 0.000227 AA missense_variant 1.0 benign(0.001) Unknown tolerated(0.79) Q53HC5.121 KLHL26 HGNC 1 A0A024R7N5.57 1.0 UPI0000071AC2 SNV KLHL26,missense_variant,p.R228H,ENST00000300976,NM_001345982.2&NM_018316.3&NM_001345981.2,c.683G>A,MODERATE,YES,tolerated(0.79),benign(0.001),1;KLHL26,intron_variant,,ENST00000599006,NM_001345984.2,c.405+278G>A,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000595182,NM_001345985.2,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000595423,,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000596843,NM_001345983.1,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000600657,,,MODIFIER,,,,1 710/4351 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.541e-05 0.0001279 2.905e-05 0.0 5.529e-05 0.0 1.885e-05 0.0 0.0 7.434440340148285e-05 0.0001215360025526 0.0 6.621640204684809e-05 0.0 0.0 0.0 afr 0.0001215360025526 0.0 7.716049731243402e-05 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 40 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KLHL26,intron_variant,,ENST00000599006.5,c.405+278G>A,MODIFIER,;KLHL26,missense_variant,p.R228H,ENST00000300976.9,c.683G>A,MODERATE,YES +SUGP2 10147 BI GRCh38 19 19004330 19004330 + missense_variant Missense_Mutation SNP C C T rs144507791 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 8 4 c.2767G>A p.Gly923Ser p.G923S ENST00000337018.10 NM_001321697.2 923 Ggc/Agc 7/11 P4 T G/S protein_coding CCDS12392.1 2767/3249 AAGGCCGTCGG PANTHER:PTHR23340;PANTHER:PTHR23340:SF2;MobiDB_lite:mobidb-lite ENSP00000337926 0.000227 0.0 7/11 rs144507791 ENST00000337018 Transcript ENSG00000064607 HGNC:18641 MODERATE 0.000227 AA missense_variant benign(0.005) Unknown tolerated_low_confidence(0.15) Q8IX01.150 SUGP2 HGNC -1 1.0 UPI000019825D Q8IX01-1 SNV SUGP2,missense_variant,p.G923S,ENST00000452918,NM_001017392.5,c.2767G>A,MODERATE,,tolerated_low_confidence(0.15),benign(0.005),-1;SUGP2,missense_variant,p.G923S,ENST00000601879,NM_001352071.2,c.2767G>A,MODERATE,,tolerated_low_confidence(0.15),benign(0.005),-1;SUGP2,missense_variant,p.G937S,ENST00000600377,NM_001321698.1&NM_001321699.1,c.2809G>A,MODERATE,YES,tolerated_low_confidence(0.13),benign(0.125),-1;SUGP2,missense_variant,p.G923S,ENST00000337018,NM_001321697.2&NM_014884.5,c.2767G>A,MODERATE,,tolerated_low_confidence(0.15),benign(0.005),-1;SUGP2,3_prime_UTR_variant,,ENST00000600239,,c.*342G>A,MODIFIER,,,,-1;SUGP2,3_prime_UTR_variant,,ENST00000598240,,c.*1817G>A,MODIFIER,,,,-1;SUGP2,intron_variant,,ENST00000330854,,c.2668-57G>A,MODIFIER,,,,-1;SUGP2,intron_variant,,ENST00000594773,,c.2668-57G>A,MODIFIER,,,,-1;SUGP2,upstream_gene_variant,,ENST00000593795,,,MODIFIER,,,,-1;SUGP2,upstream_gene_variant,,ENST00000597280,,,MODIFIER,,,,-1 2901/3640 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.001e-05 0.000186 0.0 0.0 5.463e-05 0.0 0.0 0.0 3.277e-05 2.0276000213925727e-05 4.862869900534861e-05 0.0 0.0 0.0 0.0 0.0 afr 4.862869900534861e-05 0.0 0.0 0.0 0.0002084199950331 0 27 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SUGP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000598240.1,c.*1817G>A,MODIFIER,;SUGP2,missense_variant,p.G937S,ENST00000600377.1,c.2809G>A,MODERATE,;SUGP2,missense_variant,p.G923S,ENST00000601879.5,c.2767G>A,MODERATE,;SUGP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000600239.5,c.*342G>A,MODIFIER,;SUGP2,intron_variant,NMD_transcript_variant,,ENST00000330854.15,c.2668-57G>A,MODIFIER,;SUGP2,missense_variant,p.G923S,ENST00000337018.10,c.2767G>A,MODERATE,;SUGP2,missense_variant,p.G923S,ENST00000452918.7,c.2767G>A,MODERATE,YES;SUGP2,intron_variant,NMD_transcript_variant,,ENST00000594773.5,c.2668-57G>A,MODIFIER, +LRFN3 79414 BI GRCh38 19 35939726 35939726 + missense_variant Missense_Mutation SNP G G A rs760444261 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 9 18 c.301G>A p.Gly101Ser p.G101S ENST00000246529.4 NM_024509.2 101 Ggc/Agc 2/3 P1 A G/S protein_coding YES CCDS12483.1 301/1887 CTGCCGGCGCC Low_complexity_(Seg):seg;PANTHER:PTHR45842;PANTHER:PTHR45842:SF5;Pfam:PF13855;Gene3D:3.80.10.10;SMART:SM00369;Superfamily:SSF52058 ENSP00000246529 2/3 rs760444261 ENST00000246529 Transcript ENSG00000126243 HGNC:28370 MODERATE NM_024509.2 0.0001743 gnomAD_OTH missense_variant 1.0 benign(0.056) Unknown tolerated(0.4) Q9BTN0.163 LRFN3 HGNC 1 1.0 UPI0000070E5A SNV LRFN3,missense_variant,p.G101S,ENST00000246529,NM_024509.2,c.301G>A,MODERATE,YES,tolerated(0.4),benign(0.056),1;LRFN3,missense_variant,p.G101S,ENST00000588831,,c.301G>A,MODERATE,,tolerated(0.4),benign(0.056),1;LRFN3,downstream_gene_variant,,ENST00000585876,,,MODIFIER,,,,1;LRFN3,downstream_gene_variant,,ENST00000587257,,,MODIFIER,,,,1 1499/4690 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.746e-05 0.0 0.0 0.0 0.0 0.0 2.94e-05 0.0001743 0.0 6.758859854016919e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 27 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRFN3,missense_variant,p.G101S,ENST00000246529.4,c.301G>A,MODERATE,YES;LRFN3,missense_variant,p.G101S,ENST00000588831.5,c.301G>A,MODERATE, +SIPA1L3 23094 BI GRCh38 19 38083019 38083019 + missense_variant Missense_Mutation SNP C C T rs778077624 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 29 6 c.1454C>T p.Thr485Met p.T485M ENST00000222345.11 NM_015073.3 485 aCg/aTg 3/22 P1 T T/M protein_coding YES CCDS33007.1 1454/5346 GCGGACGCAGA PANTHER:PTHR15711;PANTHER:PTHR15711:SF15 ENSP00000222345 3/22 rs778077624 ENST00000222345 Transcript 1.0 ENSG00000105738 HGNC:23801 MODERATE NM_015073.3 6.533e-05 gnomAD_SAS missense_variant 1.0 benign(0.067) Unknown tolerated(0.17) O60292.156 SIPA1L3 HGNC 1 1.0 UPI00001D8160 SNV SIPA1L3,missense_variant,p.T485M,ENST00000222345,NM_015073.3,c.1454C>T,MODERATE,YES,tolerated(0.17),benign(0.067),1;SIPA1L3,downstream_gene_variant,,ENST00000476317,,,MODIFIER,,,,1;SIPA1L3,upstream_gene_variant,,ENST00000595982,,,MODIFIER,,,,1 1983/8004 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.067e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.533e-05 6.758220024494221e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000494070991408 0.0 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 35 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SIPA1L3,missense_variant,p.T485M,ENST00000222345.11,c.1454C>T,MODERATE,YES +LRFN1 57622 BI GRCh38 19 39314441 39314441 + missense_variant Missense_Mutation SNP G G A rs1219603059 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 4 8 c.896C>T p.Pro299Leu p.P299L ENST00000248668.5 NM_020862.2 299 cCg/cTg 4/5 P1 A P/L protein_coding YES CCDS46071.1 896/2316 TCAGCGGGGGC PROSITE_profiles:PS50835;PANTHER:PTHR45842;PANTHER:PTHR45842:SF7;Gene3D:3.80.10.10;Superfamily:SSF48726;Superfamily:SSF52058 ENSP00000248668 4/5 rs1219603059 ENST00000248668 Transcript ENSG00000128011 HGNC:29290 MODERATE NM_020862.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q9P244.160 LRFN1 HGNC -1 1.0 UPI00001A5C55 SNV LRFN1,missense_variant,p.P299L,ENST00000248668,NM_020862.2,c.896C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1 1092/3579 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 24 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 12 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LRFN1,missense_variant,p.P299L,ENST00000248668.5,c.896C>T,MODERATE,YES +ZNF546 339327 BI GRCh38 19 40015125 40015125 + stop_gained Nonsense_Mutation SNP C C T rs765037445 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 9 c.1855C>T p.Arg619Ter p.R619* ENST00000347077.9 NM_178544.5 619 Cga/Tga 7/7 P4 T R/* protein_coding YES CCDS12548.1 1855/2511 CCTTTCGATTT Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR23226;PANTHER:PTHR23226;PANTHER:PTHR23226:SF133;PANTHER:PTHR23226:SF133;SMART:SM00355;Superfamily:SSF57667 ENSP00000339823 7/7 rs765037445 ENST00000347077 Transcript ENSG00000187187 HGNC:28671 HIGH NM_178544.5 0.0001639 gnomAD_OTH stop_gained 1.0 Unknown Q86UE3.149 ZNF546 HGNC 1 1.0 UPI00001984E3 SNV ZNF546,stop_gained,p.R619*,ENST00000347077,NM_178544.5,c.1855C>T,HIGH,YES,,,1;ZNF546,stop_gained,p.R593*,ENST00000600094,NM_001297763.2,c.1777C>T,HIGH,,,,1;ZNF546,intron_variant,,ENST00000596894,,c.77-1303C>T,MODIFIER,,,,1;ZNF546,downstream_gene_variant,,ENST00000599504,,,MODIFIER,,,,1;ZNF546,downstream_gene_variant,,ENST00000601138,,,MODIFIER,,,,1;ZNF546,3_prime_UTR_variant,,ENST00000651981,,c.*1809C>T,MODIFIER,,,,1 2087/8000 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.985e-05 0.0 5.79e-05 0.0 0.0001632 0.0 1.762e-05 0.0001639 6.537e-05 6.807819772802759e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5496700143557973e-05 0.0 0.0 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF546,stop_gained,p.R593*,ENST00000600094.5,c.1777C>T,HIGH,;ZNF546,stop_gained,p.R619*,ENST00000347077.9,c.1855C>T,HIGH,YES;ZNF546,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000651981.1,c.*1809C>T,MODIFIER,;ZNF546,intron_variant,,ENST00000596894.5,c.77-1303C>T,MODIFIER, +SPTBN4 57731 BI GRCh38 19 40502458 40502458 + missense_variant Missense_Mutation SNP G G A rs748767389 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 57 10 c.1154G>A p.Arg385His p.R385H ENST00000352632.7 385 cGt/cAt 10/36 P2 A R/H protein_coding CCDS12559.1 1154/7695 CAACCGTCGCC COSM4581049;COSM4581050 Gene3D:1.20.58.1940;Pfam:PF00435;PIRSF:PIRSF002297;PANTHER:PTHR11915;PANTHER:PTHR11915:SF232;Superfamily:SSF46966 ENSP00000263373 10/36 rs748767389;COSV58943967 ENST00000352632 Transcript 1.0 ENSG00000160460 HGNC:14896 MODERATE 0.000435 gnomAD_EAS missense_variant 0;1 probably_damaging(0.962) Unknown deleterious(0.01) 0;1 Q9H254.178 SPTBN4 HGNC 1 5.0 UPI0000135DBB Q9H254-1 SNV SPTBN4,missense_variant,p.R385H,ENST00000598249,NM_020971.3,c.1154G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.962),1;SPTBN4,missense_variant,p.R385H,ENST00000338932,,c.1154G>A,MODERATE,,deleterious(0.01),probably_damaging(0.956),1;SPTBN4,missense_variant,p.R385H,ENST00000352632,,c.1154G>A,MODERATE,,deleterious(0.01),probably_damaging(0.962),1;SPTBN4,missense_variant,p.R385H,ENST00000392025,,c.1154G>A,MODERATE,,deleterious(0.01),probably_damaging(0.956),1;SPTBN4,missense_variant,p.R385H,ENST00000595535,,c.1154G>A,MODERATE,,deleterious(0.04),possibly_damaging(0.83),1;SPTBN4,non_coding_transcript_exon_variant,,ENST00000598775,,n.546G>A,MODIFIER,,,,1 1240/8676 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.783e-05 0.0 0.0 0.0 0.000435 0.0 3.527e-05 0.0 0.0 4.732609886559658e-05 0.0 0.0 0.0 0.0 0.0002016939979512 0.0 nfe 9.256970224669205e-05 0.0 9.256970224669205e-05 0.0 0.0 0 88 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 67 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SPTBN4,non_coding_transcript_exon_variant,,ENST00000598775.1,n.546G>A,MODIFIER,;SPTBN4,missense_variant,p.R385H,ENST00000598249.6,c.1154G>A,MODERATE,YES;SPTBN4,missense_variant,p.R385H,ENST00000595535.5,c.1154G>A,MODERATE,;SPTBN4,missense_variant,p.R385H,ENST00000352632.7,c.1154G>A,MODERATE, +LTBP4 8425 BI GRCh38 19 40623949 40623949 + synonymous_variant Silent SNP C C T rs778594212 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 18 7 c.3900C>T p.Cys1300= p.C1300= ENST00000308370.11 NM_001042544.1 1300 tgC/tgT 29/33 A2 T C protein_coding YES CCDS74369.1 3900/4875 likely_benign GAGTGCGCCGA Gene3D:2.10.25.10;Pfam:PF07645;PROSITE_patterns:PS01187;PROSITE_profiles:PS50026;PANTHER:PTHR24034;PANTHER:PTHR24034:SF43;SMART:SM00179;SMART:SM00181;Superfamily:SSF57196;Superfamily:SSF57196;CDD:cd00054 ENSP00000311905 29/33 rs778594212 ENST00000308370 Transcript 1.0 ENSG00000090006 HGNC:6717 LOW 6.513e-05 gnomAD_AFR synonymous_variant 1 1.0 Unknown Q8N2S1.161 LTBP4 HGNC 1 1.0 UPI0000DACAC4 Q8N2S1-1 SNV LTBP4,synonymous_variant,p.C1263=,ENST00000204005,NM_003573.2,c.3789C>T,LOW,,,,1;LTBP4,synonymous_variant,p.C1233=,ENST00000396819,NM_001042545.2,c.3699C>T,LOW,,,,1;LTBP4,synonymous_variant,p.C1300=,ENST00000308370,NM_001042544.1,c.3900C>T,LOW,YES,,,1;LTBP4,synonymous_variant,p.C633=,ENST00000243562,,c.1899C>T,LOW,,,,1;LTBP4,synonymous_variant,p.C446=,ENST00000601032,,c.1338C>T,LOW,,,,1;LTBP4,synonymous_variant,p.C209=,ENST00000599724,,c.627C>T,LOW,,,,1;LTBP4,synonymous_variant,p.C176=,ENST00000622457,,c.528C>T,LOW,,,,1;LTBP4,downstream_gene_variant,,ENST00000593463,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000597071,,,MODIFIER,,,,1;LTBP4,upstream_gene_variant,,ENST00000598166,,,MODIFIER,,,,1;LTBP4,upstream_gene_variant,,ENST00000599225,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000612121,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000618486,,,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000595118,,n.1204C>T,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000318809,,n.626C>T,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000597816,,n.595C>T,MODIFIER,,,,1;LTBP4,non_coding_transcript_exon_variant,,ENST00000597151,,n.44C>T,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000594116,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000594448,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000595665,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000596351,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000598178,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000600499,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000610893,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000612845,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000622107,,,MODIFIER,,,,1;LTBP4,downstream_gene_variant,,ENST00000622565,,,MODIFIER,,,,1 3900/4948 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.611e-05 6.513e-05 0.0 0.0 0.0 0.0 2.669e-05 0.0 0.0 2.703360041778069e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.172079883981496e-05 0.0 6.172079883981496e-05 0.0 0.0 0 45 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LTBP4,non_coding_transcript_exon_variant,,ENST00000597151.1,n.44C>T,MODIFIER,;LTBP4,missense_variant,p.A176V,ENST00000622457.1,c.527C>T,MODERATE,;LTBP4,non_coding_transcript_exon_variant,,ENST00000597816.5,n.595C>T,MODIFIER,;LTBP4,non_coding_transcript_exon_variant,,ENST00000318809.11,n.626C>T,MODIFIER,;LTBP4,non_coding_transcript_exon_variant,,ENST00000595118.5,n.1204C>T,MODIFIER,;LTBP4,synonymous_variant,p.C209=,ENST00000599724.5,c.627C>T,LOW,;LTBP4,missense_variant,p.R446C,ENST00000601032.5,c.1336C>T,MODERATE,;LTBP4,missense_variant,p.A633V,ENST00000243562.13,c.1898C>T,MODERATE,;LTBP4,synonymous_variant,p.C1233=,ENST00000396819.8,c.3699C>T,LOW,YES;LTBP4,synonymous_variant,p.C1300=,ENST00000308370.11,c.3900C>T,LOW,;LTBP4,synonymous_variant,p.C1263=,ENST00000204005.13,c.3789C>T,LOW, +GPR4 2828 BI GRCh38 19 45591824 45591824 + missense_variant Missense_Mutation SNP C C T rs763872953 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 7 c.43G>A p.Val15Met p.V15M ENST00000323040.5 NM_005282.3 15 Gtg/Atg 2/2 P1 T V/M protein_coding YES CCDS12669.1 43/1089 GTCCACGCGCG COSM3104377 Gene3D:1.20.1070.10;Prints:PR01147;PANTHER:PTHR24234;PANTHER:PTHR24234:SF10;Superfamily:SSF81321 ENSP00000319744 2/2 rs763872953;COSV59918250 ENST00000323040 Transcript ENSG00000177464 HGNC:4497 MODERATE NM_005282.3 0.001163 gnomAD_EAS missense_variant 0;1 1.0 possibly_damaging(0.584) Unknown deleterious(0.03) 0;1 P46093.161 GPR4 HGNC -1 1.0 UPI0000050428 SNV GPR4,missense_variant,p.V15M,ENST00000323040,NM_005282.3,c.43G>A,MODERATE,YES,deleterious(0.03),possibly_damaging(0.584),-1;OPA3,intron_variant,,ENST00000544371,,c.-18+10271G>A,MODIFIER,,,,-1;GPR4,downstream_gene_variant,,ENST00000591614,,,MODIFIER,,,,-1 992/3052 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001148 0.0 0.0001231 0.0 0.001163 0.0 1.9e-05 0.0 0.0 0.0001013810033327 2.4304899852722883e-05 0.0 0.000198701993213 0.0 0.0008071030024439 0.0 eas 0.0008071030024439 0.0 0.0001080279980669 0.0 0.0 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GPR4,missense_variant,p.V15M,ENST00000323040.5,c.43G>A,MODERATE,YES;OPA3,intron_variant,,ENST00000544371.1,c.-18+10271G>A,MODIFIER, +FBXO46 23403 BI GRCh38 19 45712819 45712819 + missense_variant Missense_Mutation SNP C C T rs764409127 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 5 c.677G>A p.Arg226His p.R226H ENST00000317683.4 NM_001329633.2 226 cGt/cAt 2/2 P1 T R/H protein_coding YES CCDS46116.1 677/1812 CTACACGGCTG PANTHER:PTHR16271;PANTHER:PTHR16271:SF10 ENSP00000410007 2/2 rs764409127;COSV100480209 ENST00000317683 Transcript ENSG00000177051 HGNC:25069 MODERATE NM_001080469.2 2.915e-05 gnomAD_AMR missense_variant 0;1 1.0 benign(0.04) Unknown deleterious(0) 0;1 Q6PJ61.123 FBXO46 HGNC -1 2.0 UPI00002026A5 SNV FBXO46,missense_variant,p.R226H,ENST00000317683,NM_001329633.2&NM_001080469.2&NM_001329634.1&NM_001329632.1,c.677G>A,MODERATE,YES,deleterious(0),benign(0.04),-1;FBXO46,downstream_gene_variant,,ENST00000586899,,,MODIFIER,,,,-1;FBXO46,downstream_gene_variant,,ENST00000591686,,,MODIFIER,,,,-1;AC007191.1,downstream_gene_variant,,ENST00000623179,,,MODIFIER,YES,,,-1 803/2993 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.642e-05 0.0 2.915e-05 0.0 0.0 0.0 2.752e-05 0.0 0.0 6.759590178262442e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435000022989698e-05 0.0 0.0 0 23 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS FBXO46,missense_variant,p.R226H,ENST00000317683.4,c.677G>A,MODERATE,YES +CCDC8 83987 BI GRCh38 19 46412095 46412095 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 21 c.716C>T p.Ala239Val p.A239V ENST00000307522.5 NM_032040.5 239 gCg/gTg 1/1 P1 A A/V protein_coding YES CCDS12685.1 716/1617 CTGGCGCCGAT PANTHER:PTHR47741;MobiDB_lite:mobidb-lite ENSP00000303158 1/1 ENST00000307522 Transcript 1.0 ENSG00000169515 HGNC:25367 MODERATE NM_032040.5 missense_variant 1.0 benign(0.001) Unknown tolerated_low_confidence(0.67) Q9H0W5.141 CCDC8 HGNC -1 UPI00000730F2 SNV CCDC8,missense_variant,p.A239V,ENST00000307522,NM_032040.5,c.716C>T,MODERATE,YES,tolerated_low_confidence(0.67),benign(0.001),-1 1470/3236 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 53 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CCDC8,missense_variant,p.A239V,ENST00000307522.5,c.716C>T,MODERATE,YES;CCDC8,missense_variant,p.A309V,ENST00000697726.1,c.926C>T,MODERATE, +BICRA 29998 BI GRCh38 19 47701336 47701336 + missense_variant Missense_Mutation SNP G G A rs536150980 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 5 4 c.3604G>A p.Val1202Met p.V1202M ENST00000396720.7 NM_015711.3 1202 Gtg/Atg 15/15 P2 A V/M protein_coding YES CCDS46134.1 3604/4683 AGTACGTGTCT COSM4687290 PANTHER:PTHR15572;PANTHER:PTHR15572:SF1 ENSP00000379946 15/15 rs536150980;COSV67604295 ENST00000396720 Transcript ENSG00000063169 HGNC:4332 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.998) Unknown tolerated(0.05) 0;1 Q9NZM4.129 BICRA HGNC 1 5.0 UPI00016278EE Q9NZM4-1 SNV BICRA,missense_variant,p.V1202M,ENST00000396720,NM_015711.3,c.3604G>A,MODERATE,YES,tolerated(0.05),probably_damaging(0.998),1;BICRA,missense_variant,p.V960M,ENST00000614245,,c.2878G>A,MODERATE,,tolerated(0.05),probably_damaging(0.998),1;BICRA,non_coding_transcript_exon_variant,,ENST00000602258,,n.1372G>A,MODIFIER,,,,1;AC010519.1,intron_variant,,ENST00000599924,,n.87-30729G>A,MODIFIER,YES,,,1 3798/5739 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 22 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 10 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS BICRA,non_coding_transcript_exon_variant,,ENST00000602258.1,n.1372G>A,MODIFIER,;BICRA,missense_variant,p.V960M,ENST00000614245.2,c.2878G>A,MODERATE,;BICRA,missense_variant,p.V1202M,ENST00000594866.3,c.3604G>A,MODERATE,YES;BICRA,missense_variant,p.V1202M,ENST00000396720.7,c.3604G>A,MODERATE,;ENSG00000268746,intron_variant,,ENST00000599924.1,n.87-30729G>A,MODIFIER,YES +MED25 81857 BI GRCh38 19 49830789 49830789 + missense_variant Missense_Mutation SNP G G A rs1018204701 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 6 c.1003G>A p.Ala335Thr p.A335T ENST00000312865.10 NM_030973.4 335 Gcc/Acc 9/18 A A/T protein_coding CCDS33075.1 1003/2244 CTGGCGCCCCC COSM4080213;COSM4080214 Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR12433;PANTHER:PTHR12433:SF10;Pfam:PF11235 ENSP00000326767 9/18 rs1018204701;COSV57204006 ENST00000312865 Transcript 1.0 ENSG00000104973 HGNC:28845 MODERATE NM_030973.4 5.466e-05 gnomAD_EAS missense_variant 0;1 benign(0.338) Unknown tolerated(0.26) 0;1 Q71SY5.126 MED25 HGNC 1 1.0 UPI00002029A3 Q71SY5-1 SNV MED25,missense_variant,p.A335T,ENST00000593767,NM_001378355.1,c.1003G>A,MODERATE,YES,tolerated(0.21),possibly_damaging(0.53),1;MED25,missense_variant,p.A335T,ENST00000312865,NM_030973.4,c.1003G>A,MODERATE,,tolerated(0.26),benign(0.338),1;MED25,missense_variant,p.A122T,ENST00000538643,,c.364G>A,MODERATE,,tolerated_low_confidence(0.21),possibly_damaging(0.608),1;MED25,intron_variant,,ENST00000595185,,c.688+841G>A,MODIFIER,,,,1;MIR6800,upstream_gene_variant,,ENST00000614963,,,MODIFIER,YES,,,1;MED25,upstream_gene_variant,,ENST00000594998,,,MODIFIER,,,,1;MED25,upstream_gene_variant,,ENST00000599722,,,MODIFIER,,,,1 1056/2332 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.043e-06 0.0 0.0 0.0 5.466e-05 0.0 0.0 0.0 0.0 6.784629931644304e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5459800124517642e-05 0.0 0.0 0 28 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MED25,intron_variant,,ENST00000595185.5,c.688+841G>A,MODIFIER,;MED25,missense_variant,p.A122T,ENST00000538643.5,c.364G>A,MODERATE,;MED25,missense_variant,p.A335T,ENST00000593767.3,c.1003G>A,MODERATE,;MED25,missense_variant,p.A335T,ENST00000312865.10,c.1003G>A,MODERATE,YES +POLD1 5424 BI GRCh38 19 50413825 50413825 + synonymous_variant Silent SNP C C T rs1472994995 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 11 c.2334C>T p.Ala778= p.A778= ENST00000440232.7 NM_002691.4 778 gcC/gcT 19/27 P1 T A protein_coding CCDS12795.1 2334/3324 likely_benign GAGGCCGCGGA PDB-ENSP_mappings:6s1m.A;PDB-ENSP_mappings:6s1n.A;PDB-ENSP_mappings:6s1o.A;PDB-ENSP_mappings:6tny.A;PDB-ENSP_mappings:6tnz.A;CDD:cd05533;PANTHER:PTHR10322:SF23;PANTHER:PTHR10322;Gene3D:3.90.1600.10;TIGRFAM:TIGR00592;Pfam:PF00136;Superfamily:SSF56672 ENSP00000406046 19/27 rs1472994995 ENST00000440232 Transcript 1.0 ENSG00000062822 HGNC:9175 LOW NM_002691.4 3.281e-05 gnomAD_SAS synonymous_variant 1 Unknown P28340.204 POLD1 HGNC 1 A0A024R4F4.52 1.0 UPI000007288E SNV POLD1,synonymous_variant,p.A778=,ENST00000601098,,c.2334C>T,LOW,,,,1;POLD1,synonymous_variant,p.A804=,ENST00000595904,NM_001308632.1,c.2412C>T,LOW,YES,,,1;POLD1,synonymous_variant,p.A778=,ENST00000599857,NM_001256849.1,c.2334C>T,LOW,,,,1;POLD1,synonymous_variant,p.A778=,ENST00000440232,NM_002691.4,c.2334C>T,LOW,,,,1;POLD1,synonymous_variant,p.A754=,ENST00000613923,,c.2262C>T,LOW,,,,1;POLD1,synonymous_variant,p.A404=,ENST00000644560,,c.1212C>T,LOW,,,,1;POLD1,synonymous_variant,p.A35=,ENST00000593407,,c.105C>T,LOW,,,,1;POLD1,upstream_gene_variant,,ENST00000593981,,,MODIFIER,,,,1;AC020909.1,upstream_gene_variant,,ENST00000599632,,,MODIFIER,YES,,,1;POLD1,synonymous_variant,p.A778=,ENST00000600859,,c.2334C>T,LOW,,,,1;POLD1,3_prime_UTR_variant,,ENST00000643407,,c.*121C>T,MODIFIER,,,,1;POLD1,upstream_gene_variant,,ENST00000596221,,,MODIFIER,,,,1;POLD1,upstream_gene_variant,,ENST00000596648,,,MODIFIER,,,,1;POLD1,upstream_gene_variant,,ENST00000597963,,,MODIFIER,,,,1 2379/3436 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.026e-06 0.0 0.0 0.0 0.0 0.0 8.868e-06 0.0 3.281e-05 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS POLD1,missense_variant,p.R35C,ENST00000593407.5,c.103C>T,MODERATE,;POLD1,synonymous_variant,p.A780=,ENST00000644560.2,c.2340C>T,LOW,;POLD1,synonymous_variant,p.A778=,ENST00000687454.1,c.2334C>T,LOW,;POLD1,synonymous_variant,p.A778=,ENST00000593887.2,c.2334C>T,LOW,;POLD1,synonymous_variant,p.A804=,ENST00000595904.6,c.2412C>T,LOW,;POLD1,synonymous_variant,p.A778=,ENST00000440232.7,c.2334C>T,LOW,YES;POLD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643407.1,c.*121C>T,MODIFIER,;POLD1,synonymous_variant,p.A778=,ENST00000601098.6,c.2334C>T,LOW,;POLD1,synonymous_variant,p.A754=,ENST00000613923.6,c.2262C>T,LOW,;POLD1,synonymous_variant,p.A778=,ENST00000599857.7,c.2334C>T,LOW,;POLD1,non_coding_transcript_exon_variant,,ENST00000600746.2,n.2525C>T,MODIFIER,;POLD1,synonymous_variant,NMD_transcript_variant,p.A778=,ENST00000600859.5,c.2334C>T,LOW, +MYBPC2 4606 BI GRCh38 19 50455596 50455596 + missense_variant Missense_Mutation SNP G G A rs1439007318 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 47 18 c.2290G>A p.Gly764Arg p.G764R ENST00000357701.6 NM_004533.4 764 Ggg/Agg 20/28 P1 A G/R protein_coding YES CCDS46152.1 2290/3426 GGATCGGGGCA COSM999734 Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR13817;PANTHER:PTHR13817:SF17;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000350332 20/28 rs1439007318;COSV63099333 ENST00000357701 Transcript ENSG00000086967 HGNC:7550 MODERATE NM_004533.4 8.851e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q14324.178 MYBPC2 HGNC 1 A0A140VJQ0.20 1.0 UPI000013C628 SNV MYBPC2,missense_variant,p.G764R,ENST00000357701,NM_004533.4,c.2290G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1 2352/3604 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.013e-06 0.0 0.0 0.0 0.0 0.0 8.851e-06 0.0 0.0 0 100 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 65 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MYBPC2,missense_variant,p.G764R,ENST00000357701.6,c.2290G>A,MODERATE,YES +MIR516A2 574499 BI GRCh38 19 53761153 53761153 + mature_miRNA_variant mature_miRNA_variant SNP G G A rs754319127 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 50 36 n.21G>A ENST00000384888.1 1/1 A miRNA YES TTCTCGAGGAA COSN23015444 1/1 rs754319127 ENST00000384888 Transcript ENSG00000207620 HGNC:32131 MODIFIER 0.0001235 gnomAD_AFR mature_miRNA_variant 1.0 Unknown MIR516A2 HGNC 1 SNV MIR516A2,mature_miRNA_variant,,ENST00000384888,,n.21G>A,MODIFIER,YES,,,1;MIR519A2,upstream_gene_variant,,ENST00000384990,,,MODIFIER,YES,,,1;MIR516A1,downstream_gene_variant,,ENST00000385033,,,MODIFIER,YES,,,1;MIR1283-2,downstream_gene_variant,,ENST00000408621,,,MODIFIER,YES,,,1;RNU6-1041P,upstream_gene_variant,,ENST00000516254,,,MODIFIER,YES,,,-1;AC011453.1,upstream_gene_variant,,ENST00000597619,,,MODIFIER,YES,,,1 21/90 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.391e-05 0.0001235 2.896e-05 0.0 0.0 0.0 2.646e-05 0.0 0.0 3.389739867998287e-05 9.763240086613224e-05 0.0 0.0 0.0 0.0 0.0 afr 9.763240086613224e-05 0.0 1.544539918540977e-05 0.0 0.0 0 miRNA_stem 127 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 86 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MIR516A2,mature_miRNA_variant,,ENST00000384888.1,n.21G>A,MODIFIER,YES;ENSG00000269842,intron_variant,,ENST00000710695.1,n.497-2443G>A,MODIFIER,;ENSG00000269842,intron_variant,,ENST00000710694.1,n.831-2443G>A,MODIFIER,;ENSG00000269842,intron_variant,,ENST00000710698.1,n.954-2443G>A,MODIFIER,;ENSG00000269842,intron_variant,,ENST00000710737.1,n.2298-2443G>A,MODIFIER,;ENSG00000269842,intron_variant,,ENST00000710696.1,n.1476-2443G>A,MODIFIER,;ENSG00000269842,intron_variant,,ENST00000710708.1,n.1392-2443G>A,MODIFIER,YES +KIR2DL4 3805 BI GRCh38 19 54804819 54804819 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 65 7 c.103G>A p.Ala35Thr p.A35T ENST00000345540.10 NM_001080770.2 35 Gcc/Acc 3/7 P4 A A/T protein_coding YES 220/1251 GCTCTGCCTGG PANTHER:PTHR11738;PANTHER:PTHR11738:SF158;Pfam:PF00047;Gene3D:2.60.40.10;Superfamily:SSF48726 ENSP00000379580 3/8 ENST00000396284 Transcript ENSG00000189013 HGNC:6332 MODERATE missense_variant 1.0 benign(0.364) Unknown deleterious(0) KIR2DL4 HGNC 1 E7EST5.69 1.0 UPI0004E4C8FD SNV KIR2DL4,missense_variant,p.A74T,ENST00000396284,,c.220G>A,MODERATE,YES,deleterious(0),benign(0.364),1;KIR2DL4,missense_variant,p.A34T,ENST00000396289,,c.100G>A,MODERATE,,deleterious(0),possibly_damaging(0.718),1;KIR2DL4,missense_variant,p.A35T,ENST00000359085,NM_001080772.2,c.103G>A,MODERATE,,deleterious(0),possibly_damaging(0.505),1;KIR2DL4,missense_variant,p.A35T,ENST00000345540,NM_001080770.2,c.103G>A,MODERATE,,deleterious(0),probably_damaging(0.991),1;KIR2DL4,missense_variant,p.A35T,ENST00000357494,,c.103G>A,MODERATE,,deleterious(0.02),probably_damaging(0.998),1;KIR2DL4,intron_variant,,ENST00000346587,,c.76+893G>A,MODIFIER,,,,1;KIR2DL4,intron_variant,,ENST00000396293,,c.76+893G>A,MODIFIER,,,,1;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000463062,,n.115G>A,MODIFIER,,,,1;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000486965,,n.115G>A,MODIFIER,,,,1 220/1656 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 110 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS KIR2DL4,missense_variant,p.C33Y,ENST00000396289.5,c.98G>A,MODERATE,;KIR2DL4,intron_variant,,ENST00000346587.8,c.76+893G>A,MODIFIER,;KIR2DL4,intron_variant,,ENST00000396293.5,c.76+893G>A,MODIFIER,;KIR2DL4,missense_variant,p.A35T,ENST00000357494.8,c.103G>A,MODERATE,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000463062.1,n.115G>A,MODIFIER,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000486965.6,n.115G>A,MODIFIER,;KIR2DL4,missense_variant,p.A35T,ENST00000359085.8,c.103G>A,MODERATE,;KIR2DL4,missense_variant,p.A35T,ENST00000345540.10,c.103G>A,MODERATE,YES +ZSCAN1 284312 BI GRCh38 19 58038101 58038101 + missense_variant Missense_Mutation SNP G G A rs148253808 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 9 c.265G>A p.Ala89Thr p.A89T ENST00000282326.6 NM_182572.4 89 Gcg/Acg 3/6 0.0002 0.0 0.0 0.0 0.0 0.001 P1 A A/T protein_coding YES CCDS12969.1 265/1227 TGGGCGCGCTG COSM242447;COSM3938345 PROSITE_profiles:PS50804;CDD:cd07936;PANTHER:PTHR23226:SF162;PANTHER:PTHR23226;Gene3D:1.10.4020.10;Pfam:PF02023;SMART:SM00431;Superfamily:SSF47353 ENSP00000282326 0.0002276 0.0 3/6 rs148253808 ENST00000282326 Transcript ENSG00000152467 HGNC:23712 MODERATE NM_182572.4 0.001 SAS missense_variant 1.0 possibly_damaging(0.687) Unknown deleterious(0.02) Q8NBB4.148 ZSCAN1 HGNC 1 2.0 UPI000013DCD2 Q8NBB4-1 SNV ZSCAN1,missense_variant,p.A89T,ENST00000282326,NM_182572.4,c.265G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.687),1;ZSCAN1,missense_variant,p.A89T,ENST00000391700,,c.265G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.459),1;ZSCAN1,missense_variant,p.A89T,ENST00000601162,,c.265G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.459),1 553/2095 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.67e-05 6.522e-05 2.912e-05 0.0 0.0 0.0 9.114e-06 0.0 0.0001965 6.756759830750525e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002081599959637 0 22 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZSCAN1,missense_variant,p.A89T,ENST00000601162.1,c.265G>A,MODERATE,;ZSCAN1,missense_variant,p.A89T,ENST00000391700.5,c.265G>A,MODERATE,;ZSCAN1,missense_variant,p.A89T,ENST00000282326.6,c.265G>A,MODERATE,YES +ZNF324 25799 BI GRCh38 19 58471742 58471742 + missense_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 25 c.1250G>A p.Arg417His p.R417H ENST00000196482.4 NM_014347.3 417 cGc/cAc 4/4 P1 A R/H protein_coding CCDS12981.1 1250/1662 CCAGCGCGTGC COSM4082430 Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF670;SMART:SM00355;Superfamily:SSF57667 ENSP00000196482 4/4 COSV52180241 ENST00000196482 Transcript ENSG00000083812 HGNC:14096 MODERATE NM_014347.3 missense_variant 1 probably_damaging(0.996) Unknown deleterious(0) 1 O75467.171 ZNF324 HGNC 1 A0A024R4R8.47 1.0 UPI000013C359 SNV ZNF324,missense_variant,p.R417H,ENST00000536459,,c.1250G>A,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;ZNF324,missense_variant,p.R417H,ENST00000196482,NM_014347.3,c.1250G>A,MODERATE,,deleterious(0),probably_damaging(0.996),1;ZNF324,missense_variant,p.R276H,ENST00000593925,,c.827G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ZNF446,upstream_gene_variant,,ENST00000335841,,,MODIFIER,,,,1;ZNF324,downstream_gene_variant,,ENST00000535298,,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000594369,NM_017908.4,,MODIFIER,YES,,,1;ZNF446,upstream_gene_variant,,ENST00000596341,NM_001304453.1,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000600013,,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000610298,,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000622313,,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000391694,,,MODIFIER,,,,1;ZNF446,upstream_gene_variant,,ENST00000594468,,,MODIFIER,,,,1;AC012313.7,downstream_gene_variant,,ENST00000598051,,,MODIFIER,YES,,,-1 1360/5054 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 45 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZNF324,synonymous_variant,p.A275=,ENST00000593925.1,c.825G>A,LOW,;ZNF324,missense_variant,p.R417H,ENST00000196482.4,c.1250G>A,MODERATE,YES;ZNF324,missense_variant,p.R417H,ENST00000536459.6,c.1250G>A,MODERATE, +ANGPT4 51378 BI GRCh38 20 879782 879782 + missense_variant Missense_Mutation SNP C C T rs746445808 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 7 c.1018G>A p.Val340Met p.V340M ENST00000381922.5 NM_001322809.2 340 Gtg/Atg 6/9 P1 T V/M protein_coding YES CCDS13009.1 1018/1512 ATTCACGGTGC COSM1495118 Gene3D:3.90.215.10;Pfam:PF00147;PROSITE_profiles:PS51406;PANTHER:PTHR19143;PANTHER:PTHR19143:SF31;SMART:SM00186;Superfamily:SSF56496;CDD:cd00087 ENSP00000371347 6/9 rs746445808;COSV67921665 ENST00000381922 Transcript ENSG00000101280 HGNC:487 MODERATE NM_015985.4 0.0001967 gnomAD_SAS missense_variant 0;1 1.0 benign(0.193) Unknown deleterious(0.04) 0;1 Q9Y264.150 ANGPT4 HGNC -1 1.0 UPI0000062232 Q9Y264-1 SNV ANGPT4,missense_variant,p.V340M,ENST00000381922,NM_001322809.2&NM_015985.4,c.1018G>A,MODERATE,YES,deleterious(0.04),benign(0.193),-1 1138/4692 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.793e-05 0.0 0.0 0.0 0.0 0.0 8.816e-06 0.0 0.0001967 6.759680218237918e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002082470018649 0 59 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 38 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ANGPT4,missense_variant,p.V340M,ENST00000381922.5,c.1018G>A,MODERATE,YES +PSMF1 9491 BI GRCh38 20 1163158 1163158 + missense_variant Missense_Mutation SNP G G A rs762622706 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 14 c.580G>A p.Gly194Arg p.G194R ENST00000333082.7 NM_178578.4 194 Ggg/Agg 6/8 P1 A G/R protein_coding CCDS13010.1 580/816 TTGTCGGGGGA Pfam:PF08577;PANTHER:PTHR13266 ENSP00000327704 6/8 rs762622706 ENST00000333082 Transcript ENSG00000125818 HGNC:9571 MODERATE 0.0001629 gnomAD_OTH missense_variant probably_damaging(1) Unknown deleterious(0) Q92530.174 PSMF1 HGNC 1 A0A140VJT2.18 1.0 UPI000013CBCB SNV PSMF1,missense_variant,p.G194R,ENST00000335877,NM_001323409.2&NM_006814.5,c.580G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;PSMF1,missense_variant,p.G194R,ENST00000333082,NM_178578.3,c.580G>A,MODERATE,,deleterious(0),probably_damaging(1),1;PSMF1,missense_variant,p.G194R,ENST00000246015,NM_001323407.2&NM_001323410.2&NM_001323408.2,c.580G>A,MODERATE,,deleterious(0),probably_damaging(1),1;PSMF1,missense_variant,p.G20R,ENST00000381898,,c.58G>A,MODERATE,,tolerated_low_confidence(0.05),probably_damaging(0.971),1;PSMF1,intron_variant,,ENST00000435720,,c.130-1160G>A,MODIFIER,,,,1;PSMF1,non_coding_transcript_exon_variant,,ENST00000484891,,n.496G>A,MODIFIER,,,,1;PSMF1,non_coding_transcript_exon_variant,,ENST00000479715,,n.555G>A,MODIFIER,,,,1;PSMF1,upstream_gene_variant,,ENST00000418246,,,MODIFIER,,,,1;PSMF1,missense_variant,p.G194R,ENST00000652336,,c.580G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ACTG1P3,downstream_gene_variant,,ENST00000431775,,,MODIFIER,YES,,,1 748/3686 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.989e-05 0.0 0.0 0.0 5.437e-05 0.0 8.796e-06 0.0001629 6.534e-05 1.3520800166588742e-05 4.865229857387021e-05 0.0 0.0 0.0 0.0 0.0 afr 4.865229857387021e-05 0.0 0.0 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 26 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PSMF1,missense_variant,p.G20R,ENST00000381898.5,c.58G>A,MODERATE,;PSMF1,intron_variant,,ENST00000435720.5,c.130-1160G>A,MODIFIER,;PSMF1,non_coding_transcript_exon_variant,,ENST00000484891.1,n.496G>A,MODIFIER,;PSMF1,missense_variant,p.G194R,ENST00000335877.11,c.580G>A,MODERATE,YES;PSMF1,missense_variant,p.G194R,ENST00000246015.8,c.580G>A,MODERATE,;PSMF1,non_coding_transcript_exon_variant,,ENST00000479715.5,n.555G>A,MODIFIER,;PSMF1,missense_variant,p.G194R,ENST00000333082.7,c.580G>A,MODERATE,;PSMF1,missense_variant,NMD_transcript_variant,p.G194R,ENST00000652336.1,c.580G>A,MODERATE, +LZTS3 9762 BI GRCh38 20 3164549 3164549 + missense_variant Missense_Mutation SNP C C T rs144495581 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 21 c.1927G>A p.Ala643Thr p.A643T ENST00000337576.7 NM_001388193.1 643 Gca/Aca 5/5 P1 T A/T protein_coding YES 1927/2022 CCCTGCGGCCC PANTHER:PTHR19354;PANTHER:PTHR19354:SF6;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000332123 3/3 rs144495581;COSV99418141 ENST00000329152 Transcript ENSG00000088899 HGNC:30139 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 benign(0.081) Unknown tolerated(0.9) 0;1 O60299.148 LZTS3 HGNC -1 1.0 UPI0000139A8C O60299-1 SNV LZTS3,missense_variant,p.A643T,ENST00000329152,,c.1927G>A,MODERATE,YES,tolerated(0.9),benign(0.081),-1;LZTS3,missense_variant,p.A643T,ENST00000337576,NM_001367609.1&NM_001365618.1,c.1927G>A,MODERATE,,tolerated(0.9),benign(0.081),-1;LZTS3,missense_variant,p.A597T,ENST00000360342,NM_001282533.2,c.1789G>A,MODERATE,,tolerated(0.91),benign(0.216),-1;LZTS3,missense_variant,p.A597T,ENST00000645462,,c.1789G>A,MODERATE,,tolerated(0.91),benign(0.216),-1;UBOX5,upstream_gene_variant,,ENST00000217173,NM_001267584.2&NM_014948.4,,MODIFIER,YES,,,-1;UBOX5,upstream_gene_variant,,ENST00000348031,NM_199415.3,,MODIFIER,,,,-1;FASTKD5,upstream_gene_variant,,ENST00000380266,NM_021826.5,,MODIFIER,YES,,,-1;UBOX5,upstream_gene_variant,,ENST00000449731,,,MODIFIER,,,,-1 3325/5257 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.757759820175124e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 45 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS LZTS3,missense_variant,p.A643T,ENST00000329152.7,c.1927G>A,MODERATE,;LZTS3,missense_variant,p.A597T,ENST00000360342.7,c.1789G>A,MODERATE,;LZTS3,missense_variant,p.A597T,ENST00000645462.1,c.1789G>A,MODERATE,;LZTS3,missense_variant,p.A643T,ENST00000337576.7,c.1927G>A,MODERATE,YES +PLCB4 5332 BI GRCh38 20 9409106 9409106 + missense_variant Missense_Mutation SNP G G A rs1568763104 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 59 13 c.1834G>A p.Asp612Asn p.D612N ENST00000278655.9 NM_182797.3 630 Gat/Aat 21/36 P4 A D/N protein_coding CCDS13105.1 1888/3528 likely_pathogenic GAGTCGATTCC COSM1681538;COSM4294769 Gene3D:3.20.20.190;Pfam:PF00387;PIRSF:PIRSF000956;Prints:PR00390;PROSITE_profiles:PS50008;PANTHER:PTHR10336;PANTHER:PTHR10336:SF106;SMART:SM00149;Superfamily:SSF51695;CDD:cd08591 ENSP00000278655 21/36 rs1568763104;COSV53793606;COSV53801055 ENST00000278655 Transcript 1.0 ENSG00000101333 HGNC:9059 MODERATE missense_variant 1;1;1 probably_damaging(0.983) Unknown tolerated(0.05) 0;1;1 Q15147.204 PLCB4 HGNC 1 1.0 UPI0000131A94 Q15147-1 SNV PLCB4,missense_variant,p.D630N,ENST00000378501,NM_001377134.2&NM_000933.4&NM_001377135.1,c.1888G>A,MODERATE,,deleterious(0.05),benign(0.32),1;PLCB4,missense_variant,p.D630N,ENST00000378493,,c.1888G>A,MODERATE,,tolerated(0.05),probably_damaging(0.983),1;PLCB4,missense_variant,p.D642N,ENST00000378473,NM_001377142.1&NM_001377143.1,c.1924G>A,MODERATE,YES,tolerated(0.05),possibly_damaging(0.855),1;PLCB4,missense_variant,p.D630N,ENST00000278655,NM_182797.3&NM_001377136.1,c.1888G>A,MODERATE,,tolerated(0.05),probably_damaging(0.983),1;PLCB4,missense_variant,p.D642N,ENST00000414679,NM_001172646.2,c.1924G>A,MODERATE,,tolerated(0.05),possibly_damaging(0.448),1;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,,n.1903G>A,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,,n.1665G>A,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,,n.1615G>A,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,,n.1579G>A,MODIFIER,,,,1 1966/5430 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 60 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 73 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLCB4,non_coding_transcript_exon_variant,,ENST00000688465.1,n.728G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000688049.1,n.1399G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000689976.1,n.979G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000687147.1,n.1456G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151.5,n.1579G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123.1,n.1615G>A,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199.5,n.1665G>A,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000689392.1,c.*1839G>A,MODIFIER,;PLCB4,missense_variant,NMD_transcript_variant,p.D630N,ENST00000492632.5,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D612N,ENST00000278655.9,c.1834G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000693005.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000688656.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000685310.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D535N,ENST00000693090.1,c.1603G>A,MODERATE,;PLCB4,missense_variant,p.D612N,ENST00000686253.1,c.1834G>A,MODERATE,;PLCB4,missense_variant,p.D535N,ENST00000692395.1,c.1603G>A,MODERATE,;PLCB4,missense_variant,p.D634N,ENST00000686893.1,c.1900G>A,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000685446.1,n.2086G>A,MODIFIER,;PLCB4,missense_variant,p.D479N,ENST00000685482.1,c.1435G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000692085.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D562N,ENST00000689010.1,c.1684G>A,MODERATE,;PLCB4,missense_variant,p.D642N,ENST00000691112.1,c.1924G>A,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000686532.1,n.2122G>A,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686163.1,c.*380G>A,MODIFIER,;PLCB4,missense_variant,p.D642N,ENST00000690960.1,c.1924G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000693160.1,c.1888G>A,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000693492.1,c.*1167G>A,MODIFIER,;PLCB4,missense_variant,p.D642N,ENST00000685568.1,c.1924G>A,MODERATE,;PLCB4,missense_variant,p.D535N,ENST00000686117.1,c.1603G>A,MODERATE,;PLCB4,missense_variant,p.D642N,ENST00000685823.1,c.1924G>A,MODERATE,;PLCB4,missense_variant,p.D612N,ENST00000687446.1,c.1834G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000686976.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000691007.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000686313.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000684997.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D642N,ENST00000378473.9,c.1924G>A,MODERATE,YES;PLCB4,missense_variant,p.D529N,ENST00000690729.1,c.1585G>A,MODERATE,;PLCB4,missense_variant,p.D642N,ENST00000685298.1,c.1924G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000689910.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000685859.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630N,ENST00000686584.1,c.1888G>A,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000687299.1,c.*894G>A,MODIFIER,;PLCB4,missense_variant,p.D577N,ENST00000693502.1,c.1729G>A,MODERATE,;PLCB4,missense_variant,p.D535N,ENST00000693544.1,c.1603G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000693752.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000688325.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000414679.7,c.1888G>A,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630N,ENST00000685148.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000688837.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000686871.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630N,ENST00000687765.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000685110.1,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000378493.6,c.1888G>A,MODERATE,;PLCB4,missense_variant,p.D630N,ENST00000378501.3,c.1888G>A,MODERATE, +CFAP61 26074 BI GRCh38 20 20196635 20196635 + synonymous_variant Silent SNP C C T rs78795550 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 32 15 c.1656C>T p.Arg552= p.R552= ENST00000245957.10 NM_015585.4 552 cgC/cgT 16/27 0.0002 0.0 0.0 0.001 0.0 0.0 P1 T R protein_coding YES CCDS33447.1 1656/3714 CAGCGCGAAGA COSM5343551 Low_complexity_(Seg):seg;PANTHER:PTHR21178 ENSP00000245957 0.000227 0.0 16/27 rs78795550 ENST00000245957 Transcript ENSG00000089101 HGNC:15872 LOW NM_015585.4 0.001 EAS synonymous_variant 1.0 Unknown Q8NHU2.133 CFAP61 HGNC 1 1.0 UPI0000206AE4 Q8NHU2-1 SNV CFAP61,synonymous_variant,p.R552=,ENST00000245957,NM_015585.4,c.1656C>T,LOW,YES,,,1;CFAP61,synonymous_variant,p.R526=,ENST00000674269,,c.1578C>T,LOW,,,,1;CFAP61,synonymous_variant,p.R92=,ENST00000431753,,c.276C>T,LOW,,,,1;CFAP61,upstream_gene_variant,,ENST00000476414,,,MODIFIER,,,,1 1752/4098 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 9.145e-05 0.0006152 0.0001156 0.0 0.0002718 4.619e-05 8.79e-06 0.0001629 3.266e-05 0.0002908000024035 0.0009734730119816 0.0 0.0 0.0 0.0002013689954765 0.0 afr 0.0009734730119816 0.0 1.5432100553880446e-05 0.000494070991408 0.0 0 71 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 47 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CFAP61,missense_variant,p.A92V,ENST00000431753.1,c.275C>T,MODERATE,;CFAP61,synonymous_variant,p.R526=,ENST00000674269.1,c.1578C>T,LOW,;CFAP61,synonymous_variant,p.R552=,ENST00000245957.10,c.1656C>T,LOW,YES +SUN5 140732 BI GRCh38 20 32983867 32983867 + missense_variant Missense_Mutation SNP C C T rs766701001 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 71 11 c.1067G>A p.Arg356His p.R356H ENST00000356173.8 NM_080675.4 356 cGc/cAc 13/13 P4 T R/H protein_coding YES CCDS13209.1 1067/1140 GCACGCGGTAC COSM1411147 PROSITE_profiles:PS51469;PANTHER:PTHR12911;PANTHER:PTHR12911:SF39;Pfam:PF07738;Gene3D:2.60.120.260 ENSP00000348496 13/13 rs766701001;COSV62180343 ENST00000356173 Transcript 1.0 ENSG00000167098 HGNC:16252 MODERATE NM_080675.4 2.687e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q8TC36.136 SUN5 HGNC -1 A0A384MDU5.9 1.0 UPI0000135D7C SNV SUN5,missense_variant,p.R356H,ENST00000356173,NM_080675.4,c.1067G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SUN5,missense_variant,p.R331H,ENST00000375523,,c.992G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1 1160/1252 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.236e-05 0.0 0.0 0.0 0.0 0.0 2.687e-05 0.0 0.0 0 141 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 82 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SUN5,missense_variant,p.R356H,ENST00000356173.8,c.1067G>A,MODERATE,YES;SUN5,missense_variant,p.R331H,ENST00000375523.7,c.992G>A,MODERATE, +PIGU 128869 BI GRCh38 20 34581570 34581570 + synonymous_variant Silent SNP G G A rs776500928 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 11 6 c.1029C>T p.Pro343= p.P343= ENST00000217446.8 NM_080476.5 343 ccC/ccT 10/12 P1 A P protein_coding YES CCDS13239.1 1029/1308 CACACGGGGAA PANTHER:PTHR13121;Pfam:PF06728 ENSP00000217446 10/12 rs776500928 ENST00000217446 Transcript 1.0 ENSG00000101464 HGNC:15791 LOW NM_080476.5 6.555e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q9H490.145 PIGU HGNC -1 1.0 UPI0000131ABC Q9H490-1 SNV PIGU,synonymous_variant,p.P343=,ENST00000217446,NM_080476.5,c.1029C>T,LOW,YES,,,-1;PIGU,synonymous_variant,p.P323=,ENST00000374820,,c.969C>T,LOW,,,,-1;PIGU,synonymous_variant,p.P89=,ENST00000438215,,c.267C>T,LOW,,,,-1;PIGU,non_coding_transcript_exon_variant,,ENST00000480175,,n.347C>T,MODIFIER,,,,-1 1036/1639 muse;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.201e-05 0.0 0.0 0.0 0.0 0.0 8.864e-06 0.0 6.555e-05 1.3521699656848796e-05 0.0 0.0 0.0 0.0 0.0002015320060309 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 12 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 17 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PIGU,non_coding_transcript_exon_variant,,ENST00000480175.1,n.347C>T,MODIFIER,;PIGU,synonymous_variant,p.P89=,ENST00000438215.1,c.267C>T,LOW,;PIGU,synonymous_variant,p.P323=,ENST00000374820.6,c.969C>T,LOW,;PIGU,synonymous_variant,p.P343=,ENST00000217446.8,c.1029C>T,LOW,YES +NCOA6 23054 BI GRCh38 20 34740664 34740664 + synonymous_variant Silent SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 35 36 c.5592C>T p.Leu1864= p.L1864= ENST00000359003.7 NM_014071.5 1864 ctC/ctT 11/15 P3 A L protein_coding CCDS13241.1 5592/6192 CCCATGAGCCC PANTHER:PTHR15690 ENSP00000351894 11/15 COSV100750322 ENST00000359003 Transcript ENSG00000198646 HGNC:15936 LOW NM_014071.5 synonymous_variant 1 Unknown 1 Q14686.181 NCOA6 HGNC -1 1.0 UPI000013C634 SNV NCOA6,synonymous_variant,p.L1864=,ENST00000374796,NM_001318240.1,c.5592C>T,LOW,YES,,,-1;NCOA6,synonymous_variant,p.L1864=,ENST00000359003,NM_014071.5,c.5592C>T,LOW,,,,-1;NCOA6,intron_variant,,ENST00000612493,NM_001242539.2,c.2915-3906C>T,MODIFIER,,,,-1;NCOA6,intron_variant,,ENST00000616167,,c.2915-1732C>T,MODIFIER,,,,-1;NCOA6,intron_variant,,ENST00000628752,,c.303-3906C>T,MODIFIER,,,,-1;AL109824.1,upstream_gene_variant,,ENST00000655046,,,MODIFIER,YES,,,1 5935/7083 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 85 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 72 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NCOA6,intron_variant,,ENST00000616167.1,c.2915-1732C>T,MODIFIER,;NCOA6,intron_variant,,ENST00000612493.4,c.2915-3906C>T,MODIFIER,;NCOA6,synonymous_variant,p.L1864=,ENST00000359003.7,c.5592C>T,LOW,YES;NCOA6,synonymous_variant,p.L1864=,ENST00000374796.6,c.5592C>T,LOW,;NCOA6,intron_variant,,ENST00000628752.2,c.303-3906C>T,MODIFIER, +RBL1 5933 BI GRCh38 20 37007427 37007427 + missense_variant Missense_Mutation SNP G G A rs374029496 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 25 7 c.2855C>T p.Ala952Val p.A952V ENST00000373664.8 NM_001323281.2 952 gCg/gTg 20/22 P1 A A/V protein_coding YES CCDS13289.1 2855/3207 GATTCGCCAAG COSM2760395 PDB-ENSP_mappings:4yoo.A;PDB-ENSP_mappings:4yos.A;PDB-ENSP_mappings:4yoz.A;PANTHER:PTHR13742;PANTHER:PTHR13742:SF20;SMART:SM01369;Superfamily:SSF47954 ENSP00000362768 0.0 0.0001163 20/22 rs374029496;COSV60330080 ENST00000373664 Transcript ENSG00000080839 HGNC:9893 MODERATE NM_002895.5 0.0001163 EA missense_variant 0;1 1.0 benign(0.052) Unknown tolerated(0.05) 0;1 P28749.208 RBL1 HGNC -1 1.0 UPI000013D34E P28749-1 SNV RBL1,missense_variant,p.A952V,ENST00000373664,NM_001323281.2&NM_002895.5&NM_001323282.2,c.2855C>T,MODERATE,YES,tolerated(0.05),benign(0.052),-1;RBL1,missense_variant,p.A952V,ENST00000344359,NM_183404.4,c.2855C>T,MODERATE,,deleterious(0.05),benign(0.049),-1 2924/5686 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.986e-06 0.0 0.0 0.0 0.0 0.0 8.805e-06 0.0 0.0 6.769379979232326e-06 2.4372400730499063e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RBL1,missense_variant,p.A952V,ENST00000344359.7,c.2855C>T,MODERATE,;RBL1,missense_variant,p.A952V,ENST00000373664.8,c.2855C>T,MODERATE,YES +ZHX3 23051 BI GRCh38 20 41202578 41202578 + missense_variant Missense_Mutation SNP C C T rs371613858 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 92 9 c.2339G>A p.Arg780Gln p.R780Q ENST00000309060.7 780 cGg/cAg 4/5 P1 T R/Q protein_coding CCDS13315.1 2339/2871 GCTGCCGCAGC COSM4098403 Gene3D:1.10.10.60;PROSITE_profiles:PS50071;PANTHER:PTHR15467;PANTHER:PTHR15467:SF6;SMART:SM00389;Superfamily:SSF46689;CDD:cd00086 ENSP00000312222 0.000227 0.0 4/5 rs371613858 ENST00000309060 Transcript ENSG00000174306 HGNC:15935 MODERATE 0.000294 gnomAD_SAS missense_variant possibly_damaging(0.489) Unknown deleterious(0.01) Q9H4I2.174 ZHX3 HGNC -1 5.0 UPI000000D72C Q9H4I2-1 SNV ZHX3,missense_variant,p.R780Q,ENST00000309060,,c.2339G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.489),-1;ZHX3,missense_variant,p.R489Q,ENST00000421422,,c.1466G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;ZHX3,missense_variant,p.R780Q,ENST00000559234,,c.2339G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.489),-1;ZHX3,missense_variant,p.R780Q,ENST00000560361,,c.2339G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.489),-1;ZHX3,missense_variant,p.R780Q,ENST00000544979,,c.2339G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.687),-1;ZHX3,missense_variant,p.R780Q,ENST00000432768,NM_015035.4,c.2339G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.489),-1;ZHX3,intron_variant,,ENST00000558993,,c.672+1667G>A,MODIFIER,,,,-1;ZHX3,intron_variant,,ENST00000560364,,c.672+1667G>A,MODIFIER,,,,-1;ZHX3,downstream_gene_variant,,ENST00000373261,,,MODIFIER,,,,-1;ZHX3,downstream_gene_variant,,ENST00000419740,,,MODIFIER,,,,-1;ZHX3,downstream_gene_variant,,ENST00000436099,,,MODIFIER,,,,-1;ZHX3,downstream_gene_variant,,ENST00000436440,,,MODIFIER,,,,-1;ZHX3,downstream_gene_variant,,ENST00000441102,,,MODIFIER,,,,-1;ZHX3,upstream_gene_variant,,ENST00000559436,,,MODIFIER,,,,-1 2755/10030 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 4.386e-05 0.0 0.0 0.0 0.0 0.0 1.765e-05 0.0 0.000294 1.352520030195592e-05 2.4330900487257168e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5431100109708495e-05 0.0 0.0 0 125 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 102 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZHX3,missense_variant,p.R780Q,ENST00000432768.6,c.2339G>A,MODERATE,;ZHX3,missense_variant,p.R780Q,ENST00000560361.5,c.2339G>A,MODERATE,;ZHX3,intron_variant,,ENST00000558993.1,c.672+1667G>A,MODIFIER,;ZHX3,missense_variant,p.R780Q,ENST00000544979.6,c.2339G>A,MODERATE,;ZHX3,missense_variant,p.R780Q,ENST00000559234.5,c.2339G>A,MODERATE,;ZHX3,intron_variant,,ENST00000560364.5,c.672+1667G>A,MODIFIER,;ZHX3,missense_variant,p.R780Q,ENST00000683867.1,c.2339G>A,MODERATE,YES;ZHX3,synonymous_variant,p.A488=,ENST00000421422.1,c.1464G>A,LOW,;ZHX3,missense_variant,p.R780Q,ENST00000309060.7,c.2339G>A,MODERATE, +JPH2 57158 BI GRCh38 20 44159889 44159889 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 5 c.898C>T p.Arg300Cys p.R300C ENST00000372980.4 NM_020433.5 300 Cgc/Tgc 2/6 P1 A R/C protein_coding YES CCDS13325.1 898/2091 CGAGCGTTTGT Gene3D:2.20.110.10;Pfam:PF02493;PIRSF:PIRSF037387;PANTHER:PTHR23085;PANTHER:PTHR23085:SF26;SMART:SM00698;Superfamily:SSF82185 ENSP00000362071 2/6 ENST00000372980 Transcript 1.0 ENSG00000149596 HGNC:14202 MODERATE NM_020433.5 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q9BR39.161 JPH2 HGNC -1 5.0 UPI000012DAC2 Q9BR39-1 SNV JPH2,missense_variant,p.R300C,ENST00000372980,NM_020433.5,c.898C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1 1381/9502 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 20 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 21 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS JPH2,missense_variant,p.R300C,ENST00000372980.4,c.898C>T,MODERATE,YES +GDAP1L1 78997 BI GRCh38 20 44257258 44257258 + missense_variant Missense_Mutation SNP G G A rs777303313 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 16 7 c.286G>A p.Glu96Lys p.E96K ENST00000342560.10 NM_024034.6 96 Gag/Aag 2/6 P1 A E/K protein_coding CCDS13328.1 286/1104 TGGGCGAGGAG COSM3939359;COSM724520 PROSITE_profiles:PS50404;CDD:cd03052;PANTHER:PTHR44188;PANTHER:PTHR44188:SF2;Gene3D:3.40.30.10;Pfam:PF13417;Superfamily:SSF52833 ENSP00000341782 2/6 rs777303313;COSV61157481 ENST00000342560 Transcript ENSG00000124194 HGNC:4213 MODERATE NM_024034.6 0.0001089 gnomAD_EAS missense_variant 0;1 probably_damaging(0.913) Unknown tolerated(0.08) 0;1 Q96MZ0.141 GDAP1L1 HGNC 1 1.0 UPI0000038D5C Q96MZ0-1 SNV GDAP1L1,missense_variant,p.E96K,ENST00000537864,NM_001256737.1,c.286G>A,MODERATE,YES,tolerated(0.13),probably_damaging(0.941),1;GDAP1L1,missense_variant,p.E96K,ENST00000342560,NM_024034.6,c.286G>A,MODERATE,,tolerated(0.08),probably_damaging(0.913),1;GDAP1L1,missense_variant,p.E7K,ENST00000617075,NM_001256738.1,c.19G>A,MODERATE,,tolerated(0.09),probably_damaging(0.913),1;GDAP1L1,missense_variant,p.E96K,ENST00000612599,NM_001256740.1,c.286G>A,MODERATE,,tolerated(0.07),possibly_damaging(0.891),1;GDAP1L1,missense_variant,p.E96K,ENST00000438466,NM_001256739.2,c.286G>A,MODERATE,,tolerated(0.1),probably_damaging(0.993),1;GDAP1L1,missense_variant,p.E43K,ENST00000445952,,c.127G>A,MODERATE,,tolerated(0.08),probably_damaging(0.97),1;GDAP1L1,missense_variant,p.E96K,ENST00000372952,,c.286G>A,MODERATE,,tolerated(0.07),possibly_damaging(0.861),1 313/2778 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.197e-05 0.0 0.0 9.948e-05 0.0001089 0.0 0.0 0.0 0.0 6.759410098311491e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 26 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 23 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS GDAP1L1,missense_variant,p.R42Q,ENST00000445952.2,c.125G>A,MODERATE,;GDAP1L1,missense_variant,p.E96K,ENST00000372952.7,c.286G>A,MODERATE,;GDAP1L1,missense_variant,p.E96K,ENST00000438466.5,c.286G>A,MODERATE,;GDAP1L1,missense_variant,p.E96K,ENST00000342560.10,c.286G>A,MODERATE,YES;GDAP1L1,missense_variant,p.E96K,ENST00000537864.5,c.286G>A,MODERATE,;GDAP1L1,missense_variant,p.E96K,ENST00000612599.4,c.286G>A,MODERATE,;GDAP1L1,missense_variant,p.E7K,ENST00000617075.4,c.19G>A,MODERATE, +DIDO1 11083 BI GRCh38 20 62879909 62879909 + missense_variant Missense_Mutation SNP G G A rs762357648 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 46 33 c.6047C>T p.Pro2016Leu p.P2016L ENST00000266070.8 NM_033081.3 2016 cCg/cTg 16/16 P3 A P/L protein_coding YES CCDS33506.1 6047/6723 CCTGCGGGGCC MobiDB_lite:mobidb-lite ENSP00000266070 16/16 rs762357648 ENST00000266070 Transcript ENSG00000101191 HGNC:2680 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.178) Unknown deleterious(0.01) Q9BTC0.186 DIDO1 HGNC -1 5.0 UPI0000206380 Q9BTC0-4 SNV DIDO1,missense_variant,p.P2016L,ENST00000266070,NM_033081.2,c.6047C>T,MODERATE,YES,deleterious(0.01),benign(0.178),-1;DIDO1,missense_variant,p.P2016L,ENST00000395343,NM_001193369.2,c.6047C>T,MODERATE,,deleterious(0.01),benign(0.178),-1 6403/8574 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 113 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 79 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DIDO1,missense_variant,p.P2016L,ENST00000395343.6,c.6047C>T,MODERATE,YES;DIDO1,missense_variant,p.P2016L,ENST00000266070.8,c.6047C>T,MODERATE, +RUNX1 861 BI GRCh38 21 34799369 34799369 + missense_variant Missense_Mutation SNP G G A rs758682659 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 70 17 c.899C>T p.Thr300Met p.T300M ENST00000300305.7 300 aCg/aTg 7/8 A2 A T/M protein_coding CCDS42922.1 818/1362 uncertain_significance TGGGCGTTGCT PIRSF:PIRSF009374;PANTHER:PTHR11950;PANTHER:PTHR11950:SF40 ENSP00000340690 5/6 rs758682659;COSV55866372 ENST00000344691 Transcript 1.0 ENSG00000159216 HGNC:10471 MODERATE 5.274e-05 gnomAD_NFE missense_variant 1;1 possibly_damaging(0.818) Unknown deleterious(0) 0;1 Q01196.238 RUNX1 HGNC -1 1.0 UPI0000141569 Q01196-1 SNV RUNX1,missense_variant,p.T273M,ENST00000344691,NM_001001890.3,c.818C>T,MODERATE,,deleterious(0),possibly_damaging(0.818),-1;RUNX1,missense_variant,p.T300M,ENST00000300305,,c.899C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.795),-1;RUNX1,missense_variant,p.T300M,ENST00000675419,NM_001754.5,c.899C>T,MODERATE,,deleterious(0),possibly_damaging(0.795),-1;RUNX1,missense_variant,p.T300M,ENST00000437180,,c.899C>T,MODERATE,,deleterious(0),possibly_damaging(0.795),-1;RUNX1,missense_variant,p.T209M,ENST00000399240,,c.626C>T,MODERATE,,tolerated(0.09),possibly_damaging(0.855),-1;RUNX1,3_prime_UTR_variant,,ENST00000482318,,c.*489C>T,MODIFIER,,,,-1 2396/7274 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.783e-05 0.0 2.891e-05 0.0 0.0 0.0 5.274e-05 0.0 0.0 6.757400115020573e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542919926578179e-05 0.0 0.0 0 97 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 87 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RUNX1,missense_variant,p.T209M,ENST00000399240.5,c.626C>T,MODERATE,;RUNX1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000482318.5,c.*489C>T,MODIFIER,;RUNX1,missense_variant,p.T300M,ENST00000300305.7,c.899C>T,MODERATE,;RUNX1,missense_variant,p.T273M,ENST00000344691.8,c.818C>T,MODERATE,;RUNX1,missense_variant,p.T300M,ENST00000675419.1,c.899C>T,MODERATE,YES +HLCS 3141 BI GRCh38 21 36765054 36765054 + synonymous_variant Silent SNP G G A rs536830110 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 26 18 c.1638C>T p.Ser546= p.S546= ENST00000336648.8 NM_001352515.2 546 tcC/tcT 9/12 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 A S protein_coding CCDS13647.1 1638/2181 GCCACGGACAT COSM3550571 PROSITE_profiles:PS51733;CDD:cd16442;PANTHER:PTHR12835;PANTHER:PTHR12835:SF9;Pfam:PF03099;TIGRFAM:TIGR00121;Gene3D:3.30.930.10;Superfamily:SSF55681 ENSP00000338387 9/12 rs536830110;COSV60793644 ENST00000336648 Transcript 1.0 ENSG00000159267 HGNC:4976 LOW 0.0008 AFR synonymous_variant 0;1 Unknown 0;1 P50747.190 HLCS HGNC -1 1.0 UPI0000126A8C SNV HLCS,synonymous_variant,p.S546=,ENST00000674895,NM_001352518.1&NM_001352514.2&NM_001242784.3,c.1638C>T,LOW,YES,,,-1;HLCS,synonymous_variant,p.S546=,ENST00000399120,,c.1638C>T,LOW,,,,-1;HLCS,synonymous_variant,p.S546=,ENST00000612277,NM_001352517.1&NM_001242785.2,c.1638C>T,LOW,,,,-1;HLCS,synonymous_variant,p.S546=,ENST00000336648,NM_001352515.2&NM_000411.8,c.1638C>T,LOW,,,,-1;HLCS,synonymous_variant,p.S546=,ENST00000675307,NM_001352516.2,c.1638C>T,LOW,,,,-1;HLCS,synonymous_variant,p.S546=,ENST00000675057,,c.1638C>T,LOW,,,,-1 2109/6010 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.988e-05 6.152e-05 0.0 0.0 0.0 0.0 2.637e-05 0.0 3.266e-05 1.3520500033337156e-05 2.4323799152625725e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5431100109708495e-05 0.0 0.0 0 57 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HLCS,synonymous_variant,NMD_transcript_variant,p.S546=,ENST00000675057.1,c.1638C>T,LOW,;HLCS,synonymous_variant,p.S546=,ENST00000675307.1,c.1638C>T,LOW,;HLCS,synonymous_variant,p.S546=,ENST00000399120.5,c.1638C>T,LOW,;HLCS,synonymous_variant,p.S546=,ENST00000336648.8,c.1638C>T,LOW,;HLCS,synonymous_variant,p.S546=,ENST00000612277.4,c.1638C>T,LOW,;HLCS,synonymous_variant,p.S693=,ENST00000674895.3,c.2079C>T,LOW,YES +TRPM2 7226 BI GRCh38 21 44364243 44364243 + synonymous_variant Silent SNP C C T rs143653746 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 22 12 c.384C>T p.Gly128= p.G128= ENST00000300482.9 128 ggC/ggT 4/33 0.0002 0.0008 0.0 0.0 0.0 0.0 P4 T G protein_coding CCDS13710.1 384/4512 TTTGGCGACAT COSM5774477 PDB-ENSP_mappings:6mix.A;PDB-ENSP_mappings:6mix.B;PDB-ENSP_mappings:6mix.C;PDB-ENSP_mappings:6mix.D;PDB-ENSP_mappings:6miz.A;PDB-ENSP_mappings:6miz.B;PDB-ENSP_mappings:6miz.C;PDB-ENSP_mappings:6miz.D;PDB-ENSP_mappings:6mj2.A;PDB-ENSP_mappings:6mj2.B;PDB-ENSP_mappings:6mj2.C;PDB-ENSP_mappings:6mj2.D;PDB-ENSP_mappings:6puo.A;PDB-ENSP_mappings:6puo.B;PDB-ENSP_mappings:6puo.C;PDB-ENSP_mappings:6puo.D;PDB-ENSP_mappings:6pur.A;PDB-ENSP_mappings:6pur.B;PDB-ENSP_mappings:6pur.C;PDB-ENSP_mappings:6pur.D;PDB-ENSP_mappings:6pus.A;PDB-ENSP_mappings:6pus.B;PDB-ENSP_mappings:6pus.C;PDB-ENSP_mappings:6pus.D;PDB-ENSP_mappings:6puu.A;PDB-ENSP_mappings:6puu.B;PDB-ENSP_mappings:6puu.C;PDB-ENSP_mappings:6puu.D;PANTHER:PTHR13800;PANTHER:PTHR13800:SF2 ENSP00000300482 0.0006809 0.0 4/33 rs143653746 ENST00000300482 Transcript ENSG00000142185 HGNC:12339 LOW 0.0008 AFR synonymous_variant Unknown O94759.185 TRPM2 HGNC 1 1.0 UPI0000169D60 O94759-1 SNV TRPM2,synonymous_variant,p.G128=,ENST00000397928,NM_003307.3,c.384C>T,LOW,,,,1;TRPM2,synonymous_variant,p.G128=,ENST00000300482,,c.384C>T,LOW,,,,1;TRPM2,synonymous_variant,p.G128=,ENST00000300481,NM_001320351.1,c.384C>T,LOW,,,,1;TRPM2,synonymous_variant,p.G128=,ENST00000397932,NM_001320350.1,c.384C>T,LOW,YES,,,1;TRPM2,synonymous_variant,p.G128=,ENST00000431901,,c.384C>T,LOW,,,,1;TRPM2,upstream_gene_variant,,ENST00000498430,,,MODIFIER,,,,1 597/5989 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.363e-05 0.0005537 0.0 0.0 0.0 0.0 3.517e-05 0.0001629 6.533e-05 0.0001419360050931 0.0004376790020614 0.0 6.622519867960364e-05 0.0 0.0 0.0 afr 0.0004376790020614 0.0 1.5430699932039715e-05 0.0 0.0002084199950331 0 67 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 34 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TRPM2,synonymous_variant,p.G128=,ENST00000397932.6,c.384C>T,LOW,;TRPM2,synonymous_variant,p.G128=,ENST00000300481.13,c.384C>T,LOW,;TRPM2,synonymous_variant,p.G128=,ENST00000397928.6,c.384C>T,LOW,YES;TRPM2,synonymous_variant,p.G128=,ENST00000431901.5,c.384C>T,LOW,;TRPM2,synonymous_variant,p.G128=,ENST00000300482.9,c.384C>T,LOW, +SLC25A18 83733 BI GRCh38 22 17589654 17589654 + synonymous_variant Silent SNP C C T rs556042476 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 8 c.795C>T p.Thr265= p.T265= ENST00000327451.11 NM_031481.3 265 acC/acT 10/11 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 T T protein_coding YES CCDS13744.1 795/948 ATCACCGACTG Gene3D:1.50.40.10;Pfam:PF00153;PROSITE_profiles:PS50920;PANTHER:PTHR45678;PANTHER:PTHR45678:SF11;Superfamily:SSF103506 ENSP00000329033 10/11 rs556042476;COSV53660170 ENST00000327451 Transcript ENSG00000182902 HGNC:10988 LOW NM_031481.3 0.0008 AFR synonymous_variant 0;1 1.0 Unknown 0;1 Q9H1K4.155 SLC25A18 HGNC 1 A0A024R0W0.47 1.0 UPI00000015FA SNV SLC25A18,synonymous_variant,p.T265=,ENST00000327451,NM_031481.3,c.795C>T,LOW,YES,,,1;SLC25A18,synonymous_variant,p.T265=,ENST00000399813,NM_001303484.1,c.795C>T,LOW,,,,1;ATP6V1E1,downstream_gene_variant,,ENST00000253413,NM_001696.4,,MODIFIER,YES,,,-1;ATP6V1E1,downstream_gene_variant,,ENST00000399796,NM_001039367.1,,MODIFIER,,,,-1;ATP6V1E1,downstream_gene_variant,,ENST00000399798,NM_001039366.1,,MODIFIER,,,,-1;ATP6V1E1,downstream_gene_variant,,ENST00000413576,,,MODIFIER,,,,-1;ATP6V1E1,downstream_gene_variant,,ENST00000473248,,,MODIFIER,,,,-1;AC007666.1,upstream_gene_variant,,ENST00000443935,,,MODIFIER,YES,,,-1;AC007666.1,upstream_gene_variant,,ENST00000611039,,,MODIFIER,,,,-1 1274/2186 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.955e-06 6.152e-05 0.0 0.0 5.437e-05 0.0 0.0 0.0 0.0 1.3524299902201165e-05 2.4329699954250827e-05 0.0 6.635700265178457e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 50 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC25A18,synonymous_variant,p.T265=,ENST00000327451.11,c.795C>T,LOW,YES;SLC25A18,synonymous_variant,p.T265=,ENST00000399813.1,c.795C>T,LOW, +YPEL1 29799 BI GRCh38 22 21703381 21703381 + missense_variant Missense_Mutation SNP C C T rs1188706968 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 28 c.259G>A p.Gly87Arg p.G87R ENST00000339468.8 NM_013313.5 87 Ggg/Agg 4/5 P1 T G/R protein_coding CCDS13794.1 259/360 CCACCCGAGCG PROSITE_profiles:PS51792;PANTHER:PTHR13848;PANTHER:PTHR13848:SF1;Pfam:PF03226 ENSP00000342832 4/5 rs1188706968 ENST00000339468 Transcript ENSG00000100027 HGNC:12845 MODERATE NM_013313.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant probably_damaging(1) Unknown deleterious(0) O60688.129 YPEL1 HGNC -1 1.0 UPI000013BE05 SNV YPEL1,missense_variant,p.G87R,ENST00000339468,NM_013313.5,c.259G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;YPEL1,missense_variant,p.G122R,ENST00000672036,,c.364G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;PPIL2,downstream_gene_variant,,ENST00000335025,NM_148175.3,,MODIFIER,,,,1;YPEL1,downstream_gene_variant,,ENST00000403503,,,MODIFIER,,,,-1;YPEL1,non_coding_transcript_exon_variant,,ENST00000477675,,n.954G>A,MODIFIER,,,,-1 603/4297 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 61 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS YPEL1,missense_variant,p.G122R,ENST00000672036.2,c.364G>A,MODERATE,;YPEL1,non_coding_transcript_exon_variant,,ENST00000477675.1,n.954G>A,MODIFIER,;YPEL1,missense_variant,p.G87R,ENST00000339468.8,c.259G>A,MODERATE,YES +ZMAT5 55954 BI GRCh38 22 29738432 29738432 + missense_variant Missense_Mutation SNP C C T rs1276287888 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 19 5 c.281G>A p.Arg94Gln p.R94Q ENST00000344318.4 NM_001318129.2 94 cGa/cAa 5/6 P1 T R/Q protein_coding YES CCDS13868.1 281/513 TGGCTCGCCTC PANTHER:PTHR16465;Gene3D:4.10.1000.10 ENSP00000344241 5/6 rs1276287888 ENST00000344318 Transcript ENSG00000100319 HGNC:28046 MODERATE NM_001003692.2 missense_variant 1.0 benign(0.054) Unknown tolerated(0.25) Q9UDW3.146 ZMAT5 HGNC -1 A0A024R1I1.42 1.0 UPI0000072567 SNV ZMAT5,missense_variant,p.R94Q,ENST00000344318,NM_001318129.1&NM_001003692.2&NM_019103.2,c.281G>A,MODERATE,YES,tolerated(0.25),benign(0.054),-1 444/945 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.78490005157073e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5459299902431667e-05 0.0 0.0 0 39 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 24 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZMAT5,missense_variant,p.R94Q,ENST00000344318.4,c.281G>A,MODERATE,YES +DEPDC5 9681 BI GRCh38 22 31843112 31843112 + missense_variant,NMD_transcript_variant Missense_Mutation SNP C C T rs780652126 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 38 6 c.2299C>T p.Arg767Cys p.R767C ENST00000400246.7 767 Cgc/Tgc 26/41 T R/C nonsense_mediated_decay 2299/4032 GAAACCGCCCT COSM4601644;COSM4601645;COSM4601646 ENSP00000383105 26/41 rs780652126;COSV56704980 ENST00000400246 Transcript 1.0 ENSG00000100150 HGNC:18423 MODERATE 6.591e-05 gnomAD_SAS missense_variant 0;1 possibly_damaging(0.905) Unknown deleterious(0.01) 0;1 DEPDC5 HGNC 1 A0A5F9UWT1.3 1.0 UPI001149352F SNV DEPDC5,missense_variant,p.R845C,ENST00000651528,NM_001242896.3,c.2533C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.891),1;DEPDC5,missense_variant,p.R836C,ENST00000642696,NM_001369903.1,c.2506C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.791),1;DEPDC5,missense_variant,p.R836C,ENST00000645711,NM_001136029.3,c.2506C>T,MODERATE,,deleterious(0),possibly_damaging(0.719),1;DEPDC5,missense_variant,p.R845C,ENST00000382112,NM_001364318.1,c.2533C>T,MODERATE,,deleterious(0),possibly_damaging(0.891),1;DEPDC5,missense_variant,p.R845C,ENST00000644331,NM_001363852.2,c.2533C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.897),1;DEPDC5,missense_variant,p.R845C,ENST00000400249,NM_001364320.1,c.2533C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.897),1;DEPDC5,missense_variant,p.R817C,ENST00000433147,NM_001369902.1&NM_001369901.1,c.2449C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.88),1;DEPDC5,missense_variant,p.R836C,ENST00000400248,NM_014662.5,c.2506C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.791),1;DEPDC5,missense_variant,p.R767C,ENST00000646969,NM_001364319.1,c.2299C>T,MODERATE,,deleterious(0),probably_damaging(0.975),1;DEPDC5,missense_variant,p.R767C,ENST00000646465,,c.2299C>T,MODERATE,,deleterious(0.01),probably_damaging(0.975),1;DEPDC5,missense_variant,p.R845C,ENST00000382111,,c.2533C>T,MODERATE,,deleterious(0),probably_damaging(0.949),1;DEPDC5,missense_variant,p.R767C,ENST00000645560,NM_001363854.2,c.2299C>T,MODERATE,,deleterious(0),probably_damaging(0.975),1;DEPDC5,missense_variant,p.R767C,ENST00000535622,NM_001242897.2,c.2299C>T,MODERATE,,deleterious(0),possibly_damaging(0.891),1;DEPDC5,missense_variant,p.R853C,ENST00000645407,,c.2557C>T,MODERATE,,deleterious(0.01),probably_damaging(0.996),1;DEPDC5,missense_variant,p.R817C,ENST00000647343,,c.2449C>T,MODERATE,,deleterious(0),possibly_damaging(0.88),1;Z82190.2,intron_variant,,ENST00000646701,,c.1786+23887C>T,MODIFIER,YES,,,1;DEPDC5,upstream_gene_variant,,ENST00000494060,,,MODIFIER,,,,1;DEPDC5,missense_variant,p.R767C,ENST00000400246,,c.2299C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.905),1;DEPDC5,missense_variant,p.R845C,ENST00000646515,,c.2533C>T,MODERATE,,deleterious(0),possibly_damaging(0.88),1;DEPDC5,missense_variant,p.R845C,ENST00000646998,,c.2533C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;DEPDC5,missense_variant,p.R845C,ENST00000643751,,c.2533C>T,MODERATE,,deleterious(0),possibly_damaging(0.88),1;DEPDC5,missense_variant,p.R767C,ENST00000643395,,c.2299C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;DEPDC5,missense_variant,p.R197C,ENST00000448753,,c.589C>T,MODERATE,,deleterious(0),probably_damaging(0.915),1;DEPDC5,3_prime_UTR_variant,,ENST00000642684,,c.*2226C>T,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000645494,,c.*517C>T,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000642771,,c.*544C>T,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000644162,,c.*1161C>T,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000645755,,c.*1405C>T,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000642551,,n.2269C>T,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000645893,,n.1390C>T,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000490731,,n.487C>T,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000471914,,n.451C>T,MODIFIER,,,,1;DEPDC5,downstream_gene_variant,,ENST00000462414,,,MODIFIER,,,,1;DEPDC5,upstream_gene_variant,,ENST00000646135,,,MODIFIER,,,,1 2398/5725 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.054e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.591e-05 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 44 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS DEPDC5,non_coding_transcript_exon_variant,,ENST00000490731.1,n.487C>T,MODIFIER,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000471914.5,n.451C>T,MODIFIER,;DEPDC5,missense_variant,NMD_transcript_variant,p.R197C,ENST00000448753.6,c.589C>T,MODERATE,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000645893.1,n.1390C>T,MODIFIER,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000642551.1,n.2269C>T,MODIFIER,;DEPDC5,missense_variant,p.R853C,ENST00000645407.1,c.2557C>T,MODERATE,;ENSG00000285404,intron_variant,,ENST00000646701.1,c.1786+23887C>T,MODIFIER,YES;DEPDC5,missense_variant,p.R845C,ENST00000382111.6,c.2533C>T,MODERATE,;DEPDC5,missense_variant,p.R845C,ENST00000400249.7,c.2533C>T,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.R767C,ENST00000643395.1,c.2299C>T,MODERATE,;DEPDC5,missense_variant,p.R767C,ENST00000646465.1,c.2299C>T,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645494.1,c.*517C>T,MODIFIER,;DEPDC5,missense_variant,NMD_transcript_variant,p.R845C,ENST00000646998.1,c.2533C>T,MODERATE,;DEPDC5,missense_variant,p.R845C,ENST00000651528.2,c.2533C>T,MODERATE,YES;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642684.1,c.*2226C>T,MODIFIER,;DEPDC5,missense_variant,p.R817C,ENST00000647343.1,c.2449C>T,MODERATE,;DEPDC5,missense_variant,p.R836C,ENST00000642696.1,c.2506C>T,MODERATE,;DEPDC5,missense_variant,p.R767C,ENST00000646969.1,c.2299C>T,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.R845C,ENST00000643751.2,c.2533C>T,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.R845C,ENST00000646515.1,c.2533C>T,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642771.1,c.*544C>T,MODIFIER,;DEPDC5,missense_variant,p.R836C,ENST00000400248.7,c.2506C>T,MODERATE,;DEPDC5,missense_variant,p.R845C,ENST00000382112.8,c.2533C>T,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644162.1,c.*1161C>T,MODIFIER,;DEPDC5,missense_variant,NMD_transcript_variant,p.R767C,ENST00000400246.7,c.2299C>T,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645755.1,c.*1405C>T,MODIFIER,;DEPDC5,missense_variant,p.R817C,ENST00000433147.2,c.2449C>T,MODERATE,;DEPDC5,missense_variant,p.R767C,ENST00000645560.1,c.2299C>T,MODERATE,;DEPDC5,missense_variant,p.R845C,ENST00000644331.1,c.2533C>T,MODERATE,;DEPDC5,missense_variant,p.R836C,ENST00000645711.1,c.2506C>T,MODERATE,;DEPDC5,missense_variant,p.R767C,ENST00000535622.6,c.2299C>T,MODERATE, +TXN2 25828 BI GRCh38 22 36480689 36480689 + missense_variant Missense_Mutation SNP C C T rs780339679 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 37 25 c.149G>A p.Arg50Gln p.R50Q ENST00000216185.7 NM_012473.4 50 cGg/cAg 2/4 P1 T R/Q protein_coding YES CCDS13928.1 149/501 TTGTCCGGGCT PROSITE_profiles:PS51352 ENSP00000216185 2/4 rs780339679;COSV53397339 ENST00000216185 Transcript 1.0 ENSG00000100348 HGNC:17772 MODERATE NM_012473.4 0.0005204 gnomAD_AMR missense_variant 0;1 1.0 benign(0.406) Unknown tolerated(0.08) 0;1 Q99757.189 TXN2 HGNC -1 1.0 UPI0000001BCB SNV TXN2,missense_variant,p.R50Q,ENST00000216185,NM_012473.4,c.149G>A,MODERATE,YES,tolerated(0.08),benign(0.406),-1;TXN2,missense_variant,p.R50Q,ENST00000403313,,c.149G>A,MODERATE,,tolerated(0.08),benign(0.406),-1;TXN2,5_prime_UTR_variant,,ENST00000416967,,c.-158G>A,MODIFIER,,,,-1;TXN2,non_coding_transcript_exon_variant,,ENST00000487725,,n.129G>A,MODIFIER,,,,-1;TXN2,missense_variant,p.R50Q,ENST00000411915,,c.149G>A,MODERATE,,tolerated(0.06),probably_damaging(0.937),-1 226/1336 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.158e-05 0.0 0.0005204 0.0 0.0 0.0 0.0 0.0 0.0 1.3526099792215971e-05 0.0 0.0 6.628660048590973e-05 0.0 0.0002016939979512 0.0 0.0 0.0 0.0 0.0 0 68 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 62 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS TXN2,missense_variant,NMD_transcript_variant,p.R50Q,ENST00000411915.1,c.149G>A,MODERATE,;TXN2,missense_variant,p.R50Q,ENST00000403313.5,c.149G>A,MODERATE,;TXN2,non_coding_transcript_exon_variant,,ENST00000487725.1,n.129G>A,MODIFIER,;TXN2,missense_variant,p.R50Q,ENST00000216185.7,c.149G>A,MODERATE,YES;TXN2,5_prime_UTR_variant,,ENST00000416967.1,c.-158G>A,MODIFIER, +RAC2 5880 BI GRCh38 22 37232820 37232820 + missense_variant Missense_Mutation SNP G G A rs1443752435 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 12 16 c.206C>T p.Pro69Leu p.P69L ENST00000249071.11 NM_002872.5 69 cCg/cTg 3/7 P1 A P/L protein_coding YES CCDS13945.1 206/579 AGAGCGGCCGG PDB-ENSP_mappings:1ds6.A;PDB-ENSP_mappings:2w2t.A;PDB-ENSP_mappings:2w2v.A;PDB-ENSP_mappings:2w2v.B;PDB-ENSP_mappings:2w2v.C;PDB-ENSP_mappings:2w2v.D;PDB-ENSP_mappings:2w2x.A;PDB-ENSP_mappings:2w2x.B;PROSITE_profiles:PS51420;CDD:cd01871;PANTHER:PTHR24072;PANTHER:PTHR24072:SF169;TIGRFAM:TIGR00231;Gene3D:3.40.50.300;Pfam:PF00071;SMART:SM00176;SMART:SM00174;SMART:SM00173;SMART:SM00175;Superfamily:SSF52540 ENSP00000249071 3/7 rs1443752435 ENST00000249071 Transcript 1.0 ENSG00000128340 HGNC:9802 MODERATE NM_002872.5 missense_variant 1.0 probably_damaging(0.991) Unknown deleterious_low_confidence(0) P15153.216 RAC2 HGNC -1 A0A024R1P2.50 1.0 UPI00001110AB SNV RAC2,missense_variant,p.P69L,ENST00000249071,NM_002872.5,c.206C>T,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.991),-1;RAC2,missense_variant,p.P25L,ENST00000406508,,c.74C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),-1;RAC2,missense_variant,p.P62L,ENST00000405484,,c.185C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),-1;RAC2,missense_variant,p.P69L,ENST00000441619,,c.206C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),-1;RAC2,non_coding_transcript_exon_variant,,ENST00000469532,,n.336C>T,MODIFIER,,,,-1;RAC2,upstream_gene_variant,,ENST00000481215,,,MODIFIER,,,,-1 327/1472 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 6.759859843441518e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 32 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 28 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RAC2,non_coding_transcript_exon_variant,,ENST00000469532.1,n.336C>T,MODIFIER,;RAC2,missense_variant,p.P69L,ENST00000441619.5,c.206C>T,MODERATE,;RAC2,missense_variant,p.P62L,ENST00000405484.5,c.185C>T,MODERATE,;RAC2,missense_variant,p.P25L,ENST00000406508.5,c.74C>T,MODERATE,;RAC2,non_coding_transcript_exon_variant,,ENST00000699915.1,n.264C>T,MODIFIER,;RAC2,missense_variant,p.P69L,ENST00000249071.11,c.206C>T,MODERATE,YES +PLA2G6 8398 BI GRCh38 22 38135023 38135023 + missense_variant Missense_Mutation SNP C C T rs752794250 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 24 13 c.859G>A p.Gly287Arg p.G287R ENST00000332509.8 NM_001349864.2 287 Gga/Aga 6/17 P1 T G/R protein_coding CCDS13967.1 859/2421 GGCTCCGTAAC PROSITE_profiles:PS50297;PANTHER:PTHR24139:SF34;PANTHER:PTHR24139;Gene3D:1.25.40.20;SMART:SM00248;Superfamily:SSF48403 ENSP00000333142 6/17 rs752794250;COSV100140488;COSV100140501 ENST00000332509 Transcript 1.0 ENSG00000184381 HGNC:9039 MODERATE NM_003560.4 3.266e-05 gnomAD_SAS missense_variant 0;1;1 probably_damaging(0.971) Unknown deleterious(0) 0;1;1 O60733.200 PLA2G6 HGNC -1 1.0 UPI00001310F3 O60733-1 SNV PLA2G6,missense_variant,p.G287R,ENST00000332509,NM_001349864.2&NM_003560.4,c.859G>A,MODERATE,,deleterious(0),probably_damaging(0.971),-1;PLA2G6,missense_variant,p.G287R,ENST00000660610,,c.859G>A,MODERATE,,deleterious(0),probably_damaging(0.971),-1;PLA2G6,missense_variant,p.G287R,ENST00000663895,NM_001349868.2&NM_001349867.2,c.859G>A,MODERATE,,deleterious(0),probably_damaging(0.971),-1;PLA2G6,missense_variant,p.G287R,ENST00000335539,NM_001349865.2&NM_001004426.2,c.859G>A,MODERATE,,deleterious(0),possibly_damaging(0.884),-1;PLA2G6,missense_variant,p.G287R,ENST00000402064,NM_001349866.2&NM_001199562.3&NM_001349869.2,c.859G>A,MODERATE,,deleterious(0),possibly_damaging(0.884),-1;PLA2G6,missense_variant,p.G287R,ENST00000664587,,c.859G>A,MODERATE,,deleterious(0),possibly_damaging(0.844),-1;PLA2G6,missense_variant,p.G287R,ENST00000668949,,c.859G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.802),-1;PLA2G6,missense_variant,p.G287R,ENST00000667521,,c.859G>A,MODERATE,,deleterious(0),probably_damaging(0.971),-1;PLA2G6,missense_variant,p.G109R,ENST00000427114,,c.325G>A,MODERATE,,deleterious(0),possibly_damaging(0.884),-1;PLA2G6,missense_variant,p.G109R,ENST00000498338,,c.325G>A,MODERATE,,deleterious(0),probably_damaging(0.971),-1;PLA2G6,missense_variant,p.G118R,ENST00000452542,,c.352G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000671093,,n.953G>A,MODIFIER,,,,-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000668208,,n.989G>A,MODIFIER,,,,-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000427453,,n.114G>A,MODIFIER,,,,-1;PLA2G6,missense_variant,p.R224Q,ENST00000655142,,c.671G>A,MODERATE,,deleterious_low_confidence(0.02),unknown(0),-1;PLA2G6,missense_variant,p.G14R,ENST00000448094,,c.40G>A,MODERATE,,deleterious(0),probably_damaging(0.947),-1;PLA2G6,3_prime_UTR_variant,,ENST00000668499,,c.*690G>A,MODIFIER,,,,-1;PLA2G6,3_prime_UTR_variant,,ENST00000665987,,c.*760G>A,MODIFIER,,,,-1;PLA2G6,3_prime_UTR_variant,,ENST00000673413,,c.*690G>A,MODIFIER,,,,-1;PLA2G6,3_prime_UTR_variant,,ENST00000436218,,c.*219G>A,MODIFIER,,,,-1;PLA2G6,intron_variant,,ENST00000471636,,n.412+5111G>A,MODIFIER,,,,-1;PLA2G6,upstream_gene_variant,,ENST00000452794,,,MODIFIER,,,,-1;AL022322.2,non_coding_transcript_exon_variant,,ENST00000624072,,n.4808C>T,MODIFIER,YES,,,1 1071/3299 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 8.005e-06 0.0 0.0 0.0 0.0 0.0 8.898e-06 0.0 3.266e-05 6.763610144844279e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435900422744453e-05 0.0 0.0 0 35 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLA2G6,missense_variant,p.G109R,ENST00000498338.1,c.325G>A,MODERATE,;ENSG00000279080,non_coding_transcript_exon_variant,,ENST00000624072.1,n.4808C>T,MODIFIER,YES;PLA2G6,synonymous_variant,p.T117=,ENST00000452542.5,c.351G>A,LOW,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000427453.5,n.114G>A,MODIFIER,;PLA2G6,intron_variant,,ENST00000471636.5,n.412+5111G>A,MODIFIER,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000668208.1,n.989G>A,MODIFIER,;PLA2G6,missense_variant,NMD_transcript_variant,p.G14R,ENST00000448094.5,c.40G>A,MODERATE,;PLA2G6,missense_variant,p.G109R,ENST00000427114.6,c.325G>A,MODERATE,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000436218.6,c.*219G>A,MODIFIER,;PLA2G6,missense_variant,p.G287R,ENST00000668949.1,c.859G>A,MODERATE,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000671093.1,n.953G>A,MODIFIER,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673413.1,c.*690G>A,MODIFIER,;PLA2G6,missense_variant,p.G287R,ENST00000667521.1,c.859G>A,MODERATE,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000665987.1,c.*760G>A,MODIFIER,;PLA2G6,missense_variant,p.G287R,ENST00000660610.1,c.859G>A,MODERATE,;PLA2G6,missense_variant,NMD_transcript_variant,p.R224Q,ENST00000655142.1,c.671G>A,MODERATE,;PLA2G6,missense_variant,p.G287R,ENST00000664587.1,c.859G>A,MODERATE,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000668499.1,c.*690G>A,MODIFIER,;PLA2G6,missense_variant,p.G287R,ENST00000402064.5,c.859G>A,MODERATE,;PLA2G6,missense_variant,p.G287R,ENST00000335539.7,c.859G>A,MODERATE,;PLA2G6,missense_variant,p.G287R,ENST00000663895.1,c.859G>A,MODERATE,;PLA2G6,missense_variant,p.G287R,ENST00000332509.8,c.859G>A,MODERATE,YES +PLA2G6 8398 BI GRCh38 22 38143149 38143149 + missense_variant Missense_Mutation SNP C C T rs755993359 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 151 54 c.565G>A p.Val189Ile p.V189I ENST00000332509.8 NM_001349864.2 189 Gtc/Atc 4/17 P1 T V/I protein_coding CCDS13967.1 565/2421 GAAGACGGTCT PROSITE_profiles:PS50297;PANTHER:PTHR24139:SF34;PANTHER:PTHR24139;Gene3D:1.25.40.20;Pfam:PF12796;SMART:SM00248;Superfamily:SSF48403 ENSP00000333142 4/17 rs755993359;COSV59268678 ENST00000332509 Transcript 1.0 ENSG00000184381 HGNC:9039 MODERATE NM_003560.4 0.0001631 gnomAD_EAS missense_variant 0;1 benign(0.037) Unknown tolerated(0.21) 0;1 O60733.200 PLA2G6 HGNC -1 1.0 UPI00001310F3 O60733-1 SNV PLA2G6,missense_variant,p.V189I,ENST00000332509,NM_001349864.2&NM_003560.4,c.565G>A,MODERATE,,tolerated(0.21),benign(0.037),-1;PLA2G6,missense_variant,p.V189I,ENST00000660610,,c.565G>A,MODERATE,,tolerated(0.21),benign(0.037),-1;PLA2G6,missense_variant,p.V189I,ENST00000663895,NM_001349868.2&NM_001349867.2,c.565G>A,MODERATE,,tolerated(0.21),benign(0.037),-1;PLA2G6,missense_variant,p.V189I,ENST00000335539,NM_001349865.2&NM_001004426.2,c.565G>A,MODERATE,,tolerated(0.21),benign(0.035),-1;PLA2G6,missense_variant,p.V189I,ENST00000402064,NM_001349866.2&NM_001199562.3&NM_001349869.2,c.565G>A,MODERATE,,tolerated(0.21),benign(0.035),-1;PLA2G6,missense_variant,p.V189I,ENST00000664587,,c.565G>A,MODERATE,,tolerated(0.21),benign(0.053),-1;PLA2G6,missense_variant,p.V189I,ENST00000668949,,c.565G>A,MODERATE,YES,tolerated(0.26),benign(0.065),-1;PLA2G6,missense_variant,p.V189I,ENST00000667521,,c.565G>A,MODERATE,,tolerated(0.21),benign(0.037),-1;PLA2G6,missense_variant,p.V11I,ENST00000427114,,c.31G>A,MODERATE,,tolerated(0.11),benign(0.035),-1;PLA2G6,missense_variant,p.V11I,ENST00000498338,,c.31G>A,MODERATE,,tolerated(0.23),benign(0.037),-1;PLA2G6,missense_variant,p.V117I,ENST00000430886,,c.349G>A,MODERATE,,tolerated(0.43),benign(0.094),-1;PLA2G6,missense_variant,p.V23I,ENST00000452542,,c.67G>A,MODERATE,,tolerated(0.2),benign(0.014),-1;PLA2G6,downstream_gene_variant,,ENST00000455341,,,MODIFIER,,,,-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000671093,,n.659G>A,MODIFIER,,,,-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000668208,,n.695G>A,MODIFIER,,,,-1;PLA2G6,non_coding_transcript_exon_variant,,ENST00000479641,,n.491G>A,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000417303,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000420435,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000426674,,,MODIFIER,,,,-1;PLA2G6,upstream_gene_variant,,ENST00000427453,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000435484,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000445591,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000447598,,,MODIFIER,,,,-1;PLA2G6,downstream_gene_variant,,ENST00000452972,,,MODIFIER,,,,-1;PLA2G6,missense_variant,p.V189I,ENST00000655142,,c.565G>A,MODERATE,,tolerated(0.15),possibly_damaging(0.712),-1;PLA2G6,3_prime_UTR_variant,,ENST00000668499,,c.*396G>A,MODIFIER,,,,-1;PLA2G6,3_prime_UTR_variant,,ENST00000665987,,c.*466G>A,MODIFIER,,,,-1;PLA2G6,3_prime_UTR_variant,,ENST00000673413,,c.*396G>A,MODIFIER,,,,-1;PLA2G6,intron_variant,,ENST00000436218,,c.425+2289G>A,MODIFIER,,,,-1;PLA2G6,intron_variant,,ENST00000471636,,n.376+2414G>A,MODIFIER,,,,-1;AL022322.2,non_coding_transcript_exon_variant,,ENST00000624072,,n.12934C>T,MODIFIER,YES,,,1 777/3299 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.988e-05 0.0 2.891e-05 0.0 0.0001631 0.0 0.0 0.0 3.266e-05 6.758580184396124e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.000494070991408 0.0 0 272 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 205 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PLA2G6,non_coding_transcript_exon_variant,,ENST00000479641.5,n.491G>A,MODIFIER,;PLA2G6,missense_variant,p.V117I,ENST00000430886.5,c.349G>A,MODERATE,;PLA2G6,missense_variant,p.V11I,ENST00000498338.1,c.31G>A,MODERATE,;ENSG00000279080,non_coding_transcript_exon_variant,,ENST00000624072.1,n.12934C>T,MODIFIER,YES;PLA2G6,synonymous_variant,p.P22=,ENST00000452542.5,c.66G>A,LOW,;PLA2G6,intron_variant,,ENST00000471636.5,n.376+2414G>A,MODIFIER,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000668208.1,n.695G>A,MODIFIER,;PLA2G6,missense_variant,p.V11I,ENST00000427114.6,c.31G>A,MODERATE,;PLA2G6,intron_variant,NMD_transcript_variant,,ENST00000436218.6,c.425+2289G>A,MODIFIER,;PLA2G6,missense_variant,p.V189I,ENST00000668949.1,c.565G>A,MODERATE,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000671093.1,n.659G>A,MODIFIER,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673413.1,c.*396G>A,MODIFIER,;PLA2G6,missense_variant,p.V189I,ENST00000667521.1,c.565G>A,MODERATE,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000665987.1,c.*466G>A,MODIFIER,;PLA2G6,missense_variant,p.V189I,ENST00000660610.1,c.565G>A,MODERATE,;PLA2G6,missense_variant,NMD_transcript_variant,p.V189I,ENST00000655142.1,c.565G>A,MODERATE,;PLA2G6,missense_variant,p.V189I,ENST00000664587.1,c.565G>A,MODERATE,;PLA2G6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000668499.1,c.*396G>A,MODIFIER,;PLA2G6,missense_variant,p.V189I,ENST00000402064.5,c.565G>A,MODERATE,;PLA2G6,missense_variant,p.V189I,ENST00000335539.7,c.565G>A,MODERATE,;PLA2G6,missense_variant,p.V189I,ENST00000663895.1,c.565G>A,MODERATE,;PLA2G6,missense_variant,p.V189I,ENST00000332509.8,c.565G>A,MODERATE,YES +L3MBTL2 83746 BI GRCh38 22 41225883 41225883 + synonymous_variant Silent SNP C C T rs764759330 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 14 c.1446C>T p.His482= p.H482= ENST00000216237.10 NM_031488.5 482 caC/caT 12/17 P1 T H protein_coding YES CCDS14011.1 1446/2118 TCCCACGCCAT PDB-ENSP_mappings:3cey.A;PDB-ENSP_mappings:3cey.B;PDB-ENSP_mappings:3f70.A;PDB-ENSP_mappings:3f70.B;PROSITE_profiles:PS51079;PANTHER:PTHR12247;PANTHER:PTHR12247:SF64;Pfam:PF02820;Gene3D:2.30.30.140;SMART:SM00561;Superfamily:SSF63748 ENSP00000216237 12/17 rs764759330 ENST00000216237 Transcript ENSG00000100395 HGNC:18594 LOW NM_031488.5 3.266e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q969R5.180 L3MBTL2 HGNC 1 A0A0S2Z5X6.34 1.0 UPI000012E77E Q969R5-1 SNV L3MBTL2,synonymous_variant,p.H482=,ENST00000216237,NM_031488.5,c.1446C>T,LOW,YES,,,1;CHADL,downstream_gene_variant,,ENST00000216241,NM_138481.2,,MODIFIER,YES,,,-1;CHADL,downstream_gene_variant,,ENST00000417999,,,MODIFIER,,,,-1;L3MBTL2,downstream_gene_variant,,ENST00000449635,,,MODIFIER,,,,1;L3MBTL2,synonymous_variant,p.H482=,ENST00000452106,,c.1446C>T,LOW,,,,1;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000479978,,n.3704C>T,MODIFIER,,,,1;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000466589,,n.1500C>T,MODIFIER,,,,1;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000481902,,n.1569C>T,MODIFIER,,,,1;L3MBTL2,downstream_gene_variant,,ENST00000450939,,,MODIFIER,,,,1;L3MBTL2-AS1,intron_variant,,ENST00000657161,,n.227+2391G>A,MODIFIER,,,,-1 1497/3189 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.956e-06 0.0 0.0 0.0 0.0 0.0 8.795e-06 0.0 3.266e-05 6.758580184396124e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002081599959637 0 53 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 38 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS L3MBTL2-AS1,intron_variant,,ENST00000657161.1,n.227+2391G>A,MODIFIER,YES;L3MBTL2,synonymous_variant,NMD_transcript_variant,p.H482=,ENST00000452106.5,c.1446C>T,LOW,;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000479978.5,n.3704C>T,MODIFIER,;L3MBTL2,synonymous_variant,p.H482=,ENST00000216237.10,c.1446C>T,LOW,YES;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000466589.5,n.1500C>T,MODIFIER,;L3MBTL2,non_coding_transcript_exon_variant,,ENST00000481902.5,n.1569C>T,MODIFIER, +CELSR1 9620 BI GRCh38 22 46464099 46464099 + missense_variant Missense_Mutation SNP G G A rs1227807619 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 68 6 c.3791C>T p.Ala1264Val p.A1264V ENST00000262738.9 NM_014246.4 1264 gCg/gTg 2/35 P2 A A/V protein_coding CCDS14076.1 3791/9045 GCAGCGCCGAG PANTHER:PTHR24026;PANTHER:PTHR24026:SF36 ENSP00000262738 2/35 rs1227807619;COSV99418150 ENST00000262738 Transcript ENSG00000075275 HGNC:1850 MODERATE missense_variant 0;1 possibly_damaging(0.478) Unknown tolerated(0.2) 0;1 Q9NYQ6.193 CELSR1 HGNC -1 1.0 UPI0000040648 Q9NYQ6-1 SNV CELSR1,missense_variant,p.A1264V,ENST00000262738,NM_014246.4,c.3791C>T,MODERATE,,tolerated(0.2),possibly_damaging(0.478),-1;CELSR1,missense_variant,p.A1264V,ENST00000674500,NM_001378328.1,c.3791C>T,MODERATE,YES,tolerated(0.2),benign(0.044),-1;CELSR1,missense_variant,p.A1264V,ENST00000454637,,c.3791C>T,MODERATE,,tolerated(0.21),benign(0.163),-1 4241/11839 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.3515000318875536e-05 0.0 0.0 0.0 0.0 0.0 9.407340257894248e-05 0.0 1.543019970995374e-05 0.0 0.0 0 91 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 74 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CELSR1,missense_variant,p.A1264V,ENST00000454637.2,c.3791C>T,MODERATE,;CELSR1,missense_variant,p.A1264V,ENST00000674500.2,c.3791C>T,MODERATE,YES;CELSR1,missense_variant,p.A1264V,ENST00000262738.9,c.3791C>T,MODERATE, +MLC1 23209 BI GRCh38 22 50077433 50077433 + missense_variant Missense_Mutation SNP G G A rs757541925 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 23 19 c.493C>T p.Arg165Trp p.R165W ENST00000311597.10 NM_001376484.1 165 Cgg/Tgg 6/12 P1 A R/W protein_coding CCDS14083.1 493/1134 GGACCGTGCAG PANTHER:PTHR17597 ENSP00000310375 6/12 rs757541925 ENST00000311597 Transcript 1.0 ENSG00000100427 HGNC:17082 MODERATE NM_015166.4 3.268e-05 gnomAD_SAS missense_variant probably_damaging(0.997) Unknown deleterious_low_confidence(0) Q15049.174 MLC1 HGNC -1 A0A024R4V4.35 1.0 UPI000004AD09 Q15049-1 SNV MLC1,missense_variant,p.R165W,ENST00000395876,NM_001376474.1&NM_001376475.1&NM_001376476.1&NM_001376473.1&NM_001376483.1&NM_001376478.1&NM_139202.3&NM_001376477.1&NM_001376472.1,c.493C>T,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.997),-1;MLC1,missense_variant,p.R165W,ENST00000311597,NM_001376484.1&NM_001376480.1&NM_001376482.1&NM_001376481.1&NM_001376479.1&NM_015166.4,c.493C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.997),-1;MLC1,missense_variant,p.R135W,ENST00000442311,,c.403C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.997),-1;MLC1,upstream_gene_variant,,ENST00000470008,,,MODIFIER,,,,-1;MLC1,upstream_gene_variant,,ENST00000483836,,,MODIFIER,,,,-1 624/3457 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 7.973e-06 0.0 0.0 0.0 0.0 0.0 8.83e-06 0.0 3.268e-05 0 51 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 42 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MLC1,missense_variant,p.R135W,ENST00000442311.1,c.403C>T,MODERATE,;MLC1,missense_variant,p.R165W,ENST00000311597.10,c.493C>T,MODERATE,YES;MLC1,missense_variant,p.R165W,ENST00000395876.6,c.493C>T,MODERATE, +PPP6R2 9701 BI GRCh38 22 50423531 50423531 + missense_variant Missense_Mutation SNP C C T rs775856214 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 33 8 c.1042C>T p.Arg348Cys p.R348C ENST00000216061.9 NM_001365836.1 348 Cgc/Tgc 11/25 A2 T R/C protein_coding YES 1042/2901 GCGCCCGCCTC Pfam:PF04499;PANTHER:PTHR12634;PANTHER:PTHR12634:SF15;Superfamily:SSF48371 ENSP00000216061 11/25 rs775856214 ENST00000216061 Transcript ENSG00000100239 HGNC:19253 MODERATE 0.0001231 gnomAD_AFR missense_variant 1.0 probably_damaging(0.991) Unknown deleterious(0) O75170.162 PPP6R2 HGNC 1 1.0 UPI00001B31C3 O75170-1 SNV PPP6R2,missense_variant,p.R348C,ENST00000612753,NM_001351643.2&NM_001351641.2&NM_001351642.2&NM_001242898.2&NM_001351647.2,c.1042C>T,MODERATE,,deleterious(0),probably_damaging(0.984),1;PPP6R2,missense_variant,p.R348C,ENST00000359139,NM_001242900.2,c.1042C>T,MODERATE,,deleterious(0),probably_damaging(0.977),1;PPP6R2,missense_variant,p.R348C,ENST00000216061,NM_001365836.1,c.1042C>T,MODERATE,YES,deleterious(0),probably_damaging(0.991),1;PPP6R2,missense_variant,p.R349C,ENST00000395741,NM_001242899.2,c.1045C>T,MODERATE,,deleterious(0),probably_damaging(0.977),1;PPP6R2,missense_variant,p.R348C,ENST00000395744,NM_001351645.2&NM_001351644.2&NM_014678.5&NM_001351646.2&NM_001351648.2,c.1042C>T,MODERATE,,deleterious(0),probably_damaging(0.984),1;PPP6R2,missense_variant,p.R74C,ENST00000401672,,c.220C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;PPP6R2,upstream_gene_variant,,ENST00000427222,,,MODIFIER,,,,1 1412/3415 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.591e-05 0.0001231 0.0 0.0 0.0 0.0 1.759e-05 0.0 0.0 1.351730043097632e-05 4.863580033998005e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863580033998005e-05 0.0 0.0 0.0 0.0 0 48 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 41 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPP6R2,missense_variant,p.P73L,ENST00000401672.7,c.218C>T,MODERATE,;PPP6R2,missense_variant,p.R348C,ENST00000216061.9,c.1042C>T,MODERATE,;PPP6R2,missense_variant,p.R348C,ENST00000395744.7,c.1042C>T,MODERATE,;PPP6R2,missense_variant,p.R348C,ENST00000612753.5,c.1042C>T,MODERATE,YES;PPP6R2,missense_variant,p.R349C,ENST00000395741.7,c.1045C>T,MODERATE,;PPP6R2,missense_variant,p.R348C,ENST00000359139.7,c.1042C>T,MODERATE, +SBF1 6305 BI GRCh38 22 50460630 50460630 + missense_variant Missense_Mutation SNP G G A rs780146082 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 62 21 c.3050C>T p.Pro1017Leu p.P1017L ENST00000380817.8 NM_002972.4 1017 cCg/cTg 24/41 P3 A P/L protein_coding YES CCDS14091.2 3050/5682 CCGGCGGGTAC COSM1417117;COSM1417118 Pfam:PF02893;PANTHER:PTHR10807;PANTHER:PTHR10807:SF43;Superfamily:SSF50729 ENSP00000370196 24/41 rs780146082;COSV62369515 ENST00000380817 Transcript 1.0 ENSG00000100241 HGNC:10542 MODERATE NM_002972.4 6.461e-05 gnomAD_AFR missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 O95248.186 SBF1 HGNC -1 1.0 UPI00001D69ED O95248-5 SNV SBF1,missense_variant,p.P1017L,ENST00000380817,NM_002972.4,c.3050C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SBF1,missense_variant,p.P1018L,ENST00000348911,NM_001365819.1,c.3053C>T,MODERATE,,deleterious(0),possibly_damaging(0.579),-1;SBF1,upstream_gene_variant,,ENST00000476293,,,MODIFIER,,,,-1;SBF1,upstream_gene_variant,,ENST00000470434,,,MODIFIER,,,,-1 3245/8019 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.203e-05 6.461e-05 0.0 0.0 0.0 0.0 1.766e-05 0.0 0.0 1.3514400052372366e-05 2.4304899852722883e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 137 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 83 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000688030.1,c.*166C>T,MODIFIER,;SBF1,missense_variant,p.P298L,ENST00000685386.1,c.893C>T,MODERATE,;SBF1,missense_variant,p.P19L,ENST00000692006.1,c.56C>T,MODERATE,;SBF1,non_coding_transcript_exon_variant,,ENST00000693499.1,n.3141C>T,MODIFIER,;SBF1,missense_variant,NMD_transcript_variant,p.P1013L,ENST00000686801.1,c.3038C>T,MODERATE,;SBF1,missense_variant,p.P1017L,ENST00000688066.1,c.3050C>T,MODERATE,;SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686427.1,c.*63C>T,MODIFIER,;SBF1,non_coding_transcript_exon_variant,,ENST00000689177.1,n.901C>T,MODIFIER,;SBF1,missense_variant,p.P1017L,ENST00000691792.1,c.3050C>T,MODERATE,;SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686222.1,c.*2472C>T,MODIFIER,;SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000687704.1,c.*864C>T,MODIFIER,;SBF1,missense_variant,NMD_transcript_variant,p.P19L,ENST00000688985.1,c.56C>T,MODERATE,;SBF1,missense_variant,p.P1018L,ENST00000684986.1,c.3053C>T,MODERATE,;SBF1,non_coding_transcript_exon_variant,,ENST00000690369.1,n.3068C>T,MODIFIER,;SBF1,missense_variant,p.P1010L,ENST00000687016.1,c.3029C>T,MODERATE,;SBF1,missense_variant,p.P1017L,ENST00000693052.1,c.3050C>T,MODERATE,;SBF1,non_coding_transcript_exon_variant,,ENST00000691345.1,n.1551C>T,MODIFIER,;SBF1,missense_variant,p.P1014L,ENST00000685809.1,c.3041C>T,MODERATE,;SBF1,missense_variant,p.P1016L,ENST00000691233.1,c.3047C>T,MODERATE,;SBF1,missense_variant,p.P1016L,ENST00000693440.1,c.3047C>T,MODERATE,;SBF1,missense_variant,p.P1015L,ENST00000690990.1,c.3044C>T,MODERATE,;SBF1,missense_variant,p.P1017L,ENST00000689981.1,c.3050C>T,MODERATE,;SBF1,missense_variant,p.P1017L,ENST00000348911.11,c.3050C>T,MODERATE,;SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000688848.1,c.*2472C>T,MODIFIER,;SBF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000688124.1,c.*2044C>T,MODIFIER,;SBF1,non_coding_transcript_exon_variant,,ENST00000685390.1,n.1293C>T,MODIFIER,;SBF1,missense_variant,p.P1017L,ENST00000380817.8,c.3050C>T,MODERATE,YES;SBF1,non_coding_transcript_exon_variant,,ENST00000691959.1,n.2929C>T,MODIFIER,;SBF1,missense_variant,p.P1018L,ENST00000689129.1,c.3053C>T,MODERATE,;SBF1,non_coding_transcript_exon_variant,,ENST00000685180.1,n.2392C>T,MODIFIER, +CSF2RA 1438 BI GRCh38 X 1294422 1294422 + synonymous_variant Silent SNP G G A rs761160075 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 53 13 c.741G>A p.Ser247= p.S247= ENST00000381524.8 NM_001379163.1 247 tcG/tcA 8/13 A2 A S protein_coding CCDS35191.1 741/1203 CTGTCGTACCT PDB-ENSP_mappings:4nkq.B;PDB-ENSP_mappings:4rs1.B;PROSITE_profiles:PS50853;PANTHER:PTHR23036;PANTHER:PTHR23036:SF94;Gene3D:2.60.40.10;Superfamily:SSF49265 ENSP00000370935 8/13 rs761160075;COSV100817685;COSV62627212 ENST00000381524 Transcript 1.0 ENSG00000198223 HGNC:2435 LOW 6.533e-05 gnomAD_SAS synonymous_variant 0;1;1 Unknown 0;1;1 P15509.203 CSF2RA HGNC 1 1.0 UPI0000000C45 P15509-1 SNV CSF2RA,synonymous_variant,p.S247=,ENST00000381524,NM_001379163.1&NM_001379164.1,c.741G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000417535,NM_001379154.1&NM_001161530.2&NM_001379153.1,c.741G>A,LOW,YES,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000432318,NM_001161529.2,c.741G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000381529,NM_001379159.1&NM_001379162.1&NM_001379165.1&NM_001379161.1&NM_006140.6&NM_172245.4&NM_001379160.1&NM_001379166.1&NM_001379158.1&NM_001379156.1,c.741G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000355432,NM_172246.4,c.741G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S114=,ENST00000501036,NM_001161532.2,c.342G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000381509,NM_001161531.2&NM_001379155.1,c.741G>A,LOW,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000381500,NM_001379167.1&NM_001379169.1&NM_172247.3&NM_001379168.1,c.741G>A,LOW,,,,1;CSF2RA,intron_variant,,ENST00000355805,NM_172249.4,c.646+3913G>A,MODIFIER,,,,1;CSF2RA,intron_variant,,ENST00000494969,,c.244+7224G>A,MODIFIER,,,,1;CSF2RA,downstream_gene_variant,,ENST00000412290,,,MODIFIER,,,,1;MIR3690,downstream_gene_variant,,ENST00000580266,,,MODIFIER,YES,,,1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000498153,,n.95G>A,MODIFIER,,,,1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312,,n.778G>A,MODIFIER,,,,1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000475259,,n.152G>A,MODIFIER,,,,1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000491683,,n.198G>A,MODIFIER,,,,1;CSF2RA,synonymous_variant,p.S247=,ENST00000486791,,c.741G>A,LOW,,,,1 927/2291 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.195e-05 0.0 0.0 0.0 0.0 4.619e-05 0.0 0.0 6.533e-05 2.705040060391184e-05 7.303179882001132e-05 0.0 0.0 0.0 0.0 0.0 afr 7.303179882001132e-05 0.0 1.5429699487867765e-05 0.0 0.0 0 69 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 66 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CSF2RA,non_coding_transcript_exon_variant,,ENST00000491683.6,n.198G>A,MODIFIER,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000475259.6,n.152G>A,MODIFIER,;CSF2RA,synonymous_variant,p.S247=,ENST00000381500.6,c.741G>A,LOW,;CSF2RA,intron_variant,,ENST00000355805.7,c.646+3913G>A,MODIFIER,;CSF2RA,synonymous_variant,p.S247=,ENST00000355432.8,c.741G>A,LOW,;CSF2RA,synonymous_variant,NMD_transcript_variant,p.S247=,ENST00000486791.6,c.741G>A,LOW,;CSF2RA,synonymous_variant,p.S247=,ENST00000381509.8,c.741G>A,LOW,;CSF2RA,intron_variant,,ENST00000494969.7,c.244+7224G>A,MODIFIER,;CSF2RA,synonymous_variant,p.S247=,ENST00000432318.8,c.741G>A,LOW,;CSF2RA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696230.1,c.*824G>A,MODIFIER,;CSF2RA,synonymous_variant,p.S247=,ENST00000381529.9,c.741G>A,LOW,YES;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312.6,n.778G>A,MODIFIER,;CSF2RA,synonymous_variant,p.S247=,ENST00000381524.8,c.741G>A,LOW,;CSF2RA,synonymous_variant,p.S247=,ENST00000498153.7,c.741G>A,LOW, +ASB11 140456 BI GRCh38 X 15287908 15287908 + missense_variant Missense_Mutation SNP C C T rs760467867 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 40 9 c.820G>A p.Val274Met p.V274M ENST00000480796.6 NM_080873.3 274 Gtg/Atg 6/7 P4 T V/M protein_coding YES CCDS14164.1 820/972 CTCCACGCTGC COSM1245531;COSM1245532 PDB-ENSP_mappings:4uuc.A;PROSITE_profiles:PS50225;PROSITE_profiles:PS50297;PANTHER:PTHR24136;PANTHER:PTHR24136:SF14;Gene3D:1.25.40.20;Pfam:PF13637;Superfamily:SSF48403 ENSP00000417914 6/7 rs760467867;COSV60355288;COSV60355922 ENST00000480796 Transcript ENSG00000165192 HGNC:17186 MODERATE NM_080873.3 0.0001546 gnomAD_AFR missense_variant 0;1;1 1.0 probably_damaging(0.999) Unknown deleterious(0.04) 0;1;1 Q8WXH4.148 ASB11 HGNC -1 1.0 UPI00000474F1 Q8WXH4-1 SNV ASB11,missense_variant,p.V274M,ENST00000480796,NM_080873.3,c.820G>A,MODERATE,YES,deleterious(0.04),probably_damaging(0.999),-1;ASB11,missense_variant,p.V257M,ENST00000380470,NM_001201583.2,c.769G>A,MODERATE,,deleterious(0.03),probably_damaging(0.981),-1;ASB11,missense_variant,p.V253M,ENST00000344384,NM_001012428.2,c.757G>A,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1;ASB11,3_prime_UTR_variant,,ENST00000485437,,c.*263G>A,MODIFIER,,,,-1 855/2815 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.681e-05 0.0001546 0.0 0.0 0.0 0.0 1.251e-05 0.0 0.0 2.732639950409066e-05 9.735520143294708e-05 0.0 0.0 0.0 0.0 0.0 afr 9.735520143294708e-05 0.0 0.0 0.0 0.0 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 49 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ASB11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000485437.2,c.*263G>A,MODIFIER,;ASB11,missense_variant,p.V253M,ENST00000344384.8,c.757G>A,MODERATE,;ASB11,missense_variant,p.V257M,ENST00000380470.7,c.769G>A,MODERATE,;ASB11,missense_variant,p.V274M,ENST00000480796.6,c.820G>A,MODERATE,YES +PPEF1 5475 BI GRCh38 X 18757692 18757692 + synonymous_variant Silent SNP G G A rs143899775 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 128 103 c.462G>A p.Pro154= p.P154= ENST00000361511.9 154 ccG/ccA 11/22 0.0008 0.003 0.0 0.0 0.0 0.0 P1 A P protein_coding YES CCDS14188.1 462/1962 ATGCCGAATTT CDD:cd07420;PIRSF:PIRSF000912;Pfam:PF08321;SMART:SM00156;Superfamily:SSF56300;PANTHER:PTHR45668;PANTHER:PTHR45668:SF1 ENSP00000354871 0.0007823 0.0 8/19 rs143899775 ENST00000361511 Transcript ENSG00000086717 HGNC:9243 LOW 0.003 AFR synonymous_variant 1.0 Unknown O14829.200 PPEF1 HGNC 1 A0A024RBZ9.40 1.0 UPI0000001C4F O14829-1 SNV PPEF1,synonymous_variant,p.P154=,ENST00000361511,NM_001378382.1&NM_001378381.1&NM_001377986.1&NM_152224.1&NM_006240.4&NM_001377993.1&NM_001377996.1&NM_001377995.1&NM_001377994.1,c.462G>A,LOW,YES,,,1;PPEF1,synonymous_variant,p.P154=,ENST00000349874,NM_152226.1,c.462G>A,LOW,,,,1;PPEF1,synonymous_variant,p.P2=,ENST00000496075,,c.6G>A,LOW,,,,1;PPEF1,synonymous_variant,p.P64=,ENST00000472826,,c.192G>A,LOW,,,,1;PPEF1,non_coding_transcript_exon_variant,,ENST00000379962,,n.433G>A,MODIFIER,,,,1 956/2890 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0001258 0.00114 0.0001466 0.0 0.0 0.0 3.676e-05 0.0 5.265e-05 0.0002483309945091 0.0008535499800927 0.0 0.0 0.0 0.0 0.0 afr 0.0008535499800927 0.0 1.9606699424912225e-05 0.0 0.0 0 213 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 231 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PPEF1,synonymous_variant,p.P154=,ENST00000349874.10,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P2=,ENST00000496075.2,c.6G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000470157.2,c.462G>A,LOW,YES;PPEF1,synonymous_variant,NMD_transcript_variant,p.P154=,ENST00000379962.4,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P64=,ENST00000496616.6,c.192G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000471570.6,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000692488.1,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000472826.6,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000361511.9,c.462G>A,LOW,;PPEF1,synonymous_variant,p.P154=,ENST00000689646.1,c.462G>A,LOW, +PHKA2 5256 BI GRCh38 X 18926515 18926515 + missense_variant Missense_Mutation SNP G G A rs191267737 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 105 12 c.1397C>T p.Ala466Val p.A466V ENST00000379942.5 NM_000292.3 466 gCg/gTg 14/33 0.0003 0.0 0.0 0.0013 0.0 0.0 P1 A A/V protein_coding YES CCDS14190.1 1397/3708 TGTCCGCGATA COSM457216 Pfam:PF00723;PANTHER:PTHR10749;PANTHER:PTHR10749:SF5 ENSP00000369274 14/33 rs191267737;COSV66055277 ENST00000379942 Transcript 1.0 ENSG00000044446 HGNC:8926 MODERATE NM_000292.3 0.0013 EAS missense_variant 0;1 1.0 benign(0.117) Unknown deleterious(0.03) 0;1 P46019.195 PHKA2 HGNC -1 1.0 UPI000012DF4B SNV PHKA2,missense_variant,p.A466V,ENST00000379942,NM_000292.3,c.1397C>T,MODERATE,YES,deleterious(0.03),benign(0.117),-1;PHKA2,upstream_gene_variant,,ENST00000464455,,,MODIFIER,,,,-1 1579/5077 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 2.724e-05 0.0 0.0 0.0 0.0001443 0.0 2.44e-05 0.0 5.241e-05 9.143190254690126e-06 0.0 0.0 0.0 0.0 0.0002943770086858 0.0 0.0 0.0 0.0 0.0 0 150 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 117 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PHKA2,missense_variant,p.A466V,ENST00000379942.5,c.1397C>T,MODERATE,YES +MBTPS2 51360 BI GRCh38 X 21868491 21868491 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 175 8 c.695C>T p.Ala232Val p.A232V ENST00000379484.10 NM_015884.4 232 gCa/gTa 6/11 P1 T A/V protein_coding YES CCDS14201.1 695/1560 CCTTGCACTCT Pfam:PF02163;PANTHER:PTHR13325;PANTHER:PTHR13325:SF3;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000368798 6/11 ENST00000379484 Transcript 1.0 ENSG00000012174 HGNC:15455 MODERATE NM_015884.4 missense_variant 1.0 benign(0.023) Unknown tolerated(0.19) O43462.174 MBTPS2 HGNC 1 1.0 UPI000012F5A0 SNV MBTPS2,missense_variant,p.A232V,ENST00000365779,,c.695C>T,MODERATE,,tolerated(0.18),benign(0.067),1;MBTPS2,missense_variant,p.A232V,ENST00000379484,NM_015884.4,c.695C>T,MODERATE,YES,tolerated(0.19),benign(0.023),1;Y_RNA,upstream_gene_variant,,ENST00000383912,,,MODIFIER,YES,,,1 813/4446 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 256 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 183 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MBTPS2,missense_variant,p.A232V,ENST00000365779.2,c.695C>T,MODERATE,;MBTPS2,missense_variant,p.A232V,ENST00000379484.10,c.695C>T,MODERATE,YES +NYX 60506 BI GRCh38 X 41474287 41474287 + synonymous_variant Silent SNP C C T rs766462613 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 20 9 c.819C>T p.Ala273= p.A273= ENST00000342595.3 NM_022567.3 273 gcC/gcT 2/2 P1 T A protein_coding YES CCDS14256.1 834/1446 CTGGCCGAGCT Low_complexity_(Seg):seg;PANTHER:PTHR24373;PANTHER:PTHR24373:SF264;Gene3D:3.80.10.10;Pfam:PF13855;SMART:SM00369;Superfamily:SSF52058 ENSP00000340328 2/2 rs766462613 ENST00000342595 Transcript 1.0 ENSG00000188937 HGNC:8082 LOW 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q9GZU5.158 NYX HGNC 1 1.0 UPI0000130B37 SNV NYX,synonymous_variant,p.A278=,ENST00000342595,NM_022567.2,c.834C>T,LOW,YES,,,1;NYX,synonymous_variant,p.A278=,ENST00000378220,NM_001378477.1,c.834C>T,LOW,,,,1;NYX,downstream_gene_variant,,ENST00000486842,,,MODIFIER,,,,1;GEMIN7P1,upstream_gene_variant,,ENST00000451718,,,MODIFIER,YES,,,-1 1290/2713 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 9.069800398719964e-06 0.0 0.0 0.0 0.0003977720043621 0.0 0.0 0.0 0.0 0.0 0.0 0 25 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 29 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS NYX,synonymous_variant,p.A273=,ENST00000342595.3,c.819C>T,LOW,;NYX,synonymous_variant,p.A273=,ENST00000378220.3,c.819C>T,LOW,YES +MAOB 4129 BI GRCh38 X 43843705 43843705 + missense_variant Missense_Mutation SNP G G A rs778570953 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 43 16 c.106C>T p.Arg36Trp p.R36W ENST00000378069.5 NM_000898.5 36 Cgg/Tgg 2/15 P1 A R/W protein_coding YES CCDS14261.1 106/1563 GTCCCGGGCTT PDB-ENSP_mappings:1gos.A;PDB-ENSP_mappings:1gos.B;PDB-ENSP_mappings:1oj9.A;PDB-ENSP_mappings:1oj9.B;PDB-ENSP_mappings:1oja.A;PDB-ENSP_mappings:1oja.B;PDB-ENSP_mappings:1ojc.A;PDB-ENSP_mappings:1ojc.B;PDB-ENSP_mappings:1ojd.A;PDB-ENSP_mappings:1ojd.B;PDB-ENSP_mappings:1ojd.C;PDB-ENSP_mappings:1ojd.D;PDB-ENSP_mappings:1ojd.E;PDB-ENSP_mappings:1ojd.F;PDB-ENSP_mappings:1ojd.G;PDB-ENSP_mappings:1ojd.H;PDB-ENSP_mappings:1ojd.I;PDB-ENSP_mappings:1ojd.L;PDB-ENSP_mappings:1s2q.A;PDB-ENSP_mappings:1s2q.B;PDB-ENSP_mappings:1s2y.A;PDB-ENSP_mappings:1s2y.B;PDB-ENSP_mappings:1s3b.A;PDB-ENSP_mappings:1s3b.B;PDB-ENSP_mappings:1s3e.A;PDB-ENSP_mappings:1s3e.B;PDB-ENSP_mappings:2bk3.A;PDB-ENSP_mappings:2bk3.B;PDB-ENSP_mappings:2bk4.A;PDB-ENSP_mappings:2bk4.B;PDB-ENSP_mappings:2bk5.A;PDB-ENSP_mappings:2bk5.B;PDB-ENSP_mappings:2byb.A;PDB-ENSP_mappings:2byb.B;PDB-ENSP_mappings:2c64.A;PDB-ENSP_mappings:2c64.B;PDB-ENSP_mappings:2c65.A;PDB-ENSP_mappings:2c65.B;PDB-ENSP_mappings:2c66.A;PDB-ENSP_mappings:2c66.B;PDB-ENSP_mappings:2c67.A;PDB-ENSP_mappings:2c67.B;PDB-ENSP_mappings:2c70.A;PDB-ENSP_mappings:2c70.B;PDB-ENSP_mappings:2c72.A;PDB-ENSP_mappings:2c72.B;PDB-ENSP_mappings:2c73.A;PDB-ENSP_mappings:2c73.B;PDB-ENSP_mappings:2c75.A;PDB-ENSP_mappings:2c75.B;PDB-ENSP_mappings:2c76.A;PDB-ENSP_mappings:2c76.B;PDB-ENSP_mappings:2v5z.A;PDB-ENSP_mappings:2v5z.B;PDB-ENSP_mappings:2v60.A;PDB-ENSP_mappings:2v60.B;PDB-ENSP_mappings:2v61.A;PDB-ENSP_mappings:2v61.B;PDB-ENSP_mappings:2vrl.A;PDB-ENSP_mappings:2vrl.B;PDB-ENSP_mappings:2vrm.A;PDB-ENSP_mappings:2vrm.B;PDB-ENSP_mappings:2vz2.A;PDB-ENSP_mappings:2vz2.B;PDB-ENSP_mappings:2xcg.A;PDB-ENSP_mappings:2xcg.B;PDB-ENSP_mappings:2xfn.A;PDB-ENSP_mappings:2xfn.B;PDB-ENSP_mappings:2xfo.A;PDB-ENSP_mappings:2xfo.B;PDB-ENSP_mappings:2xfp.A;PDB-ENSP_mappings:2xfp.B;PDB-ENSP_mappings:2xfq.A;PDB-ENSP_mappings:2xfq.B;PDB-ENSP_mappings:2xfu.A;PDB-ENSP_mappings:2xfu.B;Gene3D:3.50.50.60;PDB-ENSP_mappings:3po7.A;PDB-ENSP_mappings:3po7.B;PDB-ENSP_mappings:3zyx.A;PDB-ENSP_mappings:3zyx.B;PDB-ENSP_mappings:4a79.A;PDB-ENSP_mappings:4a79.B;PDB-ENSP_mappings:4a7a.A;PDB-ENSP_mappings:4a7a.B;PDB-ENSP_mappings:4crt.A;PDB-ENSP_mappings:4crt.B;PDB-ENSP_mappings:5mrl.A;PDB-ENSP_mappings:5mrl.B;PDB-ENSP_mappings:6fvz.A;PDB-ENSP_mappings:6fvz.B;PDB-ENSP_mappings:6fw0.A;PDB-ENSP_mappings:6fw0.B;PDB-ENSP_mappings:6fwc.A;PDB-ENSP_mappings:6fwc.B;PDB-ENSP_mappings:6rkb.A;PDB-ENSP_mappings:6rkb.B;PDB-ENSP_mappings:6rkp.A;PDB-ENSP_mappings:6rkp.B;PDB-ENSP_mappings:6rle.A;PDB-ENSP_mappings:6rle.B;PDB-ENSP_mappings:6yt2.A;PDB-ENSP_mappings:6yt2.B;Pfam:PF01593;PANTHER:PTHR43563;PANTHER:PTHR43563:SF5;Superfamily:SSF51905 ENSP00000367309 2/15 rs778570953 ENST00000378069 Transcript ENSG00000069535 HGNC:6834 MODERATE NM_000898.5 missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) P27338.202 MAOB HGNC -1 1.0 UPI0000049071 P27338-1 SNV MAOB,missense_variant,p.R36W,ENST00000378069,NM_000898.5,c.106C>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;MAOB,non_coding_transcript_exon_variant,,ENST00000487544,,n.432C>T,MODIFIER,,,,-1;MAOB,downstream_gene_variant,,ENST00000468431,,,MODIFIER,,,,-1 257/2570 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 63 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 60 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS MAOB,non_coding_transcript_exon_variant,,ENST00000487544.1,n.432C>T,MODIFIER,;MAOB,missense_variant,p.R36W,ENST00000378069.5,c.106C>T,MODERATE,YES +CFP 5199 BI GRCh38 X 47626475 47626475 + stop_gained Nonsense_Mutation SNP G G A rs1603083122 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 17 7 c.985C>T p.Arg329Ter p.R329* ENST00000247153.7 NM_002621.2 329 Cga/Tga 8/10 P1 A R/* protein_coding CCDS14282.1 985/1410 CCGTCGGATAC PDB-ENSP_mappings:1w0r.A;PDB-ENSP_mappings:1w0r.B;PDB-ENSP_mappings:1w0s.A;PDB-ENSP_mappings:1w0s.B;PDB-ENSP_mappings:1w0s.C;Gene3D:2.20.100.10;PDB-ENSP_mappings:6rur.V;PDB-ENSP_mappings:6rur.Y;PDB-ENSP_mappings:6rus.B;PDB-ENSP_mappings:6ruv.V;PDB-ENSP_mappings:6ruv.Y;PDB-ENSP_mappings:6rv6.B;PDB-ENSP_mappings:6s08.A;PDB-ENSP_mappings:6s0a.A;PDB-ENSP_mappings:6s0b.A;PDB-ENSP_mappings:6sej.B;Pfam:PF00090;PROSITE_profiles:PS50092;PANTHER:PTHR22906;PANTHER:PTHR22906:SF11;SMART:SM00209;Superfamily:SSF82895 ENSP00000247153 8/10 COSV99901751 ENST00000247153 Transcript 1.0 ENSG00000126759 HGNC:8864 HIGH stop_gained 1 Unknown 1 P27918.189 CFP HGNC -1 A0A0S2Z4I5.37 5.0 UPI0000132325 SNV CFP,stop_gained,p.R329*,ENST00000396992,NM_001145252.3,c.985C>T,HIGH,YES,,,-1;CFP,stop_gained,p.R329*,ENST00000247153,NM_002621.2,c.985C>T,HIGH,,,,-1;CFP,stop_gained,p.R329*,ENST00000377005,,c.985C>T,HIGH,,,,-1;CFP,downstream_gene_variant,,ENST00000469388,,,MODIFIER,,,,-1;CFP,downstream_gene_variant,,ENST00000480317,,,MODIFIER,,,,-1;CFP,non_coding_transcript_exon_variant,,ENST00000485991,,n.2282C>T,MODIFIER,,,,-1;Z84466.1,non_coding_transcript_exon_variant,,ENST00000638776,,n.1223C>T,MODIFIER,YES,,,-1;CFP,non_coding_transcript_exon_variant,,ENST00000640573,,n.1223C>T,MODIFIER,,,,-1;CFP,non_coding_transcript_exon_variant,,ENST00000478222,,n.106C>T,MODIFIER,,,,-1 1227/1713 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 35 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 25 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CFP,stop_gained,p.R329*,ENST00000377005.6,c.985C>T,HIGH,;CFP,non_coding_transcript_exon_variant,,ENST00000485991.5,n.2282C>T,MODIFIER,;CFP,stop_gained,p.R329*,ENST00000247153.7,c.985C>T,HIGH,;CFP,non_coding_transcript_exon_variant,,ENST00000478222.1,n.106C>T,MODIFIER,;CFP,stop_gained,p.R329*,ENST00000396992.8,c.985C>T,HIGH,YES;CFP,non_coding_transcript_exon_variant,,ENST00000640573.1,n.1223C>T,MODIFIER,;ENSG00000283743,non_coding_transcript_exon_variant,,ENST00000638776.2,n.1223C>T,MODIFIER,YES +HUWE1 10075 BI GRCh38 X 53575665 53575665 + missense_variant Missense_Mutation SNP G G A rs782477771 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 6 c.6008C>T p.Thr2003Met p.T2003M ENST00000262854.11 NM_031407.7 2003 aCg/aTg 45/84 P2 A T/M protein_coding CCDS35301.1 6008/13125 ACTGCGTATCA COSM3845059;COSM3845060 PANTHER:PTHR11254;PANTHER:PTHR11254:SF291 ENSP00000262854 45/84 rs782477771;COSV53343668 ENST00000262854 Transcript 1.0 ENSG00000086758 HGNC:30892 MODERATE NM_031407.7 1.223e-05 gnomAD_NFE missense_variant 0;1 benign(0.197) Unknown deleterious_low_confidence(0.02) 0;1 Q7Z6Z7.186 HUWE1 HGNC -1 A0A024R9W5.52 1.0 UPI00004A0DAC Q7Z6Z7-1 SNV HUWE1,missense_variant,p.T2003M,ENST00000342160,,c.6008C>T,MODERATE,YES,deleterious_low_confidence(0.02),benign(0.197),-1;HUWE1,missense_variant,p.T2003M,ENST00000262854,NM_031407.7,c.6008C>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.197),-1;HUWE1,missense_variant,p.T1994M,ENST00000612484,,c.5981C>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.254),-1 6401/14731 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 5.458e-06 0.0 0.0 0.0 0.0 0.0 1.223e-05 0.0 0.0 0 55 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 48 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS HUWE1,missense_variant,p.T2002M,ENST00000704099.1,c.6005C>T,MODERATE,;HUWE1,missense_variant,p.T2003M,ENST00000342160.7,c.6008C>T,MODERATE,;HUWE1,missense_variant,p.T1994M,ENST00000612484.4,c.5981C>T,MODERATE,;HUWE1,missense_variant,p.T2003M,ENST00000262854.11,c.6008C>T,MODERATE,YES +RTL5 340526 BI GRCh38 X 72129931 72129931 + missense_variant,NMD_transcript_variant Missense_Mutation SNP C C T rs373524278 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 28 4 c.1610G>A p.Arg537His p.R537H ENST00000479991.1 537 cGt/cAt 1/2 T R/H nonsense_mediated_decay CCDS55446.1 1610/1710 CTAAACGACCT ENSP00000418667 0.001208 0.0 1/2 rs373524278;COSV101029985;COSV65453092 ENST00000479991 Transcript ENSG00000242732 HGNC:29430 MODERATE 0.001208 AA missense_variant 0;1;1 benign(0.166) Unknown tolerated_low_confidence(0.16) 0;1;1 Q5HYW3.108 RTL5 HGNC -1 1.0 UPI00001C2079 SNV RTL5,missense_variant,p.R537H,ENST00000609883,NM_001024455.4,c.1610G>A,MODERATE,YES,tolerated_low_confidence(0.16),benign(0.166),-1;NHSL2,intron_variant,,ENST00000631375,,c.68-8510C>T,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000632230,,c.44-8510C>T,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000633930,NM_001013627.2,c.281-2148C>T,MODIFIER,YES,,,1;NHSL2,upstream_gene_variant,,ENST00000510661,,,MODIFIER,,,,1;NHSL2,upstream_gene_variant,,ENST00000639939,,,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000631833,,n.220-2148C>T,MODIFIER,,,,1;RTL5,missense_variant,p.R537H,ENST00000479991,,c.1610G>A,MODERATE,,tolerated_low_confidence(0.16),benign(0.166),-1;NHSL2,upstream_gene_variant,,ENST00000373677,,,MODIFIER,,,,1 1971/4339 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.656e-05 0.0002423 0.0 0.0 0.0 0.0 0.0 0.0 0.0 4.601760156219825e-05 9.869399946182966e-05 0.0 0.0 0.0 0.0 0.0 afr 9.869399946182966e-05 0.0 1.968929973372724e-05 0.0 0.0003847629996016 0 34 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 32 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RTL5,missense_variant,p.R537H,ENST00000609883.3,c.1610G>A,MODERATE,YES;RTL5,missense_variant,NMD_transcript_variant,p.R537H,ENST00000479991.1,c.1610G>A,MODERATE,;NHSL2,intron_variant,,ENST00000632230.1,c.44-8510C>T,MODIFIER,;NHSL2,intron_variant,,ENST00000631375.1,c.68-8510C>T,MODIFIER,;NHSL2,intron_variant,,ENST00000631833.1,n.220-2148C>T,MODIFIER,;NHSL2,intron_variant,,ENST00000633930.2,c.281-2148C>T,MODIFIER,YES +RTL5 340526 BI GRCh38 X 72130982 72130982 + missense_variant,NMD_transcript_variant Missense_Mutation SNP G G A TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 46 6 c.559C>T p.Arg187Trp p.R187W ENST00000479991.1 187 Cgg/Tgg 1/2 A R/W nonsense_mediated_decay CCDS55446.1 559/1710 CACCCGCTCGG COSM3096051 ENSP00000418667 1/2 COSV65454048 ENST00000479991 Transcript ENSG00000242732 HGNC:29430 MODERATE missense_variant 1 possibly_damaging(0.719) Unknown tolerated(0.06) 1 Q5HYW3.108 RTL5 HGNC -1 1.0 UPI00001C2079 SNV RTL5,missense_variant,p.R187W,ENST00000609883,NM_001024455.4,c.559C>T,MODERATE,YES,tolerated(0.06),possibly_damaging(0.719),-1;NHSL2,intron_variant,,ENST00000631375,,c.68-7459G>A,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000632230,,c.44-7459G>A,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000633930,NM_001013627.2,c.281-1097G>A,MODIFIER,YES,,,1;NHSL2,upstream_gene_variant,,ENST00000510661,,,MODIFIER,,,,1;NHSL2,upstream_gene_variant,,ENST00000639939,,,MODIFIER,,,,1;NHSL2,intron_variant,,ENST00000631833,,n.220-1097G>A,MODIFIER,,,,1;RTL5,missense_variant,p.R187W,ENST00000479991,,c.559C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.719),-1;NHSL2,upstream_gene_variant,,ENST00000373677,,,MODIFIER,,,,1 920/4339 mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 62 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 52 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS RTL5,missense_variant,p.R187W,ENST00000609883.3,c.559C>T,MODERATE,YES;RTL5,missense_variant,NMD_transcript_variant,p.R187W,ENST00000479991.1,c.559C>T,MODERATE,;NHSL2,intron_variant,,ENST00000632230.1,c.44-7459G>A,MODIFIER,;NHSL2,intron_variant,,ENST00000631375.1,c.68-7459G>A,MODIFIER,;NHSL2,intron_variant,,ENST00000631833.1,n.220-1097G>A,MODIFIER,;NHSL2,intron_variant,,ENST00000633930.2,c.281-1097G>A,MODIFIER,YES +ERCC6L 54821 BI GRCh38 X 72207249 72207249 + synonymous_variant Silent SNP G G A rs1037136790 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 64 21 c.1518C>T p.Ile506= p.I506= ENST00000334463.4 NM_017669.4 506 atC/atT 2/2 P1 A I protein_coding YES CCDS35329.1 1518/3753 CCATCGATTCG Gene3D:3.40.50.300;Pfam:PF00271;PROSITE_profiles:PS51194;PANTHER:PTHR45629;PANTHER:PTHR45629:SF2;SMART:SM00490;Superfamily:SSF52540;CDD:cd18793 ENSP00000334675 2/2 rs1037136790 ENST00000334463 Transcript ENSG00000186871 HGNC:20794 LOW NM_017669.4 3.652e-05 gnomAD_AMR synonymous_variant 1.0 Unknown Q2NKX8.140 ERCC6L HGNC -1 1.0 UPI000021233E SNV ERCC6L,synonymous_variant,p.I383=,ENST00000373657,NM_001009954.3,c.1149C>T,LOW,,,,-1;ERCC6L,synonymous_variant,p.I506=,ENST00000334463,NM_017669.4,c.1518C>T,LOW,YES,,,-1;PIN4,intron_variant,,ENST00000423432,NM_001170747.1,c.312+10345G>A,MODIFIER,,,,1;PIN4,intron_variant,,ENST00000496835,,c.237+10345G>A,MODIFIER,,,,1;PIN4,intron_variant,,ENST00000652108,,c.264+10345G>A,MODIFIER,,,,1;PIN4,intron_variant,,ENST00000439980,,c.237+10345G>A,MODIFIER,,,,1 1634/4218 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.094e-05 0.0 3.652e-05 0.0 0.0 0.0 1.227e-05 0.0 0.0 1.837339914345648e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.9251099224202335e-05 0.0 3.9251099224202335e-05 0.0 0.0 0 133 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 86 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ERCC6L,synonymous_variant,p.I506=,ENST00000334463.4,c.1518C>T,LOW,YES;ERCC6L,synonymous_variant,p.I383=,ENST00000373657.2,c.1149C>T,LOW,;PIN4,intron_variant,,ENST00000496835.7,c.237+10345G>A,MODIFIER,;PIN4,intron_variant,,ENST00000652108.2,c.264+10345G>A,MODIFIER,;PIN4,intron_variant,NMD_transcript_variant,,ENST00000439980.7,c.237+10345G>A,MODIFIER,;PIN4,intron_variant,,ENST00000423432.6,c.312+10345G>A,MODIFIER, +XIST 7503 BI GRCh38 X 73851224 73851224 + non_coding_transcript_exon_variant RNA SNP G G A novel TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 52 42 n.1500C>T ENST00000429829.6 1/6 A misc_RNA YES AATGCGGCAAG 653.0 ENST00000618930 Transcript ENSG00000278039 MODIFIER downstream_gene_variant Unknown AL353804.7 Clone_based_ensembl_gene 1 SNV AL353804.7,downstream_gene_variant,,ENST00000618930,,,MODIFIER,YES,,,1;XIST,non_coding_transcript_exon_variant,,ENST00000429829,,n.1500C>T,MODIFIER,YES,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000650627,,n.369C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000648970,,n.492C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000650637,,n.644C>T,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000434839,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000635841,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000650186,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000650366,,,MODIFIER,,,,-1 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 124 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 95 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS XIST,non_coding_transcript_exon_variant,,ENST00000648970.1,n.492C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000650637.1,n.644C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000429829.6,n.1500C>T,MODIFIER,YES;XIST,non_coding_transcript_exon_variant,,ENST00000650627.1,n.369C>T,MODIFIER, +SLC16A2 6567 BI GRCh38 X 74531383 74531383 + missense_variant Missense_Mutation SNP G G A rs752570148 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 31 32 c.1450G>A p.Gly484Ser p.G484S ENST00000587091.6 NM_006517.5 484 Ggt/Agt 6/6 P1 A G/S protein_coding YES CCDS14426.2 1450/1620 TTGCCGGTGTG Gene3D:1.20.1250.20;PROSITE_profiles:PS50850;PANTHER:PTHR11360;PANTHER:PTHR11360:SF123;Superfamily:SSF103473;Transmembrane_helices:TMhelix;CDD:cd17420 ENSP00000465734 6/6 rs752570148 ENST00000587091 Transcript 1.0 ENSG00000147100 HGNC:10923 MODERATE NM_006517.5 5.243e-05 gnomAD_SAS missense_variant 1.0 probably_damaging(0.97) Unknown deleterious(0) P36021.157 SLC16A2 HGNC 1 1.0 UPI000019C3D5 SNV SLC16A2,missense_variant,p.G484S,ENST00000587091,NM_006517.5,c.1450G>A,MODERATE,YES,deleterious(0),probably_damaging(0.97),1;SLC16A2,synonymous_variant,p.P221=,ENST00000590447,,c.663G>A,LOW,,,,1;SLC16A2,3_prime_UTR_variant,,ENST00000636771,,c.*1151G>A,MODIFIER,,,,1 1595/4128 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.092e-05 0.0 0.0 0.0 0.0 0.0 1.226e-05 0.0 5.243e-05 0 59 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 63 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SLC16A2,missense_variant,p.G221S,ENST00000590447.1,c.661G>A,MODERATE,;SLC16A2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636771.1,c.*1151G>A,MODIFIER,;SLC16A2,missense_variant,p.G484S,ENST00000587091.6,c.1450G>A,MODERATE,YES +PGAM4 441531 BI GRCh38 X 77969172 77969172 + missense_variant Missense_Mutation SNP G G A rs782085897 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 86 32 c.467C>T p.Pro156Leu p.P156L ENST00000458128.3 NM_001029891.3 156 cCg/cTg 1/1 P1 A P/L protein_coding YES CCDS35338.1 467/765 CCTTCGGACTC HAMAP:MF_01039;CDD:cd07067;PANTHER:PTHR11931;PANTHER:PTHR11931:SF14;TIGRFAM:TIGR01258;Gene3D:3.40.50.1240;SMART:SM00855;Superfamily:SSF53254 ENSP00000412189 1/1 rs782085897 ENST00000458128 Transcript ENSG00000226784 HGNC:21731 MODERATE NM_001029891.3 0.0002213 gnomAD_OTH missense_variant benign(0) Unknown tolerated(1) Q8N0Y7.147 PGAM4 HGNC -1 UPI0000131CD2 SNV PGAM4,missense_variant,p.P156L,ENST00000458128,NM_001029891.3,c.467C>T,MODERATE,YES,tolerated(1),benign(0),-1;ATP7A,intron_variant,,ENST00000341514,NM_000052.7,c.-21-2449G>A,MODIFIER,YES,,,1;ATP7A,intron_variant,,ENST00000343533,NM_001282224.1,c.-21-2449G>A,MODIFIER,,,,1;ATP7A,intron_variant,,ENST00000642651,,c.-21-2449G>A,MODIFIER,,,,1;PGK1,intron_variant,,ENST00000644362,,c.-20+58337G>A,MODIFIER,,,,1;ATP7A,intron_variant,,ENST00000645454,,c.-21-2449G>A,MODIFIER,,,,1;AL356235.1,downstream_gene_variant,,ENST00000602791,,,MODIFIER,YES,,,1;ATP7A,intron_variant,,ENST00000645094,,c.-21-2449G>A,MODIFIER,,,,1 467/1690 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.274e-05 0.0001524 7.291e-05 0.0 0.0 0.0 0.0 0.0002213 5.241e-05 6.454529648181051e-05 0.000164565994055 0.0 9.591410344000906e-05 0.0 0.0 0.0 afr 0.000164565994055 0.0 1.966960007848684e-05 0.0 0.0 0 166 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 118 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ATP7A,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000689872.1,c.-2470G>A,MODIFIER,;PGAM4,missense_variant,p.P156L,ENST00000458128.3,c.467C>T,MODERATE,YES;ATP7A,intron_variant,,ENST00000687416.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000691456.1,n.271-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687628.1,n.81-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689767.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687325.1,n.283-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000692110.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000688165.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000693398.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686133.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689541.1,n.289-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000642651.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,NMD_transcript_variant,,ENST00000645094.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000685208.1,n.142-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689731.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686416.1,n.334-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000691152.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000685434.1,n.98-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687984.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000685885.1,c.16-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689649.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000684798.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000693167.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686464.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000682742.2,n.142-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000692729.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686688.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686560.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686480.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686543.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000688249.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687082.1,n.98-2449G>A,MODIFIER,;ATP7A,intron_variant,NMD_transcript_variant,,ENST00000693387.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686896.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686033.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000645454.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689891.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686050.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,NMD_transcript_variant,,ENST00000688889.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000343533.10,c.10-2449G>A,MODIFIER,;PGK1,intron_variant,,ENST00000644362.1,c.-20+58337G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687599.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000692908.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000689530.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686999.1,n.291-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000687086.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000686515.1,n.120-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000685264.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000688338.1,c.-21-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000688746.1,n.132-2449G>A,MODIFIER,;ATP7A,intron_variant,,ENST00000341514.11,c.-21-2449G>A,MODIFIER,YES;ATP7A,intron_variant,,ENST00000693051.1,c.-21-2449G>A,MODIFIER, +PCDH19 57526 BI GRCh38 X 100407744 100407744 + missense_variant Missense_Mutation SNP G G A rs1364286555 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 64 20 c.854C>T p.Thr285Met p.T285M ENST00000373034.8 NM_001184880.2 285 aCg/aTg 1/6 A2 A T/M protein_coding YES CCDS55462.1 854/3447 CGCGCGTGCGG Gene3D:2.60.40.60;PDB-ENSP_mappings:6vfu.A;PDB-ENSP_mappings:6vfu.B;PDB-ENSP_mappings:6vfu.C;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF40;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000362125 1/6 ENST00000373034 Transcript 1.0 ENSG00000165194 HGNC:14270 MODERATE NM_001184880.2 missense_variant 1.0 probably_damaging(0.918) Unknown deleterious(0.01) Q8TAB3.164 PCDH19 HGNC -1 1.0 UPI00001D7BCD Q8TAB3-1 SNV PCDH19,missense_variant,p.T285M,ENST00000373034,NM_001184880.2,c.854C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.918),-1;PCDH19,missense_variant,p.T285M,ENST00000255531,NM_001105243.2,c.854C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.637),-1;PCDH19,missense_variant,p.T285M,ENST00000420881,NM_020766.3,c.854C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.752),-1;PCDH19,upstream_gene_variant,,ENST00000636150,,,MODIFIER,,,,-1 2530/9756 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 0 90 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 84 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS PCDH19,missense_variant,p.T285M,ENST00000255531.8,c.854C>T,MODERATE,;PCDH19,missense_variant,p.T285M,ENST00000373034.8,c.854C>T,MODERATE,YES;PCDH19,missense_variant,p.T285M,ENST00000420881.6,c.854C>T,MODERATE, +ARMCX1 51309 BI GRCh38 X 101553027 101553027 + missense_variant Missense_Mutation SNP G G A rs1556027265 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 34 3 c.97G>A p.Glu33Lys p.E33K ENST00000372829.8 NM_016608.2 33 Gag/Aag 4/4 P1 A E/K protein_coding YES CCDS14487.1 97/1362 GAGACGAGAAC COSM4606486 PANTHER:PTHR15712;PANTHER:PTHR15712:SF14 ENSP00000361917 4/4 rs1556027265;COSV65704919 ENST00000372829 Transcript ENSG00000126947 HGNC:18073 MODERATE NM_016608.2 missense_variant 0;1 1.0 probably_damaging(0.959) Unknown tolerated_low_confidence(0.06) 0;1 Q9P291.139 ARMCX1 HGNC 1 A0A024RCI6.41 1.0 UPI00000411D9 SNV ARMCX1,missense_variant,p.E33K,ENST00000372829,NM_016608.2,c.97G>A,MODERATE,YES,tolerated_low_confidence(0.06),probably_damaging(0.959),1 452/2125 muse;mutect2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 9.197429790219758e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.9636299839476123e-05 0.0 0.0 0 44 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 37 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ARMCX1,missense_variant,p.E33K,ENST00000372829.8,c.97G>A,MODERATE,YES +ARMCX2 9823 BI GRCh38 X 101657033 101657033 + missense_variant Missense_Mutation SNP C C T rs782307127 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 41 22 c.556G>A p.Glu186Lys p.E186K ENST00000328766.9 NM_014782.7 186 Gaa/Aaa 5/5 P1 T E/K protein_coding CCDS14490.1 556/1899 CGCTTCGGTAG PANTHER:PTHR15712;PANTHER:PTHR15712:SF9;MobiDB_lite:mobidb-lite ENSP00000331662 5/5 rs782307127;COSV100168205 ENST00000328766 Transcript ENSG00000184867 HGNC:16869 MODERATE 0.0001581 gnomAD_AFR missense_variant 0;1 benign(0) Unknown tolerated_low_confidence(0.54) 0;1 Q7L311.134 ARMCX2 HGNC -1 A0A024RCG7.48 1.0 UPI0000071305 SNV ARMCX2,missense_variant,p.E186K,ENST00000356824,NM_001282231.2&NM_177949.4,c.556G>A,MODERATE,YES,tolerated_low_confidence(0.54),benign(0),-1;ARMCX2,missense_variant,p.E186K,ENST00000328766,NM_014782.7,c.556G>A,MODERATE,,tolerated_low_confidence(0.54),benign(0),-1;ARMCX2,missense_variant,p.E186K,ENST00000330154,,c.556G>A,MODERATE,,tolerated_low_confidence(0.54),benign(0),-1;ARMCX2,downstream_gene_variant,,ENST00000413506,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000431597,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000433318,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000440675,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000458024,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000467416,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000475854,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000479333,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000488982,,,MODIFIER,,,,-1;ARMCX2,downstream_gene_variant,,ENST00000496581,,,MODIFIER,,,,-1 1010/2762 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.677e-05 0.0001581 0.0 0.0 0.0 0.0 1.27e-05 0.0 0.0 5.495410005096346e-05 0.0001962389942491 0.0 0.0 0.0 0.0 0.0 afr 0.0001962389942491 0.0 0.0 0.0 0.0 0 68 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 63 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ARMCX2,missense_variant,p.E186K,ENST00000356824.9,c.556G>A,MODERATE,YES;ARMCX2,missense_variant,p.E186K,ENST00000330154.6,c.556G>A,MODERATE,;ARMCX2,missense_variant,p.E186K,ENST00000328766.9,c.556G>A,MODERATE, +ZMAT1 84460 BI GRCh38 X 101904329 101904329 + synonymous_variant,splice_region_variant Silent SNP G G A rs141888312 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 14 5 c.123C>T p.Asp41= p.D41= ENST00000372782.4 NM_001011657.4 41 gaC/gaT 3/7 A2 A D protein_coding CCDS35348.1 123/1917 ATGGCGTCTGT COSM1464454 PANTHER:PTHR46742;PANTHER:PTHR46742:SF2;Superfamily:SSF57667 ENSP00000361868 0.0 0.0002974 3/7 rs141888312;COSV65658316 ENST00000372782 Transcript ENSG00000166432 HGNC:29377 LOW 0.0002974 EA splice_region_variant 0;1 Unknown 0;1 Q5H9K5.128 ZMAT1 HGNC -1 1.0 UPI0001DD37FB SNV ZMAT1,splice_region_variant,p.D98=,ENST00000651725,NM_001282401.2,c.294C>T,LOW,YES,,,-1;ZMAT1,splice_region_variant,p.D41=,ENST00000372782,NM_001011657.4,c.123C>T,LOW,,,,-1;ZMAT1,splice_region_variant,p.D41=,ENST00000540921,,c.123C>T,LOW,,,,-1;ZMAT1,splice_region_variant,,ENST00000458570,,n.317C>T,LOW,,,,-1;ZMAT1,splice_region_variant,,ENST00000488347,NM_001282400.2,n.313C>T,LOW,,,,-1 171/3185 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 3.03e-05 0.0 0.0 0.0 8.079e-05 0.0 5.243e-05 0.0 0.0 9.208530173054896e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.9645600332296453e-05 0.0 0.0 0 40 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 19 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS ZMAT1,non_coding_transcript_exon_variant,,ENST00000488347.5,n.313C>T,MODIFIER,;ZMAT1,non_coding_transcript_exon_variant,,ENST00000458570.5,n.317C>T,MODIFIER,;ZMAT1,synonymous_variant,splice_region_variant,p.D98=,ENST00000651725.2,c.294C>T,LOW,YES;ZMAT1,synonymous_variant,splice_region_variant,p.D41=,ENST00000372782.4,c.123C>T,LOW,;ZMAT1,synonymous_variant,splice_region_variant,p.D41=,ENST00000540921.5,c.123C>T,LOW, +SEPTIN6 23157 BI GRCh38 X 119640778 119640778 + missense_variant Missense_Mutation SNP G G A rs764588243 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 36 19 c.701C>T p.Pro234Leu p.P234L ENST00000343984.5 NM_015129.6 234 cCg/cTg 6/10 A1 A P/L protein_coding YES CCDS14584.1 701/1305 CAAACGGCAGG COSM4972215;COSM4972216;COSM4972217 PDB-ENSP_mappings:2qag.B;PROSITE_profiles:PS51719;CDD:cd01850;PANTHER:PTHR18884;PANTHER:PTHR18884:SF55;Pfam:PF00735;Gene3D:3.40.50.300;PIRSF:PIRSF006698;Superfamily:SSF52540 ENSP00000341524 6/10 rs764588243;COSV59715333 ENST00000343984 Transcript 1.0 ENSG00000125354 HGNC:15848 MODERATE 0.0001337 gnomAD_ASJ missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0.02) 0;1 Q14141.184 SEPTIN6 HGNC -1 1.0 UPI0000001C54 Q14141-1 SNV SEPTIN6,missense_variant,p.P234L,ENST00000354416,,c.701C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;SEPTIN6,missense_variant,p.P234L,ENST00000394610,NM_145799.4,c.701C>T,MODERATE,,deleterious(0.02),probably_damaging(1),-1;SEPTIN6,missense_variant,p.P234L,ENST00000343984,NM_015129.6,c.701C>T,MODERATE,YES,deleterious(0.02),probably_damaging(1),-1;SEPTIN6,missense_variant,p.P234L,ENST00000360156,NM_145800.4,c.701C>T,MODERATE,,deleterious(0.02),probably_damaging(1),-1;SEPTIN6,missense_variant,p.P234L,ENST00000489216,,c.701C>T,MODERATE,,deleterious(0.02),probably_damaging(1),-1;SEPTIN6,missense_variant,p.P234L,ENST00000354228,NM_145802.4,c.701C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;SEPTIN6,missense_variant,p.P234L,ENST00000460411,,c.701C>T,MODERATE,,deleterious(0.01),probably_damaging(0.997),-1 966/2693 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.093e-05 0.0 0.0 0.0001337 0.0 0.0 1.222e-05 0.0 0.0 9.20827005757019e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.9652899936772883e-05 0.0 0.0 0 72 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 56 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS SEPTIN6,missense_variant,p.P234L,ENST00000343984.5,c.701C>T,MODERATE,;SEPTIN6,missense_variant,p.P234L,ENST00000394610.7,c.701C>T,MODERATE,YES;SEPTIN6,missense_variant,p.P234L,ENST00000354416.7,c.701C>T,MODERATE,;SEPTIN6,missense_variant,p.P234L,ENST00000489216.5,c.701C>T,MODERATE,;SEPTIN6,missense_variant,p.P234L,ENST00000354228.8,c.701C>T,MODERATE,;SEPTIN6,missense_variant,NMD_transcript_variant,p.P234L,ENST00000460411.5,c.701C>T,MODERATE,;SEPTIN6,missense_variant,p.P234L,ENST00000360156.11,c.701C>T,MODERATE, +CNGA2 1260 BI GRCh38 X 151739704 151739704 + missense_variant Missense_Mutation SNP G G A rs748063457 TCGA-YZ-A985-01A TCGA-YZ-A985-10A Somatic 42 13 c.346G>A p.Asp116Asn p.D116N ENST00000329903.5 NM_005140.3 116 Gac/Aac 4/7 P1 A D/N protein_coding YES CCDS14701.1 346/1995 AAGGCGACAAG COSM1715796 Low_complexity_(Seg):seg;PANTHER:PTHR45638;PANTHER:PTHR45638:SF3 ENSP00000328478 3/6 rs748063457;COSV61703945 ENST00000329903 Transcript 1.0 ENSG00000183862 HGNC:2149 MODERATE 2.449e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0.023) Unknown tolerated(0.41) 0;1 Q16280.160 CNGA2 HGNC 1 5.0 UPI000003E7AE SNV CNGA2,missense_variant,p.D116N,ENST00000329903,NM_005140.1,c.346G>A,MODERATE,YES,tolerated(0.41),benign(0.023),1 379/2834 muse;mutect2;varscan2 ebdabfcb-1c68-4ca1-8b7f-3ea9cdac3a6a 1.092e-05 0.0 0.0 0.0 0.0 0.0 2.449e-05 0.0 0.0 1.838510070228949e-05 3.281699900981039e-05 0.0 9.603380021872e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 84 676bc937-88a3-43b1-b476-8dc9d1ec0fb7 55 29e27ae3-1ca6-4f87-88da-71cdebd3e0fc SUCCESS CNGA2,missense_variant,p.D116N,ENST00000329903.5,c.346G>A,MODERATE,YES +IGSF9 57549 BI GRCh38 1 159931508 159931508 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 38 4 c.1458C>T p.Cys486= p.C486= ENST00000368094.6 NM_001135050.2 486 tgC/tgT 12/21 P1 A C protein_coding YES CCDS44254.1 1458/3540 GCACTGCATTC Gene3D:2.60.40.10;Pfam:PF13927;PROSITE_profiles:PS50835;PANTHER:PTHR44170;PANTHER:PTHR44170:SF19;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096 ENSP00000357073 12/21 ENST00000368094 Transcript ENSG00000085552 HGNC:18132 LOW NM_001135050.2 synonymous_variant 1.0 Unknown Q9P2J2.154 IGSF9 HGNC -1 1.0 UPI000004A10B Q9P2J2-1 SNV IGSF9,synonymous_variant,p.C486=,ENST00000368094,NM_001135050.2,c.1458C>T,LOW,YES,,,-1;IGSF9,synonymous_variant,p.C470=,ENST00000361509,NM_020789.4,c.1410C>T,LOW,,,,-1;IGSF9,intron_variant,,ENST00000611023,,c.1345+321C>T,MODIFIER,,,,-1;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102,,n.1653C>T,MODIFIER,,,,-1;IGSF9,non_coding_transcript_exon_variant,,ENST00000496645,,n.962C>T,MODIFIER,,,,-1;IGSF9,intron_variant,,ENST00000493195,,n.1541-247C>T,MODIFIER,,,,-1 1673/4059 muse;mutect2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 38 e787ca90-093c-4bdf-a0b5-de95d6ba129b 42 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS IGSF9,synonymous_variant,p.C486=,ENST00000368094.6,c.1458C>T,LOW,YES;IGSF9,intron_variant,,ENST00000493195.5,n.1541-247C>T,MODIFIER,;IGSF9,non_coding_transcript_exon_variant,,ENST00000496645.5,n.962C>T,MODIFIER,;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102.1,n.1653C>T,MODIFIER,;IGSF9,synonymous_variant,p.C470=,ENST00000361509.7,c.1410C>T,LOW, +PDGFRA 5156 BI GRCh38 4 54287442 54287442 + missense_variant Missense_Mutation SNP G G A rs1060501520 TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 83 27 c.2575G>A p.Val859Met p.V859M ENST00000257290.10 NM_001347828.2 859 Gtg/Atg 19/23 P1 A V/M protein_coding YES CCDS3495.1 2575/3270 uncertain_significance TGCCCGTGAAG Gene3D:1.10.510.10;PDB-ENSP_mappings:5grn.A;PDB-ENSP_mappings:5k5x.A;PDB-ENSP_mappings:6a32.A;PDB-ENSP_mappings:6joi.A;PDB-ENSP_mappings:6joj.A;PDB-ENSP_mappings:6jok.A;PDB-ENSP_mappings:6jol.A;Pfam:PF07714;PIRSF:PIRSF000615;PIRSF:PIRSF500950;PROSITE_profiles:PS50011;PANTHER:PTHR24416;PANTHER:PTHR24416:SF52;SMART:SM00219;SMART:SM00220;Superfamily:SSF56112;CDD:cd05105 ENSP00000257290 19/23 rs1060501520;COSV57265097 ENST00000257290 Transcript 1.0 ENSG00000134853 HGNC:8803 MODERATE NM_006206.6 3.266e-05 gnomAD_SAS missense_variant 1;1 1.0 probably_damaging(0.954) Unknown deleterious(0.02) 0;1 P16234.225 PDGFRA HGNC 1 1.0 UPI0000131793 P16234-1 SNV PDGFRA,missense_variant,p.V859M,ENST00000257290,NM_001347828.2&NM_006206.6&NM_001347829.2&NM_001347830.1,c.2575G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.954),1;AC058822.1,missense_variant,p.V619M,ENST00000507166,,c.1855G>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.998),1 2710/6378 muse;mutect2;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 3.993e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.266e-05 6.759590178262442e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 112 e787ca90-093c-4bdf-a0b5-de95d6ba129b 110 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS PDGFRA,missense_variant,p.V859M,ENST00000257290.10,c.2575G>A,MODERATE,YES;ENSG00000282278,missense_variant,p.V619M,ENST00000507166.5,c.1855G>A,MODERATE,YES +FLNC 2318 BI GRCh38 7 128846424 128846424 + missense_variant Missense_Mutation SNP G G C rs750856173 TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 37 16 c.4088G>C p.Gly1363Ala p.G1363A ENST00000325888.13 NM_001458.5 1363 gGc/gCc 23/48 C G/A protein_coding YES CCDS43644.1 4088/8178 GGGTGGCTTGG Gene3D:2.60.40.10;Pfam:PF00630;PROSITE_profiles:PS50194;PANTHER:PTHR38537;PANTHER:PTHR38537:SF6;SMART:SM00557;Superfamily:SSF81296 ENSP00000327145 23/48 rs750856173 ENST00000325888 Transcript 1.0 ENSG00000128591 HGNC:3756 MODERATE NM_001458.5 missense_variant 1.0 benign(0.251) Unknown tolerated(0.27) Q14315.214 FLNC HGNC 1 1.0 UPI000006DE6D Q14315-1 SNV FLNC,missense_variant,p.G1363A,ENST00000325888,NM_001458.5,c.4088G>C,MODERATE,YES,tolerated(0.27),benign(0.251),1;FLNC,missense_variant,p.G1363A,ENST00000346177,NM_001127487.2,c.4088G>C,MODERATE,,tolerated(0.28),probably_damaging(0.999),1;FLNC,downstream_gene_variant,,ENST00000388853,,,MODIFIER,,,,1;FLNC-AS1,downstream_gene_variant,,ENST00000469965,,,MODIFIER,YES,,,-1 4320/9159 muse;mutect2;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 65 e787ca90-093c-4bdf-a0b5-de95d6ba129b 53 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS FLNC,missense_variant,p.G1363A,ENST00000346177.6,c.4088G>C,MODERATE,;FLNC,missense_variant,NMD_transcript_variant,p.G1363A,ENST00000714185.1,c.4088G>C,MODERATE,;FLNC,missense_variant,p.G1267A,ENST00000714184.1,c.3800G>C,MODERATE,;FLNC,missense_variant,NMD_transcript_variant,p.G1363A,ENST00000714186.1,c.4088G>C,MODERATE,;FLNC,missense_variant,p.G1363A,ENST00000714183.1,c.4088G>C,MODERATE,;FLNC,missense_variant,p.G1363A,ENST00000325888.13,c.4088G>C,MODERATE,YES +PCGF6 84108 BI GRCh38 10 103314225 103314226 + frameshift_variant Frame_Shift_Ins INS - - A novel TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 83 28 c.956dup p.Arg320LysfsTer9 p.R320Kfs*9 ENST00000369847.4 NM_001011663.2 319 cta/ctTa 9/10 P1 A L/LX protein_coding YES CCDS31275.1 956-957/1053 TCCCTTAGAGT CDD:cd17085;PANTHER:PTHR45893;PANTHER:PTHR45893:SF2;Gene3D:3.10.20.90;Superfamily:SSF54236 ENSP00000358862 9/10 ENST00000369847 Transcript ENSG00000156374 HGNC:21156 HIGH NM_001011663.2 frameshift_variant 1.0 Unknown Q9BYE7.172 PCGF6 HGNC -1 1.0 UPI00001F9669 Q9BYE7-1 insertion PCGF6,frameshift_variant,p.R320Kfs*9,ENST00000369847,NM_001011663.2,c.956dup,HIGH,YES,,,-1;PCGF6,frameshift_variant,p.R245Kfs*9,ENST00000337211,NM_032154.4,c.731dup,HIGH,,,,-1;RNU11-3P,upstream_gene_variant,,ENST00000391111,,,MODIFIER,YES,,,-1;PCGF6,non_coding_transcript_exon_variant,,ENST00000490296,,n.993dup,MODIFIER,,,,-1;PCGF6,3_prime_UTR_variant,,ENST00000647574,,c.*597dup,MODIFIER,,,,-1 1030-1031/2236 mutect2;pindel;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 84 e787ca90-093c-4bdf-a0b5-de95d6ba129b 111 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS PCGF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647574.1,c.*597_*598insT,MODIFIER,;PCGF6,non_coding_transcript_exon_variant,,ENST00000490296.1,n.993_994insT,MODIFIER,;PCGF6,frameshift_variant,p.R245Kfs*9,ENST00000337211.8,c.731dup,HIGH,;PCGF6,frameshift_variant,p.R320Kfs*9,ENST00000369847.4,c.956dup,HIGH,YES +RAB38 23682 BI GRCh38 11 88149824 88149824 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 89 42 c.334T>G p.Leu112Val p.L112V ENST00000243662.11 NM_022337.3 112 Tta/Gta 2/3 P1 C L/V protein_coding YES CCDS8281.1 334/636 ACTTAACTTGG PDB-ENSP_mappings:6hdu.A;PDB-ENSP_mappings:6hdu.B;PDB-ENSP_mappings:6hdu.C;PDB-ENSP_mappings:6hdu.D;PROSITE_profiles:PS51419;CDD:cd04107;PANTHER:PTHR24073;PANTHER:PTHR24073:SF839;TIGRFAM:TIGR00231;Gene3D:3.40.50.300;Pfam:PF00071;SMART:SM00174;SMART:SM00176;SMART:SM00173;SMART:SM00175;Superfamily:SSF52540 ENSP00000243662 2/3 ENST00000243662 Transcript ENSG00000123892 HGNC:9776 MODERATE NM_022337.3 missense_variant 1.0 benign(0.006) Unknown tolerated(1) P57729.170 RAB38 HGNC -1 A0A024R191.49 1.0 UPI000003F780 SNV RAB38,missense_variant,p.L112V,ENST00000243662,NM_022337.3,c.334T>G,MODERATE,YES,tolerated(1),benign(0.006),-1;RAB38,missense_variant,p.L111V,ENST00000526372,,c.331T>G,MODERATE,,tolerated(1),probably_damaging(0.969),-1;RAB38,intron_variant,,ENST00000531138,,c.251+25359T>G,MODIFIER,,,,-1 393/1432 muse;mutect2;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 128 e787ca90-093c-4bdf-a0b5-de95d6ba129b 131 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS RAB38,missense_variant,p.V110G,ENST00000526372.1,c.329T>G,MODERATE,;RAB38,intron_variant,,ENST00000531138.1,c.251+25359T>G,MODIFIER,;RAB38,missense_variant,p.L112V,ENST00000243662.11,c.334T>G,MODERATE,YES +ZNF555 148254 BI GRCh38 19 2852697 2852697 + missense_variant Missense_Mutation SNP G G A rs764653741 TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 48 27 c.632G>A p.Arg211His p.R211H ENST00000334241.9 NM_152791.5 211 cGt/cAt 4/4 P4 A R/H protein_coding YES CCDS12096.1 632/1887 TCCTCGTACTT COSM2749722 Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF320;SMART:SM00355;Superfamily:SSF57667;Superfamily:SSF57667 ENSP00000334853 4/4 rs764653741;COSV62073279;COSV62073849 ENST00000334241 Transcript ENSG00000186300 HGNC:28382 MODERATE NM_152791.5 6.152e-05 gnomAD_AFR missense_variant 0;1;1 1.0 benign(0.012) Unknown tolerated(0.54) 0;1;1 Q8NEP9.156 ZNF555 HGNC 1 1.0 UPI0000203006 Q8NEP9-1 SNV ZNF555,missense_variant,p.R211H,ENST00000334241,NM_152791.5,c.632G>A,MODERATE,YES,tolerated(0.54),benign(0.012),1;ZNF555,missense_variant,p.R210H,ENST00000591539,NM_001172775.2,c.629G>A,MODERATE,,tolerated(0.54),benign(0.109),1;ZNF555,downstream_gene_variant,,ENST00000585966,,,MODIFIER,,,,1;AC006130.1,intron_variant,,ENST00000589365,,n.398-5313C>T,MODIFIER,YES,,,-1 730/8504 muse;mutect2;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 1.193e-05 6.152e-05 2.891e-05 0.0 0.0 0.0 8.794e-06 0.0 0.0 6.765079888282344e-06 2.4345099518541247e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 80 e787ca90-093c-4bdf-a0b5-de95d6ba129b 75 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS ENSG00000267063,intron_variant,,ENST00000589365.1,n.398-5313C>T,MODIFIER,YES;ZNF555,missense_variant,p.R211H,ENST00000334241.9,c.632G>A,MODERATE,YES;ZNF555,missense_variant,p.R210H,ENST00000591539.1,c.629G>A,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 36 25 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 52 e787ca90-093c-4bdf-a0b5-de95d6ba129b 61 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +BPI 671 BI GRCh38 20 38326345 38326345 + synonymous_variant Silent SNP C C G TCGA-V4-A9F3-01A TCGA-V4-A9F3-10A Somatic 10 8 c.1086C>G p.Thr362= p.T362= ENST00000262865.9 358 acC/acG 13/16 A2 G T protein_coding YES CCDS13303.1 1086/1464 CCCACCGGCCT PDB-ENSP_mappings:1bp1.A;PDB-ENSP_mappings:1ewf.A;CDD:cd00026;PANTHER:PTHR10504;PANTHER:PTHR10504:SF84;Pfam:PF02886;Gene3D:3.15.20.10;PIRSF:PIRSF002417;SMART:SM00329;Superfamily:SSF55394 ENSP00000262865 10/15 COSV99480796 ENST00000262865 Transcript ENSG00000101425 HGNC:1095 LOW synonymous_variant 1 1.0 Unknown 1 P17213.188 BPI HGNC 1 1.0 UPI000013D349 SNV BPI,synonymous_variant,p.T362=,ENST00000262865,,c.1086C>G,LOW,YES,,,1;BPI,synonymous_variant,p.T358=,ENST00000642449,NM_001725.3,c.1074C>G,LOW,,,,1;BPI,synonymous_variant,p.T161=,ENST00000417318,,c.483C>G,LOW,,,,1;BPI,downstream_gene_variant,,ENST00000489039,,,MODIFIER,,,,1;BPI,3_prime_UTR_variant,,ENST00000489102,,c.*263C>G,MODIFIER,,,,1;AL359555.1,intron_variant,,ENST00000437016,,n.183+9G>C,MODIFIER,YES,,,-1 1148/1845 muse;mutect2;varscan2 e21d8018-8fe9-4c92-8b36-28d7d3f7df2b 0 31 e787ca90-093c-4bdf-a0b5-de95d6ba129b 18 d7a150a1-28a7-4557-baa3-0497a4f02dea SUCCESS BPI,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000489102.2,c.*263C>G,MODIFIER,;BPI,synonymous_variant,p.T161=,ENST00000417318.3,c.483C>G,LOW,;BPI,synonymous_variant,p.T358=,ENST00000642449.2,c.1074C>G,LOW,YES;BPI,synonymous_variant,p.T362=,ENST00000262865.9,c.1086C>G,LOW,;ENSG00000206249,intron_variant,,ENST00000437016.1,n.183+9G>C,MODIFIER,YES +GNB1 2782 BI GRCh38 1 1804448 1804448 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 26 18 c.401G>A p.Arg134His p.R134H ENST00000378609.9 NM_002074.5 134 cGc/cAc 7/12 P1 T R/H protein_coding YES CCDS34.1 401/1023 TCACGCGCACG Gene3D:2.130.10.10;PDB-ENSP_mappings:4kfm.B;PDB-ENSP_mappings:4pnk.B;PDB-ENSP_mappings:5he0.B;PDB-ENSP_mappings:5he1.B;PDB-ENSP_mappings:5he2.B;PDB-ENSP_mappings:5he3.B;PDB-ENSP_mappings:5ukk.B;PDB-ENSP_mappings:5ukl.B;PDB-ENSP_mappings:5ukm.B;PDB-ENSP_mappings:5uz7.B;PDB-ENSP_mappings:6b3j.B;PDB-ENSP_mappings:6crk.B;PDB-ENSP_mappings:6d9h.B;PDB-ENSP_mappings:6dde.B;PDB-ENSP_mappings:6ddf.B;PDB-ENSP_mappings:6e3y.B;PDB-ENSP_mappings:6eg8.A;PDB-ENSP_mappings:6eg8.B;PDB-ENSP_mappings:6eg8.D;PDB-ENSP_mappings:6eg8.F;PDB-ENSP_mappings:6g79.B;PDB-ENSP_mappings:6gdg.B;PDB-ENSP_mappings:6kpf.B;PDB-ENSP_mappings:6kpg.B;PDB-ENSP_mappings:6li3.B;PDB-ENSP_mappings:6lmk.B;PDB-ENSP_mappings:6lml.B;PDB-ENSP_mappings:6m1h.E;PDB-ENSP_mappings:6m1i.E;PDB-ENSP_mappings:6m8s.C;PDB-ENSP_mappings:6m8s.D;PDB-ENSP_mappings:6m8s.G;PDB-ENSP_mappings:6m8s.H;PDB-ENSP_mappings:6m8s.K;PDB-ENSP_mappings:6n4b.B;PDB-ENSP_mappings:6ni3.B;PDB-ENSP_mappings:6niy.B;PDB-ENSP_mappings:6oij.B;PDB-ENSP_mappings:6oik.B;PDB-ENSP_mappings:6omm.B;PDB-ENSP_mappings:6orv.BP;PDB-ENSP_mappings:6os9.B;PDB-ENSP_mappings:6osa.B;PDB-ENSP_mappings:6ot0.B;PDB-ENSP_mappings:6p9x.B;PDB-ENSP_mappings:6p9y.B;PDB-ENSP_mappings:6pb0.B;PDB-ENSP_mappings:6pb1.B;PDB-ENSP_mappings:6pt0.B;PDB-ENSP_mappings:6uun.B;PDB-ENSP_mappings:6uus.B;PDB-ENSP_mappings:6uva.B;PDB-ENSP_mappings:6vms.B;PDB-ENSP_mappings:6whc.B;PIRSF:PIRSF002394;PROSITE_profiles:PS50294;PANTHER:PTHR19850;PANTHER:PTHR19850:SF29;SMART:SM00320;Superfamily:SSF50978;CDD:cd00200 ENSP00000367872 7/12 ENST00000378609 Transcript 1.0 ENSG00000078369 HGNC:4396 MODERATE NM_002074.5 missense_variant 1.0 possibly_damaging(0.73) Unknown deleterious(0.01) P62873.178 GNB1 HGNC -1 A0A140VJJ8.3 1.0 UPI00000230B3 P62873-1 SNV GNB1,missense_variant,p.R134H,ENST00000378609,NM_002074.5,c.401G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.73),-1;GNB1,missense_variant,p.R134H,ENST00000610897,NM_001282539.1,c.401G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.73),-1;GNB1,missense_variant,p.R34H,ENST00000615252,NM_001282538.1,c.101G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.73),-1;GNB1,missense_variant,p.R134H,ENST00000434686,,c.401G>A,MODERATE,,deleterious(0),possibly_damaging(0.73),-1;GNB1,missense_variant,p.R121H,ENST00000439272,,c.362G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.894),-1;GNB1,downstream_gene_variant,,ENST00000437146,,,MODIFIER,,,,-1;GNB1,non_coding_transcript_exon_variant,,ENST00000471354,,n.1005G>A,MODIFIER,,,,-1 764/3163 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 6.763149940525182e-06 2.4322600438608788e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 55 5d15cc8f-6836-434b-8fe5-f0168503446c 44 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS GNB1,missense_variant,p.R134H,ENST00000434686.6,c.401G>A,MODERATE,;GNB1,non_coding_transcript_exon_variant,,ENST00000471354.1,n.1005G>A,MODIFIER,;GNB1,missense_variant,p.R134H,ENST00000703711.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703710.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703709.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703708.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R121H,ENST00000703707.1,c.362G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703706.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R90H,ENST00000703705.1,c.269G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703704.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703703.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703702.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703701.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703699.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703700.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703697.1,c.401G>A,MODERATE,;GNB1,missense_variant,NMD_transcript_variant,p.R134H,ENST00000703695.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703694.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703693.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703696.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000703692.1,c.401G>A,MODERATE,;GNB1,missense_variant,p.R121H,ENST00000439272.7,c.362G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000378609.9,c.401G>A,MODERATE,YES;GNB1,missense_variant,p.R34H,ENST00000615252.5,c.101G>A,MODERATE,;GNB1,missense_variant,p.R134H,ENST00000610897.4,c.401G>A,MODERATE, +DNAH11 8701 BI GRCh38 7 21571944 21571944 + missense_variant Missense_Mutation SNP A A G rs186667584 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 7 12 c.1564A>G p.Thr522Ala p.T522A ENST00000409508.8 NM_001277115.2 522 Act/Gct 8/82 0.0002 0.0008 0.0 0.0 0.0 0.0 P4 G T/A protein_coding CCDS64602.1 1564/13551 AGAGCACTTAT Pfam:PF08385;PANTHER:PTHR45703;PANTHER:PTHR45703:SF12 ENSP00000475939 0.0005423 0.0 8/82 rs186667584 ENST00000409508 Transcript 1.0 ENSG00000105877 HGNC:2942 MODERATE NM_001277115.2 0.0008 AFR missense_variant benign(0.005) Unknown tolerated(0.46) Q96DT5.168 DNAH11 HGNC 1 5.0 UPI0002B8CE70 SNV DNAH11,missense_variant,p.T522A,ENST00000409508,NM_001277115.2,c.1564A>G,MODERATE,,tolerated(0.46),benign(0.005),1;DNAH11,missense_variant,p.T522A,ENST00000328843,,c.1564A>G,MODERATE,YES,tolerated(0.46),benign(0.009),1;DNAH11,missense_variant,p.T522A,ENST00000620169,,c.1564A>G,MODERATE,,tolerated(0.46),benign(0.005),1;DNAH11,downstream_gene_variant,,ENST00000496218,,,MODIFIER,,,,1 1771/14343 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 8.64e-06 0.0001348 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0280400349292904e-05 7.294659735634923e-05 0.0 0.0 0.0 0.0 0.0 afr 7.294659735634923e-05 0.0 0.0 0.0 0.0 0 34 5d15cc8f-6836-434b-8fe5-f0168503446c 19 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS DNAH11,missense_variant,p.T522A,ENST00000409508.8,c.1564A>G,MODERATE,YES +PTPRD 5789 BI GRCh38 9 8389348 8389348 + missense_variant Missense_Mutation SNP C C T rs1564475749 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 103 10 c.4270G>A p.Ala1424Thr p.A1424T ENST00000356435.9 NM_001378058.1 1424 Gcc/Acc 26/35 P1 T A/T protein_coding CCDS43786.1 4270/5739 ATAGGCATTTT Gene3D:3.90.190.10;Pfam:PF00102;PROSITE_profiles:PS50055;PANTHER:PTHR19134;PANTHER:PTHR19134:SF203;SMART:SM00194;Superfamily:SSF52799;CDD:cd14624 ENSP00000348812 26/35 rs1564475749;COSV100643528;COSV61970813 ENST00000356435 Transcript 1.0 ENSG00000153707 HGNC:9668 MODERATE missense_variant 0;1;1 probably_damaging(0.997) Unknown deleterious(0) 0;1;1 P23468.211 PTPRD HGNC -1 5.0 UPI0000132990 P23468-1 SNV PTPRD,missense_variant,p.A1424T,ENST00000381196,NM_002839.4,c.4270G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;PTPRD,missense_variant,p.A1424T,ENST00000356435,NM_001378058.1&NM_001377958.1,c.4270G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;PTPRD,missense_variant,p.A1018T,ENST00000355233,NM_130392.3,c.3052G>A,MODERATE,,deleterious(0),probably_damaging(0.983),-1;PTPRD,missense_variant,p.A1017T,ENST00000397617,,c.3049G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PTPRD,missense_variant,p.A1014T,ENST00000397611,NM_001377947.1&NM_001040712.2,c.3040G>A,MODERATE,,deleterious(0),probably_damaging(0.991),-1;PTPRD,missense_variant,p.A1008T,ENST00000537002,NM_130393.3,c.3022G>A,MODERATE,,deleterious(0),probably_damaging(0.983),-1;PTPRD,missense_variant,p.A1424T,ENST00000540109,,c.4270G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;PTPRD,missense_variant,p.A1017T,ENST00000486161,NM_130391.4,c.3049G>A,MODERATE,,deleterious(0),probably_damaging(0.983),-1;PTPRD,missense_variant,p.A1017T,ENST00000397606,NM_001171025.2&NM_001377946.1,c.3049G>A,MODERATE,,deleterious(0),probably_damaging(0.968),-1;PTPRD,non_coding_transcript_exon_variant,,ENST00000651105,,n.3648G>A,MODIFIER,,,,-1 4376/9472 muse;mutect2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 6.763340024917852e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435900422744453e-05 0.0 0.0 0 124 5d15cc8f-6836-434b-8fe5-f0168503446c 113 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS PTPRD,missense_variant,p.A1017T,ENST00000397606.7,c.3049G>A,MODERATE,;PTPRD,missense_variant,p.A1017T,ENST00000486161.5,c.3049G>A,MODERATE,;PTPRD,missense_variant,p.A1424T,ENST00000540109.5,c.4270G>A,MODERATE,;PTPRD,non_coding_transcript_exon_variant,,ENST00000651105.1,n.3648G>A,MODIFIER,;PTPRD,missense_variant,p.A1424T,ENST00000356435.9,c.4270G>A,MODERATE,;PTPRD,missense_variant,p.A1018T,ENST00000355233.9,c.3052G>A,MODERATE,;PTPRD,missense_variant,p.A1008T,ENST00000537002.5,c.3022G>A,MODERATE,;PTPRD,missense_variant,p.A1020T,ENST00000397617.8,c.3058G>A,MODERATE,;PTPRD,missense_variant,p.A1014T,ENST00000397611.7,c.3040G>A,MODERATE,;PTPRD,missense_variant,p.A1424T,ENST00000381196.9,c.4270G>A,MODERATE,YES +HHEX 3087 BI GRCh38 10 92692750 92692750 + stop_gained,splice_region_variant Nonsense_Mutation SNP C C T novel TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 37 22 c.589C>T p.Gln197Ter p.Q197* ENST00000282728.10 NM_002729.5 197 Cag/Tag 3/4 P1 T Q/* protein_coding YES CCDS7423.1 589/813 TAAAACAGGTA MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Gene3D:1.10.10.60;SMART:SM00389;PANTHER:PTHR24324;PANTHER:PTHR24324:SF5 ENSP00000282728 3/4 ENST00000282728 Transcript ENSG00000152804 HGNC:4901 HIGH NM_002729.5 stop_gained 1.0 Unknown Q03014.193 HHEX HGNC 1 1.0 UPI000012CA59 SNV HHEX,stop_gained,p.Q197*,ENST00000282728,NM_002729.5,c.589C>T,HIGH,YES,,,1;HHEX,stop_gained,p.Q25*,ENST00000472590,,c.73C>T,HIGH,,,,1;HHEX,stop_gained,p.Q25*,ENST00000492654,,c.73C>T,HIGH,,,,1;HHEX,downstream_gene_variant,,ENST00000551454,,,MODIFIER,,,,1 621/1724 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 85 5d15cc8f-6836-434b-8fe5-f0168503446c 59 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS HHEX,stop_gained,splice_region_variant,p.Q25*,ENST00000492654.3,c.73C>T,HIGH,;HHEX,stop_gained,splice_region_variant,p.Q25*,ENST00000472590.6,c.73C>T,HIGH,;HHEX,stop_gained,splice_region_variant,p.Q197*,ENST00000282728.10,c.589C>T,HIGH,YES +OR51L1 119682 BI GRCh38 11 4999067 4999067 + missense_variant Missense_Mutation SNP C C A novel TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 100 7 c.85C>A p.Leu29Ile p.L29I ENST00000641819.1 NM_001004755.2 29 Ctc/Atc 3/3 P1 A L/I protein_coding YES CCDS31369.1 85/948 CTTGGCTCTCC Gene3D:1.20.1070.10;Prints:PR00237;PANTHER:PTHR26450;PANTHER:PTHR26450:SF37;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15222 ENSP00000493015 3/3 ENST00000641819 Transcript ENSG00000176798 HGNC:14759 MODERATE missense_variant 1.0 benign(0.034) Unknown tolerated(1) Q8NGJ5.138 OR51L1 HGNC 1 A0A126GVJ8.32 UPI0000041B76 SNV OR51L1,missense_variant,p.L29I,ENST00000641819,NM_001004755.1,c.85C>A,MODERATE,YES,tolerated(1),benign(0.034),1;OR51L1,intron_variant,,ENST00000641624,,n.587+1484C>A,MODIFIER,,,,1;OR51L1,intron_variant,,ENST00000642056,,n.587+1484C>A,MODIFIER,,,,1 831/7300 muse;mutect2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 110 5d15cc8f-6836-434b-8fe5-f0168503446c 108 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS OR51L1,intron_variant,,ENST00000641624.1,n.587+1484C>A,MODIFIER,;OR51L1,missense_variant,p.L29I,ENST00000641819.1,c.85C>A,MODERATE,YES;OR51L1,intron_variant,,ENST00000642056.1,n.587+1484C>A,MODIFIER, +COL2A1 1280 BI GRCh38 12 47978700 47978700 + missense_variant Missense_Mutation SNP G G T novel TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 18 17 c.2792C>A p.Ala931Asp p.A931D ENST00000380518.8 NM_001844.5 931 gCt/gAt 42/54 P1 T A/D protein_coding YES CCDS41778.1 2792/4464 CTCGAGCACCT PANTHER:PTHR24023;PANTHER:PTHR24023:SF954;MobiDB_lite:mobidb-lite ENSP00000369889 42/54 ENST00000380518 Transcript 1.0 ENSG00000139219 HGNC:2200 MODERATE NM_001844.5 missense_variant 1.0 benign(0.029) Unknown tolerated(0.64) P02458.236 COL2A1 HGNC -1 1.0 UPI0000D79713 P02458-2 SNV COL2A1,missense_variant,p.A931D,ENST00000380518,NM_001844.5,c.2792C>A,MODERATE,YES,tolerated(0.64),benign(0.029),-1;COL2A1,missense_variant,p.A862D,ENST00000337299,NM_033150.3,c.2585C>A,MODERATE,,tolerated(0.31),benign(0.063),-1;COL2A1,non_coding_transcript_exon_variant,,ENST00000493991,,n.1878C>A,MODIFIER,,,,-1;COL2A1,downstream_gene_variant,,ENST00000483376,,,MODIFIER,,,,-1;COL2A1,upstream_gene_variant,,ENST00000546974,,,MODIFIER,,,,-1 2947/5059 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 40 5d15cc8f-6836-434b-8fe5-f0168503446c 35 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS COL2A1,missense_variant,p.A862D,ENST00000337299.7,c.2585C>A,MODERATE,;COL2A1,non_coding_transcript_exon_variant,,ENST00000493991.5,n.1878C>A,MODIFIER,;COL2A1,missense_variant,p.A931D,ENST00000380518.8,c.2792C>A,MODERATE,YES +XRCC3 7517 BI GRCh38 14 103703210 103703210 + missense_variant Missense_Mutation SNP A A G rs1419229375 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 8 9 c.524T>C p.Phe175Ser p.F175S ENST00000352127.11 NM_001100118.2 175 tTt/tCt 6/9 P1 G F/S protein_coding CCDS9984.1 524/1041 TGCCAAATCGG PROSITE_profiles:PS50162;CDD:cd01123;PANTHER:PTHR46487;Gene3D:3.40.50.300;PIRSF:PIRSF005856;Pfam:PF08423;Superfamily:SSF52540 ENSP00000343392 6/9 rs1419229375;COSV100573113 ENST00000352127 Transcript 1.0 ENSG00000126215 HGNC:12830 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 possibly_damaging(0.799) Unknown deleterious(0) 0;1 O43542.173 XRCC3 HGNC -1 Q53XC8.135 1.0 UPI000000CC78 SNV XRCC3,missense_variant,p.F175S,ENST00000553264,,c.524T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.799),-1;XRCC3,missense_variant,p.F175S,ENST00000555055,NM_005432.4&NM_001371231.1&NM_001371229.1&NM_001100119.2,c.524T>C,MODERATE,,deleterious(0),possibly_damaging(0.799),-1;XRCC3,missense_variant,p.F175S,ENST00000352127,NM_001100118.2,c.524T>C,MODERATE,,deleterious(0),possibly_damaging(0.799),-1;XRCC3,missense_variant,p.F175S,ENST00000554913,NM_001371232.1,c.524T>C,MODERATE,,deleterious(0),possibly_damaging(0.799),-1;KLC1,3_prime_UTR_variant,,ENST00000348520,NM_182923.3,c.*2011A>G,MODIFIER,,,,1;XRCC3,intron_variant,,ENST00000554974,,c.-54-3634T>C,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000334553,,,MODIFIER,YES,,,1;KLC1,downstream_gene_variant,,ENST00000452929,NM_001130107.1,,MODIFIER,,,,1;XRCC3,downstream_gene_variant,,ENST00000553361,,,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000554280,,,MODIFIER,,,,1;KLC1,downstream_gene_variant,,ENST00000555836,,,MODIFIER,,,,1;XRCC3,downstream_gene_variant,,ENST00000555964,,,MODIFIER,,,,-1;XRCC3,downstream_gene_variant,,ENST00000556980,,,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000557450,,,MODIFIER,,,,1;XRCC3,non_coding_transcript_exon_variant,,ENST00000555832,,n.28T>C,MODIFIER,,,,-1;XRCC3,non_coding_transcript_exon_variant,,ENST00000555451,,n.118T>C,MODIFIER,,,,-1;XRCC3,non_coding_transcript_exon_variant,,ENST00000554811,,n.1971T>C,MODIFIER,,,,-1;XRCC3,non_coding_transcript_exon_variant,,ENST00000554774,,n.138T>C,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000538504,,,MODIFIER,,,,1;XRCC3,downstream_gene_variant,,ENST00000553807,,,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000556986,,,MODIFIER,,,,1;XRCC3,downstream_gene_variant,,ENST00000557439,,,MODIFIER,,,,-1;KLC1,downstream_gene_variant,,ENST00000557686,,,MODIFIER,,,,1 865/2563 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 12 5d15cc8f-6836-434b-8fe5-f0168503446c 17 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS XRCC3,non_coding_transcript_exon_variant,,ENST00000555832.1,n.28T>C,MODIFIER,;XRCC3,non_coding_transcript_exon_variant,,ENST00000555451.1,n.118T>C,MODIFIER,;XRCC3,non_coding_transcript_exon_variant,,ENST00000554774.1,n.138T>C,MODIFIER,;XRCC3,intron_variant,,ENST00000554974.5,c.-54-3634T>C,MODIFIER,;XRCC3,non_coding_transcript_exon_variant,,ENST00000554811.5,n.1971T>C,MODIFIER,;XRCC3,missense_variant,p.F175S,ENST00000553264.5,c.524T>C,MODERATE,;XRCC3,missense_variant,p.F175S,ENST00000352127.11,c.524T>C,MODERATE,;XRCC3,missense_variant,p.F175S,ENST00000555055.6,c.524T>C,MODERATE,YES;XRCC3,missense_variant,p.F175S,ENST00000554913.5,c.524T>C,MODERATE,;KLC1,3_prime_UTR_variant,,ENST00000348520.10,c.*2011A>G,MODIFIER, +ZC3H7A 29066 BI GRCh38 16 11752784 11752784 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 46 30 c.2611C>T p.Gln871Ter p.Q871* ENST00000355758.9 NM_014153.4 871 Cag/Tag 22/23 P1 A Q/* protein_coding CCDS10550.1 2611/2916 CCACTGCTTCT PANTHER:PTHR14928:SF13;PANTHER:PTHR14928;Gene3D:3.30.160.60;Superfamily:SSF57667 ENSP00000347999 22/23 ENST00000355758 Transcript ENSG00000122299 HGNC:30959 HIGH NM_014153.4 stop_gained Unknown Q8IWR0.156 ZC3H7A HGNC -1 1.0 UPI000000DB79 Q8IWR0-1 SNV ZC3H7A,stop_gained,p.Q871*,ENST00000396516,,c.2611C>T,HIGH,YES,,,-1;ZC3H7A,stop_gained,p.Q871*,ENST00000355758,NM_014153.4,c.2611C>T,HIGH,,,,-1;ZC3H7A,stop_gained,p.Q67*,ENST00000575984,,c.199C>T,HIGH,,,,-1;ZC3H7A,downstream_gene_variant,,ENST00000571198,,,MODIFIER,,,,-1;Metazoa_SRP,downstream_gene_variant,,ENST00000597717,,,MODIFIER,YES,,,-1;ZC3H7A,3_prime_UTR_variant,,ENST00000571405,,c.*227C>T,MODIFIER,,,,-1;ZC3H7A,non_coding_transcript_exon_variant,,ENST00000570918,,n.379C>T,MODIFIER,,,,-1;ZC3H7A,downstream_gene_variant,,ENST00000570862,,,MODIFIER,,,,-1 2780/3805 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 97 5d15cc8f-6836-434b-8fe5-f0168503446c 77 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS ZC3H7A,stop_gained,p.Q871*,ENST00000355758.9,c.2611C>T,HIGH,YES;ZC3H7A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000571405.5,c.*227C>T,MODIFIER,;ZC3H7A,stop_gained,p.Q67*,ENST00000575984.1,c.199C>T,HIGH,;ZC3H7A,non_coding_transcript_exon_variant,,ENST00000570918.1,n.379C>T,MODIFIER,;ZC3H7A,stop_gained,p.Q871*,ENST00000396516.6,c.2611C>T,HIGH, +CEP131 22994 BI GRCh38 17 81192811 81192811 + missense_variant Missense_Mutation SNP G G A rs754140951 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 17 10 c.2363C>T p.Ala788Val p.A788V ENST00000269392.8 NM_001319228.2 788 gCg/gTg 19/26 P4 A A/V protein_coding YES CCDS82215.1 2363/3252 GCAGCGCCCAC PANTHER:PTHR31540;Low_complexity_(Seg):seg ENSP00000269392 19/26 rs754140951 ENST00000269392 Transcript ENSG00000141577 HGNC:29511 MODERATE 0.0001134 gnomAD_EAS missense_variant 1.0 benign(0.046) Unknown tolerated(0.13) Q9UPN4.158 CEP131 HGNC -1 1.0 UPI00001C1FC8 Q9UPN4-1 SNV CEP131,missense_variant,p.A788V,ENST00000269392,NM_001319228.2,c.2363C>T,MODERATE,YES,tolerated(0.13),benign(0.046),-1;CEP131,missense_variant,p.A785V,ENST00000450824,NM_014984.4,c.2354C>T,MODERATE,,tolerated(0.13),benign(0.012),-1;CEP131,missense_variant,p.A224V,ENST00000573053,,c.671C>T,MODERATE,,tolerated(0.1),benign(0.012),-1;CEP131,intron_variant,,ENST00000374782,NM_001009811.4,c.2322-218C>T,MODIFIER,,,,-1;CEP131,intron_variant,,ENST00000570817,,c.104-218C>T,MODIFIER,,,,-1;CEP131,intron_variant,,ENST00000575907,NM_001319229.2,c.2331-218C>T,MODIFIER,,,,-1;CEP131,upstream_gene_variant,,ENST00000571292,,,MODIFIER,,,,-1;AC027601.2,upstream_gene_variant,,ENST00000571085,,,MODIFIER,YES,,,1 2611/3673 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 2.208e-05 0.0 0.0 0.0 0.0001134 0.0 2.939e-05 0.0 0.0 4.734269896289334e-05 0.0001216960008605 0.0 0.0 0.0 0.0002021020045503 0.0 afr 0.0001216960008605 0.0 1.5439200069522485e-05 0.0 0.0 0 42 5d15cc8f-6836-434b-8fe5-f0168503446c 28 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS CEP131,intron_variant,,ENST00000575907.5,c.2331-218C>T,MODIFIER,;CEP131,missense_variant,p.A224V,ENST00000573053.5,c.671C>T,MODERATE,;CEP131,intron_variant,,ENST00000570817.5,c.104-218C>T,MODIFIER,;CEP131,missense_variant,p.A785V,ENST00000450824.7,c.2354C>T,MODERATE,YES;CEP131,missense_variant,p.A788V,ENST00000269392.8,c.2363C>T,MODERATE,;CEP131,intron_variant,,ENST00000374782.7,c.2322-218C>T,MODIFIER, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 19 20 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 78 5d15cc8f-6836-434b-8fe5-f0168503446c 40 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ZNF628 89887 BI GRCh38 19 55481817 55481817 + synonymous_variant Silent SNP C C T rs747118126 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 6 5 c.624C>T p.Leu208= p.L208= ENST00000598519.2 NM_033113.3 208 ctC/ctT 3/3 P1 T L protein_coding YES CCDS33116.3 624/3180 CCGCTCTGCCC Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF781;SMART:SM00355;Superfamily:SSF57667 ENSP00000469591 3/3 rs747118126 ENST00000598519 Transcript ENSG00000197483 HGNC:28054 LOW NM_033113.3 6.939e-05 gnomAD_SAS synonymous_variant 1.0 Unknown Q5EBL2.132 ZNF628 HGNC 1 1.0 UPI00026B9C6E SNV ZNF628,synonymous_variant,p.L208=,ENST00000598519,NM_033113.3,c.624C>T,LOW,YES,,,1;ZNF628,synonymous_variant,p.L207=,ENST00000391718,,c.621C>T,LOW,,,,1;NAT14,upstream_gene_variant,,ENST00000205194,NM_020378.4,,MODIFIER,YES,,,1;NAT14,upstream_gene_variant,,ENST00000587400,,,MODIFIER,,,,1;NAT14,upstream_gene_variant,,ENST00000588985,,,MODIFIER,,,,1;ZNF628,downstream_gene_variant,,ENST00000591164,,,MODIFIER,,,,1;NAT14,upstream_gene_variant,,ENST00000591590,,,MODIFIER,,,,1;NAT14,upstream_gene_variant,,ENST00000592719,,,MODIFIER,,,,1 892/3562 muse;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 9.052e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.939e-05 0 10 5d15cc8f-6836-434b-8fe5-f0168503446c 12 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS ZNF628,synonymous_variant,p.L208=,ENST00000598519.2,c.624C>T,LOW,YES +BRD1 23774 BI GRCh38 22 49823028 49823028 + synonymous_variant Silent SNP T T C TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 59 74 c.1290A>G p.Ala430= p.A430= ENST00000216267.12 NM_001394550.1 430 gcA/gcG 1/12 P3 C A protein_coding CCDS14080.1 1290/3177 TTTTTTGCCTT PANTHER:PTHR13793;PANTHER:PTHR13793:SF17;Low_complexity_(Seg):seg ENSP00000216267 1/12 COSV53455138 ENST00000216267 Transcript ENSG00000100425 HGNC:1102 LOW synonymous_variant 1 Unknown 1 O95696.173 BRD1 HGNC -1 A0A024R4W4.48 1.0 UPI0000126ACA O95696-1 SNV BRD1,synonymous_variant,p.A430=,ENST00000457780,NM_001349941.1&NM_001349942.1,c.1290A>G,LOW,YES,,,-1;BRD1,synonymous_variant,p.A430=,ENST00000216267,NM_001349940.1,c.1290A>G,LOW,,,,-1;BRD1,synonymous_variant,p.A430=,ENST00000404760,NM_001304808.3,c.1290A>G,LOW,,,,-1;BRD1,synonymous_variant,p.A430=,ENST00000404034,NM_001304809.1,c.1290A>G,LOW,,,,-1;BRD1,non_coding_transcript_exon_variant,,ENST00000459821,,n.274A>G,MODIFIER,,,,-1;BRD1,non_coding_transcript_exon_variant,,ENST00000494833,,n.178A>G,MODIFIER,,,,-1;BRD1,synonymous_variant,p.A62=,ENST00000438393,,c.186A>G,LOW,,,,-1 1777/4614 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 188 5d15cc8f-6836-434b-8fe5-f0168503446c 133 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS BRD1,non_coding_transcript_exon_variant,,ENST00000494833.1,n.178A>G,MODIFIER,;BRD1,non_coding_transcript_exon_variant,,ENST00000459821.1,n.274A>G,MODIFIER,;BRD1,synonymous_variant,p.A430=,ENST00000457780.3,c.1290A>G,LOW,;BRD1,synonymous_variant,p.A430=,ENST00000216267.12,c.1290A>G,LOW,;BRD1,synonymous_variant,p.A430=,ENST00000404760.6,c.1290A>G,LOW,YES;BRD1,synonymous_variant,p.A430=,ENST00000404034.5,c.1290A>G,LOW,;BRD1,synonymous_variant,NMD_transcript_variant,p.A62=,ENST00000438393.5,c.186A>G,LOW, +NHS 4810 BI GRCh38 X 17725949 17725949 + missense_variant Missense_Mutation SNP G G A rs767956070 TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 51 45 c.1780G>A p.Val594Ile p.V594I ENST00000380060.7 NM_198270.4 594 Gtc/Atc 6/8 P2 A V/I protein_coding CCDS14181.1 1780/4893 CTGGCGTCCTC COSM4850146;COSM4850147 Pfam:PF15273;PANTHER:PTHR23039;PANTHER:PTHR23039:SF5 ENSP00000369400 6/8 rs767956070;COSV66272541;COSV66282606 ENST00000380060 Transcript 1.0 ENSG00000188158 HGNC:7820 MODERATE 5.242e-05 gnomAD_SAS missense_variant 0;1;1 possibly_damaging(0.833) Unknown tolerated(0.06) 0;1;1 Q6T4R5.132 NHS HGNC 1 1.0 UPI00001DFBF3 Q6T4R5-2 SNV NHS,missense_variant,p.V615I,ENST00000676302,NM_001291867.2,c.1843G>A,MODERATE,YES,tolerated(0.06),benign(0.071),1;NHS,missense_variant,p.V435I,ENST00000615422,,c.1303G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.626),1;NHS,missense_variant,p.V594I,ENST00000380060,NM_198270.4,c.1780G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.833),1;NHS,missense_variant,p.V438I,ENST00000398097,NM_001136024.4,c.1312G>A,MODERATE,,deleterious(0.02),benign(0.042),1;NHS,missense_variant,p.V411I,ENST00000617601,NM_001291868.2,c.1231G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.715),1;NHS,downstream_gene_variant,,ENST00000485305,,,MODIFIER,,,,1 2118/8761 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 2.184e-05 0.0 3.647e-05 0.0 0.0 0.0 2.45e-05 0.0 5.242e-05 1.8470100258127783e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.943450064980425e-05 0.0 3.943450064980425e-05 0.0 0.0 0 112 5d15cc8f-6836-434b-8fe5-f0168503446c 96 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS NHS,non_coding_transcript_exon_variant,,ENST00000690608.1,n.800G>A,MODIFIER,;NHS,non_coding_transcript_exon_variant,,ENST00000615422.2,n.2238G>A,MODIFIER,;NHS,missense_variant,p.V438I,ENST00000398097.7,c.1312G>A,MODERATE,;NHS,missense_variant,p.V411I,ENST00000617601.4,c.1231G>A,MODERATE,;NHS,missense_variant,p.V594I,ENST00000380060.7,c.1780G>A,MODERATE,;NHS,missense_variant,p.V615I,ENST00000676302.1,c.1843G>A,MODERATE,YES +EIF1AX 1964 BI GRCh38 X 20138595 20138595 + missense_variant Missense_Mutation SNP C C T TCGA-V4-A9F7-01A TCGA-V4-A9F7-10A Somatic 60 17 c.44G>A p.Gly15Asp p.G15D ENST00000379607.10 NM_001412.4 15 gGt/gAt 2/7 P1 T G/D protein_coding YES CCDS14196.1 44/435 TCTTACCCCTG COSM3973544 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;TIGRFAM:TIGR00523;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309310;COSV63309316 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1;1 1.0 probably_damaging(0.977) Unknown deleterious(0) 1;1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G15D,ENST00000379607,NM_001412.4,c.44G>A,MODERATE,YES,deleterious(0),probably_damaging(0.977),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2754G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 242/4414 muse;mutect2;varscan2 64422cc5-5e5b-4ef9-a9e2-214cebf8dfbc 0 203 5d15cc8f-6836-434b-8fe5-f0168503446c 78 9e3dab4a-aff7-44d9-8bf9-00a06939f673 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2754G>A,MODIFIER,;EIF1AX,missense_variant,p.G15D,ENST00000379607.10,c.44G>A,MODERATE,YES +PADI2 11240 BI GRCh38 1 17069112 17069112 + stop_gained Nonsense_Mutation SNP C C A novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 38 25 c.1930G>T p.Glu644Ter p.E644* ENST00000375486.9 NM_007365.3 644 Gaa/Taa 16/16 P1 A E/* protein_coding YES CCDS177.1 1930/1998 GACTTCCCCCA PDB-ENSP_mappings:4n20.A;PDB-ENSP_mappings:4n22.A;PDB-ENSP_mappings:4n24.A;PDB-ENSP_mappings:4n25.A;PDB-ENSP_mappings:4n26.A;PDB-ENSP_mappings:4n28.A;PDB-ENSP_mappings:4n2a.A;PDB-ENSP_mappings:4n2b.A;PDB-ENSP_mappings:4n2c.A;PDB-ENSP_mappings:4n2d.A;PDB-ENSP_mappings:4n2e.A;PDB-ENSP_mappings:4n2f.A;PDB-ENSP_mappings:4n2g.A;PDB-ENSP_mappings:4n2h.A;PDB-ENSP_mappings:4n2i.A;PDB-ENSP_mappings:4n2k.A;PDB-ENSP_mappings:4n2l.A;PDB-ENSP_mappings:4n2m.A;PDB-ENSP_mappings:4n2n.A;PANTHER:PTHR10837;PANTHER:PTHR10837:SF12;Gene3D:3.75.10.10;PIRSF:PIRSF001247;Pfam:PF03068;Superfamily:SSF55909 ENSP00000364635 16/16 ENST00000375486 Transcript ENSG00000117115 HGNC:18341 HIGH NM_007365.3 stop_gained 1.0 Unknown Q9Y2J8.159 PADI2 HGNC -1 1.0 UPI00001314AF Q9Y2J8-1 SNV PADI2,stop_gained,p.E644*,ENST00000375486,NM_007365.3,c.1930G>T,HIGH,YES,,,-1;PADI2,non_coding_transcript_exon_variant,,ENST00000466151,,n.2286G>T,MODIFIER,,,,-1;PADI2,non_coding_transcript_exon_variant,,ENST00000479534,,n.877G>T,MODIFIER,,,,-1 2010/4361 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 93 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 63 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS PADI2,non_coding_transcript_exon_variant,,ENST00000466151.1,n.2286G>T,MODIFIER,;PADI2,non_coding_transcript_exon_variant,,ENST00000479534.5,n.877G>T,MODIFIER,;PADI2,stop_gained,p.E644*,ENST00000375486.9,c.1930G>T,HIGH,YES +DCDC2B 149069 BI GRCh38 1 32212091 32212091 + synonymous_variant Silent SNP G G A novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 23 5 c.417G>A p.Leu139= p.L139= ENST00000409358.2 NM_001099434.2 139 ctG/ctA 4/9 P1 A L protein_coding YES CCDS44100.1 417/1050 GACCTGGTAAG PROSITE_profiles:PS50309;CDD:cd17153;PANTHER:PTHR23004;PANTHER:PTHR23004:SF10;Gene3D:3.10.20.230;SMART:SM00537;Superfamily:SSF89837 ENSP00000386870 4/9 ENST00000409358 Transcript ENSG00000222046 HGNC:32576 LOW synonymous_variant 1.0 Unknown A2VCK2.90 DCDC2B HGNC 1 1.0 UPI0000DD78AB SNV DCDC2B,synonymous_variant,p.L139=,ENST00000409358,NM_001099434.1,c.417G>A,LOW,YES,,,1;IQCC,downstream_gene_variant,,ENST00000291358,NM_018134.3,,MODIFIER,,,,1;TMEM234,downstream_gene_variant,,ENST00000309777,NM_019118.5,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000344461,NM_001366191.2,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000373593,,,MODIFIER,YES,,,-1;IQCC,downstream_gene_variant,,ENST00000537469,NM_001160042.2,,MODIFIER,YES,,,1;TMEM234,downstream_gene_variant,,ENST00000485689,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000495091,,,MODIFIER,,,,-1;DCDC2B,non_coding_transcript_exon_variant,,ENST00000487056,,n.647G>A,MODIFIER,,,,1;TMEM234,downstream_gene_variant,,ENST00000461402,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000466796,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000483001,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000484490,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000487174,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000489170,,,MODIFIER,,,,-1;TMEM234,downstream_gene_variant,,ENST00000491434,,,MODIFIER,,,,-1;IQCC,downstream_gene_variant,,ENST00000617816,,,MODIFIER,,,,1 417/1349 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 29 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 28 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS DCDC2B,non_coding_transcript_exon_variant,,ENST00000487056.1,n.647G>A,MODIFIER,;DCDC2B,synonymous_variant,p.L139=,ENST00000409358.2,c.417G>A,LOW,YES +ADGRL4 64123 BI GRCh38 1 78917995 78917995 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 63 35 c.1517C>T p.Ala506Val p.A506V ENST00000370742.4 NM_022159.4 506 gCa/gTa 11/15 P2 A A/V protein_coding YES CCDS41352.1 1517/2073 TCCATGCAAAA Transmembrane_helices:TMhelix;CDD:cd15437;Gene3D:1.20.1070.10;Pfam:PF00002;PROSITE_profiles:PS50261;PANTHER:PTHR12011:SF59;PANTHER:PTHR12011;Prints:PR00249 ENSP00000359778 11/15 ENST00000370742 Transcript ENSG00000162618 HGNC:20822 MODERATE NM_022159.4 missense_variant 1.0 possibly_damaging(0.656) Unknown deleterious(0.02) Q9HBW9.165 ADGRL4 HGNC -1 1.0 UPI00004561FF SNV ADGRL4,missense_variant,p.A461V,ENST00000661030,,c.1382C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.656),-1;ADGRL4,missense_variant,p.A506V,ENST00000370742,NM_022159.4,c.1517C>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.656),-1;ADGRL4,missense_variant,p.A448V,ENST00000671209,,c.1343C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.526),-1;ADGRL4,missense_variant,p.A461V,ENST00000655029,,c.1382C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.656),-1;ADGRL4,missense_variant,p.A461V,ENST00000656841,,c.1382C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.656),-1;ADGRL4,upstream_gene_variant,,ENST00000401034,,,MODIFIER,,,,-1;ADGRL4,non_coding_transcript_exon_variant,,ENST00000661361,,n.551C>T,MODIFIER,,,,-1;ADGRL4,3_prime_UTR_variant,,ENST00000640664,,c.*450C>T,MODIFIER,,,,-1;ADGRL4,3_prime_UTR_variant,,ENST00000662895,,c.*423C>T,MODIFIER,,,,-1;ADGRL4,non_coding_transcript_exon_variant,,ENST00000664452,,n.139C>T,MODIFIER,,,,-1 1593/3539 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 91 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 98 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS ADGRL4,non_coding_transcript_exon_variant,,ENST00000664452.1,n.139C>T,MODIFIER,;ADGRL4,non_coding_transcript_exon_variant,,ENST00000661361.1,n.551C>T,MODIFIER,;ADGRL4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000662895.1,c.*423C>T,MODIFIER,;ADGRL4,missense_variant,p.A461V,ENST00000656841.1,c.1382C>T,MODERATE,;ADGRL4,missense_variant,p.A461V,ENST00000655029.1,c.1382C>T,MODERATE,;ADGRL4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000640664.2,c.*450C>T,MODIFIER,;ADGRL4,missense_variant,p.A461V,ENST00000661030.1,c.1382C>T,MODERATE,;ADGRL4,missense_variant,p.A448V,ENST00000671209.1,c.1343C>T,MODERATE,;ADGRL4,missense_variant,p.A506V,ENST00000370742.4,c.1517C>T,MODERATE,YES +MCEE 84693 BI GRCh38 2 71124373 71124373 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 48 30 c.211G>A p.Ala71Thr p.A71T ENST00000244217.6 NM_032601.4 71 Gcc/Acc 2/3 P1 T A/T protein_coding YES CCDS1915.1 211/531 CTGGGCCCCCA PDB-ENSP_mappings:3rmu.A;PDB-ENSP_mappings:3rmu.B;PDB-ENSP_mappings:3rmu.C;PDB-ENSP_mappings:3rmu.D;PDB-ENSP_mappings:6qh4.A;PDB-ENSP_mappings:6qh4.B;PDB-ENSP_mappings:6qh4.C;PDB-ENSP_mappings:6qh4.D;PROSITE_profiles:PS51819;CDD:cd07249;PANTHER:PTHR43048;PANTHER:PTHR43048:SF3;Gene3D:3.10.180.10;TIGRFAM:TIGR03081;Pfam:PF13669;Superfamily:SSF54593 ENSP00000244217 2/3 ENST00000244217 Transcript 1.0 ENSG00000124370 HGNC:16732 MODERATE NM_032601.4 missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0.02) Q96PE7.147 MCEE HGNC -1 1.0 UPI000003CA39 SNV MCEE,missense_variant,p.A71T,ENST00000244217,NM_032601.4,c.211G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.994),-1;MCEE,missense_variant,p.A27T,ENST00000413592,,c.79G>A,MODERATE,,deleterious(0.01),probably_damaging(0.964),-1;MCEE,5_prime_UTR_variant,,ENST00000494660,,c.-75G>A,MODIFIER,,,,-1;MCEE,5_prime_UTR_variant,,ENST00000486135,,c.-75G>A,MODIFIER,,,,-1 221/824 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 96 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 78 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS MCEE,5_prime_UTR_variant,,ENST00000494660.6,c.-75G>A,MODIFIER,;MCEE,5_prime_UTR_variant,,ENST00000486135.1,c.-75G>A,MODIFIER,;MCEE,missense_variant,p.A71T,ENST00000244217.6,c.211G>A,MODERATE,YES;MCEE,missense_variant,p.A27T,ENST00000413592.5,c.79G>A,MODERATE, +STAG1 10274 BI GRCh38 3 136422519 136422519 + stop_gained Nonsense_Mutation SNP A A C novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 152 17 c.1928T>G p.Leu643Ter p.L643* ENST00000383202.7 NM_005862.3 643 tTa/tGa 19/34 P1 C L/* protein_coding YES CCDS3090.1 1928/3777 TGCATAAGATA PDB-ENSP_mappings:5qsm.A;PDB-ENSP_mappings:5qsm.B;PDB-ENSP_mappings:5qsn.A;PDB-ENSP_mappings:5qsn.B;PDB-ENSP_mappings:5qso.A;PDB-ENSP_mappings:5qso.B;PDB-ENSP_mappings:5qsp.A;PDB-ENSP_mappings:5qsp.B;PDB-ENSP_mappings:5qsq.A;PDB-ENSP_mappings:5qsq.B;PDB-ENSP_mappings:5qsr.A;PDB-ENSP_mappings:5qsr.B;PDB-ENSP_mappings:5qss.A;PDB-ENSP_mappings:5qss.B;PDB-ENSP_mappings:5qsy.A;PDB-ENSP_mappings:5qsy.B;PDB-ENSP_mappings:5qsz.A;PDB-ENSP_mappings:5qsz.B;PDB-ENSP_mappings:6r7o.A;PDB-ENSP_mappings:6r7o.B;PDB-ENSP_mappings:6rrk.A;PDB-ENSP_mappings:6rrk.B;PDB-ENSP_mappings:6wg3.D;PANTHER:PTHR11199;PANTHER:PTHR11199:SF6;Superfamily:SSF48371 ENSP00000372689 19/34 ENST00000383202 Transcript 1.0 ENSG00000118007 HGNC:11354 HIGH NM_005862.3 stop_gained 1.0 Unknown Q8WVM7.170 STAG1 HGNC -1 1.0 UPI000020A2DE Q8WVM7-1 SNV STAG1,stop_gained,p.L643*,ENST00000383202,NM_005862.3,c.1928T>G,HIGH,YES,,,-1;STAG1,stop_gained,p.L643*,ENST00000236698,,c.1928T>G,HIGH,,,,-1;STAG1,stop_gained,p.L417*,ENST00000434713,,c.1250T>G,HIGH,,,,-1;STAG1,3_prime_UTR_variant,,ENST00000629124,,c.*1567T>G,MODIFIER,,,,-1;STAG1,downstream_gene_variant,,ENST00000492318,,,MODIFIER,,,,-1;STAG1,3_prime_UTR_variant,,ENST00000483235,,c.*2020T>G,MODIFIER,,,,-1;STAG1,3_prime_UTR_variant,,ENST00000487065,,c.*1567T>G,MODIFIER,,,,-1 2195/6062 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 142 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 169 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS STAG1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000487065.5,c.*1567T>G,MODIFIER,;STAG1,3_prime_UTR_variant,,ENST00000629124.2,c.*1567T>G,MODIFIER,;STAG1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000483235.5,c.*2020T>G,MODIFIER,;STAG1,stop_gained,p.L417*,ENST00000434713.6,c.1250T>G,HIGH,;STAG1,stop_gained,p.L643*,ENST00000236698.9,c.1928T>G,HIGH,;STAG1,stop_gained,p.L643*,ENST00000383202.7,c.1928T>G,HIGH,YES +UGT2B17 7367 BI GRCh38 4 68560566 68560566 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 38 10 c.976G>A p.Ala326Thr p.A326T ENST00000317746.3 NM_001077.4 326 Gca/Aca 4/7 P1 T A/T protein_coding YES CCDS3523.1 976/1593 TGATGCAATCA CDD:cd03784;PANTHER:PTHR11926;Gene3D:3.40.50.2000;Pfam:PF00201;Superfamily:SSF53756 ENSP00000320401 3/6 ENST00000317746 Transcript 1.0 ENSG00000197888 HGNC:12547 MODERATE missense_variant 1.0 possibly_damaging(0.883) Unknown deleterious(0) O75795.151 UGT2B17 HGNC -1 1.0 UPI0000137A9C SNV UGT2B17,missense_variant,p.A326T,ENST00000317746,NM_001077.3,c.976G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.883),-1 1019/2077 mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 248 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 48 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS UGT2B17,missense_variant,p.A76T,ENST00000684088.1,c.226G>A,MODERATE,;UGT2B17,missense_variant,p.A326T,ENST00000317746.3,c.976G>A,MODERATE,YES +PCDHA2 56146 BI GRCh38 5 140795327 140795327 + synonymous_variant Silent SNP G G T TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 118 11 c.363G>T p.Val121= p.V121= ENST00000526136.2 NM_018905.3 121 gtG/gtT 1/4 P1 T V protein_coding YES CCDS54914.1 363/2847 GAAGTGGAGGT COSM360089;COSM360090 Gene3D:2.60.40.60;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF60;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000431748 1/4 COSV65368609 ENST00000526136 Transcript ENSG00000204969 HGNC:8668 LOW NM_018905.3 synonymous_variant 1 1.0 Unknown 1 Q9Y5H9.172 PCDHA2 HGNC 1 1.0 UPI00001273C9 Q9Y5H9-1 SNV PCDHA2,synonymous_variant,p.V121=,ENST00000526136,NM_018905.3,c.363G>T,LOW,YES,,,1;PCDHA2,synonymous_variant,p.V121=,ENST00000520672,NM_031496.2,c.363G>T,LOW,,,,1;PCDHA2,synonymous_variant,p.V121=,ENST00000378132,NM_031495.2,c.363G>T,LOW,,,,1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.3,c.1602+7435G>T,MODIFIER,,,,1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.4,c.2394+6643G>T,MODIFIER,YES,,,1;AC005609.5,intron_variant,,ENST00000624176,,n.470+5664C>A,MODIFIER,,,,-1;AC005609.5,intron_variant,,ENST00000624712,,n.656-6473C>A,MODIFIER,,,,-1;AC005609.5,intron_variant,,ENST00000655235,,n.658-6473C>A,MODIFIER,YES,,,-1;AC005609.5,intron_variant,,ENST00000660962,,n.362-2557C>A,MODIFIER,,,,-1 476/5370 muse;mutect2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 175 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 130 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS PCDHA2,synonymous_variant,p.V121=,ENST00000520672.2,c.363G>T,LOW,;PCDHA2,synonymous_variant,p.V121=,ENST00000526136.2,c.363G>T,LOW,YES;PCDHA2,synonymous_variant,p.V121=,ENST00000378132.2,c.363G>T,LOW,;ENSG00000279726,intron_variant,,ENST00000624176.1,n.470+5664C>A,MODIFIER,;ENSG00000279726,intron_variant,,ENST00000660962.1,n.362-2557C>A,MODIFIER,;ENSG00000279726,intron_variant,,ENST00000624712.1,n.656-6473C>A,MODIFIER,;PCDHA1,intron_variant,,ENST00000394633.7,c.1602+7435G>T,MODIFIER,;PCDHA1,intron_variant,,ENST00000504120.4,c.2394+6643G>T,MODIFIER,YES;ENSG00000279726,intron_variant,,ENST00000655235.1,n.658-6473C>A,MODIFIER,YES +OR2B2 81697 BI GRCh38 6 27912199 27912199 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 74 29 c.121G>T p.Gly41Cys p.G41C ENST00000303324.4 NM_033057.2 41 Ggc/Tgc 1/1 P1 A G/C protein_coding YES CCDS4641.1 121/1074 ATTGCCAAAGA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR26453;PANTHER:PTHR26453:SF254;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15432 ENSP00000304419 1/1 ENST00000303324 Transcript ENSG00000168131 HGNC:13966 MODERATE NM_033057.2 missense_variant 1.0 probably_damaging(0.982) Unknown deleterious(0) Q9GZK3.157 OR2B2 HGNC -1 A0A126GWD0.32 UPI000004187A SNV OR2B2,missense_variant,p.G41C,ENST00000303324,NM_033057.2,c.121G>T,MODERATE,YES,deleterious(0),probably_damaging(0.982),-1 198/1212 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 52 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 103 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS OR2B2,missense_variant,p.G41C,ENST00000303324.4,c.121G>T,MODERATE,YES +ITGB8 3696 BI GRCh38 7 20381804 20381804 + synonymous_variant Silent SNP T T C novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 64 12 c.879T>C p.Asp293= p.D293= ENST00000222573.5 NM_002214.3 293 gaT/gaC 6/14 P1 C D protein_coding YES CCDS5370.1 879/2310 CTTGATAGCAA PDB-ENSP_mappings:6djp.B;PDB-ENSP_mappings:6om1.B;PDB-ENSP_mappings:6om1.D;PDB-ENSP_mappings:6om1.F;PDB-ENSP_mappings:6om1.H;PDB-ENSP_mappings:6om2.B;PDB-ENSP_mappings:6om2.D;PDB-ENSP_mappings:6uja.B;PDB-ENSP_mappings:6ujb.B;PDB-ENSP_mappings:6ujc.B;PANTHER:PTHR10082:SF9;PANTHER:PTHR10082;PIRSF:PIRSF002512;Pfam:PF00362;Gene3D:3.40.50.410;Gene3D:2.60.40.1510;SMART:SM00187;Superfamily:SSF53300;Prints:PR01186 ENSP00000222573 6/14 ENST00000222573 Transcript ENSG00000105855 HGNC:6163 LOW NM_002214.3 synonymous_variant 1.0 Unknown P26012.194 ITGB8 HGNC 1 1.0 UPI000012DA14 P26012-1 SNV ITGB8,synonymous_variant,p.D293=,ENST00000222573,NM_002214.3,c.879T>C,LOW,YES,,,1;ITGB8,synonymous_variant,p.D158=,ENST00000537992,,c.474T>C,LOW,,,,1;AC004130.1,downstream_gene_variant,,ENST00000363883,,,MODIFIER,YES,,,1;ITGB8,non_coding_transcript_exon_variant,,ENST00000477859,,n.5296T>C,MODIFIER,,,,1;ITGB8,non_coding_transcript_exon_variant,,ENST00000478974,,n.1584T>C,MODIFIER,,,,1 1786/8974 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 77 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 76 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS ITGB8,non_coding_transcript_exon_variant,,ENST00000477859.1,n.5296T>C,MODIFIER,;ITGB8,non_coding_transcript_exon_variant,,ENST00000478974.1,n.1584T>C,MODIFIER,;ITGB8,synonymous_variant,p.D293=,ENST00000222573.5,c.879T>C,LOW,YES;ITGB8,synonymous_variant,p.D158=,ENST00000537992.5,c.474T>C,LOW, +CA2 760 BI GRCh38 8 85477119 85477119 + splice_acceptor_variant Splice_Site SNP G G A TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 58 93 c.508-1G>A p.X170_splice p.X170_splice ENST00000285379.10 NM_000067.3 170 P1 A protein_coding YES CCDS6239.1 TTCTAGGGCAA ENSP00000285379 CS920730 ENST00000285379 Transcript NonExonic 1.0 ENSG00000104267 HGNC:1373 HIGH 5/6 NM_000067.3 splice_acceptor_variant 1 1.0 Unknown P00918.249 CA2 HGNC 1 V9HW21.43 1.0 UPI0000110BA2 SNV CA2,splice_acceptor_variant,p.X170_splice,ENST00000285379,NM_001293675.1&NM_000067.3,c.508-1G>A,HIGH,YES,,,1;CA2,splice_acceptor_variant,,ENST00000520127,,c.*95-1G>A,HIGH,,,,1;CA2,splice_acceptor_variant,,ENST00000522742,,c.*282-1G>A,HIGH,,,,1;CA2,downstream_gene_variant,,ENST00000518231,,,MODIFIER,,,,1;CA2,downstream_gene_variant,,ENST00000520996,,,MODIFIER,,,,1 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 122 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 151 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS CA2,splice_acceptor_variant,NMD_transcript_variant,,ENST00000522742.1,c.*282-1G>A,HIGH,;CA2,splice_acceptor_variant,p.X170_splice,ENST00000285379.10,c.508-1G>A,HIGH,YES;CA2,splice_acceptor_variant,NMD_transcript_variant,,ENST00000520127.5,c.*95-1G>A,HIGH, +MUSK 4593 BI GRCh38 9 110687150 110687150 + synonymous_variant Silent SNP T T C rs1203375135 TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 78 10 c.240T>C p.Asn80= p.N80= ENST00000374448.9 NM_005592.4 80 aaT/aaC 3/15 P4 C N protein_coding YES CCDS48005.1 240/2610 GAGAATGGGCA CDD:cd00096;Pfam:PF07679;Gene3D:2.60.40.10;PIRSF:PIRSF000615;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;PROSITE_profiles:PS50835;PANTHER:PTHR24416:SF317;PANTHER:PTHR24416 ENSP00000363571 3/15 rs1203375135 ENST00000374448 Transcript 1.0 ENSG00000030304 HGNC:7525 LOW NM_005592.4 0.0001655 gnomAD_OTH synonymous_variant 1.0 Unknown O15146.176 MUSK HGNC 1 5.0 UPI000006D2F7 O15146-1 SNV MUSK,synonymous_variant,p.N80=,ENST00000374448,NM_005592.4,c.240T>C,LOW,YES,,,1;MUSK,synonymous_variant,p.N80=,ENST00000416899,NM_001166281.2,c.240T>C,LOW,,,,1;MUSK,synonymous_variant,p.N80=,ENST00000189978,NM_001166280.2,c.240T>C,LOW,,,,1;MUSK,synonymous_variant,p.N80=,ENST00000374440,,c.240T>C,LOW,,,,1;MUSK,upstream_gene_variant,,ENST00000374439,,,MODIFIER,,,,1 354/8294 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 4.016e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0001655 0.0 0 90 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 88 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS MUSK,synonymous_variant,p.N80=,ENST00000189978.10,c.240T>C,LOW,;MUSK,synonymous_variant,p.N80=,ENST00000374448.9,c.240T>C,LOW,YES;MUSK,synonymous_variant,p.N80=,ENST00000416899.7,c.240T>C,LOW, +CD163 9332 BI GRCh38 12 7496916 7496916 + missense_variant Missense_Mutation SNP G G C TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 16 26 c.996C>G p.Ser332Arg p.S332R ENST00000359156.8 NM_001370146.1 332 agC/agG 5/17 A2 C S/R protein_coding YES CCDS8578.1 996/3471 GAAACGCTGTC Gene3D:3.10.250.10;Pfam:PF00530;PROSITE_profiles:PS50287;PANTHER:PTHR19331;PANTHER:PTHR19331:SF441;SMART:SM00202;Superfamily:SSF56487 ENSP00000352071 5/17 COSV63132618 ENST00000359156 Transcript ENSG00000177575 HGNC:1631 MODERATE missense_variant 1 1.0 possibly_damaging(0.66) Unknown tolerated(0.46) 1 Q86VB7.142 CD163 HGNC -1 1.0 UPI00004565CC Q86VB7-1 SNV CD163,missense_variant,p.S332R,ENST00000359156,NM_001370146.1&NM_004244.5,c.996C>G,MODERATE,YES,tolerated(0.46),possibly_damaging(0.66),-1;CD163,missense_variant,p.S332R,ENST00000432237,NM_001370145.1&NM_203416.4,c.996C>G,MODERATE,,tolerated(0.45),benign(0.005),-1;CD163,missense_variant,p.S332R,ENST00000396620,,c.996C>G,MODERATE,,tolerated(0.45),possibly_damaging(0.66),-1;CD163,missense_variant,p.S320R,ENST00000541972,,c.960C>G,MODERATE,,tolerated(0.45),possibly_damaging(0.529),-1;CD163,non_coding_transcript_exon_variant,,ENST00000537044,,n.1082C>G,MODIFIER,,,,-1 1199/4268 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 51 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 42 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS CD163,missense_variant,p.S332R,ENST00000396620.7,c.996C>G,MODERATE,;CD163,missense_variant,p.S320R,ENST00000541972.5,c.960C>G,MODERATE,;CD163,non_coding_transcript_exon_variant,,ENST00000537044.1,n.1082C>G,MODIFIER,;CD163,missense_variant,p.S332R,ENST00000359156.8,c.996C>G,MODERATE,;CD163,missense_variant,p.S332R,ENST00000432237.3,c.996C>G,MODERATE,YES +DVL2 1856 BI GRCh38 17 7230328 7230328 + missense_variant Missense_Mutation SNP C C T rs761312377 TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 32 28 c.367G>A p.Glu123Lys p.E123K ENST00000005340.10 NM_004422.3 123 Gag/Aag 3/15 P2 T E/K protein_coding YES CCDS11091.1 367/2211 CCTCTCGGGTG Pfam:PF02377;PANTHER:PTHR10878;PANTHER:PTHR10878:SF8;Low_complexity_(Seg):seg ENSP00000005340 3/15 rs761312377;COSV99138281 ENST00000005340 Transcript ENSG00000004975 HGNC:3086 MODERATE NM_004422.3 8.792e-06 gnomAD_NFE missense_variant 0;1 1.0 possibly_damaging(0.833) Unknown deleterious(0.05) 0;1 O14641.203 DVL2 HGNC -1 1.0 UPI0000000DE9 SNV DVL2,missense_variant,p.E123K,ENST00000005340,NM_004422.3,c.367G>A,MODERATE,YES,deleterious(0.05),possibly_damaging(0.833),-1;DVL2,missense_variant,p.E123K,ENST00000575458,,c.367G>A,MODERATE,,deleterious(0.05),probably_damaging(0.956),-1;DVL2,missense_variant,p.E123K,ENST00000575756,,c.367G>A,MODERATE,,deleterious(0.04),probably_damaging(0.982),-1;DVL2,missense_variant,p.E61K,ENST00000574143,,c.181G>A,MODERATE,,deleterious(0.04),probably_damaging(0.992),-1;PHF23,downstream_gene_variant,,ENST00000320316,NM_024297.3,,MODIFIER,YES,,,-1;PHF23,downstream_gene_variant,,ENST00000454255,NM_001284518.1,,MODIFIER,,,,-1;PHF23,downstream_gene_variant,,ENST00000571362,NM_001284517.2,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000575086,,,MODIFIER,,,,-1;PHF23,downstream_gene_variant,,ENST00000576955,,,MODIFIER,,,,-1;DVL2,non_coding_transcript_exon_variant,,ENST00000574642,,n.64G>A,MODIFIER,,,,-1;DVL2,non_coding_transcript_exon_variant,,ENST00000572285,,n.328G>A,MODIFIER,,,,-1;DVL2,non_coding_transcript_exon_variant,,ENST00000576949,,n.919G>A,MODIFIER,,,,-1;DVL2,non_coding_transcript_exon_variant,,ENST00000576439,,n.155G>A,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000571745,,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000573354,,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000574591,,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000576285,,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000576840,,,MODIFIER,,,,-1;DVL2,upstream_gene_variant,,ENST00000577154,,,MODIFIER,,,,-1 622/2989 muse;mutect2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.792e-06 0.0 0.0 0 87 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 60 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS DVL2,non_coding_transcript_exon_variant,,ENST00000576949.1,n.919G>A,MODIFIER,;DVL2,non_coding_transcript_exon_variant,,ENST00000576439.1,n.155G>A,MODIFIER,;DVL2,non_coding_transcript_exon_variant,,ENST00000572285.5,n.328G>A,MODIFIER,;DVL2,non_coding_transcript_exon_variant,,ENST00000574642.5,n.64G>A,MODIFIER,;DVL2,missense_variant,p.E61K,ENST00000574143.1,c.181G>A,MODERATE,;DVL2,missense_variant,p.E123K,ENST00000575756.5,c.367G>A,MODERATE,;DVL2,missense_variant,p.E123K,ENST00000575458.5,c.367G>A,MODERATE,;DVL2,missense_variant,p.E123K,ENST00000005340.10,c.367G>A,MODERATE,YES +SPECC1 92521 BI GRCh38 17 20205142 20205142 + missense_variant Missense_Mutation SNP G G A rs367591049 TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 92 9 c.1093G>A p.Val365Ile p.V365I ENST00000261503.9 NM_001033553.3 365 Gta/Ata 4/15 P3 A V/I protein_coding CCDS32590.1 1093/3207 ACAGCGTAAGT Coiled-coils_(Ncoils):Coil;PANTHER:PTHR23167;PANTHER:PTHR23167:SF3;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000261503 0.0 0.0001163 4/15 rs367591049 ENST00000261503 Transcript 1.0 ENSG00000128487 HGNC:30615 MODERATE 0.000347 gnomAD_AMR missense_variant benign(0) Unknown tolerated(0.87) Q5M775.131 SPECC1 HGNC 1 A0A024QYY9.49 1.0 UPI000020187D Q5M775-1 SNV SPECC1,missense_variant,p.V284I,ENST00000395530,NM_001033555.3,c.850G>A,MODERATE,,tolerated(0.83),benign(0.001),1;SPECC1,missense_variant,p.V365I,ENST00000676570,,c.1093G>A,MODERATE,,tolerated(0.95),benign(0.003),1;SPECC1,missense_variant,p.V365I,ENST00000679049,,c.1093G>A,MODERATE,,tolerated(0.95),benign(0.003),1;SPECC1,missense_variant,p.V365I,ENST00000395529,NM_152904.4,c.1093G>A,MODERATE,,tolerated(0.95),benign(0.003),1;SPECC1,missense_variant,p.V365I,ENST00000679048,,c.1093G>A,MODERATE,,tolerated(0.95),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000678019,,c.1093G>A,MODERATE,,tolerated(0.87),benign(0.015),1;SPECC1,missense_variant,p.V365I,ENST00000677148,,c.1093G>A,MODERATE,,tolerated(0.95),benign(0.024),1;SPECC1,missense_variant,p.V365I,ENST00000679255,,c.1093G>A,MODERATE,YES,tolerated(0.87),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000677914,,c.1093G>A,MODERATE,,tolerated(0.87),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000679058,,c.1093G>A,MODERATE,,tolerated(0.87),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000261503,NM_001033553.2,c.1093G>A,MODERATE,,tolerated(0.87),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000678321,,c.1093G>A,MODERATE,,tolerated(0.86),benign(0.015),1;SPECC1,missense_variant,p.V365I,ENST00000395527,NM_001243439.2,c.1093G>A,MODERATE,,tolerated(0.87),benign(0),1;SPECC1,missense_variant,p.V284I,ENST00000395522,NM_001243438.2,c.850G>A,MODERATE,,tolerated(0.95),benign(0.005),1;SPECC1,missense_variant,p.V365I,ENST00000583463,,c.1093G>A,MODERATE,,tolerated(0.96),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000578321,,c.1093G>A,MODERATE,,tolerated(0.96),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000581973,,c.1093G>A,MODERATE,,tolerated(0.96),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000583482,,c.1093G>A,MODERATE,,tolerated(0.96),benign(0),1;SPECC1,missense_variant,p.V365I,ENST00000580934,,c.1093G>A,MODERATE,,tolerated(0.96),benign(0),1;SPECC1,missense_variant,p.V284I,ENST00000395525,NM_001033554.3,c.850G>A,MODERATE,,tolerated(0.95),benign(0.005),1;SPECC1,intron_variant,,ENST00000472876,,c.-117-22271G>A,MODIFIER,,,,1;SPECC1,intron_variant,,ENST00000581399,,c.-117-22271G>A,MODIFIER,,,,1;SPECC1,intron_variant,,ENST00000583528,,c.382-22271G>A,MODIFIER,,,,1;SPECC1,upstream_gene_variant,,ENST00000582226,,,MODIFIER,,,,1;SPECC1,upstream_gene_variant,,ENST00000584527,,,MODIFIER,,,,1;SPECC1,non_coding_transcript_exon_variant,,ENST00000678651,,n.1365G>A,MODIFIER,,,,1;SPECC1,non_coding_transcript_exon_variant,,ENST00000579688,,n.946G>A,MODIFIER,,,,1;SPECC1,downstream_gene_variant,,ENST00000582063,,,MODIFIER,,,,1;SPECC1,missense_variant,p.V365I,ENST00000678315,,c.1093G>A,MODERATE,,tolerated(0.95),benign(0.024),1;SPECC1,intron_variant,,ENST00000467722,,c.284-22271G>A,MODIFIER,,,,1;AC004702.1,intron_variant,,ENST00000580225,,n.105+19956G>A,MODIFIER,YES,,,1 1144/3948 muse;mutect2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 5.973e-05 0.0 0.000347 0.0 5.438e-05 0.0 1.762e-05 0.0 0.0 4.734719914267771e-05 0.0 0.0 6.631299766013399e-05 0.0 0.0 0.0 nfe 9.259259968530388e-05 0.0 9.259259968530388e-05 0.0 0.0 0 94 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 101 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS ENSG00000263494,intron_variant,,ENST00000580225.1,n.105+19956G>A,MODIFIER,YES;SPECC1,missense_variant,p.V284I,ENST00000395525.7,c.850G>A,MODERATE,;SPECC1,missense_variant,p.V284I,ENST00000395522.6,c.850G>A,MODERATE,;SPECC1,intron_variant,,ENST00000681731.1,n.180-22271G>A,MODIFIER,;SPECC1,intron_variant,,ENST00000679740.1,c.-117-22271G>A,MODIFIER,;SPECC1,missense_variant,p.V284I,ENST00000679801.1,c.850G>A,MODERATE,;SPECC1,missense_variant,NMD_transcript_variant,p.V284I,ENST00000681545.1,c.850G>A,MODERATE,;SPECC1,missense_variant,NMD_transcript_variant,p.V284I,ENST00000680373.1,c.850G>A,MODERATE,;SPECC1,intron_variant,,ENST00000679819.1,c.-117-22271G>A,MODIFIER,;SPECC1,intron_variant,,ENST00000581399.6,c.-117-22271G>A,MODIFIER,;SPECC1,missense_variant,p.V284I,ENST00000395530.6,c.850G>A,MODERATE,;SPECC1,non_coding_transcript_exon_variant,,ENST00000579688.2,n.946G>A,MODIFIER,;SPECC1,intron_variant,NMD_transcript_variant,,ENST00000680740.1,c.284-22271G>A,MODIFIER,;SPECC1,missense_variant,p.V365I,ENST00000580934.2,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000581973.7,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000261503.9,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000395529.7,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000679058.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000680604.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000681875.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000680572.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000681116.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000681564.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000583463.6,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000680374.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000578321.2,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000677914.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000681202.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000679255.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000583482.7,c.1093G>A,MODERATE,;SPECC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680830.1,c.*753G>A,MODIFIER,;SPECC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680124.1,c.*753G>A,MODIFIER,;SPECC1,missense_variant,p.V365I,ENST00000681593.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000395527.9,c.1093G>A,MODERATE,YES;SPECC1,missense_variant,p.V365I,ENST00000680019.1,c.1093G>A,MODERATE,;SPECC1,intron_variant,,ENST00000583528.6,c.382-22271G>A,MODIFIER,;SPECC1,intron_variant,NMD_transcript_variant,,ENST00000467722.3,c.284-22271G>A,MODIFIER,;SPECC1,intron_variant,,ENST00000472876.5,c.-117-22271G>A,MODIFIER,;SPECC1,missense_variant,p.V365I,ENST00000679049.1,c.1093G>A,MODERATE,;SPECC1,non_coding_transcript_exon_variant,,ENST00000678651.1,n.1365G>A,MODIFIER,;SPECC1,missense_variant,p.V365I,ENST00000679048.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,NMD_transcript_variant,p.V365I,ENST00000678315.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000676570.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000678321.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000678019.1,c.1093G>A,MODERATE,;SPECC1,missense_variant,p.V365I,ENST00000677148.1,c.1093G>A,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 19 16 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 77 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 35 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +DSCAM 1826 BI GRCh38 21 40692940 40692940 + stop_gained Nonsense_Mutation SNP A A T novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 121 21 c.378T>A p.Tyr126Ter p.Y126* ENST00000400454.6 NM_001271534.3 126 taT/taA 3/33 P1 T Y/* protein_coding YES CCDS42929.1 378/6039 ACTGTATAGGG Gene3D:2.60.40.10;PROSITE_profiles:PS50835;PANTHER:PTHR10075;PANTHER:PTHR10075:SF51 ENSP00000383303 3/33 ENST00000400454 Transcript ENSG00000171587 HGNC:3039 HIGH NM_001389.5 stop_gained 1.0 Unknown O60469.189 DSCAM HGNC -1 1.0 UPI00000422DF O60469-1 SNV DSCAM,stop_gained,p.Y126*,ENST00000400454,NM_001271534.3&NM_001389.5,c.378T>A,HIGH,YES,,,-1 875/8571 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 57 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 142 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS DSCAM,stop_gained,p.Y126*,ENST00000400454.6,c.378T>A,HIGH,YES +SMC1A 8243 BI GRCh38 X 53383144 53383144 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 19 16 c.3083T>C p.Met1028Thr p.M1028T ENST00000322213.9 NM_006306.4 1028 aTg/aCg 20/25 P1 G M/T protein_coding YES CCDS14352.1 3083/3702 TTTCCATGGCC Gene3D:3.40.50.300;PDB-ENSP_mappings:6wg3.A;PDB-ENSP_mappings:6wge.A;Coiled-coils_(Ncoils):Coil;Pfam:PF02463;PIRSF:PIRSF005719;PANTHER:PTHR18937;PANTHER:PTHR18937:SF170;Superfamily:SSF52540 ENSP00000323421 20/25 ENST00000322213 Transcript 1.0 ENSG00000072501 HGNC:11111 MODERATE NM_006306.4 missense_variant 1.0 benign(0.028) Unknown tolerated(0.14) Q14683.211 SMC1A HGNC -1 A0A384MR33.11 1.0 UPI0000135A4D SNV SMC1A,missense_variant,p.M1006T,ENST00000375340,NM_001281463.1,c.3017T>C,MODERATE,,tolerated(0.17),benign(0.018),-1;SMC1A,missense_variant,p.M1006T,ENST00000675504,,c.3017T>C,MODERATE,,tolerated(0.17),benign(0.018),-1;SMC1A,missense_variant,p.M1028T,ENST00000322213,NM_006306.4,c.3083T>C,MODERATE,YES,tolerated(0.14),benign(0.028),-1;SMC1A,missense_variant,p.M772T,ENST00000674590,,c.2315T>C,MODERATE,,tolerated(0.06),benign(0.13),-1;SMC1A,missense_variant,p.M125T,ENST00000470241,,c.374T>C,MODERATE,,tolerated(0.17),benign(0.287),-1;SMC1A,upstream_gene_variant,,ENST00000469129,,,MODIFIER,,,,-1 3137/9710 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 33 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 36 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS SMC1A,missense_variant,p.W125R,ENST00000470241.2,c.373T>C,MODERATE,;SMC1A,missense_variant,p.M772T,ENST00000674590.1,c.2315T>C,MODERATE,;SMC1A,missense_variant,p.M1028T,ENST00000322213.9,c.3083T>C,MODERATE,YES;SMC1A,missense_variant,p.M1006T,ENST00000675504.1,c.3017T>C,MODERATE,;SMC1A,missense_variant,p.M1006T,ENST00000375340.10,c.3017T>C,MODERATE, +FRMD7 90167 BI GRCh38 X 132078640 132078640 + missense_variant Missense_Mutation SNP T T C rs1927703171 TCGA-VD-A8KG-01A TCGA-VD-A8KG-10A Somatic 108 60 c.1377A>G p.Ile459Met p.I459M ENST00000298542.9 NM_194277.3 459 atA/atG 12/12 P4 C I/M protein_coding YES CCDS35397.1 1377/2145 GAATATATGCT PANTHER:PTHR23280:SF34;PANTHER:PTHR23280 ENSP00000298542 12/12 ENST00000298542 Transcript 1.0 ENSG00000165694 HGNC:8079 MODERATE NM_194277.3 missense_variant 1.0 benign(0) Unknown tolerated(0.16) Q6ZUT3.142 FRMD7 HGNC -1 1.0 UPI00001C0AED Q6ZUT3-1 SNV FRMD7,missense_variant,p.I459M,ENST00000298542,NM_194277.3,c.1377A>G,MODERATE,YES,tolerated(0.16),benign(0),-1;FRMD7,missense_variant,p.I339M,ENST00000370879,,c.1017A>G,MODERATE,,tolerated(0.18),benign(0),-1;FRMD7,missense_variant,p.I444M,ENST00000464296,NM_001306193.1,c.1332A>G,MODERATE,,tolerated(0.16),benign(0.001),-1;STK26,downstream_gene_variant,,ENST00000354719,,,MODIFIER,,,,1;STK26,downstream_gene_variant,,ENST00000394334,NM_016542.4,,MODIFIER,,,,1;STK26,downstream_gene_variant,,ENST00000394335,NM_001042453.2,,MODIFIER,,,,1;STK26,downstream_gene_variant,,ENST00000481105,,,MODIFIER,YES,,,1;STK26,downstream_gene_variant,,ENST00000496850,NM_001042452.2,,MODIFIER,,,,1 1553/3203 muse;mutect2;varscan2 9f57834a-4dc4-45ed-97de-ed4da9d0598d 0 182 c5fe96e4-39a7-4e39-89ef-62a03a7f04fc 168 35b6e6bc-1919-4759-8be7-c3c978218462 SUCCESS FRMD7,missense_variant,p.I444M,ENST00000464296.1,c.1332A>G,MODERATE,;FRMD7,missense_variant,p.I339M,ENST00000370879.5,c.1017A>G,MODERATE,;FRMD7,missense_variant,p.I459M,ENST00000298542.9,c.1377A>G,MODERATE,YES +ODC1 4953 BI GRCh38 2 10442083 10442083 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 59 7 c.842C>T p.Ala281Val p.A281V ENST00000234111.9 NM_001287188.2 281 gCa/gTa 9/12 P1 A A/V protein_coding YES CCDS1672.1 842/1386 CTGATGCAACA PDB-ENSP_mappings:1d7k.A;PDB-ENSP_mappings:1d7k.B;PDB-ENSP_mappings:2on3.A;PDB-ENSP_mappings:2on3.B;PDB-ENSP_mappings:2oo0.A;PDB-ENSP_mappings:2oo0.B;PDB-ENSP_mappings:4zgy.A;PDB-ENSP_mappings:5bwa.A;Prints:PR01179;Superfamily:SSF51419;Superfamily:SSF50621;Pfam:PF02784;Gene3D:2.40.37.10;Pfam:PF00278;PANTHER:PTHR11482:SF42;PANTHER:PTHR11482;CDD:cd00622 ENSP00000234111 9/12 ENST00000234111 Transcript 1.0 ENSG00000115758 HGNC:8109 MODERATE NM_002539.3 missense_variant 1.0 benign(0.323) Unknown deleterious(0.01) P11926.212 ODC1 HGNC -1 1.0 UPI0000001283 SNV ODC1,missense_variant,p.A281V,ENST00000234111,NM_001287188.2&NM_002539.3,c.842C>T,MODERATE,YES,deleterious(0.01),benign(0.323),-1;ODC1,missense_variant,p.A281V,ENST00000405333,NM_001287190.2&NM_001287189.2,c.842C>T,MODERATE,,deleterious(0.01),benign(0.323),-1;ODC1,downstream_gene_variant,,ENST00000443218,,,MODIFIER,,,,-1;SNORA80B,downstream_gene_variant,,ENST00000383906,,,MODIFIER,YES,,,-1;ODC1,downstream_gene_variant,,ENST00000446285,,,MODIFIER,,,,-1 1176/2476 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 92 28923e0a-1644-41ab-bb2b-ee513b41ab49 66 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS ODC1,missense_variant,p.A281V,ENST00000443218.2,c.842C>T,MODERATE,;ODC1,missense_variant,p.A281V,ENST00000405333.5,c.842C>T,MODERATE,;ODC1,missense_variant,p.A281V,ENST00000699836.1,c.842C>T,MODERATE,;ODC1,missense_variant,p.A281V,ENST00000699835.1,c.842C>T,MODERATE,;ODC1,missense_variant,p.A281V,ENST00000234111.9,c.842C>T,MODERATE,YES;ODC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000446285.6,c.*610C>T,MODIFIER, +NFE2L2 4780 BI GRCh38 2 177231524 177231524 + stop_gained Nonsense_Mutation SNP G G T TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 154 21 c.1079C>A p.Ser360Ter p.S360* ENST00000397062.8 NM_001313903.1 360 tCa/tAa 5/5 P4 T S/* protein_coding YES CCDS42782.1 1079/1818 CCACTGAGTGT MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR24411:SF3;PANTHER:PTHR24411 ENSP00000380252 5/5 COSV67960995 ENST00000397062 Transcript 1.0 ENSG00000116044 HGNC:7782 HIGH NM_006164.5 stop_gained 1 1.0 Unknown 1 Q16236.199 NFE2L2 HGNC -1 1.0 UPI000012FFD0 Q16236-1 SNV NFE2L2,stop_gained,p.S344*,ENST00000464747,,c.1031C>A,HIGH,,,,-1;NFE2L2,stop_gained,p.S344*,ENST00000397063,NM_001313900.1&NM_001313901.1&NM_001313904.1&NM_001145412.3,c.1031C>A,HIGH,,,,-1;NFE2L2,stop_gained,p.S360*,ENST00000397062,NM_001313903.1&NM_001313902.1&NM_006164.5,c.1079C>A,HIGH,YES,,,-1;NFE2L2,stop_gained,p.S337*,ENST00000446151,NM_001145413.3,c.1010C>A,HIGH,,,,-1;NFE2L2,stop_gained,p.S88*,ENST00000449627,,c.263C>A,HIGH,,,,-1;NFE2L2,intron_variant,,ENST00000458603,,c.96+868C>A,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000421929,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000423513,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000430047,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000448782,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000586532,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000588123,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000462023,,,MODIFIER,,,,-1;NFE2L2,downstream_gene_variant,,ENST00000477534,,,MODIFIER,,,,-1;DNAJC19P5,upstream_gene_variant,,ENST00000443295,,,MODIFIER,YES,,,-1 1230/2446 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 166 28923e0a-1644-41ab-bb2b-ee513b41ab49 175 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS NFE2L2,stop_gained,p.S359*,ENST00000699304.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000699351.1,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S347*,ENST00000699412.1,c.1040C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699435.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S347*,ENST00000699411.1,c.1040C>A,HIGH,;NFE2L2,stop_gained,p.S317*,ENST00000699302.1,c.950C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699303.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699350.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699410.1,c.1076C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000699349.1,n.2268C>A,MODIFIER,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000699332.1,n.1817C>A,MODIFIER,;NFE2L2,3_prime_UTR_variant,,ENST00000699307.1,c.*814C>A,MODIFIER,;NFE2L2,stop_gained,p.S359*,ENST00000699348.1,c.1076C>A,HIGH,;NFE2L2,3_prime_UTR_variant,,ENST00000699347.1,c.*814C>A,MODIFIER,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000699306.1,n.1849C>A,MODIFIER,;NFE2L2,stop_gained,p.S359*,ENST00000699331.1,c.1076C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000462023.2,n.2565C>A,MODIFIER,;NFE2L2,stop_gained,p.S344*,ENST00000699409.1,c.1031C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000477534.2,n.2500C>A,MODIFIER,;NFE2L2,stop_gained,p.S359*,ENST00000699345.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S406*,ENST00000699346.1,c.1217C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000423513.6,n.2218C>A,MODIFIER,;NFE2L2,stop_gained,p.S347*,ENST00000699344.1,c.1040C>A,HIGH,;NFE2L2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000699299.1,c.*729C>A,MODIFIER,;NFE2L2,stop_gained,p.S359*,ENST00000699305.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S314*,ENST00000699407.1,c.941C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000699343.1,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000448782.6,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000699408.1,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699406.1,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000699330.1,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699301.1,c.1076C>A,HIGH,;NFE2L2,3_prime_UTR_variant,,ENST00000699224.1,c.*477C>A,MODIFIER,;NFE2L2,stop_gained,p.S344*,ENST00000699434.1,c.1031C>A,HIGH,;NFE2L2,3_prime_UTR_variant,,ENST00000699298.1,c.*477C>A,MODIFIER,;NFE2L2,stop_gained,p.S360*,ENST00000397062.8,c.1079C>A,HIGH,YES;NFE2L2,stop_gained,p.S330*,ENST00000699300.1,c.989C>A,HIGH,;NFE2L2,stop_gained,p.S287*,ENST00000699223.1,c.860C>A,HIGH,;NFE2L2,stop_gained,p.S337*,ENST00000446151.6,c.1010C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000699433.1,n.1827C>A,MODIFIER,;NFE2L2,stop_gained,p.S344*,ENST00000421929.6,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000464747.5,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000586532.6,c.1076C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000699328.1,c.1031C>A,HIGH,;NFE2L2,non_coding_transcript_exon_variant,,ENST00000699329.1,n.3888C>A,MODIFIER,;NFE2L2,stop_gained,p.S353*,ENST00000699264.1,c.1058C>A,HIGH,;NFE2L2,stop_gained,p.S344*,ENST00000397063.9,c.1031C>A,HIGH,;NFE2L2,stop_gained,p.S359*,ENST00000699265.1,c.1076C>A,HIGH,;NFE2L2,intron_variant,,ENST00000458603.2,c.546+868C>A,MODIFIER,;NFE2L2,intron_variant,NMD_transcript_variant,,ENST00000699327.1,c.549+868C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699405.1,c.714+365C>A,MODIFIER,;NFE2L2,intron_variant,NMD_transcript_variant,,ENST00000699432.1,c.549+868C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699404.1,c.711+365C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699220.1,c.594+868C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699342.1,c.714+365C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699431.1,c.666+365C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699297.1,c.546+868C>A,MODIFIER,;NFE2L2,intron_variant,,ENST00000699296.1,c.594+868C>A,MODIFIER, +PKHD1L1 93035 BI GRCh38 8 109443849 109443849 + missense_variant Missense_Mutation SNP G G A TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 93 7 c.4738G>A p.Glu1580Lys p.E1580K ENST00000378402.10 NM_177531.6 1580 Gaa/Aaa 37/78 P1 A E/K protein_coding YES CCDS47911.1 4738/12732 TAAATGAACTA COSM3924488 Gene3D:2.60.40.10;Pfam:PF01833;PANTHER:PTHR46769;PANTHER:PTHR46769:SF2;SMART:SM00429;Superfamily:SSF81296;CDD:cd00603 ENSP00000367655 37/78 COSV65736872;COSV65743471 ENST00000378402 Transcript ENSG00000205038 HGNC:20313 MODERATE NM_177531.6 missense_variant 1;1 1.0 possibly_damaging(0.474) Unknown tolerated(0.1) 1;1 Q86WI1.128 PKHD1L1 HGNC 1 1.0 UPI0000E5B020 SNV PKHD1L1,missense_variant,p.E1580K,ENST00000378402,NM_177531.6,c.4738G>A,MODERATE,YES,tolerated(0.1),possibly_damaging(0.474),1 4858/19969 muse;mutect2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 86 28923e0a-1644-41ab-bb2b-ee513b41ab49 100 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS PKHD1L1,missense_variant,p.E1580K,ENST00000378402.10,c.4738G>A,MODERATE,YES +STK33 65975 BI GRCh38 11 8413535 8413535 + missense_variant Missense_Mutation SNP G G C rs2135659382 TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 86 50 c.1304C>G p.Pro435Arg p.P435R ENST00000315204.5 NM_030906.4 435 cCt/cGt 13/14 P1 C P/R protein_coding CCDS7789.1 1304/1545 CATCAGGGACA MobiDB_lite:mobidb-lite;PANTHER:PTHR44167;PANTHER:PTHR44167:SF6 ENSP00000320754 13/14 ENST00000315204 Transcript ENSG00000130413 HGNC:14568 MODERATE missense_variant benign(0) Unknown tolerated_low_confidence(0.53) Q9BYT3.149 STK33 HGNC -1 1.0 UPI000004496E Q9BYT3-1 SNV STK33,missense_variant,p.P435R,ENST00000447869,NM_001352399.2&NM_001352393.2&NM_001352387.2&NM_001352392.2&NM_001352390.2&NM_001352391.2&NM_001352388.2&NM_001352389.2,c.1304C>G,MODERATE,YES,tolerated_low_confidence(0.53),benign(0),-1;STK33,missense_variant,p.P435R,ENST00000315204,NM_030906.4,c.1304C>G,MODERATE,,tolerated_low_confidence(0.53),benign(0),-1;STK33,missense_variant,p.P435R,ENST00000396672,NM_001289061.2,c.1304C>G,MODERATE,,tolerated_low_confidence(0.53),benign(0),-1;STK33,missense_variant,p.P248R,ENST00000358872,NM_001289059.2,c.743C>G,MODERATE,,tolerated_low_confidence(0.54),benign(0),-1;STK33,missense_variant,p.P394R,ENST00000534493,NM_001352395.2&NM_001352394.2&NM_001289058.2&NM_001352396.2&NM_001352397.2&NM_001352398.2,c.1181C>G,MODERATE,,tolerated_low_confidence(0.53),benign(0),-1;STK33,intron_variant,,ENST00000444064,,c.412-20825C>G,MODIFIER,,,,-1;STK33,non_coding_transcript_exon_variant,,ENST00000473980,,n.442C>G,MODIFIER,,,,-1;STK33,non_coding_transcript_exon_variant,,ENST00000486305,,n.3797C>G,MODIFIER,,,,-1 1827/2707 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 226 28923e0a-1644-41ab-bb2b-ee513b41ab49 136 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS STK33,missense_variant,p.P394R,ENST00000534493.5,c.1181C>G,MODERATE,;STK33,intron_variant,,ENST00000444064.6,c.412-20825C>G,MODIFIER,;STK33,missense_variant,p.P435R,ENST00000447869.5,c.1304C>G,MODERATE,;STK33,non_coding_transcript_exon_variant,,ENST00000486305.6,n.3797C>G,MODIFIER,;STK33,missense_variant,p.P435R,ENST00000315204.5,c.1304C>G,MODERATE,;STK33,missense_variant,p.P435R,ENST00000396672.5,c.1304C>G,MODERATE,;STK33,missense_variant,p.P248R,ENST00000358872.7,c.743C>G,MODERATE,;STK33,missense_variant,p.P435R,ENST00000687296.1,c.1304C>G,MODERATE,YES;STK33,non_coding_transcript_exon_variant,,ENST00000473980.5,n.442C>G,MODIFIER, +UMOD 7369 BI GRCh38 16 20346245 20346245 + missense_variant Missense_Mutation SNP C C T rs767780614 TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 38 31 c.1063G>A p.Asp355Asn p.D355N ENST00000396138.9 NM_001008389.3 355 Gac/Aac 5/11 A2 T D/N protein_coding CCDS10583.1 1063/1923 CTTGTCGAAGC COSM1376368;COSM2129639 Pfam:PF00100;SMART:SM00241;PROSITE_profiles:PS51034;PANTHER:PTHR46160;PANTHER:PTHR46160:SF2 ENSP00000306279 5/11 rs767780614;COSV56777798 ENST00000302509 Transcript 1.0 ENSG00000169344 HGNC:12559 MODERATE 6.152e-05 gnomAD_AFR missense_variant 0;1 benign(0.027) Unknown tolerated(0.17) 0;1 P07911.198 UMOD HGNC -1 5.0 UPI0000137E1A P07911-1 SNV UMOD,missense_variant,p.D355N,ENST00000302509,NM_001008389.3&NM_001378234.1&NM_003361.4&NM_001378235.1&NM_001378232.1&NM_001378233.1,c.1063G>A,MODERATE,,tolerated(0.17),benign(0.027),-1;UMOD,missense_variant,p.D388N,ENST00000396134,NM_001278614.2,c.1162G>A,MODERATE,,tolerated(0.19),benign(0.006),-1;UMOD,missense_variant,p.D404N,ENST00000396138,,c.1210G>A,MODERATE,YES,tolerated(0.17),benign(0.003),-1;UMOD,missense_variant,p.D355N,ENST00000570689,,c.1063G>A,MODERATE,,tolerated(0.17),benign(0.027),-1;UMOD,downstream_gene_variant,,ENST00000570757,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000570972,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000571174,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000573567,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000574195,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000576546,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000576688,,,MODIFIER,,,,-1;UMOD,downstream_gene_variant,,ENST00000577168,,,MODIFIER,,,,-1;UMOD,upstream_gene_variant,,ENST00000570331,,,MODIFIER,,,,-1 1355/2477 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 1.591e-05 6.152e-05 2.891e-05 0.0 5.437e-05 0.0 8.794e-06 0.0 0.0 3.378929977770895e-05 7.29395032976754e-05 0.0 6.621640204684809e-05 0.0 0.0 0.0 afr 7.29395032976754e-05 0.0 1.542919926578179e-05 0.0 0.0 0 89 28923e0a-1644-41ab-bb2b-ee513b41ab49 69 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS UMOD,missense_variant,p.D355N,ENST00000570689.5,c.1063G>A,MODERATE,;UMOD,missense_variant,p.D388N,ENST00000396134.6,c.1162G>A,MODERATE,;UMOD,missense_variant,p.D355N,ENST00000396138.9,c.1063G>A,MODERATE,YES +MBP 4155 BI GRCh38 18 77017213 77017213 + synonymous_variant Silent SNP A A C novel TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 26 14 c.195T>G p.Thr65= p.T65= ENST00000355994.7 NM_001025101.2 65 acT/acG 4/9 P3 C T protein_coding YES 195/915 GAGTCAGTCAC PANTHER:PTHR11429;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000348273 4/9 ENST00000355994 Transcript ENSG00000197971 HGNC:6925 LOW NM_001025101.2 synonymous_variant 1.0 Unknown P02686.223 MBP HGNC -1 A0A024R384.47 5.0 UPI000012ED3C P02686-1 SNV MBP,synonymous_variant,p.T65=,ENST00000397860,NM_001025100.2,c.195T>G,LOW,,,,-1;MBP,synonymous_variant,p.T65=,ENST00000397863,,c.195T>G,LOW,,,,-1;MBP,synonymous_variant,p.T65=,ENST00000355994,NM_001025101.2,c.195T>G,LOW,YES,,,-1;MBP,synonymous_variant,p.T65=,ENST00000579129,,c.195T>G,LOW,,,,-1;MBP,synonymous_variant,p.T65=,ENST00000580402,,c.195T>G,LOW,,,,-1;MBP,synonymous_variant,p.T65=,ENST00000581878,,c.195T>G,LOW,,,,-1;MBP,5_prime_UTR_variant,,ENST00000498683,,c.-205T>G,MODIFIER,,,,-1;MBP,5_prime_UTR_variant,,ENST00000354542,,c.-205T>G,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000359645,NM_002385.3,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000382582,NM_001025081.2,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000397865,NM_001025092.2,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000397866,NM_001025090.2,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000397869,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000397875,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000526111,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000527041,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000528160,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000578193,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000578873,,,MODIFIER,,,,-1;MBP,non_coding_transcript_exon_variant,,ENST00000487778,,n.679T>G,MODIFIER,,,,-1;MBP,non_coding_transcript_exon_variant,,ENST00000497479,,n.795T>G,MODIFIER,,,,-1;MBP,non_coding_transcript_exon_variant,,ENST00000495162,,n.450T>G,MODIFIER,,,,-1;MBP,non_coding_transcript_exon_variant,,ENST00000490754,,n.388T>G,MODIFIER,,,,-1;MBP,intron_variant,,ENST00000580473,,n.326-27153T>G,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000581179,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000582282,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000583266,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000585216,,,MODIFIER,,,,-1;MBP,non_coding_transcript_exon_variant,,ENST00000673800,,n.171T>G,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000397868,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000459948,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000467108,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000473302,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000482445,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000483025,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000484548,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000493623,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000527975,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000531144,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000533278,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000577755,,,MODIFIER,,,,-1;MBP,upstream_gene_variant,,ENST00000583474,,,MODIFIER,,,,-1 424/2738 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 64 28923e0a-1644-41ab-bb2b-ee513b41ab49 40 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS MBP,non_coding_transcript_exon_variant,,ENST00000497479.1,n.795T>G,MODIFIER,;MBP,non_coding_transcript_exon_variant,,ENST00000495162.5,n.450T>G,MODIFIER,;MBP,non_coding_transcript_exon_variant,,ENST00000490754.5,n.388T>G,MODIFIER,;MBP,non_coding_transcript_exon_variant,,ENST00000487778.5,n.679T>G,MODIFIER,;MBP,synonymous_variant,p.T65=,ENST00000581878.5,c.195T>G,LOW,;MBP,synonymous_variant,p.T65=,ENST00000397860.7,c.195T>G,LOW,;MBP,synonymous_variant,p.T65=,ENST00000397863.5,c.195T>G,LOW,;MBP,5_prime_UTR_variant,,ENST00000498683.2,c.-205T>G,MODIFIER,;MBP,non_coding_transcript_exon_variant,,ENST00000673800.1,n.171T>G,MODIFIER,;MBP,intron_variant,,ENST00000580473.5,n.326-27153T>G,MODIFIER,;MBP,synonymous_variant,p.T65=,ENST00000580402.5,c.195T>G,LOW,;MBP,synonymous_variant,p.T65=,ENST00000579129.5,c.195T>G,LOW,;MBP,5_prime_UTR_variant,,ENST00000354542.4,c.-205T>G,MODIFIER,;MBP,synonymous_variant,p.T65=,ENST00000355994.7,c.195T>G,LOW,YES +RGL3 57139 BI GRCh38 19 11406786 11406787 + frameshift_variant Frame_Shift_Ins INS - - G novel TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 27 18 c.715dup p.Gln239ProfsTer115 p.Q239Pfs*115 ENST00000380456.8 NM_001035223.4 239 caa/cCaa 6/19 P2 G Q/PX protein_coding CCDS32910.1 715-716/2133 GACCTTGAGGC Gene3D:1.10.840.10;PANTHER:PTHR23113;PANTHER:PTHR23113:SF220;Superfamily:SSF48366 ENSP00000369823 6/19 ENST00000380456 Transcript ENSG00000205517 HGNC:30282 HIGH NM_001035223.4 frameshift_variant Unknown RGL3 HGNC -1 A0A0A0MRX4.50 1.0 UPI000004E898 insertion RGL3,frameshift_variant,p.Q239Pfs*115,ENST00000380456,NM_001035223.4,c.715dup,HIGH,,,,-1;RGL3,frameshift_variant,p.Q239Pfs*115,ENST00000393423,NM_001161616.3,c.715dup,HIGH,YES,,,-1;Y_RNA,upstream_gene_variant,,ENST00000365487,,,MODIFIER,YES,,,1;RGL3,frameshift_variant,p.K235Qfs*463,ENST00000562663,,c.700dup,HIGH,,,,-1;RGL3,3_prime_UTR_variant,,ENST00000563726,,c.*356dup,MODIFIER,,,,-1;RGL3,non_coding_transcript_exon_variant,,ENST00000566153,,n.96dup,MODIFIER,,,,-1;RGL3,non_coding_transcript_exon_variant,,ENST00000453604,,n.506dup,MODIFIER,,,,-1;RGL3,non_coding_transcript_exon_variant,,ENST00000569439,,n.922dup,MODIFIER,,,,-1;RGL3,non_coding_transcript_exon_variant,,ENST00000565895,,n.157dup,MODIFIER,,,,-1;RGL3,downstream_gene_variant,,ENST00000561687,,,MODIFIER,,,,-1;RGL3,upstream_gene_variant,,ENST00000589032,,,MODIFIER,,,,-1 751-752/2511 muse*;mutect2;varscan2* 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 0 50 28923e0a-1644-41ab-bb2b-ee513b41ab49 45 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS RGL3,non_coding_transcript_exon_variant,,ENST00000569439.5,n.922_923insC,MODIFIER,;RGL3,non_coding_transcript_exon_variant,,ENST00000565895.1,n.157_158insC,MODIFIER,;RGL3,non_coding_transcript_exon_variant,,ENST00000453604.6,n.506_507insC,MODIFIER,;RGL3,frameshift_variant,p.Q239Pfs*115,ENST00000393423.7,c.715dup,HIGH,;RGL3,frameshift_variant,p.Q239Pfs*115,ENST00000380456.8,c.715dup,HIGH,YES;RGL3,non_coding_transcript_exon_variant,,ENST00000566153.5,n.96_97insC,MODIFIER,;RGL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000563726.5,c.*356_*357insC,MODIFIER,;RGL3,frameshift_variant,NMD_transcript_variant,p.Q234Pfs*115,ENST00000562663.5,c.700dup,HIGH, +PRR19 284338 BI GRCh38 19 42309939 42309939 + missense_variant Missense_Mutation SNP C C T rs139508954 TCGA-VD-A8KJ-01A TCGA-VD-A8KJ-10A Somatic 21 16 c.355C>T p.Arg119Trp p.R119W ENST00000341747.8 NM_199285.3 119 Cgg/Tgg 2/3 P1 T R/W protein_coding CCDS33036.1 355/1071 CCCCACGGTCC COSM5564251 Pfam:PF15455;PANTHER:PTHR37346;MobiDB_lite:mobidb-lite ENSP00000342709 0.0004539 0.0 2/3 rs139508954 ENST00000341747 Transcript ENSG00000188368 HGNC:33728 MODERATE 0.0004539 AA missense_variant benign(0.319) Unknown deleterious(0.01) A6NJB7.91 PRR19 HGNC 1 5.0 UPI000016101F A6NJB7-1 SNV PRR19,missense_variant,p.R119W,ENST00000499536,,c.355C>T,MODERATE,YES,deleterious(0.01),benign(0.319),1;PRR19,missense_variant,p.R119W,ENST00000598490,,c.355C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.237),1;PRR19,missense_variant,p.R119W,ENST00000341747,NM_199285.2,c.355C>T,MODERATE,,deleterious(0.01),benign(0.319),1;PRR19,missense_variant,p.R119W,ENST00000595750,,c.355C>T,MODERATE,,deleterious(0.01),benign(0.319),1;TMEM145,upstream_gene_variant,,ENST00000301204,NM_173633.3,,MODIFIER,,,,1;TMEM145,upstream_gene_variant,,ENST00000598766,,,MODIFIER,,,,1;TMEM145,upstream_gene_variant,,ENST00000673187,NM_001366910.1,,MODIFIER,,,,1;TMEM145,upstream_gene_variant,,ENST00000673205,,,MODIFIER,YES,,,1;TMEM145,upstream_gene_variant,,ENST00000601020,,,MODIFIER,,,,1;TMEM145,upstream_gene_variant,,ENST00000595775,,,MODIFIER,,,,1 733/1530 muse;mutect2;varscan2 7289bc25-2551-4c6d-b2fa-c7e13859b9b3 2.401e-05 0.0001869 0.0 0.0 5.45e-05 0.0 8.87e-06 0.0 3.273e-05 9.459970169700682e-05 0.0003159019979648 0.0 6.624269735766575e-05 0.0 0.0 0.0 afr 0.0003159019979648 0.0 0.0 0.0 0.0 0 48 28923e0a-1644-41ab-bb2b-ee513b41ab49 37 ae72116d-dfe8-4646-9fcd-a5232dc25321 SUCCESS PRR19,missense_variant,p.R119W,ENST00000499536.2,c.355C>T,MODERATE,;PRR19,missense_variant,p.R119W,ENST00000595750.2,c.355C>T,MODERATE,;PRR19,missense_variant,p.R119W,ENST00000341747.8,c.355C>T,MODERATE,YES;PRR19,missense_variant,p.R119W,ENST00000598490.1,c.355C>T,MODERATE, +PCDHGA2 56113 BI GRCh38 5 141339775 141339775 + missense_variant Missense_Mutation SNP C C A TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 50 47 c.804C>A p.Asp268Glu p.D268E ENST00000394576.3 NM_018915.4 268 gaC/gaA 1/4 P1 A D/E protein_coding YES CCDS47289.1 804/2799 ACTGACGCAGA CDD:cd11304;Gene3D:2.60.40.60;Pfam:PF00028;SMART:SM00112;Superfamily:SSF49313;PROSITE_profiles:PS50268;PANTHER:PTHR24028:SF134;PANTHER:PTHR24028;Prints:PR00205 ENSP00000378077 1/4 COSV53986833 ENST00000394576 Transcript ENSG00000081853 HGNC:8700 MODERATE NM_018915.4 missense_variant 1 1.0 probably_damaging(0.997) Unknown deleterious_low_confidence(0) 1 Q9Y5H1.158 PCDHGA2 HGNC 1 1.0 UPI0000072E67 Q9Y5H1-1 SNV PCDHGA2,missense_variant,p.D268E,ENST00000394576,NM_018915.4,c.804C>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.997),1;PCDHGA2,missense_variant,p.D268E,ENST00000528330,NM_032009.3,c.804C>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.994),1;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2,c.2421+6670C>A,MODIFIER,YES,,,1;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.4,,MODIFIER,YES,,,1;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1,,MODIFIER,,,,1;PCDHGA3,upstream_gene_variant,,ENST00000612467,,,MODIFIER,,,,1 1016/4813 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 127 84e49d30-ac41-421b-9126-d9abc2709947 97 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS PCDHGA2,missense_variant,p.D268E,ENST00000394576.3,c.804C>A,MODERATE,YES;PCDHGA2,missense_variant,p.D268E,ENST00000528330.2,c.804C>A,MODERATE,;PCDHGA1,intron_variant,,ENST00000517417.3,c.2421+6670C>A,MODIFIER,YES +GRIA1 2890 BI GRCh38 5 153794706 153794706 + missense_variant Missense_Mutation SNP G G A rs751038792 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 21 14 c.2356G>A p.Glu786Lys p.E786K ENST00000285900.10 NM_000827.4 786 Gag/Aag 14/16 A1 A E/K protein_coding CCDS4322.1 2356/2721 AGGGCGAGTGC Low_complexity_(Seg):seg;CDD:cd13729;PANTHER:PTHR18966:SF157;PANTHER:PTHR18966;Pfam:PF00060;Gene3D:3.40.190.10;Gene3D:1.10.287.70;Superfamily:SSF53850 ENSP00000285900 14/16 rs751038792 ENST00000285900 Transcript ENSG00000155511 HGNC:4571 MODERATE NM_000827.4 missense_variant possibly_damaging(0.784) Unknown deleterious(0.02) P42261.210 GRIA1 HGNC 1 1.0 UPI000013DE17 P42261-1 SNV GRIA1,missense_variant,p.E786K,ENST00000285900,NM_001364165.1&NM_000827.4,c.2356G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.784),1;GRIA1,missense_variant,p.E796K,ENST00000518783,NM_001258021.1,c.2386G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.996),1;GRIA1,missense_variant,p.E717K,ENST00000521843,NM_001258023.1,c.2149G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.784),1;GRIA1,missense_variant,p.E706K,ENST00000518142,NM_001258019.1,c.2116G>A,MODERATE,,deleterious(0.03),probably_damaging(0.951),1;GRIA1,intron_variant,,ENST00000340592,NM_001258020.1&NM_001114183.1&NM_001364167.1,c.2271-770G>A,MODIFIER,,,,1;GRIA1,intron_variant,,ENST00000448073,NM_001364166.1&NM_001258022.1,c.2301-770G>A,MODIFIER,,,,1 2575/5584 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 1.3535999642044771e-05 2.436050090182107e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5436400644830428e-05 0.0 0.0 0 33 84e49d30-ac41-421b-9126-d9abc2709947 35 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS GRIA1,intron_variant,,ENST00000448073.8,c.2301-770G>A,MODIFIER,;GRIA1,missense_variant,p.E796K,ENST00000518783.1,c.2386G>A,MODERATE,;GRIA1,missense_variant,p.E717K,ENST00000521843.6,c.2149G>A,MODERATE,;GRIA1,intron_variant,,ENST00000706734.1,c.2298-770G>A,MODIFIER,;GRIA1,intron_variant,,ENST00000340592.10,c.2271-770G>A,MODIFIER,;GRIA1,missense_variant,p.E786K,ENST00000285900.10,c.2356G>A,MODERATE,YES;GRIA1,missense_variant,p.E706K,ENST00000518142.5,c.2116G>A,MODERATE,;GRIA1,missense_variant,p.E786K,ENST00000706733.1,c.2356G>A,MODERATE, +PRSS16 10279 BI GRCh38 6 27254699 27254699 + missense_variant Missense_Mutation SNP C C G novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 85 33 c.1157C>G p.Thr386Ser p.T386S ENST00000230582.8 NM_005865.4 386 aCc/aGc 10/12 P1 G T/S protein_coding YES CCDS4623.1 1157/1545 TGTCACCTGTG PANTHER:PTHR11010;PANTHER:PTHR11010:SF11;Gene3D:1.20.120.980;Pfam:PF05577;Gene3D:3.40.50.1820 ENSP00000230582 10/12 ENST00000230582 Transcript ENSG00000112812 HGNC:9480 MODERATE NM_005865.4 missense_variant 1.0 possibly_damaging(0.634) Unknown deleterious(0.04) Q9NQE7.135 PRSS16 HGNC 1 1.0 UPI0000137773 SNV PRSS16,missense_variant,p.T386S,ENST00000230582,NM_005865.4,c.1157C>G,MODERATE,YES,deleterious(0.04),possibly_damaging(0.634),1;PRSS16,missense_variant,p.T129S,ENST00000421826,,c.386C>G,MODERATE,,tolerated(0.25),possibly_damaging(0.888),1;PRSS16,incomplete_terminal_codon_variant,p.*165=,ENST00000475106,,c.494C>G,LOW,,,,1;PRSS16,incomplete_terminal_codon_variant,p.*139=,ENST00000485993,,c.416C>G,LOW,,,,1;PRSS16,non_coding_transcript_exon_variant,,ENST00000484493,,n.352C>G,MODIFIER,,,,1;PRSS16,non_coding_transcript_exon_variant,,ENST00000468138,,n.570C>G,MODIFIER,,,,1;PRSS16,non_coding_transcript_exon_variant,,ENST00000471463,,n.386C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000377456,,n.454-287C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000459736,,n.323-287C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000478690,,n.181-287C>G,MODIFIER,,,,1;PRSS16,missense_variant,p.P82A,ENST00000466364,,c.244C>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.737),1;PRSS16,3_prime_UTR_variant,,ENST00000454665,,c.*48C>G,MODIFIER,,,,1;PRSS16,3_prime_UTR_variant,,ENST00000470870,,c.*115C>G,MODIFIER,,,,1;PRSS16,3_prime_UTR_variant,,ENST00000468930,,c.*237C>G,MODIFIER,,,,1;PRSS16,non_coding_transcript_exon_variant,,ENST00000485603,,n.1714C>G,MODIFIER,,,,1;PRSS16,non_coding_transcript_exon_variant,,ENST00000488649,,n.220C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000481125,,n.497-287C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000492575,,n.195-287C>G,MODIFIER,,,,1;PRSS16,intron_variant,,ENST00000495683,,n.195-287C>G,MODIFIER,,,,1;PRSS16,downstream_gene_variant,,ENST00000462664,,,MODIFIER,,,,1 1194/2887 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 107 84e49d30-ac41-421b-9126-d9abc2709947 118 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS PRSS16,non_coding_transcript_exon_variant,,ENST00000485603.1,n.1714C>G,MODIFIER,;PRSS16,non_coding_transcript_exon_variant,,ENST00000471463.5,n.386C>G,MODIFIER,;PRSS16,non_coding_transcript_exon_variant,,ENST00000468138.5,n.570C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000377456.6,n.454-287C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000459736.5,n.323-287C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000478690.5,n.181-287C>G,MODIFIER,;PRSS16,non_coding_transcript_exon_variant,,ENST00000484493.5,n.352C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000492575.5,n.195-287C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000481125.5,n.497-287C>G,MODIFIER,;PRSS16,non_coding_transcript_exon_variant,,ENST00000488649.5,n.220C>G,MODIFIER,;PRSS16,intron_variant,,ENST00000495683.5,n.195-287C>G,MODIFIER,;PRSS16,missense_variant,splice_region_variant,p.H164Q,ENST00000475106.2,c.492C>G,MODERATE,;PRSS16,missense_variant,splice_region_variant,p.H138Q,ENST00000485993.4,c.414C>G,MODERATE,;PRSS16,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000470870.5,c.*115C>G,MODIFIER,;PRSS16,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000468930.5,c.*237C>G,MODIFIER,;PRSS16,missense_variant,NMD_transcript_variant,p.P82A,ENST00000466364.2,c.244C>G,MODERATE,;PRSS16,missense_variant,p.T129S,ENST00000421826.6,c.386C>G,MODERATE,;PRSS16,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000454665.6,c.*48C>G,MODIFIER,;PRSS16,missense_variant,p.T386S,ENST00000230582.8,c.1157C>G,MODERATE,YES +COBL 23242 BI GRCh38 7 51028255 51028255 + synonymous_variant Silent SNP T T C novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 14 16 c.2841A>G p.Gly947= p.G947= ENST00000265136.12 NM_001346443.2 947 ggA/ggG 10/13 P1 C G protein_coding CCDS34637.1 2841/3786 GGGGCTCCCAC PANTHER:PTHR47008;MobiDB_lite:mobidb-lite ENSP00000265136 10/13 ENST00000265136 Transcript ENSG00000106078 HGNC:22199 LOW NM_015198.5 synonymous_variant Unknown O75128.138 COBL HGNC -1 1.0 UPI00001A9480 O75128-1 SNV COBL,synonymous_variant,p.G1004=,ENST00000395542,NM_001287436.2&NM_001346441.2,c.3012A>G,LOW,YES,,,-1;COBL,synonymous_variant,p.G947=,ENST00000265136,NM_001346443.2&NM_001346442.2&NM_015198.5,c.2841A>G,LOW,,,,-1;COBL,synonymous_variant,p.G832=,ENST00000431948,,c.2496A>G,LOW,,,,-1;COBL,synonymous_variant,p.G839=,ENST00000445054,,c.2517A>G,LOW,,,,-1;COBL,downstream_gene_variant,,ENST00000452534,,,MODIFIER,,,,-1;COBL,non_coding_transcript_exon_variant,,ENST00000462395,,n.6481A>G,MODIFIER,,,,-1 3017/5301 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 43 84e49d30-ac41-421b-9126-d9abc2709947 30 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS COBL,non_coding_transcript_exon_variant,,ENST00000462395.1,n.6481A>G,MODIFIER,;COBL,synonymous_variant,p.G1004=,ENST00000395542.6,c.3012A>G,LOW,;COBL,synonymous_variant,p.G947=,ENST00000265136.12,c.2841A>G,LOW,YES;COBL,synonymous_variant,p.G1029=,ENST00000431948.6,c.3087A>G,LOW,;COBL,synonymous_variant,p.G839=,ENST00000445054.5,c.2517A>G,LOW, +PTPRB 5787 BI GRCh38 12 70622624 70622624 + synonymous_variant Silent SNP C C T rs376545279 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 5 5 c.474G>A p.Ser158= p.S158= ENST00000334414.11 NM_001109754.4 158 tcG/tcA 3/34 P4 T S protein_coding YES CCDS44943.1 474/6648 CTCACCGAAAC COSM4549507 ENSP00000334928 0.0002713 0.0003671 3/34 rs376545279 ENST00000334414 Transcript 1.0 ENSG00000127329 HGNC:9665 LOW NM_001109754.4 0.0003671 EA synonymous_variant 1.0 Unknown P23467.195 PTPRB HGNC -1 1.0 UPI00002294FA P23467-3 SNV PTPRB,synonymous_variant,p.S158=,ENST00000334414,NM_001109754.4,c.474G>A,LOW,YES,,,-1;PTPRB,synonymous_variant,p.S158=,ENST00000550358,NM_001330204.2,c.474G>A,LOW,,,,-1;PTPRB,synonymous_variant,p.S157=,ENST00000551525,,c.471G>A,LOW,,,,-1;PTPRB,intron_variant,,ENST00000548122,,c.208-97G>A,MODIFIER,,,,-1;PTPRB,non_coding_transcript_exon_variant,,ENST00000538174,,n.493G>A,MODIFIER,,,,-1;PTPRB,non_coding_transcript_exon_variant,,ENST00000552253,,n.519G>A,MODIFIER,,,,-1 508/12301 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 5.551e-05 0.0 3.536e-05 0.0 0.0003529 0.0 5.88e-05 0.0 0.0 5.415279883891344e-05 2.4376000510528684e-05 0.0 0.0 0.0 0.0004043669905513 0.0 eas 0.0004043669905513 0.0 7.717240077909082e-05 0.0 0.0 0 9 84e49d30-ac41-421b-9126-d9abc2709947 10 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS PTPRB,non_coding_transcript_exon_variant,,ENST00000552253.1,n.519G>A,MODIFIER,;PTPRB,non_coding_transcript_exon_variant,,ENST00000538174.6,n.493G>A,MODIFIER,;PTPRB,intron_variant,,ENST00000548122.2,c.208-97G>A,MODIFIER,;PTPRB,synonymous_variant,p.S157=,ENST00000551525.5,c.471G>A,LOW,;PTPRB,synonymous_variant,p.S158=,ENST00000550358.5,c.474G>A,LOW,;PTPRB,synonymous_variant,p.S158=,ENST00000334414.11,c.474G>A,LOW,YES +PDS5B 23047 BI GRCh38 13 32651891 32651891 + missense_variant Missense_Mutation SNP G G C novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 91 56 c.196G>C p.Asp66His p.D66H ENST00000315596.15 NM_015032.4 66 Gat/Cat 3/35 P1 C D/H protein_coding YES CCDS41878.1 196/4344 CTTCAGATTTT PDB-ENSP_mappings:5hdt.A;PDB-ENSP_mappings:5hdt.B;PANTHER:PTHR12663:SF1;PANTHER:PTHR12663;Superfamily:SSF48371 ENSP00000313851 3/35 ENST00000315596 Transcript ENSG00000083642 HGNC:20418 MODERATE NM_015032.4 missense_variant 1.0 probably_damaging(0.965) Unknown deleterious(0) Q9NTI5.166 PDS5B HGNC 1 1.0 UPI000006D4A9 Q9NTI5-1 SNV PDS5B,missense_variant,p.D66H,ENST00000315596,NM_015032.4,c.196G>C,MODERATE,YES,deleterious(0),probably_damaging(0.965),1;PDS5B,missense_variant,p.D66H,ENST00000450460,,c.196G>C,MODERATE,,deleterious(0),probably_damaging(0.965),1;PDS5B,non_coding_transcript_exon_variant,,ENST00000498550,,n.266G>C,MODIFIER,,,,1;PDS5B,non_coding_transcript_exon_variant,,ENST00000493653,,n.258G>C,MODIFIER,,,,1;PDS5B,non_coding_transcript_exon_variant,,ENST00000482955,,n.354G>C,MODIFIER,,,,1;PDS5B,downstream_gene_variant,,ENST00000466078,,,MODIFIER,,,,1 357/7472 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 184 84e49d30-ac41-421b-9126-d9abc2709947 147 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS PDS5B,non_coding_transcript_exon_variant,,ENST00000493653.1,n.258G>C,MODIFIER,;PDS5B,missense_variant,NMD_transcript_variant,p.D66H,ENST00000450460.5,c.196G>C,MODERATE,;PDS5B,non_coding_transcript_exon_variant,,ENST00000498550.5,n.266G>C,MODIFIER,;PDS5B,non_coding_transcript_exon_variant,,ENST00000482955.5,n.354G>C,MODIFIER,;PDS5B,missense_variant,p.D66H,ENST00000315596.15,c.196G>C,MODERATE,YES +UNC79 57578 BI GRCh38 14 93622779 93622793 + inframe_deletion In_Frame_Del DEL AGAGAGAGTACCTCG AGAGAGAGTACCTCG - novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 21 9 c.5547_5561del p.Gln1849_Asp1854delinsHis p.Q1849_D1854delinsH ENST00000393151.6 1849 cAGAGAGAGTACCTCGac/cac 30/50 A2 - QREYLD/H protein_coding 5546-5560/7908 CTATCCAGAGAGAGTACCTCGACATC PANTHER:PTHR21696;PANTHER:PTHR21696:SF2;Superfamily:SSF48371 ENSP00000376858 30/50 ENST00000393151 Transcript ENSG00000133958 HGNC:19966 1.0 MODERATE inframe_deletion Unknown Q9P2D8.113 UNC79 HGNC 1 5.0 UPI00021CF3DC Q9P2D8-1 deletion UNC79,inframe_deletion,p.Q1871_D1876delinsH,ENST00000553484,,c.5613_5627del,MODERATE,YES,,,1;UNC79,inframe_deletion,p.Q1849_D1854delinsH,ENST00000555664,,c.5547_5561del,MODERATE,,,,1;UNC79,inframe_deletion,p.Q1672_D1677delinsH,ENST00000256339,NM_020818.5,c.5016_5030del,MODERATE,,,,1;UNC79,inframe_deletion,p.Q1849_D1854delinsH,ENST00000393151,NM_001346218.2,c.5547_5561del,MODERATE,,,,1;UNC79,inframe_deletion,p.Q1672_D1677delinsH,ENST00000621021,,c.5016_5030del,MODERATE,,,,1 5546-5560/7908 mutect2;pindel;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 52 84e49d30-ac41-421b-9126-d9abc2709947 31 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS UNC79,inframe_deletion,p.Q1672_D1677delinsH,ENST00000621021.1,c.5016_5030del,MODERATE,;UNC79,inframe_deletion,p.Q1849_D1854delinsH,ENST00000393151.6,c.5547_5561del,MODERATE,;UNC79,inframe_deletion,p.Q1899_D1904delinsH,ENST00000695013.1,c.5697_5711del,MODERATE,;UNC79,inframe_deletion,p.Q1921_D1926delinsH,ENST00000695012.1,c.5763_5777del,MODERATE,YES;UNC79,inframe_deletion,p.Q1871_D1876delinsH,ENST00000553484.5,c.5613_5627del,MODERATE,;UNC79,inframe_deletion,p.Q1849_D1854delinsH,ENST00000555664.5,c.5547_5561del,MODERATE,;UNC79,inframe_deletion,p.Q1672_D1677delinsH,ENST00000256339.8,c.5016_5030del,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 34 25 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 77 84e49d30-ac41-421b-9126-d9abc2709947 59 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ZNF229 7772 BI GRCh38 19 44429782 44429782 + synonymous_variant Silent SNP G G A rs754489162 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 20 25 c.999C>T p.Asn333= p.N333= ENST00000614049.5 NM_014518.4 333 aaC/aaT 6/6 P4 A N protein_coding YES CCDS42574.1 999/2478 TGCGTGTTCTG Gene3D:3.30.160.60;PANTHER:PTHR24376;PANTHER:PTHR24376:SF103 ENSP00000479884 6/6 rs754489162;COSV52161507 ENST00000614049 Transcript ENSG00000278318 HGNC:13022 LOW NM_014518.4 1.771e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q9UJW7.169 ZNF229 HGNC -1 1.0 UPI0001747B51 SNV ZNF229,synonymous_variant,p.N333=,ENST00000614049,NM_014518.4,c.999C>T,LOW,YES,,,-1;ZNF229,synonymous_variant,p.N327=,ENST00000613197,NM_001278510.2,c.981C>T,LOW,,,,-1;ZNF229,downstream_gene_variant,,ENST00000592308,,,MODIFIER,,,,-1;ZNF229,intron_variant,,ENST00000591289,,n.523-12236C>T,MODIFIER,,,,-1;ZNF229,3_prime_UTR_variant,,ENST00000620012,,c.*1202C>T,MODIFIER,,,,-1;AC245748.2,intron_variant,,ENST00000588655,,n.488+12781C>T,MODIFIER,YES,,,-1 1428/4956 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 8.027e-06 0.0 0.0 0.0 0.0 0.0 1.771e-05 0.0 0.0 0 50 84e49d30-ac41-421b-9126-d9abc2709947 45 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS ZNF229,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000620012.4,c.*1202C>T,MODIFIER,;ZNF229,synonymous_variant,p.N333=,ENST00000614049.5,c.999C>T,LOW,YES;ZNF229,synonymous_variant,p.N327=,ENST00000613197.4,c.981C>T,LOW,;ZNF229,intron_variant,,ENST00000591289.5,n.523-12236C>T,MODIFIER,;ENSG00000267188,intron_variant,,ENST00000588655.1,n.488+12781C>T,MODIFIER,YES +LRRC4B 94030 BI GRCh38 19 50518073 50518073 + missense_variant Missense_Mutation SNP C C T novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 18 10 c.1640G>A p.Arg547Gln p.R547Q ENST00000389201.7 547 cGg/cAg 3/3 P1 T R/Q protein_coding CCDS42595.1 1640/2142 TGGGCCGCGAG PANTHER:PTHR24369;PANTHER:PTHR24369:SF8;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000373853 3/3 ENST00000389201 Transcript ENSG00000131409 HGNC:25042 MODERATE missense_variant possibly_damaging(0.567) Unknown tolerated(0.12) Q9NT99.150 LRRC4B HGNC -1 A0A024R4I8.56 2.0 UPI00000497E7 SNV LRRC4B,missense_variant,p.R547Q,ENST00000652263,NM_001080457.2,c.1640G>A,MODERATE,YES,tolerated(0.12),possibly_damaging(0.567),-1;LRRC4B,missense_variant,p.R547Q,ENST00000599957,NM_001348568.1,c.1640G>A,MODERATE,,tolerated(0.12),possibly_damaging(0.567),-1;LRRC4B,missense_variant,p.R547Q,ENST00000389201,,c.1640G>A,MODERATE,,tolerated(0.12),possibly_damaging(0.567),-1;ASPDH,upstream_gene_variant,,ENST00000376916,NM_001024656.3,,MODIFIER,,,,-1;ASPDH,upstream_gene_variant,,ENST00000389208,NM_001114598.2,,MODIFIER,YES,,,-1;ASPDH,upstream_gene_variant,,ENST00000598657,,,MODIFIER,,,,-1;LRRC4B,downstream_gene_variant,,ENST00000600381,,,MODIFIER,,,,-1;ASPDH,upstream_gene_variant,,ENST00000601207,,,MODIFIER,,,,-1;ASPDH,upstream_gene_variant,,ENST00000597030,,,MODIFIER,,,,-1;ASPDH,upstream_gene_variant,,ENST00000593569,,,MODIFIER,,,,-1;ASPDH,upstream_gene_variant,,ENST00000601287,,,MODIFIER,,,,-1 1777/2958 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 19 84e49d30-ac41-421b-9126-d9abc2709947 28 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS LRRC4B,missense_variant,p.R547Q,ENST00000652263.1,c.1640G>A,MODERATE,YES;LRRC4B,missense_variant,p.R547Q,ENST00000389201.7,c.1640G>A,MODERATE,;LRRC4B,missense_variant,p.R547Q,ENST00000599957.5,c.1640G>A,MODERATE, +MIR518E 574487 BI GRCh38 19 53729875 53729875 + mature_miRNA_variant mature_miRNA_variant SNP T T G novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 54 64 n.38T>G ENST00000385252.1 1/1 G miRNA YES TTCTGTTGGCT 1/1 ENST00000385252 Transcript ENSG00000207987 HGNC:32119 MODIFIER non_coding_transcript_exon_variant 1.0 Unknown MIR518E HGNC 1 SNV MIR518E,non_coding_transcript_exon_variant,,ENST00000385252,,n.38T>G,MODIFIER,YES,,,1;MIR518A1,upstream_gene_variant,,ENST00000385068,,,MODIFIER,YES,,,1;MIR516B2,downstream_gene_variant,,ENST00000385190,,,MODIFIER,YES,,,1;MIR526A2,downstream_gene_variant,,ENST00000390198,,,MODIFIER,YES,,,1;RNU6-980P,downstream_gene_variant,,ENST00000516925,,,MODIFIER,YES,,,-1 38/88 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 miRNA_loop 151 84e49d30-ac41-421b-9126-d9abc2709947 118 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS MIR518E,mature_miRNA_variant,,ENST00000385252.1,n.38T>G,MODIFIER,YES;ENSG00000269842,intron_variant,,ENST00000710708.1,n.586-16328T>G,MODIFIER,YES +KIR3DL2 3812 BI GRCh38 19 54852222 54852222 + missense_variant Missense_Mutation SNP C C T rs376049512 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 61 53 c.295C>T p.Arg99Cys p.R99C ENST00000326321.7 NM_006737.4 99 Cgc/Tgc 3/9 P4 T R/C protein_coding YES CCDS12906.1 295/1368 GTTCACGCCCA COSM440298 CDD:cd05711;PANTHER:PTHR11738;PANTHER:PTHR11738:SF166;Gene3D:2.60.40.10;Pfam:PF00047;SMART:SM00409;Superfamily:SSF48726 ENSP00000325525 3/9 rs376049512;COSV54390025 ENST00000326321 Transcript ENSG00000240403 HGNC:6339 MODERATE NM_006737.4 0.0001674 gnomAD_EAS missense_variant 0;1 1.0 benign(0.009) Unknown tolerated(0.07) 0;1 P43630.188 KIR3DL2 HGNC 1 A0A0U1WNF3.34 1.0 UPI000012DB25 P43630-1 SNV KIR3DL2,missense_variant,p.R99C,ENST00000326321,NM_006737.4,c.295C>T,MODERATE,YES,tolerated(0.07),benign(0.009),1;KIR3DL2,missense_variant,p.R99C,ENST00000270442,NM_001242867.2,c.295C>T,MODERATE,,tolerated(0.07),possibly_damaging(0.663),1;KIR2DS4,downstream_gene_variant,,ENST00000339924,,,MODIFIER,YES,,,1 328/1877 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 2.154e-05 0.0 0.0 0.0 0.0001674 0.0 1.877e-05 0.0 0.0 3.391530117369257e-05 9.83478021225892e-05 0.0 0.0 0.0 0.0 0.0 afr 9.83478021225892e-05 0.0 1.5433999578817748e-05 0.0 0.0 0 124 84e49d30-ac41-421b-9126-d9abc2709947 114 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS KIR3DL2,missense_variant,p.R99C,ENST00000270442.5,c.295C>T,MODERATE,;KIR3DL2,missense_variant,p.R99C,ENST00000326321.7,c.295C>T,MODERATE,YES +NLRP11 204801 BI GRCh38 19 55796245 55796245 + missense_variant Missense_Mutation SNP A A G rs773018512 TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 37 36 c.2177T>C p.Met726Thr p.M726T ENST00000589093.6 NM_001385453.2 726 aTg/aCg 6/10 P1 G M/T protein_coding YES CCDS12935.1 2177/3102 ATTTCATCAAG PANTHER:PTHR45690:SF5;PANTHER:PTHR45690;Gene3D:3.80.10.10;Superfamily:SSF52047 ENSP00000466285 6/10 rs773018512 ENST00000589093 Transcript ENSG00000179873 HGNC:22945 MODERATE missense_variant 1.0 benign(0.024) Unknown tolerated(0.23) P59045.158 NLRP11 HGNC -1 1.0 UPI000013ED9D P59045-1 SNV NLRP11,missense_variant,p.M726T,ENST00000589093,NM_145007.3,c.2177T>C,MODERATE,YES,tolerated(0.23),benign(0.024),-1;NLRP11,missense_variant,p.M672T,ENST00000589824,,c.2015T>C,MODERATE,,tolerated(0.06),benign(0.054),-1;NLRP11,missense_variant,p.M627T,ENST00000592953,NM_001297743.1,c.1880T>C,MODERATE,,tolerated(0.3),benign(0.024),-1;NLRP11,synonymous_variant,p.D652=,ENST00000590409,,c.1956T>C,LOW,,,,-1;NLRP11,3_prime_UTR_variant,,ENST00000593244,,c.*153T>C,MODIFIER,,,,-1 2271/3417 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 98 84e49d30-ac41-421b-9126-d9abc2709947 73 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS NLRP11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000593244.5,c.*153T>C,MODIFIER,;NLRP11,synonymous_variant,NMD_transcript_variant,p.D652=,ENST00000590409.5,c.1956T>C,LOW,;NLRP11,missense_variant,p.M627T,ENST00000592953.5,c.1880T>C,MODERATE,;NLRP11,missense_variant,p.M726T,ENST00000589093.6,c.2177T>C,MODERATE,YES;NLRP11,missense_variant,p.M672T,ENST00000589824.6,c.2015T>C,MODERATE, +EIF1AX 1964 BI GRCh38 X 20134004 20134004 + missense_variant Missense_Mutation SNP A A T novel TCGA-V3-A9ZY-01A TCGA-V3-A9ZY-10A Somatic 4 47 c.208T>A p.Trp70Arg p.W70R ENST00000379607.10 NM_001412.4 70 Tgg/Agg 4/7 P1 T W/R protein_coding YES CCDS14196.1 208/435 TATCCAAACCT PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;HAMAP:MF_00216;PROSITE_profiles:PS50832;CDD:cd05793;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;TIGRFAM:TIGR00523;Gene3D:2.40.50.140;Pfam:PF01176;SMART:SM00652;Superfamily:SSF50249 ENSP00000368927 4/7 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0.01) P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.W70R,ENST00000379607,NM_001412.4,c.208T>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.994),-1;EIF1AX,missense_variant,p.W42R,ENST00000379593,,c.124T>A,MODERATE,,deleterious(0.01),probably_damaging(0.999),-1;AL732366.1,downstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,downstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1 406/4414 muse;mutect2;varscan2 2112a42a-9b85-475a-a31b-4ce7751cdeb9 0 63 84e49d30-ac41-421b-9126-d9abc2709947 51 199ce6fe-b695-497a-af5d-4da200e80972 SUCCESS EIF1AX,missense_variant,p.W42R,ENST00000379593.1,c.124T>A,MODERATE,;EIF1AX,missense_variant,p.W70R,ENST00000379607.10,c.208T>A,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 36 22 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 94 cce93d67-2a44-4dff-b044-2cf1ba613c0c 58 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +ADD1 118 BI GRCh38 4 2875995 2875995 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 49 32 c.80G>C p.Arg27Pro p.R27P ENST00000398129.5 NM_001354754.2 27 cGa/cCa 1/14 A2 C R/P protein_coding CCDS43205.1 80/2214 CGACCGAGTAG PANTHER:PTHR10672:SF4;PANTHER:PTHR10672 ENSP00000381197 1/14 ENST00000398129 Transcript 1.0 ENSG00000087274 HGNC:243 MODERATE missense_variant probably_damaging(0.996) Unknown deleterious(0) P35611.199 ADD1 HGNC 1 2.0 UPI0000125501 P35611-1 SNV ADD1,missense_variant,p.R27P,ENST00000355842,NM_001354762.2&NM_001354759.2&NM_001286645.1,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.998),1;ADD1,missense_variant,p.R27P,ENST00000651918,NM_001354757.2&NM_014190.4&NM_001354758.1,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.998),1;ADD1,missense_variant,p.R27P,ENST00000398125,NM_176801.2,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.983),1;ADD1,missense_variant,p.R27P,ENST00000264758,NM_001354761.2&NM_014189.3,c.80G>C,MODERATE,YES,deleterious(0),probably_damaging(0.995),1;ADD1,missense_variant,p.R27P,ENST00000398129,NM_001354754.2&NM_001354756.2&NM_001119.5&NM_001354755.1,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.996),1;ADD1,missense_variant,p.R27P,ENST00000446856,,c.80G>C,MODERATE,,deleterious(0.01),probably_damaging(0.998),1;ADD1,missense_variant,p.R27P,ENST00000503455,,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.996),1;ADD1,missense_variant,p.R27P,ENST00000513328,,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.996),1;ADD1,missense_variant,p.R27P,ENST00000398123,,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.983),1;ADD1,missense_variant,p.R27P,ENST00000511797,,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.996),1;ADD1,missense_variant,p.R27P,ENST00000508277,,c.80G>C,MODERATE,,deleterious(0),probably_damaging(0.995),1;ADD1,missense_variant,p.R27P,ENST00000510101,,c.80G>C,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.997),1;ADD1,non_coding_transcript_exon_variant,,ENST00000508684,,n.268G>C,MODIFIER,,,,1;ADD1,non_coding_transcript_exon_variant,,ENST00000503169,,n.355G>C,MODIFIER,,,,1;ADD1,non_coding_transcript_exon_variant,,ENST00000509039,,n.146G>C,MODIFIER,,,,1;ADD1,non_coding_transcript_exon_variant,,ENST00000540541,,n.136G>C,MODIFIER,,,,1 100/3787 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 102 cce93d67-2a44-4dff-b044-2cf1ba613c0c 81 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS ADD1,missense_variant,p.R27P,ENST00000398123.6,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000398129.5,c.80G>C,MODERATE,;ADD1,non_coding_transcript_exon_variant,,ENST00000503169.5,n.355G>C,MODIFIER,;ADD1,missense_variant,p.R27P,ENST00000651918.1,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000355842.7,c.80G>C,MODERATE,;ADD1,non_coding_transcript_exon_variant,,ENST00000540541.1,n.136G>C,MODIFIER,;ADD1,missense_variant,p.R27P,ENST00000503455.6,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000508277.5,c.80G>C,MODERATE,;ADD1,non_coding_transcript_exon_variant,,ENST00000509039.5,n.146G>C,MODIFIER,;ADD1,missense_variant,p.R27P,ENST00000513328.6,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000511797.5,c.80G>C,MODERATE,;ADD1,missense_variant,NMD_transcript_variant,p.R27P,ENST00000510101.5,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000264758.11,c.80G>C,MODERATE,;ADD1,non_coding_transcript_exon_variant,,ENST00000508684.5,n.268G>C,MODIFIER,;ADD1,missense_variant,p.R27P,ENST00000398125.5,c.80G>C,MODERATE,;ADD1,missense_variant,p.R27P,ENST00000683351.1,c.80G>C,MODERATE,YES +CENPE 1062 BI GRCh38 4 103141750 103141750 + missense_variant,splice_region_variant Missense_Mutation SNP C C G TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 6 9 c.5463G>C p.Lys1821Asn p.K1821N ENST00000265148.9 NM_001813.3 1821 aaG/aaC 35/49 P4 G K/N protein_coding YES CCDS34042.1 5463/8106 AATACCTTTTC Coiled-coils_(Ncoils):Coil ENSP00000265148 35/49 COSV99477638 ENST00000265148 Transcript 1.0 ENSG00000138778 HGNC:1856 MODERATE NM_001813.3 missense_variant 1 1.0 probably_damaging(0.94) Unknown deleterious(0.01) 1 Q02224.202 CENPE HGNC -1 2.0 UPI000020B28A Q02224-1 SNV CENPE,missense_variant,p.K1796N,ENST00000380026,NM_001286734.2,c.5388G>C,MODERATE,,deleterious(0.02),probably_damaging(0.998),-1;CENPE,missense_variant,p.K1821N,ENST00000265148,NM_001813.3,c.5463G>C,MODERATE,YES,deleterious(0.01),probably_damaging(0.94),-1;CENPE,missense_variant,p.K1821N,ENST00000611174,,c.5463G>C,MODERATE,,deleterious(0.03),benign(0.386),-1;CENPE,downstream_gene_variant,,ENST00000515478,,,MODIFIER,,,,-1 5487/8541 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 91 cce93d67-2a44-4dff-b044-2cf1ba613c0c 15 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS CENPE,missense_variant,splice_region_variant,p.K1821N,ENST00000265148.9,c.5463G>C,MODERATE,YES;CENPE,missense_variant,splice_region_variant,p.K1796N,ENST00000380026.8,c.5388G>C,MODERATE, +CSMD3 114788 BI GRCh38 8 112689968 112689968 + synonymous_variant Silent SNP A A T novel TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 195 75 c.2055T>A p.Val685= p.V685= ENST00000297405.10 NM_001363185.1 685 gtT/gtA 14/71 P1 T V protein_coding YES CCDS6315.1 2055/11124 CTTAAAACATC Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR45656;PANTHER:PTHR45656:SF9;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000297405 14/71 ENST00000297405 Transcript 1.0 ENSG00000164796 HGNC:19291 LOW NM_198123.2 synonymous_variant 1.0 Unknown Q7Z407.139 CSMD3 HGNC -1 1.0 UPI00001E0584 Q7Z407-1 SNV CSMD3,synonymous_variant,p.V685=,ENST00000297405,NM_001363185.1&NM_198123.2,c.2055T>A,LOW,YES,,,-1;CSMD3,synonymous_variant,p.V645=,ENST00000343508,NM_198124.2,c.1935T>A,LOW,,,,-1;CSMD3,synonymous_variant,p.V581=,ENST00000455883,NM_052900.3,c.1743T>A,LOW,,,,-1;CSMD3,synonymous_variant,p.V25=,ENST00000339701,,c.75T>A,LOW,,,,-1 2140/13052 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 274 cce93d67-2a44-4dff-b044-2cf1ba613c0c 271 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS CSMD3,synonymous_variant,p.V581=,ENST00000455883.2,c.1743T>A,LOW,;CSMD3,synonymous_variant,p.V25=,ENST00000339701.7,c.75T>A,LOW,;CSMD3,synonymous_variant,p.V645=,ENST00000343508.7,c.1935T>A,LOW,;CSMD3,synonymous_variant,p.V685=,ENST00000297405.10,c.2055T>A,LOW,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 63 49 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 137 cce93d67-2a44-4dff-b044-2cf1ba613c0c 112 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +ZNF484 83744 BI GRCh38 9 92846506 92846506 + missense_variant Missense_Mutation SNP A A C TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 68 44 c.2281T>G p.Ser761Ala p.S761A ENST00000375495.8 NM_031486.4 761 Tca/Gca 5/5 P4 C S/A protein_coding CCDS35066.1 2281/2559 TTGTGATTTCT Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24376;PANTHER:PTHR24376:SF48;SMART:SM00355;Superfamily:SSF57667 ENSP00000364645 5/5 COSV100214823 ENST00000375495 Transcript ENSG00000127081 HGNC:23385 MODERATE NM_031486.4 missense_variant 1 benign(0.018) Unknown deleterious(0.02) 1 Q5JVG2.147 ZNF484 HGNC -1 1.0 UPI00001B64FA Q5JVG2-1 SNV ZNF484,missense_variant,p.S761A,ENST00000375495,NM_031486.4,c.2281T>G,MODERATE,,deleterious(0.02),benign(0.018),-1;ZNF484,missense_variant,p.S725A,ENST00000395506,NM_001261460.2&NM_001261459.2&NM_001354536.1,c.2173T>G,MODERATE,,deleterious(0.02),benign(0.018),-1;ZNF484,missense_variant,p.S763A,ENST00000395505,NM_001261458.2&NM_001354537.1,c.2287T>G,MODERATE,YES,deleterious(0.02),benign(0.018),-1;ZNF484,missense_variant,p.S725A,ENST00000332591,NM_001007101.3,c.2173T>G,MODERATE,,deleterious(0.02),benign(0.018),-1;AL136981.2,upstream_gene_variant,,ENST00000617319,,,MODIFIER,YES,,,-1;AL136981.4,intron_variant,,ENST00000473204,,n.2103+8766A>C,MODIFIER,YES,,,1 2460/4784 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 175 cce93d67-2a44-4dff-b044-2cf1ba613c0c 112 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS ZNF484,missense_variant,p.S725A,ENST00000332591.6,c.2173T>G,MODERATE,;ZNF484,missense_variant,p.S725A,ENST00000395506.7,c.2173T>G,MODERATE,;ZNF484,missense_variant,p.S763A,ENST00000395505.6,c.2287T>G,MODERATE,;ZNF484,missense_variant,p.S761A,ENST00000375495.8,c.2281T>G,MODERATE,YES;ENSG00000288271,intron_variant,,ENST00000473204.5,n.2103+8766A>C,MODIFIER,YES +DNAJC1 64215 BI GRCh38 10 21766266 21766266 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 63 65 c.1142C>G p.Ser381Cys p.S381C ENST00000376980.8 NM_022365.4 381 tCc/tGc 10/12 P1 C S/C protein_coding YES CCDS7136.1 1142/1665 CTGGGGAGCAG PDB-ENSP_mappings:2cqq.A;Gene3D:1.10.10.60;PANTHER:PTHR44653 ENSP00000366179 10/12 ENST00000376980 Transcript ENSG00000136770 HGNC:20090 MODERATE NM_022365.4 missense_variant 1.0 possibly_damaging(0.628) Unknown deleterious(0.01) Q96KC8.166 DNAJC1 HGNC -1 1.0 UPI0000049FEF SNV DNAJC1,missense_variant,p.S381C,ENST00000376980,NM_022365.4,c.1142C>G,MODERATE,YES,deleterious(0.01),possibly_damaging(0.628),-1;DNAJC1,non_coding_transcript_exon_variant,,ENST00000483085,,n.327C>G,MODIFIER,,,,-1 1438/2100 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 147 cce93d67-2a44-4dff-b044-2cf1ba613c0c 129 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS DNAJC1,non_coding_transcript_exon_variant,,ENST00000483085.1,n.327C>G,MODIFIER,;DNAJC1,missense_variant,p.S381C,ENST00000376980.8,c.1142C>G,MODERATE,YES +CDHR1 92211 BI GRCh38 10 84196556 84196556 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 29 31 c.203C>T p.Ser68Phe p.S68F ENST00000623527.4 NM_033100.4 68 tCc/tTc 3/17 P2 T S/F protein_coding YES CCDS7372.1 203/2580 CATCTCCTACC Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF263;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000485478 3/17 ENST00000623527 Transcript 1.0 ENSG00000148600 HGNC:14550 MODERATE NM_033100.4 missense_variant 1.0 possibly_damaging(0.878) Unknown tolerated(0.53) Q96JP9.142 CDHR1 HGNC 1 F1T0L2.85 1.0 UPI0000161C2F Q96JP9-1 SNV CDHR1,missense_variant,p.S68F,ENST00000623527,NM_033100.4,c.203C>T,MODERATE,YES,tolerated(0.53),possibly_damaging(0.878),1;CDHR1,missense_variant,p.S68F,ENST00000332904,NM_001171971.3,c.203C>T,MODERATE,,tolerated(0.05),probably_damaging(0.937),1 427/6877 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 83 cce93d67-2a44-4dff-b044-2cf1ba613c0c 60 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS CDHR1,missense_variant,p.S68F,ENST00000332904.7,c.203C>T,MODERATE,;CDHR1,missense_variant,p.S68F,ENST00000623527.4,c.203C>T,MODERATE,YES +GP2 2813 BI GRCh38 16 20319697 20319697 + synonymous_variant Silent SNP G G T rs768974673 TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 84 86 c.939C>A p.Ile313= p.I313= ENST00000381362.8 NM_001007240.3 313 atC/atA 7/12 A2 T I protein_coding YES CCDS42128.1 939/1614 TTGAGGATGGT PROSITE_profiles:PS51034;PANTHER:PTHR14002:SF16;PANTHER:PTHR14002;Pfam:PF00100;SMART:SM00241 ENSP00000370767 7/12 rs768974673;COSV56892363 ENST00000381362 Transcript ENSG00000169347 HGNC:4441 LOW synonymous_variant 0;1 1.0 Unknown 0;1 P55259.160 GP2 HGNC -1 1.0 UPI000059D333 P55259-1 SNV GP2,synonymous_variant,p.I310=,ENST00000302555,NM_001502.4,c.930C>A,LOW,,,,-1;GP2,synonymous_variant,p.I313=,ENST00000381362,NM_001007240.3,c.939C>A,LOW,YES,,,-1;GP2,synonymous_variant,p.I166=,ENST00000381360,NM_001007241.3,c.498C>A,LOW,,,,-1;GP2,synonymous_variant,p.I163=,ENST00000341642,NM_001007242.3,c.489C>A,LOW,,,,-1;GP2,downstream_gene_variant,,ENST00000572347,,,MODIFIER,,,,-1;GP2,downstream_gene_variant,,ENST00000572478,,,MODIFIER,,,,-1;GP2,downstream_gene_variant,,ENST00000575449,,,MODIFIER,,,,-1;GP2,downstream_gene_variant,,ENST00000575582,,,MODIFIER,,,,-1;GP2,non_coding_transcript_exon_variant,,ENST00000573897,,n.464C>A,MODIFIER,,,,-1;GP2,downstream_gene_variant,,ENST00000575730,,,MODIFIER,,,,-1;GP2,downstream_gene_variant,,ENST00000574982,,,MODIFIER,,,,-1 1016/2425 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 6.758670224371599e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 209 cce93d67-2a44-4dff-b044-2cf1ba613c0c 171 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS GP2,non_coding_transcript_exon_variant,,ENST00000573897.5,n.464C>A,MODIFIER,;GP2,synonymous_variant,p.I163=,ENST00000341642.9,c.489C>A,LOW,;GP2,synonymous_variant,p.I166=,ENST00000381360.9,c.498C>A,LOW,;GP2,synonymous_variant,p.I313=,ENST00000381362.8,c.939C>A,LOW,;GP2,synonymous_variant,p.I310=,ENST00000302555.10,c.930C>A,LOW,YES +HASPIN 83903 BI GRCh38 17 3725407 3725407 + missense_variant Missense_Mutation SNP G G C TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 44 27 c.1472G>C p.Gly491Ala p.G491A ENST00000325418.5 NM_031965.2 491 gGg/gCg 1/1 P1 C G/A protein_coding YES CCDS11036.1 1472/2397 GATTGGGGAAG PDB-ENSP_mappings:2vuw.A;PDB-ENSP_mappings:2wb8.A;Gene3D:3.30.200.20;PDB-ENSP_mappings:3dlz.A;PDB-ENSP_mappings:3e7v.A;PDB-ENSP_mappings:3f2n.A;PDB-ENSP_mappings:3fmd.A;PDB-ENSP_mappings:3iq7.A;PDB-ENSP_mappings:4ouc.A;PDB-ENSP_mappings:4qtc.A;PDB-ENSP_mappings:5htb.A;PDB-ENSP_mappings:5htc.A;PDB-ENSP_mappings:6g34.A;PDB-ENSP_mappings:6g35.A;PDB-ENSP_mappings:6g36.A;PDB-ENSP_mappings:6g37.A;PDB-ENSP_mappings:6g38.A;PDB-ENSP_mappings:6g39.A;PDB-ENSP_mappings:6g3a.A;PDB-ENSP_mappings:6z56.A;PDB-ENSP_mappings:6z57.A;PDB-ENSP_mappings:6z58.A;PDB-ENSP_mappings:6z59.A;PDB-ENSP_mappings:6z5a.A;PDB-ENSP_mappings:6z5b.A;PDB-ENSP_mappings:6z5c.A;PDB-ENSP_mappings:6z5d.A;PDB-ENSP_mappings:6z5e.A;Pfam:PF12330;PROSITE_patterns:PS00107;PROSITE_profiles:PS50011;PANTHER:PTHR24419;PANTHER:PTHR24419:SF18;SMART:SM00220;Superfamily:SSF56112 ENSP00000325290 1/1 COSV99561621 ENST00000325418 Transcript ENSG00000177602 HGNC:19682 MODERATE NM_031965.2 missense_variant 1 probably_damaging(0.994) Unknown deleterious(0) 1 Q8TF76.171 HASPIN HGNC 1 UPI0000141654 Q8TF76-1 SNV HASPIN,missense_variant,p.G491A,ENST00000325418,NM_031965.2,c.1472G>C,MODERATE,YES,deleterious(0),probably_damaging(0.994),1;ITGAE,intron_variant,,ENST00000263087,NM_002208.5,c.3085-1663C>G,MODIFIER,YES,,,-1;ITGAE,downstream_gene_variant,,ENST00000574026,,,MODIFIER,,,,-1;ITGAE,intron_variant,,ENST00000571185,,n.578-663C>G,MODIFIER,,,,-1;ITGAE,upstream_gene_variant,,ENST00000570360,,,MODIFIER,,,,-1;ITGAE,upstream_gene_variant,,ENST00000572179,,,MODIFIER,,,,-1;ITGAE,intron_variant,,ENST00000570415,,n.479-1663C>G,MODIFIER,,,,-1;ITGAE,upstream_gene_variant,,ENST00000572433,,,MODIFIER,,,,-1;AC116914.2,downstream_gene_variant,,ENST00000571741,,,MODIFIER,YES,,,1;AC116914.1,upstream_gene_variant,,ENST00000575043,,,MODIFIER,YES,,,1 1505/2797 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 98 cce93d67-2a44-4dff-b044-2cf1ba613c0c 71 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS ITGAE,intron_variant,,ENST00000571185.1,n.578-663C>G,MODIFIER,;HASPIN,missense_variant,p.G491A,ENST00000325418.5,c.1472G>C,MODERATE,YES;ITGAE,intron_variant,,ENST00000570415.5,n.479-1663C>G,MODIFIER,;ITGAE,intron_variant,,ENST00000263087.9,c.3085-1663C>G,MODIFIER,YES +ADAMTS10 81794 BI GRCh38 19 8592040 8592040 + missense_variant Missense_Mutation SNP C C A TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 37 6 c.1651G>T p.Gly551Trp p.G551W ENST00000597188.6 NM_030957.4 551 Ggg/Tgg 14/26 P1 A G/W protein_coding YES CCDS12206.1 1651/3312 CGGCCCCCAGG Gene3D:2.20.100.10;Pfam:PF00090;PROSITE_profiles:PS50092;PANTHER:PTHR13723;PANTHER:PTHR13723:SF26;SMART:SM00209;Superfamily:SSF82895 ENSP00000471851 14/26 COSV99546603 ENST00000597188 Transcript 1.0 ENSG00000142303 HGNC:13201 MODERATE NM_030957.4 missense_variant 1 1.0 probably_damaging(0.967) Unknown deleterious(0) 1 ADAMTS10 HGNC -1 A0A0A0MQW6.50 5.0 UPI00025D3090 SNV ADAMTS10,missense_variant,p.G551W,ENST00000597188,NM_030957.4,c.1651G>T,MODERATE,YES,deleterious(0),probably_damaging(0.967),-1;ADAMTS10,missense_variant,p.G551W,ENST00000270328,,c.1651G>T,MODERATE,,deleterious(0),probably_damaging(0.967),-1;ADAMTS10,synonymous_variant,p.G41=,ENST00000595838,NM_001282352.1,c.123G>T,LOW,,,,-1;ADAMTS10,synonymous_variant,p.G41=,ENST00000593826,,c.123G>T,LOW,,,,-1;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,,c.*786G>T,MODIFIER,,,,-1;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,,c.*528G>T,MODIFIER,,,,-1;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000601163,,n.933G>T,MODIFIER,,,,-1;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000603221,,n.818G>T,MODIFIER,,,,-1;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000596236,,n.135G>T,MODIFIER,,,,-1;ADAMTS10,upstream_gene_variant,,ENST00000596911,,,MODIFIER,,,,-1;ADAMTS10,downstream_gene_variant,,ENST00000601872,,,MODIFIER,,,,-1 1937/4251 muse;mutect2;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 70 cce93d67-2a44-4dff-b044-2cf1ba613c0c 43 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS ADAMTS10,non_coding_transcript_exon_variant,,ENST00000601163.1,n.933G>T,MODIFIER,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000603221.5,n.818G>T,MODIFIER,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000596236.5,n.135G>T,MODIFIER,;ADAMTS10,synonymous_variant,NMD_transcript_variant,p.G41=,ENST00000593826.1,c.123G>T,LOW,;ADAMTS10,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000596851.5,c.*786G>T,MODIFIER,;ADAMTS10,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000593913.5,c.*528G>T,MODIFIER,;ADAMTS10,missense_variant,p.G551W,ENST00000270328.8,c.1651G>T,MODERATE,;ADAMTS10,synonymous_variant,p.G41=,ENST00000595838.5,c.123G>T,LOW,;ADAMTS10,missense_variant,p.G551W,ENST00000597188.6,c.1651G>T,MODERATE,YES +C20orf96 140680 BI GRCh38 20 277379 277380 + frameshift_variant Frame_Shift_Del DEL AA AA - novel TCGA-V4-A9E9-01A TCGA-V4-A9E9-10A Somatic 126 77 c.569_570del p.Glu191AlafsTer11 p.E191Afs*11 ENST00000360321.7 NM_153269.3 190 cTT/c 7/11 P4 - L/X protein_coding YES CCDS12994.1 569-570/1092 CTGCTCAAGATCT Coiled-coils_(Ncoils):Coil;Pfam:PF15397;PANTHER:PTHR28574 ENSP00000353470 7/11 ENST00000360321 Transcript ENSG00000196476 HGNC:16227 HIGH NM_153269.3 frameshift_variant 1.0 Unknown Q9NUD7.117 C20orf96 HGNC -1 1.0 UPI00001285F1 deletion C20orf96,frameshift_variant,p.L189Rfs*12,ENST00000400269,NM_080571.1,c.566_567del,HIGH,,,,-1;C20orf96,frameshift_variant,p.L190Rfs*12,ENST00000360321,NM_153269.3,c.569_570del,HIGH,YES,,,-1;C20orf96,frameshift_variant,p.L155Rfs*12,ENST00000382369,,c.464_465del,HIGH,,,,-1 709-710/1576 mutect2;pindel;varscan2 418152bd-7d33-4f0a-b890-2356b30d6f44 0 229 cce93d67-2a44-4dff-b044-2cf1ba613c0c 203 9765b327-ac71-48b9-915f-1a07497beddc SUCCESS C20orf96,frameshift_variant,p.E191Afs*11,ENST00000360321.7,c.569_570del,HIGH,YES;C20orf96,frameshift_variant,p.E156Afs*11,ENST00000382369.9,c.464_465del,HIGH,;C20orf96,frameshift_variant,p.E190Afs*11,ENST00000400269.4,c.566_567del,HIGH, +RYR2 6262 BI GRCh38 1 237614294 237614294 + missense_variant Missense_Mutation SNP C C A novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 9 12 c.5166C>A p.Asn1722Lys p.N1722K ENST00000366574.7 NM_001035.3 1722 aaC/aaA 37/105 P1 A N/K protein_coding YES CCDS55691.1 5166/14904 ATGAACAACGA PANTHER:PTHR12864;PANTHER:PTHR12864:SF45 ENSP00000355533 37/105 ENST00000366574 Transcript 1.0 ENSG00000198626 HGNC:10484 MODERATE NM_001035.3 missense_variant 1.0 benign(0.038) Unknown tolerated(0.49) Q92736.216 RYR2 HGNC 1 1.0 UPI0000DD0308 Q92736-1 SNV RYR2,missense_variant,p.N1722K,ENST00000366574,NM_001035.3,c.5166C>A,MODERATE,YES,tolerated(0.49),benign(0.038),1;RYR2,missense_variant,p.N1706K,ENST00000360064,,c.5118C>A,MODERATE,,tolerated(0.47),benign(0.062),1 5504/16583 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 31 2de35814-8434-456e-bcc8-3a84e342c1da 21 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS RYR2,missense_variant,p.N1067K,ENST00000714022.1,c.3201C>A,MODERATE,;RYR2,missense_variant,p.N1722K,ENST00000661330.2,c.5166C>A,MODERATE,;RYR2,missense_variant,p.N1710K,ENST00000714019.1,c.5130C>A,MODERATE,;RYR2,missense_variant,p.N1722K,ENST00000659194.3,c.5166C>A,MODERATE,;RYR2,missense_variant,p.N1722K,ENST00000366574.7,c.5166C>A,MODERATE,YES;RYR2,missense_variant,p.N1722K,ENST00000660292.2,c.5166C>A,MODERATE,;RYR2,missense_variant,p.N1685K,ENST00000714018.1,c.5055C>A,MODERATE,;RYR2,missense_variant,NMD_transcript_variant,p.N1722K,ENST00000609119.2,c.5166C>A,MODERATE,;RYR2,missense_variant,p.N1722K,ENST00000714021.1,c.5166C>A,MODERATE, +OR2L3 391192 BI GRCh38 1 248061557 248061557 + synonymous_variant Silent SNP G G A rs772101099 TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 37 15 c.876G>A p.Arg292= p.R292= ENST00000359959.4 NM_001004687.2 292 agG/agA 2/2 P1 A R protein_coding CCDS31104.1 876/939 CTGAGGAACAA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;Prints:PR00245;PANTHER:PTHR26453;PANTHER:PTHR26453:SF632;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15421 ENSP00000353044 2/2 rs772101099;COSV63456267 ENST00000359959 Transcript ENSG00000198128 HGNC:15009 LOW synonymous_variant 0;1 Unknown 0;1 Q8NG85.129 OR2L3 HGNC 1 UPI0000061EB8 SNV OR2L3,synonymous_variant,p.R292=,ENST00000641649,,c.876G>A,LOW,YES,,,1;OR2L3,synonymous_variant,p.R292=,ENST00000641161,NM_001004687.1,c.876G>A,LOW,,,,1;OR2L3,synonymous_variant,p.R292=,ENST00000359959,,c.876G>A,LOW,,,,1 942/2792 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 6.767089871573262e-06 2.4365299395867623e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 62 2de35814-8434-456e-bcc8-3a84e342c1da 52 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS OR2L3,synonymous_variant,p.R292=,ENST00000641161.1,c.876G>A,LOW,;OR2L3,synonymous_variant,p.R292=,ENST00000641649.1,c.876G>A,LOW,;OR2L3,synonymous_variant,p.R292=,ENST00000359959.4,c.876G>A,LOW,YES +PSME4 23198 BI GRCh38 2 53869402 53869402 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 124 54 c.5237C>T p.Ser1746Phe p.S1746F ENST00000404125.6 NM_014614.3 1746 tCt/tTt 44/47 P1 A S/F protein_coding YES CCDS33197.2 5237/5532 CTACAGAACCA PDB-ENSP_mappings:6kwx.A;PDB-ENSP_mappings:6kwy.c;PDB-ENSP_mappings:6rey.c;PDB-ENSP_mappings:6rey.d;PANTHER:PTHR32170:SF3;PANTHER:PTHR32170;Superfamily:SSF48371 ENSP00000384211 44/47 ENST00000404125 Transcript ENSG00000068878 HGNC:20635 MODERATE NM_014614.3 missense_variant 1.0 benign(0.031) Unknown tolerated(0.25) Q14997.151 PSME4 HGNC -1 1.0 UPI0000F3BE4A Q14997-1 SNV PSME4,missense_variant,p.S1746F,ENST00000404125,NM_014614.3,c.5237C>T,MODERATE,YES,tolerated(0.25),benign(0.031),-1;PSME4,non_coding_transcript_exon_variant,,ENST00000476586,,n.410C>T,MODIFIER,,,,-1;PSME4,intron_variant,,ENST00000466539,,n.339-2522C>T,MODIFIER,,,,-1;PSME4,3_prime_UTR_variant,,ENST00000389993,,c.*3370C>T,MODIFIER,,,,-1;PSME4,non_coding_transcript_exon_variant,,ENST00000488687,,n.1559C>T,MODIFIER,,,,-1 5446/7250 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 190 2de35814-8434-456e-bcc8-3a84e342c1da 178 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS PSME4,intron_variant,,ENST00000466539.1,n.339-2522C>T,MODIFIER,;PSME4,non_coding_transcript_exon_variant,,ENST00000488687.5,n.1559C>T,MODIFIER,;PSME4,non_coding_transcript_exon_variant,,ENST00000476586.5,n.410C>T,MODIFIER,;PSME4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000389993.7,c.*3370C>T,MODIFIER,;PSME4,missense_variant,p.S1746F,ENST00000404125.6,c.5237C>T,MODERATE,YES +BAP1 8314 BI GRCh38 3 52403678 52403692 + frameshift_variant Frame_Shift_Del DEL GCTGGGGGTGGGTGA GCTGGGGGTGGGTGA TT novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 6 18 c.1453_1466delinsA p.Ser489ArgfsTer78 p.S489Rfs*78 ENST00000460680.6 NM_004656.4 485 TCACCCACCCCCAGC/AA 13/17 P1 TT SPTPS/X protein_coding YES CCDS2853.1 1453-1467/2190 TCATTGCTGGGGGTGGGTGAGGGCT MobiDB_lite:mobidb-lite;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 13/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D indel BAP1,frameshift_variant,p.S485Kfs*82,ENST00000460680,NM_004656.4,c.1453_1467delinsAA,HIGH,YES,,,-1;BAP1,frameshift_variant,p.S467Kfs*82,ENST00000296288,,c.1399_1413delinsAA,HIGH,,,,-1;BAP1,intron_variant,,ENST00000469613,,c.119+109_119+123delinsAA,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1583-1597/3600 pindel;varscan2* df941bc1-6356-4f2e-a3f5-ae190266b441 0 23 2de35814-8434-456e-bcc8-3a84e342c1da 24 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS BAP1,frameshift_variant,p.S471Rfs*78,ENST00000296288.9,c.1399_1412delinsA,HIGH,;BAP1,intron_variant,,ENST00000469613.5,c.119+109_119+122delinsA,MODIFIER,;BAP1,frameshift_variant,p.S489Rfs*78,ENST00000460680.6,c.1453_1466delinsA,HIGH,YES +ZNF354C 30832 BI GRCh38 5 179079833 179079833 + synonymous_variant Silent SNP G G A rs772333815 TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 37 20 c.1401G>A p.Pro467= p.P467= ENST00000315475.7 NM_014594.3 467 ccG/ccA 5/5 P1 A P protein_coding YES CCDS4443.1 1401/1665 AAACCGTATCA COSM4655943 Gene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF140;Superfamily:SSF57667 ENSP00000324064 5/5 rs772333815;COSV59607512 ENST00000315475 Transcript ENSG00000177932 HGNC:16736 LOW NM_014594.3 5.437e-05 gnomAD_EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q86Y25.148 ZNF354C HGNC 1 1.0 UPI0000161A6A SNV ZNF354C,synonymous_variant,p.P467=,ENST00000315475,NM_014594.3,c.1401G>A,LOW,YES,,,1;AC104117.2,downstream_gene_variant,,ENST00000523735,,,MODIFIER,YES,,,-1 1749/5893 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 1.991e-05 0.0 0.0 0.0 5.437e-05 0.0 2.642e-05 0.0 3.267e-05 2.0289999156375416e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629199975170195e-05 0.0 4.629199975170195e-05 0.0 0.0 0 61 2de35814-8434-456e-bcc8-3a84e342c1da 57 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS ZNF354C,synonymous_variant,p.P467=,ENST00000315475.7,c.1401G>A,LOW,YES +PPP1R18 170954 BI GRCh38 6 30685956 30685956 + synonymous_variant Silent SNP G G T rs965989056 TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 75 77 c.63C>A p.Ser21= p.S21= ENST00000274853.8 NM_133471.4 21 tcC/tcA 1/3 P1 T S protein_coding CCDS43444.1 63/1842 CGAACGGACGC PANTHER:PTHR21685;PANTHER:PTHR21685:SF0;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000274853 1/3 rs965989056 ENST00000274853 Transcript ENSG00000146112 HGNC:29413 LOW NM_133471.4 synonymous_variant Unknown Q6NYC8.142 PPP1R18 HGNC -1 A0A024RCJ8.34 1.0 UPI00001C1E5E Q6NYC8-1 SNV PPP1R18,synonymous_variant,p.S21=,ENST00000615527,,c.63C>A,LOW,YES,,,-1;PPP1R18,synonymous_variant,p.S21=,ENST00000274853,NM_133471.4,c.63C>A,LOW,,,,-1;PPP1R18,synonymous_variant,p.S21=,ENST00000399199,NM_001134870.2,c.63C>A,LOW,,,,-1;NRM,downstream_gene_variant,,ENST00000259953,NM_007243.2,,MODIFIER,YES,,,-1;NRM,downstream_gene_variant,,ENST00000376420,NM_001270710.2&NM_001270709.2&NM_001270708.2,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000376421,NM_001270707.2,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000444096,,,MODIFIER,,,,-1;PPP1R18,upstream_gene_variant,,ENST00000615892,,,MODIFIER,,,,-1;PPP1R18,intron_variant,,ENST00000467662,,n.45+1158C>A,MODIFIER,,,,-1;PPP1R18,intron_variant,,ENST00000488324,,n.80+1158C>A,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000462857,,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000470733,,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000474864,,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000482141,,,MODIFIER,,,,-1;NRM,downstream_gene_variant,,ENST00000495946,,,MODIFIER,,,,-1 690/3349 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 6.758129984518746e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 143 2de35814-8434-456e-bcc8-3a84e342c1da 153 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS PPP1R18,synonymous_variant,p.S21=,ENST00000615527.1,c.63C>A,LOW,;PPP1R18,intron_variant,,ENST00000488324.1,n.80+1158C>A,MODIFIER,;PPP1R18,intron_variant,,ENST00000467662.5,n.45+1158C>A,MODIFIER,;PPP1R18,synonymous_variant,p.S21=,ENST00000274853.8,c.63C>A,LOW,YES;PPP1R18,synonymous_variant,p.S21=,ENST00000399199.7,c.63C>A,LOW, +SLC7A2 6542 BI GRCh38 8 17560421 17560421 + synonymous_variant Silent SNP C C A novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 39 40 c.1392C>A p.Ser464= p.S464= ENST00000494857.6 NM_001370338.1 464 tcC/tcA 10/13 P2 A S protein_coding CCDS34852.1 1392/1977 GAGTCCCAGGT PANTHER:PTHR43243;PANTHER:PTHR43243:SF49;TIGRFAM:TIGR00906 ENSP00000419140 10/13 ENST00000494857 Transcript ENSG00000003989 HGNC:11060 LOW NM_001370338.1 synonymous_variant Unknown P52569.174 SLC7A2 HGNC 1 5.0 UPI000035CC54 P52569-1 SNV SLC7A2,synonymous_variant,p.S503=,ENST00000470360,NM_001370337.1,c.1509C>A,LOW,,,,1;SLC7A2,synonymous_variant,p.S464=,ENST00000494857,NM_001370338.1&NM_001008539.4,c.1392C>A,LOW,,,,1;SLC7A2,synonymous_variant,p.S504=,ENST00000004531,NM_001164771.2,c.1512C>A,LOW,YES,,,1;SLC7A2,synonymous_variant,p.S503=,ENST00000398090,NM_003046.6,c.1509C>A,LOW,,,,1;SLC7A2,synonymous_variant,p.S464=,ENST00000522656,,c.1392C>A,LOW,,,,1;SLC7A2,synonymous_variant,p.S489=,ENST00000640220,,c.1467C>A,LOW,,,,1 1610/7615 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 59 2de35814-8434-456e-bcc8-3a84e342c1da 79 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS SLC7A2,synonymous_variant,p.S464=,ENST00000640220.1,c.1392C>A,LOW,;SLC7A2,synonymous_variant,p.S503=,ENST00000398090.3,c.1509C>A,LOW,;SLC7A2,synonymous_variant,p.S504=,ENST00000004531.14,c.1512C>A,LOW,;SLC7A2,synonymous_variant,p.S463=,ENST00000470360.5,c.1389C>A,LOW,;SLC7A2,synonymous_variant,p.S464=,ENST00000522656.5,c.1392C>A,LOW,;SLC7A2,synonymous_variant,p.S464=,ENST00000494857.6,c.1392C>A,LOW,YES +MICU1 10367 BI GRCh38 10 72563052 72563052 + missense_variant Missense_Mutation SNP T T A rs1338617916 TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 12 6 c.173A>T p.Glu58Val p.E58V ENST00000361114.10 NM_001195518.2 58 gAa/gTa 3/12 P4 A E/V protein_coding CCDS55715.1 173/1431 GAGATTCTGCA PANTHER:PTHR12294;PANTHER:PTHR12294:SF1 ENSP00000354415 3/12 rs1338617916 ENST00000361114 Transcript 1.0 ENSG00000107745 HGNC:1530 MODERATE NM_001195518.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant possibly_damaging(0.756) Unknown tolerated_low_confidence(0.12) Q9BPX6.171 MICU1 HGNC -1 1.0 UPI0000035D9A Q9BPX6-1 SNV MICU1,missense_variant,p.E58V,ENST00000398761,,c.173A>T,MODERATE,,tolerated_low_confidence(0.12),possibly_damaging(0.72),-1;MICU1,missense_variant,p.E58V,ENST00000361114,NM_001195518.2,c.173A>T,MODERATE,,tolerated_low_confidence(0.12),possibly_damaging(0.756),-1;MICU1,missense_variant,p.E58V,ENST00000642044,NM_006077.3&NM_001363513.1,c.173A>T,MODERATE,YES,tolerated(0.09),possibly_damaging(0.653),-1;MICU1,missense_variant,p.E58V,ENST00000635239,,c.173A>T,MODERATE,,tolerated(0.09),possibly_damaging(0.493),-1;MICU1,missense_variant,p.E58V,ENST00000604238,,c.173A>T,MODERATE,,deleterious(0.04),probably_damaging(0.979),-1;MICU1,missense_variant,p.E24V,ENST00000603011,,c.71A>T,MODERATE,,tolerated(0.42),benign(0.109),-1;MICU1,non_coding_transcript_exon_variant,,ENST00000604025,,n.239A>T,MODIFIER,,,,-1;AL513185.2,downstream_gene_variant,,ENST00000425543,,,MODIFIER,YES,,,1 244/2357 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 29 2de35814-8434-456e-bcc8-3a84e342c1da 18 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS MICU1,non_coding_transcript_exon_variant,,ENST00000604025.1,n.239A>T,MODIFIER,;MICU1,missense_variant,p.E24V,ENST00000603011.5,c.71A>T,MODERATE,;MICU1,missense_variant,p.E58V,ENST00000604238.2,c.173A>T,MODERATE,;MICU1,missense_variant,p.E58V,ENST00000635239.1,c.173A>T,MODERATE,;MICU1,missense_variant,p.E58V,ENST00000642044.1,c.173A>T,MODERATE,;MICU1,missense_variant,p.E58V,ENST00000361114.10,c.173A>T,MODERATE,YES +PLCB2 5330 BI GRCh38 15 40302017 40302017 + frameshift_variant Frame_Shift_Del DEL A A - novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 4 5 c.522del p.Pro175LeufsTer39 p.P175Lfs*39 ENST00000260402.8 NM_004573.3 174 ttT/tt 7/32 P4 - F/X protein_coding YES CCDS42020.1 522/3558 AGCAGGAAACAT Gene3D:2.30.29.240;PDB-ENSP_mappings:2fju.B;PDB-ENSP_mappings:2zkm.X;PIRSF:PIRSF000956;PANTHER:PTHR10336;PANTHER:PTHR10336:SF10;Superfamily:SSF47473;CDD:cd16209 ENSP00000260402 7/32 ENST00000260402 Transcript ENSG00000137841 HGNC:9055 HIGH NM_004573.3 frameshift_variant 1.0 Unknown Q00722.190 PLCB2 HGNC -1 2.0 UPI0000D79B75 Q00722-1 deletion PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000260402,NM_004573.3,c.522del,HIGH,YES,,,-1;PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000557821,NM_001284297.2,c.522del,HIGH,,,,-1;PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000456256,NM_001284298.2,c.522del,HIGH,,,,-1;PLCB2,frameshift_variant,p.P175Lfs*75,ENST00000543785,NM_001284299.2,c.522del,HIGH,,,,-1;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588,,n.543del,MODIFIER,,,,-1;PLCB2,upstream_gene_variant,,ENST00000558409,,,MODIFIER,,,,-1;PLCB2,downstream_gene_variant,,ENST00000559634,,,MODIFIER,,,,-1;PLCB2,upstream_gene_variant,,ENST00000560093,,,MODIFIER,,,,-1;PLCB2-AS1,downstream_gene_variant,,ENST00000559520,,,MODIFIER,YES,,,1 785/4627 mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 43 2de35814-8434-456e-bcc8-3a84e342c1da 10 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS PLCB2,frameshift_variant,p.P175Lfs*75,ENST00000543785.3,c.522del,HIGH,;PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000456256.6,c.522del,HIGH,;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588.5,n.543del,MODIFIER,;PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000260402.8,c.522del,HIGH,YES;PLCB2,frameshift_variant,p.P175Lfs*39,ENST00000557821.5,c.522del,HIGH, +NACA2 342538 BI GRCh38 17 61591129 61591129 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 31 20 c.52C>T p.Gln18Ter p.Q18* ENST00000521764.3 NM_001426702.1 18 Cag/Tag 1/1 P1 A Q/* protein_coding YES CCDS11630.1 52/648 GGACTGCGGCA PANTHER:PTHR21713;PANTHER:PTHR21713:SF2;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000427802 1/1 ENST00000521764 Transcript ENSG00000253506 HGNC:23290 HIGH NM_199290.4 stop_gained 1.0 Unknown Q9H009.130 NACA2 HGNC -1 UPI0000070B04 SNV NACA2,stop_gained,p.Q18*,ENST00000521764,NM_199290.4,c.52C>T,HIGH,YES,,,-1 91/799 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 65 2de35814-8434-456e-bcc8-3a84e342c1da 52 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS NACA2,stop_gained,p.Q18*,ENST00000521764.3,c.52C>T,HIGH,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 25 13 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 67 2de35814-8434-456e-bcc8-3a84e342c1da 39 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +KDM6A 7403 BI GRCh38 X 45059100 45059100 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9E8-01A TCGA-V4-A9E8-10A Somatic 7 25 c.970A>G p.Ile324Val p.I324V ENST00000377967.9 NM_021140.4 324 Ata/Gta 11/29 A1 G I/V protein_coding CCDS14265.1 970/4206 GTTCAATAGGG PROSITE_profiles:PS50005;PROSITE_profiles:PS50293;PANTHER:PTHR14017:SF9;PANTHER:PTHR14017;Gene3D:1.25.40.10;SMART:SM00028;Superfamily:SSF48452;Superfamily:SSF48452 ENSP00000367203 11/29 ENST00000377967 Transcript 1.0 ENSG00000147050 HGNC:12637 MODERATE missense_variant possibly_damaging(0.525) Unknown deleterious(0) O15550.193 KDM6A HGNC 1 1.0 UPI000013DA92 SNV KDM6A,missense_variant,p.I324V,ENST00000611820,NM_001291415.2,c.970A>G,MODERATE,YES,deleterious(0.02),probably_damaging(0.924),1;KDM6A,missense_variant,p.I343V,ENST00000674586,,c.1027A>G,MODERATE,,deleterious(0),possibly_damaging(0.561),1;KDM6A,missense_variant,p.I324V,ENST00000382899,NM_001291416.1,c.970A>G,MODERATE,,deleterious(0.02),possibly_damaging(0.743),1;KDM6A,missense_variant,p.I324V,ENST00000377967,NM_021140.3,c.970A>G,MODERATE,,deleterious(0),possibly_damaging(0.525),1;KDM6A,missense_variant,p.I324V,ENST00000536777,NM_001291417.1,c.970A>G,MODERATE,,deleterious(0.01),benign(0.391),1;KDM6A,missense_variant,p.I324V,ENST00000675577,,c.970A>G,MODERATE,,deleterious(0),benign(0.391),1;KDM6A,missense_variant,p.I271V,ENST00000674867,,c.811A>G,MODERATE,,deleterious(0),probably_damaging(0.992),1;KDM6A,missense_variant,p.I324V,ENST00000543216,NM_001291418.1,c.970A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.511),1;KDM6A,3_prime_UTR_variant,,ENST00000621147,,c.*201A>G,MODIFIER,,,,1;KDM6A,upstream_gene_variant,,ENST00000414389,NM_001291421.1,,MODIFIER,,,,1;KDM6A,missense_variant,p.I324V,ENST00000676062,,c.970A>G,MODERATE,,deleterious(0),possibly_damaging(0.561),1;KDM6A,missense_variant,p.I324V,ENST00000674564,,c.970A>G,MODERATE,,deleterious(0),possibly_damaging(0.676),1;KDM6A,missense_variant,p.I324V,ENST00000675514,,c.970A>G,MODERATE,,deleterious(0),possibly_damaging(0.676),1;KDM6A,missense_variant,p.I324V,ENST00000676343,,c.970A>G,MODERATE,,deleterious(0),possibly_damaging(0.561),1;KDM6A,3_prime_UTR_variant,,ENST00000676133,,c.*539A>G,MODIFIER,,,,1;KDM6A,3_prime_UTR_variant,,ENST00000674541,,c.*393A>G,MODIFIER,,,,1;KDM6A,3_prime_UTR_variant,,ENST00000674659,,c.*393A>G,MODIFIER,,,,1;KDM6A,3_prime_UTR_variant,,ENST00000676085,,c.*393A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000675525,,n.3071A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000674739,,n.1334A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000675816,,n.1125A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000676389,,n.929A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000675182,,n.854A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000675157,,n.814A>G,MODIFIER,,,,1;KDM6A,non_coding_transcript_exon_variant,,ENST00000675440,,n.1125A>G,MODIFIER,,,,1;KDM6A,upstream_gene_variant,,ENST00000675546,,,MODIFIER,,,,1 1334/5761 muse;mutect2;varscan2 df941bc1-6356-4f2e-a3f5-ae190266b441 0 37 2de35814-8434-456e-bcc8-3a84e342c1da 32 0bb47585-ce4d-4360-9b69-04bbbee47a71 SUCCESS KDM6A,non_coding_transcript_exon_variant,,ENST00000675525.1,n.3071A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000675182.1,n.854A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000676389.1,n.929A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000675157.1,n.814A>G,MODIFIER,;KDM6A,missense_variant,NMD_transcript_variant,p.I324V,ENST00000684352.1,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I324V,ENST00000683021.1,c.970A>G,MODERATE,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000621147.5,c.*201A>G,MODIFIER,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000682908.1,c.*393A>G,MODIFIER,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000683425.1,c.*432A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000675440.1,n.1125A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000675816.1,n.1125A>G,MODIFIER,;KDM6A,missense_variant,p.I343V,ENST00000674586.1,c.1027A>G,MODERATE,;KDM6A,missense_variant,NMD_transcript_variant,p.I324V,ENST00000676062.1,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I324V,ENST00000611820.5,c.970A>G,MODERATE,YES;KDM6A,missense_variant,p.I324V,ENST00000536777.6,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I324V,ENST00000382899.9,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I324V,ENST00000675577.1,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I271V,ENST00000674867.1,c.811A>G,MODERATE,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676133.1,c.*539A>G,MODIFIER,;KDM6A,non_coding_transcript_exon_variant,,ENST00000674739.1,n.1334A>G,MODIFIER,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676085.1,c.*393A>G,MODIFIER,;KDM6A,missense_variant,NMD_transcript_variant,p.I324V,ENST00000675514.1,c.970A>G,MODERATE,;KDM6A,missense_variant,p.I324V,ENST00000377967.9,c.970A>G,MODERATE,;KDM6A,missense_variant,NMD_transcript_variant,p.I324V,ENST00000674564.1,c.970A>G,MODERATE,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000674541.1,c.*393A>G,MODIFIER,;KDM6A,missense_variant,p.I324V,ENST00000543216.6,c.970A>G,MODERATE,;KDM6A,missense_variant,NMD_transcript_variant,p.I324V,ENST00000676343.1,c.970A>G,MODERATE,;KDM6A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000674659.1,c.*393A>G,MODIFIER, +POLR1B 84172 BI GRCh38 2 112575029 112575029 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 62 39 c.2708C>T p.Pro903Leu p.P903L ENST00000263331.10 NM_001371969.1 903 cCt/cTt 15/15 P1 T P/L protein_coding CCDS2097.1 2708/3408 CATGCCTTTTA CDD:cd00653;PANTHER:PTHR20856:SF5;PANTHER:PTHR20856;Pfam:PF00562;Gene3D:2.40.270.10;Superfamily:SSF64484 ENSP00000263331 15/15 ENST00000263331 Transcript ENSG00000125630 HGNC:20454 MODERATE NM_019014.6 missense_variant probably_damaging(1) Unknown deleterious(0) Q9H9Y6.181 POLR1B HGNC 1 2.0 UPI00001B6B03 Q9H9Y6-1 SNV POLR1B,missense_variant,p.P903L,ENST00000263331,NM_001371969.1&NM_019014.6,c.2708C>T,MODERATE,,deleterious(0),probably_damaging(1),1;POLR1B,missense_variant,p.P941L,ENST00000541869,NM_001282772.2,c.2822C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;POLR1B,missense_variant,p.P692L,ENST00000537335,NM_001371971.1&NM_001282776.2,c.2075C>T,MODERATE,,deleterious(0),probably_damaging(1),1;POLR1B,missense_variant,p.P720L,ENST00000409894,NM_001282774.2,c.2159C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;POLR1B,missense_variant,p.P847L,ENST00000417433,NM_001371970.1&NM_001282777.2&NM_001282779.2&NM_001137604.3,c.2540C>T,MODERATE,,deleterious(0),probably_damaging(1),1;POLR1B,missense_variant,p.P288L,ENST00000458012,,c.863C>T,MODERATE,,deleterious(0),probably_damaging(1),1;Y_RNA,downstream_gene_variant,,ENST00000384653,,,MODIFIER,YES,,,-1;POLR1B,3_prime_UTR_variant,,ENST00000333990,,c.*2578C>T,MODIFIER,,,,1;POLR1B,3_prime_UTR_variant,,ENST00000448770,,c.*955C>T,MODIFIER,,,,1;POLR1B,downstream_gene_variant,,ENST00000484574,,,MODIFIER,,,,1 2738/7527 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 97 fcd6a4b2-7385-471b-8549-31da7acd99c7 101 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS POLR1B,missense_variant,p.P288L,ENST00000458012.2,c.863C>T,MODERATE,;POLR1B,missense_variant,p.P847L,ENST00000417433.6,c.2540C>T,MODERATE,;POLR1B,missense_variant,p.P903L,ENST00000263331.10,c.2708C>T,MODERATE,YES;POLR1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000448770.5,c.*955C>T,MODIFIER,;POLR1B,missense_variant,p.P720L,ENST00000409894.7,c.2159C>T,MODERATE,;POLR1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000333990.10,c.*2578C>T,MODIFIER,;POLR1B,missense_variant,p.P941L,ENST00000541869.5,c.2822C>T,MODERATE,;POLR1B,missense_variant,p.P692L,ENST00000537335.5,c.2075C>T,MODERATE, +SPHKAP 80309 BI GRCh38 2 228018872 228018872 + missense_variant Missense_Mutation SNP T T A rs368321165 TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 81 81 c.1982A>T p.Asn661Ile p.N661I ENST00000392056.8 NM_001142644.2 661 aAt/aTt 7/12 P4 A N/I protein_coding YES CCDS46537.1 1982/5103 CGACATTTTCT PANTHER:PTHR10226;PANTHER:PTHR10226:SF7 ENSP00000375909 7/12 rs368321165 ENST00000392056 Transcript ENSG00000153820 HGNC:30619 MODERATE NM_001142644.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.174) Unknown deleterious(0.04) Q2M3C7.118 SPHKAP HGNC -1 1.0 UPI0000411D7E Q2M3C7-1 SNV SPHKAP,missense_variant,p.N661I,ENST00000392056,NM_001142644.2,c.1982A>T,MODERATE,YES,deleterious(0.04),benign(0.174),-1;SPHKAP,missense_variant,p.N661I,ENST00000344657,NM_030623.3,c.1982A>T,MODERATE,,deleterious(0.03),possibly_damaging(0.807),-1 2071/6954 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 165 fcd6a4b2-7385-471b-8549-31da7acd99c7 162 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS SPHKAP,missense_variant,p.N661I,ENST00000344657.5,c.1982A>T,MODERATE,;SPHKAP,missense_variant,p.N661I,ENST00000392056.8,c.1982A>T,MODERATE,YES +PLSCR5 389158 BI GRCh38 3 146591822 146591822 + synonymous_variant Silent SNP G G C TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 17 10 c.513C>G p.Pro171= p.P171= ENST00000443512.2 NM_001085420.2 171 ccC/ccG 5/8 P1 C P protein_coding YES CCDS46931.1 513/816 AGAAAGGGGTC PANTHER:PTHR23248;PANTHER:PTHR23248:SF25;Pfam:PF03803;Superfamily:SSF54518 ENSP00000390111 5/8 COSV71648912 ENST00000443512 Transcript ENSG00000231213 HGNC:19952 LOW synonymous_variant 1 1.0 Unknown 1 A0PG75.91 PLSCR5 HGNC -1 1.0 UPI0000425F34 A0PG75-1 SNV PLSCR5,synonymous_variant,p.P171=,ENST00000443512,NM_001085420.1,c.513C>G,LOW,YES,,,-1;PLSCR5,synonymous_variant,p.P171=,ENST00000492200,,c.513C>G,LOW,,,,-1;PLSCR5,synonymous_variant,p.P159=,ENST00000482567,NM_001321245.1,c.477C>G,LOW,,,,-1;PLSCR5-AS1,downstream_gene_variant,,ENST00000473817,,,MODIFIER,YES,,,1 1517/1969 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 13 fcd6a4b2-7385-471b-8549-31da7acd99c7 27 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS PLSCR5,synonymous_variant,p.P171=,ENST00000443512.2,c.513C>G,LOW,YES;PLSCR5,synonymous_variant,p.P159=,ENST00000482567.5,c.477C>G,LOW,;PLSCR5,synonymous_variant,p.P171=,ENST00000492200.5,c.513C>G,LOW, +MUC4 4585 BI GRCh38 3 195757251 195757251 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 30 26 c.15064G>A p.Gly5022Ser p.G5022S ENST00000463781.8 NM_018406.7 5022 Ggc/Agc 18/25 P4 T G/S protein_coding YES CCDS54700.1 15064/16239 CAAGCCAATCT PANTHER:PTHR13802;PANTHER:PTHR13802:SF53 ENSP00000417498 18/25 ENST00000463781 Transcript 1.0 ENSG00000145113 HGNC:7514 MODERATE NM_018406.7 missense_variant 1.0 benign(0.055) Unknown tolerated_low_confidence(0.07) MUC4 HGNC -1 E9PDY6.64 5.0 UPI0001B3CB30 SNV MUC4,missense_variant,p.G5022S,ENST00000463781,NM_018406.7,c.15064G>A,MODERATE,YES,tolerated_low_confidence(0.07),benign(0.055),-1;MUC4,missense_variant,p.G4970S,ENST00000475231,,c.14908G>A,MODERATE,,tolerated_low_confidence(0.09),benign(0.031),-1;MUC4,missense_variant,p.G786S,ENST00000346145,NM_004532.6,c.2356G>A,MODERATE,,tolerated(0.16),benign(0.044),-1;MUC4,missense_variant,p.G735S,ENST00000349607,NM_138297.5,c.2203G>A,MODERATE,,tolerated(0.16),benign(0.044),-1;MUC4,missense_variant,p.G5022S,ENST00000478156,,c.15064G>A,MODERATE,,tolerated_low_confidence(0.08),benign(0.17),-1;MUC4,3_prime_UTR_variant,,ENST00000466475,,c.*1785G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000477756,,c.*1503G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000477086,,c.*1785G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000480843,,c.*1503G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000462323,,c.*1503G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000470451,,c.*1469G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000448861,,c.*2024G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000308466,,c.*1696G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000339251,,c.*1757G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000415455,,c.*1696G>A,MODIFIER,,,,-1;MUC4,3_prime_UTR_variant,,ENST00000392407,,c.*1785G>A,MODIFIER,,,,-1;MUC4,intron_variant,,ENST00000479406,,c.*1707+1873G>A,MODIFIER,,,,-1;MUC4,upstream_gene_variant,,ENST00000464234,,,MODIFIER,,,,-1;MUC4,upstream_gene_variant,,ENST00000467235,,,MODIFIER,,,,-1;MUC4,upstream_gene_variant,,ENST00000469992,,,MODIFIER,,,,-1 15176/16756 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 65 fcd6a4b2-7385-471b-8549-31da7acd99c7 56 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000480843.5,c.*1503G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000470451.5,c.*1469G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000477756.5,c.*1503G>A,MODIFIER,;MUC4,missense_variant,p.G4970S,ENST00000475231.5,c.14908G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000466475.5,c.*1785G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000462323.5,c.*1503G>A,MODIFIER,;MUC4,intron_variant,NMD_transcript_variant,,ENST00000479406.5,c.*1707+1873G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000477086.5,c.*1785G>A,MODIFIER,;MUC4,missense_variant,p.G5022S,ENST00000463781.8,c.15064G>A,MODERATE,YES;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000448861.5,c.*2024G>A,MODIFIER,;MUC4,missense_variant,NMD_transcript_variant,p.G5022S,ENST00000478156.5,c.15064G>A,MODERATE,;MUC4,missense_variant,p.G786S,ENST00000346145.8,c.2356G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000415455.5,c.*1696G>A,MODIFIER,;MUC4,missense_variant,p.G735S,ENST00000349607.8,c.2203G>A,MODERATE,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000392407.6,c.*1785G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000339251.9,c.*1757G>A,MODIFIER,;MUC4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000308466.12,c.*1696G>A,MODIFIER, +CALD1 800 BI GRCh38 7 134935741 134935741 + synonymous_variant Silent SNP C C T rs1357556659 TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 11 9 c.1362C>T p.Asp454= p.D454= ENST00000361675.7 NM_033138.4 454 gaC/gaT 6/15 T D protein_coding YES CCDS5835.1 1362/2382 GAAGACAAGCC Pfam:PF02029;PANTHER:PTHR18949;PANTHER:PTHR18949:SF0;MobiDB_lite:mobidb-lite ENSP00000354826 6/15 rs1357556659 ENST00000361675 Transcript ENSG00000122786 HGNC:1441 LOW NM_033138.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q05682.192 CALD1 HGNC 1 1.0 UPI0000140A64 Q05682-1 SNV CALD1,synonymous_variant,p.D454=,ENST00000361675,NM_033138.4,c.1362C>T,LOW,YES,,,1;CALD1,synonymous_variant,p.D219=,ENST00000393118,NM_033139.3,c.657C>T,LOW,,,,1;CALD1,synonymous_variant,p.D225=,ENST00000422748,NM_033157.4,c.675C>T,LOW,,,,1;CALD1,synonymous_variant,p.D219=,ENST00000495522,,c.657C>T,LOW,,,,1;CALD1,intron_variant,,ENST00000361901,NM_004342.7,c.621+2351C>T,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000417172,,c.621+2351C>T,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000424922,NM_033140.4,c.603+2351C>T,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000436461,,c.621+2351C>T,MODIFIER,,,,1;CALD1,downstream_gene_variant,,ENST00000445569,,,MODIFIER,,,,1;CALD1,downstream_gene_variant,,ENST00000496024,,,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000430085,,c.*134+2351C>T,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000443197,,c.603+2351C>T,MODIFIER,,,,1;CALD1,intron_variant,,ENST00000482470,,n.850+2351C>T,MODIFIER,,,,1;AC083870.1,intron_variant,,ENST00000665703,,n.71+62342G>A,MODIFIER,YES,,,-1 1607/5011 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 19 fcd6a4b2-7385-471b-8549-31da7acd99c7 20 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS CALD1,intron_variant,,ENST00000424922.5,c.603+2351C>T,MODIFIER,;CALD1,synonymous_variant,p.D219=,ENST00000495522.1,c.657C>T,LOW,;CALD1,intron_variant,NMD_transcript_variant,,ENST00000443197.5,c.603+2351C>T,MODIFIER,;CALD1,synonymous_variant,p.D219=,ENST00000393118.7,c.657C>T,LOW,;ENSG00000286458,intron_variant,,ENST00000665703.1,n.71+62342G>A,MODIFIER,YES;CALD1,intron_variant,,ENST00000361901.6,c.621+2351C>T,MODIFIER,;CALD1,intron_variant,,ENST00000482470.5,n.850+2351C>T,MODIFIER,;CALD1,intron_variant,NMD_transcript_variant,,ENST00000430085.5,c.*134+2351C>T,MODIFIER,;CALD1,synonymous_variant,p.D454=,ENST00000361675.7,c.1362C>T,LOW,YES;CALD1,synonymous_variant,p.D225=,ENST00000422748.5,c.675C>T,LOW,;CALD1,intron_variant,,ENST00000436461.6,c.621+2351C>T,MODIFIER,;CALD1,intron_variant,,ENST00000417172.5,c.621+2351C>T,MODIFIER, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 50 55 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 72 fcd6a4b2-7385-471b-8549-31da7acd99c7 105 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +TRIM68 55128 BI GRCh38 11 4605142 4605142 + missense_variant Missense_Mutation SNP G G C novel TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 49 25 c.363C>G p.Ser121Arg p.S121R ENST00000300747.10 NM_018073.8 121 agC/agG 2/7 P1 C S/R protein_coding YES CCDS31356.1 363/1458 GACTGGCTGCA Gene3D:3.30.40.200;Pfam:PF00643;PROSITE_profiles:PS50119;PANTHER:PTHR24103;PANTHER:PTHR24103:SF89;SMART:SM00336;Superfamily:SSF57845;CDD:cd00021 ENSP00000300747 2/7 ENST00000300747 Transcript ENSG00000167333 HGNC:21161 MODERATE NM_018073.8 missense_variant 1.0 benign(0.015) Unknown tolerated(0.94) Q6AZZ1.151 TRIM68 HGNC -1 1.0 UPI00001D6F26 Q6AZZ1-1 SNV TRIM68,missense_variant,p.S121R,ENST00000300747,NM_018073.8,c.363C>G,MODERATE,YES,tolerated(0.94),benign(0.015),-1;TRIM68,missense_variant,p.S121R,ENST00000533021,,c.363C>G,MODERATE,,tolerated(0.57),benign(0.01),-1;TRIM68,intron_variant,,ENST00000526337,NM_001304496.2,c.-243-1802C>G,MODIFIER,,,,-1;TRIM68,missense_variant,p.S121R,ENST00000531101,,c.363C>G,MODERATE,,tolerated(0.24),benign(0.003),-1;TRIM68,non_coding_transcript_exon_variant,,ENST00000532108,,n.562C>G,MODIFIER,,,,-1;TRIM68,intron_variant,,ENST00000531644,,n.151-1802C>G,MODIFIER,,,,-1;TRIM68,upstream_gene_variant,,ENST00000531717,,,MODIFIER,,,,-1 625/3324 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 63 fcd6a4b2-7385-471b-8549-31da7acd99c7 74 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS TRIM68,missense_variant,p.S121R,ENST00000533021.1,c.363C>G,MODERATE,;TRIM68,non_coding_transcript_exon_variant,,ENST00000532108.1,n.562C>G,MODIFIER,;TRIM68,intron_variant,,ENST00000531644.5,n.151-1802C>G,MODIFIER,;TRIM68,intron_variant,,ENST00000526337.5,c.-243-1802C>G,MODIFIER,;TRIM68,missense_variant,NMD_transcript_variant,p.S121R,ENST00000531101.5,c.363C>G,MODERATE,;TRIM68,missense_variant,p.S121R,ENST00000300747.10,c.363C>G,MODERATE,YES +NPAS1 4861 BI GRCh38 19 47039512 47039512 + missense_variant Missense_Mutation SNP A A T novel TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 24 29 c.910A>T p.Met304Leu p.M304L ENST00000449844.6 304 Atg/Ttg 7/11 P1 T M/L protein_coding CCDS12694.1 910/1773 GACACATGATC CDD:cd00130;PANTHER:PTHR23043:SF25;PANTHER:PTHR23043;Gene3D:3.30.450.20;SMART:SM00091 ENSP00000405290 7/11 ENST00000449844 Transcript ENSG00000130751 HGNC:7894 MODERATE missense_variant benign(0.049) Unknown deleterious(0.02) Q99742.173 NPAS1 HGNC 1 1.0 UPI0000073CD1 Q99742-1 SNV NPAS1,missense_variant,p.M304L,ENST00000602212,NM_002517.4,c.910A>T,MODERATE,YES,deleterious(0.02),benign(0.049),1;NPAS1,missense_variant,p.M304L,ENST00000449844,,c.910A>T,MODERATE,,deleterious(0.02),benign(0.049),1;NPAS1,missense_variant,p.M129L,ENST00000602189,,c.385A>T,MODERATE,,deleterious(0.02),benign(0.007),1;NPAS1,missense_variant,p.M128L,ENST00000439365,NM_001321086.2,c.382A>T,MODERATE,,deleterious(0.03),benign(0.015),1;NPAS1,missense_variant,p.M128L,ENST00000594670,,c.382A>T,MODERATE,,deleterious(0.04),benign(0.015),1;NPAS1,non_coding_transcript_exon_variant,,ENST00000600352,,n.422A>T,MODIFIER,,,,1;NPAS1,intron_variant,,ENST00000594257,,c.161-932A>T,MODIFIER,,,,1;NPAS1,intron_variant,,ENST00000601169,,n.298-932A>T,MODIFIER,,,,1 1072/2043 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 32 fcd6a4b2-7385-471b-8549-31da7acd99c7 53 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS NPAS1,non_coding_transcript_exon_variant,,ENST00000600352.1,n.422A>T,MODIFIER,;NPAS1,intron_variant,NMD_transcript_variant,,ENST00000594257.1,c.161-932A>T,MODIFIER,;NPAS1,missense_variant,p.M128L,ENST00000594670.1,c.382A>T,MODERATE,;NPAS1,intron_variant,,ENST00000601169.1,n.298-932A>T,MODIFIER,;NPAS1,missense_variant,p.M128L,ENST00000439365.6,c.382A>T,MODERATE,;NPAS1,missense_variant,p.M304L,ENST00000449844.6,c.910A>T,MODERATE,;NPAS1,missense_variant,p.M129L,ENST00000602189.5,c.385A>T,MODERATE,;NPAS1,missense_variant,p.M304L,ENST00000602212.6,c.910A>T,MODERATE,YES +TMC2 117532 BI GRCh38 20 2617287 2617287 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 38 16 c.2156C>T p.Pro719Leu p.P719L ENST00000358864.2 NM_080751.3 719 cCc/cTc 16/20 P1 T P/L protein_coding YES CCDS13029.2 2156/2721 CCCACCCTCCT PANTHER:PTHR23302;PANTHER:PTHR23302:SF17 ENSP00000351732 16/20 ENST00000358864 Transcript ENSG00000149488 HGNC:16527 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q8TDI7.131 TMC2 HGNC 1 1.0 UPI0000246C98 Q8TDI7-1 SNV TMC2,missense_variant,p.P719L,ENST00000358864,NM_080751.2,c.2156C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;TMC2,3_prime_UTR_variant,,ENST00000496948,,c.*856C>T,MODIFIER,,,,1;TMC2,non_coding_transcript_exon_variant,,ENST00000644205,,n.2407C>T,MODIFIER,,,,1 2171/3169 muse;mutect2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 48 fcd6a4b2-7385-471b-8549-31da7acd99c7 54 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS TMC2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000496948.2,c.*856C>T,MODIFIER,;TMC2,non_coding_transcript_exon_variant,,ENST00000644205.1,n.2407C>T,MODIFIER,;TMC2,missense_variant,p.P719L,ENST00000358864.2,c.2156C>T,MODERATE,YES +EIF1AX 1964 BI GRCh38 X 20138622 20138622 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-WC-A880-01A TCGA-WC-A880-10A Somatic 2 27 c.17G>A p.Gly6Asp p.G6D ENST00000379607.10 NM_001412.4 6 gGt/gAt 2/7 P1 T G/D protein_coding YES CCDS14196.1 17/435 CTTTACCTGAT COSM3736694 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309376 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1 1.0 possibly_damaging(0.894) Unknown deleterious(0.01) 1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G6D,ENST00000379607,NM_001412.4,c.17G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.894),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2781G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 215/4414 muse;mutect2;varscan2 d8e15178-d8c5-4e4e-895c-57ffe5bc80c2 0 70 fcd6a4b2-7385-471b-8549-31da7acd99c7 29 d3e9ffaf-cdee-4fe7-8cc4-7954ca088eff SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2781G>A,MODIFIER,;EIF1AX,missense_variant,splice_region_variant,p.G6D,ENST00000379607.10,c.17G>A,MODERATE,YES +MACF1 23499 BI GRCh38 1 39333168 39333168 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 22 18 c.6595C>G p.Pro2199Ala p.P2199A ENST00000372915.8 2199 Ccc/Gcc 36/96 A2 G P/A protein_coding 6595/22158 TAAAACCCCAA PANTHER:PTHR23169;PANTHER:PTHR23169:SF24 ENSP00000362006 36/96 ENST00000372915 Transcript 1.0 ENSG00000127603 HGNC:13664 MODERATE missense_variant Unknown Q9UPN3.196 MACF1 HGNC 1 5.0 Q9UPN3-1 SNV MACF1,missense_variant,p.P2194A,ENST00000564288,,c.6580C>G,MODERATE,,tolerated_low_confidence(0.09),benign(0.037),1;MACF1,missense_variant,p.P2231A,ENST00000567887,,c.6691C>G,MODERATE,YES,tolerated_low_confidence(0.12),benign(0.009),1;MACF1,missense_variant,p.P2199A,ENST00000372915,,c.6595C>G,MODERATE,,,,1;MACF1,missense_variant,p.P2143A,ENST00000672812,,c.6427C>G,MODERATE,,tolerated_low_confidence(0.09),benign(0),1;MACF1,intron_variant,,ENST00000361689,NM_012090.5,c.4629+5815C>G,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000372925,,c.2029+5815C>G,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000530262,,c.5076+5815C>G,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000671089,,c.4476+5815C>G,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000476350,,n.2029+5815C>G,MODIFIER,,,,1;MACF1,downstream_gene_variant,,ENST00000528611,,,MODIFIER,,,,1;MACF1,3_prime_UTR_variant,,ENST00000673926,,c.*2054C>G,MODIFIER,,,,1;MACF1,non_coding_transcript_exon_variant,,ENST00000289893,,n.2031C>G,MODIFIER,,,,1 6682/23431 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 43 44ce22cc-5cdc-45eb-99b6-435f63087b7b 40 43cafceb-702a-4552-be57-644be101764f SUCCESS MACF1,non_coding_transcript_exon_variant,,ENST00000289893.8,n.2031C>G,MODIFIER,;MACF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673926.1,c.*2054C>G,MODIFIER,;MACF1,intron_variant,,ENST00000476350.1,n.2029+5815C>G,MODIFIER,;MACF1,intron_variant,,ENST00000372925.6,c.2029+5815C>G,MODIFIER,;MACF1,intron_variant,,ENST00000530262.5,c.5076+5815C>G,MODIFIER,;MACF1,intron_variant,,ENST00000671089.2,c.4476+5815C>G,MODIFIER,;MACF1,missense_variant,p.P2194A,ENST00000564288.6,c.6580C>G,MODERATE,YES;MACF1,missense_variant,p.P2143A,ENST00000672812.1,c.6427C>G,MODERATE,;MACF1,missense_variant,p.P2199A,ENST00000372915.8,c.6595C>G,MODERATE,;MACF1,missense_variant,p.P2231A,ENST00000567887.5,c.6691C>G,MODERATE,;MACF1,intron_variant,,ENST00000361689.7,c.4629+5815C>G,MODIFIER, +NME7 29922 BI GRCh38 1 169287330 169287330 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 105 91 c.727A>G p.Ile243Val p.I243V ENST00000367811.8 NM_013330.5 243 Att/Gtt 7/12 P1 C I/V protein_coding YES CCDS1277.1 727/1131 AACAATGCAAC Gene3D:3.30.70.141;Pfam:PF00334;PIRSF:PIRSF036503;PANTHER:PTHR43109;PANTHER:PTHR43109:SF2;SMART:SM00562;Superfamily:SSF54919;CDD:cd04412 ENSP00000356785 7/12 ENST00000367811 Transcript 1.0 ENSG00000143156 HGNC:20461 MODERATE NM_013330.5 missense_variant 1.0 benign(0.019) Unknown tolerated(0.37) Q9Y5B8.173 NME7 HGNC -1 1.0 UPI000012FE8C Q9Y5B8-1 SNV NME7,missense_variant,p.I207V,ENST00000472647,NM_197972.2,c.619A>G,MODERATE,,tolerated(0.37),benign(0.019),-1;NME7,missense_variant,p.I243V,ENST00000367811,NM_013330.5,c.727A>G,MODERATE,YES,tolerated(0.37),benign(0.019),-1;NME7,non_coding_transcript_exon_variant,,ENST00000469474,,n.742A>G,MODIFIER,,,,-1;NME7,non_coding_transcript_exon_variant,,ENST00000480478,,n.539A>G,MODIFIER,,,,-1;NME7,intron_variant,,ENST00000483228,,n.361+11226A>G,MODIFIER,,,,-1;NME7,missense_variant,p.I243V,ENST00000525440,,c.727A>G,MODERATE,,tolerated(0.43),benign(0.107),-1;NME7,missense_variant,p.I243V,ENST00000528517,,c.727A>G,MODERATE,,tolerated(0.42),benign(0.005),-1;NME7,non_coding_transcript_exon_variant,,ENST00000524967,,n.789A>G,MODIFIER,,,,-1 814/1472 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 199 44ce22cc-5cdc-45eb-99b6-435f63087b7b 196 43cafceb-702a-4552-be57-644be101764f SUCCESS NME7,non_coding_transcript_exon_variant,,ENST00000469474.5,n.742A>G,MODIFIER,;NME7,non_coding_transcript_exon_variant,,ENST00000524967.5,n.789A>G,MODIFIER,;NME7,non_coding_transcript_exon_variant,,ENST00000480478.5,n.539A>G,MODIFIER,;NME7,missense_variant,NMD_transcript_variant,p.I243V,ENST00000528517.5,c.727A>G,MODERATE,;NME7,intron_variant,,ENST00000483228.5,n.361+11226A>G,MODIFIER,;NME7,missense_variant,NMD_transcript_variant,p.I243V,ENST00000525440.5,c.727A>G,MODERATE,;NME7,missense_variant,p.I207V,ENST00000472647.5,c.619A>G,MODERATE,;NME7,missense_variant,p.I243V,ENST00000367811.8,c.727A>G,MODERATE,YES;ATP1B1,intron_variant,NMD_transcript_variant,,ENST00000688755.1,c.*58-23317T>C,MODIFIER, +TTLL4 9654 BI GRCh38 2 218739079 218739079 + missense_variant Missense_Mutation SNP G G A rs761668602 TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 21 25 c.1403G>A p.Arg468His p.R468H ENST00000258398.8 468 cGc/cAc 1/18 P2 A R/H protein_coding CCDS2422.1 1403/3600 CACCCGCCTCT COSM270423 PANTHER:PTHR12241;PANTHER:PTHR12241:SF145 ENSP00000258398 1/18 rs761668602;COSV51437877 ENST00000258398 Transcript ENSG00000135912 HGNC:28976 MODERATE missense_variant 0;1 benign(0.001) Unknown tolerated(0.2) 0;1 Q14679.155 TTLL4 HGNC 1 A0A024R424.39 2.0 UPI000013EDFF SNV TTLL4,missense_variant,p.R468H,ENST00000392102,NM_014640.5,c.1403G>A,MODERATE,YES,tolerated(0.2),benign(0.001),1;TTLL4,missense_variant,p.R468H,ENST00000258398,,c.1403G>A,MODERATE,,tolerated(0.2),benign(0.001),1;TTLL4,missense_variant,p.R468H,ENST00000442769,,c.1403G>A,MODERATE,,tolerated(0.21),benign(0.001),1;TTLL4,missense_variant,p.R303H,ENST00000457313,,c.908G>A,MODERATE,,tolerated(0.2),benign(0.001),1;TTLL4,downstream_gene_variant,,ENST00000415717,,,MODIFIER,,,,1;TTLL4,downstream_gene_variant,,ENST00000424644,,,MODIFIER,,,,1;TTLL4,downstream_gene_variant,,ENST00000437755,,,MODIFIER,,,,1 1506/4730 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 1.35215996124316e-05 2.4321399905602448e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5433499356731772e-05 0.0 0.0 0 33 44ce22cc-5cdc-45eb-99b6-435f63087b7b 46 43cafceb-702a-4552-be57-644be101764f SUCCESS TTLL4,missense_variant,p.R468H,ENST00000258398.8,c.1403G>A,MODERATE,;TTLL4,missense_variant,p.R468H,ENST00000442769.5,c.1403G>A,MODERATE,;TTLL4,missense_variant,p.R303H,ENST00000457313.5,c.908G>A,MODERATE,;TTLL4,missense_variant,p.R468H,ENST00000392102.6,c.1403G>A,MODERATE,YES +BAP1 8314 BI GRCh38 3 52403824 52403824 + stop_gained Nonsense_Mutation SNP G G A rs1559587104 TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 4 28 c.1321C>T p.Gln441Ter p.Q441* ENST00000460680.6 NM_004656.4 441 Cag/Tag 13/17 P1 A Q/* protein_coding YES CCDS2853.1 1321/2190 pathogenic GGGCTGCAGCA PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 13/17 rs1559587104 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 stop_gained 1 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,stop_gained,p.Q441*,ENST00000460680,NM_004656.4,c.1321C>T,HIGH,YES,,,-1;BAP1,stop_gained,p.Q423*,ENST00000296288,,c.1267C>T,HIGH,,,,-1;BAP1,stop_gained,p.Q33*,ENST00000469613,,c.97C>T,HIGH,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000490804,,n.749C>T,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1451/3600 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 57 44ce22cc-5cdc-45eb-99b6-435f63087b7b 32 43cafceb-702a-4552-be57-644be101764f SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000490804.1,n.749C>T,MODIFIER,;BAP1,stop_gained,p.Q423*,ENST00000296288.9,c.1267C>T,HIGH,;BAP1,synonymous_variant,p.C32=,ENST00000469613.5,c.96C>T,LOW,;BAP1,stop_gained,p.Q441*,ENST00000460680.6,c.1321C>T,HIGH,YES +ZDHHC23 254887 BI GRCh38 3 113956418 113956418 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 4 37 c.952G>C p.Gly318Arg p.G318R ENST00000330212.7 NM_173570.5 318 Ggg/Cgg 4/6 P4 C G/R protein_coding YES CCDS33827.1 952/1230 TGTATGGGATC Pfam:PF01529;PANTHER:PTHR22883;PANTHER:PTHR22883:SF99;Transmembrane_helices:TMhelix ENSP00000330485 4/6 ENST00000330212 Transcript ENSG00000184307 HGNC:28654 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q8IYP9.128 ZDHHC23 HGNC 1 1.0 UPI0000209F9A SNV ZDHHC23,missense_variant,p.G119R,ENST00000638807,,c.355G>C,MODERATE,,deleterious(0),probably_damaging(1),1;ZDHHC23,missense_variant,p.G318R,ENST00000330212,NM_001320466.2&NM_001320468.2&NM_001320467.2&NM_173570.5,c.952G>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;ZDHHC23,missense_variant,p.G312R,ENST00000498275,,c.934G>C,MODERATE,,deleterious(0),probably_damaging(1),1;ZDHHC23,downstream_gene_variant,,ENST00000491556,,,MODIFIER,,,,1;ZDHHC23,upstream_gene_variant,,ENST00000496083,,,MODIFIER,,,,1;ZDHHC23,upstream_gene_variant,,ENST00000488129,,,MODIFIER,,,,1;ZDHHC23,missense_variant,p.G318R,ENST00000478793,NM_001363952.1,c.952G>C,MODERATE,,deleterious(0),probably_damaging(1),1 1251/3778 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 101 44ce22cc-5cdc-45eb-99b6-435f63087b7b 41 43cafceb-702a-4552-be57-644be101764f SUCCESS ZDHHC23,missense_variant,NMD_transcript_variant,p.G318R,ENST00000478793.1,c.952G>C,MODERATE,;ZDHHC23,missense_variant,p.G318R,ENST00000638807.2,c.952G>C,MODERATE,YES;ZDHHC23,missense_variant,p.G312R,ENST00000498275.5,c.934G>C,MODERATE,;ZDHHC23,missense_variant,p.G318R,ENST00000330212.7,c.952G>C,MODERATE, +ARSB 411 BI GRCh38 5 78964472 78964472 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 19 20 c.634A>G p.Thr212Ala p.T212A ENST00000264914.10 NM_000046.5 212 Aca/Gca 3/8 P1 C T/A protein_coding YES CCDS4043.1 634/1602 GTTTGTTGAAT PDB-ENSP_mappings:1fsu.A;Superfamily:SSF53649;Gene3D:3.40.720.10;Pfam:PF00884;PANTHER:PTHR10342;PANTHER:PTHR10342:SF255;CDD:cd16029 ENSP00000264914 3/8 ENST00000264914 Transcript 1.0 ENSG00000113273 HGNC:714 MODERATE NM_000046.5 missense_variant 1.0 benign(0.306) Unknown tolerated(0.1) P15848.201 ARSB HGNC -1 A0A024RAJ9.51 1.0 UPI00001260A3 P15848-1 SNV ARSB,missense_variant,p.T212A,ENST00000264914,NM_000046.5,c.634A>G,MODERATE,YES,tolerated(0.1),benign(0.306),-1;ARSB,missense_variant,p.T212A,ENST00000565165,,c.634A>G,MODERATE,,tolerated(0.06),benign(0.007),-1;ARSB,missense_variant,p.T212A,ENST00000396151,NM_198709.3,c.634A>G,MODERATE,,tolerated(0.06),benign(0.022),-1 696/4852 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 45 44ce22cc-5cdc-45eb-99b6-435f63087b7b 40 43cafceb-702a-4552-be57-644be101764f SUCCESS ARSB,missense_variant,p.T212A,ENST00000565165.2,c.634A>G,MODERATE,;ARSB,missense_variant,p.T212A,ENST00000396151.7,c.634A>G,MODERATE,;ARSB,missense_variant,p.T212A,ENST00000264914.10,c.634A>G,MODERATE,YES +FAM171A1 221061 BI GRCh38 10 15221055 15221055 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 21 14 c.760T>C p.Trp254Arg p.W254R ENST00000378116.9 NM_001010924.2 254 Tgg/Cgg 6/8 P1 G W/R protein_coding YES CCDS31154.1 760/2673 CAGCCACGTTC Pfam:PF10577;PANTHER:PTHR31626;PANTHER:PTHR31626:SF1 ENSP00000367356 6/8 ENST00000378116 Transcript ENSG00000148468 HGNC:23522 MODERATE NM_001010924.2 missense_variant 1.0 probably_damaging(0.995) Unknown deleterious(0) Q5VUB5.125 FAM171A1 HGNC -1 1.0 UPI00001414CA SNV FAM171A1,missense_variant,p.W254R,ENST00000378116,NM_001010924.2,c.760T>C,MODERATE,YES,deleterious(0),probably_damaging(0.995),-1;FAM171A1,non_coding_transcript_exon_variant,,ENST00000477161,,n.75T>C,MODIFIER,,,,-1 997/4182 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 27 44ce22cc-5cdc-45eb-99b6-435f63087b7b 35 43cafceb-702a-4552-be57-644be101764f SUCCESS FAM171A1,non_coding_transcript_exon_variant,,ENST00000477161.1,n.75T>C,MODIFIER,;FAM171A1,missense_variant,p.W254R,ENST00000378116.9,c.760T>C,MODERATE,YES +DDX51 317781 BI GRCh38 12 132140199 132140199 + synonymous_variant,splice_region_variant Silent SNP C C T rs1243377122 TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 20 18 c.1674G>A p.Leu558= p.L558= ENST00000397333.4 NM_175066.4 558 ctG/ctA 12/15 P1 T L protein_coding YES CCDS41865.1 1674/2001 ATGAGCCTGCC PROSITE_profiles:PS51194;CDD:cd18787;PANTHER:PTHR24031:SF68;PANTHER:PTHR24031;Gene3D:3.40.50.300;Pfam:PF00271;SMART:SM00490;Superfamily:SSF52540 ENSP00000380495 12/15 rs1243377122;COSV57959207 ENST00000397333 Transcript ENSG00000185163 HGNC:20082 LOW NM_175066.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS splice_region_variant 0;1 1.0 Unknown 0;1 Q8N8A6.151 DDX51 HGNC -1 1.0 UPI000049DD95 SNV DDX51,splice_region_variant,p.L558=,ENST00000397333,NM_175066.4,c.1674G>A,LOW,YES,,,-1;NOC4L,upstream_gene_variant,,ENST00000330579,NM_024078.3,,MODIFIER,YES,,,1;NOC4L,upstream_gene_variant,,ENST00000541954,,,MODIFIER,,,,1;DDX51,splice_region_variant,,ENST00000329073,,n.2170G>A,LOW,,,,-1;DDX51,splice_region_variant,,ENST00000541489,,n.320G>A,LOW,,,,-1;DDX51,upstream_gene_variant,,ENST00000462829,,,MODIFIER,,,,-1;DDX51,downstream_gene_variant,,ENST00000545991,,,MODIFIER,,,,-1;DDX51,downstream_gene_variant,,ENST00000546058,,,MODIFIER,,,,-1 1697/4702 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 38 44ce22cc-5cdc-45eb-99b6-435f63087b7b 38 43cafceb-702a-4552-be57-644be101764f SUCCESS DDX51,non_coding_transcript_exon_variant,,ENST00000329073.8,n.2170G>A,MODIFIER,;DDX51,non_coding_transcript_exon_variant,,ENST00000541489.5,n.320G>A,MODIFIER,;DDX51,synonymous_variant,splice_region_variant,p.L558=,ENST00000397333.4,c.1674G>A,LOW,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 31 11 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0 75 44ce22cc-5cdc-45eb-99b6-435f63087b7b 42 43cafceb-702a-4552-be57-644be101764f SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +SLC12A5 57468 BI GRCh38 20 46043903 46043903 + missense_variant Missense_Mutation SNP C C T rs1340483692 TCGA-V4-A9EU-01A TCGA-V4-A9EU-10A Somatic 58 31 c.1433C>T p.Ala478Val p.A478V ENST00000454036.6 NM_001134771.2 478 gCc/gTc 11/26 T A/V protein_coding YES CCDS46610.1 1433/3420 TGGGGCCTGCA Gene3D:1.20.1740.10;Pfam:PF00324;PANTHER:PTHR11827;PANTHER:PTHR11827:SF54;TIGRFAM:TIGR00930;Transmembrane_helices:TMhelix ENSP00000387694 11/26 rs1340483692 ENST00000454036 Transcript 1.0 ENSG00000124140 HGNC:13818 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.904) Unknown deleterious(0.01) Q9H2X9.164 SLC12A5 HGNC 1 5.0 UPI00015F4605 Q9H2X9-1 SNV SLC12A5,missense_variant,p.A455V,ENST00000243964,NM_020708.5,c.1364C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.508),1;SLC12A5,missense_variant,p.A478V,ENST00000454036,NM_001134771.2,c.1433C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.904),1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,,c.*682C>T,MODIFIER,,,,1;SLC12A5,intron_variant,,ENST00000616201,,c.1297+211C>T,MODIFIER,,,,1;SLC12A5,intron_variant,,ENST00000616202,,c.612+6518C>T,MODIFIER,,,,1;SLC12A5,intron_variant,,ENST00000626937,,c.509+6621C>T,MODIFIER,,,,1;SLC12A5,intron_variant,,ENST00000539566,,c.510-1975C>T,MODIFIER,,,,1;SLC12A5,downstream_gene_variant,,ENST00000372315,,,MODIFIER,,,,1;SLC12A5,downstream_gene_variant,,ENST00000608594,,,MODIFIER,,,,1;SLC12A5,downstream_gene_variant,,ENST00000622711,,,MODIFIER,,,,1;SLC12A5,downstream_gene_variant,,ENST00000625683,,,MODIFIER,,,,1;SLC12A5,upstream_gene_variant,,ENST00000626144,,,MODIFIER,,,,1;SLC12A5,downstream_gene_variant,,ENST00000629054,,,MODIFIER,,,,1 1509/3593 muse;mutect2;varscan2 df685f8c-645a-47ae-a471-63bf1973a0ae 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 112 44ce22cc-5cdc-45eb-99b6-435f63087b7b 89 43cafceb-702a-4552-be57-644be101764f SUCCESS SLC12A5,intron_variant,NMD_transcript_variant,,ENST00000539566.3,c.510-1975C>T,MODIFIER,;SLC12A5,missense_variant,p.A455V,ENST00000243964.7,c.1364C>T,MODERATE,YES;SLC12A5,3_prime_UTR_variant,,ENST00000616933.4,c.*682C>T,MODIFIER,;SLC12A5,intron_variant,,ENST00000626937.2,c.509+6621C>T,MODIFIER,;SLC12A5,intron_variant,,ENST00000616202.4,c.612+6518C>T,MODIFIER,;SLC12A5,missense_variant,p.A478V,ENST00000454036.6,c.1433C>T,MODERATE, +SLC23A3 151295 BI GRCh38 2 219168687 219168687 + synonymous_variant Silent SNP G G C novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 16 9 c.639C>G p.Ala213= p.A213= ENST00000409878.8 NM_001144889.2 213 gcC/gcG 5/12 P4 C A protein_coding CCDS46518.1 639/1833 AACTGGGCTAC Pfam:PF00860;PANTHER:PTHR11119;PANTHER:PTHR11119:SF57 ENSP00000386473 5/12 ENST00000409878 Transcript ENSG00000213901 HGNC:20601 LOW NM_001144889.2 synonymous_variant Unknown Q6PIS1.121 SLC23A3 HGNC -1 2.0 UPI0000049A90 Q6PIS1-1 SNV SLC23A3,synonymous_variant,p.A213=,ENST00000409878,NM_001144889.2,c.639C>G,LOW,,,,-1;SLC23A3,synonymous_variant,p.A221=,ENST00000455516,NM_001144890.2,c.663C>G,LOW,YES,,,-1;SLC23A3,synonymous_variant,p.A213=,ENST00000295738,NM_144712.5,c.639C>G,LOW,,,,-1;SLC23A3,synonymous_variant,p.A213=,ENST00000409370,,c.639C>G,LOW,,,,-1;SLC23A3,synonymous_variant,p.A168=,ENST00000430764,,c.504C>G,LOW,,,,-1;CNPPD1,downstream_gene_variant,,ENST00000360507,NM_001321390.2&NM_001321391.2&NM_015680.6,,MODIFIER,,,,-1;CNPPD1,downstream_gene_variant,,ENST00000409789,NM_001321389.1,,MODIFIER,YES,,,-1;CNPPD1,downstream_gene_variant,,ENST00000451647,,,MODIFIER,,,,-1;CNPPD1,downstream_gene_variant,,ENST00000453038,,,MODIFIER,,,,-1;SLC23A3,downstream_gene_variant,,ENST00000421779,,,MODIFIER,,,,-1;AC068946.1,3_prime_UTR_variant,,ENST00000318673,,c.*304C>G,MODIFIER,YES,,,-1;SLC23A3,3_prime_UTR_variant,,ENST00000414999,,c.*290C>G,MODIFIER,,,,-1;SLC23A3,non_coding_transcript_exon_variant,,ENST00000497918,,n.619C>G,MODIFIER,,,,-1;SLC23A3,non_coding_transcript_exon_variant,,ENST00000465580,,n.460C>G,MODIFIER,,,,-1;AC068946.1,intron_variant,,ENST00000498327,,n.1479+342C>G,MODIFIER,,,,-1;SLC23A3,downstream_gene_variant,,ENST00000461812,,,MODIFIER,,,,-1 684/2322 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 28 80f9a579-f252-4262-bbc1-3612fba48b47 25 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS SLC23A3,synonymous_variant,p.A168=,ENST00000430764.2,c.504C>G,LOW,;SLC23A3,non_coding_transcript_exon_variant,,ENST00000465580.3,n.460C>G,MODIFIER,;SLC23A3,synonymous_variant,p.A213=,ENST00000409370.6,c.639C>G,LOW,;SLC23A3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000414999.5,c.*290C>G,MODIFIER,;SLC23A3,non_coding_transcript_exon_variant,,ENST00000497918.5,n.619C>G,MODIFIER,;SLC23A3,synonymous_variant,p.A221=,ENST00000455516.6,c.663C>G,LOW,;SLC23A3,synonymous_variant,p.A213=,ENST00000295738.11,c.639C>G,LOW,;SLC23A3,synonymous_variant,p.A213=,ENST00000409878.8,c.639C>G,LOW,YES;ENSG00000280537,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000318673.6,c.*304C>G,MODIFIER,YES;ENSG00000280537,intron_variant,,ENST00000498327.5,n.1479+342C>G,MODIFIER, +USP13 8975 BI GRCh38 3 179730242 179730242 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 45 33 c.1142A>T p.Gln381Leu p.Q381L ENST00000263966.8 NM_003940.3 381 cAa/cTa 9/21 P1 T Q/L protein_coding YES CCDS3235.1 1142/2592 AACACAAGATT PROSITE_profiles:PS50235;CDD:cd02658;PANTHER:PTHR24006:SF682;PANTHER:PTHR24006;Pfam:PF00443;PIRSF:PIRSF016308;Gene3D:3.90.70.10;Superfamily:SSF54001 ENSP00000263966 9/21 ENST00000263966 Transcript ENSG00000058056 HGNC:12611 MODERATE NM_003940.3 missense_variant 1.0 possibly_damaging(0.83) Unknown tolerated(0.07) Q92995.172 USP13 HGNC 1 A0A0A6YZ17.43 1.0 UPI000006DC10 Q92995-1 SNV USP13,missense_variant,p.Q381L,ENST00000263966,NM_003940.3,c.1142A>T,MODERATE,YES,tolerated(0.07),possibly_damaging(0.83),1;USP13,missense_variant,p.Q316L,ENST00000496897,,c.947A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.83),1;USP13,missense_variant,p.Q27L,ENST00000497155,,c.80A>T,MODERATE,,tolerated(0.09),benign(0.033),1;USP13,non_coding_transcript_exon_variant,,ENST00000482333,,n.1318A>T,MODIFIER,,,,1 1328/8038 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 121 80f9a579-f252-4262-bbc1-3612fba48b47 78 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS USP13,non_coding_transcript_exon_variant,,ENST00000681533.1,n.84A>T,MODIFIER,;USP13,non_coding_transcript_exon_variant,,ENST00000679403.1,n.84A>T,MODIFIER,;USP13,missense_variant,p.Q27L,ENST00000497155.1,c.80A>T,MODERATE,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680605.1,c.*196A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680307.1,c.*205A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680031.1,c.*24A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681649.1,c.*205A>T,MODIFIER,;USP13,non_coding_transcript_exon_variant,,ENST00000679972.1,n.373A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680436.1,c.*46A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680651.1,c.*216A>T,MODIFIER,;USP13,missense_variant,p.Q66L,ENST00000679694.1,c.197A>T,MODERATE,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000679783.1,c.*261A>T,MODIFIER,;USP13,missense_variant,p.Q316L,ENST00000496897.5,c.947A>T,MODERATE,;USP13,missense_variant,p.Q381L,ENST00000680008.1,c.1142A>T,MODERATE,;USP13,non_coding_transcript_exon_variant,,ENST00000482333.5,n.1318A>T,MODIFIER,;USP13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681051.1,c.*24A>T,MODIFIER,;USP13,missense_variant,p.Q381L,ENST00000263966.8,c.1142A>T,MODERATE,YES;USP13,missense_variant,p.Q380L,ENST00000680587.1,c.1139A>T,MODERATE,;ENSG00000288698,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680408.1,c.*1357A>T,MODIFIER,YES +PCDHB7 56129 BI GRCh38 5 141174686 141174686 + synonymous_variant Silent SNP G G A rs1554280293 TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 124 24 c.1851G>A p.Val617= p.V617= ENST00000231137.6 NM_018940.4 617 gtG/gtA 1/1 P1 A V protein_coding YES CCDS4249.1 1851/2382 GGCGTGTGGGC CDD:cd11304;Gene3D:2.60.40.60;Pfam:PF00028;SMART:SM00112;Superfamily:SSF49313;PROSITE_profiles:PS50268;PANTHER:PTHR24028:SF69;PANTHER:PTHR24028 ENSP00000231137 1/1 rs1554280293 ENST00000231137 Transcript ENSG00000113212 HGNC:8692 LOW NM_018940.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant Unknown Q9Y5E2.157 PCDHB7 HGNC 1 UPI00001273E3 SNV PCDHB7,synonymous_variant,p.V617=,ENST00000231137,NM_018940.4,c.1851G>A,LOW,YES,,,1;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.5,,MODIFIER,YES,,,1;AC244517.11,intron_variant,,ENST00000624192,,n.73-37503C>T,MODIFIER,,,,-1;AC244517.8,upstream_gene_variant,,ENST00000623995,,,MODIFIER,YES,,,1;AC244517.2,upstream_gene_variant,,ENST00000624802,,,MODIFIER,,,,-1;AC244517.2,upstream_gene_variant,,ENST00000625128,,,MODIFIER,,,,-1 2043/3740 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 156 80f9a579-f252-4262-bbc1-3612fba48b47 148 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS PCDHB7,synonymous_variant,p.V617=,ENST00000231137.6,c.1851G>A,LOW,YES;ENSG00000280029,intron_variant,,ENST00000624192.1,n.73-37503C>T,MODIFIER,YES +CSMD3 114788 BI GRCh38 8 112682591 112682591 + missense_variant Missense_Mutation SNP G G A rs1336806392 TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 133 31 c.2528C>T p.Ala843Val p.A843V ENST00000297405.10 NM_001363185.1 843 gCa/gTa 16/71 P1 A A/V protein_coding YES CCDS6315.1 2528/11124 GCCGTGCATTG Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR45656;PANTHER:PTHR45656:SF9;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000297405 16/71 rs1336806392 ENST00000297405 Transcript 1.0 ENSG00000164796 HGNC:19291 MODERATE NM_198123.2 8.806e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q7Z407.139 CSMD3 HGNC -1 1.0 UPI00001E0584 Q7Z407-1 SNV CSMD3,missense_variant,p.A843V,ENST00000297405,NM_001363185.1&NM_198123.2,c.2528C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;CSMD3,missense_variant,p.A803V,ENST00000343508,NM_198124.2,c.2408C>T,MODERATE,,deleterious(0),probably_damaging(0.921),-1;CSMD3,missense_variant,p.A739V,ENST00000455883,NM_052900.3,c.2216C>T,MODERATE,,deleterious(0),probably_damaging(0.998),-1;CSMD3,missense_variant,p.A183V,ENST00000339701,,c.548C>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1 2613/13052 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 3.981e-06 0.0 0.0 0.0 0.0 0.0 8.806e-06 0.0 0.0 0 128 80f9a579-f252-4262-bbc1-3612fba48b47 164 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS CSMD3,missense_variant,p.A739V,ENST00000455883.2,c.2216C>T,MODERATE,;CSMD3,missense_variant,p.A183V,ENST00000339701.7,c.548C>T,MODERATE,;CSMD3,missense_variant,p.A803V,ENST00000343508.7,c.2408C>T,MODERATE,;CSMD3,missense_variant,p.A843V,ENST00000297405.10,c.2528C>T,MODERATE,YES +RABL6 55684 BI GRCh38 9 136839857 136839857 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 4 11 c.1922G>C p.Ser641Thr p.S641T ENST00000311502.12 NM_024718.5 641 aGt/aCt 13/15 P3 C S/T protein_coding CCDS48058.1 1922/2190 GAGCAGTGAGG PANTHER:PTHR14932;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000311134 13/15 ENST00000311502 Transcript 1.0 ENSG00000196642 HGNC:24703 MODERATE NM_024718.5 missense_variant possibly_damaging(0.453) Unknown deleterious_low_confidence(0.01) Q3YEC7.144 RABL6 HGNC 1 1.0 UPI0000210F94 Q3YEC7-1 SNV RABL6,missense_variant,p.S641T,ENST00000311502,NM_024718.5,c.1922G>C,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.453),1;RABL6,missense_variant,p.S642T,ENST00000371663,NM_001173988.2,c.1925G>C,MODERATE,YES,deleterious_low_confidence(0.01),possibly_damaging(0.655),1;RABL6,intron_variant,,ENST00000357466,,c.1080-628G>C,MODIFIER,,,,1;AJM1,upstream_gene_variant,,ENST00000436881,NM_001080482.4,,MODIFIER,YES,,,1;RABL6,downstream_gene_variant,,ENST00000629216,,,MODIFIER,,,,1;RABL6,downstream_gene_variant,,ENST00000461992,,,MODIFIER,,,,1;RABL6,3_prime_UTR_variant,,ENST00000464941,,c.*300G>C,MODIFIER,,,,1;RABL6,3_prime_UTR_variant,,ENST00000484471,,c.*127G>C,MODIFIER,,,,1;RABL6,non_coding_transcript_exon_variant,,ENST00000435930,,n.3288G>C,MODIFIER,,,,1;RABL6,downstream_gene_variant,,ENST00000466096,,,MODIFIER,,,,1 2171/3104 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 18 80f9a579-f252-4262-bbc1-3612fba48b47 15 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS RABL6,non_coding_transcript_exon_variant,,ENST00000435930.1,n.3288G>C,MODIFIER,;RABL6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000464941.5,c.*300G>C,MODIFIER,;RABL6,intron_variant,,ENST00000357466.6,c.1080-628G>C,MODIFIER,;RABL6,missense_variant,p.S642T,ENST00000371663.10,c.1925G>C,MODERATE,;RABL6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000484471.6,c.*127G>C,MODIFIER,;RABL6,missense_variant,p.S641T,ENST00000311502.12,c.1922G>C,MODERATE,YES +LRRTM3 347731 BI GRCh38 10 66927873 66927873 + missense_variant Missense_Mutation SNP T T A novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 60 14 c.957T>A p.Asn319Lys p.N319K ENST00000361320.5 NM_178011.5 319 aaT/aaA 2/3 P1 A N/K protein_coding YES CCDS7270.1 957/1746 AGAAATATTTG Gene3D:3.80.10.10;PANTHER:PTHR24373;PANTHER:PTHR24373:SF296;Superfamily:SSF52058 ENSP00000355187 2/3 ENST00000361320 Transcript ENSG00000198739 HGNC:19410 MODERATE NM_178011.5 missense_variant 1.0 benign(0.009) Unknown tolerated(0.49) Q86VH5.146 LRRTM3 HGNC 1 1.0 UPI0000088C0F Q86VH5-1 SNV LRRTM3,missense_variant,p.N319K,ENST00000361320,NM_178011.5,c.957T>A,MODERATE,YES,tolerated(0.49),benign(0.009),1;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2&NM_013266.4,c.1048-152349A>T,MODIFIER,YES,,,-1;CTNNA3,intron_variant,,ENST00000494580,,c.128-152349A>T,MODIFIER,,,,-1 1505/6049 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 86 80f9a579-f252-4262-bbc1-3612fba48b47 74 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS LRRTM3,missense_variant,p.N319K,ENST00000361320.5,c.957T>A,MODERATE,YES;CTNNA3,intron_variant,NMD_transcript_variant,,ENST00000682166.1,c.*744-1661A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000683771.1,n.573-152349A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000494580.1,c.128-152349A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000683272.1,n.1242-152349A>T,MODIFIER,;CTNNA3,intron_variant,NMD_transcript_variant,,ENST00000683624.1,c.*744-152349A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000682945.1,c.1048-152349A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000433211.7,c.1048-152349A>T,MODIFIER,YES;CTNNA3,intron_variant,,ENST00000682758.1,c.1048-152349A>T,MODIFIER,;CTNNA3,intron_variant,,ENST00000684154.1,c.1048-152349A>T,MODIFIER,;CTNNA3,intron_variant,NMD_transcript_variant,,ENST00000683963.1,c.*572-152349A>T,MODIFIER, +PYROXD2 84795 BI GRCh38 10 98387300 98387300 + synonymous_variant Silent SNP A A G novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 24 18 c.1455T>C p.Asp485= p.D485= ENST00000370575.5 NM_032709.3 485 gaT/gaC 14/16 P1 G D protein_coding YES CCDS7474.1 1455/1746 ATGCAATCAAA PANTHER:PTHR10668:SF103;PANTHER:PTHR10668 ENSP00000359607 14/16 ENST00000370575 Transcript ENSG00000119943 HGNC:23517 LOW NM_032709.3 synonymous_variant 1.0 Unknown Q8N2H3.142 PYROXD2 HGNC -1 1.0 UPI000013CA6A SNV PYROXD2,synonymous_variant,p.D485=,ENST00000370575,NM_032709.3,c.1455T>C,LOW,YES,,,-1;PYROXD2,non_coding_transcript_exon_variant,,ENST00000483923,,n.2341T>C,MODIFIER,,,,-1;PYROXD2,non_coding_transcript_exon_variant,,ENST00000464808,,n.311T>C,MODIFIER,,,,-1 1502/2023 muse;mutect2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 65 80f9a579-f252-4262-bbc1-3612fba48b47 42 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS PYROXD2,non_coding_transcript_exon_variant,,ENST00000464808.1,n.311T>C,MODIFIER,;PYROXD2,synonymous_variant,p.D485=,ENST00000370575.5,c.1455T>C,LOW,YES;PYROXD2,non_coding_transcript_exon_variant,,ENST00000483923.5,n.2341T>C,MODIFIER, +BLOC1S6 26258 BI GRCh38 15 45592274 45592274 + synonymous_variant,splice_region_variant Silent SNP C C T novel TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 27 24 c.222C>T p.Leu74= p.L74= ENST00000220531.9 NM_012388.4 74 ctC/ctT 2/5 P1 T L protein_coding CCDS10126.1 222/519 GAACTCACGTA Pfam:PF14712;PIRSF:PIRSF037609;PANTHER:PTHR31328;CDD:cd14582 ENSP00000220531 2/5 ENST00000220531 Transcript 1.0 ENSG00000104164 HGNC:8549 LOW NM_012388.4 splice_region_variant Unknown Q9UL45.163 BLOC1S6 HGNC 1 1.0 UPI000004A0B2 Q9UL45-1 SNV BLOC1S6,splice_region_variant,,ENST00000568816,,c.-244C>T,LOW,,,,1;BLOC1S6,splice_region_variant,p.L79=,ENST00000565323,NM_001311255.1&NM_001311256.1,c.237C>T,LOW,YES,,,1;BLOC1S6,splice_region_variant,p.L74=,ENST00000220531,NM_012388.4,c.222C>T,LOW,,,,1;BLOC1S6,splice_region_variant,,ENST00000564765,,c.-70C>T,LOW,,,,1;BLOC1S6,splice_region_variant,,ENST00000565409,,c.-70C>T,LOW,,,,1;BLOC1S6,intron_variant,,ENST00000562384,,c.-80+4749C>T,MODIFIER,,,,1;AC090527.2,intron_variant,,ENST00000564080,,c.-18+4749C>T,MODIFIER,YES,,,1;BLOC1S6,intron_variant,,ENST00000565216,,c.82+4749C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000566801,,c.-68+4478C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000567461,,c.-68+4749C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000569076,,c.-44+4749C>T,MODIFIER,,,,1;Y_RNA,downstream_gene_variant,,ENST00000363549,,,MODIFIER,YES,,,1;BLOC1S6,splice_region_variant,,ENST00000563160,,n.191C>T,LOW,,,,1;BLOC1S6,intron_variant,,ENST00000563000,,n.237+4478C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000565727,,n.105+4398C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000567740,,n.312+4749C>T,MODIFIER,,,,1;BLOC1S6,splice_region_variant,,ENST00000566753,,n.311C>T,LOW,,,,1;BLOC1S6,splice_region_variant,p.L74=,ENST00000567523,,c.222C>T,LOW,,,,1;BLOC1S6,splice_region_variant,p.L74=,ENST00000568597,,c.222C>T,LOW,,,,1;BLOC1S6,splice_region_variant,p.L52=,ENST00000564310,,c.156C>T,LOW,,,,1;BLOC1S6,splice_region_variant,,ENST00000672455,,c.*196C>T,LOW,,,,1;BLOC1S6,intron_variant,,ENST00000566184,,n.147+4749C>T,MODIFIER,,,,1;BLOC1S6,intron_variant,,ENST00000568963,,c.82+4749C>T,MODIFIER,,,,1 287/3778 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 60 80f9a579-f252-4262-bbc1-3612fba48b47 51 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS BLOC1S6,5_prime_UTR_variant,,ENST00000564765.1,c.-70C>T,MODIFIER,;BLOC1S6,5_prime_UTR_variant,,ENST00000565409.5,c.-70C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000565727.5,n.105+4398C>T,MODIFIER,;BLOC1S6,non_coding_transcript_exon_variant,,ENST00000563160.5,n.191C>T,MODIFIER,;BLOC1S6,5_prime_UTR_variant,,ENST00000568816.5,c.-244C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000566801.5,c.-68+4478C>T,MODIFIER,;BLOC1S6,synonymous_variant,splice_region_variant,p.L79=,ENST00000565323.6,c.237C>T,LOW,;BLOC1S6,intron_variant,,ENST00000563000.5,n.237+4478C>T,MODIFIER,;BLOC1S6,missense_variant,splice_region_variant,NMD_transcript_variant,p.S52L,ENST00000564310.2,c.155C>T,MODERATE,;BLOC1S6,intron_variant,,ENST00000565216.5,c.82+4749C>T,MODIFIER,;BLOC1S6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000672455.1,c.*196C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000566184.1,n.147+4749C>T,MODIFIER,;BLOC1S6,synonymous_variant,splice_region_variant,NMD_transcript_variant,p.L74=,ENST00000567523.5,c.222C>T,LOW,;BLOC1S6,synonymous_variant,splice_region_variant,p.L74=,ENST00000220531.9,c.222C>T,LOW,YES;BLOC1S6,synonymous_variant,splice_region_variant,NMD_transcript_variant,p.L74=,ENST00000568597.5,c.222C>T,LOW,;BLOC1S6,non_coding_transcript_exon_variant,,ENST00000566753.5,n.311C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000569076.5,c.-44+4749C>T,MODIFIER,;BLOC1S6,intron_variant,NMD_transcript_variant,,ENST00000568963.5,c.82+4749C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000562384.5,c.-80+4749C>T,MODIFIER,;ENSG00000260170,intron_variant,,ENST00000564080.1,c.-18+4749C>T,MODIFIER,YES;BLOC1S6,intron_variant,,ENST00000567461.5,c.-68+4749C>T,MODIFIER,;BLOC1S6,intron_variant,,ENST00000567740.5,n.312+4749C>T,MODIFIER, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9ET-01A TCGA-V4-A9ET-10A Somatic 35 26 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 5383fb57-69c2-4b34-af7f-c67208efb2b5 0 68 80f9a579-f252-4262-bbc1-3612fba48b47 61 9848f103-835a-4e3b-8719-88a893ef725d SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 39 28 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 69 4cce1c83-aca5-4466-ae62-e8b73481597d 67 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +ITPR3 3710 BI GRCh38 6 33687044 33687044 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 33 64 c.6015G>A p.Glu2005= p.E2005= ENST00000374316.9 2005 gaG/gaA 45/59 P1 A E protein_coding YES CCDS4783.1 6015/8016 ATGGAGAGCCG PDB-ENSP_mappings:6dqj.A;PDB-ENSP_mappings:6dqj.B;PDB-ENSP_mappings:6dqj.C;PDB-ENSP_mappings:6dqj.D;PDB-ENSP_mappings:6dqn.A;PDB-ENSP_mappings:6dqn.B;PDB-ENSP_mappings:6dqn.C;PDB-ENSP_mappings:6dqn.D;PDB-ENSP_mappings:6dqs.A;PDB-ENSP_mappings:6dqs.B;PDB-ENSP_mappings:6dqs.C;PDB-ENSP_mappings:6dqs.D;PDB-ENSP_mappings:6dqv.A;PDB-ENSP_mappings:6dqv.B;PDB-ENSP_mappings:6dqv.C;PDB-ENSP_mappings:6dqv.D;PDB-ENSP_mappings:6dqz.A;PDB-ENSP_mappings:6dqz.B;PDB-ENSP_mappings:6dqz.C;PDB-ENSP_mappings:6dqz.D;PDB-ENSP_mappings:6dr0.A;PDB-ENSP_mappings:6dr0.B;PDB-ENSP_mappings:6dr0.C;PDB-ENSP_mappings:6dr0.D;PDB-ENSP_mappings:6dr2.A;PDB-ENSP_mappings:6dr2.B;PDB-ENSP_mappings:6dr2.C;PDB-ENSP_mappings:6dr2.D;PDB-ENSP_mappings:6dra.A;PDB-ENSP_mappings:6dra.B;PDB-ENSP_mappings:6dra.C;PDB-ENSP_mappings:6dra.D;PDB-ENSP_mappings:6drc.A;PDB-ENSP_mappings:6drc.B;PDB-ENSP_mappings:6drc.C;PDB-ENSP_mappings:6drc.D;PDB-ENSP_mappings:6uqk.A;PDB-ENSP_mappings:6uqk.B;PDB-ENSP_mappings:6uqk.C;PDB-ENSP_mappings:6uqk.D;PANTHER:PTHR45816;PANTHER:PTHR45816:SF1 ENSP00000363435 45/59 ENST00000374316 Transcript 1.0 ENSG00000096433 HGNC:6182 LOW synonymous_variant 1.0 Unknown Q14573.197 ITPR3 HGNC 1 5.0 UPI000013CB74 SNV ITPR3,synonymous_variant,p.E2005=,ENST00000374316,,c.6015G>A,LOW,YES,,,1;ITPR3,synonymous_variant,p.E2005=,ENST00000605930,NM_002224.4,c.6015G>A,LOW,,,,1 7075/9870 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 6.762610155419679e-06 0.0 0.0 0.0 0.0 0.0002017759979935 0.0 0.0 0.0 0.0 0.0 0 83 4cce1c83-aca5-4466-ae62-e8b73481597d 97 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS ITPR3,synonymous_variant,p.E2005=,ENST00000605930.3,c.6015G>A,LOW,YES;ITPR3,synonymous_variant,p.E2005=,ENST00000374316.9,c.6015G>A,LOW, +C6orf89 221477 BI GRCh38 6 36914612 36914612 + missense_variant Missense_Mutation SNP C C T rs753250574 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 85 135 c.614C>T p.Ala205Val p.A205V ENST00000373685.1 205 gCg/gTg 6/9 P4 T A/V protein_coding CCDS69100.1 614/1044 TGAGGCGACAG COSM4667953 PANTHER:PTHR35259 ENSP00000362789 6/9 rs753250574;COSV62101231 ENST00000373685 Transcript ENSG00000198663 HGNC:21114 MODERATE 9.67e-05 gnomAD_NFE missense_variant 0;1 benign(0) Unknown tolerated(0.59) 0;1 Q6UWU4.115 C6orf89 HGNC 1 A0A024RCY0.28 5.0 UPI0000048F18 Q6UWU4-1 SNV C6orf89,missense_variant,p.A205V,ENST00000480824,NM_001286635.2,c.614C>T,MODERATE,,tolerated(0.59),benign(0),1;C6orf89,missense_variant,p.A99V,ENST00000359359,NM_001286636.2&NM_001286637.2,c.296C>T,MODERATE,,tolerated(0.55),benign(0),1;C6orf89,missense_variant,p.A205V,ENST00000373685,,c.614C>T,MODERATE,,tolerated(0.59),benign(0),1;C6orf89,missense_variant,p.A212V,ENST00000355190,NM_152734.4,c.635C>T,MODERATE,YES,tolerated(0.59),benign(0),1 889/1400 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 5.567e-05 6.152e-05 0.0 0.0 5.437e-05 0.0 9.67e-05 0.0 3.266e-05 4.05509999836795e-05 2.4310800654347983e-05 0.0 0.0 0.0 0.0 0.0 nfe 7.714860112173483e-05 0.0 7.714860112173483e-05 0.0 0.0 0 150 4cce1c83-aca5-4466-ae62-e8b73481597d 220 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS C6orf89,missense_variant,p.A205V,ENST00000480824.7,c.614C>T,MODERATE,YES;C6orf89,missense_variant,p.A205V,ENST00000373685.1,c.614C>T,MODERATE,;C6orf89,missense_variant,p.A212V,ENST00000355190.7,c.635C>T,MODERATE,;C6orf89,missense_variant,p.A99V,ENST00000359359.6,c.296C>T,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 44 42 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 0 93 4cce1c83-aca5-4466-ae62-e8b73481597d 86 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +DSCAML1 57453 BI GRCh38 11 117437242 117437242 + missense_variant Missense_Mutation SNP C C T rs527533395 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 36 7 c.4600G>A p.Gly1534Arg p.G1534R ENST00000651296.2 NM_020693.4 1534 Ggg/Agg 26/33 P1 T G/R protein_coding YES CCDS8384.1 4780/6342 CTCCCCGGAGC PROSITE_profiles:PS50853;CDD:cd00063;PANTHER:PTHR13817;PANTHER:PTHR13817:SF54;Gene3D:2.60.40.10;SMART:SM00060;Superfamily:SSF49265 ENSP00000315465 26/33 rs527533395 ENST00000321322 Transcript ENSG00000177103 HGNC:14656 MODERATE 0.0001446 gnomAD_AMR missense_variant 1.0 benign(0.375) Unknown tolerated(0.46) DSCAML1 HGNC -1 A0A384DVL8.11 1.0 UPI00000726E2 SNV DSCAML1,missense_variant,p.G1594R,ENST00000321322,,c.4780G>A,MODERATE,YES,tolerated(0.46),benign(0.375),-1;DSCAML1,missense_variant,p.G1534R,ENST00000651296,NM_020693.4,c.4600G>A,MODERATE,,tolerated(0.41),benign(0.003),-1;DSCAML1,missense_variant,p.G1594R,ENST00000651172,,c.4780G>A,MODERATE,,tolerated(0.46),benign(0.375),-1;DSCAML1,missense_variant,p.G1324R,ENST00000527706,,c.3970G>A,MODERATE,,tolerated(0.43),benign(0.009),-1 4782/6899 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 5.17e-05 6.152e-05 0.0001446 0.0 0.0 0.0 3.517e-05 0.0 9.799e-05 2.7032499929191545e-05 2.4315499103977345e-05 0.0 0.0 0.0 0.0 0.0 sas 0.0006249999860301 0.0 0.0 0.0 0.0006249999860301 0 90 4cce1c83-aca5-4466-ae62-e8b73481597d 43 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS DSCAML1,missense_variant,p.G1594R,ENST00000651172.1,c.4780G>A,MODERATE,;DSCAML1,missense_variant,p.G1324R,ENST00000527706.5,c.3970G>A,MODERATE,;DSCAML1,missense_variant,p.G1594R,ENST00000321322.6,c.4780G>A,MODERATE,;DSCAML1,missense_variant,p.G1534R,ENST00000651296.2,c.4600G>A,MODERATE,YES +ACVRL1 94 BI GRCh38 12 51915385 51915385 + synonymous_variant Silent SNP G G A rs779758131 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 22 14 c.933G>A p.Ala311= p.A311= ENST00000388922.9 NM_000020.3 311 gcG/gcA 7/10 P1 A A protein_coding CCDS31804.1 933/1512 CTGGCGCACCT PDB-ENSP_mappings:3my0.A;PDB-ENSP_mappings:3my0.B;PDB-ENSP_mappings:3my0.C;PDB-ENSP_mappings:3my0.D;PDB-ENSP_mappings:3my0.E;PDB-ENSP_mappings:3my0.F;PDB-ENSP_mappings:3my0.G;PDB-ENSP_mappings:3my0.H;PDB-ENSP_mappings:3my0.I;PDB-ENSP_mappings:3my0.J;PDB-ENSP_mappings:3my0.K;PDB-ENSP_mappings:3my0.L;PDB-ENSP_mappings:3my0.M;PDB-ENSP_mappings:3my0.N;PDB-ENSP_mappings:3my0.O;PDB-ENSP_mappings:3my0.P;PDB-ENSP_mappings:3my0.Q;PDB-ENSP_mappings:3my0.R;PDB-ENSP_mappings:3my0.S;PDB-ENSP_mappings:3my0.T;PDB-ENSP_mappings:3my0.U;PDB-ENSP_mappings:3my0.V;PDB-ENSP_mappings:3my0.W;PDB-ENSP_mappings:3my0.X;PANTHER:PTHR23255;PANTHER:PTHR23255:SF66;PROSITE_profiles:PS50011;Superfamily:SSF56112;Gene3D:1.10.510.10;Pfam:PF07714;CDD:cd14142 ENSP00000373574 7/10 rs779758131 ENST00000388922 Transcript 1.0 ENSG00000139567 HGNC:175 LOW NM_000020.3 7.941e-05 gnomAD_NFE synonymous_variant Unknown P37023.217 ACVRL1 HGNC 1 A0A0S2Z310.23 1.0 UPI000000D9F4 SNV ACVRL1,synonymous_variant,p.A311=,ENST00000388922,NM_000020.3&NM_001077401.2,c.933G>A,LOW,,,,1;ACVRL1,synonymous_variant,p.A325=,ENST00000550683,,c.975G>A,LOW,YES,,,1;ACVRL1,synonymous_variant,p.A137=,ENST00000419526,,c.411G>A,LOW,,,,1;ACVRL1,downstream_gene_variant,,ENST00000547400,,,MODIFIER,,,,1;ACVRL1,downstream_gene_variant,,ENST00000551576,,,MODIFIER,,,,1;ACVRL1,upstream_gene_variant,,ENST00000552678,,,MODIFIER,,,,1;ACVRL1,upstream_gene_variant,,ENST00000547632,,,MODIFIER,,,,1 1130/4177 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 3.986e-05 0.0 2.892e-05 0.0 0.0 0.0 7.941e-05 0.0 0.0 2.027469963650219e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.628489841707051e-05 0.0 4.628489841707051e-05 0.0 0.0 0 42 4cce1c83-aca5-4466-ae62-e8b73481597d 36 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS ACVRL1,synonymous_variant,p.A137=,ENST00000419526.6,c.411G>A,LOW,;ACVRL1,synonymous_variant,p.A325=,ENST00000550683.5,c.975G>A,LOW,;ACVRL1,synonymous_variant,p.A221=,ENST00000547400.6,c.663G>A,LOW,;ACVRL1,synonymous_variant,p.A311=,ENST00000552678.2,c.933G>A,LOW,;ACVRL1,synonymous_variant,p.A311=,ENST00000388922.9,c.933G>A,LOW,YES;ACVRL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713618.1,c.*161G>A,MODIFIER,;ACVRL1,synonymous_variant,p.A276=,ENST00000713619.1,c.828G>A,LOW,;ACVRL1,synonymous_variant,p.A311=,ENST00000551576.6,c.933G>A,LOW, +TBX6 6911 BI GRCh38 16 30090818 30090818 + missense_variant Missense_Mutation SNP C C T rs767360040 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 19 25 c.293G>A p.Arg98Gln p.R98Q ENST00000279386.6 98 cGg/cAg 2/8 P1 T R/Q protein_coding CCDS10670.1 293/1311 GCTCCCGGTTC Gene3D:2.60.40.820;Pfam:PF00907;PROSITE_profiles:PS50252;PANTHER:PTHR11267;PANTHER:PTHR11267:SF100;SMART:SM00425;Superfamily:SSF49417;CDD:cd00182 ENSP00000279386 2/8 rs767360040 ENST00000279386 Transcript 1.0 ENSG00000149922 HGNC:11605 MODERATE 9.254e-06 gnomAD_NFE missense_variant benign(0) Unknown tolerated(0.41) O95947.179 TBX6 HGNC -1 1.0 UPI000013DBC7 O95947-1 SNV TBX6,missense_variant,p.R98Q,ENST00000553607,,c.293G>A,MODERATE,,tolerated(0.29),benign(0),-1;TBX6,missense_variant,p.R98Q,ENST00000395224,NM_004608.4,c.293G>A,MODERATE,YES,tolerated(0.41),benign(0),-1;TBX6,missense_variant,p.R98Q,ENST00000279386,,c.293G>A,MODERATE,,tolerated(0.41),benign(0),-1;TBX6,missense_variant,p.R98Q,ENST00000627355,,c.293G>A,MODERATE,,tolerated(0.45),benign(0.003),-1;YPEL3,downstream_gene_variant,,ENST00000398838,NM_001145524.2,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000398841,NM_031477.5,,MODIFIER,YES,,,-1;YPEL3,downstream_gene_variant,,ENST00000562641,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000563788,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000565110,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000566134,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000566595,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000565479,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000568674,,,MODIFIER,,,,-1;TBX6,missense_variant,p.R98Q,ENST00000567664,,c.293G>A,MODERATE,,tolerated(0.29),benign(0),-1;YPEL3,downstream_gene_variant,,ENST00000566401,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000568681,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000570099,,,MODIFIER,,,,-1 349/1796 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 4.174e-06 0.0 0.0 0.0 0.0 0.0 9.254e-06 0.0 0.0 6.758220024494221e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 41 4cce1c83-aca5-4466-ae62-e8b73481597d 44 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS TBX6,missense_variant,p.R98Q,ENST00000553607.1,c.293G>A,MODERATE,;TBX6,missense_variant,NMD_transcript_variant,p.R98Q,ENST00000567664.5,c.293G>A,MODERATE,;TBX6,missense_variant,p.R98Q,ENST00000279386.6,c.293G>A,MODERATE,;TBX6,missense_variant,p.R98Q,ENST00000395224.7,c.293G>A,MODERATE,YES +CRISPLD2 83716 BI GRCh38 16 84906620 84906620 + missense_variant Missense_Mutation SNP G G A rs147087796 TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 65 13 c.1472G>A p.Arg491Gln p.R491Q ENST00000262424.10 NM_031476.4 491 cGg/cAg 15/15 0.0002 0.0 0.0014 0.0 0.0 0.0 P4 A R/Q protein_coding YES CCDS10949.1 1472/1494 CTTCCGGATCT Gene3D:2.170.130.20;Superfamily:SSF69848 ENSP00000262424 0.0002274 0.0 15/15 rs147087796 ENST00000262424 Transcript ENSG00000103196 HGNC:25248 MODERATE NM_031476.4 0.0014 AMR missense_variant 1.0 possibly_damaging(0.632) Unknown deleterious(0.02) Q9H0B8.138 CRISPLD2 HGNC 1 A0A140VK80.23 1.0 UPI00000411B0 Q9H0B8-1 SNV CRISPLD2,missense_variant,p.R491Q,ENST00000262424,NM_031476.4,c.1472G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.632),1;CRISPLD2,missense_variant,p.R490Q,ENST00000567845,,c.1469G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.893),1;CRISPLD2,intron_variant,,ENST00000566165,,c.121-13020G>A,MODIFIER,,,,1 1695/4583 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 5.567e-05 0.0 0.0001445 0.0 5.437e-05 0.0 6.154e-05 0.0001629 0.0 9.46533982641995e-05 9.72951966105029e-05 0.0 0.0005302929785102 0.0 0.0 0.0 amr 0.0005302929785102 0.0 0.0 0.0004945599939674 0.0002085940068354 0 92 4cce1c83-aca5-4466-ae62-e8b73481597d 78 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS CRISPLD2,intron_variant,NMD_transcript_variant,,ENST00000566165.1,c.121-13020G>A,MODIFIER,;CRISPLD2,missense_variant,p.R490Q,ENST00000567845.5,c.1469G>A,MODERATE,;CRISPLD2,missense_variant,p.R491Q,ENST00000262424.10,c.1472G>A,MODERATE,YES +ZSWIM1 140831 BI GRCh38 20 45882692 45882692 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 46 5 c.100A>G p.Met34Val p.M34V ENST00000372523.1 NM_080752.4 34/485 P1 G M/V protein_coding CCDS13382.2 100/1458 TGACAATGCTG PANTHER:PTHR31569;PANTHER:PTHR31569:SF0 ENSP00000361598 2/3 ENST00000372520 Transcript ENSG00000168612 HGNC:16155 MODERATE missense_variant benign(0) Unknown tolerated(0.5) Q9BR11.125 ZSWIM1 HGNC 1 1.0 UPI0000470896 SNV ZSWIM1,missense_variant,p.M34V,ENST00000372523,NM_080603.5,c.100A>G,MODERATE,YES,tolerated(0.5),benign(0),1;ZSWIM1,missense_variant,p.M34V,ENST00000372520,,c.100A>G,MODERATE,,tolerated(0.5),benign(0),1;ZSWIM3,downstream_gene_variant,,ENST00000255152,NM_080752.4,,MODIFIER,YES,,,1;SPATA25,downstream_gene_variant,,ENST00000372519,NM_080608.4,,MODIFIER,YES,,,-1 181/2168 mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 0 58 4cce1c83-aca5-4466-ae62-e8b73481597d 52 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS ZSWIM1,missense_variant,p.M34V,ENST00000372523.1,c.100A>G,MODERATE,YES +MORC2 22880 BI GRCh38 22 30936586 30936586 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EA-01A TCGA-V4-A9EA-10A Somatic 66 63 c.1662G>A p.Met554Ile p.M554I ENST00000397641.8 NM_001303256.3 554 atG/atA 17/26 P1 T M/I protein_coding YES CCDS77668.1 1662/3099 GTCTTCATGTC PDB-ENSP_mappings:5of9.A;PDB-ENSP_mappings:5of9.B;PDB-ENSP_mappings:5ofa.A;PDB-ENSP_mappings:5ofa.B;PDB-ENSP_mappings:5ofb.A;PDB-ENSP_mappings:5ofb.B;Coiled-coils_(Ncoils):Coil;PANTHER:PTHR23337;PANTHER:PTHR23337:SF7;MobiDB_lite:mobidb-lite ENSP00000380763 17/26 ENST00000397641 Transcript 1.0 ENSG00000133422 HGNC:23573 MODERATE NM_001303256.3 missense_variant 1.0 benign(0) Unknown tolerated(0.22) Q9Y6X9.178 MORC2 HGNC -1 5.0 UPI000041AB7E Q9Y6X9-1 SNV MORC2,missense_variant,p.M554I,ENST00000397641,NM_001303256.3&NM_001303257.2,c.1662G>A,MODERATE,YES,tolerated(0.22),benign(0),-1;MORC2,missense_variant,p.M492I,ENST00000215862,NM_014941.3,c.1476G>A,MODERATE,,tolerated(0.45),benign(0),-1;MORC2,upstream_gene_variant,,ENST00000445980,,,MODIFIER,,,,-1;MORC2,non_coding_transcript_exon_variant,,ENST00000675601,,n.1504G>A,MODIFIER,,,,-1;MORC2,non_coding_transcript_exon_variant,,ENST00000469915,,n.587G>A,MODIFIER,,,,-1;MORC2,non_coding_transcript_exon_variant,,ENST00000674576,,n.3108G>A,MODIFIER,,,,-1;MORC2,non_coding_transcript_exon_variant,,ENST00000676215,,n.2505G>A,MODIFIER,,,,-1;MORC2,non_coding_transcript_exon_variant,,ENST00000675317,,n.83G>A,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000674585,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000675027,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000675402,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000675570,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000675779,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000675798,,,MODIFIER,,,,-1;MORC2,upstream_gene_variant,,ENST00000676263,,,MODIFIER,,,,-1;MORC2-AS1,downstream_gene_variant,,ENST00000441558,,,MODIFIER,,,,1 2547/5657 muse;mutect2;varscan2 a9fe64a9-6d22-4e9f-96f3-f16af7d298f8 0 123 4cce1c83-aca5-4466-ae62-e8b73481597d 129 7cf1f05c-0011-41cc-b8be-2cbd69838e3c SUCCESS MORC2,non_coding_transcript_exon_variant,,ENST00000469915.1,n.587G>A,MODIFIER,;MORC2,non_coding_transcript_exon_variant,,ENST00000675317.1,n.83G>A,MODIFIER,;MORC2,non_coding_transcript_exon_variant,,ENST00000676215.1,n.2505G>A,MODIFIER,;MORC2,non_coding_transcript_exon_variant,,ENST00000675601.1,n.1504G>A,MODIFIER,;MORC2,non_coding_transcript_exon_variant,,ENST00000674576.1,n.3108G>A,MODIFIER,;MORC2,missense_variant,p.M492I,ENST00000215862.8,c.1476G>A,MODERATE,;MORC2,missense_variant,p.M554I,ENST00000397641.8,c.1662G>A,MODERATE,YES +VASH2 79805 BI GRCh38 1 212972662 212972662 + missense_variant Missense_Mutation SNP G G T TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 39 28 c.580G>T p.Val194Phe p.V194F ENST00000517399.3 NM_001301056.2 194 Gtt/Ttt 6/8 P1 T V/F protein_coding YES CCDS73026.1 580/1068 ACCACGTTGTG PDB-ENSP_mappings:6j4o.A;PDB-ENSP_mappings:6j4p.A;PDB-ENSP_mappings:6j4q.A;PDB-ENSP_mappings:6j4q.C;PDB-ENSP_mappings:6j4q.F;PDB-ENSP_mappings:6j4q.J;PDB-ENSP_mappings:6j4s.A;PDB-ENSP_mappings:6j4v.A;PDB-ENSP_mappings:6qby.A;PDB-ENSP_mappings:6qby.C;Pfam:PF14822;PANTHER:PTHR15750;PANTHER:PTHR15750:SF4 ENSP00000428324 5/7 COSV55118238 ENST00000517399 Transcript ENSG00000143494 HGNC:25723 MODERATE missense_variant 1 1.0 possibly_damaging(0.889) Unknown deleterious(0) 1 Q86V25.118 VASH2 HGNC 1 1.0 UPI0000205E4B Q86V25-1 SNV VASH2,missense_variant,p.V129F,ENST00000366968,NM_001136474.3,c.385G>T,MODERATE,,deleterious(0),possibly_damaging(0.889),1;VASH2,missense_variant,p.V150F,ENST00000366965,NM_024749.5,c.448G>T,MODERATE,,deleterious(0),probably_damaging(0.958),1;VASH2,missense_variant,p.V129F,ENST00000366966,,c.385G>T,MODERATE,,deleterious(0),possibly_damaging(0.889),1;VASH2,missense_variant,p.V90F,ENST00000366967,NM_001136475.3,c.268G>T,MODERATE,,deleterious(0),possibly_damaging(0.889),1;VASH2,missense_variant,p.V194F,ENST00000517399,NM_001301056.2,c.580G>T,MODERATE,YES,deleterious(0),possibly_damaging(0.889),1;VASH2,downstream_gene_variant,,ENST00000366964,,,MODIFIER,,,,1;VASH2,non_coding_transcript_exon_variant,,ENST00000271776,,n.453G>T,MODIFIER,,,,1;VASH2,non_coding_transcript_exon_variant,,ENST00000366969,,n.223G>T,MODIFIER,,,,1 580/1068 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 81 5863ab9d-3c9f-462e-9242-c6590f8ee908 67 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS VASH2,non_coding_transcript_exon_variant,,ENST00000366969.2,n.223G>T,MODIFIER,;VASH2,missense_variant,p.V90F,ENST00000366967.6,c.268G>T,MODERATE,;VASH2,non_coding_transcript_exon_variant,,ENST00000271776.4,n.453G>T,MODIFIER,;VASH2,missense_variant,p.V150F,ENST00000366965.6,c.448G>T,MODERATE,;VASH2,missense_variant,p.V129F,ENST00000366968.8,c.385G>T,MODERATE,;VASH2,missense_variant,p.V194F,ENST00000517399.3,c.580G>T,MODERATE,YES;VASH2,missense_variant,p.V129F,ENST00000366966.6,c.385G>T,MODERATE, +LRP1B 53353 BI GRCh38 2 140334479 140334479 + missense_variant Missense_Mutation SNP A A G rs1160561610 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 26 24 c.12197T>C p.Val4066Ala p.V4066A ENST00000389484.8 NM_018557.3 4066 gTa/gCa 79/91 P1 G V/A protein_coding YES CCDS2182.1 12197/13800 TTTGTACTAAA PANTHER:PTHR22722:SF6;PANTHER:PTHR22722;PROSITE_profiles:PS51120;Superfamily:SSF63825;SMART:SM00135;Pfam:PF00058;Gene3D:2.120.10.30 ENSP00000374135 79/91 rs1160561610 ENST00000389484 Transcript 1.0 ENSG00000168702 HGNC:6693 MODERATE NM_018557.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.253) Unknown deleterious(0.01) Q9NZR2.166 LRP1B HGNC -1 1.0 UPI00001B045B SNV LRP1B,missense_variant,p.V4066A,ENST00000389484,NM_018557.3,c.12197T>C,MODERATE,YES,deleterious(0.01),benign(0.253),-1;LRP1B,missense_variant,p.V298A,ENST00000437977,,c.893T>C,MODERATE,,deleterious(0),possibly_damaging(0.557),-1 12484/15850 muse;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 50 5863ab9d-3c9f-462e-9242-c6590f8ee908 50 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS LRP1B,missense_variant,p.Y298H,ENST00000437977.5,c.892T>C,MODERATE,;LRP1B,missense_variant,p.V4066A,ENST00000389484.8,c.12197T>C,MODERATE,YES +GOLGA4 2803 BI GRCh38 3 37327495 37327495 + missense_variant Missense_Mutation SNP A A C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 10 24 c.5609A>C p.His1870Pro p.H1870P ENST00000361924.7 NM_002078.5 1870 cAt/cCt 14/24 P4 C H/P protein_coding CCDS2666.1 5609/6693 AGTACATAGAG Coiled-coils_(Ncoils):Coil;PANTHER:PTHR19327 ENSP00000354486 14/24 ENST00000361924 Transcript ENSG00000144674 HGNC:4427 MODERATE missense_variant benign(0.007) Unknown tolerated(0.07) Q13439.190 GOLGA4 HGNC 1 1.0 UPI000012B8DE Q13439-1 SNV GOLGA4,missense_variant,p.H1870P,ENST00000361924,NM_002078.5,c.5609A>C,MODERATE,,tolerated(0.07),benign(0.007),1;GOLGA4,missense_variant,p.H1892P,ENST00000356847,NM_001172713.2,c.5675A>C,MODERATE,YES,deleterious(0.04),benign(0.027),1;GOLGA4,missense_variant,p.H1741P,ENST00000437131,,c.5222A>C,MODERATE,,tolerated(0.07),benign(0.027),1;GOLGA4,intron_variant,,ENST00000444882,,c.478-38585A>C,MODIFIER,,,,1;GOLGA4,downstream_gene_variant,,ENST00000429018,,,MODIFIER,,,,1;GOLGA4,downstream_gene_variant,,ENST00000497537,,,MODIFIER,,,,1;GOLGA4,upstream_gene_variant,,ENST00000498250,,,MODIFIER,,,,1 5983/7772 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 58 5863ab9d-3c9f-462e-9242-c6590f8ee908 34 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS GOLGA4,missense_variant,p.H1892P,ENST00000699996.1,c.5675A>C,MODERATE,;GOLGA4,missense_variant,p.H1925P,ENST00000706569.1,c.5774A>C,MODERATE,;GOLGA4,missense_variant,p.H1870P,ENST00000361924.7,c.5609A>C,MODERATE,YES;GOLGA4,missense_variant,p.H1892P,ENST00000356847.8,c.5675A>C,MODERATE,;GOLGA4,intron_variant,,ENST00000444882.5,c.478-38585A>C,MODIFIER,;GOLGA4,missense_variant,p.H1925P,ENST00000431105.2,c.5774A>C,MODERATE,;GOLGA4,missense_variant,p.H1892P,ENST00000699995.1,c.5675A>C,MODERATE,;GOLGA4,missense_variant,p.H1892P,ENST00000437131.2,c.5675A>C,MODERATE,;GOLGA4,missense_variant,p.H1892P,ENST00000699994.1,c.5675A>C,MODERATE, +TMEM39A 55254 BI GRCh38 3 119436939 119436939 + missense_variant Missense_Mutation SNP G G C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 55 37 c.964C>G p.Leu322Val p.L322V ENST00000319172.10 NM_018266.3 322 Ctc/Gtc 7/9 P1 C L/V protein_coding YES CCDS2987.1 964/1467 AATGAGGTGCT Transmembrane_helices:TMhelix;PANTHER:PTHR12995:SF3;PANTHER:PTHR12995;Pfam:PF10271 ENSP00000326063 7/9 ENST00000319172 Transcript ENSG00000176142 HGNC:25600 MODERATE NM_018266.3 missense_variant 1.0 possibly_damaging(0.89) Unknown tolerated(0.45) Q9NV64.125 TMEM39A HGNC -1 1.0 UPI00000715E5 Q9NV64-1 SNV TMEM39A,missense_variant,p.L322V,ENST00000319172,NM_018266.3,c.964C>G,MODERATE,YES,tolerated(0.45),possibly_damaging(0.89),-1;TMEM39A,downstream_gene_variant,,ENST00000491685,,,MODIFIER,,,,-1;TMEM39A,downstream_gene_variant,,ENST00000486159,,,MODIFIER,,,,-1;TMEM39A,3_prime_UTR_variant,,ENST00000438581,,c.*632C>G,MODIFIER,,,,-1;TMEM39A,non_coding_transcript_exon_variant,,ENST00000468545,,n.225C>G,MODIFIER,,,,-1;TMEM39A,upstream_gene_variant,,ENST00000473684,,,MODIFIER,,,,-1 1318/4853 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 171 5863ab9d-3c9f-462e-9242-c6590f8ee908 92 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS TMEM39A,non_coding_transcript_exon_variant,,ENST00000468545.1,n.225C>G,MODIFIER,;TMEM39A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000438581.6,c.*632C>G,MODIFIER,;TMEM39A,missense_variant,p.L322V,ENST00000319172.10,c.964C>G,MODERATE,YES +PCDHGB1 56104 BI GRCh38 5 141350587 141350587 + missense_variant Missense_Mutation SNP C C A novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 28 3 c.327C>A p.Asn109Lys p.N109K ENST00000523390.2 NM_018922.3 109 aaC/aaA 1/4 P1 A N/K protein_coding YES CCDS54923.1 327/2784 GAAAACCCAAT Gene3D:2.60.40.60;Pfam:PF08266;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF106;SMART:SM00112;CDD:cd11304 ENSP00000429273 1/4 ENST00000523390 Transcript ENSG00000254221 HGNC:8708 MODERATE missense_variant 1.0 benign(0.158) Unknown tolerated(0.15) Q9Y5G3.151 PCDHGB1 HGNC 1 1.0 UPI0000073588 Q9Y5G3-1 SNV PCDHGB1,missense_variant,p.N109K,ENST00000523390,NM_018922.2,c.327C>A,MODERATE,YES,tolerated(0.15),benign(0.158),1;PCDHGB1,missense_variant,p.N109K,ENST00000611598,NM_032095.1,c.327C>A,MODERATE,,tolerated(0.12),benign(0.149),1;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.4,c.2424+4130C>A,MODIFIER,YES,,,1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.4,c.2424+9192C>A,MODIFIER,YES,,,1;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2,c.2421+17482C>A,MODIFIER,YES,,,1;PCDHGA4,upstream_gene_variant,,ENST00000571252,NM_018917.4,,MODIFIER,YES,,,1;PCDHGA4,upstream_gene_variant,,ENST00000612927,NM_032053.3,,MODIFIER,,,,1;PCDHGA3,downstream_gene_variant,,ENST00000619750,NM_032011.1,,MODIFIER,,,,1;PCDHGA3,intron_variant,,ENST00000612467,,c.*2003+4130C>A,MODIFIER,,,,1;AC005618.3,non_coding_transcript_exon_variant,,ENST00000625053,,n.76G>T,MODIFIER,YES,,,-1 327/4590 muse;mutect2 df291bbf-fc62-4c40-9582-289ac78225fd 0 54 5863ab9d-3c9f-462e-9242-c6590f8ee908 32 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS ENSG00000280026,non_coding_transcript_exon_variant,,ENST00000625053.1,n.76G>T,MODIFIER,YES;PCDHGB1,missense_variant,p.N109K,ENST00000611598.1,c.327C>A,MODERATE,;PCDHGB1,missense_variant,p.N109K,ENST00000523390.2,c.327C>A,MODERATE,YES;PCDHGA3,intron_variant,NMD_transcript_variant,,ENST00000612467.1,c.*2003+4130C>A,MODIFIER,;PCDHGA3,intron_variant,,ENST00000253812.8,c.2424+4130C>A,MODIFIER,YES;PCDHGA2,intron_variant,,ENST00000394576.3,c.2424+9192C>A,MODIFIER,YES;PCDHGA1,intron_variant,,ENST00000517417.3,c.2421+17482C>A,MODIFIER,YES +SNAP91 9892 BI GRCh38 6 83582260 83582260 + missense_variant Missense_Mutation SNP G G A rs764466153 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 30 18 c.2111C>T p.Thr704Met p.T704M ENST00000369694.7 NM_001376723.1 704 aCg/aTg 23/30 P4 A T/M protein_coding CCDS47455.1 2111/2724 AAGGCGTTGTC PANTHER:PTHR22951;PANTHER:PTHR22951:SF4;Low_complexity_(Seg):seg ENSP00000358708 23/30 rs764466153;COSV99536847 ENST00000369694 Transcript ENSG00000065609 HGNC:14986 MODERATE 9.805e-05 gnomAD_SAS missense_variant 0;1 possibly_damaging(0.904) Unknown tolerated(0.06) 0;1 O60641.166 SNAP91 HGNC -1 5.0 UPI0000124FB3 O60641-1 SNV SNAP91,missense_variant,p.T704M,ENST00000521485,NM_001376685.1&NM_001376686.1,c.2111C>T,MODERATE,,deleterious(0.04),benign(0.127),-1;SNAP91,missense_variant,p.T704M,ENST00000439399,NM_014841.2&NM_001376695.1&NM_001376702.1&NM_001376676.1&NM_001376720.1&NM_001376693.1&NM_001376683.1&NM_001376718.1&NM_001376703.1&NM_001376675.1&NM_001376726.1&NM_001376698.1&NM_001376706.1&NM_001376680.1&NM_001376707.1&NM_001376681.1&NM_001376682.1&NM_001376728.1,c.2111C>T,MODERATE,YES,tolerated(0.06),possibly_damaging(0.904),-1;SNAP91,missense_variant,p.T704M,ENST00000369694,NM_001242792.1&NM_001376723.1&NM_001376696.1&NM_001376687.1&NM_001376684.1&NM_001376705.1&NM_001376694.1&NM_001376678.1&NM_001376721.1&NM_001376679.1,c.2111C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.904),-1;SNAP91,missense_variant,p.T704M,ENST00000195649,NM_001376688.1&NM_001376717.1&NM_001376701.1&NM_001376713.1&NM_001376699.1&NM_001376689.1&NM_001256718.1&NM_001376714.1&NM_001376700.1&NM_001376690.1&NM_001376735.1&NM_001376691.1&NM_001376692.1&NM_001376715.1&NM_001363677.1,c.2111C>T,MODERATE,,deleterious(0.04),benign(0.127),-1;SNAP91,missense_variant,p.T704M,ENST00000521743,NM_001376716.1&NM_001376697.1&NM_001376712.1&NM_001376704.1&NM_001376677.1,c.2111C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.904),-1;SNAP91,missense_variant,p.T674M,ENST00000520302,NM_001242793.1&NM_001256717.1&NM_001376708.1&NM_001376736.1&NM_001376733.1&NM_001376731.1&NM_001376709.1&NM_001376737.1&NM_001376734.1&NM_001376719.1&NM_001376710.1&NM_001376711.1,c.2021C>T,MODERATE,,deleterious(0.04),probably_damaging(0.964),-1;SNAP91,missense_variant,p.T397M,ENST00000520213,NM_001242794.1&NM_001376739.1&NM_001376740.1&NM_001376738.1,c.1190C>T,MODERATE,,tolerated(0.14),probably_damaging(0.975),-1;SNAP91,missense_variant,p.T517M,ENST00000521931,,c.1550C>T,MODERATE,,tolerated(0.08),probably_damaging(0.976),-1;SNAP91,missense_variant,p.T45M,ENST00000523448,,c.134C>T,MODERATE,,deleterious(0.02),probably_damaging(0.969),-1;SNAP91,upstream_gene_variant,,ENST00000519133,,,MODIFIER,,,,-1;SNAP91,3_prime_UTR_variant,,ENST00000518312,,c.*2202C>T,MODIFIER,,,,-1;SNAP91,3_prime_UTR_variant,,ENST00000521616,,c.*1836C>T,MODIFIER,,,,-1 2425/4449 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 2.008e-05 0.0 0.0 0.0 0.0 0.0 1.773e-05 0.0 9.805e-05 2.7074600438936614e-05 0.0 0.0 0.0 0.0 0.0 0.0 sas 0.0004171880136709 0.0 3.087089862674475e-05 0.0 0.0004171880136709 0 52 5863ab9d-3c9f-462e-9242-c6590f8ee908 48 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS SNAP91,missense_variant,p.T517M,ENST00000521931.5,c.1550C>T,MODERATE,;SNAP91,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000521616.5,c.*1836C>T,MODIFIER,;SNAP91,missense_variant,p.T45M,ENST00000523448.5,c.134C>T,MODERATE,;SNAP91,missense_variant,p.T397M,ENST00000520213.5,c.1190C>T,MODERATE,;SNAP91,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000518312.5,c.*2202C>T,MODIFIER,;SNAP91,missense_variant,p.T704M,ENST00000521743.5,c.2111C>T,MODERATE,;SNAP91,missense_variant,p.T674M,ENST00000520302.5,c.2021C>T,MODERATE,;SNAP91,missense_variant,p.T704M,ENST00000369694.7,c.2111C>T,MODERATE,YES;SNAP91,missense_variant,p.T704M,ENST00000195649.10,c.2111C>T,MODERATE,;SNAP91,missense_variant,p.T704M,ENST00000439399.6,c.2111C>T,MODERATE,;SNAP91,missense_variant,p.T704M,ENST00000521485.5,c.2111C>T,MODERATE, +OPRM1 4988 BI GRCh38 6 154090123 154090123 + synonymous_variant Silent SNP C C T TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 37 26 c.588C>T p.Leu196= p.L196= ENST00000330432.12 NM_001285522.1 196 ctC/ctT 2/4 P4 T L protein_coding CCDS55070.1 588/1203 ATCCTCTCTTC COSM3920935;COSM3920936;COSM3920937;COSM3920938;COSM3920939;COSM3920940 Gene3D:1.20.1070.10;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24229;PANTHER:PTHR24229:SF7;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15090 ENSP00000328264 2/4 COSV57677335 ENST00000330432 Transcript ENSG00000112038 HGNC:8156 LOW NM_000914.5 synonymous_variant 1 Unknown 1 P35372.198 OPRM1 HGNC 1 1.0 UPI0000130D9C P35372-1 SNV OPRM1,synonymous_variant,p.L196=,ENST00000330432,NM_001285522.1&NM_000914.5,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000414028,NM_001145284.3,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L96=,ENST00000522236,NM_001145287.2,c.288C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L96=,ENST00000522555,NM_001285526.1,c.288C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000435918,NM_001145283.2,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L289=,ENST00000434900,NM_001145279.4&NM_001285524.1,c.867C>T,LOW,YES,,,1;OPRM1,synonymous_variant,p.L258=,ENST00000360422,NM_001285523.3&NM_001285528.2,c.774C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L96=,ENST00000520708,NM_001145280.4&NM_001285527.1,c.288C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000428397,NM_001008504.4,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000229768,NM_001008505.2,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000419506,NM_001145286.3,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000337049,NM_001008503.3,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000452687,NM_001145282.2,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000524163,NM_001145285.3,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L115=,ENST00000518759,NM_001145281.3,c.345C>T,LOW,,,,1;OPRM1,downstream_gene_variant,,ENST00000520282,,,MODIFIER,,,,1;OPRM1,non_coding_transcript_exon_variant,,ENST00000522382,,n.362C>T,MODIFIER,,,,1;OPRM1,non_coding_transcript_exon_variant,,ENST00000519613,,n.520C>T,MODIFIER,,,,1;OPRM1,non_coding_transcript_exon_variant,,ENST00000521106,,n.298C>T,MODIFIER,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000519083,,c.588C>T,LOW,,,,1;OPRM1,synonymous_variant,p.L196=,ENST00000522739,,c.588C>T,LOW,,,,1;OPRM1,intron_variant,,ENST00000524150,,c.291-829C>T,MODIFIER,,,,1 893/15143 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 102 5863ab9d-3c9f-462e-9242-c6590f8ee908 63 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS OPRM1,non_coding_transcript_exon_variant,,ENST00000521106.1,n.298C>T,MODIFIER,;OPRM1,non_coding_transcript_exon_variant,,ENST00000522382.1,n.362C>T,MODIFIER,;OPRM1,synonymous_variant,p.L96=,ENST00000522236.1,c.288C>T,LOW,;OPRM1,synonymous_variant,p.L96=,ENST00000522555.5,c.288C>T,LOW,;OPRM1,non_coding_transcript_exon_variant,,ENST00000519613.5,n.520C>T,MODIFIER,;OPRM1,synonymous_variant,p.L196=,ENST00000524163.5,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000435918.6,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000229768.9,c.588C>T,LOW,;OPRM1,synonymous_variant,NMD_transcript_variant,p.L196=,ENST00000519083.5,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000414028.6,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000337049.8,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000419506.6,c.588C>T,LOW,;OPRM1,intron_variant,NMD_transcript_variant,,ENST00000524150.2,c.291-829C>T,MODIFIER,;OPRM1,synonymous_variant,NMD_transcript_variant,p.L196=,ENST00000522739.5,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000452687.6,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000428397.6,c.588C>T,LOW,;OPRM1,synonymous_variant,p.L196=,ENST00000330432.12,c.588C>T,LOW,YES;OPRM1,synonymous_variant,p.L258=,ENST00000360422.8,c.774C>T,LOW,;OPRM1,synonymous_variant,p.L96=,ENST00000520708.5,c.288C>T,LOW,;OPRM1,synonymous_variant,p.L289=,ENST00000434900.6,c.867C>T,LOW,;OPRM1,synonymous_variant,p.L115=,ENST00000518759.5,c.345C>T,LOW, +ERMARD 55780 BI GRCh38 6 169776007 169776007 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 29 23 c.1462C>T p.His488Tyr p.H488Y ENST00000366773.8 NM_018341.3 488 Cac/Tac 15/18 P4 T H/Y protein_coding YES CCDS34576.1 1462/2037 TGTATCACCAT PANTHER:PTHR31701 ENSP00000355735 15/18 ENST00000366773 Transcript 1.0 ENSG00000130023 HGNC:21056 MODERATE NM_018341.3 missense_variant 1.0 benign(0) Unknown tolerated(0.68) Q5T6L9.110 ERMARD HGNC 1 2.0 UPI000020DF6E Q5T6L9-1 SNV ERMARD,missense_variant,p.H488Y,ENST00000366773,NM_018341.3,c.1462C>T,MODERATE,YES,tolerated(0.68),benign(0),1;ERMARD,missense_variant,p.H352Y,ENST00000588451,,c.1054C>T,MODERATE,,tolerated(0.68),benign(0.009),1;ERMARD,missense_variant,p.H488Y,ENST00000366772,NM_001278531.2,c.1462C>T,MODERATE,,tolerated(0.48),benign(0.003),1;ERMARD,missense_variant,p.H362Y,ENST00000392095,NM_001278532.2,c.1084C>T,MODERATE,,tolerated(0.51),benign(0),1;ERMARD,missense_variant,p.H488Y,ENST00000418781,NM_001278533.2,c.1462C>T,MODERATE,,tolerated(0.5),benign(0.003),1;ERMARD,non_coding_transcript_exon_variant,,ENST00000366771,,n.1560C>T,MODIFIER,,,,1;ERMARD,non_coding_transcript_exon_variant,,ENST00000477995,,n.130C>T,MODIFIER,,,,1;ERMARD,non_coding_transcript_exon_variant,,ENST00000492738,,n.504C>T,MODIFIER,,,,1;AL354892.3,downstream_gene_variant,,ENST00000586101,,,MODIFIER,YES,,,1 1498/2160 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 74 5863ab9d-3c9f-462e-9242-c6590f8ee908 52 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS ERMARD,non_coding_transcript_exon_variant,,ENST00000477995.1,n.130C>T,MODIFIER,;ERMARD,non_coding_transcript_exon_variant,,ENST00000492738.1,n.504C>T,MODIFIER,;ERMARD,non_coding_transcript_exon_variant,,ENST00000366771.5,n.1560C>T,MODIFIER,;ERMARD,missense_variant,p.H352Y,ENST00000588451.1,c.1054C>T,MODERATE,;ERMARD,missense_variant,p.H488Y,ENST00000418781.7,c.1462C>T,MODERATE,;ERMARD,missense_variant,p.H362Y,ENST00000392095.8,c.1084C>T,MODERATE,;ERMARD,missense_variant,p.H488Y,ENST00000366772.6,c.1462C>T,MODERATE,;ERMARD,missense_variant,p.H488Y,ENST00000366773.8,c.1462C>T,MODERATE,YES +PTPRD 5789 BI GRCh38 9 8331704 8331704 + synonymous_variant Silent SNP C C T novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 126 11 c.5412G>A p.Gln1804= p.Q1804= ENST00000356435.9 NM_001378058.1 1804 caG/caA 33/35 P1 T Q protein_coding CCDS43786.1 5412/5739 GTGAACTGGAA Gene3D:3.90.190.10;Pfam:PF00102;PROSITE_profiles:PS50055;PANTHER:PTHR19134;PANTHER:PTHR19134:SF203;SMART:SM00194;SMART:SM00404;Superfamily:SSF52799;CDD:cd14628 ENSP00000348812 33/35 ENST00000356435 Transcript 1.0 ENSG00000153707 HGNC:9668 LOW synonymous_variant Unknown P23468.211 PTPRD HGNC -1 5.0 UPI0000132990 P23468-1 SNV PTPRD,synonymous_variant,p.Q1804=,ENST00000381196,NM_002839.4,c.5412G>A,LOW,YES,,,-1;PTPRD,synonymous_variant,p.Q1804=,ENST00000356435,NM_001378058.1&NM_001377958.1,c.5412G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1398=,ENST00000355233,NM_130392.3,c.4194G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1397=,ENST00000397617,,c.4191G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1394=,ENST00000397611,NM_001377947.1&NM_001040712.2,c.4182G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1388=,ENST00000537002,NM_130393.3,c.4164G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1804=,ENST00000540109,,c.5412G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1397=,ENST00000486161,NM_130391.4,c.4191G>A,LOW,,,,-1;PTPRD,synonymous_variant,p.Q1397=,ENST00000397606,NM_001171025.2&NM_001377946.1,c.4191G>A,LOW,,,,-1;PTPRD,non_coding_transcript_exon_variant,,ENST00000651105,,n.4790G>A,MODIFIER,,,,-1 5518/9472 muse;mutect2 df291bbf-fc62-4c40-9582-289ac78225fd 0 181 5863ab9d-3c9f-462e-9242-c6590f8ee908 137 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS PTPRD,synonymous_variant,p.Q1397=,ENST00000397606.7,c.4191G>A,LOW,;PTPRD,synonymous_variant,p.Q1397=,ENST00000486161.5,c.4191G>A,LOW,;PTPRD,synonymous_variant,p.Q1804=,ENST00000540109.5,c.5412G>A,LOW,;PTPRD,non_coding_transcript_exon_variant,,ENST00000651105.1,n.4790G>A,MODIFIER,;PTPRD,synonymous_variant,p.Q1804=,ENST00000356435.9,c.5412G>A,LOW,;PTPRD,synonymous_variant,p.Q1398=,ENST00000355233.9,c.4194G>A,LOW,;PTPRD,synonymous_variant,p.Q1388=,ENST00000537002.5,c.4164G>A,LOW,;PTPRD,synonymous_variant,p.Q1400=,ENST00000397617.8,c.4200G>A,LOW,;PTPRD,synonymous_variant,p.Q1394=,ENST00000397611.7,c.4182G>A,LOW,;PTPRD,synonymous_variant,p.Q1804=,ENST00000381196.9,c.5412G>A,LOW,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 39 29 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 88 5863ab9d-3c9f-462e-9242-c6590f8ee908 68 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +GABBR2 9568 BI GRCh38 9 98541891 98541891 + synonymous_variant Silent SNP G G A rs142025089 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 17 11 c.612C>T p.Asp204= p.D204= ENST00000259455.4 NM_005458.8 204 gaC/gaT 3/19 0.0006 0.0023 0.0 0.0 0.0 0.0 P1 A D protein_coding YES CCDS6736.1 612/2826 TGAACGTCTTG COSM3902492 Gene3D:3.40.50.2300;Gene3D:3.40.50.2300;PDB-ENSP_mappings:4f11.A;PDB-ENSP_mappings:4f12.A;PDB-ENSP_mappings:4mqe.B;PDB-ENSP_mappings:4mqf.B;PDB-ENSP_mappings:4mr7.B;PDB-ENSP_mappings:4mr8.B;PDB-ENSP_mappings:4mr9.B;PDB-ENSP_mappings:4mrm.B;PDB-ENSP_mappings:4ms1.B;PDB-ENSP_mappings:4ms3.B;PDB-ENSP_mappings:4ms4.B;PDB-ENSP_mappings:6uo8.B;PDB-ENSP_mappings:6uo9.B;PDB-ENSP_mappings:6uoa.B;PDB-ENSP_mappings:6vjm.B;Pfam:PF01094;PANTHER:PTHR10519;PANTHER:PTHR10519:SF20;Superfamily:SSF53822;CDD:cd06366 ENSP00000259455 0.0004539 0.0 3/19 rs142025089 ENST00000259455 Transcript 1.0 ENSG00000136928 HGNC:4507 LOW NM_005458.8 0.0023 AFR synonymous_variant 1.0 Unknown O75899.192 GABBR2 HGNC -1 H9NIL8.73 1.0 UPI0000035832 SNV GABBR2,synonymous_variant,p.D204=,ENST00000259455,NM_005458.8,c.612C>T,LOW,YES,,,-1;GABBR2,synonymous_variant,p.D76=,ENST00000637717,,c.228C>T,LOW,,,,-1;GABBR2,non_coding_transcript_exon_variant,,ENST00000637410,,n.390C>T,MODIFIER,,,,-1;GABBR2,non_coding_transcript_exon_variant,,ENST00000477471,,n.399C>T,MODIFIER,,,,-1;GABBR2,non_coding_transcript_exon_variant,,ENST00000634227,,n.386C>T,MODIFIER,,,,-1;GABBR2,downstream_gene_variant,,ENST00000638001,,,MODIFIER,,,,-1 810/5499 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 3.187e-05 0.0003076 2.892e-05 0.0 0.0 0.0 0.0 0.0 6.534e-05 5.4054798965808e-05 0.0001701089931884 0.0 6.621640204684809e-05 0.0 0.0 0.0 afr 0.0001701089931884 0.0 0.0 0.0 0.0 0 42 5863ab9d-3c9f-462e-9242-c6590f8ee908 28 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS GABBR2,synonymous_variant,p.D76=,ENST00000637717.1,c.228C>T,LOW,;GABBR2,non_coding_transcript_exon_variant,,ENST00000634227.1,n.386C>T,MODIFIER,;GABBR2,non_coding_transcript_exon_variant,,ENST00000477471.1,n.399C>T,MODIFIER,;GABBR2,non_coding_transcript_exon_variant,,ENST00000637410.1,n.390C>T,MODIFIER,;GABBR2,synonymous_variant,p.D204=,ENST00000259455.4,c.612C>T,LOW,YES +PRRC2B 84726 BI GRCh38 9 131475511 131475511 + missense_variant Missense_Mutation SNP C C T rs559310957 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 13 4 c.3382C>T p.Arg1128Trp p.R1128W ENST00000683519.1 NM_001384822.1 1128 Cgg/Tgg 16/32 0.0002 0.0008 0.0 0.0 0.0 0.0 P4 T R/W protein_coding YES CCDS48044.1 3382/6690 CCCGACGGAGA COSM4607178;COSM4607179 PANTHER:PTHR14038;PANTHER:PTHR14038:SF4;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000349856 16/32 rs559310957;COSV61942815 ENST00000357304 Transcript ENSG00000130723 HGNC:28121 MODERATE 0.0008 AFR missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q5JSZ5.129 PRRC2B HGNC 1 5.0 UPI00002374A3 Q5JSZ5-1 SNV PRRC2B,missense_variant,p.R1128W,ENST00000357304,NM_013318.3,c.3382C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;PRRC2B,intron_variant,,ENST00000405995,,c.2324+1787C>T,MODIFIER,,,,1;PRRC2B,downstream_gene_variant,,ENST00000422467,,,MODIFIER,,,,1;PRRC2B,upstream_gene_variant,,ENST00000451855,,,MODIFIER,,,,1;PRRC2B,upstream_gene_variant,,ENST00000651535,,,MODIFIER,,,,1 3648/11253 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 1.656e-05 0.0 2.967e-05 0.0 0.0 0.0 2.763e-05 0.0 0.0 6.759680218237918e-06 2.430960012134165e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 22 5863ab9d-3c9f-462e-9242-c6590f8ee908 17 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS PRRC2B,intron_variant,,ENST00000682501.1,c.2324+1787C>T,MODIFIER,;PRRC2B,missense_variant,p.R1128W,ENST00000683519.1,c.3382C>T,MODERATE,YES;PRRC2B,missense_variant,p.R1128W,ENST00000684596.1,c.3382C>T,MODERATE, +PTPMT1 114971 BI GRCh38 11 47569720 47569720 + synonymous_variant Silent SNP C C T rs1428676655 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 17 12 c.276C>T p.Val92= p.V92= ENST00000326674.10 NM_175732.3 92 gtC/gtT 3/4 P1 T V protein_coding YES CCDS41643.1 276/606 GGAGTCGAGCA CDD:cd14524;PANTHER:PTHR46712;Pfam:PF00782;Gene3D:3.90.190.10;SMART:SM00195;Superfamily:SSF52799 ENSP00000325958 3/4 rs1428676655;COSV58597688 ENST00000326674 Transcript ENSG00000110536 HGNC:26965 LOW NM_175732.3 6.592e-05 gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 Q8WUK0.164 PTPMT1 HGNC 1 1.0 UPI00000472C6 Q8WUK0-1 SNV PTPMT1,stop_gained,p.R129*,ENST00000534775,,c.385C>T,HIGH,,,,1;PTPMT1,synonymous_variant,p.V92=,ENST00000326674,NM_175732.3,c.276C>T,LOW,YES,,,1;PTPMT1,intron_variant,,ENST00000326656,,c.256-1751C>T,MODIFIER,,,,1;PTPMT1,intron_variant,,ENST00000426530,NM_001143984.1,c.365-1751C>T,MODIFIER,,,,1;KBTBD4,downstream_gene_variant,,ENST00000395288,NM_001318721.1&NM_001318722.1&NM_001318723.1&NM_001318724.1&NM_016506.6&NM_001318725.1&NM_001318716.1,,MODIFIER,,,,-1;KBTBD4,downstream_gene_variant,,ENST00000430070,NM_001318719.1&NM_001318717.1&NM_001318720.1&NM_018095.6,,MODIFIER,,,,-1;CELF1,upstream_gene_variant,,ENST00000525841,,,MODIFIER,,,,-1;KBTBD4,downstream_gene_variant,,ENST00000526005,,,MODIFIER,,,,-1;CELF1,upstream_gene_variant,,ENST00000526419,,,MODIFIER,,,,-1;CELF1,upstream_gene_variant,,ENST00000530151,,,MODIFIER,,,,-1;KBTBD4,downstream_gene_variant,,ENST00000533290,NM_001318718.1,,MODIFIER,YES,,,-1;PTPMT1,non_coding_transcript_exon_variant,,ENST00000527079,,n.110C>T,MODIFIER,,,,1;NDUFS3,intron_variant,,ENST00000533507,,n.543-1751C>T,MODIFIER,,,,1 300/2462 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 1.214e-05 0.0 0.0 0.0 0.0 0.0 8.92e-06 0.0 6.592e-05 2.707020030356944e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.63049000245519e-05 0.0 4.63049000245519e-05 0.0004970179870724 0.0 0 28 5863ab9d-3c9f-462e-9242-c6590f8ee908 29 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS PTPMT1,non_coding_transcript_exon_variant,,ENST00000527079.2,n.110C>T,MODIFIER,;PTPMT1,synonymous_variant,p.V92=,ENST00000326674.10,c.276C>T,LOW,YES;PTPMT1,intron_variant,,ENST00000326656.12,c.256-1751C>T,MODIFIER,;PTPMT1,stop_gained,p.R129*,ENST00000534775.1,c.385C>T,HIGH,;PTPMT1,intron_variant,,ENST00000426530.2,c.365-1751C>T,MODIFIER,;NDUFS3,intron_variant,,ENST00000533507.5,n.543-1751C>T,MODIFIER, +CD4 920 BI GRCh38 12 6814202 6814202 + missense_variant Missense_Mutation SNP T T C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 38 38 c.275T>C p.Phe92Ser p.F92S ENST00000011653.9 NM_001382707.1 92 tTt/tCt 4/10 P1 C F/S protein_coding YES CCDS8562.1 275/1377 AAACTTTCCCC PDB-ENSP_mappings:1cdh.A;PDB-ENSP_mappings:1cdi.A;PDB-ENSP_mappings:1cdj.A;PDB-ENSP_mappings:1cdu.A;PDB-ENSP_mappings:1cdy.A;PDB-ENSP_mappings:1g9m.C;PDB-ENSP_mappings:1g9n.C;PDB-ENSP_mappings:1gc1.C;PDB-ENSP_mappings:1jl4.D;PDB-ENSP_mappings:1rzj.C;PDB-ENSP_mappings:1rzk.C;PDB-ENSP_mappings:1wio.A;PDB-ENSP_mappings:1wio.B;PDB-ENSP_mappings:1wip.A;PDB-ENSP_mappings:1wip.B;PDB-ENSP_mappings:1wiq.A;PDB-ENSP_mappings:1wiq.B;Gene3D:2.60.40.10;PDB-ENSP_mappings:2b4c.C;PDB-ENSP_mappings:2nxy.B;PDB-ENSP_mappings:2nxz.B;PDB-ENSP_mappings:2ny0.B;PDB-ENSP_mappings:2ny1.B;PDB-ENSP_mappings:2ny2.B;PDB-ENSP_mappings:2ny3.B;PDB-ENSP_mappings:2ny4.B;PDB-ENSP_mappings:2ny5.C;PDB-ENSP_mappings:2ny6.B;PDB-ENSP_mappings:2qad.B;PDB-ENSP_mappings:2qad.F;PDB-ENSP_mappings:3cd4.A;PDB-ENSP_mappings:3j70.C;PDB-ENSP_mappings:3j70.O;PDB-ENSP_mappings:3j70.T;PDB-ENSP_mappings:3jcb.D;PDB-ENSP_mappings:3jcc.D;PDB-ENSP_mappings:3jwd.C;PDB-ENSP_mappings:3jwd.D;PDB-ENSP_mappings:3jwo.C;PDB-ENSP_mappings:3lqa.C;PDB-ENSP_mappings:3o2d.A;PDB-ENSP_mappings:3s4s.G;PDB-ENSP_mappings:3s4s.H;PDB-ENSP_mappings:3s5l.G;PDB-ENSP_mappings:3s5l.H;PDB-ENSP_mappings:3t0e.E;PDB-ENSP_mappings:4h8w.C;PDB-ENSP_mappings:4jm2.F;PDB-ENSP_mappings:4p9h.C;PDB-ENSP_mappings:4q6i.C;PDB-ENSP_mappings:4q6i.I;PDB-ENSP_mappings:4q6i.J;PDB-ENSP_mappings:4q6i.K;PDB-ENSP_mappings:4r2g.B;PDB-ENSP_mappings:4r2g.F;PDB-ENSP_mappings:4r2g.H;PDB-ENSP_mappings:4r2g.L;PDB-ENSP_mappings:4r4h.B;PDB-ENSP_mappings:4rqs.B;PDB-ENSP_mappings:5a7x.B;PDB-ENSP_mappings:5a7x.F;PDB-ENSP_mappings:5a7x.J;PDB-ENSP_mappings:5a8h.B;PDB-ENSP_mappings:5a8h.H;PDB-ENSP_mappings:5a8h.N;PDB-ENSP_mappings:5cay.B;PDB-ENSP_mappings:5thr.G;PDB-ENSP_mappings:5thr.H;PDB-ENSP_mappings:5thr.I;PDB-ENSP_mappings:5u1f.M;PDB-ENSP_mappings:5vn3.C;PDB-ENSP_mappings:5vn3.E;PDB-ENSP_mappings:5vn3.F;PDB-ENSP_mappings:6cm3.G;PDB-ENSP_mappings:6cm3.H;PDB-ENSP_mappings:6cm3.I;PDB-ENSP_mappings:6edu.G;PDB-ENSP_mappings:6edu.H;PDB-ENSP_mappings:6edu.I;PDB-ENSP_mappings:6l1y.C;PDB-ENSP_mappings:6meo.A;PDB-ENSP_mappings:6met.A;PDB-ENSP_mappings:6u0l.D;PDB-ENSP_mappings:6u0l.E;PDB-ENSP_mappings:6u0l.F;PDB-ENSP_mappings:6u0n.D;PDB-ENSP_mappings:6u0n.E;PDB-ENSP_mappings:6u0n.F;Pfam:PF00047;PROSITE_profiles:PS50835;PANTHER:PTHR11422;PANTHER:PTHR11422:SF0;SMART:SM00406;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd07690 ENSP00000011653 4/10 ENST00000011653 Transcript 1.0 ENSG00000010610 HGNC:1678 MODERATE NM_000616.5 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) P01730.230 CD4 HGNC 1 A0A4Y5UGE4.6 1.0 UPI0000001294 SNV CD4,missense_variant,p.F92S,ENST00000011653,NM_001382707.1&NM_001382706.1&NM_000616.5&NM_001382714.1&NM_001382705.1&NM_001195015.3&NM_001195014.3&NM_001195016.3&NM_001195017.3,c.275T>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;CD4,missense_variant,p.F37S,ENST00000541982,,c.110T>C,MODERATE,,deleterious(0),probably_damaging(1),1;CD4,non_coding_transcript_exon_variant,,ENST00000538827,,n.188T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000536610,,n.577T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000536563,,n.112T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000536590,,n.505T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000437800,,n.188T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000544344,,n.188T>C,MODIFIER,,,,1;CD4,non_coding_transcript_exon_variant,,ENST00000543755,,n.149T>C,MODIFIER,,,,1 477/3049 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 119 5863ab9d-3c9f-462e-9242-c6590f8ee908 76 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS CD4,non_coding_transcript_exon_variant,,ENST00000543755.1,n.149T>C,MODIFIER,;CD4,non_coding_transcript_exon_variant,,ENST00000536563.1,n.112T>C,MODIFIER,;CD4,non_coding_transcript_exon_variant,,ENST00000536590.1,n.505T>C,MODIFIER,;CD4,non_coding_transcript_exon_variant,,ENST00000538827.5,n.188T>C,MODIFIER,;CD4,non_coding_transcript_exon_variant,,ENST00000437800.6,n.188T>C,MODIFIER,;CD4,missense_variant,p.F37S,ENST00000541982.5,c.110T>C,MODERATE,;CD4,non_coding_transcript_exon_variant,,ENST00000544344.5,n.188T>C,MODIFIER,;CD4,missense_variant,p.F92S,ENST00000011653.9,c.275T>C,MODERATE,YES;CD4,non_coding_transcript_exon_variant,,ENST00000536610.5,n.577T>C,MODIFIER, +KRT79 338785 BI GRCh38 12 52823103 52823103 + missense_variant Missense_Mutation SNP C C T rs775879705 TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 18 17 c.1280G>A p.Arg427His p.R427H ENST00000330553.6 NM_175834.3 427 cGt/cAt 7/9 P1 T R/H protein_coding YES CCDS8839.1 1280/1608 AGTCACGCAGC COSM1362606 Coiled-coils_(Ncoils):Coil;PROSITE_profiles:PS51842;PANTHER:PTHR45616:SF10;PANTHER:PTHR45616;Gene3D:1.20.5.170;Pfam:PF00038;SMART:SM01391;Superfamily:SSF64593 ENSP00000328358 7/9 rs775879705;COSV57938097;COSV57938701 ENST00000330553 Transcript ENSG00000185640 HGNC:28930 MODERATE NM_175834.3 0.000196 gnomAD_SAS missense_variant 0;1;1 1.0 benign(0.248) Unknown deleterious(0.01) 0;1;1 Q5XKE5.134 KRT79 HGNC -1 1.0 UPI0000198204 SNV KRT79,missense_variant,p.R427H,ENST00000330553,NM_175834.3,c.1280G>A,MODERATE,YES,deleterious(0.01),benign(0.248),-1;KRT79,missense_variant,p.R13H,ENST00000549255,,c.38G>A,MODERATE,,deleterious(0),probably_damaging(0.956),-1;KRT79,non_coding_transcript_exon_variant,,ENST00000546453,,n.752G>A,MODIFIER,,,,-1 1331/2123 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 4.375e-05 0.0 0.0 0.0 0.0001087 0.0 1.759e-05 0.0001629 0.000196 0 100 5863ab9d-3c9f-462e-9242-c6590f8ee908 35 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS KRT79,missense_variant,p.R13H,ENST00000549255.1,c.38G>A,MODERATE,;KRT79,non_coding_transcript_exon_variant,,ENST00000546453.1,n.752G>A,MODIFIER,;KRT79,missense_variant,p.R427H,ENST00000330553.6,c.1280G>A,MODERATE,YES +PROSER1 80209 BI GRCh38 13 39013381 39013381 + missense_variant Missense_Mutation SNP T T C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 62 46 c.1871A>G p.His624Arg p.H624R ENST00000352251.8 NM_025138.5 624 cAt/cGt 11/13 P2 C H/R protein_coding YES CCDS9368.2 1871/2835 CAGAATGAGAT PANTHER:PTHR14880 ENSP00000332034 11/13 ENST00000352251 Transcript ENSG00000120685 HGNC:20291 MODERATE NM_025138.5 missense_variant 1.0 benign(0.087) Unknown tolerated(0.88) Q86XN7.117 PROSER1 HGNC -1 1.0 UPI00001FCC65 Q86XN7-1 SNV PROSER1,missense_variant,p.H624R,ENST00000352251,NM_025138.5,c.1871A>G,MODERATE,YES,tolerated(0.88),benign(0.087),-1;PROSER1,missense_variant,p.H602R,ENST00000625998,NM_170719.3,c.1805A>G,MODERATE,,tolerated(0.78),probably_damaging(0.99),-1;PROSER1,intron_variant,,ENST00000484434,,n.709-1192A>G,MODIFIER,,,,-1;PROSER1,upstream_gene_variant,,ENST00000468017,,,MODIFIER,,,,-1;PROSER1,upstream_gene_variant,,ENST00000492646,,,MODIFIER,,,,-1;PROSER1,downstream_gene_variant,,ENST00000602512,,,MODIFIER,,,,-1;PROSER1,downstream_gene_variant,,ENST00000602899,,,MODIFIER,,,,-1 2718/5182 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 122 5863ab9d-3c9f-462e-9242-c6590f8ee908 109 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS PROSER1,intron_variant,,ENST00000484434.3,n.709-1192A>G,MODIFIER,;PROSER1,missense_variant,p.H602R,ENST00000625998.2,c.1805A>G,MODERATE,;PROSER1,missense_variant,p.H624R,ENST00000352251.8,c.1871A>G,MODERATE,YES +PCK2 5106 BI GRCh38 14 24100054 24100054 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 35 34 c.1075G>A p.Ala359Thr p.A359T ENST00000216780.9 NM_004563.4 359 Gcc/Acc 7/10 P1 A A/T protein_coding YES CCDS9609.1 1075/1923 CCTCTGCCACC HAMAP:MF_00452;CDD:cd00819;PANTHER:PTHR11561;PANTHER:PTHR11561:SF11;Pfam:PF00821;PIRSF:PIRSF001348;Gene3D:3.90.228.20;Gene3D:2.170.8.10;Superfamily:SSF53795 ENSP00000216780 7/10 ENST00000216780 Transcript 1.0 ENSG00000100889 HGNC:8725 MODERATE NM_004563.4 missense_variant 1.0 benign(0.009) Unknown tolerated(0.46) Q16822.200 PCK2 HGNC 1 A0A384MTT2.9 1.0 UPI0000169DF3 Q16822-1 SNV PCK2,missense_variant,p.A225T,ENST00000545054,NM_001308054.2,c.673G>A,MODERATE,,tolerated(0.47),benign(0.017),1;PCK2,missense_variant,p.A225T,ENST00000558096,,c.673G>A,MODERATE,,tolerated(0.45),benign(0.005),1;PCK2,missense_variant,p.A359T,ENST00000216780,NM_004563.4,c.1075G>A,MODERATE,YES,tolerated(0.46),benign(0.009),1;PCK2,missense_variant,p.A225T,ENST00000561286,NM_001291556.2,c.673G>A,MODERATE,,tolerated(0.47),benign(0.017),1;PCK2,missense_variant,p.A359T,ENST00000396973,NM_001018073.3,c.1075G>A,MODERATE,,tolerated(0.47),benign(0.402),1;PCK2,missense_variant,p.A371T,ENST00000559250,,c.1111G>A,MODERATE,,tolerated(0.43),benign(0.01),1;NRL,intron_variant,,ENST00000558280,,c.-254+14668C>T,MODIFIER,,,,-1;NRL,intron_variant,,ENST00000561028,NM_001354768.3&NM_001354770.2&NM_006177.5,c.-28+14668C>T,MODIFIER,YES,,,-1;NRL,upstream_gene_variant,,ENST00000396997,NM_001354769.1,,MODIFIER,,,,-1;PCK2,upstream_gene_variant,,ENST00000559171,,,MODIFIER,,,,1;PCK2,downstream_gene_variant,,ENST00000559837,,,MODIFIER,,,,1;PCK2,downstream_gene_variant,,ENST00000560736,,,MODIFIER,,,,1;PCK2,downstream_gene_variant,,ENST00000560657,,,MODIFIER,,,,1;PCK2,3_prime_UTR_variant,,ENST00000559503,,c.*222G>A,MODIFIER,,,,1;PCK2,non_coding_transcript_exon_variant,,ENST00000558674,,n.1940G>A,MODIFIER,,,,1;PCK2,non_coding_transcript_exon_variant,,ENST00000561050,,n.1667G>A,MODIFIER,,,,1;PCK2,upstream_gene_variant,,ENST00000557969,,,MODIFIER,,,,1;PCK2,downstream_gene_variant,,ENST00000559584,,,MODIFIER,,,,1;PCK2,downstream_gene_variant,,ENST00000560106,,,MODIFIER,,,,1 1170/2179 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 107 5863ab9d-3c9f-462e-9242-c6590f8ee908 69 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS PCK2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000559503.1,c.*222G>A,MODIFIER,;PCK2,missense_variant,p.A225T,ENST00000558096.5,c.673G>A,MODERATE,;PCK2,non_coding_transcript_exon_variant,,ENST00000558674.5,n.1940G>A,MODIFIER,;PCK2,missense_variant,p.A225T,ENST00000561286.5,c.673G>A,MODERATE,;PCK2,non_coding_transcript_exon_variant,,ENST00000561050.5,n.1667G>A,MODIFIER,;PCK2,missense_variant,p.A359T,ENST00000216780.9,c.1075G>A,MODERATE,YES;PCK2,missense_variant,p.A225T,ENST00000545054.6,c.673G>A,MODERATE,;PCK2,missense_variant,p.A359T,ENST00000396973.8,c.1075G>A,MODERATE,;PCK2,missense_variant,p.A371T,ENST00000559250.5,c.1111G>A,MODERATE,;NRL,intron_variant,,ENST00000558280.1,c.-254+14668C>T,MODIFIER,;NRL,intron_variant,,ENST00000561028.6,c.-28+14668C>T,MODIFIER,YES +FES 2242 BI GRCh38 15 90889867 90889867 + synonymous_variant Silent SNP T T G novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 76 9 c.954T>G p.Ala318= p.A318= ENST00000328850.8 NM_002005.4 318 gcT/gcG 8/19 P1 G A protein_coding YES CCDS10365.1 954/2469 CTGGCTGTGGC PDB-ENSP_mappings:4dyl.A;Gene3D:1.10.287.160;PIRSF:PIRSF000632;PANTHER:PTHR24418;PANTHER:PTHR24418:SF197 ENSP00000331504 8/19 ENST00000328850 Transcript 1.0 ENSG00000182511 HGNC:3657 LOW NM_002005.4 synonymous_variant 1.0 Unknown P07332.218 FES HGNC 1 A0A024RC92.54 1.0 UPI0000001C30 P07332-1 SNV FES,synonymous_variant,p.A318=,ENST00000328850,NM_002005.4,c.954T>G,LOW,YES,,,1;FES,synonymous_variant,p.A260=,ENST00000414248,NM_001143785.2,c.780T>G,LOW,,,,1;FES,synonymous_variant,p.A260=,ENST00000394300,NM_001143783.1,c.780T>G,LOW,,,,1;FES,synonymous_variant,p.A318=,ENST00000444422,NM_001143784.1,c.954T>G,LOW,,,,1;FES,synonymous_variant,p.A260=,ENST00000394302,,c.780T>G,LOW,,,,1;FES,downstream_gene_variant,,ENST00000416779,,,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000443697,,,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000452243,,,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000559355,,,MODIFIER,,,,1;FES,non_coding_transcript_exon_variant,,ENST00000448367,,n.115T>G,MODIFIER,,,,1;FES,synonymous_variant,p.A318=,ENST00000464684,,c.954T>G,LOW,,,,1;FES,non_coding_transcript_exon_variant,,ENST00000496379,,n.28T>G,MODIFIER,,,,1;FES,non_coding_transcript_exon_variant,,ENST00000494259,,n.459T>G,MODIFIER,,,,1;FES,non_coding_transcript_exon_variant,,ENST00000462476,,n.19T>G,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000470152,,,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000481665,,,MODIFIER,,,,1;FES,downstream_gene_variant,,ENST00000497945,,,MODIFIER,,,,1 1004/2737 muse;mutect2 df291bbf-fc62-4c40-9582-289ac78225fd 0 142 5863ab9d-3c9f-462e-9242-c6590f8ee908 86 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS FES,non_coding_transcript_exon_variant,,ENST00000462476.1,n.19T>G,MODIFIER,;FES,non_coding_transcript_exon_variant,,ENST00000496379.5,n.28T>G,MODIFIER,;FES,non_coding_transcript_exon_variant,,ENST00000448367.5,n.115T>G,MODIFIER,;FES,non_coding_transcript_exon_variant,,ENST00000494259.1,n.459T>G,MODIFIER,;FES,synonymous_variant,p.A260=,ENST00000394300.7,c.780T>G,LOW,;FES,synonymous_variant,p.A318=,ENST00000444422.2,c.954T>G,LOW,;FES,synonymous_variant,NMD_transcript_variant,p.A318=,ENST00000464684.5,c.954T>G,LOW,;FES,synonymous_variant,p.A318=,ENST00000328850.8,c.954T>G,LOW,YES;FES,synonymous_variant,p.A260=,ENST00000394302.5,c.780T>G,LOW,;FES,synonymous_variant,p.A260=,ENST00000414248.6,c.780T>G,LOW, +TBX6 6911 BI GRCh38 16 30088613 30088613 + missense_variant,splice_region_variant Missense_Mutation SNP G G C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 52 46 c.771C>G p.Ile257Met p.I257M ENST00000279386.6 257 atC/atG 5/8 P1 C I/M protein_coding CCDS10670.1 771/1311 TGTGTGATCTG Gene3D:2.60.40.820;Pfam:PF00907;Prints:PR00937;PROSITE_profiles:PS50252;PANTHER:PTHR11267;PANTHER:PTHR11267:SF100;SMART:SM00425;Superfamily:SSF49417;CDD:cd00182 ENSP00000279386 5/8 ENST00000279386 Transcript 1.0 ENSG00000149922 HGNC:11605 MODERATE missense_variant probably_damaging(0.999) Unknown deleterious(0) O95947.179 TBX6 HGNC -1 1.0 UPI000013DBC7 O95947-1 SNV TBX6,missense_variant,p.I257M,ENST00000553607,,c.771C>G,MODERATE,,deleterious(0),probably_damaging(0.999),-1;TBX6,missense_variant,p.I257M,ENST00000395224,NM_004608.4,c.771C>G,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;TBX6,missense_variant,p.I257M,ENST00000279386,,c.771C>G,MODERATE,,deleterious(0),probably_damaging(0.999),-1;TBX6,intron_variant,,ENST00000627355,,c.808+37C>G,MODIFIER,,,,-1;PPP4C,downstream_gene_variant,,ENST00000279387,NM_001303503.2&NM_001303506.2&NM_002720.3&NM_001303507.2,,MODIFIER,YES,,,1;YPEL3,downstream_gene_variant,,ENST00000398838,NM_001145524.2,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000398841,NM_031477.5,,MODIFIER,YES,,,-1;PPP4C,downstream_gene_variant,,ENST00000561610,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000562222,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000562664,NM_001303504.2,,MODIFIER,,,,1;YPEL3,downstream_gene_variant,,ENST00000563788,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000565110,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000566134,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000566595,,,MODIFIER,,,,-1;PPP4C,downstream_gene_variant,,ENST00000627746,,,MODIFIER,,,,1;YPEL3,downstream_gene_variant,,ENST00000565479,,,MODIFIER,,,,-1;YPEL3,downstream_gene_variant,,ENST00000568674,,,MODIFIER,,,,-1;TBX6,missense_variant,p.I257M,ENST00000567664,,c.771C>G,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PPP4C,downstream_gene_variant,,ENST00000563200,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000563597,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000563732,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000566749,,,MODIFIER,,,,1;PPP4C,downstream_gene_variant,,ENST00000567040,,,MODIFIER,,,,1;YPEL3,downstream_gene_variant,,ENST00000570099,,,MODIFIER,,,,-1 827/1796 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 145 5863ab9d-3c9f-462e-9242-c6590f8ee908 98 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS TBX6,missense_variant,splice_region_variant,p.I257M,ENST00000553607.1,c.771C>G,MODERATE,;TBX6,missense_variant,splice_region_variant,NMD_transcript_variant,p.I257M,ENST00000567664.5,c.771C>G,MODERATE,;TBX6,missense_variant,splice_region_variant,p.I257M,ENST00000279386.6,c.771C>G,MODERATE,;TBX6,missense_variant,splice_region_variant,p.I257M,ENST00000395224.7,c.771C>G,MODERATE,YES +MPP3 4356 BI GRCh38 17 43801786 43801786 + missense_variant Missense_Mutation SNP A A C novel TCGA-YZ-A983-01A TCGA-YZ-A983-10B Somatic 54 37 c.1673T>G p.Leu558Arg p.L558R ENST00000398389.9 NM_001932.6 558 cTc/cGc 20/20 P1 C L/R protein_coding CCDS42344.1 1673/1758 CCTGGAGATCC Gene3D:3.40.50.300;Coiled-coils_(Ncoils):Coil;Pfam:PF00625;PROSITE_profiles:PS50052;PANTHER:PTHR23122;PANTHER:PTHR23122:SF33;SMART:SM00072;Superfamily:SSF52540 ENSP00000381425 20/20 ENST00000398389 Transcript ENSG00000161647 HGNC:7221 MODERATE NM_001932.6 missense_variant possibly_damaging(0.873) Unknown deleterious(0) Q13368.163 MPP3 HGNC -1 1.0 UPI0000167B23 SNV MPP3,missense_variant,p.L583R,ENST00000398393,NM_001330233.1,c.1748T>G,MODERATE,YES,deleterious(0),possibly_damaging(0.873),-1;MPP3,missense_variant,p.L558R,ENST00000398389,NM_001353080.1&NM_001932.6,c.1673T>G,MODERATE,,deleterious(0),possibly_damaging(0.873),-1;MPP3,3_prime_UTR_variant,,ENST00000496503,,c.*704T>G,MODIFIER,,,,-1 1815/2790 muse;mutect2;varscan2 df291bbf-fc62-4c40-9582-289ac78225fd 0 100 5863ab9d-3c9f-462e-9242-c6590f8ee908 91 be6dde0b-5d96-4608-9424-bd37470f2e2e SUCCESS MPP3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000496503.5,c.*704T>G,MODIFIER,;MPP3,missense_variant,p.L558R,ENST00000398389.9,c.1673T>G,MODERATE,YES;MPP3,missense_variant,p.L583R,ENST00000398393.5,c.1748T>G,MODERATE, +PRAMEF5 343068 BI GRCh38 1 13263004 13263004 + missense_variant Missense_Mutation SNP G G T novel TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 142 12 c.1324G>T p.Val442Leu p.V442L ENST00000622421.3 NM_001013407.5 442 Gtg/Ttg 4/4 P1 T V/L protein_coding YES CCDS72708.1 1324/1431 AGAGAGTGAGG PANTHER:PTHR14224:SF19;PANTHER:PTHR14224;PIRSF:PIRSF038286 ENSP00000480122 4/4 ENST00000622421 Transcript ENSG00000270601 HGNC:27995 MODERATE missense_variant 1.0 benign(0.02) Unknown tolerated(1) Q5TYX0.128 PRAMEF5 HGNC 1 1.0 UPI0004423C15 SNV PRAMEF5,missense_variant,p.V442L,ENST00000622421,NM_001013407.3,c.1324G>T,MODERATE,YES,tolerated(1),benign(0.02),1 1410/1720 muse;mutect2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 248 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 154 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS PRAMEF5,missense_variant,p.V442L,ENST00000622421.3,c.1324G>T,MODERATE,YES +GSDME 1687 BI GRCh38 7 24719149 24719149 + missense_variant Missense_Mutation SNP C C G novel TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 42 28 c.474G>C p.Leu158Phe p.L158F ENST00000342947.9 NM_004403.3 158 ttG/ttC 4/10 P1 G L/F protein_coding YES CCDS5389.1 474/1491 TGTGTCAAAAC Pfam:PF04598;PANTHER:PTHR15207 ENSP00000339587 4/10 ENST00000342947 Transcript 1.0 ENSG00000105928 HGNC:2810 MODERATE missense_variant 1.0 probably_damaging(0.989) Unknown deleterious(0) O60443.149 GSDME HGNC -1 A0A024RA58.46 1.0 UPI00001291FC O60443-1 SNV GSDME,missense_variant,p.L158F,ENST00000342947,NM_004403.3,c.474G>C,MODERATE,YES,deleterious(0),probably_damaging(0.989),-1;GSDME,missense_variant,p.L158F,ENST00000645220,NM_001127453.2,c.474G>C,MODERATE,,deleterious(0),probably_damaging(0.989),-1;GSDME,missense_variant,p.L158F,ENST00000414428,,c.474G>C,MODERATE,,deleterious(0.01),probably_damaging(0.972),-1;GSDME,5_prime_UTR_variant,,ENST00000419307,NM_001127454.2,c.-19G>C,MODIFIER,,,,-1;GSDME,5_prime_UTR_variant,,ENST00000409970,,c.-19G>C,MODIFIER,,,,-1;GSDME,upstream_gene_variant,,ENST00000415480,,,MODIFIER,,,,-1;GSDME,upstream_gene_variant,,ENST00000446822,,,MODIFIER,,,,-1;GSDME,non_coding_transcript_exon_variant,,ENST00000411476,,n.243G>C,MODIFIER,,,,-1;GSDME,non_coding_transcript_exon_variant,,ENST00000559637,,n.169G>C,MODIFIER,,,,-1;GSDME,non_coding_transcript_exon_variant,,ENST00000493723,,n.493G>C,MODIFIER,,,,-1 726/2414 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 93 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 71 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS GSDME,non_coding_transcript_exon_variant,,ENST00000493723.5,n.493G>C,MODIFIER,;GSDME,non_coding_transcript_exon_variant,,ENST00000411476.3,n.243G>C,MODIFIER,;GSDME,non_coding_transcript_exon_variant,,ENST00000559637.6,n.169G>C,MODIFIER,;GSDME,missense_variant,p.L158F,ENST00000414428.2,c.474G>C,MODERATE,;GSDME,5_prime_UTR_variant,,ENST00000419307.6,c.-19G>C,MODIFIER,;GSDME,5_prime_UTR_variant,,ENST00000409970.6,c.-19G>C,MODIFIER,;GSDME,missense_variant,p.L158F,ENST00000645220.1,c.474G>C,MODERATE,YES;GSDME,missense_variant,p.L158F,ENST00000342947.9,c.474G>C,MODERATE, +TNS2 23371 BI GRCh38 12 53055825 53055825 + synonymous_variant Silent SNP C C T novel TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 87 46 c.741C>T p.His247= p.H247= ENST00000314250.11 NM_001416202.1 247 caC/caT 10/29 P4 T H protein_coding CCDS8843.1 741/4230 ATGCACTACAG PROSITE_profiles:PS51181;CDD:cd14562;PANTHER:PTHR45734:SF1;PANTHER:PTHR45734;Gene3D:3.90.190.10;Superfamily:SSF52799 ENSP00000319684 10/29 ENST00000314250 Transcript ENSG00000111077 HGNC:19737 LOW NM_170754.4 synonymous_variant Unknown Q63HR2.145 TNS2 HGNC 1 1.0 UPI000013F7A1 Q63HR2-1 SNV TNS2,synonymous_variant,p.H257=,ENST00000314276,NM_015319.2,c.771C>T,LOW,YES,,,1;TNS2,synonymous_variant,p.H247=,ENST00000314250,NM_170754.4,c.741C>T,LOW,,,,1;TNS2,synonymous_variant,p.H123=,ENST00000379902,NM_198316.2,c.369C>T,LOW,,,,1;TNS2,synonymous_variant,p.H247=,ENST00000552570,,c.741C>T,LOW,,,,1;TNS2,synonymous_variant,p.H247=,ENST00000549700,,c.741C>T,LOW,,,,1;TNS2,synonymous_variant,p.H247=,ENST00000546602,,c.741C>T,LOW,,,,1;TNS2,upstream_gene_variant,,ENST00000602335,,,MODIFIER,,,,1;MIR6757,upstream_gene_variant,,ENST00000612099,,,MODIFIER,YES,,,1;TNS2,non_coding_transcript_exon_variant,,ENST00000549311,,n.876C>T,MODIFIER,,,,1;TNS2,non_coding_transcript_exon_variant,,ENST00000549498,,n.816C>T,MODIFIER,,,,1;TNS2,upstream_gene_variant,,ENST00000546759,,,MODIFIER,,,,1;TNS2,upstream_gene_variant,,ENST00000546772,,,MODIFIER,,,,1;TNS2,upstream_gene_variant,,ENST00000547223,,,MODIFIER,,,,1;TNS2,upstream_gene_variant,,ENST00000549789,,,MODIFIER,,,,1;TNS2,downstream_gene_variant,,ENST00000551302,,,MODIFIER,,,,1;TNS2,upstream_gene_variant,,ENST00000551583,,,MODIFIER,,,,1;TNS2,downstream_gene_variant,,ENST00000551693,,,MODIFIER,,,,1;TNS2,downstream_gene_variant,,ENST00000552403,,,MODIFIER,,,,1;AC068888.1,upstream_gene_variant,,ENST00000546793,,,MODIFIER,YES,,,-1;AC068888.1,upstream_gene_variant,,ENST00000550601,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000551890,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000654457,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000657514,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000657729,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000662446,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000662901,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000666649,,,MODIFIER,,,,-1;AC068888.1,upstream_gene_variant,,ENST00000668380,,,MODIFIER,,,,-1 862/4848 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 172 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 133 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS TNS2,synonymous_variant,p.H247=,ENST00000546602.5,c.741C>T,LOW,;TNS2,synonymous_variant,p.H247=,ENST00000552570.5,c.741C>T,LOW,;TNS2,synonymous_variant,p.H247=,ENST00000549700.5,c.741C>T,LOW,;TNS2,synonymous_variant,p.H247=,ENST00000314250.11,c.741C>T,LOW,YES;TNS2,non_coding_transcript_exon_variant,,ENST00000549311.7,n.876C>T,MODIFIER,;TNS2,non_coding_transcript_exon_variant,,ENST00000549498.5,n.816C>T,MODIFIER,;TNS2,synonymous_variant,p.H257=,ENST00000314276.7,c.771C>T,LOW,;TNS2,synonymous_variant,p.H123=,ENST00000379902.7,c.369C>T,LOW, +GGA2 23062 BI GRCh38 16 23470094 23470094 + missense_variant Missense_Mutation SNP C C T rs1446470734 TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 43 15 c.1522G>A p.Ala508Thr p.A508T ENST00000309859.8 NM_015044.4 508 Gcc/Acc 15/17 P1 T A/T protein_coding YES CCDS10611.1 1522/1842 AGGGGCTCCCG PROSITE_profiles:PS50180;PANTHER:PTHR45905:SF2;PANTHER:PTHR45905;Gene3D:2.60.40.1230;Pfam:PF02883;SMART:SM00809;Superfamily:SSF49348 ENSP00000311962 15/17 rs1446470734 ENST00000309859 Transcript ENSG00000103365 HGNC:16064 MODERATE NM_015044.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.584) Unknown tolerated(0.07) Q9UJY4.190 GGA2 HGNC -1 1.0 UPI000013EF46 SNV GGA2,missense_variant,p.A508T,ENST00000309859,NM_015044.4,c.1522G>A,MODERATE,YES,tolerated(0.07),possibly_damaging(0.584),-1;GGA2,intron_variant,,ENST00000567468,,c.625-4696G>A,MODIFIER,,,,-1;GGA2,upstream_gene_variant,,ENST00000566685,,,MODIFIER,,,,-1;GGA2,upstream_gene_variant,,ENST00000567339,,,MODIFIER,,,,-1;GGA2,downstream_gene_variant,,ENST00000569182,,,MODIFIER,,,,-1;GGA2,upstream_gene_variant,,ENST00000568922,,,MODIFIER,,,,-1 1605/5973 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 66 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 58 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS GGA2,intron_variant,,ENST00000567468.5,c.625-4696G>A,MODIFIER,;GGA2,missense_variant,p.A508T,ENST00000309859.8,c.1522G>A,MODERATE,YES +CFAP52 146845 BI GRCh38 17 9586794 9586794 + missense_variant Missense_Mutation SNP G G C TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 50 45 c.367G>C p.Asp123His p.D123H ENST00000352665.10 NM_145054.5 123 Gat/Cat 3/14 P1 C D/H protein_coding YES CCDS11149.2 367/1863 CAAATGATTTG Gene3D:2.130.10.10;Pfam:PF00400;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR13720;PANTHER:PTHR13720:SF14;SMART:SM00320;Superfamily:SSF50978 ENSP00000339449 3/14 COSV55349070 ENST00000352665 Transcript 1.0 ENSG00000166596 HGNC:16053 MODERATE NM_145054.5 missense_variant 1 1.0 probably_damaging(0.963) Unknown deleterious(0.01) 1 Q8N1V2.150 CFAP52 HGNC 1 1.0 UPI00001AECC1 Q8N1V2-1 SNV CFAP52,missense_variant,p.D123H,ENST00000352665,NM_145054.5,c.367G>C,MODERATE,YES,deleterious(0.01),probably_damaging(0.963),1;CFAP52,missense_variant,p.D55H,ENST00000396219,NM_001080556.2,c.163G>C,MODERATE,,deleterious(0.01),possibly_damaging(0.86),1;CFAP52,missense_variant,p.M121I,ENST00000576499,,c.363G>C,MODERATE,,,unknown(0),1;CFAP52,3_prime_UTR_variant,,ENST00000576630,,c.*428G>C,MODIFIER,,,,1;CFAP52,3_prime_UTR_variant,,ENST00000575247,,c.*71G>C,MODIFIER,,,,1;CFAP52,3_prime_UTR_variant,,ENST00000572333,,c.*71G>C,MODIFIER,,,,1;CFAP52,non_coding_transcript_exon_variant,,ENST00000576320,,n.164G>C,MODIFIER,,,,1;CFAP52,intron_variant,,ENST00000574937,,c.70+10029G>C,MODIFIER,,,,1;RPL19P18,downstream_gene_variant,,ENST00000466869,,,MODIFIER,YES,,,-1 421/2166 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 92 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 95 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS CFAP52,non_coding_transcript_exon_variant,,ENST00000576320.1,n.164G>C,MODIFIER,;CFAP52,missense_variant,p.M121I,ENST00000576499.1,c.363G>C,MODERATE,;CFAP52,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000572333.5,c.*71G>C,MODIFIER,;CFAP52,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000576630.5,c.*428G>C,MODIFIER,;CFAP52,intron_variant,NMD_transcript_variant,,ENST00000574937.5,c.70+10029G>C,MODIFIER,;CFAP52,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000575247.5,c.*71G>C,MODIFIER,;CFAP52,missense_variant,p.D123H,ENST00000352665.10,c.367G>C,MODERATE,YES;CFAP52,missense_variant,p.D55H,ENST00000396219.7,c.163G>C,MODERATE, +C17orf80 55028 BI GRCh38 17 73242972 73242972 + synonymous_variant Silent SNP C C G novel TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 16 13 c.1698C>G p.Val566= p.V566= ENST00000535032.7 NM_001351264.2 566 gtC/gtG 5/6 P4 G V protein_coding YES CCDS11694.1 1698/1830 TTCGTCCTGTG PANTHER:PTHR16270;Transmembrane_helices:TMhelix ENSP00000351937 5/6 ENST00000359042 Transcript ENSG00000141219 HGNC:29601 LOW synonymous_variant Unknown Q9BSJ5.121 C17orf80 HGNC 1 5.0 UPI000014128C Q9BSJ5-1 SNV C17orf80,synonymous_variant,p.V566=,ENST00000359042,NM_017941.5,c.1698C>G,LOW,YES,,,1;C17orf80,synonymous_variant,p.V530=,ENST00000268942,NM_001351265.2&NM_001100621.3,c.1590C>G,LOW,,,,1;C17orf80,synonymous_variant,p.V530=,ENST00000255557,NM_001288771.3,c.1590C>G,LOW,,,,1;C17orf80,synonymous_variant,p.V566=,ENST00000535032,NM_001351264.2,c.1698C>G,LOW,,,,1;C17orf80,synonymous_variant,p.V566=,ENST00000426147,NM_001100622.4,c.1698C>G,LOW,,,,1;C17orf80,synonymous_variant,p.V530=,ENST00000577615,NM_001288770.3,c.1590C>G,LOW,,,,1;C17orf80,synonymous_variant,p.V35=,ENST00000582793,,c.105C>G,LOW,,,,1;AC087301.1,upstream_gene_variant,,ENST00000579037,,,MODIFIER,YES,,,1 1907/3645 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 37 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 29 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS C17orf80,synonymous_variant,p.V35=,ENST00000582793.1,c.105C>G,LOW,;C17orf80,synonymous_variant,p.V566=,ENST00000426147.6,c.1698C>G,LOW,;C17orf80,synonymous_variant,p.V530=,ENST00000268942.12,c.1590C>G,LOW,;C17orf80,synonymous_variant,p.V566=,ENST00000359042.6,c.1698C>G,LOW,;C17orf80,synonymous_variant,p.V530=,ENST00000577615.5,c.1590C>G,LOW,;C17orf80,synonymous_variant,p.V566=,ENST00000535032.7,c.1698C>G,LOW,YES;C17orf80,synonymous_variant,p.V530=,ENST00000255557.8,c.1590C>G,LOW, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 32 21 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 79 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 53 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +MIR125A 406910 BI GRCh38 19 51693260 51693260 + mature_miRNA_variant mature_miRNA_variant SNP T T A novel TCGA-V3-A9ZX-01A TCGA-V3-A9ZX-10A Somatic 6 4 n.7T>A ENST00000385273.1 1/1 P1 A protein_coding YES CCDS82386.1 GCCAGTCTCTA 70.0 ENSP00000490829 ENST00000637797 Transcript ENSG00000182310 HGNC:27113 MODIFIER NM_001316972.2 upstream_gene_variant 1.0 Unknown W5XKT8.33 SPACA6 HGNC 1 1.0 UPI0006B2D8C0 W5XKT8-1 SNV SPACA6,intron_variant,,ENST00000646845,,c.368-1218T>A,MODIFIER,,,,1;SPACA6,upstream_gene_variant,,ENST00000637797,NM_001316994.2&NM_001316972.2,,MODIFIER,YES,,,1;MIR125A,non_coding_transcript_exon_variant,,ENST00000385273,,n.7T>A,MODIFIER,YES,,,1;MIRLET7E,downstream_gene_variant,,ENST00000362102,,,MODIFIER,YES,,,1;MIR99B,downstream_gene_variant,,ENST00000384819,,,MODIFIER,YES,,,1;SPACA6,upstream_gene_variant,,ENST00000571328,,,MODIFIER,,,,1;SPACA6,upstream_gene_variant,,ENST00000573266,,,MODIFIER,,,,1;SPACA6,upstream_gene_variant,,ENST00000574072,,,MODIFIER,,,,1;SPACA6,upstream_gene_variant,,ENST00000576093,,,MODIFIER,,,,1;SPACA6,upstream_gene_variant,,ENST00000576494,,,MODIFIER,,,,1;SPACA6P-AS,non_coding_transcript_exon_variant,,ENST00000602324,,n.197A>T,MODIFIER,YES,,,-1 muse;mutect2 5019e7f1-db46-4a07-9e7b-b6e5d1481b84 0 13 9e53e568-2eb6-4662-9a22-91d6d6b00fa8 10 5f90cb58-960e-442c-a0ba-760c36f73a74 SUCCESS MIR125A,mature_miRNA_variant,,ENST00000385273.1,n.7T>A,MODIFIER,YES;SPACA6,intron_variant,,ENST00000646845.1,c.368-1218T>A,MODIFIER,;SPACA6,intron_variant,,ENST00000710615.1,c.-41-1218T>A,MODIFIER,;SPACA6-AS1,non_coding_transcript_exon_variant,,ENST00000602324.1,n.197A>T,MODIFIER,YES +JAK1 3716 BI GRCh38 1 64873369 64873369 + splice_donor_variant Splice_Site SNP C C T novel TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 3 8 c.483+1G>A p.X161_splice p.X161_splice ENST00000342505.5 NM_001321857.2 161 P1 T protein_coding CCDS41346.1 TCCTACCTGAG ENSP00000343204 ENST00000342505 Transcript NonExonic 1.0 ENSG00000162434 HGNC:6190 HIGH 5/24 NM_002227.4 splice_donor_variant Unknown P23458.218 JAK1 HGNC -1 5.0 UPI0000054C7D SNV JAK1,splice_donor_variant,p.X161_splice,ENST00000342505,NM_001321857.2&NM_002227.4,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000671929,,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000671954,NM_001321852.2,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000672179,NM_001321856.1&NM_001320923.1,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000672247,NM_001321855.2,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000672434,NM_001321854.2&NM_001321853.2,c.483+1G>A,HIGH,YES,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000672751,,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000673046,,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X43_splice,ENST00000673246,,c.127+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000673254,,c.483+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,p.X161_splice,ENST00000673502,,c.483+1G>A,HIGH,,,,-1;JAK1,downstream_gene_variant,,ENST00000672099,,,MODIFIER,,,,-1;JAK1,upstream_gene_variant,,ENST00000672903,,,MODIFIER,,,,-1;JAK1,splice_donor_variant,,ENST00000671746,,c.*391+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,,ENST00000673220,,c.*3043+1G>A,HIGH,,,,-1;JAK1,splice_donor_variant,,ENST00000673314,,n.589+1G>A,HIGH,,,,-1 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 60 1d9e059e-86a6-4259-9368-9ce7e3d725ca 11 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS JAK1,splice_donor_variant,p.X161_splice,ENST00000699263.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000699262.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,NMD_transcript_variant,p.X130_splice,ENST00000673220.1,c.*3043+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000673254.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000673046.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,,ENST00000673502.2,n.934+1G>A,HIGH,;JAK1,splice_donor_variant,NMD_transcript_variant,p.X161_splice,ENST00000699261.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,NMD_transcript_variant,p.X161_splice,ENST00000699313.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000672574.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,,ENST00000673314.2,n.792+1G>A,HIGH,;JAK1,splice_donor_variant,NMD_transcript_variant,,ENST00000671746.2,c.*391+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000672247.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000672751.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000673246.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000672179.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,NMD_transcript_variant,p.X161_splice,ENST00000699311.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000699312.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000699310.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000671954.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000699260.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000671929.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000699259.1,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000672434.2,c.483+1G>A,HIGH,;JAK1,splice_donor_variant,p.X161_splice,ENST00000342505.5,c.483+1G>A,HIGH,YES +NOP14 8602 BI GRCh38 4 2950117 2950117 + missense_variant Missense_Mutation SNP C C T rs145122268 TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 88 67 c.1099G>A p.Gly367Arg p.G367R ENST00000314262.10 NM_003703.3 367 Ggg/Agg 8/19 P1 T G/R protein_coding CCDS33945.1 1099/2574 CTCCCCGCCTG Pfam:PF04147;PANTHER:PTHR23183;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000315674 8/19 rs145122268 ENST00000314262 Transcript ENSG00000087269 HGNC:16821 MODERATE missense_variant benign(0.001) Unknown tolerated(0.45) P78316.160 NOP14 HGNC -1 1.0 UPI00001A9472 P78316-1 SNV NOP14,missense_variant,p.G367R,ENST00000416614,NM_001291978.2,c.1099G>A,MODERATE,YES,tolerated(0.45),benign(0.001),-1;NOP14,missense_variant,p.G367R,ENST00000314262,NM_003703.3,c.1099G>A,MODERATE,,tolerated(0.45),benign(0.001),-1;NOP14,missense_variant,p.G367R,ENST00000502735,,c.1099G>A,MODERATE,,tolerated(0.45),benign(0),-1;NOP14,missense_variant,p.G367R,ENST00000398071,NM_001291979.2,c.1099G>A,MODERATE,,tolerated(0.47),benign(0),-1;NOP14-AS1,intron_variant,,ENST00000503709,,n.828-36C>T,MODIFIER,,,,1;NOP14-AS1,intron_variant,,ENST00000515194,,n.3582-36C>T,MODIFIER,YES,,,1;NOP14-AS1,intron_variant,,ENST00000664833,,n.443-36C>T,MODIFIER,,,,1;NOP14-AS1,intron_variant,,ENST00000671407,,n.3212-36C>T,MODIFIER,,,,1;NOP14-AS1,intron_variant,,ENST00000671608,,n.671-36C>T,MODIFIER,,,,1;NOP14-AS1,downstream_gene_variant,,ENST00000505731,,,MODIFIER,,,,1;NOP14-AS1,downstream_gene_variant,,ENST00000507702,,,MODIFIER,,,,1 1148/2889 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 2.0278799638617784e-05 2.4323799152625725e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.086039941990748e-05 0.0 3.086039941990748e-05 0.0 0.0 0 222 1d9e059e-86a6-4259-9368-9ce7e3d725ca 156 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS NOP14,missense_variant,p.G367R,ENST00000398071.4,c.1099G>A,MODERATE,;NOP14,missense_variant,p.G367R,ENST00000502735.5,c.1099G>A,MODERATE,;NOP14,missense_variant,p.G367R,ENST00000314262.10,c.1099G>A,MODERATE,;NOP14,missense_variant,p.G367R,ENST00000416614.7,c.1099G>A,MODERATE,YES;NOP14-AS1,intron_variant,,ENST00000503709.1,n.828-36C>T,MODIFIER,YES;NOP14-AS1,intron_variant,,ENST00000671608.1,n.671-36C>T,MODIFIER,;NOP14-AS1,intron_variant,,ENST00000664833.1,n.443-36C>T,MODIFIER,;NOP14-AS1,intron_variant,,ENST00000515194.6,n.3582-36C>T,MODIFIER,;NOP14-AS1,intron_variant,,ENST00000671407.1,n.3212-36C>T,MODIFIER, +UBA6 55236 BI GRCh38 4 67665264 67665264 + synonymous_variant Silent SNP A A G rs1414055928 TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 45 35 c.822T>C p.Gly274= p.G274= ENST00000322244.10 NM_018227.6 274 ggT/ggC 10/33 P1 G G protein_coding YES CCDS3516.1 822/3159 GTGTCACCAAT CDD:cd01491;PANTHER:PTHR10953;PANTHER:PTHR10953:SF186;Pfam:PF00899;Gene3D:3.40.50.12550;TIGRFAM:TIGR01408;Gene3D:2.40.30.180;Pfam:PF16190;Superfamily:SSF69572 ENSP00000313454 10/33 rs1414055928 ENST00000322244 Transcript ENSG00000033178 HGNC:25581 LOW NM_018227.6 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown A0AVT1.134 UBA6 HGNC -1 A1LT96.3 1.0 UPI000004A4F7 A0AVT1-1 SNV UBA6,synonymous_variant,p.G274=,ENST00000322244,NM_018227.6,c.822T>C,LOW,YES,,,-1;UBA6,synonymous_variant,p.G274=,ENST00000420827,,c.822T>C,LOW,,,,-1;UBA6,non_coding_transcript_exon_variant,,ENST00000429659,,n.851T>C,MODIFIER,,,,-1 858/9540 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 124 1d9e059e-86a6-4259-9368-9ce7e3d725ca 80 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS UBA6,non_coding_transcript_exon_variant,,ENST00000429659.7,n.851T>C,MODIFIER,;UBA6,synonymous_variant,p.G274=,ENST00000420827.2,c.822T>C,LOW,;UBA6,synonymous_variant,p.G274=,ENST00000322244.10,c.822T>C,LOW,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 42 27 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 108 1d9e059e-86a6-4259-9368-9ce7e3d725ca 69 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +ZNF462 58499 BI GRCh38 9 106929017 106929017 + missense_variant Missense_Mutation SNP G G A novel TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 20 10 c.5105G>A p.Cys1702Tyr p.C1702Y ENST00000277225.10 NM_021224.6 1702 tGt/tAt 3/13 P1 A C/Y protein_coding YES CCDS35096.1 5105/7521 CCTGTGTGCCT Gene3D:3.30.160.60;PANTHER:PTHR24403;PANTHER:PTHR24403:SF58;SMART:SM00355 ENSP00000277225 3/13 ENST00000277225 Transcript 1.0 ENSG00000148143 HGNC:21684 MODERATE NM_021224.6 missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0) Q96JM2.157 ZNF462 HGNC 1 1.0 UPI0000470106 Q96JM2-1 SNV ZNF462,missense_variant,p.C1702Y,ENST00000277225,NM_021224.6&NM_001347997.2,c.5105G>A,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;ZNF462,missense_variant,p.C585Y,ENST00000374686,,c.1754G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;ZNF462,missense_variant,p.C547Y,ENST00000441147,,c.1640G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;ZNF462,intron_variant,,ENST00000472574,,c.281-1508G>A,MODIFIER,,,,1;ZNF462,intron_variant,,ENST00000480607,,n.241-1508G>A,MODIFIER,,,,1;ZNF462,upstream_gene_variant,,ENST00000469433,,,MODIFIER,,,,1;ZNF462,upstream_gene_variant,,ENST00000471032,,,MODIFIER,,,,1;ZNF462,upstream_gene_variant,,ENST00000479166,,,MODIFIER,,,,1;ZNF462,upstream_gene_variant,,ENST00000497489,,,MODIFIER,,,,1 5325/10345 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 40 1d9e059e-86a6-4259-9368-9ce7e3d725ca 30 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS ZNF462,missense_variant,p.C547Y,ENST00000441147.6,c.1640G>A,MODERATE,;ZNF462,missense_variant,p.C585Y,ENST00000374686.6,c.1754G>A,MODERATE,;ZNF462,intron_variant,,ENST00000480607.5,n.241-1508G>A,MODIFIER,;ZNF462,missense_variant,p.C1702Y,ENST00000277225.10,c.5105G>A,MODERATE,YES;ZNF462,intron_variant,,ENST00000472574.1,c.281-1508G>A,MODIFIER, +USP15 9958 BI GRCh38 12 62384085 62384085 + missense_variant Missense_Mutation SNP C C T rs1483593421 TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 38 26 c.1256C>T p.Ala419Val p.A419V ENST00000280377.10 NM_001351159.2 419 gCc/gTc 11/22 P3 T A/V protein_coding YES CCDS58251.1 1256/2946 GGTTGCCGAAG PDB-ENSP_mappings:6cpm.C;PDB-ENSP_mappings:6cpm.D;PDB-ENSP_mappings:6crn.A;PDB-ENSP_mappings:6crn.B;PDB-ENSP_mappings:6crn.C;PDB-ENSP_mappings:6crn.D;PDB-ENSP_mappings:6gh9.A;PDB-ENSP_mappings:6gh9.B;PDB-ENSP_mappings:6gha.A;PDB-ENSP_mappings:6ml1.A;PDB-ENSP_mappings:6ml1.B;PROSITE_profiles:PS50235;PANTHER:PTHR21646;PANTHER:PTHR21646:SF45;Pfam:PF00443;Gene3D:3.90.70.10;Superfamily:SSF54001 ENSP00000280377 11/22 rs1483593421 ENST00000280377 Transcript ENSG00000135655 HGNC:12613 MODERATE NM_001252078.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) Q9Y4E8.199 USP15 HGNC 1 1.0 UPI00001379F8 Q9Y4E8-1 SNV USP15,missense_variant,p.A419V,ENST00000280377,NM_001351159.2&NM_001252078.2,c.1256C>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;USP15,missense_variant,p.A390V,ENST00000353364,NM_001351165.2&NM_001351166.2&NM_001351163.2&NM_001351164.2&NM_006313.3&NM_001351160.2,c.1169C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;USP15,downstream_gene_variant,,ENST00000547317,,,MODIFIER,,,,1;USP15,non_coding_transcript_exon_variant,,ENST00000549268,,n.614C>T,MODIFIER,,,,1 1267/14971 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 73 1d9e059e-86a6-4259-9368-9ce7e3d725ca 65 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS USP15,non_coding_transcript_exon_variant,,ENST00000549268.1,n.614C>T,MODIFIER,;USP15,missense_variant,p.A419V,ENST00000280377.10,c.1256C>T,MODERATE,YES;USP15,missense_variant,p.A390V,ENST00000353364.7,c.1169C>T,MODERATE, +PSG4 5672 BI GRCh38 19 43203939 43203939 + missense_variant Missense_Mutation SNP T T A novel TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 124 76 c.377A>T p.Lys126Met p.K126M ENST00000405312.8 NM_001316339.2 126 aAg/aTg 2/6 P1 A K/M protein_coding YES CCDS46093.1 377/1260 GTCGCTTTATG CDD:cd05774;PANTHER:PTHR44427;PANTHER:PTHR44427:SF17;Pfam:PF07686;Gene3D:2.60.40.10;SMART:SM00409;Superfamily:SSF48726 ENSP00000384770 2/6 ENST00000405312 Transcript ENSG00000243137 HGNC:9521 MODERATE NM_002780.5 missense_variant 1.0 benign(0.088) Unknown deleterious(0.03) Q00888.188 PSG4 HGNC -1 1.0 UPI000034ECBA Q00888-1 SNV PSG4,missense_variant,p.K126M,ENST00000405312,NM_001316339.2&NM_002780.5,c.377A>T,MODERATE,YES,deleterious(0.03),benign(0.088),-1;PSG4,missense_variant,p.K126M,ENST00000433626,NM_001276495.1,c.377A>T,MODERATE,,tolerated(0.05),possibly_damaging(0.657),-1;PSG4,missense_variant,p.K126M,ENST00000244295,NM_213633.3,c.377A>T,MODERATE,,deleterious(0.04),benign(0.328),-1;PSG4,missense_variant,p.K142M,ENST00000451895,,c.425A>T,MODERATE,,tolerated(0.07),benign(0.378),-1;PSG4,missense_variant,p.K105M,ENST00000599746,,c.314A>T,MODERATE,,tolerated(0.06),benign(0.041),-1;PSG4,missense_variant,p.K55M,ENST00000600572,,c.164A>T,MODERATE,,deleterious(0.04),benign(0.088),-1;PSG4,intron_variant,,ENST00000596907,,c.64+1534A>T,MODIFIER,,,,-1;PSG4,intron_variant,,ENST00000599391,,c.64+1534A>T,MODIFIER,,,,-1;PSG4,non_coding_transcript_exon_variant,,ENST00000597912,,n.1444A>T,MODIFIER,,,,-1;PSG4,non_coding_transcript_exon_variant,,ENST00000495316,,n.113A>T,MODIFIER,,,,-1;PSG4,intron_variant,,ENST00000595949,,c.64+1534A>T,MODIFIER,,,,-1;PSG4,intron_variant,,ENST00000596199,,n.166+1534A>T,MODIFIER,,,,-1;PSG4,intron_variant,,ENST00000601041,,c.64+1534A>T,MODIFIER,,,,-1 479/2032 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 253 1d9e059e-86a6-4259-9368-9ce7e3d725ca 200 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS PSG4,non_coding_transcript_exon_variant,,ENST00000597912.1,n.1444A>T,MODIFIER,;PSG4,missense_variant,p.K55M,ENST00000600572.1,c.164A>T,MODERATE,;PSG4,missense_variant,p.K142M,ENST00000451895.1,c.425A>T,MODERATE,;PSG4,intron_variant,,ENST00000596199.5,n.166+1534A>T,MODIFIER,;PSG4,non_coding_transcript_exon_variant,,ENST00000495316.2,n.113A>T,MODIFIER,;PSG4,intron_variant,NMD_transcript_variant,,ENST00000595949.1,c.64+1534A>T,MODIFIER,;PSG4,missense_variant,p.S105C,ENST00000599746.5,c.313A>T,MODERATE,;PSG4,intron_variant,NMD_transcript_variant,,ENST00000601041.1,c.64+1534A>T,MODIFIER,;PSG4,intron_variant,,ENST00000599391.1,c.64+1534A>T,MODIFIER,;PSG4,intron_variant,,ENST00000596907.5,c.64+1534A>T,MODIFIER,;PSG4,missense_variant,p.K126M,ENST00000244295.13,c.377A>T,MODERATE,;PSG4,missense_variant,p.K126M,ENST00000433626.6,c.377A>T,MODERATE,;PSG4,missense_variant,p.K126M,ENST00000405312.8,c.377A>T,MODERATE,YES +MATN4 8785 BI GRCh38 20 45298262 45298262 + missense_variant Missense_Mutation SNP C C T rs150948243 TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 17 38 c.1457G>A p.Arg486His p.R486H ENST00000372754.5 486 cGt/cAt 7/10 0.0002 0.0 0.0014 0.0 0.0 0.0 P4 T R/H protein_coding YES 1457/1869 GGGCACGGGGC COSM5047886;COSM5047887 Pfam:PF00092;Gene3D:3.40.50.410;SMART:SM00327;Superfamily:SSF53300;PROSITE_profiles:PS50234;PANTHER:PTHR24020;PANTHER:PTHR24020:SF14 ENSP00000361840 0.0 0.0004651 7/10 rs150948243 ENST00000372754 Transcript ENSG00000124159 HGNC:6910 MODERATE 0.0014 AMR missense_variant 1.0 probably_damaging(0.909) Unknown O95460.185 MATN4 HGNC -1 5.0 UPI00004708AD O95460-1 SNV MATN4,missense_variant,p.R486H,ENST00000372754,,c.1457G>A,MODERATE,YES,,probably_damaging(0.909),-1;MATN4,missense_variant,p.R404H,ENST00000360607,NM_030590.4,c.1211G>A,MODERATE,,,possibly_damaging(0.813),-1;MATN4,missense_variant,p.R445H,ENST00000372756,NM_003833.4,c.1334G>A,MODERATE,,,possibly_damaging(0.852),-1;MATN4,missense_variant,p.R445H,ENST00000537548,,c.1334G>A,MODERATE,,,possibly_damaging(0.852),-1;MATN4,missense_variant,p.R363H,ENST00000353917,NM_030592.3,c.1088G>A,MODERATE,,tolerated(0.55),probably_damaging(0.953),-1 1466/2200 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0.0001644 6.198e-05 5.791e-05 0.0 0.0 9.262e-05 0.0003209 0.0 0.0 9.4631701358594e-05 2.4311999368364923e-05 0.0 0.0001986489951377 0.0 0.0 0.0 amr 0.0001986489951377 0.0 0.0001543399994261 0.0 0.0 0 61 1d9e059e-86a6-4259-9368-9ce7e3d725ca 55 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS MATN4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686119.1,c.*1141G>A,MODIFIER,;MATN4,missense_variant,p.R404H,ENST00000360607.10,c.1211G>A,MODERATE,;MATN4,missense_variant,p.R445H,ENST00000372756.6,c.1334G>A,MODERATE,YES;MATN4,missense_variant,p.R445H,ENST00000537548.3,c.1334G>A,MODERATE,;MATN4,missense_variant,p.R363H,ENST00000353917.10,c.1088G>A,MODERATE,;MATN4,missense_variant,p.R486H,ENST00000372754.5,c.1457G>A,MODERATE, +EMID1 129080 BI GRCh38 22 29225200 29225200 + synonymous_variant Silent SNP G G T novel TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 38 28 c.387G>T p.Arg129= p.R129= ENST00000334018.11 NM_133455.4 129 cgG/cgT 4/15 P4 T R protein_coding CCDS33630.1 387/1332 CTTCGGCCCAC PANTHER:PTHR15427:SF23;PANTHER:PTHR15427 ENSP00000335481 4/15 ENST00000334018 Transcript ENSG00000186998 HGNC:18036 LOW NM_133455.4 synonymous_variant Unknown Q96A84.136 EMID1 HGNC 1 1.0 UPI00001A796B Q96A84-3 SNV EMID1,synonymous_variant,p.R129=,ENST00000334018,NM_133455.4&NM_001267895.2,c.387G>T,LOW,,,,1;EMID1,synonymous_variant,p.R129=,ENST00000404820,,c.387G>T,LOW,YES,,,1;EMID1,synonymous_variant,p.R129=,ENST00000404755,,c.387G>T,LOW,,,,1;EMID1,synonymous_variant,p.R129=,ENST00000429226,,c.387G>T,LOW,,,,1;EMID1,intron_variant,,ENST00000430127,,c.320-1290G>T,MODIFIER,,,,1;EMID1,non_coding_transcript_exon_variant,,ENST00000484039,,n.122G>T,MODIFIER,,,,1;EMID1,intron_variant,,ENST00000435427,,c.102-5820G>T,MODIFIER,,,,1 530/2128 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 75 1d9e059e-86a6-4259-9368-9ce7e3d725ca 66 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS EMID1,non_coding_transcript_exon_variant,,ENST00000484039.5,n.122G>T,MODIFIER,;EMID1,intron_variant,NMD_transcript_variant,,ENST00000435427.5,c.102-5820G>T,MODIFIER,;EMID1,intron_variant,,ENST00000430127.1,c.320-1290G>T,MODIFIER,;EMID1,synonymous_variant,p.R129=,ENST00000404820.7,c.387G>T,LOW,;EMID1,synonymous_variant,p.R129=,ENST00000404755.7,c.387G>T,LOW,;EMID1,synonymous_variant,p.R129=,ENST00000429226.5,c.387G>T,LOW,;EMID1,synonymous_variant,p.R129=,ENST00000334018.11,c.387G>T,LOW,YES +DGKK 139189 BI GRCh38 X 50470357 50470357 + missense_variant Missense_Mutation SNP C C G novel TCGA-WC-A883-01A TCGA-WC-A883-10A Somatic 110 94 c.322G>C p.Glu108Gln p.E108Q ENST00000611977.2 NM_001013742.4 108 Gag/Cag 1/28 P1 G E/Q protein_coding YES CCDS75980.1 322/3816 CGGCTCTGTGG MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000477515 1/28 ENST00000611977 Transcript ENSG00000274588 HGNC:32395 MODERATE NM_001013742.4 missense_variant 1.0 possibly_damaging(0.813) Unknown tolerated_low_confidence(0.12) Q5KSL6.127 DGKK HGNC -1 1.0 UPI00004BA922 SNV DGKK,missense_variant,p.E108Q,ENST00000611977,NM_001013742.4,c.322G>C,MODERATE,YES,tolerated_low_confidence(0.12),possibly_damaging(0.813),-1 469/7494 muse;mutect2;varscan2 a08e4c1d-5d92-43ec-b0b9-87b2286d685e 0 291 1d9e059e-86a6-4259-9368-9ce7e3d725ca 204 cb6cbe14-3c2a-45ae-8df0-f6a7b210adb2 SUCCESS DGKK,missense_variant,p.E108Q,ENST00000611977.2,c.322G>C,MODERATE,YES +SLC30A1 7779 BI GRCh38 1 211575933 211575933 + missense_variant Missense_Mutation SNP T T C rs771486914 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 57 40 c.979A>G p.Ile327Val p.I327V ENST00000367001.5 NM_021194.3 327 Ata/Gta 2/2 P1 C I/V protein_coding YES CCDS1499.1 979/1524 AAGTATACAAA PANTHER:PTHR45820;PANTHER:PTHR45820:SF1;Transmembrane_helices:TMhelix ENSP00000355968 2/2 rs771486914 ENST00000367001 Transcript ENSG00000170385 HGNC:11012 MODERATE NM_021194.3 4.409e-05 gnomAD_NFE missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0.01) Q9Y6M5.164 SLC30A1 HGNC -1 1.0 UPI000013EBA0 SNV SLC30A1,missense_variant,p.I327V,ENST00000367001,NM_021194.3,c.979A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.994),-1 1528/5893 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 1.996e-05 0.0 0.0 0.0 0.0 0.0 4.409e-05 0.0 0.0 0 105 f7f46f33-0972-422b-bff2-d5881c96898b 97 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS SLC30A1,missense_variant,p.I327V,ENST00000367001.5,c.979A>G,MODERATE,YES +DYNC1I2 1781 BI GRCh38 2 171744157 171744157 + synonymous_variant Silent SNP T T C rs1489997404 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 24 5 c.1645T>C p.Leu549= p.L549= ENST00000397119.8 NM_001378.3 549 Ttg/Ctg 16/18 A1 C L protein_coding YES CCDS46450.1 1645/1917 GGAGATTGGAT PDB-ENSP_mappings:6f1t.g;PDB-ENSP_mappings:6f1t.h;PDB-ENSP_mappings:6f1t.o;PDB-ENSP_mappings:6f1t.p;PDB-ENSP_mappings:6f1u.h;PDB-ENSP_mappings:6f1z.o;PDB-ENSP_mappings:6f1z.p;PDB-ENSP_mappings:6f38.g;PDB-ENSP_mappings:6f38.h;PDB-ENSP_mappings:6f38.o;PDB-ENSP_mappings:6f38.p;PDB-ENSP_mappings:6f3a.g;PDB-ENSP_mappings:6f3a.h;PROSITE_profiles:PS50294;PANTHER:PTHR12442;PANTHER:PTHR12442:SF37;Gene3D:2.130.10.10;SMART:SM00320;Superfamily:SSF50978 ENSP00000380308 16/18 rs1489997404 ENST00000397119 Transcript 1.0 ENSG00000077380 HGNC:2964 LOW NM_001378.3 synonymous_variant 1.0 Unknown Q13409.203 DYNC1I2 HGNC 1 A0A140VKE9.23 1.0 UPI0000129A05 Q13409-1 SNV DYNC1I2,synonymous_variant,p.L549=,ENST00000397119,NM_001378.3,c.1645T>C,LOW,YES,,,1;DYNC1I2,synonymous_variant,p.L523=,ENST00000340296,NM_001271788.2,c.1567T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L549=,ENST00000409773,NM_001271785.2,c.1645T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L523=,ENST00000409197,NM_001271789.2,c.1567T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L549=,ENST00000409453,,c.1645T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L523=,ENST00000508530,NM_001271790.2&NM_001320884.2,c.1567T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L543=,ENST00000409317,NM_001320882.2&NM_001378455.1&NM_001320883.2&NM_001378456.1,c.1627T>C,LOW,,,,1;DYNC1I2,synonymous_variant,p.L541=,ENST00000410079,NM_001271786.2&NM_001271787.2,c.1621T>C,LOW,,,,1;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000482454,,n.1798T>C,MODIFIER,,,,1;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000479806,,n.1008T>C,MODIFIER,,,,1 1813/4354 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 6.761139957234263e-06 2.4324999685632065e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 32 f7f46f33-0972-422b-bff2-d5881c96898b 29 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS DYNC1I2,non_coding_transcript_exon_variant,,ENST00000479806.1,n.1008T>C,MODIFIER,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000482454.5,n.1798T>C,MODIFIER,;DYNC1I2,synonymous_variant,p.L549=,ENST00000409453.5,c.1645T>C,LOW,;DYNC1I2,synonymous_variant,p.L549=,ENST00000409773.5,c.1645T>C,LOW,;DYNC1I2,synonymous_variant,p.L543=,ENST00000409317.5,c.1627T>C,LOW,;DYNC1I2,synonymous_variant,p.L523=,ENST00000409197.5,c.1567T>C,LOW,;DYNC1I2,synonymous_variant,p.L523=,ENST00000508530.5,c.1567T>C,LOW,;DYNC1I2,synonymous_variant,p.L541=,ENST00000410079.7,c.1621T>C,LOW,;DYNC1I2,synonymous_variant,p.L549=,ENST00000397119.8,c.1645T>C,LOW,YES;DYNC1I2,synonymous_variant,p.L523=,ENST00000340296.8,c.1567T>C,LOW, +SPEG 10290 BI GRCh38 2 219480101 219480101 + missense_variant Missense_Mutation SNP T T C rs1382597576 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 39 24 c.5303T>C p.Ile1768Thr p.I1768T ENST00000312358.12 NM_005876.5 1768 aTt/aCt 25/41 P1 C I/T protein_coding YES CCDS42824.1 5303/9804 CGAGATTGTCA Gene3D:1.10.510.10;Pfam:PF00069;PROSITE_profiles:PS50011;PANTHER:PTHR47633;PANTHER:PTHR47633:SF3;SMART:SM00220;Superfamily:SSF49265;Superfamily:SSF56112;CDD:cd14108 ENSP00000311684 25/41 rs1382597576 ENST00000312358 Transcript 1.0 ENSG00000072195 HGNC:16901 MODERATE NM_005876.5 9.934e-05 gnomAD_ASJ missense_variant probably_damaging(0.994) Unknown deleterious(0.01) Q15772.182 SPEG HGNC 1 5.0 UPI000066D99E Q15772-5 SNV SPEG,missense_variant,p.I1768T,ENST00000312358,NM_005876.5,c.5303T>C,MODERATE,YES,deleterious(0.01),probably_damaging(0.994),1;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,,n.4546T>C,MODIFIER,,,,1;ASIC4-AS1,downstream_gene_variant,,ENST00000429882,,,MODIFIER,YES,,,-1 5438/10782 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 4.013e-06 0.0 0.0 9.934e-05 0.0 0.0 0.0 0.0 0.0 0 48 f7f46f33-0972-422b-bff2-d5881c96898b 63 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS SPEG,non_coding_transcript_exon_variant,,ENST00000485813.5,n.4546T>C,MODIFIER,;SPEG,missense_variant,p.I1768T,ENST00000312358.12,c.5303T>C,MODERATE,YES +BAP1 8314 BI GRCh38 3 52408526 52408526 + missense_variant Missense_Mutation SNP T T C rs1194652468 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 1 11 c.203A>G p.Asp68Gly p.D68G ENST00000460680.6 NM_004656.4 68 gAt/gGt 4/17 P1 C D/G protein_coding YES CCDS2853.1 203/2190 ACGTATCATCC Low_complexity_(Seg):seg;CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 4/17 rs1194652468;COSV56240608 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 MODERATE NM_004656.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 benign(0.029) Unknown deleterious(0) 0;1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,missense_variant,p.D68G,ENST00000460680,NM_004656.4,c.203A>G,MODERATE,YES,deleterious(0),benign(0.029),-1;BAP1,missense_variant,p.D68G,ENST00000296288,,c.203A>G,MODERATE,,deleterious(0),benign(0.017),-1;BAP1,5_prime_UTR_variant,,ENST00000470173,,c.-35A>G,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000614886,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000615126,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000472337,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,,n.203A>G,MODIFIER,,,,-1;BAP1,intron_variant,,ENST00000490917,,c.123-449A>G,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 333/3600 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 17 f7f46f33-0972-422b-bff2-d5881c96898b 12 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS BAP1,5_prime_UTR_variant,,ENST00000470173.1,c.-35A>G,MODIFIER,;BAP1,intron_variant,NMD_transcript_variant,,ENST00000490917.1,c.123-449A>G,MODIFIER,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984.5,n.203A>G,MODIFIER,;BAP1,missense_variant,p.D68G,ENST00000296288.9,c.203A>G,MODERATE,;BAP1,missense_variant,p.D68G,ENST00000460680.6,c.203A>G,MODERATE,YES +B4GALT4 8702 BI GRCh38 3 119226961 119226961 + missense_variant Missense_Mutation SNP G G A rs781226310 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 10 21 c.334C>T p.Arg112Trp p.R112W ENST00000359213.7 NM_212543.2 112 Cgg/Tgg 5/9 P1 A R/W protein_coding CCDS2986.1 334/1035 ATACCGGCCTC PANTHER:PTHR19300:SF9;PANTHER:PTHR19300;Pfam:PF13733;Gene3D:3.90.550.10;Superfamily:SSF53448 ENSP00000352144 5/9 rs781226310 ENST00000359213 Transcript ENSG00000121578 HGNC:927 MODERATE 0.0001087 gnomAD_EAS missense_variant possibly_damaging(0.867) Unknown deleterious(0) O60513.181 B4GALT4 HGNC -1 B2RAZ5.111 2.0 UPI00000389DB SNV B4GALT4,missense_variant,p.R112W,ENST00000467604,,c.334C>T,MODERATE,,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,missense_variant,p.R112W,ENST00000483209,,c.334C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,missense_variant,p.R112W,ENST00000359213,NM_212543.2,c.334C>T,MODERATE,,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,missense_variant,p.R112W,ENST00000393765,NM_003778.4,c.334C>T,MODERATE,,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,missense_variant,p.R112W,ENST00000475803,,c.334C>T,MODERATE,,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,missense_variant,p.R112W,ENST00000479150,,c.334C>T,MODERATE,,deleterious(0),possibly_damaging(0.867),-1;B4GALT4,5_prime_UTR_variant,,ENST00000491906,,c.-78C>T,MODIFIER,,,,-1;B4GALT4,intron_variant,,ENST00000471675,,c.165+28C>T,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000459778,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000459820,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000470111,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000473887,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000493932,,,MODIFIER,,,,-1;B4GALT4,non_coding_transcript_exon_variant,,ENST00000460321,,n.328C>T,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000460395,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000472471,,,MODIFIER,,,,-1;B4GALT4,downstream_gene_variant,,ENST00000484595,,,MODIFIER,,,,-1;B4GALT4,missense_variant,p.R112W,ENST00000480814,,c.334C>T,MODERATE,,deleterious(0),probably_damaging(0.915),-1;B4GALT4-AS1,intron_variant,,ENST00000470790,,n.196+280G>A,MODIFIER,YES,,,1;B4GALT4-AS1,intron_variant,,ENST00000657819,,n.175+280G>A,MODIFIER,,,,1 877/2385 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 2.785e-05 0.0 5.783e-05 0.0 0.0001087 0.0 2.64e-05 0.0 0.0 1.352500021312153e-05 0.0 0.0 0.0 0.0 0.0002017759979935 0.0 0.0 1.543260077596642e-05 0.0 0.0 0 48 f7f46f33-0972-422b-bff2-d5881c96898b 31 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS B4GALT4,missense_variant,p.R112W,ENST00000479150.5,c.334C>T,MODERATE,;B4GALT4,missense_variant,p.R112W,ENST00000475803.5,c.334C>T,MODERATE,;B4GALT4,5_prime_UTR_variant,,ENST00000491906.5,c.-78C>T,MODIFIER,;B4GALT4-AS1,intron_variant,,ENST00000657819.1,n.175+280G>A,MODIFIER,;B4GALT4-AS1,intron_variant,,ENST00000470790.1,n.196+280G>A,MODIFIER,YES;B4GALT4,non_coding_transcript_exon_variant,,ENST00000460321.5,n.328C>T,MODIFIER,;B4GALT4,missense_variant,NMD_transcript_variant,p.R112W,ENST00000480814.5,c.334C>T,MODERATE,;B4GALT4,missense_variant,p.R112W,ENST00000359213.7,c.334C>T,MODERATE,;B4GALT4,intron_variant,,ENST00000471675.1,c.165+28C>T,MODIFIER,;B4GALT4,missense_variant,p.R112W,ENST00000393765.7,c.334C>T,MODERATE,YES;B4GALT4,missense_variant,p.R112W,ENST00000467604.5,c.334C>T,MODERATE,;B4GALT4,missense_variant,p.R112W,ENST00000483209.5,c.334C>T,MODERATE, +N4BP2 55728 BI GRCh38 4 40144642 40144642 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 56 61 c.4985A>C p.His1662Pro p.H1662P ENST00000261435.11 NM_001318359.2 1662 cAt/cCt 16/18 P1 C H/P protein_coding YES CCDS3457.1 4985/5313 TCTTCATGAGC PDB-ENSP_mappings:2vkc.A;Pfam:PF08590;PANTHER:PTHR46535;SMART:SM01162 ENSP00000261435 16/18 ENST00000261435 Transcript 1.0 ENSG00000078177 HGNC:29851 MODERATE NM_018177.6 missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) Q86UW6.158 N4BP2 HGNC 1 5.0 UPI00001A962C Q86UW6-1 SNV N4BP2,missense_variant,p.H1662P,ENST00000261435,NM_001318359.2&NM_018177.6,c.4985A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;N4BP2,missense_variant,p.H1292P,ENST00000513269,,c.3875A>C,MODERATE,,deleterious(0),probably_damaging(1),1;N4BP2,3_prime_UTR_variant,,ENST00000511480,,c.*4776A>C,MODIFIER,,,,1;AC095057.1,upstream_gene_variant,,ENST00000507583,,,MODIFIER,YES,,,-1 5377/9720 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 135 f7f46f33-0972-422b-bff2-d5881c96898b 117 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS N4BP2,synonymous_variant,p.S1291=,ENST00000513269.1,c.3873A>C,LOW,;N4BP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000511480.5,c.*4776A>C,MODIFIER,;N4BP2,missense_variant,p.H1662P,ENST00000261435.11,c.4985A>C,MODERATE,YES;N4BP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706658.1,c.*4776A>C,MODIFIER, +ADAMTS12 81792 BI GRCh38 5 33576093 33576093 + synonymous_variant Silent SNP G G A TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 106 14 c.3933C>T p.Gly1311= p.G1311= ENST00000504830.6 NM_030955.4 1311 ggC/ggT 19/24 P1 A G protein_coding YES CCDS34140.1 3933/4785 CCGTGGCCGTT Gene3D:2.20.100.10;PANTHER:PTHR13723;PANTHER:PTHR13723:SF189 ENSP00000422554 19/24 COSV100711108 ENST00000504830 Transcript ENSG00000151388 HGNC:14605 LOW NM_030955.4 synonymous_variant 1 1.0 Unknown 1 P58397.184 ADAMTS12 HGNC -1 1.0 UPI000013DC51 P58397-1 SNV ADAMTS12,synonymous_variant,p.G1311=,ENST00000504830,NM_030955.4,c.3933C>T,LOW,YES,,,-1;ADAMTS12,synonymous_variant,p.G1226=,ENST00000352040,NM_001324512.2,c.3678C>T,LOW,,,,-1;ADAMTS12,downstream_gene_variant,,ENST00000504582,,,MODIFIER,,,,-1 4067/8572 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 119 f7f46f33-0972-422b-bff2-d5881c96898b 120 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS ADAMTS12,synonymous_variant,p.G1226=,ENST00000352040.7,c.3678C>T,LOW,;ADAMTS12,synonymous_variant,p.G1311=,ENST00000504830.6,c.3933C>T,LOW,YES +IQGAP2 10788 BI GRCh38 5 76673488 76673488 + synonymous_variant Silent SNP A A G novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 78 10 c.3108A>G p.Thr1036= p.T1036= ENST00000274364.11 NM_006633.5 1036 acA/acG 25/36 P1 G T protein_coding YES CCDS34188.1 3108/4728 CTAACATACCC Gene3D:1.10.506.10;PDB-ENSP_mappings:5cjp.E;PDB-ENSP_mappings:5cjp.F;Pfam:PF00616;PROSITE_profiles:PS50018;PANTHER:PTHR14149;PANTHER:PTHR14149:SF12;SMART:SM00323;Superfamily:SSF48350 ENSP00000274364 25/36 ENST00000274364 Transcript ENSG00000145703 HGNC:6111 LOW NM_006633.5 synonymous_variant 1.0 Unknown Q13576.190 IQGAP2 HGNC 1 1.0 UPI000020CB2C Q13576-1 SNV IQGAP2,synonymous_variant,p.T1036=,ENST00000274364,NM_006633.5,c.3108A>G,LOW,YES,,,1;IQGAP2,synonymous_variant,p.T986=,ENST00000379730,NM_001285460.1,c.2958A>G,LOW,,,,1;IQGAP2,synonymous_variant,p.T986=,ENST00000505766,,c.2958A>G,LOW,,,,1;IQGAP2,synonymous_variant,p.T532=,ENST00000502745,NM_001285462.2,c.1596A>G,LOW,,,,1;IQGAP2,synonymous_variant,p.T532=,ENST00000396234,NM_001285461.2,c.1596A>G,LOW,,,,1;IQGAP2,downstream_gene_variant,,ENST00000514001,,,MODIFIER,,,,1;IQGAP2,non_coding_transcript_exon_variant,,ENST00000512383,,n.352A>G,MODIFIER,,,,1;IQGAP2,non_coding_transcript_exon_variant,,ENST00000504558,,n.154A>G,MODIFIER,,,,1;IQGAP2,upstream_gene_variant,,ENST00000504477,,,MODIFIER,,,,1;IQGAP2,upstream_gene_variant,,ENST00000509741,,,MODIFIER,,,,1;IQGAP2,upstream_gene_variant,,ENST00000512256,,,MODIFIER,,,,1 3369/5808 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 83 f7f46f33-0972-422b-bff2-d5881c96898b 88 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS IQGAP2,non_coding_transcript_exon_variant,,ENST00000504558.1,n.154A>G,MODIFIER,;IQGAP2,non_coding_transcript_exon_variant,,ENST00000512383.1,n.352A>G,MODIFIER,;IQGAP2,intron_variant,,ENST00000685564.1,c.58-9627A>G,MODIFIER,;IQGAP2,synonymous_variant,p.T532=,ENST00000502745.5,c.1596A>G,LOW,;IQGAP2,synonymous_variant,p.T532=,ENST00000396234.7,c.1596A>G,LOW,;IQGAP2,synonymous_variant,p.T986=,ENST00000379730.7,c.2958A>G,LOW,;IQGAP2,synonymous_variant,p.T1036=,ENST00000274364.11,c.3108A>G,LOW,YES +ANKRD6 22881 BI GRCh38 6 89618010 89618018 + inframe_deletion In_Frame_Del DEL TCTCCTTAC TCTCCTTAC - novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 66 39 c.772_780del p.Leu258_Thr260del p.L258_T260del ENST00000339746.9 NM_001242809.2 257 ctTCTCCTTACt/ctt 9/16 P4 - LLLT/L protein_coding YES CCDS56441.1 771-779/2184 TGCTCTTCTCCTTACTAAAG PROSITE_profiles:PS50297;PANTHER:PTHR24203;PANTHER:PTHR24203:SF7;Pfam:PF12796;Gene3D:1.25.40.20;SMART:SM00248;Superfamily:SSF48403 ENSP00000345767 9/16 ENST00000339746 Transcript ENSG00000135299 HGNC:17280 1.0 MODERATE NM_001242809.2 inframe_deletion 1.0 Unknown Q9Y2G4.172 ANKRD6 HGNC 1 1.0 UPI000020D325 Q9Y2G4-2 deletion ANKRD6,inframe_deletion,p.L258_T260del,ENST00000339746,NM_001242809.2,c.772_780del,MODERATE,YES,,,1;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000369408,NM_001242813.1,c.772_780del,MODERATE,,,,1;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000522441,NM_001242811.1,c.772_780del,MODERATE,,,,1;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000447838,NM_014942.4,c.772_780del,MODERATE,,,,1;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000485637,,c.772_780del,MODERATE,,,,1;ANKRD6,intron_variant,,ENST00000518150,,c.121-5399_121-5391del,MODIFIER,,,,1;ANKRD6,intron_variant,,ENST00000520793,NM_001242814.1,c.615+1354_615+1362del,MODIFIER,,,,1;LYRM2,intron_variant,,ENST00000626778,,c.*117+3703_*117+3711del,MODIFIER,YES,,,-1;ANKRD6,downstream_gene_variant,,ENST00000465722,,,MODIFIER,,,,1;LYRM2,downstream_gene_variant,,ENST00000520441,,,MODIFIER,,,,-1;LYRM2,intron_variant,,ENST00000520897,,n.562+3703_562+3711del,MODIFIER,,,,-1;LYRM2,downstream_gene_variant,,ENST00000523793,,,MODIFIER,,,,-1;ANKRD6,3_prime_UTR_variant,,ENST00000524056,,c.*108_*116del,MODIFIER,,,,1;ANKRD6,non_coding_transcript_exon_variant,,ENST00000518253,,n.589_597del,MODIFIER,,,,1;ANKRD6,non_coding_transcript_exon_variant,,ENST00000520839,,n.318_326del,MODIFIER,,,,1;LYRM2,intron_variant,,ENST00000412237,,c.*117+3703_*117+3711del,MODIFIER,,,,-1;ANKRD6,upstream_gene_variant,,ENST00000415924,,,MODIFIER,,,,1;ANKRD6,upstream_gene_variant,,ENST00000479572,,,MODIFIER,,,,1 1138-1146/5368 mutect2;pindel;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 105 f7f46f33-0972-422b-bff2-d5881c96898b 105 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS ANKRD6,non_coding_transcript_exon_variant,,ENST00000520839.1,n.317_325del,MODIFIER,;ANKRD6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000524056.5,c.*107_*115del,MODIFIER,;ANKRD6,non_coding_transcript_exon_variant,,ENST00000518253.5,n.588_596del,MODIFIER,;LYRM2,intron_variant,NMD_transcript_variant,,ENST00000412237.6,c.*117+3703_*117+3711del,MODIFIER,;LYRM2,intron_variant,,ENST00000626778.2,c.*117+3703_*117+3711del,MODIFIER,;LYRM2,intron_variant,,ENST00000520897.5,n.562+3703_562+3711del,MODIFIER,;ANKRD6,intron_variant,,ENST00000520793.5,c.615+1353_615+1361del,MODIFIER,;ANKRD6,intron_variant,,ENST00000518150.5,c.121-5400_121-5392del,MODIFIER,;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000485637.5,c.772_780del,MODERATE,;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000522441.5,c.772_780del,MODERATE,;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000447838.6,c.772_780del,MODERATE,;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000369408.9,c.772_780del,MODERATE,;ANKRD6,inframe_deletion,p.L258_T260del,ENST00000339746.9,c.772_780del,MODERATE,YES;ANKRD6,inframe_deletion,p.L283_T285del,ENST00000710308.1,c.847_855del,MODERATE, +ING3 54556 BI GRCh38 7 120969066 120969067 + frameshift_variant Frame_Shift_Ins INS - - TAAT novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 37 16 c.771_774dup p.Asn257IlefsTer3 p.N257Ifs*3 ENST00000315870.10 NM_019071.3 257 aat/aaTAATt 9/12 P1 TAAT N/NNX protein_coding YES CCDS5778.1 770-771/1257 TAAGAATAATG PANTHER:PTHR10333:SF96;PANTHER:PTHR10333 ENSP00000320566 9/12 ENST00000315870 Transcript ENSG00000071243 HGNC:14587 4.0 HIGH NM_019071.3 frameshift_variant 1.0 Unknown Q9NXR8.171 ING3 HGNC 1 1.0 UPI00000373B3 Q9NXR8-1 insertion ING3,frameshift_variant,p.D259*,ENST00000315870,NM_019071.3,c.771_774dup,HIGH,YES,,,1;ING3,frameshift_variant,p.D244*,ENST00000431467,,c.726_729dup,HIGH,,,,1;ING3,3_prime_UTR_variant,,ENST00000427726,,c.*392_*395dup,MODIFIER,,,,1;ING3,non_coding_transcript_exon_variant,,ENST00000497502,,n.368_371dup,MODIFIER,,,,1 890-891/3749 mutect2;pindel;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 67 f7f46f33-0972-422b-bff2-d5881c96898b 53 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS ING3,non_coding_transcript_exon_variant,,ENST00000497502.1,n.367_368insTAAT,MODIFIER,;ING3,frameshift_variant,p.N242Ifs*3,ENST00000431467.1,c.726_729dup,HIGH,;ING3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000427726.5,c.*391_*392insTAAT,MODIFIER,;ING3,frameshift_variant,p.N257Ifs*3,ENST00000315870.10,c.771_774dup,HIGH,YES +XKR4 114786 BI GRCh38 8 55102909 55102909 + stop_gained Nonsense_Mutation SNP C C T TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 99 13 c.421C>T p.Gln141Ter p.Q141* ENST00000327381.7 NM_052898.2 141 Cag/Tag 1/3 P1 T Q/* protein_coding YES CCDS34893.1 421/1953 GCGGCCAGCGC Pfam:PF09815;PANTHER:PTHR16024;PANTHER:PTHR16024:SF16 ENSP00000328326 1/3 COSV59325910 ENST00000327381 Transcript ENSG00000206579 HGNC:29394 HIGH NM_052898.2 stop_gained 1 1.0 Unknown 1 Q5GH76.105 XKR4 HGNC 1 1.0 UPI000016098C SNV XKR4,stop_gained,p.Q141*,ENST00000327381,NM_052898.2,c.421C>T,HIGH,YES,,,1;XKR4,stop_gained,p.Q141*,ENST00000622811,,c.421C>T,HIGH,,,,1 882/20241 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 60 f7f46f33-0972-422b-bff2-d5881c96898b 112 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS XKR4,stop_gained,p.Q141*,ENST00000327381.7,c.421C>T,HIGH,YES +NDUFAF6 137682 BI GRCh38 8 95052225 95052225 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 71 54 c.868C>T p.Gln290Ter p.Q290* ENST00000396124.9 NM_001354516.2 290 Cag/Tag 8/9 P1 T Q/* protein_coding YES CCDS6266.2 868/1002 TTCTTCAGACG Gene3D:1.10.600.10;Pfam:PF00494;PANTHER:PTHR21181;PANTHER:PTHR21181:SF13;Superfamily:SSF48576 ENSP00000379430 8/9 ENST00000396124 Transcript 1.0 ENSG00000156170 HGNC:28625 HIGH NM_152416.4 stop_gained 1.0 Unknown Q330K2.114 NDUFAF6 HGNC 1 2.0 UPI0000F0A5CF Q330K2-1 SNV NDUFAF6,stop_gained,p.Q198*,ENST00000396113,,c.592C>T,HIGH,,,,1;NDUFAF6,stop_gained,p.Q198*,ENST00000396111,NM_001354514.1&NM_001354525.1&NM_001354524.1&NM_001354522.1&NM_001354515.1&NM_001354528.1&NM_001354527.1&NM_001354518.1&NM_001354532.1&NM_001330582.1&NM_001354521.1&NM_001354519.1&NM_001354530.1&NM_001354533.1&NM_001354529.1&NM_001354531.1&NM_001354517.1,c.592C>T,HIGH,,,,1;NDUFAF6,stop_gained,p.Q290*,ENST00000396124,NM_001354516.1&NM_152416.4,c.868C>T,HIGH,YES,,,1;RNU6-1209P,upstream_gene_variant,,ENST00000363655,,,MODIFIER,YES,,,1;NDUFAF6,intron_variant,,ENST00000523184,,n.93+3667C>T,MODIFIER,,,,1;NDUFAF6,3_prime_UTR_variant,,ENST00000520757,,c.*506C>T,MODIFIER,,,,1;NDUFAF6,3_prime_UTR_variant,,ENST00000518258,,c.*843C>T,MODIFIER,,,,1;NDUFAF6,3_prime_UTR_variant,,ENST00000517976,,c.*759C>T,MODIFIER,,,,1;NDUFAF6,3_prime_UTR_variant,,ENST00000454358,,c.*566C>T,MODIFIER,,,,1 888/1795 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 112 f7f46f33-0972-422b-bff2-d5881c96898b 125 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS NDUFAF6,intron_variant,,ENST00000523184.5,n.93+3667C>T,MODIFIER,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000520757.1,c.*506C>T,MODIFIER,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000454358.6,c.*566C>T,MODIFIER,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000517976.5,c.*759C>T,MODIFIER,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000518258.5,c.*843C>T,MODIFIER,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000519804.2,c.*662C>T,MODIFIER,;NDUFAF6,stop_gained,p.Q290*,ENST00000396124.9,c.868C>T,HIGH,YES;NDUFAF6,stop_gained,p.Q198*,ENST00000396111.6,c.592C>T,HIGH,;NDUFAF6,stop_gained,p.Q198*,ENST00000697364.1,c.592C>T,HIGH,;NDUFAF6,stop_gained,p.Q198*,ENST00000396113.5,c.592C>T,HIGH,;NDUFAF6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697355.1,c.*638C>T,MODIFIER, +MROH1 727957 BI GRCh38 8 144180436 144180436 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 66 69 c.475G>A p.Val159Ile p.V159I ENST00000326134.10 NM_032450.3 159 Gtc/Atc 7/44 P4 A V/I protein_coding CCDS47938.1 475/4926 GCGTAGTCCCC PANTHER:PTHR23120;PANTHER:PTHR23120:SF0;Superfamily:SSF48371;Low_complexity_(Seg):seg ENSP00000321737 5/42 ENST00000326134 Transcript ENSG00000179832 HGNC:26958 MODERATE missense_variant benign(0.232) Unknown deleterious(0) Q8NDA8.139 MROH1 HGNC 1 5.0 UPI0001AE6FA6 Q8NDA8-1 SNV MROH1,missense_variant,p.V159I,ENST00000528919,NM_032450.3,c.475G>A,MODERATE,YES,deleterious(0),benign(0.232),1;MROH1,missense_variant,p.V159I,ENST00000326134,,c.475G>A,MODERATE,,deleterious(0),benign(0.232),1;MROH1,missense_variant,p.V159I,ENST00000534366,NM_001288814.1,c.475G>A,MODERATE,,deleterious(0),benign(0.232),1;MROH1,missense_variant,p.V159I,ENST00000423230,NM_001099280.3&NM_001099281.3,c.475G>A,MODERATE,,deleterious(0),probably_damaging(0.918),1;MROH1,non_coding_transcript_exon_variant,,ENST00000527552,,n.604G>A,MODIFIER,,,,1;MROH1,non_coding_transcript_exon_variant,,ENST00000532255,,n.592G>A,MODIFIER,,,,1;MROH1,non_coding_transcript_exon_variant,,ENST00000525287,,n.711G>A,MODIFIER,,,,1;MROH1,non_coding_transcript_exon_variant,,ENST00000534508,,n.307G>A,MODIFIER,,,,1 532/5183 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 72 f7f46f33-0972-422b-bff2-d5881c96898b 135 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS MROH1,non_coding_transcript_exon_variant,,ENST00000534508.1,n.307G>A,MODIFIER,;MROH1,missense_variant,p.V159I,ENST00000528919.5,c.475G>A,MODERATE,;MROH1,non_coding_transcript_exon_variant,,ENST00000527552.5,n.604G>A,MODIFIER,;MROH1,missense_variant,p.V159I,ENST00000534366.5,c.475G>A,MODERATE,;MROH1,missense_variant,p.V159I,ENST00000423230.6,c.475G>A,MODERATE,;MROH1,non_coding_transcript_exon_variant,,ENST00000525287.5,n.711G>A,MODIFIER,;MROH1,non_coding_transcript_exon_variant,,ENST00000532255.5,n.592G>A,MODIFIER,;MROH1,missense_variant,p.V159I,ENST00000326134.10,c.475G>A,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 43 38 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 81 f7f46f33-0972-422b-bff2-d5881c96898b 82 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +CCDC89 220388 BI GRCh38 11 85686091 85686091 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 70 11 c.40A>C p.Met14Leu p.M14L ENST00000316398.5 NM_152723.3 14 Atg/Ctg 1/1 P1 G M/L protein_coding YES CCDS8270.1 40/1125 GTCCATCCTGG MobiDB_lite:mobidb-lite;PANTHER:PTHR34768;PANTHER:PTHR34768:SF1 ENSP00000320649 1/1 ENST00000316398 Transcript ENSG00000179071 HGNC:26762 MODERATE NM_152723.3 missense_variant 1.0 possibly_damaging(0.529) Unknown deleterious_low_confidence(0.02) Q8N998.114 CCDC89 HGNC -1 UPI000000DAB1 SNV CCDC89,missense_variant,p.M14L,ENST00000316398,NM_152723.3,c.40A>C,MODERATE,YES,deleterious_low_confidence(0.02),possibly_damaging(0.529),-1;CREBZF,upstream_gene_variant,,ENST00000534224,,,MODIFIER,,,,-1;CREBZF,upstream_gene_variant,,ENST00000531515,,,MODIFIER,,,,-1 105/2348 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 91 f7f46f33-0972-422b-bff2-d5881c96898b 81 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS CCDC89,missense_variant,p.M14L,ENST00000316398.5,c.40A>C,MODERATE,YES +NCKAP5L 57701 BI GRCh38 12 49796170 49796170 + missense_variant Missense_Mutation SNP G G A rs764426987 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 17 16 c.1690C>T p.Arg564Trp p.R564W ENST00000335999.7 NM_001037806.4 564 Cgg/Tgg 8/13 P1 A R/W protein_coding YES CCDS41781.2 1690/4005 GCTCCGAGAAA PANTHER:PTHR21740;PANTHER:PTHR21740:SF3;MobiDB_lite:mobidb-lite ENSP00000337998 8/13 rs764426987 ENST00000335999 Transcript ENSG00000167566 HGNC:29321 MODERATE NM_001037806.4 3.322e-05 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.742) Unknown deleterious(0.02) Q9HCH0.121 NCKAP5L HGNC -1 5.0 UPI00006C1298 SNV NCKAP5L,missense_variant,p.R564W,ENST00000335999,NM_001037806.4&NM_001368048.1,c.1690C>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.742),-1;NCKAP5L,missense_variant,p.R279W,ENST00000433948,,c.835C>T,MODERATE,,deleterious(0.02),probably_damaging(0.91),-1 1880/4882 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 8.248e-06 0.0 0.0 0.0 0.0 0.0 9.142e-06 0.0 3.322e-05 1.3521200344257522e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435000022989698e-05 0.0 0.0002085070009343 0 29 f7f46f33-0972-422b-bff2-d5881c96898b 33 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS NCKAP5L,missense_variant,p.R564W,ENST00000335999.7,c.1690C>T,MODERATE,YES;NCKAP5L,missense_variant,p.S278L,ENST00000433948.5,c.833C>T,MODERATE, +GPC5 2262 BI GRCh38 13 92866404 92866405 + frameshift_variant Frame_Shift_Ins INS - - T novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 80 70 c.1685dup p.Ile562TyrfsTer23 p.I562Yfs*23 ENST00000377067.9 NM_004466.6 562 ata/aTta 8/8 P1 T I/IX protein_coding YES CCDS9468.1 1684-1685/1719 CTCTGATAAGT Pfam:PF01153 ENSP00000366267 8/8 ENST00000377067 Transcript 1.0 ENSG00000179399 HGNC:4453 1.0 HIGH NM_004466.6 frameshift_variant 1.0 Unknown P78333.163 GPC5 HGNC 1 1.0 UPI0000001C85 insertion GPC5,frameshift_variant,p.S563Kfs*22,ENST00000377067,NM_004466.6,c.1685dup,HIGH,YES,,,1;GPC5,frameshift_variant,p.S43Kfs*51,ENST00000618283,,c.124dup,HIGH,,,,1 2110-2111/2943 mutect2;pindel;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 115 f7f46f33-0972-422b-bff2-d5881c96898b 150 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS GPC5,frameshift_variant,p.*41Cfs*12,ENST00000618283.1,c.124dup,HIGH,;GPC5,frameshift_variant,p.I562Yfs*23,ENST00000377067.9,c.1685dup,HIGH,YES +VPS35L 57020 BI GRCh38 16 19610352 19610352 + synonymous_variant Silent SNP A A C novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 11 14 c.960A>C p.Thr320= p.T320= ENST00000417362.7 NM_020314.7 320 acA/acC 12/31 P4 C T protein_coding 960/2892 TTGACATGCAT PANTHER:PTHR13673 ENSP00000395973 12/31 ENST00000417362 Transcript ENSG00000103544 HGNC:24641 LOW NM_020314.7 synonymous_variant Unknown Q7Z3J2.111 VPS35L HGNC 1 1.0 UPI000018CE96 Q7Z3J2-1 SNV VPS35L,synonymous_variant,p.T409=,ENST00000251143,,c.1227A>C,LOW,YES,,,1;VPS35L,synonymous_variant,p.T409=,ENST00000438132,,c.1227A>C,LOW,,,,1;VPS35L,synonymous_variant,p.T320=,ENST00000417362,NM_020314.7&NM_001365293.2&NM_001365294.2,c.960A>C,LOW,,,,1;VPS35L,synonymous_variant,p.T170=,ENST00000448695,,c.510A>C,LOW,,,,1;VPS35L,synonymous_variant,p.T69=,ENST00000543152,NM_001365295.2,c.207A>C,LOW,,,,1;VPS35L,synonymous_variant,p.T409=,ENST00000542263,NM_001300743.3,c.1227A>C,LOW,,,,1;VPS35L,synonymous_variant,p.T320=,ENST00000513947,,c.960A>C,LOW,,,,1;VPS35L,5_prime_UTR_variant,,ENST00000538552,,c.-4A>C,MODIFIER,,,,1;VPS35L,non_coding_transcript_exon_variant,,ENST00000540101,,n.249A>C,MODIFIER,,,,1;VPS35L,non_coding_transcript_exon_variant,,ENST00000535164,,n.297A>C,MODIFIER,,,,1;VPS35L,non_coding_transcript_exon_variant,,ENST00000539705,,n.144A>C,MODIFIER,,,,1;VPS35L,non_coding_transcript_exon_variant,,ENST00000541153,,n.277A>C,MODIFIER,,,,1;VPS35L,non_coding_transcript_exon_variant,,ENST00000546175,,n.288A>C,MODIFIER,,,,1;VPS35L,downstream_gene_variant,,ENST00000539322,,,MODIFIER,,,,1;VPS35L,downstream_gene_variant,,ENST00000540240,,,MODIFIER,,,,1 987/3606 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 26 f7f46f33-0972-422b-bff2-d5881c96898b 25 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS VPS35L,non_coding_transcript_exon_variant,,ENST00000540101.2,n.249A>C,MODIFIER,;VPS35L,5_prime_UTR_variant,,ENST00000538552.5,c.-4A>C,MODIFIER,;VPS35L,non_coding_transcript_exon_variant,,ENST00000541153.5,n.277A>C,MODIFIER,;VPS35L,non_coding_transcript_exon_variant,,ENST00000539705.5,n.144A>C,MODIFIER,;VPS35L,non_coding_transcript_exon_variant,,ENST00000535164.5,n.297A>C,MODIFIER,;VPS35L,non_coding_transcript_exon_variant,,ENST00000546175.5,n.288A>C,MODIFIER,;VPS35L,synonymous_variant,p.T69=,ENST00000543152.5,c.207A>C,LOW,;VPS35L,synonymous_variant,p.T320=,ENST00000513947.8,c.960A>C,LOW,;VPS35L,synonymous_variant,p.T320=,ENST00000417362.7,c.960A>C,LOW,YES;VPS35L,synonymous_variant,p.T320=,ENST00000542263.5,c.960A>C,LOW,;VPS35L,synonymous_variant,p.T409=,ENST00000251143.9,c.1227A>C,LOW, +TRPV2 51393 BI GRCh38 17 16417675 16417675 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 88 9 c.7T>G p.Ser3Ala p.S3A ENST00000338560.12 NM_016113.5 3 Tca/Gca 2/15 P1 G S/A protein_coding YES CCDS32576.1 7/2295 TGACCTCACCC PANTHER:PTHR10582;PANTHER:PTHR10582:SF5;MobiDB_lite:mobidb-lite ENSP00000342222 2/15 ENST00000338560 Transcript ENSG00000187688 HGNC:18082 MODERATE NM_016113.5 missense_variant 1.0 benign(0.058) Unknown tolerated_low_confidence(0.08) Q9Y5S1.169 TRPV2 HGNC 1 1.0 UPI0000032F4E SNV TRPV2,missense_variant,p.S3A,ENST00000338560,NM_016113.5,c.7T>G,MODERATE,YES,tolerated_low_confidence(0.08),benign(0.058),1;TRPV2,upstream_gene_variant,,ENST00000455666,,,MODIFIER,,,,1;AC093484.2,upstream_gene_variant,,ENST00000580996,,,MODIFIER,YES,,,-1 377/2779 muse;mutect2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 79 f7f46f33-0972-422b-bff2-d5881c96898b 98 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS TRPV2,missense_variant,p.S3A,ENST00000338560.12,c.7T>G,MODERATE,YES +SMCR8 140775 BI GRCh38 17 18317935 18317935 + missense_variant Missense_Mutation SNP C C A novel TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 47 17 c.2146C>A p.Gln716Lys p.Q716K ENST00000406438.5 NM_144775.3 716 Cag/Aag 1/2 P1 A Q/K protein_coding YES CCDS11195.2 2146/2814 TCCGCCAGTAC PDB-ENSP_mappings:6lt0.B;PDB-ENSP_mappings:6lt0.E;PROSITE_profiles:PS51834;PANTHER:PTHR31334 ENSP00000385025 1/2 ENST00000406438 Transcript ENSG00000176994 HGNC:17921 MODERATE NM_144775.3 missense_variant 1.0 probably_damaging(0.989) Unknown deleterious(0.01) Q8TEV9.120 SMCR8 HGNC 1 1.0 UPI0000E0322D Q8TEV9-1 SNV SMCR8,missense_variant,p.Q716K,ENST00000406438,NM_144775.3,c.2146C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.989),1;TOP3A,upstream_gene_variant,,ENST00000321105,NM_001320759.2&NM_004618.5,,MODIFIER,YES,,,-1;TOP3A,upstream_gene_variant,,ENST00000542570,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000580095,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000582230,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000584669,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000584887,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000461127,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000472959,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000580713,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000582981,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000583328,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000584582,,,MODIFIER,,,,-1;TOP3A,upstream_gene_variant,,ENST00000585031,,,MODIFIER,,,,-1;RPL21P121,downstream_gene_variant,,ENST00000439258,,,MODIFIER,YES,,,1 2643/8297 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 60 f7f46f33-0972-422b-bff2-d5881c96898b 64 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS SMCR8,missense_variant,p.Q716K,ENST00000406438.5,c.2146C>A,MODERATE,YES +RYR1 6261 BI GRCh38 19 38460564 38460564 + synonymous_variant Silent SNP C C T rs757850226 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 49 21 c.2550C>T p.Phe850= p.F850= ENST00000359596.8 NM_000540.3 850 ttC/ttT 20/106 A2 T F protein_coding YES CCDS33011.1 2550/15117 GACTTCGTGCC COSM3222312 Gene3D:1.10.490.160;Pfam:PF02026;PANTHER:PTHR13715;PANTHER:PTHR13715:SF15 ENSP00000352608 20/106 rs757850226;COSV100615193;COSV62101418 ENST00000359596 Transcript 1.0 ENSG00000196218 HGNC:10483 LOW NM_000540.3 3.266e-05 gnomAD_SAS synonymous_variant 0;1;1 1.0 Unknown 0;1;1 P21817.226 RYR1 HGNC 1 5.0 UPI0000D7E62F P21817-1 SNV RYR1,synonymous_variant,p.F850=,ENST00000359596,NM_000540.3,c.2550C>T,LOW,YES,,,1;RYR1,synonymous_variant,p.F850=,ENST00000355481,NM_001042723.2,c.2550C>T,LOW,,,,1 2689/15400 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 1.199e-05 0.0 0.0 0.0 0.0 0.0 1.763e-05 0.0 3.266e-05 6.757300070603378e-06 0.0 0.0 0.0 0.0 0.0002014500059885 0.0 0.0 0.0 0.0 0.0 0 62 f7f46f33-0972-422b-bff2-d5881c96898b 71 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS RYR1,synonymous_variant,NMD_transcript_variant,p.F850=,ENST00000599547.7,c.2550C>T,LOW,;RYR1,synonymous_variant,p.F850=,ENST00000355481.8,c.2550C>T,LOW,;RYR1,synonymous_variant,p.F810=,ENST00000713953.1,c.2430C>T,LOW,;RYR1,synonymous_variant,p.F850=,ENST00000689936.2,c.2550C>T,LOW,;RYR1,synonymous_variant,p.F850=,ENST00000359596.8,c.2550C>T,LOW,YES;RYR1,synonymous_variant,NMD_transcript_variant,p.F850=,ENST00000688602.2,c.2550C>T,LOW,;RYR1,synonymous_variant,p.F850=,ENST00000713952.1,c.2550C>T,LOW,;RYR1,synonymous_variant,NMD_transcript_variant,p.F850=,ENST00000594335.6,c.2550C>T,LOW,;RYR1,synonymous_variant,NMD_transcript_variant,p.F850=,ENST00000593322.2,c.2550C>T,LOW, +MED12 9968 BI GRCh38 X 71119761 71119761 + missense_variant Missense_Mutation SNP C C T rs2147773280 TCGA-V4-A9F8-01A TCGA-V4-A9F8-10A Somatic 0 12 c.280C>T p.Pro94Ser p.P94S ENST00000374080.8 NM_005120.3 94 Ccc/Tcc 3/45 P4 T P/S protein_coding YES CCDS43970.1 280/6534 GGAAGCCCCAA PANTHER:PTHR46007;PANTHER:PTHR46007:SF2 ENSP00000363193 3/45 ENST00000374080 Transcript 1.0 ENSG00000184634 HGNC:11957 MODERATE NM_005120.3 missense_variant 1.0 possibly_damaging(0.792) Unknown tolerated(0.05) Q93074.195 MED12 HGNC 1 1.0 UPI00004257E2 Q93074-1 SNV MED12,missense_variant,p.P94S,ENST00000374080,NM_005120.3,c.280C>T,MODERATE,YES,tolerated(0.05),possibly_damaging(0.792),1;MED12,missense_variant,p.P94S,ENST00000374102,,c.280C>T,MODERATE,,tolerated(0.05),probably_damaging(0.999),1;MED12,missense_variant,p.P79S,ENST00000429213,,c.235C>T,MODERATE,,tolerated(0.13),benign(0.068),1;MED12,5_prime_UTR_variant,,ENST00000333646,,c.-180C>T,MODIFIER,,,,1 439/6925 muse;mutect2;varscan2 64bd88bd-1d5a-4569-9f46-f668d448c336 0 13 f7f46f33-0972-422b-bff2-d5881c96898b 12 9956eaf5-261a-45ee-a012-0f1dd2567dd8 SUCCESS MED12,non_coding_transcript_exon_variant,,ENST00000688718.1,n.216C>T,MODIFIER,;MED12,missense_variant,p.P94S,ENST00000691468.1,c.280C>T,MODERATE,;MED12,missense_variant,p.P94S,ENST00000690145.1,c.280C>T,MODERATE,;MED12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000689008.1,c.*176C>T,MODIFIER,;MED12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686548.1,c.*176C>T,MODIFIER,;MED12,missense_variant,p.P94S,ENST00000693324.1,c.280C>T,MODERATE,;MED12,missense_variant,p.P94S,ENST00000374102.6,c.280C>T,MODERATE,;MED12,non_coding_transcript_exon_variant,,ENST00000690828.1,n.436C>T,MODIFIER,;MED12,missense_variant,p.P94S,ENST00000374080.8,c.280C>T,MODERATE,YES;MED12,missense_variant,p.P94S,ENST00000333646.11,c.280C>T,MODERATE,;MED12,missense_variant,NMD_transcript_variant,p.P94S,ENST00000688663.1,c.280C>T,MODERATE,;MED12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000429213.3,c.*29C>T,MODIFIER,;MED12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000692864.1,c.*176C>T,MODIFIER,;MED12,missense_variant,p.P94S,ENST00000687382.1,c.280C>T,MODERATE,;MED12,missense_variant,p.P94S,ENST00000692304.1,c.280C>T,MODERATE,;MED12,missense_variant,p.P94S,ENST00000690242.1,c.280C>T,MODERATE, +TET3 200424 BI GRCh38 2 74047971 74047972 + frameshift_variant Frame_Shift_Del DEL CC CC - novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 35 28 c.2057_2058del p.Pro686GlnfsTer19 p.P686Qfs*19 ENST00000409262.8 NM_001287491.2 685 tCC/t 4/12 P1 - S/X protein_coding YES CCDS46339.2 2054-2055/5388 TGAGGTCCCCCAG PANTHER:PTHR23358;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000386869 3/11 ENST00000409262 Transcript 1.0 ENSG00000187605 HGNC:28313 3.0 HIGH frameshift_variant 1.0 Unknown O43151.142 TET3 HGNC 1 1.0 UPI0002A87FCB O43151-1 deletion TET3,frameshift_variant,p.P686Qfs*19,ENST00000409262,NM_001287491.2,c.2057_2058del,HIGH,YES,,,1;TET3,frameshift_variant,p.P593Qfs*19,ENST00000305799,NM_001366022.1,c.1778_1779del,HIGH,,,,1;TET3,non_coding_transcript_exon_variant,,ENST00000475405,,n.815_816del,MODIFIER,,,,1 2054-2055/11388 mutect2;pindel;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 20 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 63 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS TET3,non_coding_transcript_exon_variant,,ENST00000475405.2,n.812_813del,MODIFIER,;TET3,frameshift_variant,p.P593Qfs*19,ENST00000305799.8,c.1778_1779del,HIGH,;TET3,frameshift_variant,p.P686Qfs*19,ENST00000409262.8,c.2057_2058del,HIGH,YES +OR2B3 442184 BI GRCh38 6 29086376 29086376 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 49 13 c.873C>A p.Ser291Arg p.S291R ENST00000377173.4 NM_001005226.2 291 agC/agA 1/1 P1 T S/R protein_coding YES CCDS34358.1 873/942 CTAAGGCTGTA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;Prints:PR00245;PANTHER:PTHR26453;PANTHER:PTHR26453:SF103;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15947 ENSP00000366378 1/1 ENST00000377173 Transcript ENSG00000204703 HGNC:8238 MODERATE NM_001005226.2 missense_variant 1.0 benign(0.276) Unknown deleterious(0) O76000.168 OR2B3 HGNC -1 A0A126GV76.30 UPI0000041DB9 SNV OR2B3,missense_variant,p.S291R,ENST00000377173,NM_001005226.2,c.873C>A,MODERATE,YES,deleterious(0),benign(0.276),-1 938/1106 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 47 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 62 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS OR2B3,missense_variant,p.S291R,ENST00000377173.4,c.873C>A,MODERATE,YES +ACTB 60 BI GRCh38 7 5528692 5528692 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 43 44 c.391G>A p.Ala131Thr p.A131T ENST00000646664.1 NM_001101.5 131 Gcc/Acc 4/6 P1 T A/T protein_coding YES CCDS5341.1 391/1128 CATGGCTGGGG CDD:cd00012;PANTHER:PTHR11937;PANTHER:PTHR11937:SF243;Pfam:PF00022;Gene3D:3.30.420.40;SMART:SM00268;Superfamily:SSF53067 ENSP00000502821 4/6 ENST00000674681 Transcript 1.0 ENSG00000075624 HGNC:132 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious_low_confidence(0.02) ACTB HGNC -1 Q1KLZ0.132 UPI000000082D SNV ACTB,missense_variant,p.A131T,ENST00000674681,,c.391G>A,MODERATE,YES,deleterious_low_confidence(0.02),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000642480,,c.391G>A,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000675515,,c.391G>A,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000646664,NM_001101.5,c.391G>A,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000676397,,c.391G>A,MODERATE,,deleterious_low_confidence(0.01),benign(0.001),-1;ACTB,missense_variant,p.A88T,ENST00000473257,,c.262G>A,MODERATE,,deleterious_low_confidence(0.01),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000493945,,c.391G>A,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(1),-1;ACTB,missense_variant,p.A131T,ENST00000432588,,c.391G>A,MODERATE,,deleterious_low_confidence(0.01),benign(0.001),-1;ACTB,missense_variant,p.A9T,ENST00000647275,,c.25G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(1),-1;ACTB,intron_variant,,ENST00000645576,,c.364-21G>A,MODIFIER,,,,-1;ACTB,intron_variant,,ENST00000676319,,c.87+879G>A,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000414620,,,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000417101,,,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000443528,,,MODIFIER,,,,-1;ACTB,upstream_gene_variant,,ENST00000464611,,,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000484841,,,MODIFIER,,,,-1;ACTB,synonymous_variant,p.Q130=,ENST00000676189,,c.390G>A,LOW,,,,-1;ACTB,3_prime_UTR_variant,,ENST00000425660,,c.*54G>A,MODIFIER,,,,-1;ACTB,non_coding_transcript_exon_variant,,ENST00000477812,,n.938G>A,MODIFIER,,,,-1;ACTB,non_coding_transcript_exon_variant,,ENST00000462494,,n.916G>A,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000480301,,,MODIFIER,,,,-1;ACTB,downstream_gene_variant,,ENST00000645025,,,MODIFIER,,,,-1 478/2554 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 99 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 87 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS ACTB,missense_variant,p.A9T,ENST00000647275.1,c.25G>A,MODERATE,;ACTB,intron_variant,,ENST00000645576.1,c.364-21G>A,MODIFIER,;ACTB,missense_variant,p.A131T,ENST00000432588.6,c.391G>A,MODERATE,;ACTB,missense_variant,p.A131T,ENST00000493945.6,c.391G>A,MODERATE,;ACTB,non_coding_transcript_exon_variant,,ENST00000462494.5,n.916G>A,MODIFIER,;ACTB,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000425660.5,c.*54G>A,MODIFIER,;ACTB,non_coding_transcript_exon_variant,,ENST00000477812.2,n.938G>A,MODIFIER,;ACTB,missense_variant,p.A131T,ENST00000675515.1,c.391G>A,MODERATE,;ACTB,missense_variant,p.A131T,ENST00000646664.1,c.391G>A,MODERATE,YES;ACTB,intron_variant,,ENST00000676319.1,c.87+879G>A,MODIFIER,;ACTB,missense_variant,p.A88T,ENST00000473257.3,c.262G>A,MODERATE,;ACTB,missense_variant,p.A131T,ENST00000676397.1,c.391G>A,MODERATE,;ACTB,missense_variant,p.A131T,ENST00000642480.2,c.391G>A,MODERATE,;ACTB,synonymous_variant,NMD_transcript_variant,p.Q130=,ENST00000676189.1,c.390G>A,LOW,;ACTB,missense_variant,p.A131T,ENST00000674681.1,c.391G>A,MODERATE, +TRAM1 23471 BI GRCh38 8 70608177 70608177 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 38 40 c.23C>G p.Thr8Ser p.T8S ENST00000262213.7 NM_001317804.2 8 aCc/aGc 1/11 P1 C T/S protein_coding YES CCDS6207.1 23/1125 TCTTGGTGCTT PIRSF:PIRSF005449;PANTHER:PTHR12371:SF3;PANTHER:PTHR12371 ENSP00000262213 1/11 ENST00000262213 Transcript ENSG00000067167 HGNC:20568 MODERATE NM_014294.6 missense_variant 1.0 benign(0) Unknown tolerated(0.86) Q15629.168 TRAM1 HGNC -1 Q6FHL3.131 1.0 UPI0000001C66 Q15629-1 SNV TRAM1,missense_variant,p.T8S,ENST00000262213,NM_001317804.2&NM_014294.6,c.23C>G,MODERATE,YES,tolerated(0.86),benign(0),-1;TRAM1,intron_variant,,ENST00000518678,,c.-30-41C>G,MODIFIER,,,,-1;TRAM1,upstream_gene_variant,,ENST00000521425,NM_001317805.2,,MODIFIER,,,,-1;TRAM1,non_coding_transcript_exon_variant,,ENST00000521049,,n.163C>G,MODIFIER,,,,-1;TRAM1,intron_variant,,ENST00000520700,,n.90+86C>G,MODIFIER,,,,-1;LACTB2-AS1,upstream_gene_variant,,ENST00000499227,,,MODIFIER,YES,,,1;LACTB2-AS1,upstream_gene_variant,,ENST00000518152,,,MODIFIER,,,,1;LACTB2-AS1,upstream_gene_variant,,ENST00000518553,,,MODIFIER,,,,1;LACTB2-AS1,upstream_gene_variant,,ENST00000519358,,,MODIFIER,,,,1 240/3056 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 67 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 78 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS TRAM1,intron_variant,,ENST00000518678.1,c.-30-41C>G,MODIFIER,;TRAM1,intron_variant,,ENST00000520700.1,n.90+86C>G,MODIFIER,;TRAM1,non_coding_transcript_exon_variant,,ENST00000521049.5,n.163C>G,MODIFIER,;TRAM1,missense_variant,p.T8S,ENST00000262213.7,c.23C>G,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 55 43 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 99 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 98 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +ARAP1 116985 BI GRCh38 11 72697486 72697486 + synonymous_variant,splice_region_variant Silent SNP C C T novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 28 19 c.2790G>A p.Arg930= p.R930= ENST00000393609.8 NM_001040118.3 930 agG/agA 21/35 P3 T R protein_coding YES CCDS41687.1 2790/4353 AGTGTCCTGGG CDD:cd13257;PANTHER:PTHR45899;PANTHER:PTHR45899:SF3;SMART:SM00233;Superfamily:SSF50729 ENSP00000377233 21/35 ENST00000393609 Transcript ENSG00000186635 HGNC:16925 LOW splice_region_variant 1.0 Unknown Q96P48.181 ARAP1 HGNC -1 2.0 UPI000053F81B Q96P48-6 SNV ARAP1,splice_region_variant,p.R930=,ENST00000359373,,c.2790G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R930=,ENST00000393609,NM_001040118.2,c.2790G>A,LOW,YES,,,-1;ARAP1,splice_region_variant,p.R685=,ENST00000334211,NM_015242.4,c.2055G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R690=,ENST00000393605,,c.2070G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R685=,ENST00000426523,NM_001369489.1,c.2055G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R624=,ENST00000429686,NM_001135190.1,c.1872G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R170=,ENST00000455638,,c.510G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R218=,ENST00000427971,,c.654G>A,LOW,,,,-1;ARAP1,splice_region_variant,p.R218=,ENST00000452383,,c.654G>A,LOW,,,,-1;ARAP1,upstream_gene_variant,,ENST00000542596,,,MODIFIER,,,,-1;ARAP1,splice_region_variant,,ENST00000495878,,n.633G>A,LOW,,,,-1;ARAP1,upstream_gene_variant,,ENST00000544958,,,MODIFIER,,,,-1;ARAP1,splice_region_variant,,ENST00000465814,,n.3127G>A,LOW,,,,-1;ARAP1,upstream_gene_variant,,ENST00000536993,,,MODIFIER,,,,-1;ARAP1,upstream_gene_variant,,ENST00000543868,,,MODIFIER,,,,-1;ARAP1,upstream_gene_variant,,ENST00000546293,,,MODIFIER,,,,-1;ARAP1-AS2,upstream_gene_variant,,ENST00000500163,,,MODIFIER,YES,,,1;ARAP1-AS1,downstream_gene_variant,,ENST00000542022,,,MODIFIER,YES,,,1;AP003065.1,downstream_gene_variant,,ENST00000669205,,,MODIFIER,YES,,,1 2993/5145 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 28 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 47 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS ARAP1,synonymous_variant,splice_region_variant,p.R218=,ENST00000452383.2,c.654G>A,LOW,;ARAP1,synonymous_variant,splice_region_variant,p.R218=,ENST00000427971.6,c.654G>A,LOW,;ARAP1,synonymous_variant,splice_region_variant,p.R624=,ENST00000429686.5,c.1872G>A,LOW,;ARAP1,synonymous_variant,splice_region_variant,p.R685=,ENST00000426523.5,c.2055G>A,LOW,;ARAP1,synonymous_variant,splice_region_variant,p.R690=,ENST00000393605.7,c.2070G>A,LOW,;ARAP1,synonymous_variant,splice_region_variant,p.R685=,ENST00000334211.12,c.2055G>A,LOW,;ARAP1,non_coding_transcript_exon_variant,,ENST00000465814.5,n.3127G>A,MODIFIER,;ARAP1,non_coding_transcript_exon_variant,,ENST00000495878.5,n.633G>A,MODIFIER,;ARAP1,synonymous_variant,splice_region_variant,p.R930=,ENST00000393609.8,c.2790G>A,LOW,YES;ARAP1,synonymous_variant,splice_region_variant,p.R930=,ENST00000359373.9,c.2790G>A,LOW, +EIF1AX 1964 BI GRCh38 X 20138617 20138619 + inframe_deletion In_Frame_Del DEL CTT CTT - novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 1 35 c.20_22del p.Gly9del p.G9del ENST00000379607.10 NM_001412.4 7 aAAGga/aga 2/7 P1 - KG/R protein_coding YES CCDS14196.1 20-22/435 TACCTCCTTTACCT PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 inframe_deletion 1.0 Unknown P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF deletion EIF1AX,inframe_deletion,p.K7_G8delinsR,ENST00000379607,NM_001412.4,c.20_22del,MODERATE,YES,,,-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2778_17-2776del,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 218-220/4414 mutect2;pindel;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 70 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 36 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2778_17-2776del,MODIFIER,;EIF1AX,inframe_deletion,p.G9del,ENST00000379607.10,c.20_22del,MODERATE,YES +XIST 7503 BI GRCh38 X 73842764 73842764 + non_coding_transcript_exon_variant RNA SNP G G A novel TCGA-VD-A8KO-01A TCGA-VD-A8KO-10A Somatic 0 18 n.9960C>T ENST00000429829.6 1/6 A lncRNA YES AAAGGGCCTTG 1/6 ENST00000429829 Transcript 1.0 ENSG00000229807 HGNC:12810 MODIFIER non_coding_transcript_exon_variant 1.0 Unknown XIST HGNC -1 1.0 SNV XIST,non_coding_transcript_exon_variant,,ENST00000429829,,n.9960C>T,MODIFIER,YES,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000650627,,n.8829C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000650366,,n.3507C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000650186,,n.4237C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000648991,,n.1320C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000648607,,n.1445C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000669898,,n.770C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000666309,,n.2030C>T,MODIFIER,,,,-1;XIST,non_coding_transcript_exon_variant,,ENST00000665247,,n.228C>T,MODIFIER,,,,-1;XIST,intron_variant,,ENST00000434839,,n.164+8166C>T,MODIFIER,,,,-1;XIST,intron_variant,,ENST00000635841,,n.124-1443C>T,MODIFIER,,,,-1;XIST,intron_variant,,ENST00000648970,,n.1215-1291C>T,MODIFIER,,,,-1;XIST,intron_variant,,ENST00000650637,,n.1367-1291C>T,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000421322,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000602863,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000647696,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000647913,,,MODIFIER,,,,-1;XIST,upstream_gene_variant,,ENST00000650548,,,MODIFIER,,,,-1 9960/19245 muse;mutect2;varscan2 014d4b17-d683-438b-9287-33fcec82bf5a 0 16 a57f05ff-06a3-4f57-9df9-1c0f4ec3111a 18 58b56b6d-066e-45da-b4dc-06799b01b169 SUCCESS XIST,non_coding_transcript_exon_variant,,ENST00000665247.1,n.228C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000666309.1,n.2030C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000648991.1,n.1320C>T,MODIFIER,;XIST,intron_variant,,ENST00000648970.1,n.1215-1291C>T,MODIFIER,;XIST,intron_variant,,ENST00000650637.1,n.1367-1291C>T,MODIFIER,;XIST,intron_variant,,ENST00000635841.2,n.124-1443C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000650186.1,n.4237C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000648607.1,n.1445C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000650366.1,n.3507C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000429829.6,n.9960C>T,MODIFIER,YES;XIST,non_coding_transcript_exon_variant,,ENST00000650627.1,n.8829C>T,MODIFIER,;XIST,intron_variant,,ENST00000434839.3,n.164+8166C>T,MODIFIER,;XIST,non_coding_transcript_exon_variant,,ENST00000669898.1,n.770C>T,MODIFIER, +SF3B1 23451 BI GRCh38 2 197402636 197402636 + missense_variant Missense_Mutation SNP T T G rs374250186 TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 35 28 c.1997A>C p.Lys666Thr p.K666T ENST00000335508.11 NM_012433.4 666 aAg/aCg 14/25 P1 G K/T protein_coding YES CCDS33356.1 1997/3915 likely_pathogenic CAATCTTAATA COSM131556 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs374250186;COSV59205833;COSV59206062;COSV59207657 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 2.639e-05 gnomAD_NFE missense_variant 1;1;1;1 1.0 23634996 probably_damaging(0.992) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.K666T,ENST00000335508,NM_012433.4,c.1997A>C,MODERATE,YES,deleterious(0),probably_damaging(0.992),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*3064A>C,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2256A>C,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3881A>C,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 2026/6463 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 1.193e-05 0.0 0.0 0.0 0.0 0.0 2.639e-05 0.0 0.0 6.758129984518746e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 44 7c0bdb87-3555-4578-9586-692a6a37e156 63 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3881A>C,MODIFIER,;SF3B1,missense_variant,p.K666T,ENST00000335508.11,c.1997A>C,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*3064A>C,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2256A>C,MODIFIER, +BAP1 8314 BI GRCh38 3 52407201 52407201 + missense_variant Missense_Mutation SNP C C G TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 0 22 c.553G>C p.Gly185Arg p.G185R ENST00000460680.6 NM_004656.4 185 Ggg/Cgg 7/17 P1 G G/R protein_coding YES CCDS2853.1 553/2190 CAGCCCATCCA CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001;Prints:PR00707 ENSP00000417132 7/17 COSV56230214 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 MODERATE NM_004656.4 missense_variant 1 1.0 probably_damaging(1) Unknown deleterious(0.04) 1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,missense_variant,p.G185R,ENST00000460680,NM_004656.4,c.553G>C,MODERATE,YES,deleterious(0.04),probably_damaging(1),-1;BAP1,missense_variant,p.G185R,ENST00000296288,,c.553G>C,MODERATE,,deleterious(0.04),probably_damaging(1),-1;BAP1,missense_variant,p.G106R,ENST00000470173,,c.316G>C,MODERATE,,deleterious(0.02),probably_damaging(1),-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,3_prime_UTR_variant,,ENST00000490917,,c.*294G>C,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000471532,,n.268G>C,MODIFIER,,,,-1;BAP1,intron_variant,,ENST00000483984,,n.437+198G>C,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 683/3600 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 0 39 7c0bdb87-3555-4578-9586-692a6a37e156 22 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS BAP1,missense_variant,p.G106R,ENST00000470173.1,c.316G>C,MODERATE,;BAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000490917.1,c.*294G>C,MODIFIER,;BAP1,intron_variant,,ENST00000483984.5,n.437+198G>C,MODIFIER,;BAP1,non_coding_transcript_exon_variant,,ENST00000471532.5,n.268G>C,MODIFIER,;BAP1,missense_variant,p.G185R,ENST00000296288.9,c.553G>C,MODERATE,;BAP1,missense_variant,p.G185R,ENST00000460680.6,c.553G>C,MODERATE,YES +FBXL17 64839 BI GRCh38 5 107881056 107881056 + missense_variant Missense_Mutation SNP C C A novel TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 85 50 c.1946G>T p.Gly649Val p.G649V ENST00000542267.7 NM_001163315.3 649 gGg/gTg 8/9 P2 A G/V protein_coding YES CCDS54886.1 1946/2106 TCAGCCCCAAA Gene3D:3.80.10.10;SMART:SM00367;Superfamily:SSF52047 ENSP00000437464 8/9 ENST00000542267 Transcript ENSG00000145743 HGNC:13615 MODERATE NM_001163315.3 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0.01) Q9UF56.159 FBXL17 HGNC -1 1.0 UPI00019B21FB Q9UF56-1 SNV FBXL17,missense_variant,p.G649V,ENST00000542267,NM_001163315.3,c.1946G>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),-1;FBXL17,missense_variant,p.G411V,ENST00000619412,,c.1232G>T,MODERATE,,deleterious(0),probably_damaging(1),-1;FBXL17,missense_variant,p.G319V,ENST00000496714,,c.956G>T,MODERATE,,deleterious(0),probably_damaging(0.992),-1 2353/5198 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 0 109 7c0bdb87-3555-4578-9586-692a6a37e156 135 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS FBXL17,synonymous_variant,p.G318=,ENST00000496714.2,c.954G>T,LOW,;FBXL17,missense_variant,p.G649V,ENST00000542267.7,c.1946G>T,MODERATE,YES +APC 324 BI GRCh38 5 112844005 112844005 + missense_variant Missense_Mutation SNP A A C novel TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 40 47 c.8411A>C p.Gln2804Pro p.Q2804P ENST00000257430.9 NM_001354895.2 2804 cAg/cCg 16/16 P1 C Q/P protein_coding YES CCDS4107.1 8411/8532 ATCTCAGATCC Pfam:PF05937;PANTHER:PTHR12607;PANTHER:PTHR12607:SF11;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000257430 16/16 ENST00000257430 Transcript 1.0 ENSG00000134982 HGNC:583 MODERATE NM_000038.6 missense_variant probably_damaging(0.985) Unknown tolerated_low_confidence(0.14) P25054.248 APC HGNC 1 5.0 UPI000013CF60 P25054-1 SNV APC,missense_variant,p.Q2804P,ENST00000257430,NM_001354895.2&NM_001354906.2&NM_001354896.2&NM_000038.6&NM_001354903.2&NM_001354899.2&NM_001354900.2&NM_001354901.2&NM_001354905.2,c.8411A>C,MODERATE,YES,tolerated_low_confidence(0.14),probably_damaging(0.985),1;APC,missense_variant,p.Q2804P,ENST00000508376,NM_001127510.3&NM_001354898.2&NM_001354904.2,c.8411A>C,MODERATE,,tolerated_low_confidence(0.14),probably_damaging(0.985),1;APC,downstream_gene_variant,,ENST00000507379,NM_001354897.2&NM_001354902.2&NM_001127511.3,,MODIFIER,,,,1;APC,downstream_gene_variant,,ENST00000512211,,,MODIFIER,,,,1;AC008575.1,intron_variant,,ENST00000520401,,c.231-12644A>C,MODIFIER,YES,,,1;APC,downstream_gene_variant,,ENST00000502371,,,MODIFIER,,,,1;APC,downstream_gene_variant,,ENST00000508624,,,MODIFIER,,,,1 8470/10704 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 0 52 7c0bdb87-3555-4578-9586-692a6a37e156 87 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS ENSG00000258864,intron_variant,NMD_transcript_variant,,ENST00000520401.1,c.231-12644A>C,MODIFIER,YES;APC,missense_variant,p.Q2804P,ENST00000512211.7,c.8411A>C,MODERATE,;APC,missense_variant,p.Q2804P,ENST00000508376.6,c.8411A>C,MODERATE,;APC,missense_variant,p.Q2698P,ENST00000713639.1,c.8093A>C,MODERATE,;APC,missense_variant,p.Q2822P,ENST00000504915.3,c.8465A>C,MODERATE,;APC,3_prime_UTR_variant,,ENST00000713638.1,c.*6393A>C,MODIFIER,;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713637.1,c.*7900A>C,MODIFIER,;APC,missense_variant,p.Q2804P,ENST00000257430.9,c.8411A>C,MODERATE,YES;APC,missense_variant,p.Q2786P,ENST00000507379.6,c.8357A>C,MODERATE,;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000505350.2,c.*8417A>C,MODIFIER,;APC,missense_variant,p.Q2804P,ENST00000509732.6,c.8411A>C,MODERATE, +FLRT1 23769 BI GRCh38 11 64116944 64116944 + missense_variant Missense_Mutation SNP G G A rs771760157 TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 17 7 c.677G>A p.Arg226His p.R226H ENST00000246841.3 NM_001384466.1 226 cGc/cAc 2/2 P1 A R/H protein_coding YES CCDS8057.1 677/2025 GCGGCGCCTGG COSM1207245 PROSITE_profiles:PS51450;PANTHER:PTHR45712:SF15;PANTHER:PTHR45712;Gene3D:3.80.10.10;Pfam:PF13855;SMART:SM00369;Superfamily:SSF52058 ENSP00000246841 2/2 rs771760157;COSV55358981 ENST00000246841 Transcript 1.0 ENSG00000126500 HGNC:3760 MODERATE 2.661e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.996) Unknown tolerated(0.06) 0;1 Q9NZU1.171 FLRT1 HGNC 1 1.0 UPI0000039F94 SNV FLRT1,missense_variant,p.R226H,ENST00000246841,NM_013280.4,c.677G>A,MODERATE,YES,tolerated(0.06),probably_damaging(0.996),1;MACROD1,intron_variant,,ENST00000255681,NM_014067.4,c.517+34295C>T,MODIFIER,,,,-1;MACROD1,intron_variant,,ENST00000675777,,c.517+34295C>T,MODIFIER,YES,,,-1;MACROD1,intron_variant,,ENST00000542359,,n.298+34295C>T,MODIFIER,,,,-1;MACROD1,intron_variant,,ENST00000543422,,n.81+9910C>T,MODIFIER,,,,-1;MACROD1,intron_variant,,ENST00000545464,,n.629+34295C>T,MODIFIER,,,,-1;AP006333.1,downstream_gene_variant,,ENST00000543817,,,MODIFIER,YES,,,-1 1720/3949 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 1.21e-05 0.0 0.0 0.0 0.0 0.0 2.661e-05 0.0 0.0 4.05630016757641e-05 0.0 0.0 6.625150126637891e-05 0.0 0.0 0.0 nfe 7.716529944445938e-05 0.0 7.716529944445938e-05 0.0 0.0 0 23 7c0bdb87-3555-4578-9586-692a6a37e156 24 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS FLRT1,missense_variant,p.R226H,ENST00000246841.3,c.677G>A,MODERATE,;FLRT1,missense_variant,p.R226H,ENST00000682287.1,c.677G>A,MODERATE,YES;MACROD1,intron_variant,,ENST00000542359.5,n.298+34295C>T,MODIFIER,;MACROD1,intron_variant,,ENST00000545464.5,n.629+34295C>T,MODIFIER,;MACROD1,intron_variant,,ENST00000543422.5,n.81+9910C>T,MODIFIER,;MACROD1,intron_variant,,ENST00000675777.1,c.517+34295C>T,MODIFIER,;MACROD1,intron_variant,,ENST00000255681.7,c.517+34295C>T,MODIFIER,YES +CNPY2 10330 BI GRCh38 12 56311288 56311288 + missense_variant Missense_Mutation SNP G G A rs768166554 TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 120 100 c.331C>T p.Arg111Trp p.R111W ENST00000273308.9 NM_014255.7 111 Cgg/Tgg 4/6 P1 A R/W protein_coding YES CCDS8914.1 331/549 ATTCCGGCCCA PROSITE_profiles:PS50015;PANTHER:PTHR13341;PANTHER:PTHR13341:SF6;Pfam:PF11938 ENSP00000273308 4/6 rs768166554;COSV99076045 ENST00000273308 Transcript ENSG00000257727 HGNC:13529 MODERATE NM_014255.7 0.0001631 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.991) Unknown deleterious(0) 0;1 Q9Y2B0.153 CNPY2 HGNC -1 1.0 UPI000004C630 Q9Y2B0-1 SNV CNPY2,missense_variant,p.R111W,ENST00000273308,NM_014255.7,c.331C>T,MODERATE,YES,deleterious(0),probably_damaging(0.991),-1;AC073896.1,missense_variant,p.R111W,ENST00000549318,,c.331C>T,MODERATE,YES,deleterious(0),probably_damaging(0.994),-1;CNPY2,missense_variant,p.R111W,ENST00000551475,,c.331C>T,MODERATE,,deleterious(0),probably_damaging(0.991),-1;CNPY2,missense_variant,p.R59W,ENST00000551286,,c.175C>T,MODERATE,,deleterious(0),probably_damaging(0.991),-1;AC073896.1,intron_variant,,ENST00000547423,,c.204+3563C>T,MODIFIER,,,,-1;AC073896.1,intron_variant,,ENST00000548360,,c.204+3563C>T,MODIFIER,,,,-1;PAN2,downstream_gene_variant,,ENST00000610546,,,MODIFIER,YES,,,-1;CNPY2,downstream_gene_variant,,ENST00000551276,,,MODIFIER,,,,-1;CNPY2,downstream_gene_variant,,ENST00000551720,,,MODIFIER,,,,-1;CNPY2,missense_variant,p.R9W,ENST00000546466,,c.25C>T,MODERATE,,deleterious(0),probably_damaging(0.991),-1;CNPY2,3_prime_UTR_variant,,ENST00000553191,,c.*160C>T,MODIFIER,,,,-1;CNPY2,non_coding_transcript_exon_variant,,ENST00000546937,,n.642C>T,MODIFIER,,,,-1;CNPY2,downstream_gene_variant,,ENST00000546388,,,MODIFIER,,,,-1;CNPY2,downstream_gene_variant,,ENST00000547570,,,MODIFIER,,,,-1;CNPY2,downstream_gene_variant,,ENST00000548013,NM_001190991.2,,MODIFIER,,,,-1;CNPY2,downstream_gene_variant,,ENST00000553164,,,MODIFIER,,,,-1;AC073896.2,intron_variant,,ENST00000549565,,n.113-1119G>A,MODIFIER,,,,1;AC073896.2,intron_variant,,ENST00000549860,,n.158-3241G>A,MODIFIER,,,,1;AC073896.2,intron_variant,,ENST00000660360,,n.76-3241G>A,MODIFIER,YES,,,1;AC073896.3,downstream_gene_variant,,ENST00000546789,,,MODIFIER,YES,,,1 524/1450 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 3.181e-05 0.0 0.0 0.0 0.0001631 0.0 1.758e-05 0.0 9.799e-05 6.765810212527867e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002085940068354 0 145 7c0bdb87-3555-4578-9586-692a6a37e156 220 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS CNPY2,missense_variant,p.R59W,ENST00000551286.1,c.175C>T,MODERATE,;CNPY2,missense_variant,p.R111W,ENST00000551475.5,c.331C>T,MODERATE,;CNPY2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000553191.1,c.*160C>T,MODIFIER,;CNPY2,non_coding_transcript_exon_variant,,ENST00000546937.5,n.642C>T,MODIFIER,;CNPY2,missense_variant,p.R111W,ENST00000273308.9,c.331C>T,MODERATE,YES;CNPY2,missense_variant,NMD_transcript_variant,p.R9W,ENST00000546466.5,c.25C>T,MODERATE,;CNPY2-AS1,intron_variant,,ENST00000549860.1,n.158-3241G>A,MODIFIER,;ENSG00000144785,intron_variant,,ENST00000548360.1,c.204+3563C>T,MODIFIER,;CNPY2-AS1,intron_variant,,ENST00000660360.2,n.95-3241G>A,MODIFIER,YES;CNPY2-AS1,intron_variant,,ENST00000549565.4,n.114-1119G>A,MODIFIER,;ENSG00000144785,intron_variant,,ENST00000547423.5,c.204+3563C>T,MODIFIER,;ENSG00000144785,missense_variant,p.R111W,ENST00000549318.5,c.331C>T,MODERATE,YES +TPCN1 53373 BI GRCh38 12 113285941 113285941 + stop_gained Nonsense_Mutation SNP C C G novel TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 29 43 c.1506C>G p.Tyr502Ter p.Y502* ENST00000335509.11 NM_017901.6 502 taC/taG 18/28 P1 G Y/* protein_coding CCDS31908.1 1506/2451 GAGTACTTGTC Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR46474;Superfamily:SSF81324 ENSP00000335300 18/28 ENST00000335509 Transcript ENSG00000186815 HGNC:18182 HIGH NM_017901.6 stop_gained Unknown Q9ULQ1.152 TPCN1 HGNC 1 1.0 UPI0000041252 Q9ULQ1-1 SNV TPCN1,stop_gained,p.Y574*,ENST00000550785,NM_001143819.3,c.1722C>G,HIGH,YES,,,1;TPCN1,stop_gained,p.Y502*,ENST00000335509,NM_017901.6,c.1506C>G,HIGH,,,,1;TPCN1,stop_gained,p.Y574*,ENST00000541517,,c.1722C>G,HIGH,,,,1;TPCN1,stop_gained,p.Y434*,ENST00000392569,NM_001351346.2&NM_001301214.1&NM_001351347.1,c.1302C>G,HIGH,,,,1;TPCN1,stop_gained,p.Y171*,ENST00000546781,,c.513C>G,HIGH,,,,1;TPCN1,stop_gained,p.Y37*,ENST00000547955,,c.111C>G,HIGH,,,,1;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077,,n.1772C>G,MODIFIER,,,,1;TPCN1,non_coding_transcript_exon_variant,,ENST00000551127,,n.480C>G,MODIFIER,,,,1;TPCN1,non_coding_transcript_exon_variant,,ENST00000428632,,n.1635C>G,MODIFIER,,,,1;TPCN1,non_coding_transcript_exon_variant,,ENST00000550543,,n.120C>G,MODIFIER,,,,1;TPCN1,upstream_gene_variant,,ENST00000546907,,,MODIFIER,,,,1 1794/5248 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 0 52 7c0bdb87-3555-4578-9586-692a6a37e156 72 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS TPCN1,missense_variant,NMD_transcript_variant,p.L37V,ENST00000547955.5,c.109C>G,MODERATE,;TPCN1,non_coding_transcript_exon_variant,,ENST00000550543.1,n.120C>G,MODIFIER,;TPCN1,non_coding_transcript_exon_variant,,ENST00000551127.5,n.480C>G,MODIFIER,;TPCN1,missense_variant,p.L171V,ENST00000546781.5,c.511C>G,MODERATE,;TPCN1,non_coding_transcript_exon_variant,,ENST00000428632.7,n.1635C>G,MODIFIER,;TPCN1,stop_gained,p.Y434*,ENST00000392569.8,c.1302C>G,HIGH,;TPCN1,stop_gained,p.Y574*,ENST00000541517.5,c.1722C>G,HIGH,;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077.5,n.1772C>G,MODIFIER,;TPCN1,stop_gained,p.Y502*,ENST00000335509.11,c.1506C>G,HIGH,YES;TPCN1,stop_gained,p.Y574*,ENST00000550785.5,c.1722C>G,HIGH, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-AA9A-01A TCGA-WC-AA9A-10A Somatic 33 16 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 01b18f83-da8a-4d3f-b722-f00fe7559c60 0 56 7c0bdb87-3555-4578-9586-692a6a37e156 49 e6bf1acb-1f4d-4f34-a95e-74e28bc1aac4 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ASPM 259266 BI GRCh38 1 197142406 197142406 + missense_variant Missense_Mutation SNP T T G novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 78 82 c.1846A>C p.Lys616Gln p.K616Q ENST00000367409.9 NM_018136.5 616 Aaa/Caa 3/28 P1 G K/Q protein_coding YES CCDS1389.1 1846/10434 TGTTTTCTTAA PANTHER:PTHR22590;PANTHER:PTHR22590:SF4 ENSP00000356379 3/28 ENST00000367409 Transcript 1.0 ENSG00000066279 HGNC:19048 MODERATE NM_018136.5 missense_variant 1.0 benign(0.045) Unknown tolerated(0.11) Q8IZT6.170 ASPM HGNC -1 1.0 UPI0000458904 Q8IZT6-1 SNV ASPM,missense_variant,p.K616Q,ENST00000367409,NM_018136.5,c.1846A>C,MODERATE,YES,tolerated(0.11),benign(0.045),-1;ASPM,missense_variant,p.K616Q,ENST00000294732,NM_001206846.1,c.1846A>C,MODERATE,,tolerated(0.11),benign(0.127),-1;SEPTIN14P12,upstream_gene_variant,,ENST00000442280,,,MODIFIER,YES,,,-1 2078/10863 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 180 e17c8362-e46f-44d9-997d-36b362cda7fa 160 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ASPM,non_coding_transcript_exon_variant,,ENST00000679766.1,n.2063A>C,MODIFIER,;ASPM,missense_variant,NMD_transcript_variant,p.K616Q,ENST00000681879.1,c.1846A>C,MODERATE,;ASPM,missense_variant,p.K616Q,ENST00000680710.1,c.1846A>C,MODERATE,;ASPM,missense_variant,p.K616Q,ENST00000294732.11,c.1846A>C,MODERATE,;ASPM,missense_variant,p.K616Q,ENST00000680265.1,c.1846A>C,MODERATE,;ASPM,missense_variant,p.K616Q,ENST00000367409.9,c.1846A>C,MODERATE,YES +ASPM 259266 BI GRCh38 1 197142407 197142407 + synonymous_variant Silent SNP C C T TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 80 82 c.1845G>A p.Lys615= p.K615= ENST00000367409.9 NM_018136.5 615 aaG/aaA 3/28 P1 T K protein_coding YES CCDS1389.1 1845/10434 GTTTTCTTAAC PANTHER:PTHR22590;PANTHER:PTHR22590:SF4 ENSP00000356379 3/28 COSV54126894 ENST00000367409 Transcript 1.0 ENSG00000066279 HGNC:19048 LOW NM_018136.5 synonymous_variant 1 1.0 Unknown 1 Q8IZT6.170 ASPM HGNC -1 1.0 UPI0000458904 Q8IZT6-1 SNV ASPM,synonymous_variant,p.K615=,ENST00000367409,NM_018136.5,c.1845G>A,LOW,YES,,,-1;ASPM,synonymous_variant,p.K615=,ENST00000294732,NM_001206846.1,c.1845G>A,LOW,,,,-1;SEPTIN14P12,upstream_gene_variant,,ENST00000442280,,,MODIFIER,YES,,,-1 2077/10863 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 180 e17c8362-e46f-44d9-997d-36b362cda7fa 162 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ASPM,non_coding_transcript_exon_variant,,ENST00000679766.1,n.2062G>A,MODIFIER,;ASPM,synonymous_variant,NMD_transcript_variant,p.K615=,ENST00000681879.1,c.1845G>A,LOW,;ASPM,synonymous_variant,p.K615=,ENST00000680710.1,c.1845G>A,LOW,;ASPM,synonymous_variant,p.K615=,ENST00000294732.11,c.1845G>A,LOW,;ASPM,synonymous_variant,p.K615=,ENST00000680265.1,c.1845G>A,LOW,;ASPM,synonymous_variant,p.K615=,ENST00000367409.9,c.1845G>A,LOW,YES +HTR3E 285242 BI GRCh38 3 184101493 184101493 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 52 34 c.243G>T p.Gln81His p.Q81H ENST00000415389.6 NM_001256613.2 81 caG/caT 3/9 P4 T Q/H protein_coding CCDS58868.1 243/1371 GAACAGCTGCA CDD:cd19013;PANTHER:PTHR18945;PANTHER:PTHR18945:SF811;Pfam:PF02931;Gene3D:2.70.170.10;Superfamily:SSF63712 ENSP00000401444 3/9 ENST00000415389 Transcript ENSG00000186038 HGNC:24005 MODERATE missense_variant benign(0.023) Unknown tolerated(0.13) A5X5Y0.122 HTR3E HGNC 1 1.0 UPI000156575F A5X5Y0-1 SNV HTR3E,missense_variant,p.Q81H,ENST00000415389,NM_001256613.1,c.243G>T,MODERATE,,tolerated(0.13),benign(0.023),1;HTR3E,missense_variant,p.Q96H,ENST00000335304,NM_182589.2,c.288G>T,MODERATE,,tolerated(0.13),benign(0.015),1;HTR3E,missense_variant,p.Q10H,ENST00000431041,,c.30G>T,MODERATE,,tolerated(0.1),benign(0.023),1;HTR3E,intron_variant,,ENST00000425359,NM_198313.2,c.234+842G>T,MODIFIER,,,,1;HTR3E,intron_variant,,ENST00000436361,NM_198314.2,c.279+842G>T,MODIFIER,,,,1;HTR3E,intron_variant,,ENST00000440596,NM_001256614.1,c.279+842G>T,MODIFIER,YES,,,1;HTR3E-AS1,intron_variant,,ENST00000431427,,n.282+2667C>A,MODIFIER,YES,,,-1 709/2139 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 116 e17c8362-e46f-44d9-997d-36b362cda7fa 86 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS HTR3E,intron_variant,,ENST00000436361.6,c.279+842G>T,MODIFIER,;HTR3E,intron_variant,,ENST00000440596.2,c.279+842G>T,MODIFIER,;HTR3E,missense_variant,p.Q10H,ENST00000431041.5,c.30G>T,MODERATE,;HTR3E,missense_variant,p.Q96H,ENST00000335304.6,c.288G>T,MODERATE,;HTR3E,intron_variant,,ENST00000425359.6,c.234+842G>T,MODIFIER,;HTR3E,missense_variant,p.Q81H,ENST00000415389.6,c.243G>T,MODERATE,YES;HTR3E-AS1,intron_variant,,ENST00000431427.1,n.282+2667C>A,MODIFIER,YES +GAB1 2549 BI GRCh38 4 143415642 143415642 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 23 15 c.238G>A p.Glu80Lys p.E80K ENST00000262994.9 NM_002039.4 80 Gaa/Aaa 2/10 A2 A E/K protein_coding CCDS3759.1 238/2085 AGTTTGAAAAC PROSITE_profiles:PS50003;CDD:cd01266;PANTHER:PTHR45960;PANTHER:PTHR45960:SF5;Pfam:PF00169;Gene3D:2.30.29.30;SMART:SM00233;Superfamily:SSF50729 ENSP00000262994 2/10 ENST00000262994 Transcript 1.0 ENSG00000109458 HGNC:4066 MODERATE missense_variant probably_damaging(0.994) Unknown deleterious(0) Q13480.183 GAB1 HGNC 1 1.0 UPI000013D37B Q13480-1 SNV GAB1,missense_variant,p.E80K,ENST00000262995,NM_207123.3,c.238G>A,MODERATE,YES,deleterious(0),probably_damaging(0.993),1;GAB1,missense_variant,p.E80K,ENST00000262994,NM_002039.4,c.238G>A,MODERATE,,deleterious(0),probably_damaging(0.994),1;GAB1,missense_variant,p.E59K,ENST00000509992,,c.175G>A,MODERATE,,deleterious(0),possibly_damaging(0.876),1;GAB1,missense_variant,p.E80K,ENST00000514639,,c.238G>A,MODERATE,,deleterious(0),probably_damaging(0.989),1;GAB1,5_prime_UTR_variant,,ENST00000505913,,c.-72G>A,MODIFIER,,,,1;GAB1,5_prime_UTR_variant,,ENST00000515366,,c.-72G>A,MODIFIER,,,,1;GAB1,missense_variant,p.E46K,ENST00000511836,,c.136G>A,MODERATE,,tolerated(0.11),possibly_damaging(0.519),1 540/2648 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 50 e17c8362-e46f-44d9-997d-36b362cda7fa 38 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS GAB1,stop_retained_variant,NMD_transcript_variant,p.*45=,ENST00000511836.1,c.134G>A,LOW,;GAB1,missense_variant,p.E59K,ENST00000509992.1,c.175G>A,MODERATE,;GAB1,5_prime_UTR_variant,,ENST00000505913.5,c.-72G>A,MODIFIER,;GAB1,5_prime_UTR_variant,,ENST00000515366.5,c.-72G>A,MODIFIER,;GAB1,missense_variant,p.E80K,ENST00000514639.6,c.238G>A,MODERATE,;GAB1,missense_variant,p.E80K,ENST00000262995.9,c.238G>A,MODERATE,;GAB1,missense_variant,p.E80K,ENST00000262994.9,c.238G>A,MODERATE,YES +ZNF474 133923 BI GRCh38 5 122152780 122152830 + inframe_deletion In_Frame_Del DEL CAGAAGCCTCAGCCCCTTCCGAATGCACAGTCCAGCCAAGCGGGACCAAAT CAGAAGCCTCAGCCCCTTCCGAATGCACAGTCCAGCCAAGCGGGACCAAAT - novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 36 8 c.792_842del p.Lys265_Gln281del p.K265_Q281del ENST00000296600.5 NM_207317.3 264 CAGAAGCCTCAGCCCCTTCCGAATGCACAGTCCAGCCAAGCGGGACCAAAT/- 2/2 P1 - QKPQPLPNAQSSQAGPN/- protein_coding YES CCDS4130.1 790-840/1095 CTCCCACAGAAGCCTCAGCCCCTTCCGAATGCACAGTCCAGCCAAGCGGGACCAAATCAAGC PANTHER:PTHR13555;PANTHER:PTHR13555:SF36;Low_complexity_(Seg):seg ENSP00000296600 2/2 ENST00000296600 Transcript ENSG00000164185 HGNC:23245 2.0 MODERATE NM_207317.3 inframe_deletion 1.0 Unknown Q6S9Z5.125 ZNF474 HGNC 1 1.0 UPI0000160642 deletion ZNF474,inframe_deletion,p.K265_Q281del,ENST00000296600,NM_207317.3,c.792_842del,MODERATE,YES,,,1;AC010255.2,intron_variant,,ENST00000514925,,c.-185+911_-185+961del,MODIFIER,,,,1;ZNF474,downstream_gene_variant,,ENST00000504912,,,MODIFIER,,,,1;ZNF474,downstream_gene_variant,,ENST00000505843,,,MODIFIER,,,,1;AC010255.2,upstream_gene_variant,,ENST00000515596,,,MODIFIER,,,,1;AC010255.1,intron_variant,,ENST00000504829,,n.233+1794_233+1844del,MODIFIER,,,,-1;ZNF474-AS1,downstream_gene_variant,,ENST00000505209,,,MODIFIER,YES,,,-1 1140-1190/1929 mutect2;pindel 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 48 e17c8362-e46f-44d9-997d-36b362cda7fa 44 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ZNF475,intron_variant,,ENST00000514925.1,c.-185+909_-185+959del,MODIFIER,;ZNF474,inframe_deletion,p.K265_Q281del,ENST00000698749.1,c.792_842del,MODERATE,;ZNF474,intron_variant,,ENST00000698748.1,c.682+108_682+158del,MODIFIER,;ZNF474,inframe_deletion,p.K265_Q281del,ENST00000296600.5,c.792_842del,MODERATE,YES;ENSG00000247311,intron_variant,,ENST00000504829.1,n.233+1794_233+1844del,MODIFIER,YES +FAM217A 222826 BI GRCh38 6 4069572 4069572 + missense_variant Missense_Mutation SNP G G C rs149448787 TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 56 27 c.651C>G p.Ser217Arg p.S217R ENST00000274673.8 NM_173563.3 217 agC/agG 7/7 A2 C S/R protein_coding CCDS4489.1 651/1527 AAATAGCTGAG PANTHER:PTHR22145;PANTHER:PTHR22145:SF4;Pfam:PF15344 ENSP00000274673 7/7 ENST00000274673 Transcript ENSG00000145975 HGNC:21362 MODERATE NM_173563.3 missense_variant possibly_damaging(0.643) Unknown deleterious(0.01) Q8IXS0.113 FAM217A HGNC -1 1.0 UPI0000160AA7 SNV FAM217A,missense_variant,p.S217R,ENST00000274673,NM_173563.3,c.651C>G,MODERATE,,deleterious(0.01),possibly_damaging(0.643),-1;FAM217A,missense_variant,p.S351R,ENST00000639338,,c.1053C>G,MODERATE,YES,deleterious(0),probably_damaging(0.915),-1;PRPF4B,downstream_gene_variant,,ENST00000337659,NM_003913.5,,MODIFIER,YES,,,1;FAM217A,downstream_gene_variant,,ENST00000492651,,,MODIFIER,,,,-1;FAM217A,downstream_gene_variant,,ENST00000498677,,,MODIFIER,,,,-1;FAM217A,non_coding_transcript_exon_variant,,ENST00000380188,,n.1060C>G,MODIFIER,,,,-1;FAM217A,intron_variant,,ENST00000469157,,n.391+3703C>G,MODIFIER,,,,-1;PRPF4B,downstream_gene_variant,,ENST00000461612,,,MODIFIER,,,,1;FAM217A,downstream_gene_variant,,ENST00000478714,,,MODIFIER,,,,-1;PRPF4B,downstream_gene_variant,,ENST00000463634,,,MODIFIER,,,,1;PRPF4B,downstream_gene_variant,,ENST00000480058,,,MODIFIER,,,,1;PRPF4B,downstream_gene_variant,,ENST00000481109,,,MODIFIER,,,,1 971/2176 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 99 e17c8362-e46f-44d9-997d-36b362cda7fa 83 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS FAM217A,missense_variant,p.S351R,ENST00000639338.1,c.1053C>G,MODERATE,;FAM217A,missense_variant,p.S217R,ENST00000274673.8,c.651C>G,MODERATE,YES;FAM217A,non_coding_transcript_exon_variant,,ENST00000380188.2,n.1060C>G,MODIFIER,;FAM217A,intron_variant,,ENST00000469157.5,n.391+3703C>G,MODIFIER, +ENSG00000284292 0 BI GRCh38 7 99388198 99388198 + missense_variant Missense_Mutation SNP A A G rs1377946182 TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 44 27 c.1325A>G p.Lys442Arg p.K442R ENST00000638617.1 442 aAg/aGg 11/17 P1 G K/R protein_coding YES 1325/2055 GAACAAGTTTG Gene3D:2.130.10.10;PANTHER:PTHR10709;PANTHER:PTHR10709:SF11;SMART:SM00320;Superfamily:SSF50978 ENSP00000491073 11/17 ENST00000638617 Transcript ENSG00000284292 MODERATE missense_variant probably_damaging(0.989) Unknown deleterious(0) AC004922.1 Clone_based_ensembl_gene 1 A0A1W2PNV4.13 5.0 UPI00097BA602 SNV AC004922.1,missense_variant,p.K442R,ENST00000638617,,c.1325A>G,MODERATE,YES,deleterious(0),probably_damaging(0.989),1;ARPC1B,missense_variant,p.K110R,ENST00000443222,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.95),1;ARPC1B,missense_variant,p.K110R,ENST00000451682,,c.329A>G,MODERATE,YES,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000645391,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000427217,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000455009,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000646101,NM_005720.4,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000431816,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000458033,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,missense_variant,p.K110R,ENST00000417330,,c.329A>G,MODERATE,,deleterious(0),probably_damaging(0.971),1;ARPC1B,downstream_gene_variant,,ENST00000414376,,,MODIFIER,,,,1;ARPC1B,downstream_gene_variant,,ENST00000418347,,,MODIFIER,,,,1;ARPC1B,downstream_gene_variant,,ENST00000429246,,,MODIFIER,,,,1;ARPC1B,non_coding_transcript_exon_variant,,ENST00000474880,,n.344A>G,MODIFIER,,,,1;ARPC1B,non_coding_transcript_exon_variant,,ENST00000493403,,n.487A>G,MODIFIER,,,,1;PDAP1,downstream_gene_variant,,ENST00000496335,,,MODIFIER,,,,-1;ARPC1B,missense_variant,p.K110R,ENST00000432343,,c.329A>G,MODERATE,,deleterious(0.02),probably_damaging(0.971),1;ARPC1B,3_prime_UTR_variant,,ENST00000445924,,c.*328A>G,MODIFIER,,,,1;ARPC1B,non_coding_transcript_exon_variant,,ENST00000484375,,n.417A>G,MODIFIER,,,,1;ARPC1B,non_coding_transcript_exon_variant,,ENST00000484600,,n.394A>G,MODIFIER,,,,1;AC004922.1,downstream_gene_variant,,ENST00000441989,,,MODIFIER,,,,1;ARPC1B,upstream_gene_variant,,ENST00000468337,,,MODIFIER,,,,1;ARPC1B,upstream_gene_variant,,ENST00000481997,,,MODIFIER,,,,1;ARPC1B,upstream_gene_variant,,ENST00000491294,,,MODIFIER,,,,1 1480/2430 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 48 e17c8362-e46f-44d9-997d-36b362cda7fa 71 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ARPC1B,non_coding_transcript_exon_variant,,ENST00000493403.1,n.487A>G,MODIFIER,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000445924.5,n.442A>G,MODIFIER,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000474880.5,n.344A>G,MODIFIER,;ARPC1B,missense_variant,NMD_transcript_variant,p.K110R,ENST00000432343.1,c.329A>G,MODERATE,;ARPC1B,missense_variant,p.K110R,ENST00000417330.6,c.329A>G,MODERATE,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000695609.1,n.394A>G,MODIFIER,;ARPC1B,missense_variant,p.K110R,ENST00000431816.6,c.329A>G,MODERATE,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000484600.6,n.394A>G,MODIFIER,;ARPC1B,missense_variant,p.K110R,ENST00000458033.6,c.329A>G,MODERATE,;ARPC1B,missense_variant,p.K110R,ENST00000427217.6,c.329A>G,MODERATE,;ARPC1B,missense_variant,p.K110R,ENST00000646101.2,c.329A>G,MODERATE,YES;ARPC1B,missense_variant,p.K110R,ENST00000451682.5,c.329A>G,MODERATE,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000695608.1,n.399A>G,MODIFIER,;ARPC1B,missense_variant,p.K110R,ENST00000455009.6,c.329A>G,MODERATE,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000484375.5,n.417A>G,MODIFIER,;ARPC1B,non_coding_transcript_exon_variant,,ENST00000695607.1,n.428A>G,MODIFIER,;ARPC1B,missense_variant,p.K110R,ENST00000645391.1,c.329A>G,MODERATE,;ARPC1B,missense_variant,p.K110R,ENST00000414376.6,c.329A>G,MODERATE,;ARPC1B,missense_variant,p.K110R,ENST00000443222.6,c.329A>G,MODERATE,;ENSG00000284292,missense_variant,p.K442R,ENST00000638617.1,c.1325A>G,MODERATE,YES +STRIP2 57464 BI GRCh38 7 129485631 129485631 + synonymous_variant Silent SNP C C T novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 72 17 c.2307C>T p.Ala769= p.A769= ENST00000249344.7 NM_020704.3 769 gcC/gcT 21/21 P1 T A protein_coding YES CCDS34752.1 2307/2505 AGGGCCAACAT PANTHER:PTHR13239;PANTHER:PTHR13239:SF6;Pfam:PF11882;SMART:SM01293 ENSP00000249344 21/21 ENST00000249344 Transcript ENSG00000128578 HGNC:22209 LOW NM_020704.3 synonymous_variant 1.0 Unknown Q9ULQ0.125 STRIP2 HGNC 1 1.0 UPI00001C1E68 Q9ULQ0-1 SNV STRIP2,synonymous_variant,p.A769=,ENST00000249344,NM_020704.3,c.2307C>T,LOW,YES,,,1;STRIP2,downstream_gene_variant,,ENST00000435494,NM_001134336.2,,MODIFIER,,,,1;RNU1-72P,downstream_gene_variant,,ENST00000362976,,,MODIFIER,YES,,,1 2348/5116 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 6.774329904146725e-06 2.4376000510528684e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 57 e17c8362-e46f-44d9-997d-36b362cda7fa 89 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS STRIP2,synonymous_variant,p.A769=,ENST00000249344.7,c.2307C>T,LOW,YES +PLXNA4 91584 BI GRCh38 7 132226218 132226218 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 86 74 c.1925C>T p.Thr642Ile p.T642I ENST00000321063.9 NM_001393897.1 642 aCc/aTc 8/32 P1 A T/I protein_coding CCDS43646.1 1925/5685 TGCCGGTCTCC PANTHER:PTHR22625;PANTHER:PTHR22625:SF34;Gene3D:2.60.40.10;Pfam:PF17960 ENSP00000323194 8/32 ENST00000321063 Transcript ENSG00000221866 HGNC:9102 MODERATE missense_variant possibly_damaging(0.798) Unknown deleterious(0.04) Q9HCM2.156 PLXNA4 HGNC -1 A0A024R7A6.57 5.0 UPI000004E55B Q9HCM2-1 SNV PLXNA4,missense_variant,p.T642I,ENST00000359827,,c.1925C>T,MODERATE,YES,deleterious(0.04),possibly_damaging(0.798),-1;PLXNA4,missense_variant,p.T642I,ENST00000321063,NM_020911.1,c.1925C>T,MODERATE,,deleterious(0.04),possibly_damaging(0.798),-1 2154/13061 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 109 e17c8362-e46f-44d9-997d-36b362cda7fa 160 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS PLXNA4,missense_variant,p.T642I,ENST00000359827.7,c.1925C>T,MODERATE,;PLXNA4,missense_variant,p.T642I,ENST00000321063.9,c.1925C>T,MODERATE,YES +ASIC1 41 BI GRCh38 12 50059937 50059937 + missense_variant Missense_Mutation SNP G G A rs764353781 TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 3 17 c.541G>A p.Ala181Thr p.A181T ENST00000447966.7 NM_001412756.1 181 Gct/Act 3/12 P1 A A/T protein_coding CCDS44876.1 541/1587 GCAGCGCTGAA Gene3D:1.10.287.770;Gene3D:1.10.3590.10;Gene3D:2.60.470.10;Pfam:PF00858;PANTHER:PTHR11690;PANTHER:PTHR11690:SF170;TIGRFAM:TIGR00859 ENSP00000400228 3/12 rs764353781 ENST00000447966 Transcript ENSG00000110881 HGNC:100 MODERATE NM_001095.4 6.155e-05 gnomAD_AFR missense_variant benign(0.149) Unknown deleterious(0.03) P78348.179 ASIC1 HGNC 1 1.0 UPI000016199C P78348-2 SNV ASIC1,missense_variant,p.A181T,ENST00000228468,NM_020039.4,c.541G>A,MODERATE,YES,deleterious(0.03),benign(0.045),1;ASIC1,missense_variant,p.A181T,ENST00000447966,NM_001095.4,c.541G>A,MODERATE,,deleterious(0.03),benign(0.149),1;ASIC1,missense_variant,p.A18T,ENST00000453327,,c.52G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.511),1;ASIC1,missense_variant,p.A181T,ENST00000550558,,c.541G>A,MODERATE,,tolerated(0.38),possibly_damaging(0.864),1 878/3886 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 1.196e-05 6.155e-05 0.0 0.0 5.438e-05 0.0 8.82e-06 0.0 0.0 6.76023000778514e-06 2.4324999685632065e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 45 e17c8362-e46f-44d9-997d-36b362cda7fa 20 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ASIC1,synonymous_variant,p.A17=,ENST00000453327.7,c.51G>A,LOW,;ASIC1,missense_variant,NMD_transcript_variant,p.A181T,ENST00000550558.5,c.541G>A,MODERATE,;ASIC1,missense_variant,p.A181T,ENST00000447966.7,c.541G>A,MODERATE,YES;ASIC1,missense_variant,p.A181T,ENST00000228468.8,c.541G>A,MODERATE, +CYSLTR2 57105 BI GRCh38 13 48707203 48707203 + missense_variant Missense_Mutation SNP T T A TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 142 45 c.386T>A p.Leu129Gln p.L129Q ENST00000282018.4 NM_001308471.3 129 cTg/cAg 1/1 P1 A L/Q protein_coding YES CCDS9412.1 386/1041 TTTCCTGACCG COSM1666392 Gene3D:1.20.1070.10;PDB-ENSP_mappings:6rz6.A;PDB-ENSP_mappings:6rz7.A;PDB-ENSP_mappings:6rz8.A;PDB-ENSP_mappings:6rz9.A;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24230;PANTHER:PTHR24230:SF10;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15157 ENSP00000282018 1/1 COSV56166671 ENST00000282018 Transcript 1.0 ENSG00000152207 HGNC:18274 MODERATE missense_variant 1 1.0 probably_damaging(0.997) Unknown deleterious(0) 1 Q9NS75.162 CYSLTR2 HGNC 1 Q5KU17.121 UPI000003BCCC SNV CYSLTR2,missense_variant,p.L129Q,ENST00000282018,NM_001308471.3,c.386T>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;CYSLTR2,missense_variant,p.L129Q,ENST00000614739,NM_001308465.3&NM_001308476.3&NM_001308468.3&NM_001308467.3&NM_020377.5&NM_001308469.3&NM_001308470.3,c.386T>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;CYSLTR2,downstream_gene_variant,,ENST00000617562,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000621321,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000622559,,,MODIFIER,,,,1 649/4672 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 149 e17c8362-e46f-44d9-997d-36b362cda7fa 187 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS CYSLTR2,missense_variant,p.L129Q,ENST00000282018.4,c.386T>A,MODERATE,;CYSLTR2,missense_variant,p.L129Q,ENST00000682523.1,c.386T>A,MODERATE,YES;CYSLTR2,missense_variant,p.L129Q,ENST00000614739.4,c.386T>A,MODERATE, +KCNH5 27133 BI GRCh38 14 62950522 62950522 + missense_variant Missense_Mutation SNP C C T rs587777164 TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 55 13 c.980G>A p.Arg327His p.R327H ENST00000322893.12 NM_139318.5 327 cGt/cAt 7/11 P1 T R/H protein_coding YES CCDS9756.1 980/2967 uncertain_significance;pathogenic AGAGACGCACC COSM1370447;COSM1370448 Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR10217;PANTHER:PTHR10217:SF533;Superfamily:SSF81324;Low_complexity_(Seg):seg ENSP00000321427 7/11 rs587777164;CM1310653;COSV59758318;COSV59758899 ENST00000322893 Transcript 1.0 ENSG00000140015 HGNC:6254 MODERATE NM_139318.5 missense_variant 1;1;1;1 1.0 23647072;24133262 probably_damaging(0.999) Unknown deleterious(0) 0;0;1;1 Q8NCM2.170 KCNH5 HGNC -1 1.0 UPI0000039E2D Q8NCM2-1 SNV KCNH5,missense_variant,p.R327H,ENST00000322893,NM_139318.5,c.980G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;KCNH5,missense_variant,p.R327H,ENST00000420622,NM_172375.3,c.980G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;KCNH5,missense_variant,p.R269H,ENST00000394968,,c.806G>A,MODERATE,,deleterious(0),probably_damaging(0.997),-1;KCNH5,non_coding_transcript_exon_variant,,ENST00000394964,,n.1145G>A,MODIFIER,,,,-1 1252/11283 muse;mutect2;varscan2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 31 e17c8362-e46f-44d9-997d-36b362cda7fa 68 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS KCNH5,non_coding_transcript_exon_variant,,ENST00000394964.3,n.1145G>A,MODIFIER,;KCNH5,missense_variant,p.R269H,ENST00000394968.2,c.806G>A,MODERATE,;KCNH5,missense_variant,p.R327H,ENST00000420622.6,c.980G>A,MODERATE,;KCNH5,missense_variant,p.R327H,ENST00000322893.12,c.980G>A,MODERATE,YES +ABR 29 BI GRCh38 17 1056999 1056999 + synonymous_variant,splice_region_variant Silent SNP G G A rs771481181 TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 142 96 c.1485C>T p.Asp495= p.D495= ENST00000302538.10 NM_021962.5 495 gaC/gaT 13/23 P4 A D protein_coding CCDS10999.1 1485/2580 TTACCGTCTTT PANTHER:PTHR23182;PANTHER:PTHR23182:SF5 ENSP00000303909 13/23 rs771481181 ENST00000302538 Transcript ENSG00000159842 HGNC:81 LOW 0.0001631 gnomAD_OTH splice_region_variant Unknown Q12979.185 ABR HGNC -1 1.0 UPI00001AED3D Q12979-1 SNV ABR,splice_region_variant,p.D449=,ENST00000544583,NM_001159746.3&NM_001322840.2,c.1347C>T,LOW,,,,-1;ABR,splice_region_variant,p.D495=,ENST00000302538,NM_021962.5,c.1485C>T,LOW,,,,-1;ABR,splice_region_variant,p.D507=,ENST00000574437,NM_001322841.2,c.1521C>T,LOW,YES,,,-1;ABR,splice_region_variant,p.D458=,ENST00000291107,NM_001092.5,c.1374C>T,LOW,,,,-1;ABR,splice_region_variant,p.D277=,ENST00000536794,NM_001282149.2,c.831C>T,LOW,,,,-1;ABR,splice_region_variant,p.D162=,ENST00000574544,,c.486C>T,LOW,,,,-1;ABR,intron_variant,,ENST00000576964,,n.525-6856C>T,MODIFIER,,,,-1;ABR,splice_region_variant,,ENST00000573895,,n.182C>T,LOW,,,,-1;ABR,splice_region_variant,,ENST00000575770,,c.*162C>T,LOW,,,,-1 1632/5289 muse;mutect2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 1.194e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0001631 6.539e-05 0 190 e17c8362-e46f-44d9-997d-36b362cda7fa 238 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ABR,non_coding_transcript_exon_variant,,ENST00000573895.1,n.182C>T,MODIFIER,;ABR,stop_gained,splice_region_variant,p.R162*,ENST00000574544.1,c.484C>T,HIGH,;ABR,intron_variant,,ENST00000576964.5,n.525-6856C>T,MODIFIER,;ABR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000575770.5,c.*162C>T,MODIFIER,;ABR,synonymous_variant,splice_region_variant,p.D277=,ENST00000536794.6,c.831C>T,LOW,;ABR,synonymous_variant,splice_region_variant,p.D458=,ENST00000291107.6,c.1374C>T,LOW,;ABR,synonymous_variant,splice_region_variant,p.D507=,ENST00000574437.5,c.1521C>T,LOW,;ABR,synonymous_variant,splice_region_variant,p.D449=,ENST00000544583.6,c.1347C>T,LOW,;ABR,synonymous_variant,splice_region_variant,p.D754=,ENST00000574139.7,c.2262C>T,LOW,;ABR,synonymous_variant,splice_region_variant,p.D495=,ENST00000302538.10,c.1485C>T,LOW,YES +ILVBL 10994 BI GRCh38 19 15119230 15119230 + missense_variant Missense_Mutation SNP G G T TCGA-VD-AA8O-01A TCGA-VD-AA8O-10A Somatic 114 8 c.987C>A p.His329Gln p.H329Q ENST00000263383.8 NM_006844.5 329 caC/caA 9/16 P1 T H/Q protein_coding YES CCDS12325.1 987/1899 AGGGGGTGGTT PANTHER:PTHR18968:SF155;PANTHER:PTHR18968;Pfam:PF00205;Gene3D:3.40.50.1220;Superfamily:SSF52467 ENSP00000263383 9/16 COSV99655165 ENST00000263383 Transcript ENSG00000105135 HGNC:6041 MODERATE NM_006844.5 missense_variant 1 1.0 possibly_damaging(0.653) Unknown tolerated(0.06) 1 A1L0T0.114 ILVBL HGNC -1 1.0 UPI000007055E SNV ILVBL,missense_variant,p.H329Q,ENST00000263383,NM_006844.5,c.987C>A,MODERATE,YES,tolerated(0.06),possibly_damaging(0.653),-1;ILVBL,missense_variant,p.H222Q,ENST00000534378,,c.666C>A,MODERATE,,tolerated(0.07),possibly_damaging(0.653),-1;ILVBL,missense_variant,p.H112Q,ENST00000598709,,c.336C>A,MODERATE,,tolerated(0.08),possibly_damaging(0.653),-1;SYDE1,downstream_gene_variant,,ENST00000342784,NM_033025.6,,MODIFIER,YES,,,1;ILVBL,downstream_gene_variant,,ENST00000527093,,,MODIFIER,,,,-1;ILVBL,downstream_gene_variant,,ENST00000533747,,,MODIFIER,,,,-1;SYDE1,downstream_gene_variant,,ENST00000600252,,,MODIFIER,,,,1;SYDE1,downstream_gene_variant,,ENST00000600440,NM_001300910.2,,MODIFIER,,,,1;ILVBL,downstream_gene_variant,,ENST00000600984,,,MODIFIER,,,,-1;ILVBL,downstream_gene_variant,,ENST00000531635,,,MODIFIER,,,,-1;ILVBL,3_prime_UTR_variant,,ENST00000533148,,c.*626C>A,MODIFIER,,,,-1;ILVBL,non_coding_transcript_exon_variant,,ENST00000533086,,n.1397C>A,MODIFIER,,,,-1;ILVBL,upstream_gene_variant,,ENST00000524779,,,MODIFIER,,,,-1;ILVBL,upstream_gene_variant,,ENST00000525880,,,MODIFIER,,,,-1;ILVBL,upstream_gene_variant,,ENST00000534806,,,MODIFIER,,,,-1;ILVBL,upstream_gene_variant,,ENST00000596093,,,MODIFIER,,,,-1;AC003956.1,upstream_gene_variant,,ENST00000598450,,,MODIFIER,YES,,,1 1128/2305 muse;mutect2 99d1bfcc-1989-4dd2-a5e9-78e08f6ce7cf 0 112 e17c8362-e46f-44d9-997d-36b362cda7fa 122 86a9f2ed-9b27-4568-866a-0d43f4db61fc SUCCESS ILVBL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000533148.5,c.*626C>A,MODIFIER,;ILVBL,missense_variant,p.H112Q,ENST00000598709.1,c.336C>A,MODERATE,;ILVBL,missense_variant,p.H222Q,ENST00000534378.5,c.666C>A,MODERATE,;ILVBL,missense_variant,p.H329Q,ENST00000263383.8,c.987C>A,MODERATE,YES;ILVBL,non_coding_transcript_exon_variant,,ENST00000533086.5,n.1397C>A,MODIFIER, +C1orf127 148345 BI GRCh38 1 10954127 10954127 + missense_variant Missense_Mutation SNP C C T rs757164639 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 54 31 c.991G>A p.Gly331Arg p.G331R ENST00000377004.9 NM_001170754.1 331 Gga/Aga 10/13 P1 T G/R protein_coding YES CCDS53267.1 991/2472 TCCTCCGACTT COSM5491017;COSM5491018 PANTHER:PTHR38653;Pfam:PF15094 ENSP00000366203 10/13 rs757164639;COSV65438149 ENST00000377004 Transcript ENSG00000175262 HGNC:26730 MODERATE 0.0006264 gnomAD_SAS missense_variant 0;1 1.0 benign(0.028) Unknown tolerated(1) 0;1 C1orf127 HGNC -1 G8JLG8.54 5.0 UPI0001C0B385 SNV C1orf127,missense_variant,p.G331R,ENST00000377004,NM_001170754.1,c.991G>A,MODERATE,YES,tolerated(1),benign(0.028),-1;C1orf127,missense_variant,p.G309R,ENST00000520253,,c.925G>A,MODERATE,,tolerated(1),benign(0.003),-1;C1orf127,missense_variant,p.G166R,ENST00000418570,NM_001366227.1,c.496G>A,MODERATE,,tolerated(1),benign(0),-1;C1orf127,upstream_gene_variant,,ENST00000476357,,,MODIFIER,,,,-1 991/2761 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 9.188e-05 0.0001846 2.933e-05 0.0 0.0 0.0 0.0 0.0 0.0006264 3.380939961061813e-05 4.864999937126413e-05 0.0 6.63305982016027e-05 0.0 0.0 0.0 afr 4.864999937126413e-05 0.0 3.086610013269819e-05 0.0 0.0 0 68 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 85 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS C1orf127,synonymous_variant,p.S308=,ENST00000520253.1,c.924G>A,LOW,;C1orf127,missense_variant,p.G331R,ENST00000377004.9,c.991G>A,MODERATE,YES;C1orf127,synonymous_variant,p.S165=,ENST00000418570.6,c.495G>A,LOW, +LUZP1 7798 BI GRCh38 1 23091455 23091455 + missense_variant Missense_Mutation SNP G G A rs1159342358 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 172 7 c.2807C>T p.Pro936Leu p.P936L ENST00000302291.9 NM_001142546.3 936 cCc/cTc 4/5 P4 A P/L protein_coding YES CCDS30628.1 2807/3231 TTGGGGGGTCT PANTHER:PTHR23166;PANTHER:PTHR23166:SF7;MobiDB_lite:mobidb-lite ENSP00000303758 4/5 rs1159342358;COSV56505220 ENST00000302291 Transcript ENSG00000169641 HGNC:14985 MODERATE 5.782e-05 gnomAD_AMR missense_variant 0;1 benign(0.055) Unknown deleterious_low_confidence(0.05) 0;1 Q86V48.139 LUZP1 HGNC -1 5.0 UPI000020466A Q86V48-1 SNV LUZP1,missense_variant,p.P936L,ENST00000302291,,c.2807C>T,MODERATE,YES,deleterious_low_confidence(0.05),benign(0.055),-1;LUZP1,missense_variant,p.P936L,ENST00000418342,NM_001142546.1&NM_033631.4,c.2807C>T,MODERATE,,deleterious_low_confidence(0.05),benign(0.055),-1;LUZP1,missense_variant,p.P936L,ENST00000314174,,c.2807C>T,MODERATE,,deleterious_low_confidence(0.04),benign(0.054),-1;LUZP1,downstream_gene_variant,,ENST00000471849,,,MODIFIER,,,,-1;LUZP1,downstream_gene_variant,,ENST00000475164,,,MODIFIER,,,,-1;AL031428.1,upstream_gene_variant,,ENST00000427154,,,MODIFIER,YES,,,-1 3609/8898 muse;mutect2 a9f956a0-660f-4185-a843-d9911d2484de 7.955e-06 0.0 5.782e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 146 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 179 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS LUZP1,missense_variant,p.P936L,ENST00000314174.5,c.2807C>T,MODERATE,;LUZP1,missense_variant,p.P936L,ENST00000706844.2,c.2807C>T,MODERATE,;LUZP1,missense_variant,p.P936L,ENST00000713666.1,c.2807C>T,MODERATE,;LUZP1,missense_variant,p.P936L,ENST00000302291.9,c.2807C>T,MODERATE,YES;LUZP1,missense_variant,p.P936L,ENST00000475164.3,c.2807C>T,MODERATE,;LUZP1,intron_variant,,ENST00000713667.1,n.584-2402C>T,MODIFIER,;LUZP1,missense_variant,p.P936L,ENST00000471849.6,c.2807C>T,MODERATE, +PDE4DIP 9659 BI GRCh38 1 149010556 149010556 + missense_variant Missense_Mutation SNP C C A rs1553604482 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 65 81 c.5041C>A p.Pro1681Thr p.P1681T ENST00000369354.7 NM_014644.6 1681 Ccc/Acc 31/44 A2 A P/T protein_coding CCDS72891.1 5041/7041 CAACTCCCCAG MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR46501:SF2;PANTHER:PTHR46501 ENSP00000358360 31/44 rs1553604482 ENST00000369354 Transcript 1.0 ENSG00000178104 HGNC:15580 MODERATE 8.792e-06 gnomAD_NFE missense_variant possibly_damaging(0.542) Unknown deleterious(0.01) Q5VU43.150 PDE4DIP HGNC 1 1.0 UPI0002747118 Q5VU43-1 SNV PDE4DIP,missense_variant,p.P1817T,ENST00000585156,NM_001377392.1&NM_001350521.3,c.5449C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.955),1;PDE4DIP,missense_variant,p.P1681T,ENST00000369356,NM_001198834.4,c.5041C>A,MODERATE,,deleterious(0.01),possibly_damaging(0.542),1;PDE4DIP,missense_variant,p.P1681T,ENST00000369354,NM_014644.6&NM_001350520.1,c.5041C>A,MODERATE,,deleterious(0.01),possibly_damaging(0.542),1;PDE4DIP,missense_variant,p.P1637T,ENST00000618462,NM_001350522.2&NM_001377393.1&NM_001198832.3&NM_001350523.2,c.4909C>A,MODERATE,,deleterious(0.01),probably_damaging(0.998),1;PDE4DIP,intron_variant,,ENST00000524974,,c.5335+765C>A,MODIFIER,,,,1;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000479369,,n.385C>A,MODIFIER,,,,1;PDE4DIP,intron_variant,,ENST00000530062,,c.91-16159C>A,MODIFIER,,,,1;AC239802.1,upstream_gene_variant,,ENST00000531288,,,MODIFIER,YES,,,-1 5231/8262 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.792e-06 0.0 0.0 0 143 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 147 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS PDE4DIP,non_coding_transcript_exon_variant,,ENST00000479369.6,n.385C>A,MODIFIER,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000695772.1,n.1802C>A,MODIFIER,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000695771.1,n.2311C>A,MODIFIER,;PDE4DIP,intron_variant,,ENST00000695770.1,n.3603+765C>A,MODIFIER,;PDE4DIP,intron_variant,NMD_transcript_variant,,ENST00000530062.5,c.91-16159C>A,MODIFIER,;PDE4DIP,missense_variant,p.P1843T,ENST00000704840.1,c.5527C>A,MODERATE,;PDE4DIP,missense_variant,p.P1681T,ENST00000369354.7,c.5041C>A,MODERATE,;PDE4DIP,missense_variant,p.P1681T,ENST00000369356.8,c.5041C>A,MODERATE,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000706648.1,n.4886C>A,MODIFIER,;PDE4DIP,missense_variant,p.P1747T,ENST00000695795.1,c.5239C>A,MODERATE,YES;PDE4DIP,missense_variant,p.P1637T,ENST00000618462.4,c.4909C>A,MODERATE,;PDE4DIP,missense_variant,p.P1817T,ENST00000585156.5,c.5449C>A,MODERATE,;PDE4DIP,intron_variant,,ENST00000524974.5,c.5335+765C>A,MODIFIER,;PDE4DIP,missense_variant,p.P1818T,ENST00000695794.1,c.5452C>A,MODERATE,;PDE4DIP,missense_variant,p.P1781T,ENST00000695768.1,c.5341C>A,MODERATE,;PDE4DIP,intron_variant,,ENST00000706647.1,c.5338+765C>A,MODIFIER, +BAP1 8314 BI GRCh38 3 52409596 52409597 + frameshift_variant Frame_Shift_Ins INS - - C rs397509413 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 60 115 c.79dup p.Val27GlyfsTer42 p.V27Gfs*42 ENST00000460680.6 NM_004656.4 27 gtg/gGtg 3/17 P1 C V/GX protein_coding YES CCDS2853.1 79-80/2190 pathogenic CTTGCACCCCC CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 3/17 rs397509413 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1 1.0 23684012 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D insertion BAP1,frameshift_variant,p.V27Gfs*42,ENST00000460680,NM_004656.4,c.79dup,HIGH,YES,,,-1;BAP1,frameshift_variant,p.V27Gfs*42,ENST00000296288,,c.79dup,HIGH,,,,-1;BAP1,5_prime_UTR_variant,,ENST00000470173,,c.-159dup,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000461861,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000614886,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000615126,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000472337,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,frameshift_variant,p.V27Gfs*?,ENST00000490917,,c.79dup,HIGH,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,,n.79dup,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 209-210/3600 mutect2;pindel;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 179 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 175 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS BAP1,5_prime_UTR_variant,,ENST00000470173.1,c.-159_-158insG,MODIFIER,;BAP1,frameshift_variant,NMD_transcript_variant,p.V27Gfs,ENST00000490917.1,c.79dup,HIGH,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984.5,n.79_80insG,MODIFIER,;BAP1,frameshift_variant,p.V27Gfs*42,ENST00000296288.9,c.79dup,HIGH,;BAP1,frameshift_variant,p.V27Gfs*42,ENST00000460680.6,c.79dup,HIGH,YES +SH3RF1 57630 BI GRCh38 4 169116376 169116376 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 42 3 c.2032C>T p.Pro678Ser p.P678S ENST00000284637.14 NM_020870.4 678 Ccc/Tcc 10/12 P1 A P/S protein_coding YES CCDS34099.1 2032/2667 ACTGGGCTCAG PANTHER:PTHR14167;PANTHER:PTHR14167:SF62 ENSP00000284637 10/12 ENST00000284637 Transcript ENSG00000154447 HGNC:17650 MODERATE NM_020870.4 missense_variant 1.0 benign(0.026) Unknown tolerated(0.46) Q7Z6J0.139 SH3RF1 HGNC -1 1.0 UPI0000160033 Q7Z6J0-1 SNV SH3RF1,missense_variant,p.P678S,ENST00000284637,NM_020870.4,c.2032C>T,MODERATE,YES,tolerated(0.46),benign(0.026),-1;SH3RF1,non_coding_transcript_exon_variant,,ENST00000508685,,n.1913C>T,MODIFIER,,,,-1;SH3RF1,3_prime_UTR_variant,,ENST00000511421,,c.*639C>T,MODIFIER,,,,-1 2225/5120 muse;mutect2 a9f956a0-660f-4185-a843-d9911d2484de 0 28 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 45 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS SH3RF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000511421.5,c.*639C>T,MODIFIER,;SH3RF1,non_coding_transcript_exon_variant,,ENST00000508685.1,n.1913C>T,MODIFIER,;SH3RF1,missense_variant,p.P678S,ENST00000284637.14,c.2032C>T,MODERATE,YES +PCDHB7 56129 BI GRCh38 5 141174500 141174500 + missense_variant Missense_Mutation SNP C C A TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 27 42 c.1665C>A p.Asn555Lys p.N555K ENST00000231137.6 NM_018940.4 555 aaC/aaA 1/1 P1 A N/K protein_coding YES CCDS4249.1 1665/2382 GCCAACGACAA CDD:cd11304;Gene3D:2.60.40.60;SMART:SM00112;Superfamily:SSF49313;PROSITE_profiles:PS50268;PANTHER:PTHR24028:SF69;PANTHER:PTHR24028;PROSITE_patterns:PS00232;Prints:PR00205 ENSP00000231137 1/1 COSV50753531;COSV99176308 ENST00000231137 Transcript ENSG00000113212 HGNC:8692 MODERATE NM_018940.4 missense_variant 1;1 probably_damaging(0.988) Unknown deleterious_low_confidence(0.01) 1;1 Q9Y5E2.157 PCDHB7 HGNC 1 UPI00001273E3 SNV PCDHB7,missense_variant,p.N555K,ENST00000231137,NM_018940.4,c.1665C>A,MODERATE,YES,deleterious_low_confidence(0.01),probably_damaging(0.988),1;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.5,,MODIFIER,YES,,,1;AC244517.11,intron_variant,,ENST00000624192,,n.73-37317G>T,MODIFIER,,,,-1;AC244517.8,upstream_gene_variant,,ENST00000623995,,,MODIFIER,YES,,,1;AC244517.2,upstream_gene_variant,,ENST00000624802,,,MODIFIER,,,,-1;AC244517.2,upstream_gene_variant,,ENST00000625128,,,MODIFIER,,,,-1 1857/3740 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 61 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 69 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS PCDHB7,missense_variant,p.N555K,ENST00000231137.6,c.1665C>A,MODERATE,YES;ENSG00000280029,intron_variant,,ENST00000624192.1,n.73-37317G>T,MODIFIER,YES +IGFBP3 3486 BI GRCh38 7 45917290 45917290 + missense_variant Missense_Mutation SNP G G A rs755356224 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 100 28 c.553C>T p.Arg185Cys p.R185C ENST00000613132.5 NM_000598.5 185 Cgc/Tgc 2/5 P1 A R/C protein_coding CCDS5505.1 553/876 GTAGCGCTGGC COSM218925 PANTHER:PTHR11551;PANTHER:PTHR11551:SF3;Prints:PR01979 ENSP00000275521 2/5 rs755356224;COSV51871889 ENST00000275521 Transcript ENSG00000146674 HGNC:5472 MODERATE 0.0001087 gnomAD_EAS missense_variant 0;1 probably_damaging(0.943) Unknown deleterious(0.02) 0;1 P17936.220 IGFBP3 HGNC -1 1.0 UPI000013DA64 P17936-1 SNV IGFBP3,missense_variant,p.R191C,ENST00000381083,NM_001013398.2,c.571C>T,MODERATE,YES,deleterious(0.03),benign(0.151),-1;IGFBP3,missense_variant,p.R164C,ENST00000613132,,c.490C>T,MODERATE,,deleterious(0.02),benign(0.042),-1;IGFBP3,missense_variant,p.R88C,ENST00000381086,,c.262C>T,MODERATE,,deleterious(0.02),probably_damaging(0.943),-1;IGFBP3,missense_variant,p.R185C,ENST00000275521,NM_000598.5,c.553C>T,MODERATE,,deleterious(0.02),probably_damaging(0.943),-1;IGFBP3,missense_variant,p.R37C,ENST00000428530,,c.109C>T,MODERATE,,deleterious(0.01),probably_damaging(0.987),-1;IGFBP3,missense_variant,p.R47C,ENST00000417621,,c.139C>T,MODERATE,,deleterious(0.01),probably_damaging(0.987),-1;IGFBP3,missense_variant,p.R157C,ENST00000615754,,c.469C>T,MODERATE,,deleterious(0.01),probably_damaging(0.943),-1;IGFBP3,missense_variant,p.R75C,ENST00000448817,,c.223C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;IGFBP3,non_coding_transcript_exon_variant,,ENST00000465642,,n.539C>T,MODIFIER,,,,-1;IGFBP3,non_coding_transcript_exon_variant,,ENST00000460477,,n.280C>T,MODIFIER,,,,-1;IGFBP3,upstream_gene_variant,,ENST00000460209,,,MODIFIER,,,,-1 687/2262 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 7.952e-06 0.0 0.0 0.0 0.0001087 0.0 0.0 0.0 0.0 0 93 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 128 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS IGFBP3,non_coding_transcript_exon_variant,,ENST00000460477.1,n.280C>T,MODIFIER,;IGFBP3,non_coding_transcript_exon_variant,,ENST00000465642.1,n.539C>T,MODIFIER,;IGFBP3,missense_variant,p.R75C,ENST00000448817.1,c.223C>T,MODERATE,;IGFBP3,missense_variant,p.A46V,ENST00000417621.5,c.137C>T,MODERATE,;IGFBP3,synonymous_variant,p.S36=,ENST00000428530.5,c.108C>T,LOW,;IGFBP3,missense_variant,p.R88C,ENST00000381086.9,c.262C>T,MODERATE,;IGFBP3,missense_variant,p.R191C,ENST00000381083.9,c.571C>T,MODERATE,;IGFBP3,missense_variant,p.R185C,ENST00000613132.5,c.553C>T,MODERATE,YES +ELAPOR2 222223 BI GRCh38 7 86913061 86913061 + synonymous_variant Silent SNP G G A novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 65 4 c.1875C>T p.His625= p.H625= ENST00000450689.7 NM_001142749.3 625 caC/caT 14/22 P4 A H protein_coding YES CCDS47632.1 1875/3090 ATGTAGTGGCC PANTHER:PTHR22727;PANTHER:PTHR22727:SF3;SMART:SM01411;Superfamily:SSF57184 ENSP00000413445 14/22 ENST00000450689 Transcript ENSG00000164659 HGNC:21945 LOW NM_001142749.3 synonymous_variant 1.0 Unknown A8MWY0.105 ELAPOR2 HGNC -1 5.0 UPI000173AA00 A8MWY0-1 SNV ELAPOR2,missense_variant,p.T579I,ENST00000444627,,c.1736C>T,MODERATE,,tolerated(0.15),benign(0.404),-1;ELAPOR2,synonymous_variant,p.H625=,ENST00000450689,NM_001142749.3,c.1875C>T,LOW,YES,,,-1;ELAPOR2,synonymous_variant,p.H458=,ENST00000416314,NM_001291991.1&NM_001291990.1&NM_152748.4,c.1374C>T,LOW,,,,-1;ELAPOR2,synonymous_variant,p.H586=,ENST00000423294,,c.1758C>T,LOW,,,,-1;ELAPOR2,non_coding_transcript_exon_variant,,ENST00000490995,,n.593C>T,MODIFIER,,,,-1;ELAPOR2,non_coding_transcript_exon_variant,,ENST00000474609,,n.582C>T,MODIFIER,,,,-1;ELAPOR2,3_prime_UTR_variant,,ENST00000394714,,c.*1147C>T,MODIFIER,,,,-1;ELAPOR2,non_coding_transcript_exon_variant,,ENST00000470853,,n.100C>T,MODIFIER,,,,-1;ELAPOR2,upstream_gene_variant,,ENST00000427812,,,MODIFIER,,,,-1 2016/6796 muse;mutect2 a9f956a0-660f-4185-a843-d9911d2484de 0 42 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 69 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS ELAPOR2,non_coding_transcript_exon_variant,,ENST00000474609.1,n.582C>T,MODIFIER,;ELAPOR2,non_coding_transcript_exon_variant,,ENST00000490995.5,n.593C>T,MODIFIER,;ELAPOR2,non_coding_transcript_exon_variant,,ENST00000470853.1,n.100C>T,MODIFIER,;ELAPOR2,synonymous_variant,p.L586=,ENST00000423294.5,c.1756C>T,LOW,;ELAPOR2,synonymous_variant,p.H458=,ENST00000416314.5,c.1374C>T,LOW,;ELAPOR2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000394714.6,c.*1147C>T,MODIFIER,;ELAPOR2,missense_variant,p.T579I,ENST00000444627.5,c.1736C>T,MODERATE,;ELAPOR2,synonymous_variant,p.H625=,ENST00000450689.7,c.1875C>T,LOW,YES +NRCAM 4897 BI GRCh38 7 108231036 108231036 + missense_variant Missense_Mutation SNP T T C rs1367486144 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 59 26 c.545A>G p.Asp182Gly p.D182G ENST00000379028.8 NM_001371124.1 182 gAt/gGt 8/33 P1 C D/G protein_coding YES CCDS47686.1 545/3915 AATTATCCATC Gene3D:2.60.40.10;PROSITE_profiles:PS50835;PANTHER:PTHR10075;PANTHER:PTHR10075:SF44;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726 ENSP00000368314 8/33 rs1367486144 ENST00000379028 Transcript ENSG00000091129 HGNC:7994 MODERATE NM_001037132.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.581) Unknown deleterious(0.01) Q92823.189 NRCAM HGNC -1 5.0 UPI00005E2661 Q92823-1 SNV NRCAM,missense_variant,p.D182G,ENST00000379028,NM_001371124.1&NM_001371119.1&NM_001371164.1&NM_001371143.1&NM_001371146.1&NM_001371172.1&NM_001371138.1&NM_001371169.1&NM_001037132.4&NM_001371156.1&NM_001371126.1&NM_001371131.1,c.545A>G,MODERATE,YES,deleterious(0.01),possibly_damaging(0.581),-1;NRCAM,missense_variant,p.D182G,ENST00000413765,NM_001193582.1&NM_001371123.1&NM_001371127.1&NM_001371161.1&NM_001371173.1&NM_001371149.1&NM_001371144.1&NM_001371153.1&NM_001371168.1&NM_001371128.1,c.545A>G,MODERATE,,deleterious(0.01),probably_damaging(0.998),-1;NRCAM,missense_variant,p.D176G,ENST00000351718,NM_005010.4&NM_001371151.1&NM_001371148.1&NM_001371170.1&NM_001371137.1&NM_001371134.1&NM_001371175.1&NM_001371157.1&NM_001371136.1&NM_001371152.1&NM_001371160.1&NM_001371174.1&NM_001371150.1&NM_001371159.1&NM_001371133.1&NM_001371171.1&NM_001371130.1&NM_001371180.1&NM_001371178.1&NM_001371176.1&NM_001371179.1&NM_001371182.1,c.527A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.615),-1;NRCAM,missense_variant,p.D182G,ENST00000379024,NM_001193584.1&NM_001193583.1&NM_001371122.1&NM_001371125.1&NM_001371147.1&NM_001371142.1&NM_001371154.1&NM_001371140.1&NM_001371129.1&NM_001371158.1&NM_001371145.1&NM_001371135.1&NM_001371141.1&NM_001371162.1&NM_001371139.1&NM_001371163.1&NM_001371165.1&NM_001371155.1&NM_001371166.1&NM_001371132.1&NM_001371167.1&NM_001371177.1&NM_001371181.1,c.545A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.648),-1;NRCAM,missense_variant,p.D177G,ENST00000379022,,c.530A>G,MODERATE,,deleterious(0),probably_damaging(0.998),-1;NRCAM,missense_variant,p.D176G,ENST00000613830,,c.527A>G,MODERATE,,deleterious(0),probably_damaging(0.926),-1;NRCAM,missense_variant,p.D176G,ENST00000417701,,c.527A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.803),-1;NRCAM,downstream_gene_variant,,ENST00000418239,,,MODIFIER,,,,-1;NRCAM,downstream_gene_variant,,ENST00000419936,,,MODIFIER,,,,-1;NRCAM,downstream_gene_variant,,ENST00000442580,,,MODIFIER,,,,-1;NRCAM,downstream_gene_variant,,ENST00000456431,,,MODIFIER,,,,-1 1070/6701 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 49 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 85 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS NRCAM,missense_variant,p.D176G,ENST00000417701.5,c.527A>G,MODERATE,;NRCAM,missense_variant,p.D182G,ENST00000379024.8,c.545A>G,MODERATE,;NRCAM,missense_variant,p.D176G,ENST00000351718.8,c.527A>G,MODERATE,;NRCAM,missense_variant,p.D182G,ENST00000379028.8,c.545A>G,MODERATE,YES;NRCAM,missense_variant,p.D182G,ENST00000413765.6,c.545A>G,MODERATE, +PAPPA 5069 BI GRCh38 9 116187681 116187681 + missense_variant Missense_Mutation SNP G G A rs201429158 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 13 17 c.943G>A p.Gly315Ser p.G315S ENST00000328252.4 NM_002581.5 315 Ggc/Agc 2/22 P1 A G/S protein_coding YES CCDS6813.1 943/4884 CCCACGGCTTT PANTHER:PTHR46130;PANTHER:PTHR46130:SF2 ENSP00000330658 2/22 rs201429158;COSV100075339 ENST00000328252 Transcript ENSG00000182752 HGNC:8602 MODERATE NM_002581.5 9.923e-05 gnomAD_ASJ missense_variant 0;1 1.0 benign(0.003) Unknown tolerated(0.54) 0;1 Q13219.206 PAPPA HGNC 1 1.0 UPI00001E0589 SNV PAPPA,missense_variant,p.G315S,ENST00000328252,NM_002581.5,c.943G>A,MODERATE,YES,tolerated(0.54),benign(0.003),1 1325/10971 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 3.978e-06 0.0 0.0 9.923e-05 0.0 0.0 0.0 0.0 0.0 6.758310064469697e-06 2.430720087431837e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 41 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 30 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS PAPPA,missense_variant,p.G315S,ENST00000328252.4,c.943G>A,MODERATE,YES +DYNC2I2 89891 BI GRCh38 9 128634293 128634318 + frameshift_variant Frame_Shift_Del DEL GAGGGAGAGCTGCAGCGAAGTCAAGG GAGGGAGAGCTGCAGCGAAGTCAAGG - novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 30 16 c.1280_1305del p.Lys436ProfsTer15 p.K436Pfs*15 ENST00000372715.7 NM_052844.4 427 cCCTTGACTTCGCTGCAGCTCTCCCTC/c 8/9 P1 - PLTSLQLSL/X protein_coding YES CCDS6906.2 1280-1305/1611 ATACTTGAGGGAGAGCTGCAGCGAAGTCAAGGGAGGG PDB-ENSP_mappings:6rlb.D;PDB-ENSP_mappings:6sc2.D;PROSITE_profiles:PS50294;PANTHER:PTHR12442;PANTHER:PTHR12442:SF26;Gene3D:2.130.10.10;SMART:SM00320;Superfamily:SSF50978 ENSP00000361800 8/9 ENST00000372715 Transcript 1.0 ENSG00000119333 HGNC:28296 HIGH frameshift_variant 1.0 Unknown Q96EX3.148 DYNC2I2 HGNC -1 1.0 UPI000045894D deletion DYNC2I2,frameshift_variant,p.P427Qfs*24,ENST00000372715,NM_052844.3,c.1280_1305del,HIGH,YES,,,-1;SPTAN1,downstream_gene_variant,,ENST00000358161,NM_001195532.2,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000372731,NM_003127.4,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000372739,NM_001375312.2&NM_001375311.2&NM_001375310.1&NM_001130438.3&NM_001375313.1,,MODIFIER,,,,1;DYNC2I2,downstream_gene_variant,,ENST00000419989,,,MODIFIER,,,,-1;DYNC2I2,downstream_gene_variant,,ENST00000451652,,,MODIFIER,,,,-1;SPTAN1,downstream_gene_variant,,ENST00000630804,NM_001375314.2&NM_001363765.2,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000630866,NM_001375318.1&NM_001363759.2,,MODIFIER,YES,,,1;SPTAN1,downstream_gene_variant,,ENST00000630981,,,MODIFIER,,,,1;DYNC2I2,downstream_gene_variant,,ENST00000473486,,,MODIFIER,,,,-1;DYNC2I2,downstream_gene_variant,,ENST00000480613,,,MODIFIER,,,,-1;DYNC2I2,downstream_gene_variant,,ENST00000483181,,,MODIFIER,,,,-1;SPTAN1,downstream_gene_variant,,ENST00000636010,,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000636939,,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000625980,,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000630147,,,MODIFIER,,,,1;SPTAN1,downstream_gene_variant,,ENST00000630763,,,MODIFIER,,,,1;AL356481.3,upstream_gene_variant,,ENST00000630523,,,MODIFIER,YES,,,-1 1341-1366/1755 mutect2;pindel a9f956a0-660f-4185-a843-d9911d2484de 0 93 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 46 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS DYNC2I2,frameshift_variant,p.K436Pfs*15,ENST00000372715.7,c.1280_1305del,HIGH,YES +FUBP3 8939 BI GRCh38 9 130616414 130616414 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 27 11 c.464A>T p.His155Leu p.H155L ENST00000319725.10 NM_003934.2 155 cAt/cTt 7/19 P1 T H/L protein_coding YES CCDS43893.1 464/1719 CTTTCATAATG PANTHER:PTHR10288;PANTHER:PTHR10288:SF234;Superfamily:SSF54791 ENSP00000318177 7/19 ENST00000319725 Transcript ENSG00000107164 HGNC:4005 MODERATE NM_003934.2 missense_variant 1.0 possibly_damaging(0.762) Unknown deleterious(0.02) Q96I24.176 FUBP3 HGNC 1 A0A024R8A7.35 1.0 UPI00001C1EAA Q96I24-1 SNV FUBP3,missense_variant,p.H155L,ENST00000319725,NM_003934.2,c.464A>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.762),1;FUBP3,downstream_gene_variant,,ENST00000465949,,,MODIFIER,,,,1;FUBP3,upstream_gene_variant,,ENST00000487406,,,MODIFIER,,,,1;FUBP3,3_prime_UTR_variant,,ENST00000650723,,c.*2280A>T,MODIFIER,,,,1 568/3153 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 36 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 38 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS FUBP3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000699747.1,c.*349A>T,MODIFIER,;FUBP3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000650723.1,c.*2280A>T,MODIFIER,;FUBP3,missense_variant,p.H155L,ENST00000319725.10,c.464A>T,MODERATE,YES +DHTKD1 55526 BI GRCh38 10 12117716 12117722 + frameshift_variant Frame_Shift_Del DEL TTAACCC TTAACCC - novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 43 55 c.2363_2369del p.Phe788TrpfsTer28 p.F788Wfs*28 ENST00000263035.9 NM_018706.7 788 tTTAACCCg/tg 14/17 P1 - FNP/X protein_coding YES CCDS7087.1 2363-2369/2760 CAACATTTAACCCGGTCA PANTHER:PTHR23152;PANTHER:PTHR23152:SF21;TIGRFAM:TIGR00239;Pfam:PF16870;Gene3D:3.40.50.12470;PIRSF:PIRSF000157;Gene3D:3.40.50.11610 ENSP00000263035 14/17 ENST00000263035 Transcript 1.0 ENSG00000181192 HGNC:23537 HIGH NM_018706.7 frameshift_variant 1.0 Unknown Q96HY7.141 DHTKD1 HGNC 1 1.0 UPI000013D38C deletion DHTKD1,frameshift_variant,p.F788Wfs*28,ENST00000263035,NM_018706.7,c.2363_2369del,HIGH,YES,,,1;DHTKD1,downstream_gene_variant,,ENST00000448829,,,MODIFIER,,,,1;RNU6-88P,upstream_gene_variant,,ENST00000606801,,,MODIFIER,YES,,,-1;DHTKD1,upstream_gene_variant,,ENST00000479283,,,MODIFIER,,,,1 2443-2449/5173 mutect2;pindel;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 95 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 98 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS DHTKD1,frameshift_variant,p.F788Wfs*28,ENST00000263035.9,c.2363_2369del,HIGH,YES +RPP38 10557 BI GRCh38 10 15104063 15104063 + missense_variant Missense_Mutation SNP G G A rs562959917 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 52 25 c.749G>A p.Arg250Gln p.R250Q ENST00000378197.5 NM_183005.5 250 cGg/cAg 3/3 0.0 0.0 0.0 0.0 0.0 0.0 P1 A R/Q protein_coding CCDS7108.1 749/852 CGGTCGGCAGG PDB-ENSP_mappings:6ahr.C;PDB-ENSP_mappings:6ahu.C;PANTHER:PTHR46948 ENSP00000367439 3/3 rs562959917 ENST00000378197 Transcript ENSG00000152464 HGNC:30329 MODERATE NM_183005.5 0.0002027 gnomAD_AMR missense_variant benign(0) Unknown tolerated(1) P78345.173 RPP38 HGNC 1 1.0 UPI000006F1AE SNV RPP38,missense_variant,p.R250Q,ENST00000616640,NM_001265601.1,c.749G>A,MODERATE,YES,tolerated(1),benign(0),1;RPP38,missense_variant,p.R250Q,ENST00000378197,NM_183005.5,c.749G>A,MODERATE,,tolerated(1),benign(0),1;RPP38,missense_variant,p.R250Q,ENST00000378203,NM_001097590.3,c.749G>A,MODERATE,,tolerated(1),benign(0),1;RPP38,missense_variant,p.R250Q,ENST00000378202,NM_006414.5,c.749G>A,MODERATE,,tolerated(1),benign(0),1;RPP38,intron_variant,,ENST00000378201,,c.399+350G>A,MODIFIER,,,,1;NMT2,downstream_gene_variant,,ENST00000378150,NM_001308295.2,,MODIFIER,,,,-1;NMT2,downstream_gene_variant,,ENST00000378165,NM_004808.3,,MODIFIER,YES,,,-1;RPP38,downstream_gene_variant,,ENST00000441850,,,MODIFIER,,,,1;RPP38,intron_variant,,ENST00000451677,,n.162+6665G>A,MODIFIER,,,,1;NMT2,intron_variant,,ENST00000466201,,n.128-380C>T,MODIFIER,,,,-1;NMT2,downstream_gene_variant,,ENST00000486786,,,MODIFIER,,,,-1 1290/1484 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 6.39e-05 0.0 0.0002027 0.0 0.0 0.0 5.29e-05 0.0 9.813e-05 4.059209823026322e-05 7.306029874598607e-05 0.0 6.628660048590973e-05 0.0 0.0 0.0 afr 7.306029874598607e-05 0.0 0.0 0.0004950499860569 0.0002090299967676 0 83 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 77 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS NMT2,intron_variant,,ENST00000466201.1,n.128-380C>T,MODIFIER,;RPP38,missense_variant,p.R250Q,ENST00000378197.5,c.749G>A,MODERATE,YES;RPP38,missense_variant,p.R250Q,ENST00000378202.5,c.749G>A,MODERATE,;RPP38,intron_variant,,ENST00000451677.1,n.162+6665G>A,MODIFIER,;RPP38,intron_variant,,ENST00000378201.6,c.399+350G>A,MODIFIER,;RPP38,missense_variant,p.R250Q,ENST00000616640.1,c.749G>A,MODERATE,;RPP38,missense_variant,p.R250Q,ENST00000378203.5,c.749G>A,MODERATE, +PRKG1 5592 BI GRCh38 10 50991524 50991524 + missense_variant Missense_Mutation SNP T T G novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 5 7 c.146T>G p.Val49Gly p.V49G ENST00000401604.8 NM_001098512.3 49 gTg/gGg 1/18 P1 G V/G protein_coding CCDS44399.1 146/2016 CCCAGTGCCCT PDB-ENSP_mappings:1zxa.A;PDB-ENSP_mappings:1zxa.B;PIRSF:PIRSF000559;PANTHER:PTHR24353;PANTHER:PTHR24353:SF68;CDD:cd12085 ENSP00000384200 1/18 ENST00000401604 Transcript 1.0 ENSG00000185532 HGNC:9414 MODERATE missense_variant 1.0 benign(0) Unknown tolerated(0.32) Q13976.201 PRKG1 HGNC 1 5.0 UPI000016A69C Q13976-1 SNV PRKG1,missense_variant,p.V49G,ENST00000401604,NM_001098512.3,c.146T>G,MODERATE,,tolerated(0.32),benign(0),1 637/6957 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 12 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 12 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS PRKG1,missense_variant,p.V49G,ENST00000401604.8,c.146T>G,MODERATE, +PRLHR 2834 BI GRCh38 10 118594182 118594182 + missense_variant Missense_Mutation SNP G G A rs774369942 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 24 18 c.1063C>T p.Arg355Cys p.R355C ENST00000239032.4 NM_004248.3 355 Cgc/Tgc 2/2 P1 A R/C protein_coding YES CCDS7606.1 1063/1113 CTTGCGGGGCC Gene3D:1.20.1070.10;Prints:PR01018;PANTHER:PTHR24235;PANTHER:PTHR24235:SF11;Superfamily:SSF81321 ENSP00000239032 2/2 rs774369942 ENST00000239032 Transcript ENSG00000119973 HGNC:4464 MODERATE NM_004248.3 9.651e-05 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.869) Unknown deleterious(0) P49683.170 PRLHR HGNC -1 1.0 UPI000013CA6F SNV PRLHR,missense_variant,p.R355C,ENST00000239032,NM_004248.3,c.1063C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.869),-1;PRLHR,missense_variant,p.R355C,ENST00000636925,,c.1063C>T,MODERATE,,deleterious(0),possibly_damaging(0.869),-1 1202/5387 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 1.451e-05 0.0 0.0 0.0 0.0 0.0 1.054e-05 0.0 9.651e-05 0 39 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 42 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS PRLHR,missense_variant,p.R355C,ENST00000636925.1,c.1063C>T,MODERATE,;PRLHR,missense_variant,p.R355C,ENST00000239032.4,c.1063C>T,MODERATE,YES +SLC39A5 283375 BI GRCh38 12 56231473 56231473 + missense_variant Missense_Mutation SNP C C A TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 53 38 c.199C>A p.Leu67Ile p.L67I ENST00000266980.8 NM_001135195.1 67 Cta/Ata 2/11 P1 A L/I protein_coding YES CCDS8912.2 199/1623 TGGGGCTAGGC Low_complexity_(Seg):seg;PANTHER:PTHR12191:SF17;PANTHER:PTHR12191 ENSP00000266980 2/11 COSV57191982 ENST00000266980 Transcript 1.0 ENSG00000139540 HGNC:20502 MODERATE missense_variant 1 1.0 probably_damaging(0.991) Unknown deleterious(0.01) 1 Q6ZMH5.133 SLC39A5 HGNC 1 A0A024RB24.52 1.0 UPI000035E86A SNV SLC39A5,missense_variant,p.L67I,ENST00000266980,NM_001135195.1,c.199C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.991),1;SLC39A5,missense_variant,p.L67I,ENST00000454355,NM_173596.3,c.199C>A,MODERATE,,deleterious(0.01),probably_damaging(0.991),1;SLC39A5,missense_variant,p.L38I,ENST00000436633,,c.112C>A,MODERATE,,deleterious(0.01),probably_damaging(0.996),1;SLC39A5,missense_variant,p.L67I,ENST00000419753,,c.199C>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),1;SLC39A5,missense_variant,p.L67I,ENST00000437277,,c.199C>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),1;SLC39A5,missense_variant,p.L67I,ENST00000417965,,c.199C>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),1;SLC39A5,missense_variant,p.L67I,ENST00000424625,,c.199C>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.991),1;NABP2,downstream_gene_variant,,ENST00000267023,NM_024068.4,,MODIFIER,,,,1;NABP2,downstream_gene_variant,,ENST00000341463,,,MODIFIER,,,,1;NABP2,downstream_gene_variant,,ENST00000380198,,,MODIFIER,YES,,,1;NABP2,downstream_gene_variant,,ENST00000399713,,,MODIFIER,,,,1;SLC39A5,non_coding_transcript_exon_variant,,ENST00000481103,,n.68C>A,MODIFIER,,,,1;SLC39A5,downstream_gene_variant,,ENST00000493574,,,MODIFIER,,,,1 492/2031 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 51 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 91 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS SLC39A5,missense_variant,p.L67I,ENST00000437277.1,c.199C>A,MODERATE,;SLC39A5,missense_variant,p.L67I,ENST00000266980.8,c.199C>A,MODERATE,;SLC39A5,missense_variant,p.L38I,ENST00000436633.5,c.112C>A,MODERATE,;SLC39A5,missense_variant,p.L67I,ENST00000417965.5,c.199C>A,MODERATE,;SLC39A5,non_coding_transcript_exon_variant,,ENST00000481103.5,n.68C>A,MODIFIER,;SLC39A5,missense_variant,p.L67I,ENST00000454355.7,c.199C>A,MODERATE,YES;SLC39A5,missense_variant,p.L67I,ENST00000424625.5,c.199C>A,MODERATE,;SLC39A5,missense_variant,p.L67I,ENST00000419753.5,c.199C>A,MODERATE, +GRIN2A 2903 BI GRCh38 16 9849902 9849902 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 54 5 c.1182G>T p.Lys394Asn p.K394N ENST00000330684.4 NM_001134407.3 394 aaG/aaT 5/13 P1 A K/N protein_coding YES CCDS10539.1 1182/4395 AAGGACTTGTA PDB-ENSP_mappings:6ira.B;PDB-ENSP_mappings:6ira.D;PDB-ENSP_mappings:6irf.B;PDB-ENSP_mappings:6irf.D;PDB-ENSP_mappings:6irg.B;PDB-ENSP_mappings:6irg.D;PDB-ENSP_mappings:6irh.B;PDB-ENSP_mappings:6irh.D;PANTHER:PTHR18966;PANTHER:PTHR18966:SF407 ENSP00000332549 5/13 ENST00000330684 Transcript 1.0 ENSG00000183454 HGNC:4585 MODERATE NM_001134407.3 missense_variant 1.0 benign(0) Unknown tolerated(0.81) Q12879.209 GRIN2A HGNC -1 Q547U9.140 1.0 UPI000000D7AB Q12879-1 SNV GRIN2A,missense_variant,p.K394N,ENST00000330684,NM_001134407.3,c.1182G>T,MODERATE,YES,tolerated(0.81),benign(0),-1;GRIN2A,missense_variant,p.K394N,ENST00000396573,NM_000833.5,c.1182G>T,MODERATE,,tolerated(0.81),benign(0),-1;GRIN2A,missense_variant,p.K237N,ENST00000674742,,c.711G>T,MODERATE,,tolerated(0.8),benign(0),-1;GRIN2A,missense_variant,p.K237N,ENST00000535259,,c.711G>T,MODERATE,,tolerated(0.66),benign(0.001),-1;GRIN2A,missense_variant,p.K394N,ENST00000675398,,c.1182G>T,MODERATE,,tolerated(0.25),benign(0.02),-1;GRIN2A,missense_variant,p.K394N,ENST00000562109,NM_001134408.2,c.1182G>T,MODERATE,,tolerated(0.59),benign(0),-1;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,,n.821G>T,MODIFIER,,,,-1;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566683,,n.415G>T,MODIFIER,,,,-1;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,,n.775G>T,MODIFIER,,,,-1;GRIN2A,non_coding_transcript_exon_variant,,ENST00000675189,,n.1666G>T,MODIFIER,,,,-1 1752/14706 muse;mutect2 a9f956a0-660f-4185-a843-d9911d2484de 0 50 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 60 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS GRIN2A,non_coding_transcript_exon_variant,,ENST00000566683.1,n.415G>T,MODIFIER,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000675189.1,n.1666G>T,MODIFIER,;GRIN2A,missense_variant,p.K394N,ENST00000562109.5,c.1182G>T,MODERATE,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273.2,n.775G>T,MODIFIER,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292.3,n.821G>T,MODIFIER,;GRIN2A,missense_variant,p.K394N,ENST00000675398.1,c.1182G>T,MODERATE,;GRIN2A,missense_variant,p.K237N,ENST00000674742.1,c.711G>T,MODERATE,;GRIN2A,missense_variant,p.K237N,ENST00000535259.6,c.711G>T,MODERATE,;GRIN2A,missense_variant,p.K394N,ENST00000330684.4,c.1182G>T,MODERATE,YES;GRIN2A,missense_variant,p.K394N,ENST00000396573.6,c.1182G>T,MODERATE, +PAGR1 79447 BI GRCh38 16 29819572 29819572 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 148 62 c.583C>T p.Gln195Ter p.Q195* ENST00000320330.8 NM_024516.4 195 Cag/Tag 3/3 P1 T Q/* protein_coding YES CCDS10655.1 583/765 GGAGCCAGAAA Pfam:PF15364;PANTHER:PTHR28467;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000326519 3/3 ENST00000320330 Transcript ENSG00000280789 HGNC:28707 HIGH NM_024516.4 stop_gained 1.0 Unknown Q9BTK6.134 PAGR1 HGNC 1 1.0 UPI000006FAEB SNV PAGR1,stop_gained,p.Q195*,ENST00000320330,NM_024516.4,c.583C>T,HIGH,YES,,,1;PRRT2,downstream_gene_variant,,ENST00000300797,NM_001256443.2,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000357402,NM_005115.5&NM_001293204.1&NM_001293205.1,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000358758,NM_145239.3,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000395353,NM_017458.3,,MODIFIER,YES,,,1;MVP,upstream_gene_variant,,ENST00000563558,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000563915,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000565164,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000566066,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000567659,NM_001256442.2,,MODIFIER,YES,,,1;MVP,upstream_gene_variant,,ENST00000570234,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000572820,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000636619,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000636902,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000637064,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000637403,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000637565,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000647876,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000565830,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000637425,,,MODIFIER,,,,1;AC120114.4,stop_gained,p.Q25*,ENST00000562285,,c.73C>T,HIGH,YES,,,1;AC009133.6,3_prime_UTR_variant,,ENST00000609618,,c.*524C>T,MODIFIER,YES,,,1;MVP,upstream_gene_variant,,ENST00000562463,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000563096,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000566859,,,MODIFIER,,,,1;MVP,upstream_gene_variant,,ENST00000569887,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000636131,,,MODIFIER,,,,1;PRRT2,downstream_gene_variant,,ENST00000637290,,,MODIFIER,,,,1;AC009133.1,non_coding_transcript_exon_variant,,ENST00000569809,,n.373G>A,MODIFIER,,,,-1;AC009133.1,non_coding_transcript_exon_variant,,ENST00000569039,,n.213G>A,MODIFIER,,,,-1;AC009133.1,non_coding_transcript_exon_variant,,ENST00000564980,,n.405G>A,MODIFIER,,,,-1 957/3874 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 185 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 210 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS MVP-DT,non_coding_transcript_exon_variant,,ENST00000564980.1,n.405G>A,MODIFIER,;MVP-DT,non_coding_transcript_exon_variant,,ENST00000569809.2,n.373G>A,MODIFIER,;ENSG00000281348,synonymous_variant,NMD_transcript_variant,p.A24=,ENST00000562285.1,c.72C>T,LOW,YES;PAGR1,stop_gained,p.Q195*,ENST00000320330.8,c.583C>T,HIGH,YES;ENSG00000280893,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000609618.2,c.*524C>T,MODIFIER,YES;MVP-DT,non_coding_transcript_exon_variant,,ENST00000569039.5,n.213G>A,MODIFIER,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 40 23 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 64 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 63 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ZNF341 84905 BI GRCh38 20 33770275 33770275 + synonymous_variant Silent SNP G G A rs1383763618 TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 5 30 c.1605G>A p.Lys535= p.K535= ENST00000375200.6 NM_001282933.2 535 aaG/aaA 10/15 P2 A K protein_coding YES CCDS74719.1 1605/2565 AAGAAGGACAA Gene3D:3.30.160.60;PANTHER:PTHR24388;PANTHER:PTHR24388:SF28 ENSP00000364346 10/15 ENST00000375200 Transcript 1.0 ENSG00000131061 HGNC:15992 LOW NM_001282933.2 synonymous_variant 1.0 Unknown Q9BYN7.167 ZNF341 HGNC 1 1.0 UPI0000470A07 Q9BYN7-1 SNV ZNF341,synonymous_variant,p.K528=,ENST00000342427,NM_032819.4,c.1584G>A,LOW,,,,1;ZNF341,synonymous_variant,p.K535=,ENST00000375200,NM_001282935.1&NM_001282933.2,c.1605G>A,LOW,YES,,,1;ZNF341,synonymous_variant,p.K535=,ENST00000483118,,c.1605G>A,LOW,,,,1;ZNF341,3_prime_UTR_variant,,ENST00000497876,,c.*1189G>A,MODIFIER,,,,1 1631/3343 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 6.8955100687162485e-06 0.0 0.0 6.740359822288156e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 34 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 35 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS ZNF341,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698695.1,c.*530G>A,MODIFIER,;ZNF341,synonymous_variant,NMD_transcript_variant,p.K535=,ENST00000483118.5,c.1605G>A,LOW,;ZNF341,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000497876.5,c.*1189G>A,MODIFIER,;ZNF341,intron_variant,,ENST00000698694.1,c.490-19261G>A,MODIFIER,;ZNF341,synonymous_variant,p.K535=,ENST00000375200.6,c.1605G>A,LOW,YES;ZNF341,synonymous_variant,p.K528=,ENST00000342427.6,c.1584G>A,LOW, +SHROOM2 357 BI GRCh38 X 9896513 9896513 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KL-01A TCGA-VD-A8KL-10A Somatic 9 6 c.2605A>G p.Arg869Gly p.R869G ENST00000380913.8 NM_001649.4 869 Agg/Ggg 4/10 P1 G R/G protein_coding YES CCDS14135.1 2605/4851 CGCGGAGGCTC PANTHER:PTHR15012;PANTHER:PTHR15012:SF8;MobiDB_lite:mobidb-lite ENSP00000370299 4/10 ENST00000380913 Transcript ENSG00000146950 HGNC:630 MODERATE NM_001649.4 missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0) Q13796.162 SHROOM2 HGNC 1 1.0 UPI0000125D05 SNV SHROOM2,missense_variant,p.R869G,ENST00000380913,NM_001649.4,c.2605A>G,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;SHROOM2,upstream_gene_variant,,ENST00000493668,,,MODIFIER,,,,1 2722/7474 muse;mutect2;varscan2 a9f956a0-660f-4185-a843-d9911d2484de 0 16 5ae5c385-f8dd-4fcb-8077-ba5cc4c5eacb 15 019ea45a-ab47-4f30-abdf-d495f932fa5d SUCCESS SHROOM2,missense_variant,p.R869G,ENST00000380913.8,c.2605A>G,MODERATE,YES +TNFRSF8 943 BI GRCh38 1 12104387 12104387 + missense_variant Missense_Mutation SNP G G A rs141205943 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 24 19 c.277G>A p.Val93Met p.V93M ENST00000263932.7 NM_001243.5 93 Gtg/Atg 4/15 P1 A V/M protein_coding YES CCDS144.1 277/1788 ACCTCGTGGAG COSM83873 Gene3D:2.10.50.10;PROSITE_patterns:PS00652;PROSITE_profiles:PS50050;PANTHER:PTHR47497;SMART:SM00208;Superfamily:SSF57586;CDD:cd13409 ENSP00000263932 0.000227 0.0 4/15 rs141205943 ENST00000263932 Transcript ENSG00000120949 HGNC:11923 MODERATE NM_001243.5 0.000227 AA missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) P28908.199 TNFRSF8 HGNC 1 1.0 UPI0000000971 P28908-1 SNV TNFRSF8,missense_variant,p.V93M,ENST00000263932,NM_001243.5,c.277G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;TNFRSF8,5_prime_UTR_variant,,ENST00000417814,NM_001281430.2,c.-57G>A,MODIFIER,,,,1;TNFRSF8,3_prime_UTR_variant,,ENST00000514649,,c.*21G>A,MODIFIER,,,,1 573/3760 muse;mutect2 eeab0529-31e6-4edb-bd2c-a21f2a169381 2.386e-05 0.000123 2.891e-05 0.0 0.0 0.0 1.758e-05 0.0 3.266e-05 4.73670988867525e-05 0.0001461130013922 0.0 0.0 0.0 0.0 0.0 afr 0.0001461130013922 0.0 1.5435900422744453e-05 0.0 0.0 0 74 685483a8-1b68-4ba3-8bb1-e6f49611a109 44 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS TNFRSF8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000514649.5,c.*21G>A,MODIFIER,;TNFRSF8,5_prime_UTR_variant,,ENST00000417814.3,c.-57G>A,MODIFIER,;TNFRSF8,missense_variant,p.V93M,ENST00000263932.7,c.277G>A,MODERATE,YES +RPS6KC1 26750 BI GRCh38 1 213241901 213241901 + missense_variant Missense_Mutation SNP G G T rs1177225810 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 40 39 c.2425G>T p.Val809Leu p.V809L ENST00000366960.8 NM_012424.6 809 Gta/Tta 11/15 P2 T V/L protein_coding YES CCDS1513.1 2425/3201 CAGCAGTAACT PROSITE_profiles:PS50011;PANTHER:PTHR15508;PANTHER:PTHR15508:SF2;Superfamily:SSF56112 ENSP00000355927 11/15 rs1177225810 ENST00000366960 Transcript ENSG00000136643 HGNC:10439 MODERATE NM_012424.6 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(1) Q96S38.161 RPS6KC1 HGNC 1 1.0 UPI0000071B8C Q96S38-1 SNV RPS6KC1,missense_variant,p.V809L,ENST00000366960,NM_001349646.1&NM_001349647.1&NM_012424.6,c.2425G>T,MODERATE,YES,tolerated(1),benign(0),1;RPS6KC1,missense_variant,p.V797L,ENST00000366959,NM_001136138.3,c.2389G>T,MODERATE,,tolerated(1),benign(0),1;RPS6KC1,missense_variant,p.V597L,ENST00000543470,NM_001287219.2,c.1789G>T,MODERATE,,tolerated(1),benign(0.001),1;RPS6KC1,missense_variant,p.V597L,ENST00000614059,NM_001349660.1&NM_001349654.1&NM_001287218.2&NM_001349659.1&NM_001349662.1&NM_001349661.1,c.1789G>T,MODERATE,,tolerated(1),benign(0.001),1;RPS6KC1,missense_variant,p.V628L,ENST00000543354,NM_001349651.1&NM_001349650.1&NM_001349649.1&NM_001349658.1&NM_001349648.1&NM_001349652.1&NM_001349653.1&NM_001349657.1&NM_001287221.2,c.1882G>T,MODERATE,,tolerated(1),benign(0),1;RPS6KC1,missense_variant,p.V344L,ENST00000615329,NM_001349669.1&NM_001349666.1&NM_001349664.1&NM_001349671.1&NM_001349668.1&NM_001287220.2&NM_001349670.1&NM_001349663.1&NM_001349667.1&NM_001349672.1&NM_001349665.1,c.1030G>T,MODERATE,,tolerated(1),benign(0),1;RPS6KC1,non_coding_transcript_exon_variant,,ENST00000490299,,n.2239G>T,MODIFIER,,,,1;RPS6KC1,upstream_gene_variant,,ENST00000491616,,,MODIFIER,,,,1 2589/5505 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 112 685483a8-1b68-4ba3-8bb1-e6f49611a109 79 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS RPS6KC1,non_coding_transcript_exon_variant,,ENST00000490299.5,n.2239G>T,MODIFIER,;RPS6KC1,missense_variant,p.V797L,ENST00000366959.4,c.2389G>T,MODERATE,;RPS6KC1,missense_variant,p.V809L,ENST00000366960.8,c.2425G>T,MODERATE,YES;RPS6KC1,missense_variant,p.V344L,ENST00000615329.4,c.1030G>T,MODERATE,;RPS6KC1,missense_variant,p.V628L,ENST00000543354.5,c.1882G>T,MODERATE,;RPS6KC1,missense_variant,p.V597L,ENST00000543470.5,c.1789G>T,MODERATE,;RPS6KC1,missense_variant,p.V597L,ENST00000614059.4,c.1789G>T,MODERATE, +RYR2 6262 BI GRCh38 1 237627961 237627961 + synonymous_variant Silent SNP G G T TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 18 13 c.6321G>T p.Thr2107= p.T2107= ENST00000366574.7 NM_001035.3 2107 acG/acT 41/105 P1 T T protein_coding YES CCDS55691.1 6321/14904 TACACGATAAA PANTHER:PTHR12864;PANTHER:PTHR12864:SF45 ENSP00000355533 41/105 COSV100772088;COSV63684440 ENST00000366574 Transcript 1.0 ENSG00000198626 HGNC:10484 LOW NM_001035.3 synonymous_variant 1;1 1.0 Unknown 1;1 Q92736.216 RYR2 HGNC 1 1.0 UPI0000DD0308 Q92736-1 SNV RYR2,synonymous_variant,p.T2107=,ENST00000366574,NM_001035.3,c.6321G>T,LOW,YES,,,1;RYR2,synonymous_variant,p.T2091=,ENST00000360064,,c.6273G>T,LOW,,,,1 6659/16583 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 42 685483a8-1b68-4ba3-8bb1-e6f49611a109 31 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS RYR2,synonymous_variant,p.T1452=,ENST00000714022.1,c.4356G>T,LOW,;RYR2,synonymous_variant,p.T2107=,ENST00000661330.2,c.6321G>T,LOW,;RYR2,synonymous_variant,p.T2095=,ENST00000714019.1,c.6285G>T,LOW,;RYR2,synonymous_variant,p.T2107=,ENST00000659194.3,c.6321G>T,LOW,;RYR2,synonymous_variant,p.T2107=,ENST00000366574.7,c.6321G>T,LOW,YES;RYR2,synonymous_variant,p.T2107=,ENST00000660292.2,c.6321G>T,LOW,;RYR2,synonymous_variant,p.T2070=,ENST00000714018.1,c.6210G>T,LOW,;RYR2,synonymous_variant,NMD_transcript_variant,p.T2107=,ENST00000609119.2,c.6321G>T,LOW,;RYR2,synonymous_variant,p.T2107=,ENST00000714021.1,c.6321G>T,LOW, +FANCL 55120 BI GRCh38 2 58161527 58161527 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 33 10 c.1015T>C p.Tyr339His p.Y339H ENST00000233741.9 NM_018062.4 339 Tat/Cat 12/14 P1 G Y/H protein_coding CCDS1860.1 1015/1128 CTCATATAAGC PDB-ENSP_mappings:4ccg.X;PDB-ENSP_mappings:4ccg.Y;CDD:cd16490;PANTHER:PTHR13206;Gene3D:3.30.40.10;Pfam:PF11793;SMART:SM01197;Superfamily:SSF57850 ENSP00000233741 12/14 ENST00000233741 Transcript 1.0 ENSG00000115392 HGNC:20748 MODERATE NM_018062.4 missense_variant probably_damaging(1) Unknown deleterious(0) Q9NW38.172 FANCL HGNC -1 1.0 UPI000013C98C Q9NW38-1 SNV FANCL,missense_variant,p.Y344H,ENST00000402135,NM_001114636.1,c.1030T>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;FANCL,missense_variant,p.Y339H,ENST00000233741,NM_018062.4&NM_001374615.1,c.1015T>C,MODERATE,,deleterious(0),probably_damaging(1),-1;FANCL,missense_variant,p.Y311H,ENST00000403295,,c.931T>C,MODERATE,,deleterious(0),probably_damaging(0.99),-1;FANCL,missense_variant,p.Y280H,ENST00000449070,,c.838T>C,MODERATE,,deleterious(0),probably_damaging(0.986),-1;FANCL,missense_variant,p.Y222H,ENST00000403676,,c.664T>C,MODERATE,,deleterious(0),probably_damaging(0.992),-1;VRK2,downstream_gene_variant,,ENST00000340157,NM_001130480.2&NM_001130481.2&NM_006296.7,,MODIFIER,,,,1;VRK2,downstream_gene_variant,,ENST00000412104,NM_001288839.1&NM_001288836.1,,MODIFIER,,,,1;FANCL,downstream_gene_variant,,ENST00000417361,,,MODIFIER,,,,-1;VRK2,downstream_gene_variant,,ENST00000417641,NM_001288838.1&NM_001130483.2,,MODIFIER,,,,1;FANCL,downstream_gene_variant,,ENST00000427708,,,MODIFIER,,,,-1;VRK2,downstream_gene_variant,,ENST00000435505,NM_001288837.1,,MODIFIER,YES,,,1;VRK2,downstream_gene_variant,,ENST00000440705,NM_001130482.2,,MODIFIER,,,,1;FANCL,downstream_gene_variant,,ENST00000446381,,,MODIFIER,,,,-1;VRK2,downstream_gene_variant,,ENST00000648897,,,MODIFIER,,,,1;VRK2,downstream_gene_variant,,ENST00000432057,,,MODIFIER,,,,1;FANCL,downstream_gene_variant,,ENST00000470506,,,MODIFIER,,,,-1 1027/1658 muse;mutect2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 78 685483a8-1b68-4ba3-8bb1-e6f49611a109 43 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS FANCL,missense_variant,p.Y334H,ENST00000696307.1,c.1000T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696440.1,n.2051T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696531.1,c.*547T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696570.1,c.*337T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696460.1,n.1512T>C,MODIFIER,;FANCL,missense_variant,p.Y271H,ENST00000696530.1,c.811T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696416.1,n.1023T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696532.1,n.2162T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696498.1,n.1774T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696459.1,c.*450T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696474.1,n.891T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696456.1,n.525T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696495.1,c.*761T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696529.1,n.878T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696569.1,n.1124T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696473.1,c.*698T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696494.1,n.1047T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696413.1,n.1017T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696470.1,n.3183T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696414.1,n.2061T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696363.1,n.2792T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696471.1,n.685T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696509.1,c.*892T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696436.1,n.969T>C,MODIFIER,;FANCL,synonymous_variant,NMD_transcript_variant,p.Y316=,ENST00000696415.1,c.948T>C,LOW,;FANCL,synonymous_variant,NMD_transcript_variant,p.Y292=,ENST00000696458.1,c.876T>C,LOW,;FANCL,non_coding_transcript_exon_variant,,ENST00000696496.1,n.1554T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696439.1,n.3064T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696438.1,c.*848T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696472.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696457.1,c.*1786T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696437.1,n.1432T>C,MODIFIER,;FANCL,missense_variant,p.Y163H,ENST00000696510.1,c.487T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696376.1,n.6801T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696639.1,n.3093T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696625.1,c.*465T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696638.1,n.1030T>C,MODIFIER,;FANCL,missense_variant,p.Y359H,ENST00000696326.1,c.1075T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696497.1,n.4312T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696362.1,c.*465T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696528.1,c.*68T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696637.1,n.8088T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696344.1,c.*729T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696343.1,n.2874T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696399.1,n.2289T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696397.1,n.3140T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696398.1,c.*162T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696306.1,c.*905T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696360.1,n.1800T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696325.1,n.4098T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696342.1,c.*2245T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696412.1,n.1514T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696375.1,n.7948T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696341.1,n.1523T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696396.1,n.2169T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696374.1,c.*383T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696340.1,n.3241T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696395.1,n.4456T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696394.1,n.4517T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696339.1,n.2587T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696320.1,n.2694T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696373.1,c.*2245T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696359.1,n.3365T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696372.1,n.2104T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000470506.2,n.1529T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696358.1,n.3688T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696636.1,n.3467T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696411.1,n.720T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696475.1,n.2523T>C,MODIFIER,;FANCL,missense_variant,p.Y191H,ENST00000446381.6,c.571T>C,MODERATE,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696469.1,c.*162T>C,MODIFIER,;FANCL,missense_variant,p.Y316H,ENST00000696624.1,c.946T>C,MODERATE,;FANCL,missense_variant,p.Y320H,ENST00000696305.1,c.958T>C,MODERATE,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696361.1,c.*1018T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696455.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696468.1,c.*507T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696410.1,c.*496T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696527.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696318.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696409.1,c.*532T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696324.1,c.*465T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696566.1,n.3603T>C,MODIFIER,;FANCL,missense_variant,p.Y280H,ENST00000449070.6,c.838T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696623.1,n.981T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000417361.2,c.*593T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696338.1,n.1129T>C,MODIFIER,;FANCL,missense_variant,p.Y304H,ENST00000696567.1,c.910T>C,MODERATE,;FANCL,missense_variant,p.Y336H,ENST00000696371.1,c.1006T>C,MODERATE,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696467.1,c.*511T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696622.1,n.2746T>C,MODIFIER,;FANCL,missense_variant,p.Y335H,ENST00000696547.1,c.1003T>C,MODERATE,;FANCL,synonymous_variant,NMD_transcript_variant,p.Y311=,ENST00000696317.1,c.933T>C,LOW,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696544.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696545.1,c.*683T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696543.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696621.1,c.*162T>C,MODIFIER,;FANCL,missense_variant,p.Y339H,ENST00000233741.9,c.1015T>C,MODERATE,YES;FANCL,missense_variant,p.Y203H,ENST00000696620.1,c.607T>C,MODERATE,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696493.1,c.*863T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696378.1,c.*1033T>C,MODIFIER,;FANCL,missense_variant,p.Y344H,ENST00000402135.8,c.1030T>C,MODERATE,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696634.1,c.*569T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696565.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696435.1,c.*162T>C,MODIFIER,;FANCL,non_coding_transcript_exon_variant,,ENST00000696364.1,n.1408T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696546.1,c.*794T>C,MODIFIER,;FANCL,missense_variant,p.Y331H,ENST00000696635.1,c.991T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696619.1,n.2571T>C,MODIFIER,;FANCL,intron_variant,,ENST00000696316.1,c.903+1339T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696433.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000403676.6,c.*578T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696499.1,c.*452T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696564.1,c.*68T>C,MODIFIER,;FANCL,missense_variant,p.Y325H,ENST00000696319.1,c.973T>C,MODERATE,;FANCL,missense_variant,p.Y285H,ENST00000696434.1,c.853T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696542.1,n.953T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696548.1,c.*1219T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696400.1,c.*779T>C,MODIFIER,;FANCL,missense_variant,p.Y311H,ENST00000403295.8,c.931T>C,MODERATE,;FANCL,missense_variant,p.Y354H,ENST00000427708.7,c.1060T>C,MODERATE,;FANCL,non_coding_transcript_exon_variant,,ENST00000696432.1,n.3474T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696315.1,c.*578T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696314.1,c.*68T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696454.1,c.*366T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696492.1,c.*680T>C,MODIFIER,;FANCL,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696508.1,c.*570T>C,MODIFIER, +SF3B1 23451 BI GRCh38 2 197402646 197402646 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 26 20 c.1987A>C p.Thr663Pro p.T663P ENST00000335508.11 NM_012433.4 663 Act/Cct 14/25 P1 G T/P protein_coding YES CCDS33356.1 1987/3915 ACCAGTGTGTC Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.T663P,ENST00000335508,NM_012433.4,c.1987A>C,MODERATE,YES,deleterious(0),probably_damaging(1),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*3054A>C,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2246A>C,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3871A>C,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 2016/6463 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 52 685483a8-1b68-4ba3-8bb1-e6f49611a109 46 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3871A>C,MODIFIER,;SF3B1,missense_variant,p.T663P,ENST00000335508.11,c.1987A>C,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*3054A>C,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2246A>C,MODIFIER, +SLC27A6 28965 BI GRCh38 5 128966506 128966506 + synonymous_variant Silent SNP C C T rs758990702 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 14 11 c.369C>T p.Phe123= p.F123= ENST00000262462.9 NM_001017372.3 123 ttC/ttT 1/10 P1 T F protein_coding YES CCDS4145.1 369/1860 TGGTTCGGCCT CDD:cd05938;PANTHER:PTHR43107;PANTHER:PTHR43107:SF10;Pfam:PF00501;Gene3D:3.40.50.12780;Superfamily:SSF56801 ENSP00000262462 1/10 rs758990702;COSV99322969 ENST00000262462 Transcript ENSG00000113396 HGNC:11000 LOW NM_001017372.3 0.0001703 gnomAD_OTH synonymous_variant 0;1 1.0 Unknown 0;1 Q9Y2P4.138 SLC27A6 HGNC 1 1.0 UPI0000038E83 SNV SLC27A6,synonymous_variant,p.F123=,ENST00000262462,NM_001317984.1&NM_001017372.3,c.369C>T,LOW,YES,,,1;SLC27A6,synonymous_variant,p.F123=,ENST00000395266,NM_014031.4,c.369C>T,LOW,,,,1;SLC27A6,synonymous_variant,p.F123=,ENST00000506176,,c.369C>T,LOW,,,,1;SLC27A6,intron_variant,,ENST00000508645,,c.-62-18627C>T,MODIFIER,,,,1 1019/2863 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 4.113e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0001703 0.0 6.763059900549706e-06 2.4338000002899207e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 22 685483a8-1b68-4ba3-8bb1-e6f49611a109 25 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS SLC27A6,synonymous_variant,p.F123=,ENST00000506176.1,c.369C>T,LOW,;SLC27A6,synonymous_variant,p.F123=,ENST00000395266.5,c.369C>T,LOW,;SLC27A6,synonymous_variant,p.F123=,ENST00000262462.9,c.369C>T,LOW,YES;SLC27A6,intron_variant,,ENST00000508645.5,c.-62-18627C>T,MODIFIER, +SLC39A7 7922 BI GRCh38 6 33201430 33201431 + frameshift_variant Frame_Shift_Ins INS - - T novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 38 26 c.186dup p.His62LeufsTer25 p.H62Lfs*25 ENST00000374675.7 NM_001077516.2 62 cat/caTt 2/8 P1 T H/HX protein_coding CCDS43453.1 185-186/1410 TGCCCATGGCC PANTHER:PTHR16950;PANTHER:PTHR16950:SF25;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000363807 2/8 ENST00000374675 Transcript ENSG00000112473 HGNC:4927 1.0 HIGH frameshift_variant Unknown Q92504.172 SLC39A7 HGNC 1 A0A024RCX7.35 1.0 UPI0000046C3F insertion SLC39A7,frameshift_variant,p.G63Wfs*24,ENST00000374677,NM_006979.3&NM_001288777.2,c.186dup,HIGH,YES,,,1;SLC39A7,frameshift_variant,p.G63Wfs*24,ENST00000374675,NM_001077516.2,c.186dup,HIGH,,,,1;SLC39A7,intron_variant,,ENST00000444757,,c.142-314dup,MODIFIER,,,,1;HSD17B8,upstream_gene_variant,,ENST00000374662,NM_014234.5,,MODIFIER,YES,,,1;RXRB,upstream_gene_variant,,ENST00000374680,NM_021976.5,,MODIFIER,,,,-1;RXRB,upstream_gene_variant,,ENST00000374685,NM_001291989.1&NM_001270401.2,,MODIFIER,YES,,,-1;RNY4P10,downstream_gene_variant,,ENST00000365571,,,MODIFIER,YES,,,1;SLC39A7,upstream_gene_variant,,ENST00000463972,,,MODIFIER,,,,1;HSD17B8,upstream_gene_variant,,ENST00000469186,,,MODIFIER,,,,1;RXRB,upstream_gene_variant,,ENST00000481441,,,MODIFIER,,,,-1;RXRB,upstream_gene_variant,,ENST00000483281,,,MODIFIER,,,,-1 302-303/2153 mutect2;pindel;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 49 685483a8-1b68-4ba3-8bb1-e6f49611a109 64 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS SLC39A7,non_coding_transcript_exon_variant,,ENST00000698689.1,n.238_239insT,MODIFIER,;SLC39A7,frameshift_variant,p.H62Lfs*25,ENST00000698687.1,c.186dup,HIGH,;SLC39A7,frameshift_variant,NMD_transcript_variant,p.H62Lfs*25,ENST00000698688.1,c.186dup,HIGH,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698686.1,n.241_242insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698685.1,n.251_252insT,MODIFIER,;SLC39A7,frameshift_variant,p.H62Lfs*25,ENST00000374677.8,c.186dup,HIGH,YES;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698684.1,n.605_606insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698681.1,n.605_606insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698682.1,n.605_606insT,MODIFIER,;SLC39A7,frameshift_variant,p.H62Lfs*25,ENST00000374675.7,c.186dup,HIGH,;SLC39A7,frameshift_variant,p.H62Lfs*25,ENST00000698680.1,c.186dup,HIGH,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698683.1,n.605_606insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698679.1,n.979_980insT,MODIFIER,;SLC39A7,intron_variant,,ENST00000444757.5,c.142-315_142-314insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698678.1,n.1009_1010insT,MODIFIER,;SLC39A7,non_coding_transcript_exon_variant,,ENST00000698677.1,n.823_824insT,MODIFIER, +KLHL31 401265 BI GRCh38 6 53654338 53654338 + missense_variant Missense_Mutation SNP C C T rs893752130 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 63 58 c.935G>A p.Arg312Gln p.R312Q ENST00000370905.4 NM_001003760.5 312 cGa/cAa 2/3 P1 T R/Q protein_coding YES CCDS34478.1 935/1905 CACCTCGGATT Gene3D:2.120.10.80;PIRSF:PIRSF037037;PANTHER:PTHR45632;PANTHER:PTHR45632:SF17 ENSP00000359942 2/3 rs893752130 ENST00000370905 Transcript ENSG00000124743 HGNC:21353 MODERATE NM_001003760.5 missense_variant 1.0 probably_damaging(0.992) Unknown deleterious(0) Q9H511.138 KLHL31 HGNC -1 1.0 UPI000006D624 SNV KLHL31,missense_variant,p.R312Q,ENST00000370905,NM_001003760.5,c.935G>A,MODERATE,YES,deleterious(0),probably_damaging(0.992),-1;KLHL31,missense_variant,p.R312Q,ENST00000407079,,c.935G>A,MODERATE,,deleterious(0),probably_damaging(0.992),-1 1124/5776 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 128 685483a8-1b68-4ba3-8bb1-e6f49611a109 121 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS KLHL31,missense_variant,p.R312Q,ENST00000407079.1,c.935G>A,MODERATE,;KLHL31,missense_variant,p.R312Q,ENST00000370905.4,c.935G>A,MODERATE,YES;LINC01564,intron_variant,,ENST00000701539.1,n.320-12373C>T,MODIFIER,YES +TYRP1 7306 BI GRCh38 9 12695537 12695541 + frameshift_variant Frame_Shift_Del DEL AAGTA AAGTA - rs769074792 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 74 14 c.411_415del p.Ser137ArgfsTer42 p.S137Rfs*42 ENST00000388918.10 NM_000550.3 136 ttAAGTAaa/ttaa 3/8 P1 - LSK/LX protein_coding YES CCDS34990.1 408-412/1614 GGACTTAAGTAAAGAA Gene3D:1.10.1280.10;PDB-ENSP_mappings:5m8l.A;PDB-ENSP_mappings:5m8l.B;PDB-ENSP_mappings:5m8l.C;PDB-ENSP_mappings:5m8l.D;PDB-ENSP_mappings:5m8m.A;PDB-ENSP_mappings:5m8m.B;PDB-ENSP_mappings:5m8m.C;PDB-ENSP_mappings:5m8m.D;PDB-ENSP_mappings:5m8n.A;PDB-ENSP_mappings:5m8n.B;PDB-ENSP_mappings:5m8n.C;PDB-ENSP_mappings:5m8n.D;PDB-ENSP_mappings:5m8o.A;PDB-ENSP_mappings:5m8o.B;PDB-ENSP_mappings:5m8o.C;PDB-ENSP_mappings:5m8o.D;PDB-ENSP_mappings:5m8p.A;PDB-ENSP_mappings:5m8p.B;PDB-ENSP_mappings:5m8p.C;PDB-ENSP_mappings:5m8p.D;PDB-ENSP_mappings:5m8q.A;PDB-ENSP_mappings:5m8q.B;PDB-ENSP_mappings:5m8q.C;PDB-ENSP_mappings:5m8q.D;PDB-ENSP_mappings:5m8r.A;PDB-ENSP_mappings:5m8r.B;PDB-ENSP_mappings:5m8r.C;PDB-ENSP_mappings:5m8r.D;PDB-ENSP_mappings:5m8s.A;PDB-ENSP_mappings:5m8s.B;PDB-ENSP_mappings:5m8s.C;PDB-ENSP_mappings:5m8s.D;PDB-ENSP_mappings:5m8t.A;PDB-ENSP_mappings:5m8t.B;PDB-ENSP_mappings:5m8t.C;PDB-ENSP_mappings:5m8t.D;PANTHER:PTHR11474;PANTHER:PTHR11474:SF3;Superfamily:SSF48056 ENSP00000373570 3/8 rs769074792 ENST00000388918 Transcript 1.0 ENSG00000107165 HGNC:12450 3.0 HIGH NM_000550.3 4.62e-05 gnomAD_FIN frameshift_variant 1.0 Unknown P17643.195 TYRP1 HGNC 1 1.0 UPI0000039DCA deletion TYRP1,frameshift_variant,p.S137Rfs*42,ENST00000388918,NM_000550.3,c.411_415del,HIGH,YES,,,1;TYRP1,upstream_gene_variant,,ENST00000381136,,,MODIFIER,,,,1;TYRP1,downstream_gene_variant,,ENST00000473763,,,MODIFIER,,,,1;TYRP1,upstream_gene_variant,,ENST00000381142,,,MODIFIER,,,,1;TYRP1,downstream_gene_variant,,ENST00000459790,,,MODIFIER,,,,1;LURAP1L-AS1,downstream_gene_variant,,ENST00000417638,,,MODIFIER,,,,-1;LURAP1L-AS1,downstream_gene_variant,,ENST00000650458,,,MODIFIER,,,,-1;LURAP1L-AS1,downstream_gene_variant,,ENST00000654076,,,MODIFIER,,,,-1 587-591/2896 mutect2;pindel eeab0529-31e6-4edb-bd2c-a21f2a169381 7.974e-06 0.0 0.0 0.0 0.0 4.62e-05 8.834e-06 0.0 0.0 0 77 685483a8-1b68-4ba3-8bb1-e6f49611a109 89 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS TYRP1,frameshift_variant,p.S137Rfs*42,ENST00000388918.10,c.411_415del,HIGH,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 51 50 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 83 685483a8-1b68-4ba3-8bb1-e6f49611a109 101 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +SETX 23064 BI GRCh38 9 132329807 132329807 + missense_variant Missense_Mutation SNP G G C rs1338284039 TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 17 7 c.1791C>G p.Phe597Leu p.F597L ENST00000224140.6 NM_015046.7 597 ttC/ttG 10/26 P1 C F/L protein_coding YES CCDS6947.1 1791/8034 GCTTTGAATTT ENSP00000224140 10/26 rs1338284039 ENST00000224140 Transcript 1.0 ENSG00000107290 HGNC:445 MODERATE NM_015046.7 1.764e-05 gnomAD_NFE missense_variant 1.0 benign(0) Unknown tolerated(0.68) Q7Z333.169 SETX HGNC -1 1.0 UPI0000210D28 Q7Z333-1 SNV SETX,missense_variant,p.F597L,ENST00000224140,NM_015046.7&NM_001351528.2&NM_001351527.1,c.1791C>G,MODERATE,YES,tolerated(0.68),benign(0),-1 1975/11101 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 7.972e-06 0.0 0.0 0.0 0.0 0.0 1.764e-05 0.0 0.0 2.7037600375479087e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.173220026539639e-05 0.0 6.173220026539639e-05 0.0 0.0 0 63 685483a8-1b68-4ba3-8bb1-e6f49611a109 24 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS SETX,missense_variant,p.F597L,ENST00000224140.6,c.1791C>G,MODERATE,YES +PNPLA7 375775 BI GRCh38 9 137480393 137480393 + synonymous_variant Silent SNP T T C novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 14 16 c.2424A>G p.Thr808= p.T808= ENST00000277531.8 NM_152286.5 808 acA/acG 22/34 A2 C T protein_coding CCDS7045.1 2424/3954 CAGGGTGTGAG PANTHER:PTHR14226;PANTHER:PTHR14226:SF23 ENSP00000277531 22/34 ENST00000277531 Transcript ENSG00000130653 HGNC:24768 LOW synonymous_variant Unknown Q6ZV29.142 PNPLA7 HGNC -1 2.0 UPI000443805E Q6ZV29-1 SNV PNPLA7,synonymous_variant,p.T833=,ENST00000406427,NM_001098537.3,c.2499A>G,LOW,YES,,,-1;PNPLA7,synonymous_variant,p.T808=,ENST00000277531,NM_152286.5,c.2424A>G,LOW,,,,-1;PNPLA7,non_coding_transcript_exon_variant,,ENST00000469998,,n.335A>G,MODIFIER,,,,-1;PNPLA7,upstream_gene_variant,,ENST00000492278,,,MODIFIER,,,,-1 2611/4581 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 21 685483a8-1b68-4ba3-8bb1-e6f49611a109 30 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS PNPLA7,non_coding_transcript_exon_variant,,ENST00000469998.1,n.335A>G,MODIFIER,;PNPLA7,synonymous_variant,p.T808=,ENST00000277531.8,c.2424A>G,LOW,;PNPLA7,synonymous_variant,p.T833=,ENST00000406427.6,c.2499A>G,LOW,YES +HK1 3098 BI GRCh38 10 69384351 69384351 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 73 45 c.1589C>T p.Ala530Val p.A530V ENST00000359426.7 NM_000188.3 530 gCc/gTc 11/18 P1 T A/V protein_coding CCDS7292.1 1589/2754 CTTGGCCCTGG PDB-ENSP_mappings:1cza.N;PDB-ENSP_mappings:1dgk.N;PDB-ENSP_mappings:1hkb.A;PDB-ENSP_mappings:1hkb.B;PDB-ENSP_mappings:1hkc.A;PDB-ENSP_mappings:1qha.A;PDB-ENSP_mappings:1qha.B;Gene3D:3.30.420.40;Gene3D:3.40.367.20;PDB-ENSP_mappings:4f9o.A;PDB-ENSP_mappings:4f9o.B;PDB-ENSP_mappings:4foe.A;PDB-ENSP_mappings:4foe.B;PDB-ENSP_mappings:4foi.A;PDB-ENSP_mappings:4foi.B;PDB-ENSP_mappings:4fpa.A;PDB-ENSP_mappings:4fpa.B;PDB-ENSP_mappings:4fpb.A;PDB-ENSP_mappings:4fpb.B;Pfam:PF00349;Prints:PR00475;PROSITE_profiles:PS51748;PANTHER:PTHR19443;PANTHER:PTHR19443:SF10;Superfamily:SSF53067;CDD:cd00012 ENSP00000352398 11/18 ENST00000359426 Transcript 1.0 ENSG00000156515 HGNC:4922 MODERATE NM_000188.3 missense_variant possibly_damaging(0.755) Unknown deleterious(0.03) P19367.233 HK1 HGNC 1 1.0 UPI0000111BA5 P19367-1 SNV HK1,missense_variant,p.A534V,ENST00000643399,NM_001358263.1,c.1601C>T,MODERATE,YES,deleterious(0.03),probably_damaging(0.999),1;HK1,missense_variant,p.A518V,ENST00000360289,NM_033500.2,c.1553C>T,MODERATE,,deleterious(0.03),probably_damaging(1),1;HK1,missense_variant,p.A534V,ENST00000448642,NM_033498.2&NM_001322364.1,c.1601C>T,MODERATE,,deleterious(0.03),probably_damaging(0.999),1;HK1,missense_variant,p.A534V,ENST00000436817,NM_001322365.1&NM_033497.2,c.1601C>T,MODERATE,,deleterious(0.03),probably_damaging(0.999),1;HK1,missense_variant,p.A530V,ENST00000359426,NM_001322366.1&NM_000188.3&NM_001322367.1,c.1589C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.755),1;HK1,missense_variant,p.A529V,ENST00000298649,NM_033496.2,c.1586C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.619),1;HK1,3_prime_UTR_variant,,ENST00000493591,,c.*1477C>T,MODIFIER,,,,1;HK1,non_coding_transcript_exon_variant,,ENST00000494253,,n.1815C>T,MODIFIER,,,,1 1690/3602 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 139 685483a8-1b68-4ba3-8bb1-e6f49611a109 118 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS HK1,non_coding_transcript_exon_variant,,ENST00000703957.1,n.94C>T,MODIFIER,;HK1,non_coding_transcript_exon_variant,,ENST00000703955.1,n.2139C>T,MODIFIER,;HK1,non_coding_transcript_exon_variant,,ENST00000494253.1,n.1815C>T,MODIFIER,;HK1,missense_variant,p.A490V,ENST00000703954.1,c.1469C>T,MODERATE,;HK1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703953.1,c.*852C>T,MODIFIER,;HK1,intron_variant,,ENST00000703952.1,c.1265+4256C>T,MODIFIER,;HK1,intron_variant,,ENST00000703951.1,c.1265+4256C>T,MODIFIER,;HK1,missense_variant,p.A530V,ENST00000703950.1,c.1589C>T,MODERATE,;HK1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000493591.6,c.*1477C>T,MODIFIER,;HK1,missense_variant,p.A530V,ENST00000703949.1,c.1589C>T,MODERATE,;HK1,missense_variant,p.A530V,ENST00000359426.7,c.1589C>T,MODERATE,YES;HK1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703948.1,c.*1206C>T,MODIFIER,;HK1,missense_variant,p.A400V,ENST00000703947.1,c.1199C>T,MODERATE,;HK1,missense_variant,p.A530V,ENST00000470050.2,c.1589C>T,MODERATE,;HK1,intron_variant,,ENST00000703946.1,c.1265+4256C>T,MODIFIER,;HK1,missense_variant,p.A502V,ENST00000703945.1,c.1505C>T,MODERATE,;HK1,missense_variant,p.A529V,ENST00000298649.8,c.1586C>T,MODERATE,;HK1,missense_variant,p.A534V,ENST00000643399.2,c.1601C>T,MODERATE,;HK1,missense_variant,p.A534V,ENST00000436817.6,c.1601C>T,MODERATE, +COL4A2 1284 BI GRCh38 13 110445857 110445857 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 54 48 c.986G>C p.Gly329Ala p.G329A ENST00000360467.7 NM_001846.4 329 gGg/gCg 17/48 P1 C G/A protein_coding YES CCDS41907.1 986/5139 TCAAGGGCCTG Pfam:PF01391;PANTHER:PTHR24023;PANTHER:PTHR24023:SF588 ENSP00000353654 17/48 ENST00000360467 Transcript 1.0 ENSG00000134871 HGNC:2203 MODERATE NM_001846.4 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0.02) P08572.216 COL4A2 HGNC 1 A0A024RDW8.56 5.0 UPI000041C713 SNV COL4A2,missense_variant,p.G329A,ENST00000360467,NM_001846.4,c.986G>C,MODERATE,YES,deleterious(0.02),probably_damaging(0.999),1;COL4A2,missense_variant,p.G329A,ENST00000650540,,c.986G>C,MODERATE,,deleterious(0.02),benign(0.165),1;COL4A2,missense_variant,p.G82A,ENST00000617564,,c.245G>C,MODERATE,,tolerated(0.05),probably_damaging(0.998),1 1275/6446 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 92 685483a8-1b68-4ba3-8bb1-e6f49611a109 102 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS COL4A2,missense_variant,p.G329A,ENST00000650540.1,c.986G>C,MODERATE,;COL4A2,missense_variant,NMD_transcript_variant,p.G329A,ENST00000714397.1,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000617564.3,c.986G>C,MODERATE,;COL4A2,missense_variant,NMD_transcript_variant,p.G329A,ENST00000714398.1,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000649951.2,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000714399.1,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000360467.7,c.986G>C,MODERATE,YES;COL4A2,missense_variant,p.G329A,ENST00000480609.2,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000714396.1,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000494852.3,c.986G>C,MODERATE,;COL4A2,missense_variant,p.G329A,ENST00000400163.8,c.986G>C,MODERATE, +NDN 4692 BI GRCh38 15 23686854 23686854 + missense_variant Missense_Mutation SNP G G T novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 115 12 c.364C>A p.Pro122Thr p.P122T ENST00000649030.2 NM_002487.3 122 Cca/Aca 1/1 P1 T P/T protein_coding YES CCDS10014.1 364/966 GTCTGGAAACC PROSITE_profiles:PS50838;PANTHER:PTHR11736;PANTHER:PTHR11736:SF10;Gene3D:1.10.10.1200;SMART:SM01373 ENSP00000497916 1/1 ENST00000649030 Transcript 1.0 ENSG00000182636 HGNC:7675 MODERATE NM_002487.3 missense_variant 1.0 benign(0.127) Unknown tolerated(0.47) Q99608.164 NDN HGNC -1 X5D982.52 UPI000012FEF1 SNV NDN,missense_variant,p.P122T,ENST00000649030,NM_002487.3,c.364C>A,MODERATE,YES,tolerated(0.47),benign(0.127),-1 452/1906 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 134 685483a8-1b68-4ba3-8bb1-e6f49611a109 128 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS NDN,missense_variant,p.P122T,ENST00000649030.2,c.364C>A,MODERATE,YES +LRRC49 54839 BI GRCh38 15 70900988 70900988 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 20 18 c.260A>C p.Glu87Ala p.E87A ENST00000260382.10 NM_017691.5 87 gAg/gCg 4/16 P1 C E/A protein_coding CCDS32282.1 260/2061 TGAAGAGAAAA Gene3D:3.80.10.10;PANTHER:PTHR15454;PANTHER:PTHR15454:SF23;Superfamily:SSF52058 ENSP00000260382 4/16 ENST00000260382 Transcript ENSG00000137821 HGNC:25965 MODERATE NM_017691.5 missense_variant benign(0.143) Unknown deleterious(0.03) Q8IUZ0.145 LRRC49 HGNC 1 1.0 UPI000013F990 Q8IUZ0-1 SNV LRRC49,missense_variant,p.E77A,ENST00000544974,NM_001284357.1,c.230A>C,MODERATE,,deleterious(0.02),benign(0.287),1;LRRC49,missense_variant,p.E87A,ENST00000260382,NM_017691.5,c.260A>C,MODERATE,,deleterious(0.03),benign(0.143),1;LRRC49,missense_variant,p.E43A,ENST00000443425,NM_001199018.2,c.128A>C,MODERATE,,deleterious(0),benign(0.276),1;LRRC49,missense_variant,p.E92A,ENST00000560369,NM_001199017.2,c.275A>C,MODERATE,YES,deleterious(0.02),benign(0.201),1;LRRC49,5_prime_UTR_variant,,ENST00000560691,NM_001363732.1,c.-696A>C,MODIFIER,,,,1;LRRC49,5_prime_UTR_variant,,ENST00000558546,,c.-208A>C,MODIFIER,,,,1;LRRC49,5_prime_UTR_variant,,ENST00000557977,,c.-208A>C,MODIFIER,,,,1;LRRC49,downstream_gene_variant,,ENST00000560755,,,MODIFIER,,,,1;LRRC49,non_coding_transcript_exon_variant,,ENST00000436542,,n.476A>C,MODIFIER,,,,1;LRRC49,intron_variant,,ENST00000558799,,n.409-3564A>C,MODIFIER,,,,1;LRRC49,upstream_gene_variant,,ENST00000558137,,,MODIFIER,,,,1;LRRC49,3_prime_UTR_variant,,ENST00000561081,,c.*124A>C,MODIFIER,,,,1;LRRC49,3_prime_UTR_variant,,ENST00000559201,,c.*169A>C,MODIFIER,,,,1;LRRC49,non_coding_transcript_exon_variant,,ENST00000560980,,n.306A>C,MODIFIER,,,,1;LRRC49,non_coding_transcript_exon_variant,,ENST00000558271,,n.492A>C,MODIFIER,,,,1;LRRC49,intron_variant,,ENST00000558204,,c.*189-3564A>C,MODIFIER,,,,1;LRRC49,intron_variant,,ENST00000559670,,c.106-3564A>C,MODIFIER,,,,1;LRRC49,intron_variant,,ENST00000560107,,c.194-3564A>C,MODIFIER,,,,1;LRRC49,downstream_gene_variant,,ENST00000558032,,,MODIFIER,,,,1 329/6176 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 110 685483a8-1b68-4ba3-8bb1-e6f49611a109 38 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS LRRC49,non_coding_transcript_exon_variant,,ENST00000436542.6,n.476A>C,MODIFIER,;LRRC49,non_coding_transcript_exon_variant,,ENST00000558271.5,n.492A>C,MODIFIER,;LRRC49,5_prime_UTR_variant,,ENST00000560691.5,c.-696A>C,MODIFIER,;LRRC49,5_prime_UTR_variant,,ENST00000557977.5,c.-208A>C,MODIFIER,;LRRC49,intron_variant,NMD_transcript_variant,,ENST00000558204.5,c.*189-3564A>C,MODIFIER,;LRRC49,non_coding_transcript_exon_variant,,ENST00000560980.5,n.306A>C,MODIFIER,;LRRC49,missense_variant,p.E87A,ENST00000260382.10,c.260A>C,MODERATE,YES;LRRC49,intron_variant,NMD_transcript_variant,,ENST00000559670.5,c.106-3564A>C,MODIFIER,;LRRC49,missense_variant,p.E92A,ENST00000560369.5,c.275A>C,MODERATE,;LRRC49,intron_variant,NMD_transcript_variant,,ENST00000560107.6,c.194-3564A>C,MODIFIER,;LRRC49,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000559201.5,c.*169A>C,MODIFIER,;LRRC49,missense_variant,p.E43A,ENST00000443425.6,c.128A>C,MODERATE,;LRRC49,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000561081.5,c.*124A>C,MODIFIER,;LRRC49,5_prime_UTR_variant,,ENST00000558546.5,c.-208A>C,MODIFIER,;LRRC49,intron_variant,,ENST00000558799.5,n.409-3564A>C,MODIFIER,;LRRC49,missense_variant,p.E77A,ENST00000544974.6,c.230A>C,MODERATE, +KRTAP4-4 84616 BI GRCh38 17 41160533 41160533 + synonymous_variant Silent SNP G G A TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 19 13 c.159C>T p.Thr53= p.T53= ENST00000390661.5 NM_032524.2 53 acC/acT 1/1 P1 A T protein_coding YES CCDS11383.1 159/501 CAGGTGGTCTG PANTHER:PTHR23262;PANTHER:PTHR23262:SF182;Low_complexity_(Seg):seg ENSP00000375076 1/1 COSV101180521 ENST00000390661 Transcript ENSG00000171396 HGNC:16928 LOW NM_032524.2 synonymous_variant 1 1.0 Unknown 1 Q9BYR3.119 KRTAP4-4 HGNC -1 UPI000006DEC1 SNV KRTAP4-4,synonymous_variant,p.T53=,ENST00000390661,NM_032524.2,c.159C>T,LOW,YES,,,-1 216/1100 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 74 685483a8-1b68-4ba3-8bb1-e6f49611a109 32 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS KRTAP4-4,synonymous_variant,p.T53=,ENST00000390661.5,c.159C>T,LOW,YES +DSG1 1828 BI GRCh38 18 31333640 31333640 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 30 28 c.736G>A p.Ala246Thr p.A246T ENST00000257192.5 NM_001942.4 246 Gca/Aca 7/15 P1 A A/T protein_coding YES CCDS11896.1 736/3150 GCGGGGCAGAT Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24025;PANTHER:PTHR24025:SF9;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000257192 7/15 ENST00000257192 Transcript 1.0 ENSG00000134760 HGNC:3048 MODERATE NM_001942.4 missense_variant 1.0 benign(0.1) Unknown tolerated(0.16) Q02413.201 DSG1 HGNC 1 1.0 UPI000013CF4C Q02413-1 SNV DSG1,missense_variant,p.A246T,ENST00000257192,NM_001942.4,c.736G>A,MODERATE,YES,tolerated(0.16),benign(0.1),1 877/7191 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 57 685483a8-1b68-4ba3-8bb1-e6f49611a109 59 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS DSG1,missense_variant,p.A246T,ENST00000257192.5,c.736G>A,MODERATE,YES +SIM2 6493 BI GRCh38 21 36743406 36743406 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 52 10 c.1018C>T p.Leu340Phe p.L340F ENST00000290399.11 NM_005069.6 340 Ctt/Ttt 9/11 P1 T L/F protein_coding YES CCDS13646.1 1018/2004 AGGAACTTCAG Gene3D:3.30.450.20;PROSITE_profiles:PS51302;PANTHER:PTHR23043;PANTHER:PTHR23043:SF19 ENSP00000290399 9/11 ENST00000290399 Transcript ENSG00000159263 HGNC:10883 MODERATE NM_005069.6 missense_variant 1.0 possibly_damaging(0.835) Unknown deleterious(0.01) Q14190.196 SIM2 HGNC 1 1.0 UPI000013599A Q14190-1 SNV SIM2,missense_variant,p.L340F,ENST00000290399,NM_005069.6&NM_009586.5,c.1018C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.835),1;SIM2,missense_variant,p.L278F,ENST00000431229,,c.832C>T,MODERATE,,deleterious(0.01),probably_damaging(0.956),1;SIM2,non_coding_transcript_exon_variant,,ENST00000481185,,n.1631C>T,MODIFIER,,,,1 1650/4461 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 87 685483a8-1b68-4ba3-8bb1-e6f49611a109 62 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS SIM2,missense_variant,p.T277I,ENST00000431229.1,c.830C>T,MODERATE,;SIM2,non_coding_transcript_exon_variant,,ENST00000481185.1,n.1631C>T,MODIFIER,;SIM2,missense_variant,p.L340F,ENST00000290399.11,c.1018C>T,MODERATE,YES +EP300 2033 BI GRCh38 22 41177596 41177596 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 39 29 c.5885T>C p.Met1962Thr p.M1962T ENST00000263253.9 NM_001429.4 1962 aTg/aCg 31/31 P4 C M/T protein_coding YES CCDS14010.1 5885/7245 TCCCATGGCCC PANTHER:PTHR13808;PANTHER:PTHR13808:SF29;Low_complexity_(Seg):seg ENSP00000263253 31/31 ENST00000263253 Transcript 1.0 ENSG00000100393 HGNC:3373 MODERATE NM_001429.4 missense_variant 1.0 benign(0.037) Unknown tolerated(0.1) Q09472.250 EP300 HGNC 1 1.0 UPI00001AE876 SNV EP300,missense_variant,p.M1962T,ENST00000263253,NM_001429.4,c.5885T>C,MODERATE,YES,tolerated(0.1),benign(0.037),1;EP300,missense_variant,p.M1936T,ENST00000674155,NM_001362843.2,c.5807T>C,MODERATE,,tolerated(0.11),possibly_damaging(0.774),1;EP300,downstream_gene_variant,,ENST00000635083,,,MODIFIER,,,,1;AL035658.1,intron_variant,,ENST00000415054,,n.82+5467A>G,MODIFIER,YES,,,-1;EP300-AS1,intron_variant,,ENST00000420537,,n.224-2772A>G,MODIFIER,YES,,,-1 6298/8779 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 63 685483a8-1b68-4ba3-8bb1-e6f49611a109 69 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS EP300-AS1,intron_variant,,ENST00000420537.1,n.224-2772A>G,MODIFIER,YES;ENSG00000232754,intron_variant,,ENST00000415054.1,n.82+5467A>G,MODIFIER,YES;EP300,missense_variant,p.M1936T,ENST00000674155.1,c.5807T>C,MODERATE,;EP300,missense_variant,p.M1962T,ENST00000263253.9,c.5885T>C,MODERATE,YES;EP300,missense_variant,p.M1962T,ENST00000715703.1,c.5885T>C,MODERATE, +EIF1AX 1964 BI GRCh38 X 20138613 20138613 + missense_variant Missense_Mutation SNP C C T TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 25 25 c.26G>A p.Gly9Asp p.G9D ENST00000379607.10 NM_001412.4 9 gGt/gAt 2/7 P1 T G/D protein_coding YES CCDS14196.1 26/435 TTTTACCTCCT COSM3372213 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309275;COSV63309367 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1;1 1.0 probably_damaging(0.977) Unknown deleterious(0) 1;1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G9D,ENST00000379607,NM_001412.4,c.26G>A,MODERATE,YES,deleterious(0),probably_damaging(0.977),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2772G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 224/4414 muse;mutect2;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 142 685483a8-1b68-4ba3-8bb1-e6f49611a109 50 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2772G>A,MODIFIER,;EIF1AX,missense_variant,p.G9D,ENST00000379607.10,c.26G>A,MODERATE,YES +RENBP 5973 BI GRCh38 X 153941621 153941621 + frameshift_variant Frame_Shift_Del DEL G G - novel TCGA-V4-A9EC-01A TCGA-V4-A9EC-10A Somatic 46 20 c.802del p.Arg268ValfsTer15 p.R268Vfs*15 ENST00000393700.8 NM_002910.6 268 Cgt/gt 8/11 P1 - R/X protein_coding YES CCDS14738.2 802/1284 AATGACGGAGCA CDD:cd00249;PANTHER:PTHR15108;Gene3D:1.50.10.10;Pfam:PF07221;Superfamily:SSF48208 ENSP00000377303 8/11 ENST00000393700 Transcript ENSG00000102032 HGNC:9959 HIGH NM_002910.6 frameshift_variant 1.0 Unknown P51606.167 RENBP HGNC -1 1.0 UPI0000E5B00C P51606-1 deletion RENBP,frameshift_variant,p.R268Vfs*15,ENST00000393700,NM_002910.6,c.802del,HIGH,YES,,,-1;RENBP,frameshift_variant,p.R254Vfs*15,ENST00000369997,,c.760del,HIGH,,,,-1;RENBP,upstream_gene_variant,,ENST00000451114,,,MODIFIER,,,,-1;RENBP,downstream_gene_variant,,ENST00000462086,,,MODIFIER,,,,-1;RENBP,frameshift_variant,p.V146Sfs*16,ENST00000442361,,c.435del,HIGH,,,,-1;RENBP,frameshift_variant,p.R19Vfs*15,ENST00000457282,,c.53del,HIGH,,,,-1;RENBP,3_prime_UTR_variant,,ENST00000423624,,c.*623del,MODIFIER,,,,-1;RENBP,downstream_gene_variant,,ENST00000464227,,,MODIFIER,,,,-1;RENBP,downstream_gene_variant,,ENST00000471056,,,MODIFIER,,,,-1;RENBP,downstream_gene_variant,,ENST00000475904,,,MODIFIER,,,,-1 835/1334 mutect2;pindel;varscan2 eeab0529-31e6-4edb-bd2c-a21f2a169381 0 70 685483a8-1b68-4ba3-8bb1-e6f49611a109 66 7e3ea27a-346a-4fa1-8726-006561fd0374 SUCCESS RENBP,frameshift_variant,NMD_transcript_variant,p.V146Sfs*16,ENST00000442361.1,c.435del,HIGH,;RENBP,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000423624.5,c.*623del,MODIFIER,;RENBP,frameshift_variant,p.R254Vfs*15,ENST00000369997.7,c.760del,HIGH,;RENBP,frameshift_variant,NMD_transcript_variant,p.P18Rfs*99,ENST00000457282.5,c.53del,HIGH,;RENBP,frameshift_variant,p.R268Vfs*15,ENST00000393700.8,c.802del,HIGH,YES +CADM3 57863 BI GRCh38 1 159192614 159192614 + missense_variant Missense_Mutation SNP C C T rs748945624 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 57 12 c.266C>T p.Thr89Met p.T89M ENST00000368125.9 NM_001127173.3 89 aCg/aTg 3/9 A2 T T/M protein_coding CCDS44251.1 266/1197 CTCTACGCCCC COSM228815 PDB-ENSP_mappings:1z9m.A;PDB-ENSP_mappings:1z9m.B;Gene3D:2.60.40.10;Pfam:PF07686;PROSITE_profiles:PS50835;PANTHER:PTHR45889;PANTHER:PTHR45889:SF5;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd05882 ENSP00000357107 3/9 rs748945624;COSV63684507 ENST00000368125 Transcript ENSG00000162706 HGNC:17601 MODERATE NM_001127173.3 0.000123 gnomAD_AFR missense_variant 0;1 probably_damaging(0.983) Unknown deleterious(0) 0;1 Q8N126.163 CADM3 HGNC 1 1.0 UPI0000031579 Q8N126-1 SNV CADM3,missense_variant,p.T89M,ENST00000368125,NM_001127173.3&NM_001346510.2,c.266C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;CADM3,missense_variant,p.T123M,ENST00000368124,NM_021189.5,c.368C>T,MODERATE,YES,deleterious(0),probably_damaging(0.937),1;CADM3,missense_variant,p.T89M,ENST00000416746,,c.266C>T,MODERATE,,deleterious(0),probably_damaging(0.927),1;CADM3-AS1,downstream_gene_variant,,ENST00000415675,,,MODIFIER,YES,,,-1 417/3739 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 2.784e-05 0.000123 8.675e-05 0.0 0.0 0.0 1.758e-05 0.0 0.0 6.760319956811145e-05 2.4322600438608788e-05 0.0 0.0005300819757394 0.0 0.0 0.0 amr 0.0005300819757394 0.0 1.5433099179062992e-05 0.0 0.0 0 73 1625acba-43ea-4885-830b-4603a38f01e6 69 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS CADM3,missense_variant,p.T89M,ENST00000416746.1,c.266C>T,MODERATE,;CADM3,missense_variant,p.T89M,ENST00000368125.9,c.266C>T,MODERATE,YES;CADM3,missense_variant,p.T123M,ENST00000368124.8,c.368C>T,MODERATE, +DDR2 4921 BI GRCh38 1 162767302 162767302 + synonymous_variant Silent SNP C C T novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 67 22 c.1236C>T p.Leu412= p.L412= ENST00000367921.8 NM_001354982.2 412 ctC/ctT 11/18 P1 T L protein_coding CCDS1241.1 1236/2568 ATCCTCCTGGC PANTHER:PTHR24416;PANTHER:PTHR24416:SF295;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000356898 11/18 ENST00000367921 Transcript 1.0 ENSG00000162733 HGNC:2731 LOW NM_006182.4 synonymous_variant Unknown Q16832.199 DDR2 HGNC 1 A0A024R906.43 1.0 UPI000013E1B4 SNV DDR2,synonymous_variant,p.L412=,ENST00000367922,NM_001014796.3,c.1236C>T,LOW,YES,,,1;DDR2,synonymous_variant,p.L412=,ENST00000367921,NM_001354982.2&NM_006182.4,c.1236C>T,LOW,,,,1;DDR2,synonymous_variant,p.L412=,ENST00000446985,NM_001354983.2,c.1236C>T,LOW,,,,1;DDR2,non_coding_transcript_exon_variant,,ENST00000672207,,n.1622C>T,MODIFIER,,,,1;DDR2,non_coding_transcript_exon_variant,,ENST00000433757,,n.13C>T,MODIFIER,,,,1;DDR2,non_coding_transcript_exon_variant,,ENST00000458105,,n.66C>T,MODIFIER,,,,1 1595/10086 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 79 1625acba-43ea-4885-830b-4603a38f01e6 89 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS DDR2,non_coding_transcript_exon_variant,,ENST00000433757.1,n.13C>T,MODIFIER,;DDR2,non_coding_transcript_exon_variant,,ENST00000458105.1,n.66C>T,MODIFIER,;DDR2,synonymous_variant,p.L412=,ENST00000367922.7,c.1236C>T,LOW,;DDR2,synonymous_variant,p.L412=,ENST00000367921.8,c.1236C>T,LOW,YES;DDR2,non_coding_transcript_exon_variant,,ENST00000672207.1,n.1622C>T,MODIFIER,;DDR2,synonymous_variant,p.L412=,ENST00000446985.6,c.1236C>T,LOW, +SPTBN1 6711 BI GRCh38 2 54618190 54618190 + missense_variant Missense_Mutation SNP G G A TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 46 5 c.760G>A p.Glu254Lys p.E254K ENST00000356805.9 NM_003128.3 254 Gaa/Aaa 7/36 P3 A E/K protein_coding CCDS33198.1 760/7095 ACCCCGAAGGT COSM1021636;COSM1021637 Gene3D:1.10.418.10;PDB-ENSP_mappings:1aa2.A;PDB-ENSP_mappings:1bkr.A;Pfam:PF00307;PIRSF:PIRSF002297;PROSITE_profiles:PS50021;PANTHER:PTHR11915;PANTHER:PTHR11915:SF226;SMART:SM00033;Superfamily:SSF47576;CDD:cd00014 ENSP00000349259 7/36 COSV61685379;COSV61690403 ENST00000356805 Transcript 1.0 ENSG00000115306 HGNC:11275 MODERATE NM_003128.3 missense_variant 1;1 possibly_damaging(0.883) Unknown deleterious(0) 1;1 Q01082.212 SPTBN1 HGNC 1 B2ZZ89.117 1.0 UPI0000DBEE4B Q01082-1 SNV SPTBN1,missense_variant,p.E254K,ENST00000615901,,c.760G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.872),1;SPTBN1,missense_variant,p.E254K,ENST00000356805,NM_003128.3,c.760G>A,MODERATE,,deleterious(0),possibly_damaging(0.883),1;SPTBN1,missense_variant,p.E241K,ENST00000333896,NM_178313.2,c.721G>A,MODERATE,,deleterious(0),probably_damaging(0.992),1;SPTBN1,missense_variant,p.E254K,ENST00000389980,,c.760G>A,MODERATE,,deleterious(0),possibly_damaging(0.883),1 999/10211 muse;mutect2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 46 1625acba-43ea-4885-830b-4603a38f01e6 52 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS SPTBN1,missense_variant,p.E241K,ENST00000333896.5,c.721G>A,MODERATE,;SPTBN1,missense_variant,p.E254K,ENST00000389980.7,c.760G>A,MODERATE,;SPTBN1,missense_variant,p.E254K,ENST00000356805.9,c.760G>A,MODERATE,YES +SPAG16 79582 BI GRCh38 2 213930057 213930057 + missense_variant Missense_Mutation SNP G G A rs747474099 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 71 8 c.1312G>A p.Ala438Thr p.A438T ENST00000331683.10 NM_024532.5 438 Gca/Aca 12/16 P1 A A/T protein_coding YES CCDS2396.1 1312/1896 GCCGCGCAGTG Gene3D:2.130.10.10;Pfam:PF00400;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR14604;PANTHER:PTHR14604:SF3;SMART:SM00320;Superfamily:SSF50978;CDD:cd00200 ENSP00000332592 12/16 rs747474099;COSV100531553 ENST00000331683 Transcript ENSG00000144451 HGNC:23225 MODERATE NM_024532.5 0.0007618 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.938) Unknown deleterious(0.03) 0;1 Q8N0X2.158 SPAG16 HGNC 1 1.0 UPI00001AFF12 Q8N0X2-1 SNV SPAG16,missense_variant,p.A438T,ENST00000331683,NM_024532.5,c.1312G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.938),1;SPAG16,intron_variant,,ENST00000451561,,c.272+67429G>A,MODIFIER,,,,1;SPAG16,intron_variant,,ENST00000480494,,n.142+6053G>A,MODIFIER,,,,1;SPAG16,3_prime_UTR_variant,,ENST00000452556,,c.*878G>A,MODIFIER,,,,1;SPAG16,3_prime_UTR_variant,,ENST00000406979,,c.*1313G>A,MODIFIER,,,,1 1332/2102 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 6.366e-05 0.0 0.0 0.0 0.0007618 0.0 1.76e-05 0.0 0.0 2.7042000510846265e-05 0.0 0.0 0.0 0.0 0.0008064520079642 0.0 eas 0.0008064520079642 0.0 0.0 0.0 0.0 0 82 1625acba-43ea-4885-830b-4603a38f01e6 79 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS SPAG16,intron_variant,,ENST00000480494.1,n.142+6053G>A,MODIFIER,;SPAG16,intron_variant,,ENST00000451561.1,c.272+67429G>A,MODIFIER,;SPAG16,missense_variant,p.A438T,ENST00000331683.10,c.1312G>A,MODERATE,YES;SPAG16,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000452556.5,c.*878G>A,MODIFIER,;SPAG16,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000406979.6,c.*1313G>A,MODIFIER, +BAP1 8314 BI GRCh38 3 52407236 52407236 + missense_variant Missense_Mutation SNP T T C TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 22 4 c.518A>G p.Tyr173Cys p.Y173C ENST00000460680.6 NM_004656.4 173 tAt/tGt 7/17 P1 C Y/C protein_coding YES CCDS2853.1 518/2190 GCACATAGCTG COSM1666806 CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 7/17 CM156459;COSV56231551;COSV56238100 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 MODERATE NM_004656.4 missense_variant 1;1;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1;1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,missense_variant,p.Y173C,ENST00000460680,NM_004656.4,c.518A>G,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;BAP1,missense_variant,p.Y173C,ENST00000296288,,c.518A>G,MODERATE,,deleterious(0),probably_damaging(0.998),-1;BAP1,missense_variant,p.Y94C,ENST00000470173,,c.281A>G,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,3_prime_UTR_variant,,ENST00000490917,,c.*259A>G,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000471532,,n.233A>G,MODIFIER,,,,-1;BAP1,intron_variant,,ENST00000483984,,n.437+163A>G,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 648/3600 muse;mutect2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 38 1625acba-43ea-4885-830b-4603a38f01e6 26 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS BAP1,missense_variant,p.Y94C,ENST00000470173.1,c.281A>G,MODERATE,;BAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000490917.1,c.*259A>G,MODIFIER,;BAP1,intron_variant,,ENST00000483984.5,n.437+163A>G,MODIFIER,;BAP1,non_coding_transcript_exon_variant,,ENST00000471532.5,n.233A>G,MODIFIER,;BAP1,missense_variant,p.Y173C,ENST00000296288.9,c.518A>G,MODERATE,;BAP1,missense_variant,p.Y173C,ENST00000460680.6,c.518A>G,MODERATE,YES +DENND6A 201627 BI GRCh38 3 57641663 57641663 + synonymous_variant Silent SNP A A G novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 44 14 c.1122T>C p.Leu374= p.L374= ENST00000311128.10 NM_152678.3 374 ctT/ctC 12/20 P1 G L protein_coding YES CCDS33773.1 1122/1827 GGTTTAAGGTC PROSITE_profiles:PS50211;PANTHER:PTHR13677;PANTHER:PTHR13677:SF1 ENSP00000311401 12/20 ENST00000311128 Transcript ENSG00000174839 HGNC:26635 LOW NM_152678.3 synonymous_variant 1.0 Unknown Q8IWF6.119 DENND6A HGNC -1 1.0 UPI00000744F6 SNV DENND6A,synonymous_variant,p.L374=,ENST00000311128,NM_152678.3,c.1122T>C,LOW,YES,,,-1;DENND6A,synonymous_variant,p.L143=,ENST00000477344,,c.429T>C,LOW,,,,-1;DENND6A-AS1,intron_variant,,ENST00000470427,,n.69+12785A>G,MODIFIER,YES,,,1 1181/4646 muse;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 49 1625acba-43ea-4885-830b-4603a38f01e6 58 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS DENND6A,stop_lost,p.*143Qext*?,ENST00000477344.1,c.427T>C,HIGH,;DENND6A-AS1,intron_variant,,ENST00000470427.1,n.69+12785A>G,MODIFIER,YES;DENND6A,synonymous_variant,p.L374=,ENST00000311128.10,c.1122T>C,LOW,YES +GPR78 27201 BI GRCh38 4 8587242 8587242 + missense_variant Missense_Mutation SNP A A G rs1014333637 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 48 11 c.971A>G p.Asp324Gly p.D324G ENST00000382487.5 NM_080819.5 324 gAc/gGc 3/3 P1 G D/G protein_coding YES CCDS3403.1 971/1092 CCATGACAGCT PANTHER:PTHR24245;PANTHER:PTHR24245:SF7 ENSP00000371927 3/3 rs1014333637 ENST00000382487 Transcript ENSG00000155269 HGNC:4528 MODERATE NM_080819.5 missense_variant 1.0 benign(0) Unknown tolerated_low_confidence(0.23) Q96P69.134 GPR78 HGNC 1 B2R7M4.91 1.0 UPI0000037A5F SNV GPR78,missense_variant,p.D324G,ENST00000382487,NM_080819.5,c.971A>G,MODERATE,YES,tolerated_low_confidence(0.23),benign(0),1;GPR78,non_coding_transcript_exon_variant,,ENST00000509216,,n.771A>G,MODIFIER,,,,1;GPR78,non_coding_transcript_exon_variant,,ENST00000504255,,n.449A>G,MODIFIER,,,,1;GPR78,intron_variant,,ENST00000514302,,c.782+4598A>G,MODIFIER,,,,1 1562/4343 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 62 1625acba-43ea-4885-830b-4603a38f01e6 59 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS GPR78,non_coding_transcript_exon_variant,,ENST00000504255.1,n.449A>G,MODIFIER,;GPR78,missense_variant,p.D324G,ENST00000382487.5,c.971A>G,MODERATE,YES;GPR78,non_coding_transcript_exon_variant,,ENST00000509216.1,n.771A>G,MODIFIER,;GPR78,intron_variant,NMD_transcript_variant,,ENST00000514302.5,c.782+4598A>G,MODIFIER, +ARAP3 64411 BI GRCh38 5 141680419 141680419 + missense_variant Missense_Mutation SNP T T G novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 42 4 c.68A>C p.Asp23Ala p.D23A ENST00000239440.9 NM_022481.6 23 gAc/gCc 2/33 P1 G D/A protein_coding YES CCDS4266.1 68/4635 ACGTGTCTGCA PDB-ENSP_mappings:2kg5.A;PROSITE_profiles:PS50105;CDD:cd09490;PANTHER:PTHR45899:SF4;PANTHER:PTHR45899;Gene3D:1.10.150.50;Pfam:PF07647;SMART:SM00454;Superfamily:SSF47769 ENSP00000239440 2/33 ENST00000239440 Transcript ENSG00000120318 HGNC:24097 MODERATE NM_022481.6 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q8WWN8.160 ARAP3 HGNC -1 1.0 UPI0000049886 Q8WWN8-1 SNV ARAP3,missense_variant,p.D23A,ENST00000239440,NM_022481.6,c.68A>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;ARAP3,missense_variant,p.D23A,ENST00000504448,,c.68A>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;ARAP3,5_prime_UTR_variant,,ENST00000626478,,c.-167A>C,MODIFIER,,,,-1;ARAP3,5_prime_UTR_variant,,ENST00000508305,,c.-167A>C,MODIFIER,,,,-1 143/5258 muse;mutect2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 58 1625acba-43ea-4885-830b-4603a38f01e6 46 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS ARAP3,missense_variant,p.D23A,ENST00000504448.1,c.68A>C,MODERATE,;ARAP3,5_prime_UTR_variant,,ENST00000626478.2,c.-167A>C,MODIFIER,;ARAP3,missense_variant,p.D23A,ENST00000239440.9,c.68A>C,MODERATE,YES;ARAP3,5_prime_UTR_variant,,ENST00000508305.5,c.-167A>C,MODIFIER, +OR9A4 130075 BI GRCh38 7 141918929 141918929 + synonymous_variant Silent SNP C C A novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 150 12 c.54C>A p.Gly18= p.G18= ENST00000548136.1 18 ggC/ggA 1/1 P1 A G protein_coding CCDS43661.1 54/945 CCTGGCTCTGA PANTHER:PTHR24242;PANTHER:PTHR24242:SF216;Superfamily:SSF81321 ENSP00000448789 1/1 ENST00000548136 Transcript ENSG00000258083 HGNC:15095 LOW synonymous_variant Unknown Q8NGU2.139 OR9A4 HGNC 1 A0A126GVB1.27 UPI0000041D24 SNV OR9A4,synonymous_variant,p.G18=,ENST00000641559,,c.54C>A,LOW,YES,,,1;OR9A4,synonymous_variant,p.G18=,ENST00000548136,NM_001001656.2,c.54C>A,LOW,,,,1;MGAM,intron_variant,,ENST00000465654,,c.-180+11061C>A,MODIFIER,,,,1;MGAM,intron_variant,,ENST00000497554,,n.37-10848C>A,MODIFIER,,,,1 113/1093 muse;mutect2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 184 1625acba-43ea-4885-830b-4603a38f01e6 162 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS OR9A4,synonymous_variant,p.G18=,ENST00000548136.1,c.54C>A,LOW,;OR9A4,synonymous_variant,p.G18=,ENST00000641559.1,c.54C>A,LOW,YES;MGAM,intron_variant,,ENST00000497554.1,n.37-10848C>A,MODIFIER,;MGAM,intron_variant,,ENST00000465654.5,c.-180+11061C>A,MODIFIER, +CACNA1B 774 BI GRCh38 9 138121752 138121752 + missense_variant Missense_Mutation SNP C C T rs1430690049 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 31 11 c.6773C>T p.Pro2258Leu p.P2258L ENST00000371372.6 NM_000718.4 2258 cCt/cTt 47/47 P4 T P/L protein_coding CCDS59522.1 6773/7020 TGACCCTTACC PANTHER:PTHR45628;PANTHER:PTHR45628:SF6 ENSP00000360423 47/47 rs1430690049 ENST00000371372 Transcript 1.0 ENSG00000148408 HGNC:1389 MODERATE NM_000718.4 5.567e-05 gnomAD_EAS missense_variant probably_damaging(0.974) Unknown deleterious(0) Q00975.190 CACNA1B HGNC 1 5.0 UPI0000127267 Q00975-1 SNV CACNA1B,missense_variant,p.P2258L,ENST00000371372,NM_000718.4,c.6773C>T,MODERATE,,deleterious(0),probably_damaging(0.974),1;CACNA1B,missense_variant,p.P2256L,ENST00000371363,,c.6767C>T,MODERATE,,deleterious(0),possibly_damaging(0.904),1;CACNA1B,missense_variant,p.P2259L,ENST00000371355,,c.6776C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;CACNA1B,missense_variant,p.P2257L,ENST00000371357,,c.6770C>T,MODERATE,,deleterious(0),probably_damaging(0.974),1;CACNA1B,missense_variant,p.L2196F,ENST00000277549,,c.6586C>T,MODERATE,,tolerated_low_confidence(0.21),benign(0),1;CACNA1B,missense_variant,p.L2196F,ENST00000277551,NM_001243812.2,c.6586C>T,MODERATE,,tolerated_low_confidence(0.21),unknown(0),1 6925/9792 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 4.022e-06 0.0 0.0 0.0 5.567e-05 0.0 0.0 0.0 0.0 0 60 1625acba-43ea-4885-830b-4603a38f01e6 42 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS CACNA1B,missense_variant,p.P2257L,ENST00000371357.5,c.6770C>T,MODERATE,;CACNA1B,missense_variant,p.P2256L,ENST00000371363.5,c.6767C>T,MODERATE,;CACNA1B,missense_variant,p.L2196F,ENST00000277551.6,c.6586C>T,MODERATE,;CACNA1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000715547.1,c.*5189C>T,MODIFIER,;CACNA1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000715546.1,c.*5179C>T,MODIFIER,;CACNA1B,missense_variant,p.P2262L,ENST00000715549.1,c.6785C>T,MODERATE,;CACNA1B,missense_variant,p.P2279L,ENST00000715544.1,c.6836C>T,MODERATE,;CACNA1B,missense_variant,p.P2258L,ENST00000371372.6,c.6773C>T,MODERATE,YES;CACNA1B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000715545.1,c.*3487C>T,MODIFIER,;CACNA1B,missense_variant,p.P2300L,ENST00000715548.1,c.6899C>T,MODERATE, +CFAP70 118491 BI GRCh38 10 73293283 73293283 + missense_variant Missense_Mutation SNP C C T rs1302123744 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 28 7 c.1750G>A p.Ala584Thr p.A584T ENST00000310715.8 654 Gca/Aca 17/28 P4 T A/T protein_coding YES 1960/3366 TGCTGCCATCT Gene3D:1.25.40.10;PROSITE_profiles:PS50005;PROSITE_profiles:PS50293;PANTHER:PTHR44314;SMART:SM00028;Superfamily:SSF48452;Low_complexity_(Seg):seg ENSP00000310829 17/28 rs1302123744 ENST00000310715 Transcript 1.0 ENSG00000156042 HGNC:30726 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q5T0N1.138 CFAP70 HGNC -1 5.0 UPI00001AEF7A Q5T0N1-1 SNV CFAP70,missense_variant,p.A654T,ENST00000310715,,c.1960G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;CFAP70,missense_variant,p.A654T,ENST00000355577,NM_001350934.1&NM_001350933.1&NM_001367801.1,c.1960G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;CFAP70,missense_variant,p.A61T,ENST00000433268,,c.181G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;CFAP70,intron_variant,,ENST00000340329,,c.648-18733G>A,MODIFIER,,,,-1;CFAP70,upstream_gene_variant,,ENST00000394865,,,MODIFIER,,,,-1;CFAP70,non_coding_transcript_exon_variant,,ENST00000493787,,n.5540G>A,MODIFIER,,,,-1;CFAP70,upstream_gene_variant,,ENST00000462684,,,MODIFIER,,,,-1;CFAP70,upstream_gene_variant,,ENST00000495161,,,MODIFIER,,,,-1 2081/3703 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 39 1625acba-43ea-4885-830b-4603a38f01e6 35 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS CFAP70,missense_variant,p.A584T,ENST00000310715.8,c.1750G>A,MODERATE,;CFAP70,missense_variant,p.A462T,ENST00000686590.1,c.1384G>A,MODERATE,;CFAP70,intron_variant,,ENST00000340329.7,c.648-18733G>A,MODIFIER,;CFAP70,missense_variant,p.A654T,ENST00000355577.9,c.1960G>A,MODERATE,YES;CFAP70,missense_variant,p.A61T,ENST00000433268.5,c.181G>A,MODERATE,;CFAP70,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000493787.6,c.*5100G>A,MODIFIER, +OR5B21 219968 BI GRCh38 11 58507247 58507247 + missense_variant Missense_Mutation SNP A A G rs1239622308 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 136 22 c.859T>C p.Tyr287His p.Y287H ENST00000360374.3 NM_001005218.3 287 Tac/Cac 1/1 P1 G Y/H protein_coding YES CCDS31552.1 859/930 GCTGTATATCA Prints:PR00237;Prints:PR00245;Superfamily:SSF81321;Pfam:PF13853;Gene3D:1.20.1070.10;PANTHER:PTHR26452;PANTHER:PTHR26452:SF329;CDD:cd15407;PROSITE_profiles:PS50262;Transmembrane_helices:TMhelix ENSP00000353537 1/1 rs1239622308 ENST00000360374 Transcript ENSG00000198283 HGNC:19616 MODERATE 3.268e-05 gnomAD_SAS missense_variant probably_damaging(1) Unknown deleterious_low_confidence(0) A6NL26.100 OR5B21 HGNC -1 UPI000015FCAA SNV OR5B21,missense_variant,p.Y287H,ENST00000360374,NM_001005218.2,c.859T>C,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(1),-1;AP003557.1,upstream_gene_variant,,ENST00000527054,,,MODIFIER,,,,-1;AP003557.1,upstream_gene_variant,,ENST00000528978,,,MODIFIER,,,,-1;AP003557.1,upstream_gene_variant,,ENST00000531715,,,MODIFIER,YES,,,-1 859/931 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 3.98e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.268e-05 0 163 1625acba-43ea-4885-830b-4603a38f01e6 158 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS OR5B21,missense_variant,p.Y287H,ENST00000360374.3,c.859T>C,MODERATE,YES +THBS1 7057 BI GRCh38 15 39582282 39582282 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 33 5 c.157del p.Asp53ThrfsTer14 p.D53Tfs*14 ENST00000260356.6 NM_003246.4 53 Gac/ac 3/22 P1 - D/X protein_coding YES CCDS32194.1 157/3513 GGCCCCGACCCT PDB-ENSP_mappings:1z78.A;PDB-ENSP_mappings:1za4.A;Gene3D:2.60.120.200;PDB-ENSP_mappings:2erf.A;PDB-ENSP_mappings:2es3.A;PDB-ENSP_mappings:2es3.B;PDB-ENSP_mappings:2ouh.A;PDB-ENSP_mappings:2ouh.B;PDB-ENSP_mappings:2ouj.A;PANTHER:PTHR10199;PANTHER:PTHR10199:SF78;SMART:SM00210;Superfamily:SSF49899 ENSP00000260356 3/22 COSV52949951 ENST00000260356 Transcript ENSG00000137801 HGNC:11785 HIGH NM_003246.4 frameshift_variant 1 1.0 Unknown 1 P07996.240 THBS1 HGNC 1 1.0 UPI00001FE219 P07996-1 deletion THBS1,frameshift_variant,p.D53Tfs*14,ENST00000260356,NM_003246.4,c.157del,HIGH,YES,,,1;THBS1,frameshift_variant,p.D53Tfs*14,ENST00000397591,,c.157del,HIGH,,,,1;AC037198.1,upstream_gene_variant,,ENST00000478845,,,MODIFIER,YES,,,1 336/7789 mutect2;pindel;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 58 1625acba-43ea-4885-830b-4603a38f01e6 38 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS THBS1,frameshift_variant,p.D53Tfs*14,ENST00000397591.2,c.157del,HIGH,;THBS1,frameshift_variant,p.D53Tfs*14,ENST00000260356.6,c.157del,HIGH,YES +SPAG5 10615 BI GRCh38 17 28579784 28579784 + stop_gained Nonsense_Mutation SNP G G A rs756148727 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 110 14 c.2851C>T p.Arg951Ter p.R951* ENST00000321765.10 NM_006461.4 951 Cga/Tga 17/24 P1 A R/* protein_coding YES CCDS32594.1 2851/3582 TACTCGGGTGA PANTHER:PTHR15347 ENSP00000323300 17/24 rs756148727 ENST00000321765 Transcript ENSG00000076382 HGNC:13452 HIGH NM_006461.4 8.792e-06 gnomAD_NFE stop_gained 1.0 Unknown Q96R06.156 SPAG5 HGNC -1 1.0 UPI0000073414 SNV SPAG5,stop_gained,p.R951*,ENST00000321765,NM_006461.4,c.2851C>T,HIGH,YES,,,-1;ALDOC,upstream_gene_variant,,ENST00000226253,NM_005165.3,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000395319,,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000395321,,,MODIFIER,YES,,,-1;ALDOC,upstream_gene_variant,,ENST00000435638,,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000460201,,,MODIFIER,,,,-1;AC005726.1,downstream_gene_variant,,ENST00000531839,,,MODIFIER,YES,,,-1;ALDOC,upstream_gene_variant,,ENST00000578590,,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000581807,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000582076,,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000584086,,,MODIFIER,,,,-1;SPAG5,downstream_gene_variant,,ENST00000584206,,,MODIFIER,,,,-1;SPAG5,3_prime_UTR_variant,,ENST00000378976,,c.*166C>T,MODIFIER,,,,-1;SPAG5,non_coding_transcript_exon_variant,,ENST00000580406,,n.818C>T,MODIFIER,,,,-1;SPAG5,non_coding_transcript_exon_variant,,ENST00000581133,,n.132C>T,MODIFIER,,,,-1;SPAG5,non_coding_transcript_exon_variant,,ENST00000577259,,n.453C>T,MODIFIER,,,,-1;SPAG5,non_coding_transcript_exon_variant,,ENST00000580682,,n.388C>T,MODIFIER,,,,-1;AC005726.1,intron_variant,,ENST00000481916,,c.*1195+24267C>T,MODIFIER,,,,-1;SPAG5,downstream_gene_variant,,ENST00000578230,,,MODIFIER,,,,-1;SPAG5,downstream_gene_variant,,ENST00000580083,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000580377,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000580676,,,MODIFIER,,,,-1;SPAG5,upstream_gene_variant,,ENST00000582175,,,MODIFIER,,,,-1;ALDOC,upstream_gene_variant,,ENST00000582381,,,MODIFIER,,,,-1 2930/3786 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.792e-06 0.0 0.0 6.761869826732436e-06 2.4332099201274104e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 135 1625acba-43ea-4885-830b-4603a38f01e6 124 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS SPAG5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000378976.5,c.*166C>T,MODIFIER,;SPAG5,non_coding_transcript_exon_variant,,ENST00000580406.1,n.818C>T,MODIFIER,;SPAG5,non_coding_transcript_exon_variant,,ENST00000577259.1,n.453C>T,MODIFIER,;SPAG5,non_coding_transcript_exon_variant,,ENST00000580682.5,n.388C>T,MODIFIER,;SPAG5,non_coding_transcript_exon_variant,,ENST00000581133.5,n.132C>T,MODIFIER,;SPAG5,stop_gained,p.R951*,ENST00000321765.10,c.2851C>T,HIGH,YES;RSKR,intron_variant,NMD_transcript_variant,,ENST00000481916.6,c.*1195+24267C>T,MODIFIER, +SRSF2 6427 BI GRCh38 17 76736291 76736308 + inframe_deletion In_Frame_Del DEL GATCTGGAGACCGACGAG GATCTGGAGACCGACGAG - novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 51 12 c.519_536del p.Arg186_Ser191del p.R186_S191del ENST00000359995.10 NM_001195427.2 173 tcCTCGTCGGTCTCCAGATCt/tct 2/3 P1 - SSSVSRS/S protein_coding CCDS11749.1 519-536/666 GAACGAGATCTGGAGACCGACGAGGACTT PANTHER:PTHR23147;PANTHER:PTHR23147:SF119;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000353089 2/3 ENST00000359995 Transcript 1.0 ENSG00000161547 HGNC:10783 MODERATE NM_001195427.2 inframe_deletion Unknown Q01130.232 SRSF2 HGNC -1 A0A024R8U5.53 1.0 UPI0000000C2A Q01130-1 deletion SRSF2,inframe_deletion,p.S174_S179del,ENST00000392485,NM_003016.4,c.519_536del,MODERATE,YES,,,-1;SRSF2,inframe_deletion,p.S174_S179del,ENST00000359995,NM_001195427.2,c.519_536del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.S162_S167del,ENST00000508921,,c.483_500del,MODERATE,,,,-1;MFSD11,5_prime_UTR_variant,,ENST00000586622,,c.-870_-853del,MODIFIER,,,,1;AC005837.2,intron_variant,,ENST00000587459,,c.239-1989_239-1972del,MODIFIER,YES,,,1;MFSD11,upstream_gene_variant,,ENST00000336509,NM_001353019.1&NM_001242535.2&NM_024311.4&NM_001242532.4,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000341249,NM_001378349.1&NM_001378351.1&NM_001080510.5&NM_001378352.1,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000355954,NM_001242536.2,,MODIFIER,,,,1;SRSF2,downstream_gene_variant,,ENST00000358156,,,MODIFIER,,,,-1;SRSF2,downstream_gene_variant,,ENST00000583836,,,MODIFIER,,,,-1;METTL23,downstream_gene_variant,,ENST00000586200,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000586689,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586738,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586752,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000587661,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588302,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588460,NM_001353018.1,,MODIFIER,YES,,,1;METTL23,downstream_gene_variant,,ENST00000588563,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588783,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588822,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588964,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589977,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590393,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590514,NM_001242533.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000590964,NM_001206987.2&NM_001206986.2&NM_001206985.2&NM_001302704.1&NM_001378354.1,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000591571,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000591864,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000592849,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000593181,NM_001242537.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000615984,NM_001206983.2&NM_001302703.1&NM_001206984.2&NM_001302705.1&NM_001378348.1&NM_001378353.1&NM_001378350.1,,MODIFIER,YES,,,1;MFSD11,upstream_gene_variant,,ENST00000621483,NM_001242534.2&NM_001353017.1,,MODIFIER,,,,1;MIR636,downstream_gene_variant,,ENST00000384825,,,MODIFIER,YES,,,-1;SRSF2,inframe_deletion,p.S174_S179del,ENST00000585202,,c.519_536del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.S174_S179del,ENST00000452355,,c.519_536del,MODERATE,,,,-1;SRSF2,non_coding_transcript_exon_variant,,ENST00000582449,,n.248_265del,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000586778,,,MODIFIER,,,,-1;MFSD11,upstream_gene_variant,,ENST00000588031,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588670,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588768,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589581,,,MODIFIER,,,,1;SRSF2,upstream_gene_variant,,ENST00000589919,,,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000592676,,,MODIFIER,,,,-1 690-707/1888 mutect2;pindel 339490ef-6cf5-4d05-81b1-5e339e95f678 0 78 1625acba-43ea-4885-830b-4603a38f01e6 63 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS MFSD11,5_prime_UTR_variant,,ENST00000586622.5,c.-872_-855del,MODIFIER,;SRSF2,inframe_deletion,p.R174_S179del,ENST00000508921.7,c.483_500del,MODERATE,;SRSF2,inframe_deletion,NMD_transcript_variant,p.R186_S191del,ENST00000452355.7,c.519_536del,MODERATE,;SRSF2,non_coding_transcript_exon_variant,,ENST00000582449.5,n.248_265del,MODIFIER,;SRSF2,inframe_deletion,NMD_transcript_variant,p.R186_S191del,ENST00000585202.5,c.519_536del,MODERATE,;SRSF2,inframe_deletion,p.R186_S191del,ENST00000359995.10,c.519_536del,MODERATE,YES;SRSF2,inframe_deletion,p.R186_S191del,ENST00000392485.2,c.519_536del,MODERATE,;SRSF2,inframe_deletion,p.R179_S184del,ENST00000358156.7,c.498_515del,MODERATE,;ENSG00000267168,intron_variant,,ENST00000587459.1,c.239-1991_239-1974del,MODIFIER,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 34 18 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 50 1625acba-43ea-4885-830b-4603a38f01e6 52 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +KIR2DL4 3805 BI GRCh38 19 54813951 54813951 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 282 32 c.869C>T p.Thr290Ile p.T290I ENST00000345540.10 NM_001080770.2 290 aCa/aTa 7/7 P4 T T/I protein_coding YES 1091/1251 CTCAACAGATA PANTHER:PTHR11738;PANTHER:PTHR11738:SF158 ENSP00000379580 8/8 ENST00000396284 Transcript ENSG00000189013 HGNC:6332 MODERATE missense_variant 1.0 benign(0.27) Unknown tolerated(0.07) KIR2DL4 HGNC 1 E7EST5.69 1.0 UPI0004E4C8FD SNV KIR2DL4,missense_variant,p.T364I,ENST00000396284,,c.1091C>T,MODERATE,YES,tolerated(0.07),benign(0.27),1;KIR2DL4,missense_variant,p.T346I,ENST00000396289,,c.1037C>T,MODERATE,,tolerated(0.09),benign(0.293),1;KIR2DL4,missense_variant,p.T290I,ENST00000345540,NM_001080770.2,c.869C>T,MODERATE,,tolerated(0.09),benign(0.059),1;KIR2DL4,missense_variant,p.T273I,ENST00000357494,,c.818C>T,MODERATE,,deleterious(0.03),benign(0.029),1;KIR2DL4,missense_variant,p.T195I,ENST00000346587,,c.584C>T,MODERATE,,tolerated(0.09),benign(0.031),1;KIR2DL4,missense_variant,p.T178I,ENST00000396293,,c.533C>T,MODERATE,,deleterious(0.04),benign(0.033),1;KIR2DL4,3_prime_UTR_variant,,ENST00000359085,NM_001080772.2,c.*151C>T,MODIFIER,,,,1;KIR3DL1,upstream_gene_variant,,ENST00000326542,,,MODIFIER,,,,1;KIR3DL1,upstream_gene_variant,,ENST00000358178,,,MODIFIER,,,,1;KIR3DL1,upstream_gene_variant,,ENST00000391728,NM_013289.2,,MODIFIER,YES,,,1;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000463062,,n.934C>T,MODIFIER,,,,1;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000486965,,n.776C>T,MODIFIER,,,,1 1091/1656 muse;mutect2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 346 1625acba-43ea-4885-830b-4603a38f01e6 315 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS KIR2DL4,synonymous_variant,p.N345=,ENST00000396289.5,c.1035C>T,LOW,;KIR2DL4,missense_variant,p.T195I,ENST00000346587.8,c.584C>T,MODERATE,;KIR2DL4,missense_variant,p.T178I,ENST00000396293.5,c.533C>T,MODERATE,;KIR2DL4,missense_variant,p.T273I,ENST00000357494.8,c.818C>T,MODERATE,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000463062.1,n.934C>T,MODIFIER,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000486965.6,n.776C>T,MODIFIER,;KIR2DL4,3_prime_UTR_variant,,ENST00000359085.8,c.*151C>T,MODIFIER,;KIR2DL4,missense_variant,p.T290I,ENST00000345540.10,c.869C>T,MODERATE,YES +LIPI 149998 BI GRCh38 21 14181793 14181793 + missense_variant Missense_Mutation SNP G G T novel TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 61 6 c.608C>A p.Ala203Glu p.A203E ENST00000681601.1 NM_198996.4 203 gCa/gAa 4/10 P4 T A/E protein_coding YES CCDS13564.1 671/1446 ACTTTGCATCC Gene3D:3.40.50.1820;Pfam:PF00151;PIRSF:PIRSF000865;PANTHER:PTHR11610;PANTHER:PTHR11610:SF103;Superfamily:SSF53474;CDD:cd00707 ENSP00000343331 4/10 ENST00000344577 Transcript 1.0 ENSG00000188992 HGNC:18821 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q6XZB0.147 LIPI HGNC -1 1.0 UPI000462096D Q6XZB0-2 SNV LIPI,missense_variant,p.A224E,ENST00000344577,NM_198996.4,c.671C>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;LIPI,missense_variant,p.A194E,ENST00000536861,NM_001379566.1&NM_001379565.1&NM_001303000.2&NM_001303001.2&NM_001302998.2,c.581C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;LIPI,missense_variant,p.A194E,ENST00000614229,NM_001302999.2,c.581C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;LIPI,missense_variant,p.A83E,ENST00000400211,,c.248C>A,MODERATE,,deleterious(0),probably_damaging(1),-1 697/1652 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 50 1625acba-43ea-4885-830b-4603a38f01e6 67 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS LIPI,missense_variant,p.A203E,ENST00000400211.3,c.608C>A,MODERATE,;LIPI,missense_variant,p.A203E,ENST00000536861.6,c.608C>A,MODERATE,;LIPI,missense_variant,p.A38E,ENST00000679868.1,c.113C>A,MODERATE,;LIPI,missense_variant,p.A203E,ENST00000680801.1,c.608C>A,MODERATE,;LIPI,missense_variant,p.A203E,ENST00000614229.5,c.608C>A,MODERATE,;LIPI,missense_variant,NMD_transcript_variant,p.A203E,ENST00000680487.1,c.608C>A,MODERATE,;LIPI,non_coding_transcript_exon_variant,,ENST00000344577.6,n.697C>A,MODIFIER,;LIPI,missense_variant,p.A203E,ENST00000681601.1,c.608C>A,MODERATE,YES +OSM 5008 BI GRCh38 22 30265064 30265064 + missense_variant Missense_Mutation SNP G G T rs149963275 TCGA-WC-A888-01A TCGA-WC-A888-10A Somatic 89 11 c.115C>A p.Leu39Ile p.L39I ENST00000215781.3 NM_020530.6 39 Ctt/Att 2/3 P4 T L/I protein_coding YES CCDS13873.1 115/759 GCCAAGGAGCA PDB-ENSP_mappings:1evs.A;PANTHER:PTHR14261;Gene3D:1.20.1250.10;Pfam:PF01291;SMART:SM00080;Superfamily:SSF47266 ENSP00000215781 2/3 rs149963275 ENST00000215781 Transcript ENSG00000099985 HGNC:8506 MODERATE NM_020530.6 missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0.01) P13725.193 OSM HGNC -1 1.0 UPI0000130D33 SNV OSM,missense_variant,p.L39I,ENST00000215781,NM_020530.6,c.115C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.996),-1;OSM,missense_variant,p.L18I,ENST00000403389,NM_001319108.2,c.52C>A,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;OSM,intron_variant,,ENST00000403463,,c.35-600C>A,MODIFIER,,,,-1 167/1865 muse;mutect2;varscan2 339490ef-6cf5-4d05-81b1-5e339e95f678 0 148 1625acba-43ea-4885-830b-4603a38f01e6 100 e4014960-7df6-4442-b161-fb09c4a7fdfd SUCCESS OSM,intron_variant,,ENST00000403463.1,c.35-600C>A,MODIFIER,;OSM,missense_variant,p.L18I,ENST00000403389.1,c.52C>A,MODERATE,;OSM,missense_variant,p.L39I,ENST00000215781.3,c.115C>A,MODERATE,YES +MTOR 2475 BI GRCh38 1 11109317 11109317 + missense_variant Missense_Mutation SNP T T A TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 64 10 c.7501A>T p.Ile2501Phe p.I2501F ENST00000361445.9 NM_004958.4 2501 Att/Ttt 56/58 P1 A I/F protein_coding YES CCDS127.1 7501/7650 GTTAATAATCT COSM4140746 PDB-ENSP_mappings:3jbz.A;PDB-ENSP_mappings:4jsn.A;PDB-ENSP_mappings:4jsn.B;PDB-ENSP_mappings:4jsp.A;PDB-ENSP_mappings:4jsp.B;PDB-ENSP_mappings:4jsv.A;PDB-ENSP_mappings:4jsv.B;PDB-ENSP_mappings:4jsx.A;PDB-ENSP_mappings:4jsx.B;PDB-ENSP_mappings:4jt5.A;PDB-ENSP_mappings:4jt5.B;PDB-ENSP_mappings:4jt6.A;PDB-ENSP_mappings:4jt6.B;PDB-ENSP_mappings:5flc.B;PDB-ENSP_mappings:5flc.F;PDB-ENSP_mappings:5h64.A;PDB-ENSP_mappings:5h64.a;PDB-ENSP_mappings:5wbu.A;PDB-ENSP_mappings:5wbu.B;PDB-ENSP_mappings:5wby.A;PDB-ENSP_mappings:5wby.B;PDB-ENSP_mappings:5zcs.A;PDB-ENSP_mappings:5zcs.B;PDB-ENSP_mappings:6bcu.A;PDB-ENSP_mappings:6bcu.B;PDB-ENSP_mappings:6bcx.A;PDB-ENSP_mappings:6bcx.B;PDB-ENSP_mappings:6sb0.A;PDB-ENSP_mappings:6sb0.B;PDB-ENSP_mappings:6sb2.A;PDB-ENSP_mappings:6sb2.B;PROSITE_profiles:PS50290;PANTHER:PTHR11139;PANTHER:PTHR11139:SF9 ENSP00000354558 56/58 COSV63871874 ENST00000361445 Transcript 1.0 ENSG00000198793 HGNC:3942 MODERATE NM_004958.4 missense_variant 1 1.0 possibly_damaging(0.764) Unknown deleterious(0.01) 1 P42345.215 MTOR HGNC -1 1.0 UPI000012ABD3 SNV MTOR,missense_variant,p.I2501F,ENST00000361445,NM_004958.4,c.7501A>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.764),-1;MTOR,missense_variant,p.I706F,ENST00000376838,,c.2116A>T,MODERATE,,tolerated(0.05),possibly_damaging(0.764),-1;MTOR,missense_variant,p.I157F,ENST00000455339,,c.469A>T,MODERATE,,tolerated(0.08),possibly_damaging(0.764),-1;MTOR,non_coding_transcript_exon_variant,,ENST00000490931,,n.784A>T,MODIFIER,,,,-1;MTOR,non_coding_transcript_exon_variant,,ENST00000473471,,n.513A>T,MODIFIER,,,,-1 7622/8721 muse;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 110 f34ad461-9510-471b-acd0-06d324914a1d 74 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS MTOR,non_coding_transcript_exon_variant,,ENST00000455339.1,n.680A>T,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000490931.1,n.784A>T,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000473471.5,n.513A>T,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000703131.1,n.3419A>T,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703118.1,c.*2876A>T,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703142.1,c.*4331A>T,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703141.1,c.*3018A>T,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000376838.5,n.2918A>T,MODIFIER,;MTOR,missense_variant,p.I2501F,ENST00000361445.9,c.7501A>T,MODERATE,YES;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703139.2,c.*557A>T,MODIFIER,;MTOR,missense_variant,p.I2430F,ENST00000703140.1,c.7288A>T,MODERATE,;MTOR,missense_variant,p.I2501F,ENST00000703143.2,c.7501A>T,MODERATE, +MTOR 2475 BI GRCh38 1 11109355 11109355 + missense_variant Missense_Mutation SNP A A C novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 8 52 c.7463T>G p.Val2488Gly p.V2488G ENST00000361445.9 NM_001386501.1 2488 gTg/gGg 56/58 P1 C V/G protein_coding YES CCDS127.1 7463/7650 GTTTCACCAAA PDB-ENSP_mappings:3jbz.A;PDB-ENSP_mappings:4jsn.A;PDB-ENSP_mappings:4jsn.B;PDB-ENSP_mappings:4jsp.A;PDB-ENSP_mappings:4jsp.B;PDB-ENSP_mappings:4jsv.A;PDB-ENSP_mappings:4jsv.B;PDB-ENSP_mappings:4jsx.A;PDB-ENSP_mappings:4jsx.B;PDB-ENSP_mappings:4jt5.A;PDB-ENSP_mappings:4jt5.B;PDB-ENSP_mappings:4jt6.A;PDB-ENSP_mappings:4jt6.B;PDB-ENSP_mappings:5flc.B;PDB-ENSP_mappings:5flc.F;PDB-ENSP_mappings:5h64.A;PDB-ENSP_mappings:5h64.a;PDB-ENSP_mappings:5wbu.A;PDB-ENSP_mappings:5wbu.B;PDB-ENSP_mappings:5wby.A;PDB-ENSP_mappings:5wby.B;PDB-ENSP_mappings:5zcs.A;PDB-ENSP_mappings:5zcs.B;PDB-ENSP_mappings:6bcu.A;PDB-ENSP_mappings:6bcu.B;PDB-ENSP_mappings:6bcx.A;PDB-ENSP_mappings:6bcx.B;PDB-ENSP_mappings:6sb0.A;PDB-ENSP_mappings:6sb0.B;PDB-ENSP_mappings:6sb2.A;PDB-ENSP_mappings:6sb2.B;PROSITE_profiles:PS50290;PANTHER:PTHR11139;PANTHER:PTHR11139:SF9 ENSP00000354558 56/58 ENST00000361445 Transcript 1.0 ENSG00000198793 HGNC:3942 MODERATE NM_004958.4 missense_variant 1.0 benign(0.021) Unknown tolerated(0.41) P42345.215 MTOR HGNC -1 1.0 UPI000012ABD3 SNV MTOR,missense_variant,p.V2488G,ENST00000361445,NM_004958.4,c.7463T>G,MODERATE,YES,tolerated(0.41),benign(0.021),-1;MTOR,missense_variant,p.V693G,ENST00000376838,,c.2078T>G,MODERATE,,tolerated(0.38),benign(0.021),-1;MTOR,missense_variant,p.V144G,ENST00000455339,,c.431T>G,MODERATE,,tolerated(0.38),benign(0.021),-1;MTOR,non_coding_transcript_exon_variant,,ENST00000490931,,n.746T>G,MODIFIER,,,,-1;MTOR,non_coding_transcript_exon_variant,,ENST00000473471,,n.475T>G,MODIFIER,,,,-1 7584/8721 muse;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 100 f34ad461-9510-471b-acd0-06d324914a1d 60 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS MTOR,non_coding_transcript_exon_variant,,ENST00000455339.1,n.642T>G,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000490931.1,n.746T>G,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000473471.5,n.475T>G,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000703131.1,n.3381T>G,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703118.1,c.*2838T>G,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703142.1,c.*4293T>G,MODIFIER,;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703141.1,c.*2980T>G,MODIFIER,;MTOR,non_coding_transcript_exon_variant,,ENST00000376838.5,n.2880T>G,MODIFIER,;MTOR,missense_variant,p.V2488G,ENST00000361445.9,c.7463T>G,MODERATE,YES;MTOR,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703139.2,c.*519T>G,MODIFIER,;MTOR,missense_variant,p.V2417G,ENST00000703140.1,c.7250T>G,MODERATE,;MTOR,missense_variant,p.V2488G,ENST00000703143.2,c.7463T>G,MODERATE, +ARSJ 79642 BI GRCh38 4 113902570 113902570 + missense_variant Missense_Mutation SNP G G T TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 26 21 c.1504C>A p.Pro502Thr p.P502T ENST00000315366.8 NM_001354210.2 502 Cca/Aca 2/2 P1 T P/T protein_coding YES CCDS43264.1 1504/1800 ATATGGGTCGG CDD:cd16029;PANTHER:PTHR10342:SF69;PANTHER:PTHR10342;Gene3D:3.30.1120.10;Superfamily:SSF53649 ENSP00000320219 2/2 COSV59539032 ENST00000315366 Transcript ENSG00000180801 HGNC:26286 MODERATE NM_024590.4 missense_variant 1 1.0 probably_damaging(1) Unknown deleterious(0.02) 1 Q5FYB0.127 ARSJ HGNC -1 1.0 UPI000003FD84 SNV ARSJ,missense_variant,p.P502T,ENST00000315366,NM_001354210.2&NM_024590.4,c.1504C>A,MODERATE,YES,deleterious(0.02),probably_damaging(1),-1;ARSJ,downstream_gene_variant,,ENST00000636527,,,MODIFIER,,,,-1;ARSJ,3_prime_UTR_variant,,ENST00000509829,,c.*1183C>A,MODIFIER,,,,-1 2317/4603 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 56 f34ad461-9510-471b-acd0-06d324914a1d 47 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS ARSJ,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000509829.1,c.*1183C>A,MODIFIER,;ARSJ,missense_variant,p.P502T,ENST00000315366.8,c.1504C>A,MODERATE,YES +DNAH8 1769 BI GRCh38 6 38860602 38860602 + missense_variant Missense_Mutation SNP G G A rs758868992 TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 78 9 c.5453G>A p.Arg1818His p.R1818H ENST00000359357.7 NM_001371.4 1818 cGt/cAt 41/91 A2 A R/H protein_coding 5453/13473 TGATCGTCTTG COSM5756854;COSM5756855;COSM5756856 Gene3D:1.20.58.1120;Pfam:PF12774;PANTHER:PTHR10676;PANTHER:PTHR10676:SF361 ENSP00000352312 41/91 rs758868992;COSV59480066 ENST00000359357 Transcript ENSG00000124721 HGNC:2952 MODERATE 9.609e-05 gnomAD_SAS missense_variant 0;1 probably_damaging(1) Unknown deleterious(0) 0;1 Q96JB1.136 DNAH8 HGNC 1 2.0 UPI00003677EB Q96JB1-1 SNV DNAH8,missense_variant,p.R2035H,ENST00000327475,NM_001206927.2,c.6104G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;DNAH8,missense_variant,p.R1818H,ENST00000359357,NM_001371.4,c.5453G>A,MODERATE,,deleterious(0),probably_damaging(1),1;DNAH8,missense_variant,p.R2035H,ENST00000449981,,c.6104G>A,MODERATE,,deleterious(0),probably_damaging(1),1;DNAH8,upstream_gene_variant,,ENST00000394393,,,MODIFIER,,,,1 5707/13864 muse;mutect2 2bf47a88-df0a-4102-af2e-998c3d252b9c 2.584e-05 0.0 0.0 0.0 0.0 0.0 3.117e-05 0.0 9.609e-05 1.3529100215237122e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0871800845488906e-05 0.0 3.0871800845488906e-05 0.0 0.0 0 76 f34ad461-9510-471b-acd0-06d324914a1d 88 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS DNAH8,missense_variant,p.R1818H,ENST00000359357.7,c.5453G>A,MODERATE,;DNAH8,missense_variant,p.R2035H,ENST00000449981.6,c.6104G>A,MODERATE,;DNAH8,missense_variant,p.R2035H,ENST00000327475.11,c.6104G>A,MODERATE,YES +LSM1 27257 BI GRCh38 8 38163727 38163727 + missense_variant Missense_Mutation SNP C C G novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 27 22 c.345G>C p.Gln115His p.Q115H ENST00000311351.9 NM_014462.3 115 caG/caC 4/4 P1 G Q/H protein_coding YES CCDS6103.1 345/402 AGGGCCTGCAC Coiled-coils_(Ncoils):Coil;PANTHER:PTHR15588;PANTHER:PTHR15588:SF8;Gene3D:2.30.30.100 ENSP00000310596 4/4 ENST00000311351 Transcript ENSG00000175324 HGNC:20472 MODERATE NM_014462.3 missense_variant 1.0 benign(0.182) Unknown deleterious(0.01) O15116.163 LSM1 HGNC -1 A0A0S2Z590.24 1.0 UPI000012E963 SNV LSM1,missense_variant,p.Q115H,ENST00000311351,NM_014462.3,c.345G>C,MODERATE,YES,deleterious(0.01),benign(0.182),-1;LSM1,3_prime_UTR_variant,,ENST00000520755,,c.*94G>C,MODIFIER,,,,-1;RNU6-323P,downstream_gene_variant,,ENST00000521915,,,MODIFIER,YES,,,-1;LSM1,non_coding_transcript_exon_variant,,ENST00000522515,,n.1200G>C,MODIFIER,,,,-1;LSM1,non_coding_transcript_exon_variant,,ENST00000520286,,n.477G>C,MODIFIER,,,,-1;LSM1,3_prime_UTR_variant,,ENST00000523511,,c.*280G>C,MODIFIER,,,,-1;AC084024.3,non_coding_transcript_exon_variant,,ENST00000520598,,n.517C>G,MODIFIER,YES,,,1 518/906 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 57 f34ad461-9510-471b-acd0-06d324914a1d 49 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS LSM1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000523511.1,c.*280G>C,MODIFIER,;LSM1,non_coding_transcript_exon_variant,,ENST00000520286.5,n.477G>C,MODIFIER,;LSM1,non_coding_transcript_exon_variant,,ENST00000522515.5,n.1200G>C,MODIFIER,;LSM1,missense_variant,p.Q115H,ENST00000311351.9,c.345G>C,MODERATE,YES;LSM1,3_prime_UTR_variant,,ENST00000520755.5,c.*94G>C,MODIFIER,;ENSG00000253356,non_coding_transcript_exon_variant,,ENST00000520598.1,n.517C>G,MODIFIER,YES +COL14A1 7373 BI GRCh38 8 120212560 120212560 + missense_variant Missense_Mutation SNP C C T rs748226555 TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 23 103 c.1580C>T p.Thr527Met p.T527M ENST00000297848.8 NM_021110.4 527 aCg/aTg 13/48 P4 T T/M protein_coding YES CCDS34938.1 1580/5391 TGTTACGGGAC COSM5624723 Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR24020;PANTHER:PTHR24020:SF15;Superfamily:SSF49265;CDD:cd00063 ENSP00000297848 13/48 rs748226555;COSV52866169 ENST00000297848 Transcript 1.0 ENSG00000187955 HGNC:2191 MODERATE NM_021110.4 0.0001635 gnomAD_OTH missense_variant 0;1 1.0 possibly_damaging(0.825) Unknown deleterious(0.03) 0;1 Q05707.166 COL14A1 HGNC 1 5.0 UPI000046D377 Q05707-1 SNV COL14A1,missense_variant,p.T527M,ENST00000297848,NM_021110.4,c.1580C>T,MODERATE,YES,deleterious(0.03),possibly_damaging(0.825),1;COL14A1,missense_variant,p.T527M,ENST00000309791,,c.1580C>T,MODERATE,,deleterious(0.02),probably_damaging(0.933),1;COL14A1,missense_variant,p.T527M,ENST00000537875,,c.1580C>T,MODERATE,,deleterious(0),possibly_damaging(0.726),1;COL14A1,missense_variant,p.T340M,ENST00000434620,,c.1019C>T,MODERATE,,deleterious(0),probably_damaging(0.919),1;COL14A1,missense_variant,p.T284M,ENST00000523142,,c.851C>T,MODERATE,,deleterious(0),probably_damaging(0.954),1;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,,n.1814C>T,MODIFIER,,,,1;COL14A1,missense_variant,p.T527M,ENST00000498051,,c.1580C>T,MODERATE,,deleterious(0),possibly_damaging(0.726),1 1856/8009 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 1.194e-05 0.0 0.0 0.0 5.44e-05 0.0 8.806e-06 0.0001635 0.0 1.353070001641754e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0872801289660856e-05 0.0 3.0872801289660856e-05 0.0 0.0 0 57 f34ad461-9510-471b-acd0-06d324914a1d 126 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS COL14A1,missense_variant,p.T340M,ENST00000434620.5,c.1019C>T,MODERATE,;COL14A1,synonymous_variant,p.Y283=,ENST00000523142.5,c.849C>T,LOW,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943.6,n.1814C>T,MODIFIER,;COL14A1,missense_variant,p.T527M,ENST00000309791.8,c.1580C>T,MODERATE,;COL14A1,missense_variant,p.T527M,ENST00000297848.8,c.1580C>T,MODERATE,YES;COL14A1,missense_variant,p.T527M,ENST00000537875.2,c.1580C>T,MODERATE,;COL14A1,missense_variant,NMD_transcript_variant,p.T527M,ENST00000498051.6,c.1580C>T,MODERATE, +POU4F1 5457 BI GRCh38 13 78601703 78601703 + synonymous_variant Silent SNP C C T novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 24 4 c.972G>A p.Ala324= p.A324= ENST00000377208.7 NM_006237.4 324 gcG/gcA 2/2 P1 T A protein_coding YES CCDS31996.1 972/1260 TTGAGCGCGAT Gene3D:1.10.260.40;Pfam:PF00157;Prints:PR00028;PROSITE_profiles:PS51179;PANTHER:PTHR11636;PANTHER:PTHR11636:SF42;SMART:SM00352;Superfamily:SSF47413 ENSP00000366413 2/2 ENST00000377208 Transcript ENSG00000152192 HGNC:9218 LOW NM_006237.4 synonymous_variant 1.0 Unknown Q01851.188 POU4F1 HGNC -1 1.0 UPI000013DCAA Q01851-1 SNV POU4F1,synonymous_variant,p.A324=,ENST00000377208,NM_006237.4,c.972G>A,LOW,YES,,,-1;OBI1-AS1,intron_variant,,ENST00000430549,,n.430-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000444769,,n.404-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000560209,,n.154-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000560584,,n.189-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000606124,,n.385-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000606376,,n.314-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000606429,,n.385-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000607205,,n.398-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000607220,,n.237-3598C>T,MODIFIER,,,,1;OBI1-AS1,intron_variant,,ENST00000607860,,n.500-3598C>T,MODIFIER,,,,1;AL445209.1,downstream_gene_variant,,ENST00000607269,,,MODIFIER,YES,,,1 1198/4539 muse;mutect2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 25 f34ad461-9510-471b-acd0-06d324914a1d 28 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS POU4F1,synonymous_variant,p.A324=,ENST00000377208.7,c.972G>A,LOW,YES;OBI1-AS1,intron_variant,,ENST00000560584.2,n.189-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000444769.7,n.404-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000606376.5,n.314-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000560209.6,n.154-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000430549.6,n.430-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000607220.5,n.237-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000607860.5,n.500-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000606124.5,n.385-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000606429.5,n.385-3598C>T,MODIFIER,;OBI1-AS1,intron_variant,,ENST00000607205.5,n.398-3598C>T,MODIFIER, +PRKCB 5579 BI GRCh38 16 24191112 24191124 + inframe_deletion In_Frame_Del DEL AACGTCTGGGTTG AACGTCTGGGTTG T novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 67 47 c.1746_1757del p.Lys582_Cys586delinsIle p.K582_C586delinsI ENST00000643927.1 NM_002738.7 582 aAACGTCTGGGTTGt/aTt 16/17 A1 T KRLGC/I protein_coding CCDS10618.1 1745-1757/2016 AGGCAAACGTCTGGGTTGTGGAC Gene3D:1.10.510.10;PDB-ENSP_mappings:2i0e.A;PDB-ENSP_mappings:2i0e.B;Pfam:PF00069;PIRSF:PIRSF000550;PROSITE_profiles:PS50011;PANTHER:PTHR24356;PANTHER:PTHR24356:SF158;SMART:SM00220;Superfamily:SSF56112;CDD:cd05616 ENSP00000318315 16/17 ENST00000321728 Transcript 1.0 ENSG00000166501 HGNC:9395 MODERATE protein_altering_variant Unknown P05771.242 PRKCB HGNC 1 1.0 UPI000012DF67 P05771-1 indel PRKCB,protein_altering_variant,p.K582_C586delinsI,ENST00000643927,NM_002738.7,c.1745_1757delinsT,MODERATE,YES,,,1;PRKCB,protein_altering_variant,p.K582_C586delinsI,ENST00000321728,NM_212535.3,c.1745_1757delinsT,MODERATE,,,,1;PRKCB,protein_altering_variant,p.K21_C25delinsI,ENST00000466124,,c.60_72delinsT,MODERATE,,,,1 1938-1950/2707 pindel;varscan2* 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 91 f34ad461-9510-471b-acd0-06d324914a1d 114 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS PRKCB,stop_gained,inframe_deletion,p.Q20*,ENST00000466124.1,c.61_72del,HIGH,;PRKCB,inframe_deletion,p.K582_C586delinsI,ENST00000643927.1,c.1746_1757del,MODERATE,YES;PRKCB,inframe_deletion,p.K582_C586delinsI,ENST00000321728.12,c.1746_1757del,MODERATE, +PPP4R1 9989 BI GRCh38 18 9550174 9550174 + missense_variant Missense_Mutation SNP C C A novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 33 22 c.2425G>T p.Val809Leu p.V809L ENST00000400556.8 NM_001042388.3 809 Gtg/Ttg 18/20 A2 A V/L protein_coding YES CCDS42412.1 2425/2853 CTTCACCATCT PANTHER:PTHR10648;PANTHER:PTHR10648:SF8;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000383402 18/20 ENST00000400556 Transcript ENSG00000154845 HGNC:9320 MODERATE NM_001042388.3 missense_variant 1.0 benign(0.003) Unknown tolerated(1) Q8TF05.160 PPP4R1 HGNC -1 1.0 UPI000006D6DE Q8TF05-1 SNV PPP4R1,missense_variant,p.V809L,ENST00000400556,NM_001042388.3,c.2425G>T,MODERATE,YES,tolerated(1),benign(0.003),-1;PPP4R1,missense_variant,p.V792L,ENST00000400555,NM_001382562.1&NM_005134.4,c.2374G>T,MODERATE,,tolerated(1),benign(0.005),-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579609,,n.152G>T,MODIFIER,,,,-1;PPP4R1,downstream_gene_variant,,ENST00000584754,,,MODIFIER,,,,-1;PPP4R1,3_prime_UTR_variant,,ENST00000285124,,c.*2137G>T,MODIFIER,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000582594,,n.1675G>T,MODIFIER,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578010,,n.218G>T,MODIFIER,,,,-1;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578329,,n.127G>T,MODIFIER,,,,-1 2500/3923 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 61 f34ad461-9510-471b-acd0-06d324914a1d 55 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS PPP4R1,non_coding_transcript_exon_variant,,ENST00000578010.1,n.218G>T,MODIFIER,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578329.1,n.127G>T,MODIFIER,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579609.5,n.152G>T,MODIFIER,;PPP4R1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000285124.12,c.*2137G>T,MODIFIER,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000582594.5,n.1675G>T,MODIFIER,;PPP4R1,missense_variant,p.V809L,ENST00000400556.8,c.2425G>T,MODERATE,YES;PPP4R1,missense_variant,p.V792L,ENST00000400555.7,c.2374G>T,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 44 27 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 83 f34ad461-9510-471b-acd0-06d324914a1d 71 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +SHANK1 50944 BI GRCh38 19 50716751 50716751 + missense_variant Missense_Mutation SNP G G A TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 33 3 c.169C>T p.Leu57Phe p.L57F ENST00000293441.6 NM_016148.5 57 Ctc/Ttc 2/24 P4 A L/F protein_coding CCDS12799.1 169/6486 CTGGAGGCCTC PANTHER:PTHR24135;PANTHER:PTHR24135:SF3 ENSP00000293441 2/24 COSV53260380 ENST00000293441 Transcript 1.0 ENSG00000161681 HGNC:15474 MODERATE NM_016148.5 missense_variant 1 benign(0.003) Unknown deleterious(0.04) 1 Q9Y566.188 SHANK1 HGNC -1 1.0 UPI000013E109 Q9Y566-1 SNV SHANK1,missense_variant,p.L57F,ENST00000293441,NM_016148.5,c.169C>T,MODERATE,,deleterious(0.04),benign(0.003),-1;SHANK1,missense_variant,p.L57F,ENST00000391814,,c.169C>T,MODERATE,YES,deleterious(0.04),benign(0.007),-1;SHANK1,missense_variant,p.L57F,ENST00000359082,,c.169C>T,MODERATE,,deleterious(0.04),benign(0.007),-1;SHANK1,upstream_gene_variant,,ENST00000483128,,,MODIFIER,,,,-1 609/9636 muse;mutect2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 38 f34ad461-9510-471b-acd0-06d324914a1d 36 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS SHANK1,missense_variant,p.L57F,ENST00000359082.3,c.169C>T,MODERATE,;SHANK1,missense_variant,p.L57F,ENST00000391814.5,c.169C>T,MODERATE,;SHANK1,missense_variant,p.L57F,ENST00000293441.6,c.169C>T,MODERATE,YES +LILRA2 11027 BI GRCh38 19 54575468 54575468 + missense_variant Missense_Mutation SNP G G A rs368237647 TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 35 31 c.868G>A p.Gly290Arg p.G290R ENST00000391738.8 NM_001130917.3 290 Ggg/Agg 5/8 P4 A G/R protein_coding YES CCDS46179.1 868/1452 CCCACGGGGGC PROSITE_profiles:PS50835;PANTHER:PTHR11738;PANTHER:PTHR11738:SF165;Gene3D:2.60.40.10;PIRSF:PIRSF001979;SMART:SM00409;SMART:SM00408;Superfamily:SSF48726 ENSP00000375618 0.0 0.0001163 5/8 rs368237647;COSV52194613 ENST00000391738 Transcript ENSG00000239998 HGNC:6603 MODERATE NM_001130917.3 0.0001163 EA missense_variant 0;1 1.0 possibly_damaging(0.486) Unknown tolerated(0.11) 0;1 Q8N149.152 LILRA2 HGNC 1 1.0 UPI00034F238E SNV LILRA2,missense_variant,p.G290R,ENST00000391738,NM_001130917.3,c.868G>A,MODERATE,YES,tolerated(0.11),possibly_damaging(0.486),1;LILRA2,missense_variant,p.G290R,ENST00000251376,NM_006866.4&NM_001290271.2,c.868G>A,MODERATE,,tolerated(0.11),benign(0.146),1;LILRA2,missense_variant,p.G290R,ENST00000251377,,c.868G>A,MODERATE,,tolerated(0.11),possibly_damaging(0.486),1;LILRA2,missense_variant,p.G290R,ENST00000439534,,c.868G>A,MODERATE,,tolerated(0.11),benign(0.078),1;LILRA2,missense_variant,p.G278R,ENST00000391737,NM_001290270.1,c.832G>A,MODERATE,,tolerated(0.11),possibly_damaging(0.486),1;LILRA2,intron_variant,,ENST00000629481,,c.315-490G>A,MODIFIER,,,,1;LILRA2,upstream_gene_variant,,ENST00000472992,,,MODIFIER,,,,1;LILRA2,downstream_gene_variant,,ENST00000495786,,,MODIFIER,,,,1 957/4482 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 2.387e-05 0.0 0.0 0.0 0.0001087 0.0 2.639e-05 0.0 3.266e-05 2.7055199097958397e-05 0.0 0.0 0.0 0.0 0.000201938993996 0.0 nfe 4.631769843399525e-05 0.0 4.631769843399525e-05 0.0 0.0 0 56 f34ad461-9510-471b-acd0-06d324914a1d 67 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS LILRA2,missense_variant,p.G278R,ENST00000391737.3,c.832G>A,MODERATE,;LILRA2,missense_variant,p.G290R,ENST00000251376.7,c.868G>A,MODERATE,;LILRA2,missense_variant,p.G290R,ENST00000391738.8,c.868G>A,MODERATE,YES;LILRA2,missense_variant,p.G290R,ENST00000251377.7,c.868G>A,MODERATE,;LILRA2,missense_variant,p.G290R,ENST00000439534.5,c.868G>A,MODERATE, +GMEB2 26205 BI GRCh38 20 63604745 63604745 + stop_gained,splice_region_variant Nonsense_Mutation SNP A A T novel TCGA-RZ-AB0B-01A TCGA-RZ-AB0B-10A Somatic 51 9 c.227T>A p.Leu76Ter p.L76* ENST00000266068.5 76 tTa/tAa 2/9 P1 T L/* protein_coding YES CCDS13528.1 227/1593 TACCTAACACG PANTHER:PTHR10417:SF2;PANTHER:PTHR10417 ENSP00000266068 2/9 ENST00000266068 Transcript ENSG00000101216 HGNC:4371 HIGH stop_gained 1.0 Unknown Q9UKD1.161 GMEB2 HGNC -1 2.0 UPI000012B8AD SNV GMEB2,stop_gained,p.L76*,ENST00000266068,,c.227T>A,HIGH,YES,,,-1;GMEB2,stop_gained,p.L76*,ENST00000370077,NM_012384.5,c.227T>A,HIGH,,,,-1;GMEB2,stop_gained,p.L25*,ENST00000370069,,c.74T>A,HIGH,,,,-1 706/4559 muse;mutect2;varscan2 2bf47a88-df0a-4102-af2e-998c3d252b9c 0 69 f34ad461-9510-471b-acd0-06d324914a1d 60 50a1a066-41ed-4897-88f2-d5f156cd3c1e SUCCESS GMEB2,stop_gained,splice_region_variant,p.L76*,ENST00000370077.2,c.227T>A,HIGH,YES;GMEB2,stop_gained,splice_region_variant,p.L76*,ENST00000266068.5,c.227T>A,HIGH,;GMEB2,stop_gained,splice_region_variant,p.L25*,ENST00000370069.5,c.74T>A,HIGH, +ZBTB7B 51043 BI GRCh38 1 155015273 155015273 + missense_variant Missense_Mutation SNP C C T rs199978828 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 33 14 c.613C>T p.Arg205Trp p.R205W ENST00000292176.2 205 Cgg/Tgg 1/2 P2 T R/W protein_coding CCDS1081.1 613/1620 AGCCCCGGAAA PANTHER:PTHR46105;PANTHER:PTHR46105:SF4;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000292176 1/2 rs199978828 ENST00000292176 Transcript ENSG00000160685 HGNC:18668 MODERATE 5.453e-05 gnomAD_EAS missense_variant probably_damaging(0.997) Unknown deleterious(0.01) O15156.177 ZBTB7B HGNC 1 1.0 UPI0000073A63 O15156-1 SNV ZBTB7B,missense_variant,p.R239W,ENST00000417934,NM_001377451.1&NM_001252406.3,c.715C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),1;ZBTB7B,missense_variant,p.R205W,ENST00000535420,NM_001377455.1&NM_001256455.2,c.613C>T,MODERATE,,deleterious(0.01),probably_damaging(0.997),1;ZBTB7B,missense_variant,p.R205W,ENST00000368426,NM_001377454.1&NM_001377452.1&NM_001377453.1,c.613C>T,MODERATE,,deleterious(0.01),probably_damaging(0.997),1;ZBTB7B,missense_variant,p.R205W,ENST00000292176,,c.613C>T,MODERATE,,deleterious(0.01),probably_damaging(0.997),1;DCST2,downstream_gene_variant,,ENST00000368424,NM_144622.3,,MODIFIER,YES,,,-1;ZBTB7B,non_coding_transcript_exon_variant,,ENST00000487542,,n.837C>T,MODIFIER,,,,1;ZBTB7B,downstream_gene_variant,,ENST00000461530,,,MODIFIER,,,,1;ZBTB7B,downstream_gene_variant,,ENST00000483226,,,MODIFIER,,,,1;DCST2,downstream_gene_variant,,ENST00000368423,,,MODIFIER,,,,-1;DCST2,downstream_gene_variant,,ENST00000467991,,,MODIFIER,,,,-1;DCST2,downstream_gene_variant,,ENST00000485982,,,MODIFIER,,,,-1 826/2129 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 8.028e-06 0.0 2.898e-05 0.0 5.453e-05 0.0 0.0 0.0 0.0 6.759129973943345e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5432100553880446e-05 0.0 0.0 0 43 db8b8741-ca17-4605-b6b4-b55cb41197ae 47 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS ZBTB7B,missense_variant,p.R205W,ENST00000292176.2,c.613C>T,MODERATE,;ZBTB7B,missense_variant,p.R205W,ENST00000535420.6,c.613C>T,MODERATE,YES;ZBTB7B,missense_variant,p.R205W,ENST00000368426.3,c.613C>T,MODERATE,;ZBTB7B,missense_variant,p.R239W,ENST00000417934.6,c.715C>T,MODERATE, +SLC26A9 115019 BI GRCh38 1 205928032 205928032 + missense_variant Missense_Mutation SNP G G A rs769381035 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 15 14 c.971C>T p.Ser324Leu p.S324L ENST00000367135.8 NM_052934.4 324 tCg/tTg 9/21 P2 A S/L protein_coding CCDS30990.1 971/2376 CAGGCGACACC COSM3689312;COSM3689313 Pfam:PF00916;PANTHER:PTHR11814;PANTHER:PTHR11814:SF17;TIGRFAM:TIGR00815 ENSP00000356103 9/21 rs769381035;COSV61602420 ENST00000367135 Transcript ENSG00000174502 HGNC:14469 MODERATE NM_052934.4 6.184e-05 gnomAD_NFE missense_variant 0;1 benign(0) Unknown tolerated(1) 0;1 Q7LBE3.140 SLC26A9 HGNC -1 1.0 UPI000014028B Q7LBE3-1 SNV SLC26A9,missense_variant,p.S324L,ENST00000367135,NM_052934.4,c.971C>T,MODERATE,,tolerated(1),benign(0),-1;SLC26A9,missense_variant,p.S324L,ENST00000367134,NM_134325.2,c.971C>T,MODERATE,YES,tolerated(1),benign(0),-1;SLC26A9,missense_variant,p.S324L,ENST00000340781,,c.971C>T,MODERATE,,tolerated(1),benign(0),-1;SLC26A9,non_coding_transcript_exon_variant,,ENST00000491127,,n.355C>T,MODIFIER,,,,-1;SLC26A9,non_coding_transcript_exon_variant,,ENST00000469392,,n.655C>T,MODIFIER,,,,-1;SLC26A9,upstream_gene_variant,,ENST00000461505,,,MODIFIER,,,,-1 1081/4791 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 3.195e-05 6.179e-05 0.0 0.0 0.0 0.0 6.184e-05 0.0 0.0 2.705189945118036e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.173599831527099e-05 0.0 6.173599831527099e-05 0.0 0.0 0 22 db8b8741-ca17-4605-b6b4-b55cb41197ae 29 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS SLC26A9,non_coding_transcript_exon_variant,,ENST00000469392.1,n.655C>T,MODIFIER,;SLC26A9,non_coding_transcript_exon_variant,,ENST00000491127.5,n.355C>T,MODIFIER,;SLC26A9,missense_variant,p.S324L,ENST00000367134.2,c.971C>T,MODERATE,;SLC26A9,missense_variant,p.S324L,ENST00000367135.8,c.971C>T,MODERATE,YES;SLC26A9,missense_variant,p.S324L,ENST00000340781.8,c.971C>T,MODERATE, +RGS12 6002 BI GRCh38 4 3417432 3417432 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 27 16 c.2652G>A p.Leu884= p.L884= ENST00000336727.8 NM_001394155.1 884 ctG/ctA 9/18 P4 A L protein_coding CCDS3366.1 2652/4344 GAGCTGGGGGA MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR45945:SF1;PANTHER:PTHR45945;Pfam:PF16613 ENSP00000338509 8/17 ENST00000336727 Transcript ENSG00000159788 HGNC:9994 LOW synonymous_variant Unknown O14924.183 RGS12 HGNC 1 1.0 UPI0000133830 O14924-1 SNV RGS12,synonymous_variant,p.L884=,ENST00000382788,NM_002926.3,c.2652G>A,LOW,,,,1;RGS12,synonymous_variant,p.L884=,ENST00000344733,NM_198229.2,c.2652G>A,LOW,YES,,,1;RGS12,synonymous_variant,p.L884=,ENST00000336727,,c.2652G>A,LOW,,,,1;RGS12,synonymous_variant,p.L236=,ENST00000338806,NM_198227.2,c.708G>A,LOW,,,,1;RGS12,downstream_gene_variant,,ENST00000643191,,,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000508158,,n.933G>A,MODIFIER,,,,1;RGS12,downstream_gene_variant,,ENST00000503041,,,MODIFIER,,,,1;RGS12,downstream_gene_variant,,ENST00000505570,,,MODIFIER,,,,1;RGS12,downstream_gene_variant,,ENST00000512990,,,MODIFIER,,,,1;RGS12,downstream_gene_variant,,ENST00000513784,,,MODIFIER,,,,1;RGS12,upstream_gene_variant,,ENST00000515521,,,MODIFIER,,,,1;RGS12,3_prime_UTR_variant,,ENST00000514268,,c.*626G>A,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000512266,,n.1736G>A,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000504194,,n.1609G>A,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000513991,,n.1107G>A,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000506998,,n.790G>A,MODIFIER,,,,1;RGS12,non_coding_transcript_exon_variant,,ENST00000506631,,n.843G>A,MODIFIER,,,,1;RGS12,upstream_gene_variant,,ENST00000510803,,,MODIFIER,,,,1 2755/4674 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 33 db8b8741-ca17-4605-b6b4-b55cb41197ae 43 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS RGS12,non_coding_transcript_exon_variant,,ENST00000513991.5,n.1107G>A,MODIFIER,;RGS12,non_coding_transcript_exon_variant,,ENST00000512266.5,n.1736G>A,MODIFIER,;RGS12,non_coding_transcript_exon_variant,,ENST00000504194.5,n.1609G>A,MODIFIER,;RGS12,non_coding_transcript_exon_variant,,ENST00000508158.5,n.933G>A,MODIFIER,;RGS12,non_coding_transcript_exon_variant,,ENST00000506998.5,n.790G>A,MODIFIER,;RGS12,synonymous_variant,p.L236=,ENST00000338806.4,c.708G>A,LOW,;RGS12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000514268.5,c.*626G>A,MODIFIER,;RGS12,synonymous_variant,p.L884=,ENST00000382788.7,c.2652G>A,LOW,;RGS12,synonymous_variant,p.L884=,ENST00000344733.9,c.2652G>A,LOW,;RGS12,non_coding_transcript_exon_variant,,ENST00000506631.5,n.843G>A,MODIFIER,;RGS12,synonymous_variant,p.L884=,ENST00000336727.8,c.2652G>A,LOW,YES +EVC 2121 BI GRCh38 4 5797122 5797122 + missense_variant Missense_Mutation SNP C C T rs867240492 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 42 6 c.1987C>T p.Arg663Trp p.R663W ENST00000264956.11 NM_153717.3 663 Cgg/Tgg 14/21 P2 T R/W protein_coding YES CCDS3383.1 1987/2979 AGATGCGGCTA COSM4125341 PANTHER:PTHR16795;PANTHER:PTHR16795:SF13 ENSP00000264956 14/21 rs867240492;COSV53830752 ENST00000264956 Transcript 1.0 ENSG00000072840 HGNC:3497 MODERATE NM_153717.3 2.893e-05 gnomAD_AMR missense_variant 0;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1 P57679.146 EVC HGNC 1 1.0 UPI000012A2A5 SNV EVC,missense_variant,p.R663W,ENST00000264956,NM_153717.3&NM_001306090.2,c.1987C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;EVC,non_coding_transcript_exon_variant,,ENST00000515113,,n.211C>T,MODIFIER,,,,1;CRMP1,intron_variant,,ENST00000506216,,n.1647+28372G>A,MODIFIER,,,,-1;EVC,non_coding_transcript_exon_variant,,ENST00000506240,,n.305C>T,MODIFIER,,,,1 2167/6427 muse;mutect2 edbf6720-467e-4928-b1cb-0e7336358d18 3.998e-06 0.0 2.893e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.351530045212712e-05 0.0 0.0 6.620759813813493e-05 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 36 db8b8741-ca17-4605-b6b4-b55cb41197ae 48 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS EVC,non_coding_transcript_exon_variant,,ENST00000515113.1,n.211C>T,MODIFIER,;EVC,non_coding_transcript_exon_variant,,ENST00000506240.1,n.305C>T,MODIFIER,;CRMP1,intron_variant,,ENST00000506216.5,n.1647+28372G>A,MODIFIER,;EVC,missense_variant,p.R663W,ENST00000264956.11,c.1987C>T,MODERATE,YES +KIF13B 23303 BI GRCh38 8 29167395 29167395 + missense_variant Missense_Mutation SNP C C T rs1812052781 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 22 29 c.1136G>A p.Arg379Gln p.R379Q ENST00000524189.6 NM_015254.4 379 cGg/cAg 11/40 P1 T R/Q protein_coding YES CCDS55217.1 1136/5481 GCTCCCGGAGT Coiled-coils_(Ncoils):Coil ENSP00000427900 11/40 ENST00000524189 Transcript ENSG00000197892 HGNC:14405 MODERATE NM_015254.4 missense_variant 1.0 possibly_damaging(0.606) Unknown deleterious(0.02) Q9NQT8.177 KIF13B HGNC -1 1.0 UPI000035B257 Q9NQT8-1 SNV KIF13B,missense_variant,p.R379Q,ENST00000524189,NM_015254.4,c.1136G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.606),-1;KIF13B,missense_variant,p.R379Q,ENST00000521515,,c.1136G>A,MODERATE,,deleterious(0.03),benign(0.062),-1;KIF13B,3_prime_UTR_variant,,ENST00000522355,,c.*783G>A,MODIFIER,,,,-1;KIF13B,3_prime_UTR_variant,,ENST00000523968,,c.*1074G>A,MODIFIER,,,,-1 1172/8743 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 6.759500138286967e-06 2.4315499103977345e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 27 db8b8741-ca17-4605-b6b4-b55cb41197ae 51 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS KIF13B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000523968.1,c.*1074G>A,MODIFIER,;KIF13B,missense_variant,p.R379Q,ENST00000521515.1,c.1136G>A,MODERATE,;KIF13B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000522355.5,c.*783G>A,MODIFIER,;KIF13B,missense_variant,p.R379Q,ENST00000524189.6,c.1136G>A,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 32 37 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 66 db8b8741-ca17-4605-b6b4-b55cb41197ae 69 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +PMPCA 23203 BI GRCh38 9 136421879 136421879 + missense_variant Missense_Mutation SNP G G A rs1489517685 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 17 26 c.1311G>A p.Met437Ile p.M437I ENST00000371717.8 NM_015160.3 437 atG/atA 12/13 P1 A M/I protein_coding YES CCDS35180.1 1311/1578 ATGATGAACCT PANTHER:PTHR11851;PANTHER:PTHR11851:SF192;Gene3D:3.30.830.10;Superfamily:SSF63411 ENSP00000360782 12/13 rs1489517685 ENST00000371717 Transcript 1.0 ENSG00000165688 HGNC:18667 MODERATE NM_015160.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q10713.188 PMPCA HGNC 1 1.0 UPI00000703D3 Q10713-1 SNV PMPCA,missense_variant,p.M145I,ENST00000444897,,c.435G>A,MODERATE,,deleterious(0),probably_damaging(0.995),1;PMPCA,missense_variant,p.M437I,ENST00000371717,NM_015160.3,c.1311G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;PMPCA,missense_variant,p.M306I,ENST00000399219,NM_001282946.1&NM_001282944.1,c.918G>A,MODERATE,,deleterious(0),possibly_damaging(0.636),1;PMPCA,downstream_gene_variant,,ENST00000462616,,,MODIFIER,,,,1;PMPCA,downstream_gene_variant,,ENST00000612553,,,MODIFIER,,,,1;PMPCA,downstream_gene_variant,,ENST00000620895,,,MODIFIER,,,,1 1322/2086 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 36 db8b8741-ca17-4605-b6b4-b55cb41197ae 43 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706390.1,c.*805G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000399219.7,c.*775G>A,MODIFIER,;PMPCA,missense_variant,p.M437I,ENST00000371717.8,c.1311G>A,MODERATE,YES;PMPCA,non_coding_transcript_exon_variant,,ENST00000706389.1,n.3545G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706384.1,c.*831G>A,MODIFIER,;PMPCA,missense_variant,NMD_transcript_variant,p.E257K,ENST00000706379.1,c.769G>A,MODERATE,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706387.1,c.*775G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706388.1,c.*620G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706380.1,c.*620G>A,MODIFIER,;PMPCA,non_coding_transcript_exon_variant,,ENST00000706383.1,n.2195G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706386.1,c.*620G>A,MODIFIER,;PMPCA,non_coding_transcript_exon_variant,,ENST00000706381.1,n.2770G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706385.1,c.*451G>A,MODIFIER,;PMPCA,non_coding_transcript_exon_variant,,ENST00000706382.1,n.2697G>A,MODIFIER,;PMPCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000706377.1,c.*654G>A,MODIFIER,;PMPCA,non_coding_transcript_exon_variant,,ENST00000612553.5,n.1898G>A,MODIFIER,;PMPCA,non_coding_transcript_exon_variant,,ENST00000706378.1,n.1898G>A,MODIFIER,;PMPCA,missense_variant,p.M460I,ENST00000706376.1,c.1380G>A,MODERATE,;PMPCA,missense_variant,p.M437I,ENST00000444897.3,c.1311G>A,MODERATE,;PMPCA,missense_variant,NMD_transcript_variant,p.M437I,ENST00000706227.1,c.1311G>A,MODERATE,;PMPCA,missense_variant,NMD_transcript_variant,p.M437I,ENST00000706375.1,c.1311G>A,MODERATE,;PMPCA,missense_variant,NMD_transcript_variant,p.M437I,ENST00000706228.1,c.1311G>A,MODERATE, +CHAT 1103 BI GRCh38 10 49655122 49655122 + synonymous_variant Silent SNP C C T rs145370753 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 50 33 c.1662C>T p.Tyr554= p.Y554= ENST00000337653.7 NM_020549.5 554 taC/taT 12/15 P4 T Y protein_coding YES CCDS7232.1 1662/2247 ACCTACGAGAG COSM5654153;COSM5654154 PDB-ENSP_mappings:2fy2.A;PDB-ENSP_mappings:2fy3.A;PDB-ENSP_mappings:2fy4.A;PDB-ENSP_mappings:2fy5.A;PANTHER:PTHR22589;PANTHER:PTHR22589:SF14;Pfam:PF00755;Gene3D:3.30.559.40;Superfamily:SSF52777 ENSP00000337103 0.0 0.0001163 12/15 rs145370753 ENST00000337653 Transcript 1.0 ENSG00000070748 HGNC:1912 LOW NM_020549.5 0.0001163 EA synonymous_variant 1.0 Unknown P28329.189 CHAT HGNC 1 1.0 UPI000013F1B9 P28329-1 SNV CHAT,synonymous_variant,p.Y554=,ENST00000337653,NM_020549.5,c.1662C>T,LOW,YES,,,1;CHAT,synonymous_variant,p.Y472=,ENST00000395562,NM_001142933.2,c.1416C>T,LOW,,,,1;CHAT,synonymous_variant,p.Y436=,ENST00000351556,NM_020985.4&NM_001142934.2&NM_001142929.2,c.1308C>T,LOW,,,,1;CHAT,synonymous_variant,p.Y436=,ENST00000339797,NM_020984.4,c.1308C>T,LOW,,,,1;CHAT,synonymous_variant,p.Y436=,ENST00000395559,NM_020986.4,c.1308C>T,LOW,,,,1;CHAT,synonymous_variant,p.Y175=,ENST00000640822,,c.525C>T,LOW,,,,1;CHAT,3_prime_UTR_variant,,ENST00000466590,,c.*1393C>T,MODIFIER,,,,1;CHAT,3_prime_UTR_variant,,ENST00000638282,,c.*499C>T,MODIFIER,,,,1;CHAT,non_coding_transcript_exon_variant,,ENST00000638683,,n.299C>T,MODIFIER,,,,1 1815/5296 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 7.957e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 0 58 db8b8741-ca17-4605-b6b4-b55cb41197ae 83 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS CHAT,non_coding_transcript_exon_variant,,ENST00000638683.1,n.299C>T,MODIFIER,;CHAT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000638282.1,c.*499C>T,MODIFIER,;CHAT,synonymous_variant,p.Y175=,ENST00000640822.1,c.525C>T,LOW,;CHAT,synonymous_variant,p.Y554=,ENST00000337653.7,c.1662C>T,LOW,YES;CHAT,synonymous_variant,p.Y472=,ENST00000395562.2,c.1416C>T,LOW,;CHAT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000466590.6,c.*1393C>T,MODIFIER,;CHAT,synonymous_variant,p.Y436=,ENST00000395559.6,c.1308C>T,LOW,;CHAT,synonymous_variant,p.Y436=,ENST00000351556.7,c.1308C>T,LOW,;CHAT,synonymous_variant,p.Y436=,ENST00000339797.5,c.1308C>T,LOW, +OR51B6 390058 BI GRCh38 11 5351743 5351743 + missense_variant Missense_Mutation SNP T T C rs779749567 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 30 46 c.236T>C p.Val79Ala p.V79A ENST00000380219.1 NM_001004750.1 79 gTg/gCg 1/1 P1 C V/A protein_coding YES CCDS31379.1 236/939 CACAGTGCTAG Superfamily:SSF81321;Gene3D:1.20.1070.10;Pfam:PF13853;PANTHER:PTHR26450:SF22;PANTHER:PTHR26450;CDD:cd15222;PROSITE_profiles:PS50262;Transmembrane_helices:TMhelix ENSP00000369568 1/1 rs779749567 ENST00000380219 Transcript ENSG00000176239 HGNC:19600 MODERATE NM_001004750.1 8.813e-06 gnomAD_NFE missense_variant benign(0.35) Unknown deleterious(0.01) Q9H340.137 OR51B6 HGNC 1 UPI000014017D SNV OR51B6,missense_variant,p.V79A,ENST00000380219,NM_001004750.1,c.236T>C,MODERATE,YES,deleterious(0.01),benign(0.35),1;HBE1,intron_variant,,ENST00000292896,,c.-266-81587A>G,MODIFIER,YES,,,-1;HBE1,intron_variant,,ENST00000380237,,c.-309-69792A>G,MODIFIER,,,,-1;HBG2,intron_variant,,ENST00000380252,,c.-73-97229A>G,MODIFIER,,,,-1;OR51B5,intron_variant,,ENST00000415970,,n.85-4833A>G,MODIFIER,,,,-1;OR51B5,intron_variant,,ENST00000420465,,n.46-4833A>G,MODIFIER,,,,-1;OR51B5,intron_variant,,ENST00000420726,,n.46-4833A>G,MODIFIER,,,,-1;AC104389.5,intron_variant,,ENST00000380259,,c.*740-5844A>G,MODIFIER,YES,,,-1;OR51B5,intron_variant,,ENST00000418729,,c.-359-4833A>G,MODIFIER,,,,-1;AC104389.3,upstream_gene_variant,,ENST00000450768,,,MODIFIER,YES,,,1 236/939 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 3.985e-06 0.0 0.0 0.0 0.0 0.0 8.813e-06 0.0 0.0 0 70 db8b8741-ca17-4605-b6b4-b55cb41197ae 76 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS OR51B6,missense_variant,p.V79A,ENST00000380219.1,c.236T>C,MODERATE,YES;OR51B5,intron_variant,,ENST00000418729.1,c.-359-4833A>G,MODIFIER,;OR51B5,intron_variant,,ENST00000415970.6,n.85-4833A>G,MODIFIER,;OR51B5,intron_variant,,ENST00000420465.6,n.46-4833A>G,MODIFIER,;OR51B5,intron_variant,,ENST00000420726.6,n.46-4833A>G,MODIFIER,;HBE1,intron_variant,,ENST00000380237.5,c.-309-69792A>G,MODIFIER,;HBE1,intron_variant,,ENST00000292896.3,c.-266-81587A>G,MODIFIER,;ENSG00000239920,intron_variant,NMD_transcript_variant,,ENST00000380259.7,c.*740-5844A>G,MODIFIER,YES;HBG2,intron_variant,,ENST00000380252.6,c.-73-97229A>G,MODIFIER, +MTNR1B 4544 BI GRCh38 11 92969896 92969896 + synonymous_variant Silent SNP C C A rs938370725 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 8 5 c.171C>A p.Gly57= p.G57= ENST00000257068.3 NM_005959.5 57 ggC/ggA 1/2 P1 A G protein_coding YES CCDS8290.1 171/1089 GTGGGCAACCT PDB-ENSP_mappings:6me6.A;PDB-ENSP_mappings:6me6.B;PDB-ENSP_mappings:6me7.A;PDB-ENSP_mappings:6me7.B;PDB-ENSP_mappings:6me8.A;PDB-ENSP_mappings:6me8.B;PDB-ENSP_mappings:6me9.A;PDB-ENSP_mappings:6me9.B;Transmembrane_helices:TMhelix;CDD:cd15400;Gene3D:1.20.1070.10;Pfam:PF00001;SMART:SM01381;Superfamily:SSF81321;PROSITE_profiles:PS50262;PANTHER:PTHR24228:SF54;PANTHER:PTHR24228;Prints:PR00237 ENSP00000257068 1/2 rs938370725 ENST00000257068 Transcript 1.0 ENSG00000134640 HGNC:7464 LOW NM_005959.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown P49286.164 MTNR1B HGNC 1 1.0 UPI0000050408 SNV MTNR1B,missense_variant,p.Q39K,ENST00000528076,,c.115C>A,MODERATE,,,unknown(0),1;MTNR1B,synonymous_variant,p.G57=,ENST00000257068,NM_005959.5,c.171C>A,LOW,YES,,,1;MTNR1B,synonymous_variant,p.G57=,ENST00000532482,,c.171C>A,LOW,,,,1;AP003171.1,downstream_gene_variant,,ENST00000532770,,,MODIFIER,YES,,,1 246/1634 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 20 db8b8741-ca17-4605-b6b4-b55cb41197ae 13 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS MTNR1B,missense_variant,p.A38E,ENST00000528076.1,c.113C>A,MODERATE,;MTNR1B,synonymous_variant,NMD_transcript_variant,p.G57=,ENST00000532482.1,c.171C>A,LOW,;MTNR1B,synonymous_variant,p.G57=,ENST00000257068.3,c.171C>A,LOW,YES +FBN1 2200 BI GRCh38 15 48437869 48437869 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 65 37 c.6212C>T p.Ser2071Leu p.S2071L ENST00000316623.10 NM_000138.5 2071 tCa/tTa 51/66 P1 A S/L protein_coding YES CCDS32232.1 6212/8616 GTGATGAACAC Gene3D:3.90.290.10;Pfam:PF00683;PIRSF:PIRSF036312;PROSITE_profiles:PS51364;PANTHER:PTHR24039;PANTHER:PTHR24039:SF22;Superfamily:SSF57581 ENSP00000325527 51/66 ENST00000316623 Transcript 1.0 ENSG00000166147 HGNC:3603 MODERATE NM_000138.5 missense_variant 1.0 benign(0.192) Unknown tolerated(0.18) P35555.235 FBN1 HGNC -1 1.0 UPI0000EE4EBC SNV FBN1,missense_variant,p.S2071L,ENST00000316623,NM_000138.5,c.6212C>T,MODERATE,YES,tolerated(0.18),benign(0.192),-1;FBN1,missense_variant,p.S507L,ENST00000559133,,c.1520C>T,MODERATE,,tolerated(0.15),benign(0.005),-1;FBN1,missense_variant,p.S404L,ENST00000674301,,c.1211C>T,MODERATE,,tolerated(0.21),,-1;FBN1,3_prime_UTR_variant,,ENST00000537463,,c.*1975C>T,MODIFIER,,,,-1;FBN1,non_coding_transcript_exon_variant,,ENST00000560820,,n.332C>T,MODIFIER,,,,-1;FBN1,upstream_gene_variant,,ENST00000560720,,,MODIFIER,,,,-1 6528/11609 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 127 db8b8741-ca17-4605-b6b4-b55cb41197ae 102 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS FBN1,non_coding_transcript_exon_variant,,ENST00000560820.1,n.332C>T,MODIFIER,;FBN1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000537463.6,c.*1975C>T,MODIFIER,;FBN1,missense_variant,NMD_transcript_variant,p.S2071L,ENST00000674301.2,c.6212C>T,MODERATE,;FBN1,missense_variant,NMD_transcript_variant,p.S2071L,ENST00000559133.6,c.6212C>T,MODERATE,;FBN1,missense_variant,p.S2071L,ENST00000316623.10,c.6212C>T,MODERATE,YES +FBN1 2200 BI GRCh38 15 48437870 48437870 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 66 36 c.6211T>C p.Ser2071Pro p.S2071P ENST00000316623.10 NM_000138.5 2071 Tca/Cca 51/66 P1 G S/P protein_coding YES CCDS32232.1 6211/8616 TGATGAACACT Gene3D:3.90.290.10;Pfam:PF00683;PIRSF:PIRSF036312;PROSITE_profiles:PS51364;PANTHER:PTHR24039;PANTHER:PTHR24039:SF22;Superfamily:SSF57581 ENSP00000325527 51/66 ENST00000316623 Transcript 1.0 ENSG00000166147 HGNC:3603 MODERATE NM_000138.5 missense_variant 1.0 possibly_damaging(0.575) Unknown deleterious(0.03) P35555.235 FBN1 HGNC -1 1.0 UPI0000EE4EBC SNV FBN1,missense_variant,p.S2071P,ENST00000316623,NM_000138.5,c.6211T>C,MODERATE,YES,deleterious(0.03),possibly_damaging(0.575),-1;FBN1,missense_variant,p.S507P,ENST00000559133,,c.1519T>C,MODERATE,,deleterious(0.04),possibly_damaging(0.713),-1;FBN1,missense_variant,p.S404P,ENST00000674301,,c.1210T>C,MODERATE,,deleterious(0.04),,-1;FBN1,3_prime_UTR_variant,,ENST00000537463,,c.*1974T>C,MODIFIER,,,,-1;FBN1,non_coding_transcript_exon_variant,,ENST00000560820,,n.331T>C,MODIFIER,,,,-1;FBN1,upstream_gene_variant,,ENST00000560720,,,MODIFIER,,,,-1 6527/11609 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 126 db8b8741-ca17-4605-b6b4-b55cb41197ae 103 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS FBN1,non_coding_transcript_exon_variant,,ENST00000560820.1,n.331T>C,MODIFIER,;FBN1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000537463.6,c.*1974T>C,MODIFIER,;FBN1,missense_variant,NMD_transcript_variant,p.S2071P,ENST00000674301.2,c.6211T>C,MODERATE,;FBN1,missense_variant,NMD_transcript_variant,p.S2071P,ENST00000559133.6,c.6211T>C,MODERATE,;FBN1,missense_variant,p.S2071P,ENST00000316623.10,c.6211T>C,MODERATE,YES +EFL1 79631 BI GRCh38 15 82225212 82225212 + synonymous_variant Silent SNP G G A rs771171710 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 22 16 c.1245C>T p.Ser415= p.S415= ENST00000268206.12 NM_024580.6 415 tcC/tcT 12/20 P1 A S protein_coding YES CCDS42071.1 1245/3363 ATTTTGGAAAC COSM3504536 PDB-ENSP_mappings:5anb.K;PDB-ENSP_mappings:5anc.K;PANTHER:PTHR42908:SF3;PANTHER:PTHR42908;Gene3D:2.40.30.10;Superfamily:SSF50447 ENSP00000268206 12/20 rs771171710;COSV51603821 ENST00000268206 Transcript 1.0 ENSG00000140598 HGNC:25789 LOW NM_024580.6 5.62e-05 gnomAD_EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q7Z2Z2.146 EFL1 HGNC -1 1.0 UPI00001FEA35 Q7Z2Z2-1 SNV EFL1,synonymous_variant,p.S415=,ENST00000268206,NM_001322845.1&NM_024580.6,c.1245C>T,LOW,YES,,,-1;EFL1,synonymous_variant,p.S364=,ENST00000359445,NM_001040610.2&NM_001322844.1,c.1092C>T,LOW,,,,-1;EFL1,downstream_gene_variant,,ENST00000561331,,,MODIFIER,,,,-1;EFL1,3_prime_UTR_variant,,ENST00000650113,,c.*151C>T,MODIFIER,,,,-1 1385/3643 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 4.041e-06 0.0 0.0 0.0 5.62e-05 0.0 0.0 0.0 0.0 0 38 db8b8741-ca17-4605-b6b4-b55cb41197ae 38 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS EFL1,synonymous_variant,p.S369=,ENST00000557939.2,c.1107C>T,LOW,;EFL1,non_coding_transcript_exon_variant,,ENST00000561331.2,n.626C>T,MODIFIER,;EFL1,non_coding_transcript_exon_variant,,ENST00000696337.1,n.1058C>T,MODIFIER,;EFL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000561389.2,c.*983C>T,MODIFIER,;EFL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000650113.1,c.*151C>T,MODIFIER,;EFL1,synonymous_variant,NMD_transcript_variant,p.S415=,ENST00000696336.1,c.1245C>T,LOW,;EFL1,synonymous_variant,p.S415=,ENST00000268206.12,c.1245C>T,LOW,YES;EFL1,synonymous_variant,p.S415=,ENST00000696330.1,c.1245C>T,LOW,;EFL1,synonymous_variant,p.S364=,ENST00000359445.8,c.1092C>T,LOW, +HDAC5 10014 BI GRCh38 17 44080454 44080454 + missense_variant Missense_Mutation SNP C C G rs2050337556 TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 27 26 c.2772G>C p.Trp924Cys p.W924C ENST00000586802.5 924 tgG/tgC 22/27 P4 G W/C protein_coding CCDS45696.1 2772/3369 CCTGTCCATGC Gene3D:3.40.800.20;Pfam:PF00850;PIRSF:PIRSF037911;PANTHER:PTHR45364;PANTHER:PTHR45364:SF2;Superfamily:SSF52768;CDD:cd10007 ENSP00000468004 22/27 ENST00000586802 Transcript ENSG00000108840 HGNC:14068 MODERATE missense_variant probably_damaging(0.999) Unknown deleterious(0) Q9UQL6.207 HDAC5 HGNC -1 1.0 UPI0000201355 Q9UQL6-1 SNV HDAC5,missense_variant,p.W925C,ENST00000225983,NM_001015053.2,c.2775G>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;HDAC5,missense_variant,p.W839C,ENST00000336057,,c.2517G>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;HDAC5,missense_variant,p.W924C,ENST00000586802,NM_005474.5&NM_001382393.1,c.2772G>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;G6PC3,downstream_gene_variant,,ENST00000269097,NM_138387.3&NM_001319945.2,,MODIFIER,YES,,,1;G6PC3,downstream_gene_variant,,ENST00000590253,,,MODIFIER,,,,1;G6PC3,downstream_gene_variant,,ENST00000591696,,,MODIFIER,,,,1;G6PC3,downstream_gene_variant,,ENST00000585361,,,MODIFIER,,,,1;HDAC5,upstream_gene_variant,,ENST00000586339,,,MODIFIER,,,,-1;HDAC5,downstream_gene_variant,,ENST00000588419,,,MODIFIER,,,,-1;G6PC3,downstream_gene_variant,,ENST00000588558,,,MODIFIER,,,,1;G6PC3,downstream_gene_variant,,ENST00000590639,,,MODIFIER,,,,1;HDAC5,downstream_gene_variant,,ENST00000592385,,,MODIFIER,,,,-1;HDAC5,downstream_gene_variant,,ENST00000593013,,,MODIFIER,,,,-1 2983/3662 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 46 db8b8741-ca17-4605-b6b4-b55cb41197ae 53 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS HDAC5,missense_variant,p.W924C,ENST00000586802.5,c.2772G>C,MODERATE,;HDAC5,missense_variant,p.W839C,ENST00000336057.9,c.2517G>C,MODERATE,;HDAC5,missense_variant,p.W924C,ENST00000715273.1,c.2772G>C,MODERATE,;HDAC5,missense_variant,p.W924C,ENST00000682912.1,c.2772G>C,MODERATE,YES;HDAC5,missense_variant,p.W925C,ENST00000225983.10,c.2775G>C,MODERATE,;G6PC3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696392.1,c.*459C>G,MODIFIER, +SBK2 646643 BI GRCh38 19 55529801 55529801 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 24 4 c.979C>T p.Arg327Cys p.R327C ENST00000344158.4 327 Cgc/Tgc 3/3 P1 A R/C protein_coding CCDS42631.1 979/1047 GGGGCGCCCCA PROSITE_profiles:PS50011;PANTHER:PTHR24359;PANTHER:PTHR24359:SF0;Gene3D:1.10.510.10;SMART:SM00220 ENSP00000345044 3/3 ENST00000344158 Transcript ENSG00000187550 HGNC:34416 MODERATE missense_variant benign(0.01) Unknown tolerated(0.22) P0C263.103 SBK2 HGNC -1 2.0 UPI00015DFA43 SNV SBK2,missense_variant,p.R327C,ENST00000413299,NM_001370096.2,c.979C>T,MODERATE,YES,tolerated(0.22),benign(0.01),-1;SBK2,missense_variant,p.R327C,ENST00000344158,,c.979C>T,MODERATE,,tolerated(0.22),benign(0.01),-1 988/1056 muse;mutect2 edbf6720-467e-4928-b1cb-0e7336358d18 0 16 db8b8741-ca17-4605-b6b4-b55cb41197ae 28 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS SBK2,missense_variant,p.R327C,ENST00000344158.4,c.979C>T,MODERATE,;SBK2,missense_variant,p.R327C,ENST00000413299.6,c.979C>T,MODERATE,YES +DSTN 11034 BI GRCh38 20 17600822 17600826 + frameshift_variant Frame_Shift_Del DEL AAGAA AAGAA - novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 52 18 c.94_98del p.Arg32GlufsTer33 p.R32Efs*33 ENST00000246069.12 NM_006870.4 30 AAGAAa/a 2/4 P1 - KK/X protein_coding YES CCDS13127.1 88-92/498 GAAATCAAGAAAAGAA Gene3D:3.40.20.10;Pfam:PF00241;Prints:PR00006;PROSITE_profiles:PS51263;PANTHER:PTHR11913;PANTHER:PTHR11913:SF18;SMART:SM00102;Superfamily:SSF55753;CDD:cd11286 ENSP00000246069 2/4 ENST00000246069 Transcript ENSG00000125868 HGNC:15750 6.0 HIGH NM_006870.4 frameshift_variant 1.0 Unknown P60981.159 DSTN HGNC 1 V9HWA6.46 1.0 UPI00001291DE P60981-1 deletion DSTN,frameshift_variant,p.R32Efs*33,ENST00000246069,NM_006870.4,c.94_98del,HIGH,YES,,,1;DSTN,frameshift_variant,p.R15Efs*33,ENST00000474024,NM_001011546.2,c.43_47del,HIGH,,,,1;DSTN,frameshift_variant,p.R32Efs*33,ENST00000449141,,c.94_98del,HIGH,,,,1;AL132765.1,upstream_gene_variant,,ENST00000434165,,,MODIFIER,YES,,,-1 222-226/3405 pindel;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 32 db8b8741-ca17-4605-b6b4-b55cb41197ae 71 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS DSTN,frameshift_variant,NMD_transcript_variant,p.R32Efs*33,ENST00000449141.2,c.94_98del,HIGH,;DSTN,frameshift_variant,p.R15Efs*33,ENST00000474024.5,c.43_47del,HIGH,;DSTN,frameshift_variant,p.R32Efs*33,ENST00000246069.12,c.94_98del,HIGH,YES +TBC1D10A 83874 BI GRCh38 22 30294072 30294072 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 34 32 c.744G>A p.Leu248= p.L248= ENST00000215790.12 NM_031937.3 248 ctG/ctA 7/9 P1 T L protein_coding CCDS13874.1 744/1527 TGCAACAGCGA PROSITE_profiles:PS50086;PANTHER:PTHR22957;PANTHER:PTHR22957:SF215;Pfam:PF00566;Gene3D:1.10.472.80;SMART:SM00164;Superfamily:SSF47923;Superfamily:SSF47923 ENSP00000215790 7/9 ENST00000215790 Transcript ENSG00000099992 HGNC:23609 LOW NM_031937.3 synonymous_variant Unknown Q9BXI6.157 TBC1D10A HGNC -1 1.0 UPI0000001BE4 Q9BXI6-1 SNV TBC1D10A,synonymous_variant,p.L248=,ENST00000215790,NM_031937.3,c.744G>A,LOW,,,,-1;TBC1D10A,synonymous_variant,p.L255=,ENST00000403477,NM_001204240.2,c.765G>A,LOW,YES,,,-1;TBC1D10A,synonymous_variant,p.L160=,ENST00000403362,,c.480G>A,LOW,,,,-1;AC004997.1,synonymous_variant,p.L122=,ENST00000434291,,c.366G>A,LOW,YES,,,-1;TBC1D10A,downstream_gene_variant,,ENST00000393906,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000404953,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000407689,NM_001037666.3,,MODIFIER,YES,,,-1;CASTOR1,upstream_gene_variant,,ENST00000498572,,,MODIFIER,,,,-1;TBC1D10A,synonymous_variant,p.L181=,ENST00000433426,,c.543G>A,LOW,,,,-1;AC004997.1,synonymous_variant,p.L109=,ENST00000330168,,c.327G>A,LOW,,,,-1;AC004997.1,synonymous_variant,p.L122=,ENST00000447976,,c.366G>A,LOW,,,,-1;AC004997.1,synonymous_variant,p.L120=,ENST00000434987,,c.360G>A,LOW,,,,-1;AC004997.1,synonymous_variant,p.L122=,ENST00000418047,,c.366G>A,LOW,,,,-1;TBC1D10A,3_prime_UTR_variant,,ENST00000437122,,c.*356G>A,MODIFIER,,,,-1;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000462073,,n.4280G>A,MODIFIER,,,,-1;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000467596,,n.1964G>A,MODIFIER,,,,-1;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000466666,,n.93G>A,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000415484,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000421236,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000425691,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000440704,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000440839,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000463795,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000471480,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000492159,,,MODIFIER,,,,-1;CASTOR1,upstream_gene_variant,,ENST00000497605,,,MODIFIER,,,,-1 804/1972 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 69 db8b8741-ca17-4605-b6b4-b55cb41197ae 66 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS TBC1D10A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000437122.1,c.*356G>A,MODIFIER,;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000466666.5,n.93G>A,MODIFIER,;TBC1D10A,synonymous_variant,NMD_transcript_variant,p.L181=,ENST00000433426.5,c.543G>A,LOW,;TBC1D10A,synonymous_variant,p.L160=,ENST00000403362.5,c.480G>A,LOW,;TBC1D10A,synonymous_variant,p.L255=,ENST00000403477.7,c.765G>A,LOW,;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000462073.5,n.4280G>A,MODIFIER,;TBC1D10A,non_coding_transcript_exon_variant,,ENST00000467596.5,n.1964G>A,MODIFIER,;TBC1D10A,synonymous_variant,p.L248=,ENST00000215790.12,c.744G>A,LOW,YES;ENSG00000248751,synonymous_variant,NMD_transcript_variant,p.L122=,ENST00000418047.5,c.366G>A,LOW,;ENSG00000248751,synonymous_variant,NMD_transcript_variant,p.L122=,ENST00000447976.1,c.366G>A,LOW,;ENSG00000248751,synonymous_variant,p.L122=,ENST00000434291.5,c.366G>A,LOW,YES;ENSG00000248751,synonymous_variant,NMD_transcript_variant,p.L120=,ENST00000434987.5,c.360G>A,LOW,;ENSG00000248751,synonymous_variant,NMD_transcript_variant,p.L109=,ENST00000330168.9,c.327G>A,LOW, +ZNF157 7712 BI GRCh38 X 47412726 47412726 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 4 30 c.653T>C p.Phe218Ser p.F218S ENST00000377073.4 NM_003446.4 218 tTt/tCt 4/4 P1 C F/S protein_coding YES CCDS14278.1 653/1521 GCCCTTTGAAT Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF34;SMART:SM00355;Superfamily:SSF57667 ENSP00000366273 4/4 ENST00000377073 Transcript ENSG00000147117 HGNC:12942 MODERATE NM_003446.4 missense_variant 1.0 possibly_damaging(0.528) Unknown deleterious(0) P51786.179 ZNF157 HGNC 1 1.0 UPI00001AE9ED SNV ZNF157,missense_variant,p.F218S,ENST00000377073,NM_003446.4,c.653T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.528),1 744/2516 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 19 db8b8741-ca17-4605-b6b4-b55cb41197ae 34 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS ZNF157,missense_variant,p.F218S,ENST00000377073.4,c.653T>C,MODERATE,YES +GLA 2717 BI GRCh38 X 101398477 101398477 + missense_variant Missense_Mutation SNP T T C TCGA-V4-A9EE-01A TCGA-V4-A9EE-10A Somatic 14 82 c.892A>G p.Asn298Asp p.N298D ENST00000218516.4 NM_000169.3 298 Aat/Gat 6/7 P1 C N/D protein_coding CCDS14484.1 892/1290 GTCATTAGACA PDB-ENSP_mappings:1r46.A;PDB-ENSP_mappings:1r46.B;PDB-ENSP_mappings:1r47.A;PDB-ENSP_mappings:1r47.B;PDB-ENSP_mappings:3gxn.A;PDB-ENSP_mappings:3gxn.B;PDB-ENSP_mappings:3gxp.A;PDB-ENSP_mappings:3gxp.B;PDB-ENSP_mappings:3gxt.A;PDB-ENSP_mappings:3gxt.B;PDB-ENSP_mappings:3hg2.A;PDB-ENSP_mappings:3hg2.B;PDB-ENSP_mappings:3hg3.A;PDB-ENSP_mappings:3hg3.B;PDB-ENSP_mappings:3hg4.A;PDB-ENSP_mappings:3hg4.B;PDB-ENSP_mappings:3hg5.A;PDB-ENSP_mappings:3hg5.B;PDB-ENSP_mappings:3lx9.A;PDB-ENSP_mappings:3lx9.B;PDB-ENSP_mappings:3lxa.A;PDB-ENSP_mappings:3lxa.B;PDB-ENSP_mappings:3lxb.A;PDB-ENSP_mappings:3lxb.B;PDB-ENSP_mappings:3lxc.A;PDB-ENSP_mappings:3lxc.B;PDB-ENSP_mappings:3s5y.A;PDB-ENSP_mappings:3s5y.B;PDB-ENSP_mappings:3s5z.A;PDB-ENSP_mappings:3s5z.B;PDB-ENSP_mappings:3tv8.A;PDB-ENSP_mappings:3tv8.B;PDB-ENSP_mappings:4nxs.A;PDB-ENSP_mappings:4nxs.B;PDB-ENSP_mappings:6ibk.A;PDB-ENSP_mappings:6ibk.B;PDB-ENSP_mappings:6ibm.A;PDB-ENSP_mappings:6ibm.B;PDB-ENSP_mappings:6ibr.A;PDB-ENSP_mappings:6ibr.B;PDB-ENSP_mappings:6ibt.A;PDB-ENSP_mappings:6ibt.B;CDD:cd14792;PANTHER:PTHR11452;PANTHER:PTHR11452:SF14;Pfam:PF16499;Gene3D:3.20.20.70;Superfamily:SSF51445;Prints:PR00740 ENSP00000218516 6/7 CM960774 ENST00000218516 Transcript 1.0 ENSG00000102393 HGNC:4296 MODERATE NM_000169.3 missense_variant 1 probably_damaging(0.983) Unknown deleterious(0.03) P06280.223 GLA HGNC -1 Q53Y83.124 1.0 UPI0000033A30 SNV GLA,missense_variant,p.N339D,ENST00000649178,,c.1015A>G,MODERATE,YES,deleterious(0.02),probably_damaging(0.975),-1;GLA,missense_variant,p.N298D,ENST00000218516,NM_000169.3,c.892A>G,MODERATE,,deleterious(0.03),probably_damaging(0.983),-1;GLA,missense_variant,p.N286D,ENST00000676156,,c.856A>G,MODERATE,,deleterious(0.03),possibly_damaging(0.844),-1;GLA,missense_variant,p.N298D,ENST00000674634,,c.892A>G,MODERATE,,deleterious(0.02),possibly_damaging(0.743),-1;RPL36A-HNRNPH2,intron_variant,,ENST00000409170,NM_001199973.2,c.300+3020T>C,MODIFIER,YES,,,1;RPL36A-HNRNPH2,intron_variant,,ENST00000409338,NM_001199974.2,c.177+6655T>C,MODIFIER,,,,1;GLA,intron_variant,,ENST00000675592,,c.801+308A>G,MODIFIER,,,,-1;RPL36A,downstream_gene_variant,,ENST00000392994,,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000427805,,,MODIFIER,YES,,,1;RPL36A,downstream_gene_variant,,ENST00000471855,,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000553110,NM_021029.6,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000614077,,,MODIFIER,,,,1;GLA,3_prime_UTR_variant,,ENST00000675799,,c.*417A>G,MODIFIER,,,,-1;GLA,3_prime_UTR_variant,,ENST00000674127,,c.*395A>G,MODIFIER,,,,-1;GLA,3_prime_UTR_variant,,ENST00000493905,,c.*280A>G,MODIFIER,,,,-1;GLA,3_prime_UTR_variant,,ENST00000676372,,c.*145A>G,MODIFIER,,,,-1;GLA,3_prime_UTR_variant,,ENST00000486121,,c.*338A>G,MODIFIER,,,,-1;GLA,3_prime_UTR_variant,,ENST00000480513,,c.*200A>G,MODIFIER,,,,-1;GLA,non_coding_transcript_exon_variant,,ENST00000675968,,n.3763A>G,MODIFIER,,,,-1;GLA,non_coding_transcript_exon_variant,,ENST00000468823,,n.2044A>G,MODIFIER,,,,-1;GLA,non_coding_transcript_exon_variant,,ENST00000674142,,n.1196A>G,MODIFIER,,,,-1;GLA,non_coding_transcript_exon_variant,,ENST00000479445,,n.1506A>G,MODIFIER,,,,-1;GLA,non_coding_transcript_exon_variant,,ENST00000466414,,n.1028A>G,MODIFIER,,,,-1;RPL36A,downstream_gene_variant,,ENST00000372849,,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000465340,,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000465744,,,MODIFIER,,,,1;RPL36A,downstream_gene_variant,,ENST00000489407,,,MODIFIER,,,,1 914/1318 muse;mutect2;varscan2 edbf6720-467e-4928-b1cb-0e7336358d18 0 84 db8b8741-ca17-4605-b6b4-b55cb41197ae 96 41820e99-ff15-4257-83c8-cf614ac903ed SUCCESS GLA,missense_variant,p.N298D,ENST00000674634.2,c.892A>G,MODERATE,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000486121.7,c.*338A>G,MODIFIER,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000480513.6,c.*200A>G,MODIFIER,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675799.1,c.*417A>G,MODIFIER,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000674127.2,c.*395A>G,MODIFIER,;GLA,intron_variant,,ENST00000675592.1,c.801+308A>G,MODIFIER,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676372.1,c.*145A>G,MODIFIER,;GLA,missense_variant,p.N286D,ENST00000676156.1,c.856A>G,MODERATE,;GLA,non_coding_transcript_exon_variant,,ENST00000675968.1,n.3763A>G,MODIFIER,;GLA,missense_variant,p.N339D,ENST00000649178.1,c.1015A>G,MODERATE,;GLA,non_coding_transcript_exon_variant,,ENST00000479445.2,n.1506A>G,MODIFIER,;GLA,non_coding_transcript_exon_variant,,ENST00000466414.2,n.1028A>G,MODIFIER,;GLA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000493905.6,c.*280A>G,MODIFIER,;GLA,missense_variant,p.N298D,ENST00000218516.4,c.892A>G,MODERATE,YES;GLA,missense_variant,p.N323D,ENST00000710365.1,c.967A>G,MODERATE,;GLA,non_coding_transcript_exon_variant,,ENST00000468823.2,n.2044A>G,MODIFIER,;GLA,non_coding_transcript_exon_variant,,ENST00000674142.1,n.1196A>G,MODIFIER,;RPL36A-HNRNPH2,intron_variant,,ENST00000409170.3,c.300+3020T>C,MODIFIER,YES;RPL36A-HNRNPH2,intron_variant,,ENST00000409338.5,c.177+6655T>C,MODIFIER, +DNAJC8 22826 BI GRCh38 1 28228995 28228995 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 55 46 c.107T>C p.Val36Ala p.V36A ENST00000263697.6 NM_014280.3 36 gTt/gCt 2/9 P1 G V/A protein_coding YES CCDS41292.1 107/762 TTAGAACCGAG PANTHER:PTHR15606:SF7;PANTHER:PTHR15606;Superfamily:SSF46565 ENSP00000263697 2/9 ENST00000263697 Transcript ENSG00000126698 HGNC:15470 MODERATE NM_014280.3 missense_variant 1.0 possibly_damaging(0.493) Unknown tolerated(0.08) O75937.150 DNAJC8 HGNC -1 1.0 UPI0000072BF3 SNV DNAJC8,missense_variant,p.V36A,ENST00000263697,NM_014280.3,c.107T>C,MODERATE,YES,tolerated(0.08),possibly_damaging(0.493),-1;DNAJC8,non_coding_transcript_exon_variant,,ENST00000489277,,n.256T>C,MODIFIER,,,,-1;DNAJC8,non_coding_transcript_exon_variant,,ENST00000488868,,n.251T>C,MODIFIER,,,,-1;DNAJC8,non_coding_transcript_exon_variant,,ENST00000482674,,n.113T>C,MODIFIER,,,,-1 138/1763 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 77 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 101 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS DNAJC8,non_coding_transcript_exon_variant,,ENST00000488868.1,n.251T>C,MODIFIER,;DNAJC8,non_coding_transcript_exon_variant,,ENST00000482674.5,n.113T>C,MODIFIER,;DNAJC8,5_prime_UTR_variant,,ENST00000489277.6,c.-392T>C,MODIFIER,;DNAJC8,missense_variant,p.V36A,ENST00000263697.6,c.107T>C,MODERATE,YES +EPC2 26122 BI GRCh38 2 148771274 148771274 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 62 47 c.1607A>G p.Gln536Arg p.Q536R ENST00000258484.11 NM_015630.4 536 cAg/cGg 10/14 P1 G Q/R protein_coding YES CCDS46422.1 1607/2424 TTTACAGGACA PANTHER:PTHR14898;PANTHER:PTHR14898:SF4 ENSP00000258484 10/14 ENST00000258484 Transcript ENSG00000135999 HGNC:24543 MODERATE NM_015630.4 missense_variant 1.0 benign(0.047) Unknown tolerated(0.14) Q52LR7.117 EPC2 HGNC 1 1.0 UPI00005A7FE2 SNV EPC2,missense_variant,p.Q536R,ENST00000258484,NM_015630.4,c.1607A>G,MODERATE,YES,tolerated(0.14),benign(0.047),1 1874/3883 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 69 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 110 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS EPC2,missense_variant,p.Q536R,ENST00000258484.11,c.1607A>G,MODERATE,YES +ARPC2 10109 BI GRCh38 2 218228749 218228749 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 23 22 c.121G>A p.Val41Ile p.V41I ENST00000295685.14 NM_005731.3 41 Gtc/Atc 3/10 P1 A V/I protein_coding YES CCDS2410.1 121/903 ATGGGGTCCTC Gene3D:3.30.1460.20;PANTHER:PTHR12058;PANTHER:PTHR12058:SF0;Superfamily:SSF69645 ENSP00000295685 3/10 ENST00000295685 Transcript ENSG00000163466 HGNC:705 MODERATE missense_variant 1.0 benign(0.018) Unknown deleterious(0.02) O15144.175 ARPC2 HGNC 1 Q53R19.120 1.0 UPI0000125D3D SNV ARPC2,missense_variant,p.V41I,ENST00000295685,NM_005731.3,c.121G>A,MODERATE,YES,deleterious(0.02),benign(0.018),1;ARPC2,missense_variant,p.V41I,ENST00000315717,NM_152862.3,c.121G>A,MODERATE,,deleterious(0.02),benign(0.018),1;ARPC2,missense_variant,p.V41I,ENST00000420104,,c.121G>A,MODERATE,,tolerated(0.05),benign(0.018),1;ARPC2,non_coding_transcript_exon_variant,,ENST00000491780,,n.235G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000478612,,n.108G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000480062,,n.105G>A,MODIFIER,,,,1;ARPC2,upstream_gene_variant,,ENST00000484961,,,MODIFIER,,,,1;ARPC2,missense_variant,p.V41I,ENST00000420201,,c.121G>A,MODERATE,,tolerated(0.07),possibly_damaging(0.861),1;ARPC2,3_prime_UTR_variant,,ENST00000414983,,c.*106G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000489598,,n.237G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000465395,,n.137G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000471355,,n.48G>A,MODIFIER,,,,1;ARPC2,non_coding_transcript_exon_variant,,ENST00000472753,,n.48G>A,MODIFIER,,,,1;ARPC2,upstream_gene_variant,,ENST00000470146,,,MODIFIER,,,,1 382/1605 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 42 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 45 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS ARPC2,non_coding_transcript_exon_variant,,ENST00000472753.1,n.48G>A,MODIFIER,;ARPC2,non_coding_transcript_exon_variant,,ENST00000471355.5,n.48G>A,MODIFIER,;ARPC2,non_coding_transcript_exon_variant,,ENST00000465395.5,n.137G>A,MODIFIER,;ARPC2,missense_variant,p.V41I,ENST00000295685.14,c.121G>A,MODERATE,;ARPC2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000414983.5,c.*106G>A,MODIFIER,;ARPC2,non_coding_transcript_exon_variant,,ENST00000480062.5,n.105G>A,MODIFIER,;ARPC2,non_coding_transcript_exon_variant,,ENST00000478612.5,n.108G>A,MODIFIER,;ARPC2,missense_variant,p.V41I,ENST00000315717.10,c.121G>A,MODERATE,YES;ARPC2,missense_variant,NMD_transcript_variant,p.V41I,ENST00000420201.5,c.121G>A,MODERATE,;ARPC2,non_coding_transcript_exon_variant,,ENST00000491780.5,n.235G>A,MODIFIER,;ARPC2,non_coding_transcript_exon_variant,,ENST00000489598.5,n.237G>A,MODIFIER,;ARPC2,missense_variant,p.V41I,ENST00000420104.5,c.121G>A,MODERATE, +AMOTL2 51421 BI GRCh38 3 134357722 134357722 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 107 57 c.2323G>A p.Val775Met p.V775M ENST00000422605.6 NM_001363943.2 775 Gtg/Atg 10/10 A2 T V/M protein_coding CCDS87138.1 2323/2340 CTCCACCATGT PANTHER:PTHR14826:SF3;PANTHER:PTHR14826 ENSP00000409999 10/10 ENST00000422605 Transcript ENSG00000114019 HGNC:17812 MODERATE missense_variant probably_damaging(0.998) Unknown deleterious(0) Q9Y2J4.155 AMOTL2 HGNC -1 5.0 UPI000020A2BB Q9Y2J4-1 SNV AMOTL2,missense_variant,p.V776M,ENST00000249883,NM_016201.4,c.2326G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;AMOTL2,missense_variant,p.V833M,ENST00000514516,NM_001278683.1&NM_001363943.2,c.2497G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;AMOTL2,missense_variant,p.V775M,ENST00000422605,,c.2323G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;AMOTL2,missense_variant,p.V773M,ENST00000513145,NM_001278685.2,c.2317G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;RPL39P5,upstream_gene_variant,,ENST00000273411,,,MODIFIER,YES,,,-1;AMOTL2,non_coding_transcript_exon_variant,,ENST00000506326,,n.1699G>A,MODIFIER,,,,-1 2490/4335 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 125 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 164 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS AMOTL2,missense_variant,p.V773M,ENST00000513145.1,c.2317G>A,MODERATE,;AMOTL2,non_coding_transcript_exon_variant,,ENST00000506326.1,n.1699G>A,MODIFIER,;AMOTL2,missense_variant,p.V775M,ENST00000422605.6,c.2323G>A,MODERATE,;AMOTL2,missense_variant,p.V833M,ENST00000514516.5,c.2497G>A,MODERATE,;AMOTL2,missense_variant,p.V776M,ENST00000249883.10,c.2326G>A,MODERATE,YES +APC 324 BI GRCh38 5 112834981 112834981 + missense_variant Missense_Mutation SNP T T G TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 49 43 c.1774T>G p.Leu592Val p.L592V ENST00000257430.9 NM_001354895.2 592 Tta/Gta 15/16 P1 G L/V protein_coding YES CCDS4107.1 1774/8532 GTGCCTTATGG Gene3D:1.25.10.10;PDB-ENSP_mappings:3au3.A;PDB-ENSP_mappings:3nmw.A;PDB-ENSP_mappings:3nmw.B;PDB-ENSP_mappings:3nmx.A;PDB-ENSP_mappings:3nmx.B;PDB-ENSP_mappings:3nmx.C;PDB-ENSP_mappings:3nmz.A;PDB-ENSP_mappings:3nmz.B;PDB-ENSP_mappings:3qhe.A;PDB-ENSP_mappings:3qhe.C;PDB-ENSP_mappings:3t7u.A;PDB-ENSP_mappings:3t7u.B;PDB-ENSP_mappings:4yje.A;PDB-ENSP_mappings:4yjl.A;PDB-ENSP_mappings:4yjl.B;PDB-ENSP_mappings:4yjl.C;PDB-ENSP_mappings:4yjl.D;PDB-ENSP_mappings:4yjl.E;PDB-ENSP_mappings:4yjl.F;PDB-ENSP_mappings:4yk6.A;PDB-ENSP_mappings:5b6g.A;PDB-ENSP_mappings:5iz6.A;PDB-ENSP_mappings:5iz8.A;PDB-ENSP_mappings:5iz8.B;PDB-ENSP_mappings:5iz9.A;PDB-ENSP_mappings:5iza.A;PDB-ENSP_mappings:5z8h.A;PANTHER:PTHR12607;PANTHER:PTHR12607:SF11;SMART:SM00185;Superfamily:SSF48371 ENSP00000257430 15/16 CD130075 ENST00000257430 Transcript 1.0 ENSG00000134982 HGNC:583 MODERATE NM_000038.6 missense_variant 1 probably_damaging(0.94) Unknown deleterious(0) P25054.248 APC HGNC 1 5.0 UPI000013CF60 P25054-1 SNV APC,missense_variant,p.L592V,ENST00000257430,NM_001354895.2&NM_001354906.2&NM_001354896.2&NM_000038.6&NM_001354903.2&NM_001354899.2&NM_001354900.2&NM_001354901.2&NM_001354905.2,c.1774T>G,MODERATE,YES,deleterious(0),probably_damaging(0.94),1;APC,missense_variant,p.L592V,ENST00000508376,NM_001127510.3&NM_001354898.2&NM_001354904.2,c.1774T>G,MODERATE,,deleterious(0),probably_damaging(0.94),1;APC,missense_variant,p.L592V,ENST00000512211,,c.1774T>G,MODERATE,,deleterious(0),probably_damaging(0.94),1;APC,missense_variant,p.L574V,ENST00000507379,NM_001354897.2&NM_001354902.2&NM_001127511.3,c.1720T>G,MODERATE,,deleterious(0),probably_damaging(0.978),1;APC,missense_variant,p.L155V,ENST00000504915,,c.463T>G,MODERATE,,deleterious(0.02),probably_damaging(0.975),1;APC,missense_variant,p.L43R,ENST00000502371,,c.128T>G,MODERATE,,tolerated_low_confidence(0.09),possibly_damaging(0.887),1;APC,3_prime_UTR_variant,,ENST00000508624,,c.*1096T>G,MODIFIER,,,,1;AC008575.1,intron_variant,,ENST00000520401,,c.230+6009T>G,MODIFIER,YES,,,1 1833/10704 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 71 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 92 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS ENSG00000258864,intron_variant,NMD_transcript_variant,,ENST00000520401.1,c.230+6009T>G,MODIFIER,YES;APC,missense_variant,NMD_transcript_variant,p.L480R,ENST00000502371.3,c.1439T>G,MODERATE,;APC,missense_variant,p.L592V,ENST00000512211.7,c.1774T>G,MODERATE,;APC,missense_variant,p.L592V,ENST00000508376.6,c.1774T>G,MODERATE,;APC,missense_variant,p.L486V,ENST00000713639.1,c.1456T>G,MODERATE,;APC,missense_variant,p.L610V,ENST00000504915.3,c.1828T>G,MODERATE,;APC,intron_variant,,ENST00000713638.1,c.1744-2572T>G,MODIFIER,;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713637.1,c.*1263T>G,MODIFIER,;APC,missense_variant,p.L592V,ENST00000257430.9,c.1774T>G,MODERATE,YES;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000508624.5,c.*1096T>G,MODIFIER,;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713636.1,c.*1041T>G,MODIFIER,;APC,missense_variant,p.L574V,ENST00000507379.6,c.1720T>G,MODERATE,;APC,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000505350.2,c.*1780T>G,MODIFIER,;APC,missense_variant,p.L592V,ENST00000509732.6,c.1774T>G,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 47 57 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 72 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 104 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +PTGER2 5732 BI GRCh38 14 52314600 52314600 + missense_variant Missense_Mutation SNP T T C rs770164807 TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 24 15 c.52T>C p.Trp18Arg p.W18R ENST00000245457.6 NM_000956.4 18 Tgg/Cgg 1/2 P1 C W/R protein_coding YES CCDS9708.1 52/1077 GACAGTGGCTT Prints:PR00581;PANTHER:PTHR11866;PANTHER:PTHR11866:SF8 ENSP00000245457 1/2 rs770164807 ENST00000245457 Transcript 1.0 ENSG00000125384 HGNC:9594 MODERATE NM_000956.4 7.039e-05 gnomAD_SAS missense_variant 1.0 benign(0.047) Unknown tolerated(0.39) P43116.167 PTGER2 HGNC 1 1.0 UPI000013CBA3 SNV PTGER2,missense_variant,p.W18R,ENST00000245457,NM_000956.4,c.52T>C,MODERATE,YES,tolerated(0.39),benign(0.047),1;PTGER2,intron_variant,,ENST00000557436,,c.-80+99T>C,MODIFIER,,,,1 289/2458 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 5.799e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 7.039e-05 0 25 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 39 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS PTGER2,missense_variant,p.W18R,ENST00000245457.6,c.52T>C,MODERATE,YES;PTGER2,intron_variant,,ENST00000557436.1,c.-80+99T>C,MODIFIER, +RASL12 51285 BI GRCh38 15 65055036 65055036 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 22 16 c.664A>C p.Asn222His p.N222H ENST00000220062.9 NM_016563.4 222 Aac/Cac 5/5 P1 G N/H protein_coding YES CCDS10200.1 664/801 CGTGTTGAAGG PROSITE_profiles:PS51421;PANTHER:PTHR24070;PANTHER:PTHR24070:SF252 ENSP00000220062 5/5 ENST00000220062 Transcript ENSG00000103710 HGNC:30289 MODERATE NM_016563.4 missense_variant 1.0 benign(0.007) Unknown tolerated_low_confidence(0.23) Q9NYN1.158 RASL12 HGNC -1 A0A024R5Y3.39 1.0 UPI000006F3CC Q9NYN1-1 SNV RASL12,missense_variant,p.N222H,ENST00000220062,NM_016563.4,c.664A>C,MODERATE,YES,tolerated_low_confidence(0.23),benign(0.007),-1;RASL12,missense_variant,p.N203H,ENST00000421977,NM_001307930.2,c.607A>C,MODERATE,,tolerated(0.25),possibly_damaging(0.641),-1;RASL12,missense_variant,p.N211H,ENST00000434605,NM_001379429.1,c.631A>C,MODERATE,,tolerated_low_confidence(0.22),benign(0.005),-1;SLC51B,downstream_gene_variant,,ENST00000334287,NM_178859.4,,MODIFIER,YES,,,1 820/2519 muse;mutect2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 21 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 38 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS RASL12,missense_variant,p.N211H,ENST00000434605.2,c.631A>C,MODERATE,;RASL12,missense_variant,p.N203H,ENST00000421977.7,c.607A>C,MODERATE,;RASL12,missense_variant,p.N222H,ENST00000220062.9,c.664A>C,MODERATE,YES +SHPK 23729 BI GRCh38 17 3610699 3610699 + missense_variant Missense_Mutation SNP G G A rs762096736 TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 59 64 c.1298C>T p.Ala433Val p.A433V ENST00000225519.5 NM_013276.4 433 gCg/gTg 7/7 P1 A A/V protein_coding YES CCDS11030.1 1298/1437 ACAGCGCACTC Gene3D:3.30.420.40;PANTHER:PTHR10196;PANTHER:PTHR10196:SF67;Superfamily:SSF53067;CDD:cd07777 ENSP00000225519 7/7 rs762096736;COSV56650840 ENST00000225519 Transcript 1.0 ENSG00000197417 HGNC:1492 MODERATE NM_013276.4 5.437e-05 gnomAD_EAS missense_variant 0;1 1.0 possibly_damaging(0.456) Unknown tolerated(0.08) 0;1 Q9UHJ6.147 SHPK HGNC -1 1.0 UPI0000070BB8 SNV SHPK,missense_variant,p.A433V,ENST00000225519,NM_013276.4,c.1298C>T,MODERATE,YES,tolerated(0.08),possibly_damaging(0.456),-1;TRPV1,upstream_gene_variant,,ENST00000572705,NM_080704.4,,MODIFIER,,,,-1;AC027796.3,missense_variant,p.A433V,ENST00000572919,,c.1298C>T,MODERATE,YES,tolerated(0.08),possibly_damaging(0.456),-1 1329/3788 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 7.963e-06 0.0 0.0 0.0 5.437e-05 0.0 8.809e-06 0.0 0.0 6.762330031051533e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433099179062992e-05 0.0 0.0 0 105 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 123 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS SHPK,missense_variant,p.A433V,ENST00000225519.5,c.1298C>T,MODERATE,YES;ENSG00000262304,missense_variant,NMD_transcript_variant,p.A433V,ENST00000572919.1,c.1298C>T,MODERATE,YES +ELMO2 63916 BI GRCh38 20 46386230 46386230 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 59 23 c.571C>G p.Gln191Glu p.Q191E ENST00000290246.11 NM_133171.5 191 Cag/Gag 9/22 P4 C Q/E protein_coding YES CCDS13398.1 571/2163 CCTCTGAAGGA PDB-ENSP_mappings:6idx.A;PDB-ENSP_mappings:6ie1.A;PANTHER:PTHR12771;PANTHER:PTHR12771:SF8;Pfam:PF11841;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000290246 9/22 ENST00000290246 Transcript 1.0 ENSG00000062598 HGNC:17233 MODERATE NM_133171.5 missense_variant 1.0 benign(0.241) Unknown tolerated(0.12) Q96JJ3.169 ELMO2 HGNC -1 1.0 UPI000013F6C4 Q96JJ3-1 SNV ELMO2,missense_variant,p.Q103E,ENST00000372176,NM_001318253.2,c.307C>G,MODERATE,,tolerated(0.12),benign(0.241),-1;ELMO2,missense_variant,p.Q191E,ENST00000290246,NM_133171.5,c.571C>G,MODERATE,YES,tolerated(0.12),benign(0.241),-1;ELMO2,missense_variant,p.Q191E,ENST00000396391,NM_182764.2,c.571C>G,MODERATE,,tolerated(0.12),benign(0.241),-1;ELMO2,missense_variant,p.Q189E,ENST00000352077,,c.565C>G,MODERATE,,tolerated(0.12),benign(0.326),-1;ELMO2,missense_variant,p.Q191E,ENST00000450812,,c.571C>G,MODERATE,,tolerated(0.05),benign(0.241),-1;ELMO2,upstream_gene_variant,,ENST00000425546,,,MODIFIER,,,,-1;ELMO2,non_coding_transcript_exon_variant,,ENST00000488853,,n.648C>G,MODIFIER,,,,-1;ELMO2,non_coding_transcript_exon_variant,,ENST00000469801,,n.689C>G,MODIFIER,,,,-1;ELMO2,non_coding_transcript_exon_variant,,ENST00000497412,,n.671C>G,MODIFIER,,,,-1;ELMO2,non_coding_transcript_exon_variant,,ENST00000460474,,n.616C>G,MODIFIER,,,,-1;ELMO2,upstream_gene_variant,,ENST00000462491,,,MODIFIER,,,,-1;ELMO2,downstream_gene_variant,,ENST00000462593,,,MODIFIER,,,,-1;ELMO2,upstream_gene_variant,,ENST00000480042,,,MODIFIER,,,,-1;ELMO2,downstream_gene_variant,,ENST00000487583,,,MODIFIER,,,,-1;AL133227.1,intron_variant,,ENST00000612368,,n.366-1470G>C,MODIFIER,,,,1;AL133227.1,intron_variant,,ENST00000651935,,n.152-4518G>C,MODIFIER,YES,,,1 764/3666 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 81 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 83 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS ELMO2,non_coding_transcript_exon_variant,,ENST00000497412.5,n.671C>G,MODIFIER,;ELMO2,non_coding_transcript_exon_variant,,ENST00000460474.5,n.616C>G,MODIFIER,;ELMO2,non_coding_transcript_exon_variant,,ENST00000469801.5,n.689C>G,MODIFIER,;ELMO2,missense_variant,p.Q191E,ENST00000450812.5,c.571C>G,MODERATE,;ELMO2,non_coding_transcript_exon_variant,,ENST00000488853.5,n.648C>G,MODIFIER,;ELMO2,missense_variant,p.Q189E,ENST00000352077.6,c.565C>G,MODERATE,;ELMO2,missense_variant,p.Q191E,ENST00000396391.5,c.571C>G,MODERATE,;ELMO2,missense_variant,p.Q103E,ENST00000372176.5,c.307C>G,MODERATE,;ELMO2,missense_variant,p.Q191E,ENST00000290246.11,c.571C>G,MODERATE,YES;ENSG00000273828,intron_variant,,ENST00000651935.1,n.152-4518G>C,MODIFIER,YES;ENSG00000273828,intron_variant,,ENST00000612368.1,n.366-1470G>C,MODIFIER, +EIF1AX 1964 BI GRCh38 X 20138617 20138617 + missense_variant Missense_Mutation SNP C C T TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 63 46 c.22G>A p.Gly8Arg p.G8R ENST00000379607.10 NM_001412.4 8 Gga/Aga 2/7 P1 T G/R protein_coding YES CCDS14196.1 22/435 ACCTCCTTTAC COSM3372215 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309305;COSV63309328 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1;1 1.0 probably_damaging(0.991) Unknown deleterious(0.03) 1;1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G8R,ENST00000379607,NM_001412.4,c.22G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.991),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2776G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 220/4414 muse;mutect2;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 121 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 110 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2776G>A,MODIFIER,;EIF1AX,missense_variant,p.G8R,ENST00000379607.10,c.22G>A,MODERATE,YES +HUWE1 10075 BI GRCh38 X 53562207 53562209 + inframe_deletion In_Frame_Del DEL CTC CTC - novel TCGA-V4-A9EY-01A TCGA-V4-A9EY-10A Somatic 42 14 c.7240_7242del p.Glu2414_His2415delinsAsp p.E2414_H2415delinsD ENST00000262854.11 NM_031407.7 2414 GAG/- 54/84 P2 - E/- protein_coding CCDS35301.1 7240-7242/13125 AGTGTGCTCCTCCT PANTHER:PTHR11254;PANTHER:PTHR11254:SF291;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000262854 54/84 ENST00000262854 Transcript 1.0 ENSG00000086758 HGNC:30892 MODERATE NM_031407.7 inframe_deletion Unknown Q7Z6Z7.186 HUWE1 HGNC -1 A0A024R9W5.52 1.0 UPI00004A0DAC Q7Z6Z7-1 deletion HUWE1,inframe_deletion,p.E2414del,ENST00000342160,,c.7240_7242del,MODERATE,YES,,,-1;HUWE1,inframe_deletion,p.E2414del,ENST00000262854,NM_031407.7,c.7240_7242del,MODERATE,,,,-1;HUWE1,inframe_deletion,p.E2405del,ENST00000612484,,c.7213_7215del,MODERATE,,,,-1;MIRLET7F2,upstream_gene_variant,,ENST00000385277,,,MODIFIER,YES,,,-1 7633-7635/14731 pindel;varscan2 15d19ccc-52b8-41f6-b1c1-2cc55691aed5 0 28 c1d90f48-4bfe-41a1-b60f-983cb405dbbd 56 b82add51-8d4a-4b98-9732-3bd8564921bc SUCCESS HUWE1,inframe_deletion,p.E2413_H2414delinsD,ENST00000704099.1,c.7237_7239del,MODERATE,;HUWE1,inframe_deletion,p.E2414_H2415delinsD,ENST00000342160.7,c.7240_7242del,MODERATE,;HUWE1,inframe_deletion,p.E2405_H2406delinsD,ENST00000612484.4,c.7213_7215del,MODERATE,;HUWE1,inframe_deletion,p.E2414_H2415delinsD,ENST00000262854.11,c.7240_7242del,MODERATE,YES +IL1R1 3554 BI GRCh38 2 102176594 102176594 + missense_variant Missense_Mutation SNP G G C rs753616565 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 13 5 c.1545G>C p.Trp515Cys p.W515C ENST00000410023.6 NM_001320978.2 515 tgG/tgC 12/12 P1 C W/C protein_coding YES CCDS2055.1 1545/1710 CGCTGGTCAGG Gene3D:3.40.50.10140;Pfam:PF01582;Prints:PR01537;PROSITE_profiles:PS50104;PANTHER:PTHR11890;PANTHER:PTHR11890:SF26;SMART:SM00255;Superfamily:SSF52200 ENSP00000386380 12/12 rs753616565 ENST00000410023 Transcript ENSG00000115594 HGNC:5993 MODERATE NM_000877.4 0.0003759 gnomAD_AMR missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) P14778.222 IL1R1 HGNC 1 1.0 UPI0000034759 SNV IL1R1,missense_variant,p.W515C,ENST00000410023,NM_001320978.2&NM_001320980.2&NM_001320981.2&NM_001320982.2&NM_000877.4,c.1545G>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;IL1R1,missense_variant,p.W484C,ENST00000409929,NM_001288706.2,c.1452G>C,MODERATE,,deleterious(0),probably_damaging(1),1;IL1R1,3_prime_UTR_variant,,ENST00000424272,,c.*908G>C,MODIFIER,,,,1;IL1R1,intron_variant,,ENST00000409589,,c.487-608G>C,MODIFIER,,,,1;IL1R1,downstream_gene_variant,,ENST00000409288,,,MODIFIER,,,,1;IL1R1,downstream_gene_variant,,ENST00000409329,,,MODIFIER,,,,1;IL1R1,downstream_gene_variant,,ENST00000428279,NM_001320985.1&NM_001320984.1&NM_001320983.1,,MODIFIER,,,,1;IL1R1,3_prime_UTR_variant,,ENST00000413623,,c.*995G>C,MODIFIER,,,,1;IL1R1,downstream_gene_variant,,ENST00000422532,,,MODIFIER,,,,1;IL1R1-AS1,intron_variant,,ENST00000428188,,n.305+3318C>G,MODIFIER,YES,,,-1 1903/5183 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 5.174e-05 0.0 0.0003759 0.0 0.0 0.0 0.0 0.0 0.0 1.3519699677999595e-05 0.0 0.0 0.0001325030025327 0.0 0.0 0.0 amr 0.0001325030025327 0.0 0.0 0.0 0.0 0 30 38d91c00-8484-4134-a465-9621fc2d1c7c 18 933ef160-741f-490d-ad13-507272477d96 SUCCESS IL1R1-AS1,intron_variant,,ENST00000428188.1,n.305+3318C>G,MODIFIER,YES;IL1R1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000413623.5,c.*995G>C,MODIFIER,;IL1R1,missense_variant,p.W515C,ENST00000410023.6,c.1545G>C,MODERATE,YES;IL1R1,intron_variant,,ENST00000409589.5,c.487-608G>C,MODIFIER,;IL1R1,missense_variant,p.W484C,ENST00000409929.5,c.1452G>C,MODERATE,;IL1R1,3_prime_UTR_variant,,ENST00000424272.5,c.*908G>C,MODIFIER, +ATP13A5 344905 BI GRCh38 3 193354174 193354174 + missense_variant Missense_Mutation SNP C C T rs747489400 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 7 48 c.559G>A p.Ala187Thr p.A187T ENST00000342358.9 NM_198505.4 187 Gcc/Acc 6/30 P1 T A/T protein_coding YES CCDS33914.1 559/3657 AATGGCGTTGG Pfam:PF00690;PANTHER:PTHR45630;PANTHER:PTHR45630:SF4;Superfamily:SSF81665;TIGRFAM:TIGR01657;CDD:cd07542 ENSP00000341942 6/30 rs747489400;COSV100665007 ENST00000342358 Transcript ENSG00000187527 HGNC:31789 MODERATE NM_198505.4 1.767e-05 gnomAD_NFE missense_variant 0;1 1.0 benign(0.012) Unknown tolerated(0.77) 0;1 Q4VNC0.121 ATP13A5 HGNC -1 1.0 UPI000050EC1D SNV ATP13A5,missense_variant,p.A187T,ENST00000342358,NM_198505.4,c.559G>A,MODERATE,YES,tolerated(0.77),benign(0.012),-1 587/3938 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 8.006e-06 0.0 0.0 0.0 0.0 0.0 1.767e-05 0.0 0.0 5.410599987953901e-05 2.4326200218638405e-05 0.0 0.0 0.0 0.0 0.0 nfe 0.0001080380025086 0.0 0.0001080380025086 0.0 0.0 0 73 38d91c00-8484-4134-a465-9621fc2d1c7c 55 933ef160-741f-490d-ad13-507272477d96 SUCCESS ATP13A5,missense_variant,p.A187T,ENST00000342358.9,c.559G>A,MODERATE,YES +PRDM9 56979 BI GRCh38 5 23527360 23527360 + missense_variant Missense_Mutation SNP C C T TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 36 57 c.2272C>T p.Arg758Cys p.R758C ENST00000296682.4 NM_020227.4 758 Cgc/Tgc 11/11 P1 T R/C protein_coding YES CCDS43307.1 2272/2685 GCTTTCGCGAT COSM3429363 Gene3D:3.30.160.60;PDB-ENSP_mappings:5egb.A;PDB-ENSP_mappings:5eh2.E;PDB-ENSP_mappings:5eh2.F;PDB-ENSP_mappings:5ei9.E;PDB-ENSP_mappings:5ei9.F;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR16515;PANTHER:PTHR16515:SF10;SMART:SM00355;Superfamily:SSF57667 ENSP00000296682 11/11 COSV57002975 ENST00000296682 Transcript ENSG00000164256 HGNC:13994 MODERATE NM_020227.4 missense_variant 1 1.0 benign(0.139) Unknown deleterious(0.05) 1 Q9NQV7.166 PRDM9 HGNC 1 1.0 UPI00006C9E90 SNV PRDM9,missense_variant,p.R758C,ENST00000296682,NM_001310214.2&NM_001376900.1&NM_020227.4,c.2272C>T,MODERATE,YES,deleterious(0.05),benign(0.139),1;PRDM9,downstream_gene_variant,,ENST00000635252,,,MODIFIER,,,,1 2460/3193 muse;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 110 38d91c00-8484-4134-a465-9621fc2d1c7c 95 933ef160-741f-490d-ad13-507272477d96 SUCCESS PRDM9,missense_variant,p.R758C,ENST00000296682.4,c.2272C>T,MODERATE,YES;PRDM9,missense_variant,p.R758C,ENST00000502755.6,c.2272C>T,MODERATE, +TNPO1 3842 BI GRCh38 5 72888190 72888190 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 60 36 c.1416C>T p.Arg472= p.R472= ENST00000337273.10 NM_002270.4 472 cgC/cgT 13/25 T R protein_coding YES CCDS43329.1 1416/2697 AGCCGCTATGC PDB-ENSP_mappings:1qbk.B;PDB-ENSP_mappings:2h4m.A;PDB-ENSP_mappings:2h4m.B;PDB-ENSP_mappings:2ot8.A;PDB-ENSP_mappings:2ot8.B;PDB-ENSP_mappings:2qmr.A;PDB-ENSP_mappings:2qmr.B;PDB-ENSP_mappings:2qmr.C;PDB-ENSP_mappings:2qmr.D;PDB-ENSP_mappings:2z5j.A;PDB-ENSP_mappings:2z5k.A;PDB-ENSP_mappings:2z5m.A;PDB-ENSP_mappings:2z5n.A;PDB-ENSP_mappings:2z5o.A;PDB-ENSP_mappings:4fdd.A;PDB-ENSP_mappings:4fq3.A;PDB-ENSP_mappings:4jlq.A;PDB-ENSP_mappings:4oo6.A;PDB-ENSP_mappings:5j3v.A;PDB-ENSP_mappings:5j3v.B;PDB-ENSP_mappings:5tqc.A;PDB-ENSP_mappings:5yvg.A;PDB-ENSP_mappings:5yvg.B;PDB-ENSP_mappings:5yvh.A;PDB-ENSP_mappings:5yvi.A;PANTHER:PTHR10527;PANTHER:PTHR10527:SF21;Gene3D:1.25.10.10;Pfam:PF13513;Superfamily:SSF48371 ENSP00000336712 13/25 ENST00000337273 Transcript ENSG00000083312 HGNC:6401 LOW synonymous_variant 1.0 Unknown Q92973.212 TNPO1 HGNC 1 A0A024RAM0.53 1.0 UPI000020CAB6 Q92973-1 SNV TNPO1,synonymous_variant,p.R472=,ENST00000337273,NM_002270.3,c.1416C>T,LOW,YES,,,1;TNPO1,synonymous_variant,p.R464=,ENST00000506351,NM_001364292.2&NM_153188.3&NM_001364294.2&NM_001364293.2,c.1392C>T,LOW,,,,1;TNPO1,synonymous_variant,p.R422=,ENST00000523768,NM_001364295.2,c.1266C>T,LOW,,,,1;TNPO1,downstream_gene_variant,,ENST00000505082,,,MODIFIER,,,,1 1842/11183 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 87 38d91c00-8484-4134-a465-9621fc2d1c7c 96 933ef160-741f-490d-ad13-507272477d96 SUCCESS TNPO1,synonymous_variant,p.R464=,ENST00000506351.6,c.1392C>T,LOW,;TNPO1,synonymous_variant,p.R464=,ENST00000679378.1,c.1392C>T,LOW,;TNPO1,synonymous_variant,NMD_transcript_variant,p.R431=,ENST00000681711.1,c.1293C>T,LOW,;TNPO1,synonymous_variant,p.R422=,ENST00000523768.5,c.1266C>T,LOW,;TNPO1,synonymous_variant,NMD_transcript_variant,p.R472=,ENST00000680025.1,c.1416C>T,LOW,;TNPO1,synonymous_variant,p.R472=,ENST00000337273.10,c.1416C>T,LOW,YES;TNPO1,synonymous_variant,p.R472=,ENST00000680533.1,c.1416C>T,LOW, +PCDHB4 56131 BI GRCh38 5 141123526 141123526 + missense_variant Missense_Mutation SNP G G A rs782629770 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 213 34 c.1528G>A p.Gly510Ser p.G510S ENST00000194152.4 NM_018938.4 510 Ggc/Agc 1/1 P1 A G/S protein_coding YES CCDS4246.1 1528/2388 ACAACGGCCAC Gene3D:2.60.40.60;Pfam:PF00028;Prints:PR00205;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF55;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000194152 1/1 rs782629770 ENST00000194152 Transcript ENSG00000081818 HGNC:8689 MODERATE NM_018938.4 6.384e-05 gnomAD_AFR missense_variant 1.0 probably_damaging(1) Unknown deleterious_low_confidence(0) Q9Y5E5.162 PCDHB4 HGNC 1 UPI00001273DF SNV PCDHB4,missense_variant,p.G510S,ENST00000194152,NM_018938.4,c.1528G>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(1),1;PCDHB4,non_coding_transcript_exon_variant,,ENST00000623478,,n.585G>A,MODIFIER,,,,1;AC244517.2,intron_variant,,ENST00000624802,,n.365-22771C>T,MODIFIER,,,,-1;AC244517.2,intron_variant,,ENST00000625066,,n.60-22771C>T,MODIFIER,,,,-1;AC244517.2,intron_variant,,ENST00000625128,,n.208-22771C>T,MODIFIER,,,,-1;AC244517.1,downstream_gene_variant,,ENST00000606030,,,MODIFIER,YES,,,1 1709/3806 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 4.002e-06 6.384e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.757029950676952e-06 2.4304899852722883e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 282 38d91c00-8484-4134-a465-9621fc2d1c7c 247 933ef160-741f-490d-ad13-507272477d96 SUCCESS PCDHB4,non_coding_transcript_exon_variant,,ENST00000623478.1,n.585G>A,MODIFIER,;PCDHB4,missense_variant,p.G510S,ENST00000194152.4,c.1528G>A,MODERATE,YES;ENSG00000272154,intron_variant,,ENST00000624802.1,n.365-22771C>T,MODIFIER,YES;ENSG00000272154,intron_variant,,ENST00000625128.3,n.208-22771C>T,MODIFIER,;ENSG00000272154,intron_variant,,ENST00000625066.1,n.60-22771C>T,MODIFIER, +CD109 135228 BI GRCh38 6 73768188 73768188 + missense_variant Missense_Mutation SNP G G T novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 2 15 c.1631G>T p.Ser544Ile p.S544I ENST00000287097.6 NM_133493.5 544 aGt/aTt 14/33 P3 T S/I protein_coding YES CCDS4982.1 1631/4338 TATAAGTGATG Gene3D:2.60.40.1930;Pfam:PF07703;PANTHER:PTHR11412;PANTHER:PTHR11412:SF136;SMART:SM01359 ENSP00000287097 14/33 ENST00000287097 Transcript 1.0 ENSG00000156535 HGNC:21685 MODERATE NM_133493.5 missense_variant 1.0 benign(0.189) Unknown deleterious(0) Q6YHK3.136 CD109 HGNC 1 1.0 UPI000013DE92 Q6YHK3-1 SNV CD109,missense_variant,p.S544I,ENST00000437994,NM_001159587.2,c.1631G>T,MODERATE,,deleterious(0),benign(0.241),1;CD109,missense_variant,p.S467I,ENST00000422508,NM_001159588.2,c.1400G>T,MODERATE,,deleterious(0),benign(0.088),1;CD109,missense_variant,p.S544I,ENST00000287097,NM_133493.5,c.1631G>T,MODERATE,YES,deleterious(0),benign(0.189),1;CD109,non_coding_transcript_exon_variant,,ENST00000649530,,n.1603G>T,MODIFIER,,,,1 1644/9031 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 31 38d91c00-8484-4134-a465-9621fc2d1c7c 17 933ef160-741f-490d-ad13-507272477d96 SUCCESS CD109,non_coding_transcript_exon_variant,,ENST00000649530.1,n.1603G>T,MODIFIER,;CD109,missense_variant,p.S544I,ENST00000287097.6,c.1631G>T,MODERATE,YES;CD109,missense_variant,p.S467I,ENST00000422508.6,c.1400G>T,MODERATE,;CD109,missense_variant,p.S544I,ENST00000437994.6,c.1631G>T,MODERATE, +COL12A1 1303 BI GRCh38 6 75181097 75181097 + missense_variant Missense_Mutation SNP G G A rs201657576 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 7 30 c.2006C>T p.Ala669Val p.A669V ENST00000322507.13 NM_004370.6 669 gCg/gTg 11/66 0.0004 0.0008 0.0 0.001 0.0 0.0 P1 A A/V protein_coding YES CCDS43482.1 2006/9192 uncertain_significance CAGCCGCTTCC Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR24020;PANTHER:PTHR24020:SF17;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000325146 0.0005058 0.0 11/66 rs201657576;COSV59403671 ENST00000322507 Transcript 1.0 ENSG00000111799 HGNC:2188 MODERATE NM_004370.6 0.001 EAS missense_variant 1;1 1.0 benign(0.166) Unknown tolerated(0.41) 0;1 Q99715.193 COL12A1 HGNC -1 1.0 UPI000045890B Q99715-1 SNV COL12A1,missense_variant,p.A669V,ENST00000322507,NM_004370.6,c.2006C>T,MODERATE,YES,tolerated(0.41),benign(0.166),-1;COL12A1,missense_variant,p.A669V,ENST00000483888,,c.2006C>T,MODERATE,,tolerated(0.41),benign(0.086),-1;COL12A1,missense_variant,p.A669V,ENST00000416123,,c.2006C>T,MODERATE,,tolerated(0.34),benign(0.407),-1;COL12A1,5_prime_UTR_variant,,ENST00000615798,,c.-1562C>T,MODIFIER,,,,-1;COL12A1,intron_variant,,ENST00000345356,NM_080645.3,c.73+21623C>T,MODIFIER,,,,-1;COL12A1,non_coding_transcript_exon_variant,,ENST00000486533,,n.1112C>T,MODIFIER,,,,-1 2318/11725 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 6.82e-05 0.0005166 2.9e-05 9.934e-05 5.563e-05 0.0 5.308e-05 0.0 0.0 0.0001693950034677 0.0003171660064253 0.0 0.0 0.0 0.0002027580048888 0.0 afr 0.0003171660064253 0.0 0.0001698419946478 0.0 0.0 0 52 38d91c00-8484-4134-a465-9621fc2d1c7c 37 933ef160-741f-490d-ad13-507272477d96 SUCCESS COL12A1,non_coding_transcript_exon_variant,,ENST00000486533.1,n.1112C>T,MODIFIER,;COL12A1,missense_variant,p.A669V,ENST00000483888.6,c.2006C>T,MODERATE,;COL12A1,missense_variant,p.A669V,ENST00000416123.6,c.2006C>T,MODERATE,;COL12A1,intron_variant,,ENST00000345356.10,c.73+21623C>T,MODIFIER,;COL12A1,missense_variant,p.A669V,ENST00000322507.13,c.2006C>T,MODERATE,YES +FBXO10 26267 BI GRCh38 9 37518324 37518324 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 35 3 c.2315C>T p.Ala772Val p.A772V ENST00000432825.7 NM_012166.3 772 gCc/gTc 9/11 P1 A A/V protein_coding YES CCDS47966.1 2315/2871 TGTTGGCCACT Gene3D:2.160.20.10;Pfam:PF05048;PANTHER:PTHR22990;PANTHER:PTHR22990:SF15;SMART:SM00710;SMART:SM00722;Superfamily:SSF51126 ENSP00000403802 9/11 ENST00000432825 Transcript ENSG00000147912 HGNC:13589 MODERATE NM_012166.3 missense_variant 1.0 benign(0.031) Unknown tolerated(0.34) Q9UK96.159 FBXO10 HGNC -1 1.0 UPI00001C1EC6 Q9UK96-1 SNV FBXO10,missense_variant,p.A772V,ENST00000432825,NM_012166.3,c.2315C>T,MODERATE,YES,tolerated(0.34),benign(0.031),-1;AL513165.2,non_coding_transcript_exon_variant,,ENST00000544475,,n.2443C>T,MODIFIER,,,,-1;AL513165.2,non_coding_transcript_exon_variant,,ENST00000541804,,n.958C>T,MODIFIER,,,,-1;FBXO10,downstream_gene_variant,,ENST00000543968,,,MODIFIER,,,,-1;FBXO10,downstream_gene_variant,,ENST00000544208,,,MODIFIER,,,,-1;FBXO10,3_prime_UTR_variant,,ENST00000276960,,c.*522C>T,MODIFIER,,,,-1 2491/4702 muse;mutect2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 34 38d91c00-8484-4134-a465-9621fc2d1c7c 38 933ef160-741f-490d-ad13-507272477d96 SUCCESS FBXO10,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000276960.7,c.*522C>T,MODIFIER,;ENSG00000256966,non_coding_transcript_exon_variant,,ENST00000541804.1,n.958C>T,MODIFIER,;ENSG00000256966,non_coding_transcript_exon_variant,,ENST00000544475.5,n.2443C>T,MODIFIER,;FBXO10,missense_variant,p.A772V,ENST00000432825.7,c.2315C>T,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 36 41 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 69 38d91c00-8484-4134-a465-9621fc2d1c7c 77 933ef160-741f-490d-ad13-507272477d96 SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +INPP5A 3632 BI GRCh38 10 132781937 132781937 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 65 44 c.1235A>T p.Gln412Leu p.Q412L ENST00000368594.8 NM_005539.5 412 cAg/cTg 15/16 P1 T Q/L protein_coding YES CCDS7669.2 1235/1239 CGTGCAGTGAC PANTHER:PTHR12997:SF10;PANTHER:PTHR12997 ENSP00000357583 15/16 ENST00000368594 Transcript ENSG00000068383 HGNC:6076 MODERATE NM_005539.5 missense_variant 1.0 benign(0.154) Unknown deleterious_low_confidence(0) Q14642.159 INPP5A HGNC 1 1.0 UPI000012D085 SNV INPP5A,missense_variant,p.Q412L,ENST00000368594,NM_005539.5&NM_001321042.1,c.1235A>T,MODERATE,YES,deleterious_low_confidence(0),benign(0.154),1;INPP5A,intron_variant,,ENST00000445580,,c.241+40A>T,MODIFIER,,,,1;INPP5A,downstream_gene_variant,,ENST00000342652,,,MODIFIER,,,,1;NKX6-2,downstream_gene_variant,,ENST00000368592,NM_177400.3,,MODIFIER,YES,,,-1;INPP5A,downstream_gene_variant,,ENST00000368593,,,MODIFIER,,,,1;NKX6-2,downstream_gene_variant,,ENST00000441365,,,MODIFIER,,,,-1 1545/3000 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 101 38d91c00-8484-4134-a465-9621fc2d1c7c 109 933ef160-741f-490d-ad13-507272477d96 SUCCESS INPP5A,intron_variant,,ENST00000445580.1,c.241+40A>T,MODIFIER,;INPP5A,missense_variant,p.Q412L,ENST00000368594.8,c.1235A>T,MODERATE,YES +FAT3 120114 BI GRCh38 11 92887054 92887054 + missense_variant Missense_Mutation SNP G G T rs1218254092 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 12 9 c.12992G>T p.Gly4331Val p.G4331V ENST00000525166.6 NM_001367949.2 4331 gGc/gTc 25/28 P1 T G/V protein_coding YES 12992/13674 TAAAGGCAGCA MobiDB_lite:mobidb-lite;PANTHER:PTHR24026;PANTHER:PTHR24026:SF49 ENSP00000387040 24/25 rs1218254092 ENST00000409404 Transcript 1.0 ENSG00000165323 HGNC:23112 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.775) Unknown deleterious(0.02) Q8TDW7.142 FAT3 HGNC 1 5.0 UPI000050B6C7 Q8TDW7-3 SNV FAT3,missense_variant,p.G4331V,ENST00000409404,NM_001008781.3,c.12992G>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.775),1;FAT3,missense_variant,p.G4181V,ENST00000525166,NM_001367949.2,c.12542G>T,MODERATE,,deleterious(0.01),benign(0.017),1;FAT3,missense_variant,p.G666V,ENST00000533797,,c.1997G>T,MODERATE,,deleterious(0.01),possibly_damaging(0.783),1;FAT3,non_coding_transcript_exon_variant,,ENST00000489716,,n.150G>T,MODIFIER,,,,1;FAT3,non_coding_transcript_exon_variant,,ENST00000469900,,n.190G>T,MODIFIER,,,,1 13009/19030 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 9 38d91c00-8484-4134-a465-9621fc2d1c7c 21 933ef160-741f-490d-ad13-507272477d96 SUCCESS FAT3,non_coding_transcript_exon_variant,,ENST00000469900.1,n.190G>T,MODIFIER,;FAT3,non_coding_transcript_exon_variant,,ENST00000489716.1,n.150G>T,MODIFIER,;FAT3,missense_variant,p.G666V,ENST00000533797.1,c.1997G>T,MODERATE,;FAT3,missense_variant,p.G4331V,ENST00000409404.6,c.12992G>T,MODERATE,;FAT3,missense_variant,p.G4331V,ENST00000525166.6,c.12992G>T,MODERATE,YES +OR6C65 403282 BI GRCh38 12 55401361 55401361 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 29 33 c.833C>T p.Ser278Phe p.S278F ENST00000379665.3 NM_001005518.1 278 tCt/tTt 1/1 P1 T S/F protein_coding YES CCDS31821.1 833/939 TACCTCTGTTG Transmembrane_helices:TMhelix;PROSITE_profiles:PS50262;CDD:cd15912;PANTHER:PTHR26454:SF15;PANTHER:PTHR26454;Gene3D:1.20.1070.10;Pfam:PF13853;Superfamily:SSF81321;Prints:PR00237 ENSP00000368986 1/1 ENST00000379665 Transcript ENSG00000205328 HGNC:31295 MODERATE missense_variant 1.0 probably_damaging(0.958) Unknown deleterious_low_confidence(0) A6NJZ3.101 OR6C65 HGNC 1 A0A126GW71.28 UPI000044D410 SNV OR6C65,missense_variant,p.S278F,ENST00000379665,NM_001005518.1,c.833C>T,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.958),1;OR6C73P,downstream_gene_variant,,ENST00000546432,,,MODIFIER,YES,,,1 932/1076 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 73 38d91c00-8484-4134-a465-9621fc2d1c7c 63 933ef160-741f-490d-ad13-507272477d96 SUCCESS OR6C65,missense_variant,p.S278F,ENST00000379665.3,c.833C>T,MODERATE,YES +RAB2B 84932 BI GRCh38 14 21468728 21468728 + missense_variant Missense_Mutation SNP T T C rs780512676 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 33 28 c.211A>G p.Ile71Val p.I71V ENST00000397762.6 NM_032846.4 71 Atc/Gtc 4/8 P1 C I/V protein_coding YES CCDS9570.1 211/651 GGTGATAGAAC PDB-ENSP_mappings:2a5j.A;Superfamily:SSF52540;SMART:SM00175;SMART:SM00174;SMART:SM00173;SMART:SM00176;Gene3D:3.40.50.300;TIGRFAM:TIGR00231;Pfam:PF00071;PANTHER:PTHR24073;PANTHER:PTHR24073:SF869;CDD:cd01866;PROSITE_profiles:PS51419 ENSP00000380869 4/8 rs780512676 ENST00000397762 Transcript ENSG00000129472 HGNC:20246 MODERATE NM_032846.4 3.779e-05 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.664) Unknown tolerated(0.46) Q8WUD1.166 RAB2B HGNC -1 1.0 UPI000013316C Q8WUD1-1 SNV RAB2B,missense_variant,p.I71V,ENST00000397762,NM_032846.4&NM_001163380.2,c.211A>G,MODERATE,YES,tolerated(0.46),possibly_damaging(0.664),-1;RAB2B,missense_variant,p.I71V,ENST00000649801,,c.211A>G,MODERATE,,tolerated(0.47),benign(0.007),-1;RAB2B,non_coding_transcript_exon_variant,,ENST00000461909,,n.239A>G,MODIFIER,,,,-1;RAB2B,intron_variant,,ENST00000417141,,c.187-4961A>G,MODIFIER,,,,-1 298/2914 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 4.492e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.779e-05 0 34 38d91c00-8484-4134-a465-9621fc2d1c7c 61 933ef160-741f-490d-ad13-507272477d96 SUCCESS RAB2B,non_coding_transcript_exon_variant,,ENST00000461909.1,n.239A>G,MODIFIER,;RAB2B,intron_variant,NMD_transcript_variant,,ENST00000417141.5,c.187-4961A>G,MODIFIER,;RAB2B,missense_variant,p.I71V,ENST00000649801.1,c.211A>G,MODERATE,;RAB2B,missense_variant,p.I71V,ENST00000397762.6,c.211A>G,MODERATE,YES +FCSK 197258 BI GRCh38 16 70466182 70466182 + synonymous_variant Silent SNP C C T rs770830036 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 8 30 c.336C>T p.Pro112= p.P112= ENST00000288078.11 NM_145059.3 112 ccC/ccT 5/24 P1 T P protein_coding CCDS10891.2 336/3255 CTCCCCGTGGA Pfam:PF07959;PANTHER:PTHR32463 ENSP00000288078 5/24 rs770830036 ENST00000288078 Transcript 1.0 ENSG00000157353 HGNC:29500 LOW NM_145059.3 0.000165 gnomAD_OTH synonymous_variant Unknown Q8N0W3.146 FCSK HGNC 1 1.0 UPI000013DEF1 Q8N0W3-1 SNV FCSK,synonymous_variant,p.P144=,ENST00000378912,,c.432C>T,LOW,YES,,,1;FCSK,synonymous_variant,p.P112=,ENST00000288078,NM_145059.3,c.336C>T,LOW,,,,1;FCSK,synonymous_variant,p.P112=,ENST00000574784,,c.336C>T,LOW,,,,1;FCSK,synonymous_variant,p.P112=,ENST00000576453,,c.336C>T,LOW,,,,1;FCSK,synonymous_variant,p.P112=,ENST00000572784,,c.336C>T,LOW,,,,1;FCSK,intron_variant,,ENST00000571514,,c.-697-2667C>T,MODIFIER,,,,1;FCSK,downstream_gene_variant,,ENST00000573352,,,MODIFIER,,,,1;FCSK,non_coding_transcript_exon_variant,,ENST00000464499,,n.394C>T,MODIFIER,,,,1;FCSK,non_coding_transcript_exon_variant,,ENST00000571487,,n.343C>T,MODIFIER,,,,1;FCSK,non_coding_transcript_exon_variant,,ENST00000576107,,n.394C>T,MODIFIER,,,,1 394/3907 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 6.816e-05 0.0 0.0 0.0 0.0 4.638e-05 0.0001149 0.000165 6.536e-05 6.762059638276696e-05 2.4328499421244487e-05 0.0 0.0 0.0 0.0 0.0 nfe 0.0001389020035276 0.0 0.0001389020035276 0.0 0.0 0 63 38d91c00-8484-4134-a465-9621fc2d1c7c 38 933ef160-741f-490d-ad13-507272477d96 SUCCESS FCSK,synonymous_variant,p.P112=,ENST00000576453.1,c.336C>T,LOW,;FCSK,intron_variant,,ENST00000571514.5,c.-697-2667C>T,MODIFIER,;FCSK,non_coding_transcript_exon_variant,,ENST00000464499.5,n.394C>T,MODIFIER,;FCSK,synonymous_variant,p.P112=,ENST00000574784.5,c.336C>T,LOW,;FCSK,synonymous_variant,p.P144=,ENST00000378912.6,c.432C>T,LOW,;FCSK,non_coding_transcript_exon_variant,,ENST00000571487.5,n.343C>T,MODIFIER,;FCSK,synonymous_variant,p.P112=,ENST00000572784.5,c.336C>T,LOW,;FCSK,synonymous_variant,p.P112=,ENST00000288078.11,c.336C>T,LOW,YES;FCSK,non_coding_transcript_exon_variant,,ENST00000576107.5,n.394C>T,MODIFIER, +ALKBH7 84266 BI GRCh38 19 6374558 6374558 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 22 16 c.473del p.Leu158CysfsTer43 p.L158Cfs*43 ENST00000245812.8 NM_032306.4 158 Ttg/tg 3/4 P1 - L/X protein_coding YES CCDS12163.1 472/666 GAACTCTTGCTG Gene3D:2.60.120.590;PDB-ENSP_mappings:4qkb.A;PDB-ENSP_mappings:4qkb.B;PDB-ENSP_mappings:4qkb.C;PDB-ENSP_mappings:4qkd.A;PDB-ENSP_mappings:4qkd.B;PDB-ENSP_mappings:4qkd.C;PDB-ENSP_mappings:4qkf.A;PDB-ENSP_mappings:4qkf.B;PDB-ENSP_mappings:4qkf.C;Pfam:PF13532;PANTHER:PTHR21052;PANTHER:PTHR21052:SF0;Superfamily:SSF51197;Low_complexity_(Seg):seg ENSP00000245812 3/4 ENST00000245812 Transcript ENSG00000125652 HGNC:21306 1.0 HIGH NM_032306.4 frameshift_variant 1.0 Unknown Q9BT30.125 ALKBH7 HGNC 1 1.0 UPI0000039ED9 deletion ALKBH7,frameshift_variant,p.L158Cfs*43,ENST00000245812,NM_032306.4,c.473del,HIGH,YES,,,1;ALKBH7,frameshift_variant,p.L16Cfs*43,ENST00000596657,,c.47del,HIGH,,,,1;ALKBH7,frameshift_variant,p.L97Cfs*43,ENST00000599849,,c.290del,HIGH,,,,1;PSPN,downstream_gene_variant,,ENST00000245810,NM_004158.3,,MODIFIER,,,,-1;CLPP,downstream_gene_variant,,ENST00000245816,NM_006012.4,,MODIFIER,YES,,,1;PSPN,downstream_gene_variant,,ENST00000597721,,,MODIFIER,YES,,,-1 499/970 mutect2;pindel;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 0 37 38d91c00-8484-4134-a465-9621fc2d1c7c 38 933ef160-741f-490d-ad13-507272477d96 SUCCESS ALKBH7,frameshift_variant,p.L97Cfs*43,ENST00000599849.1,c.290del,HIGH,;ALKBH7,frameshift_variant,p.L16Cfs*43,ENST00000596657.1,c.47del,HIGH,;ALKBH7,frameshift_variant,p.L158Cfs*43,ENST00000245812.8,c.473del,HIGH,YES +MUC16 94025 BI GRCh38 19 8978725 8978725 + missense_variant Missense_Mutation SNP C C T rs773114784 TCGA-V4-A9E7-01A TCGA-V4-A9E7-10A Somatic 90 70 c.2414G>A p.Ser805Asn p.S805N ENST00000397910.8 NM_024690.2 805 aGt/aAt 1/84 P1 T S/N protein_coding YES CCDS54212.1 2414/43524 GGACACTCCCT MobiDB_lite:mobidb-lite ENSP00000381008 1/84 rs773114784;COSV101200642 ENST00000397910 Transcript 1.0 ENSG00000181143 HGNC:15582 MODERATE 8.853e-06 gnomAD_NFE missense_variant 0;1 1.0 benign(0.266) Unknown tolerated_low_confidence(0.05) 0;1 Q8WXI7.134 MUC16 HGNC -1 5.0 UPI000065CA24 SNV MUC16,missense_variant,p.S805N,ENST00000397910,NM_024690.2,c.2414G>A,MODERATE,YES,tolerated_low_confidence(0.05),benign(0.266),-1 2618/43816 muse;mutect2;varscan2 b5c516ba-4785-41dc-bd07-b129d47808dd 4.013e-06 0.0 0.0 0.0 0.0 0.0 8.853e-06 0.0 0.0 0 120 38d91c00-8484-4134-a465-9621fc2d1c7c 160 933ef160-741f-490d-ad13-507272477d96 SUCCESS MUC16,missense_variant,p.S805N,ENST00000397910.8,c.2414G>A,MODERATE,;MUC16,missense_variant,p.S845N,ENST00000711672.1,c.2534G>A,MODERATE,YES;MUC16,missense_variant,p.S845N,ENST00000710609.1,c.2534G>A,MODERATE,;MUC16,intron_variant,,ENST00000710610.1,c.301+6826G>A,MODIFIER, +AADACL4 343066 BI GRCh38 1 12651227 12651227 + synonymous_variant Silent SNP C C T rs770479268 TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 57 46 c.273C>T p.Asp91= p.D91= ENST00000376221.2 NM_001013630.2 91 gaC/gaT 2/4 P1 T D protein_coding YES CCDS30590.1 273/1224 ACCGACCTGCG PANTHER:PTHR23024;PANTHER:PTHR23024:SF457;PIRSF:PIRSF037251;Superfamily:SSF53474 ENSP00000365395 2/4 rs770479268;COSV100879438 ENST00000376221 Transcript ENSG00000204518 HGNC:32038 LOW 0.0001848 gnomAD_FIN synonymous_variant 0;1 1.0 Unknown 0;1 Q5VUY2.113 AADACL4 HGNC 1 5.0 UPI0000160609 SNV AADACL4,synonymous_variant,p.D91=,ENST00000376221,NM_001013630.1,c.273C>T,LOW,YES,,,1 273/1575 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 1.591e-05 0.0 0.0 0.0 0.0 0.0001848 0.0 0.0 0.0 1.3517699699150398e-05 0.0 0.0 0.0 0.0 0.0 0.0001882530050352 fin 0.0001882530050352 0.0 0.0 0.0 0.0 0 117 61513ae2-6154-46f5-b886-76e54e18599e 103 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS AADACL4,synonymous_variant,p.D91=,ENST00000376221.2,c.273C>T,LOW,YES +RPL11 6135 BI GRCh38 1 23692738 23692739 + frameshift_variant Frame_Shift_Ins INS - - AG novel TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 75 38 c.135_136dup p.Gln45SerfsTer43 p.Q45Sfs*43 ENST00000374550.8 NM_001199802.1 45 cag/cAGag 2/6 P4 AG Q/QX protein_coding CCDS85940.1 133-134/534 CAGGGCAGACC Gene3D:3.30.1440.10;Pfam:PF00281;PIRSF:PIRSF002161;PROSITE_patterns:PS00358;PANTHER:PTHR11994;PANTHER:PTHR11994:SF23;Superfamily:SSF55282 ENSP00000363676 2/6 ENST00000374550 Transcript 1.0 ENSG00000142676 HGNC:10301 3.0 HIGH frameshift_variant Unknown P62913.165 RPL11 HGNC 1 1.0 UPI0000071406 P62913-2 insertion RPL11,frameshift_variant,p.T47Rfs*42,ENST00000643754,NM_000975.5,c.138_139dup,HIGH,YES,,,1;RPL11,frameshift_variant,p.T36Rfs*42,ENST00000458455,,c.105_106dup,HIGH,,,,1;RPL11,frameshift_variant,p.T46Rfs*42,ENST00000374550,NM_001199802.1,c.135_136dup,HIGH,,,,1;RPL11,3_prime_UTR_variant,,ENST00000467075,,c.*234_*235dup,MODIFIER,,,,1;RPL11,non_coding_transcript_exon_variant,,ENST00000443624,,n.156_157dup,MODIFIER,,,,1;RPL11,non_coding_transcript_exon_variant,,ENST00000482370,,n.132_133dup,MODIFIER,,,,1 215-216/660 mutect2;pindel;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 101 61513ae2-6154-46f5-b886-76e54e18599e 113 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS RPL11,non_coding_transcript_exon_variant,,ENST00000482370.2,n.130_131insAG,MODIFIER,;RPL11,frameshift_variant,p.Q35Sfs*43,ENST00000458455.2,c.105_106dup,HIGH,;RPL11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000467075.2,c.*232_*233insAG,MODIFIER,;RPL11,non_coding_transcript_exon_variant,,ENST00000443624.6,n.154_155insAG,MODIFIER,;RPL11,frameshift_variant,p.Q46Sfs*43,ENST00000643754.2,c.138_139dup,HIGH,YES;RPL11,frameshift_variant,p.Q45Sfs*43,ENST00000374550.8,c.135_136dup,HIGH, +SEMA4A 64218 BI GRCh38 1 156176621 156176621 + missense_variant Missense_Mutation SNP C C G TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 27 15 c.1910C>G p.Ser637Cys p.S637C ENST00000355014.6 NM_001193301.2 637 tCc/tGc 15/15 P2 G S/C protein_coding CCDS1132.1 1910/2286 GATCTCCTACT PANTHER:PTHR11036;PANTHER:PTHR11036:SF15 ENSP00000347117 15/15 COSV61772484 ENST00000355014 Transcript 1.0 ENSG00000196189 HGNC:10729 MODERATE missense_variant 1 benign(0.152) Unknown deleterious(0.01) 1 Q9H3S1.176 SEMA4A HGNC 1 1.0 UPI000007217A Q9H3S1-1 SNV SEMA4A,missense_variant,p.S637C,ENST00000368282,NM_001370567.1,c.1910C>G,MODERATE,YES,deleterious(0.01),benign(0.152),1;SEMA4A,missense_variant,p.S637C,ENST00000368285,NM_001193300.2&NM_022367.4,c.1910C>G,MODERATE,,deleterious(0.01),benign(0.152),1;SEMA4A,missense_variant,p.S637C,ENST00000355014,NM_001193301.1,c.1910C>G,MODERATE,,deleterious(0.01),benign(0.152),1;SEMA4A,missense_variant,p.S599C,ENST00000368286,,c.1796C>G,MODERATE,,deleterious(0.01),benign(0.152),1;SEMA4A,missense_variant,p.S505C,ENST00000368284,NM_001370571.1&NM_001370569.1&NM_001370568.1&NM_001193302.1,c.1514C>G,MODERATE,,deleterious(0.03),benign(0.152),1;SEMA4A,non_coding_transcript_exon_variant,,ENST00000484155,,n.541C>G,MODIFIER,,,,1;SEMA4A,downstream_gene_variant,,ENST00000487358,,,MODIFIER,,,,1;SEMA4A,downstream_gene_variant,,ENST00000462892,,,MODIFIER,,,,1 2014/3137 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 40 61513ae2-6154-46f5-b886-76e54e18599e 42 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS SEMA4A,non_coding_transcript_exon_variant,,ENST00000484155.1,n.541C>G,MODIFIER,;SEMA4A,missense_variant,p.S637C,ENST00000368282.1,c.1910C>G,MODERATE,;SEMA4A,missense_variant,p.S637C,ENST00000368285.8,c.1910C>G,MODERATE,YES;SEMA4A,missense_variant,p.S505C,ENST00000368284.5,c.1514C>G,MODERATE,;SEMA4A,missense_variant,p.S637C,ENST00000355014.6,c.1910C>G,MODERATE, +PLD5 200150 BI GRCh38 1 242100706 242100706 + missense_variant Missense_Mutation SNP C C T rs747669178 TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 31 18 c.1316G>A p.Arg439His p.R439H ENST00000442594.6 439 cGc/cAc 10/11 P2 T R/H protein_coding CCDS1621.2 1316/1611 TGTTGCGATTT COSM1340695;COSM1340696;COSM4785640 Gene3D:3.30.870.10;PANTHER:PTHR10185;PANTHER:PTHR10185:SF9;SMART:SM00155;Superfamily:SSF56024;CDD:cd09149 ENSP00000414188 10/11 rs747669178;COSV59139492 ENST00000442594 Transcript ENSG00000180287 HGNC:26879 MODERATE 6.152e-05 gnomAD_AFR missense_variant 0;1 benign(0.005) Unknown tolerated(1) 0;1 Q8N7P1.140 PLD5 HGNC -1 5.0 UPI000040E1A4 Q8N7P1-1 SNV PLD5,missense_variant,p.R439H,ENST00000536534,NM_001320272.2&NM_001372062.1,c.1316G>A,MODERATE,YES,tolerated(1),benign(0.005),-1;PLD5,missense_variant,p.R439H,ENST00000442594,,c.1316G>A,MODERATE,,tolerated(1),benign(0.005),-1;PLD5,missense_variant,p.R377H,ENST00000427495,NM_001195812.2&NM_001195811.1,c.1130G>A,MODERATE,,tolerated(1),benign(0.036),-1;PLD5,3_prime_UTR_variant,,ENST00000314833,,c.*824G>A,MODIFIER,,,,-1;PLD5,3_prime_UTR_variant,,ENST00000366545,,c.*993G>A,MODIFIER,,,,-1 1543/3305 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 2.784e-05 6.152e-05 0.0 0.0 0.0 0.0 4.397e-05 0.0 3.266e-05 1.3556699741457123e-05 4.883770088781603e-05 0.0 0.0 0.0 0.0 0.0 afr 4.883770088781603e-05 0.0 0.0 0.0 0.0 0 74 61513ae2-6154-46f5-b886-76e54e18599e 49 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS PLD5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000366545.5,c.*993G>A,MODIFIER,;PLD5,missense_variant,p.R439H,ENST00000442594.6,c.1316G>A,MODERATE,;PLD5,missense_variant,p.R377H,ENST00000427495.5,c.1130G>A,MODERATE,;PLD5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000314833.10,c.*824G>A,MODIFIER,;PLD5,missense_variant,p.R439H,ENST00000536534.7,c.1316G>A,MODERATE,YES +ALPI 248 BI GRCh38 2 232458747 232458747 + synonymous_variant,splice_region_variant Silent SNP C C T rs773147145 TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 23 19 c.1299C>T p.Ser433= p.S433= ENST00000295463.4 NM_001631.5 433 agC/agT 10/11 P1 T S protein_coding YES CCDS2492.1 1299/1587 GAGAGCGGTGA Gene3D:3.40.720.10;Pfam:PF00245;PANTHER:PTHR11596;PANTHER:PTHR11596:SF69;SMART:SM00098;Superfamily:SSF53649;CDD:cd16012 ENSP00000295463 10/11 rs773147145 ENST00000295463 Transcript ENSG00000163295 HGNC:437 LOW NM_001631.5 1.768e-05 gnomAD_NFE splice_region_variant 1.0 Unknown P09923.198 ALPI HGNC 1 A0A024R4A2.38 1.0 UPI0000131FFE SNV ALPI,splice_region_variant,p.S433=,ENST00000295463,NM_001631.5,c.1299C>T,LOW,YES,,,1;ALPI,splice_region_variant,,ENST00000457560,,c.*1228C>T,LOW,,,,1 1346/3241 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 7.982e-06 0.0 0.0 0.0 0.0 0.0 1.768e-05 0.0 0.0 0 45 61513ae2-6154-46f5-b886-76e54e18599e 42 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS ALPI,synonymous_variant,splice_region_variant,p.S433=,ENST00000295463.4,c.1299C>T,LOW,YES;ALPI,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000457560.1,c.*1228C>T,MODIFIER, +BAP1 8314 BI GRCh38 3 52409577 52409577 + stop_gained Nonsense_Mutation SNP G G C TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 25 71 c.99C>G p.Tyr33Ter p.Y33* ENST00000460680.6 NM_004656.4 33 taC/taG 3/17 P1 C Y/* protein_coding YES CCDS2853.1 99/2190 AGGTCGTAGAT CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 3/17 COSV56234502 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 stop_gained 1 1.0 Unknown 1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,stop_gained,p.Y33*,ENST00000460680,NM_004656.4,c.99C>G,HIGH,YES,,,-1;BAP1,stop_gained,p.Y33*,ENST00000296288,,c.99C>G,HIGH,,,,-1;BAP1,5_prime_UTR_variant,,ENST00000470173,,c.-139C>G,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000461861,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000614886,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000615126,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000472337,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,stop_gained,p.Y33*,ENST00000490917,,c.99C>G,HIGH,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,,n.99C>G,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 229/3600 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 267 61513ae2-6154-46f5-b886-76e54e18599e 96 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS BAP1,5_prime_UTR_variant,,ENST00000470173.1,c.-139C>G,MODIFIER,;BAP1,stop_gained,NMD_transcript_variant,p.Y33*,ENST00000490917.1,c.99C>G,HIGH,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984.5,n.99C>G,MODIFIER,;BAP1,stop_gained,p.Y33*,ENST00000296288.9,c.99C>G,HIGH,;BAP1,stop_gained,p.Y33*,ENST00000460680.6,c.99C>G,HIGH,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 49 33 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 77 61513ae2-6154-46f5-b886-76e54e18599e 82 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +EPS8L2 64787 BI GRCh38 11 722155 722155 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 15 5 c.1049C>T p.Pro350Leu p.P350L ENST00000318562.13 NM_022772.4 350 cCt/cTt 12/21 P1 T P/L protein_coding CCDS31328.1 1049/2148 CGGGCCTCTGG PANTHER:PTHR12287:SF20;PANTHER:PTHR12287 ENSP00000320828 12/21 ENST00000318562 Transcript 1.0 ENSG00000177106 HGNC:21296 MODERATE NM_022772.4 missense_variant probably_damaging(0.997) Unknown deleterious(0) Q9H6S3.160 EPS8L2 HGNC 1 1.0 UPI000006226C Q9H6S3-1 SNV EPS8L2,missense_variant,p.P350L,ENST00000533256,,c.1049C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;EPS8L2,missense_variant,p.P366L,ENST00000614442,,c.1097C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;EPS8L2,missense_variant,p.P350L,ENST00000318562,NM_022772.4,c.1049C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;EPS8L2,missense_variant,p.P350L,ENST00000650127,,c.1049C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;EPS8L2,missense_variant,p.P350L,ENST00000530636,,c.1049C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;EPS8L2,missense_variant,p.P366L,ENST00000526198,,c.1097C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;EPS8L2,5_prime_UTR_variant,,ENST00000610855,,c.-351C>T,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000524763,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000531348,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000533500,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000534755,,,MODIFIER,,,,1;EPS8L2,upstream_gene_variant,,ENST00000524973,,,MODIFIER,,,,1;EPS8L2,upstream_gene_variant,,ENST00000534449,,,MODIFIER,,,,1;EPS8L2,synonymous_variant,p.A131=,ENST00000528770,,c.393C>T,LOW,,,,1;EPS8L2,3_prime_UTR_variant,,ENST00000526909,,c.*1754C>T,MODIFIER,,,,1;EPS8L2,non_coding_transcript_exon_variant,,ENST00000531393,,n.230C>T,MODIFIER,,,,1;EPS8L2,non_coding_transcript_exon_variant,,ENST00000529346,,n.1571C>T,MODIFIER,,,,1;EPS8L2,non_coding_transcript_exon_variant,,ENST00000524474,,n.713C>T,MODIFIER,,,,1;EPS8L2,non_coding_transcript_exon_variant,,ENST00000533816,,n.352C>T,MODIFIER,,,,1;EPS8L2,intron_variant,,ENST00000526651,,n.472+164C>T,MODIFIER,,,,1;EPS8L2,intron_variant,,ENST00000530452,,c.318-246C>T,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000527807,,,MODIFIER,,,,1;EPS8L2,upstream_gene_variant,,ENST00000527832,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000530118,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000531471,,,MODIFIER,,,,1;EPS8L2,downstream_gene_variant,,ENST00000532545,,,MODIFIER,,,,1;EPS8L2,upstream_gene_variant,,ENST00000534027,,,MODIFIER,,,,1;EPS8L2,upstream_gene_variant,,ENST00000534679,,,MODIFIER,,,,1;AP006621.4,intron_variant,,ENST00000527021,,n.72+4821G>A,MODIFIER,YES,,,-1 1185/3030 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 32 61513ae2-6154-46f5-b886-76e54e18599e 20 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS EPS8L2,non_coding_transcript_exon_variant,,ENST00000531393.5,n.230C>T,MODIFIER,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000533816.1,n.352C>T,MODIFIER,;EPS8L2,intron_variant,NMD_transcript_variant,,ENST00000530452.6,c.318-246C>T,MODIFIER,;EPS8L2,missense_variant,NMD_transcript_variant,p.P131L,ENST00000528770.5,c.392C>T,MODERATE,;EPS8L2,intron_variant,,ENST00000526651.5,n.472+164C>T,MODIFIER,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000524474.5,n.713C>T,MODIFIER,;EPS8L2,missense_variant,p.P366L,ENST00000526198.5,c.1097C>T,MODERATE,;ENSG00000269915,intron_variant,,ENST00000527021.2,n.72+4821G>A,MODIFIER,YES;EPS8L2,missense_variant,p.P350L,ENST00000530636.5,c.1049C>T,MODERATE,;EPS8L2,missense_variant,p.P350L,ENST00000318562.13,c.1049C>T,MODERATE,YES;EPS8L2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000526909.5,c.*1754C>T,MODIFIER,;EPS8L2,missense_variant,p.P350L,ENST00000650127.1,c.1049C>T,MODERATE,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000529346.5,n.1571C>T,MODIFIER,;EPS8L2,missense_variant,p.P366L,ENST00000614442.4,c.1097C>T,MODERATE,;EPS8L2,missense_variant,p.P350L,ENST00000533256.5,c.1049C>T,MODERATE, +C3 718 BI GRCh38 19 6684406 6684406 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 53 41 c.4154T>C p.Ile1385Thr p.I1385T ENST00000245907.11 NM_000064.4 1385 aTc/aCc 33/41 P1 G I/T protein_coding YES CCDS32883.1 4154/4992 CAAGGATCATA Gene3D:2.60.40.690;PDB-ENSP_mappings:2a73.B;PDB-ENSP_mappings:2a74.C;PDB-ENSP_mappings:2a74.F;PDB-ENSP_mappings:2i07.B;PDB-ENSP_mappings:2ice.C;PDB-ENSP_mappings:2ice.F;PDB-ENSP_mappings:2icf.B;PDB-ENSP_mappings:2qki.C;PDB-ENSP_mappings:2qki.F;PDB-ENSP_mappings:2wii.B;PDB-ENSP_mappings:2win.B;PDB-ENSP_mappings:2win.D;PDB-ENSP_mappings:2win.F;PDB-ENSP_mappings:2win.H;PDB-ENSP_mappings:2xwb.B;PDB-ENSP_mappings:2xwb.D;PDB-ENSP_mappings:2xwj.B;PDB-ENSP_mappings:2xwj.D;PDB-ENSP_mappings:2xwj.F;PDB-ENSP_mappings:2xwj.H;PDB-ENSP_mappings:3g6j.B;PDB-ENSP_mappings:3g6j.D;PDB-ENSP_mappings:3l3o.C;PDB-ENSP_mappings:3l3o.F;PDB-ENSP_mappings:3l5n.B;PDB-ENSP_mappings:3nms.C;PDB-ENSP_mappings:3ohx.C;PDB-ENSP_mappings:3ohx.F;PDB-ENSP_mappings:3t4a.C;PDB-ENSP_mappings:3t4a.F;PDB-ENSP_mappings:5fo7.B;PDB-ENSP_mappings:5fo8.B;PDB-ENSP_mappings:5fo9.B;PDB-ENSP_mappings:5fo9.E;PDB-ENSP_mappings:5foa.B;PDB-ENSP_mappings:5foa.D;PDB-ENSP_mappings:5fob.B;PDB-ENSP_mappings:5o32.B;PDB-ENSP_mappings:5o32.F;PDB-ENSP_mappings:5o35.B;PDB-ENSP_mappings:6ehg.B;PDB-ENSP_mappings:6ru5.B;PDB-ENSP_mappings:6rur.B;PDB-ENSP_mappings:6rur.H;PDB-ENSP_mappings:6ruv.B;PDB-ENSP_mappings:6ruv.H;PANTHER:PTHR11412;PANTHER:PTHR11412:SF81;Superfamily:SSF49410 ENSP00000245907 33/41 ENST00000245907 Transcript 1.0 ENSG00000125730 HGNC:1318 MODERATE NM_000064.4 missense_variant 1.0 benign(0) Unknown tolerated(0.52) P01024.244 C3 HGNC -1 V9HWA9.51 1.0 UPI000013EC9B SNV C3,missense_variant,p.I1385T,ENST00000245907,NM_000064.4,c.4154T>C,MODERATE,YES,tolerated(0.52),benign(0),-1;C3,missense_variant,p.I92T,ENST00000596548,,c.275T>C,MODERATE,,tolerated(0.45),benign(0.001),-1;C3,intron_variant,,ENST00000601008,,c.241+2340T>C,MODIFIER,,,,-1;C3,upstream_gene_variant,,ENST00000599668,,,MODIFIER,,,,-1;C3,non_coding_transcript_exon_variant,,ENST00000596179,,n.107T>C,MODIFIER,,,,-1;C3,downstream_gene_variant,,ENST00000596238,,,MODIFIER,,,,-1;C3,downstream_gene_variant,,ENST00000598805,,,MODIFIER,,,,-1;C3,upstream_gene_variant,,ENST00000599899,,,MODIFIER,,,,-1 4215/5231 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 105 61513ae2-6154-46f5-b886-76e54e18599e 95 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS C3,non_coding_transcript_exon_variant,,ENST00000596179.1,n.107T>C,MODIFIER,;C3,missense_variant,p.I92T,ENST00000596548.1,c.275T>C,MODERATE,;C3,intron_variant,,ENST00000601008.1,c.241+2340T>C,MODIFIER,;C3,missense_variant,p.I1060T,ENST00000695654.1,c.3179T>C,MODERATE,;C3,missense_variant,p.I688T,ENST00000695653.1,c.2063T>C,MODERATE,;C3,non_coding_transcript_exon_variant,,ENST00000695691.1,n.345T>C,MODIFIER,;C3,missense_variant,NMD_transcript_variant,p.I22T,ENST00000695689.1,c.65T>C,MODERATE,;C3,non_coding_transcript_exon_variant,,ENST00000695690.1,n.345T>C,MODIFIER,;C3,missense_variant,p.I1385T,ENST00000245907.11,c.4154T>C,MODERATE,YES;C3,non_coding_transcript_exon_variant,,ENST00000695651.1,n.2502T>C,MODIFIER, +PSG6 5675 BI GRCh38 19 42906950 42906950 + synonymous_variant Silent SNP G G T novel TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 119 69 c.1212C>A p.Ile404= p.I404= ENST00000292125.6 NM_002782.5 404 atC/atA 5/6 P4 T I protein_coding YES CCDS12613.1 1212/1308 TTGGAGATTTC PROSITE_profiles:PS50835;CDD:cd00096;PANTHER:PTHR44427:SF17;PANTHER:PTHR44427;Pfam:PF13895;Gene3D:2.60.40.10;SMART:SM00409;Superfamily:SSF48726 ENSP00000292125 5/6 ENST00000292125 Transcript ENSG00000170848 HGNC:9523 LOW synonymous_variant 1.0 Unknown Q00889.165 PSG6 HGNC -1 1.0 UPI00001327A1 Q00889-1 SNV PSG6,synonymous_variant,p.I404=,ENST00000187910,NM_001031850.4,c.1212C>A,LOW,,,,-1;PSG6,synonymous_variant,p.I311=,ENST00000402603,,c.933C>A,LOW,,,,-1;PSG6,synonymous_variant,p.I404=,ENST00000292125,NM_002782.5,c.1212C>A,LOW,YES,,,-1;PSG6,downstream_gene_variant,,ENST00000594375,,,MODIFIER,,,,-1;PSG6,3_prime_UTR_variant,,ENST00000599753,,c.*569C>A,MODIFIER,,,,-1;PSG6,non_coding_transcript_exon_variant,,ENST00000595062,,n.780C>A,MODIFIER,,,,-1;PSG6,downstream_gene_variant,,ENST00000402456,,,MODIFIER,,,,-1;PSG6,downstream_gene_variant,,ENST00000484292,,,MODIFIER,,,,-1 1257/1391 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 233 61513ae2-6154-46f5-b886-76e54e18599e 188 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS PSG6,non_coding_transcript_exon_variant,,ENST00000595062.1,n.780C>A,MODIFIER,;PSG6,synonymous_variant,p.I404=,ENST00000292125.6,c.1212C>A,LOW,;PSG6,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000599753.1,c.*569C>A,MODIFIER,;PSG6,synonymous_variant,p.I311=,ENST00000402603.8,c.933C>A,LOW,;PSG6,synonymous_variant,p.I404=,ENST00000187910.7,c.1212C>A,LOW,YES +TFDP3 51270 BI GRCh38 X 133217685 133217685 + missense_variant Missense_Mutation SNP T T C rs767295052 TCGA-V4-A9F1-01A TCGA-V4-A9F1-10A Somatic 18 14 c.575A>G p.Asn192Ser p.N192S ENST00000310125.5 NM_016521.3 192 aAc/aGc 1/1 P1 C N/S protein_coding YES CCDS14636.2 575/1218 CCGAGTTGGTG Gene3D:1.10.10.10;PIRSF:PIRSF009404;PANTHER:PTHR12548;PANTHER:PTHR12548:SF13 ENSP00000385461 1/1 rs767295052;COSV59537261 ENST00000310125 Transcript ENSG00000183434 HGNC:24603 MODERATE NM_016521.3 missense_variant 0;1 1.0 benign(0.125) Unknown tolerated(0.18) 0;1 Q5H9I0.135 TFDP3 HGNC -1 UPI0000212570 SNV TFDP3,missense_variant,p.N192S,ENST00000310125,NM_016521.3,c.575A>G,MODERATE,YES,tolerated(0.18),benign(0.125),-1 670/1693 muse;mutect2;varscan2 94f3d9b0-0ee4-4f6a-a8ff-ce7a4d8fab76 0 52 61513ae2-6154-46f5-b886-76e54e18599e 32 979887ce-c3e5-4119-b0b2-4bb82d25260d SUCCESS TFDP3,missense_variant,p.N192S,ENST00000310125.5,c.575A>G,MODERATE,YES +FAAP20 199990 BI GRCh38 1 2193794 2193794 + synonymous_variant Silent SNP G G A rs772593583 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 29 14 c.315C>T p.His105= p.H105= ENST00000378546.9 NM_182533.4 105 caC/caT 3/4 P1 A H protein_coding CCDS38.2 315/543 GCCCCGTGAAG PANTHER:PTHR37862;Pfam:PF15751 ENSP00000367808 3/4 rs772593583;COSV101052041 ENST00000378546 Transcript ENSG00000162585 HGNC:26428 LOW NM_182533.4 0.0002688 gnomAD_AFR synonymous_variant 0;1 Unknown 0;1 Q6NZ36.123 FAAP20 HGNC -1 1.0 UPI000155D483 Q6NZ36-1 SNV FAAP20,missense_variant,p.T60M,ENST00000400919,NM_001256945.2,c.179C>T,MODERATE,,,benign(0),-1;FAAP20,missense_variant,p.T60M,ENST00000378543,NM_001256947.2,c.179C>T,MODERATE,,,benign(0),-1;FAAP20,synonymous_variant,p.H105=,ENST00000420515,NM_001256946.2,c.315C>T,LOW,YES,,,-1;FAAP20,synonymous_variant,p.H105=,ENST00000400918,NM_001282673.2,c.315C>T,LOW,,,,-1;FAAP20,synonymous_variant,p.H105=,ENST00000378546,NM_182533.4,c.315C>T,LOW,,,,-1;FAAP20,non_coding_transcript_exon_variant,,ENST00000487186,NM_001282670.1,n.3187C>T,MODIFIER,,,,-1;FAAP20,non_coding_transcript_exon_variant,,ENST00000401813,,n.2154C>T,MODIFIER,,,,-1;FAAP20,non_coding_transcript_exon_variant,,ENST00000469733,NM_001146310.1,n.1075C>T,MODIFIER,,,,-1;FAAP20,non_coding_transcript_exon_variant,,ENST00000476803,,n.333C>T,MODIFIER,,,,-1;FAAP20,synonymous_variant,p.H103=,ENST00000428120,NM_001282671.1,c.309C>T,LOW,,,,-1;FAAP20,synonymous_variant,p.H105=,ENST00000414253,NM_001282672.1,c.315C>T,LOW,,,,-1;FAAP20,synonymous_variant,p.H57=,ENST00000440825,,c.171C>T,LOW,,,,-1;FAAP20,non_coding_transcript_exon_variant,,ENST00000497675,,n.228C>T,MODIFIER,,,,-1;FAAP20,downstream_gene_variant,,ENST00000514625,,,MODIFIER,,,,-1 338/727 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 2.549e-05 0.0002688 0.0 0.0 0.0 0.0 0.0 0.0001759 3.376e-05 9.46240033954382e-05 0.0003160559863317 0.0 6.622519867960364e-05 0.0 0.0 0.0 afr 0.0003160559863317 0.0 0.0 0.0 0.0 0 30 87a1660e-0b6f-486a-a768-e99cd8b7841a 43 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS FAAP20,missense_variant,p.T105M,ENST00000420515.1,c.314C>T,MODERATE,;FAAP20,missense_variant,NMD_transcript_variant,p.R57W,ENST00000440825.6,c.169C>T,MODERATE,;FAAP20,non_coding_transcript_exon_variant,,ENST00000476803.1,n.333C>T,MODIFIER,;FAAP20,missense_variant,p.T60M,ENST00000378543.2,c.179C>T,MODERATE,;FAAP20,synonymous_variant,p.H105=,ENST00000378546.9,c.315C>T,LOW,YES;FAAP20,non_coding_transcript_exon_variant,,ENST00000487186.5,n.3187C>T,MODIFIER,;FAAP20,non_coding_transcript_exon_variant,,ENST00000401813.7,n.2154C>T,MODIFIER,;FAAP20,non_coding_transcript_exon_variant,,ENST00000497675.2,n.228C>T,MODIFIER,;FAAP20,synonymous_variant,p.H105=,ENST00000400918.7,c.315C>T,LOW,;FAAP20,synonymous_variant,NMD_transcript_variant,p.H105=,ENST00000414253.5,c.315C>T,LOW,;FAAP20,missense_variant,NMD_transcript_variant,p.R103W,ENST00000428120.5,c.307C>T,MODERATE,;FAAP20,non_coding_transcript_exon_variant,,ENST00000469733.5,n.1075C>T,MODIFIER,;FAAP20,missense_variant,p.T60M,ENST00000400919.7,c.179C>T,MODERATE, +C1orf94 84970 BI GRCh38 1 34197631 34197631 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 20 24 c.727T>C p.Phe243Leu p.F243L ENST00000488417.2 NM_001134734.2 243 Ttc/Ctc 2/7 P2 C F/L protein_coding YES CCDS44108.1 727/1797 CCCAGTTCCCA PANTHER:PTHR35674;Pfam:PF15752 ENSP00000435634 2/7 ENST00000488417 Transcript ENSG00000142698 HGNC:28250 MODERATE NM_001134734.2 missense_variant 1.0 benign(0.011) Unknown tolerated(0.22) Q6P1W5.126 C1orf94 HGNC 1 1.0 UPI0000D4BFB0 Q6P1W5-1 SNV C1orf94,missense_variant,p.F243L,ENST00000488417,NM_001134734.2,c.727T>C,MODERATE,YES,tolerated(0.22),benign(0.011),1;C1orf94,missense_variant,p.F53L,ENST00000373374,NM_032884.5,c.157T>C,MODERATE,,tolerated(0.14),benign(0.011),1 1610/3050 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 45 87a1660e-0b6f-486a-a768-e99cd8b7841a 45 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS C1orf94,missense_variant,p.F243L,ENST00000488417.2,c.727T>C,MODERATE,YES;C1orf94,missense_variant,p.F53L,ENST00000373374.7,c.157T>C,MODERATE, +PTBP2 58155 BI GRCh38 1 96813355 96813355 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 57 35 c.1573C>G p.Leu525Val p.L525V ENST00000426398.3 NM_001300986.2 525 Ctt/Gtt 14/14 G L/V protein_coding YES 1573/1623 ATAACCTTGGA PDB-ENSP_mappings:2mju.A;PDB-ENSP_mappings:4cq1.A;PDB-ENSP_mappings:4cq1.B;PDB-ENSP_mappings:4cq1.C;PDB-ENSP_mappings:4cq1.D;PDB-ENSP_mappings:4cq1.E;PDB-ENSP_mappings:4cq1.F;PDB-ENSP_mappings:4cq1.G;PDB-ENSP_mappings:4cq1.H;PROSITE_profiles:PS50102;CDD:cd12702;PANTHER:PTHR15592;PANTHER:PTHR15592:SF16;Gene3D:3.30.70.330;Pfam:PF00076;TIGRFAM:TIGR01649;SMART:SM00360;Superfamily:SSF54928 ENSP00000412788 14/14 ENST00000426398 Transcript ENSG00000117569 HGNC:17662 MODERATE missense_variant 1.0 benign(0.001) Unknown deleterious(0.03) Q9UKA9.172 PTBP2 HGNC 1 1.0 UPI0001D54DEC Q9UKA9-1 SNV PTBP2,missense_variant,p.L517V,ENST00000609116,NM_001300989.2,c.1549C>G,MODERATE,,deleterious(0.04),benign(0.029),1;PTBP2,missense_variant,p.L490V,ENST00000676292,NM_001300987.2&NM_001300990.2,c.1468C>G,MODERATE,,deleterious(0.04),benign(0),1;PTBP2,missense_variant,p.L524V,ENST00000675735,,c.1570C>G,MODERATE,,deleterious(0.03),benign(0.021),1;PTBP2,missense_variant,p.L516V,ENST00000674951,NM_021190.4,c.1546C>G,MODERATE,,deleterious(0.04),benign(0.113),1;PTBP2,missense_variant,p.L525V,ENST00000426398,NM_001300986.2,c.1573C>G,MODERATE,YES,deleterious(0.03),benign(0.001),1;PTBP2,missense_variant,p.L522V,ENST00000370197,NM_001300985.2,c.1564C>G,MODERATE,,deleterious(0.04),benign(0.029),1;PTBP2,missense_variant,p.L521V,ENST00000370198,NM_001300988.1,c.1561C>G,MODERATE,,deleterious(0.04),benign(0),1;PTBP2,missense_variant,p.L334V,ENST00000675401,,c.1000C>G,MODERATE,,deleterious(0.04),benign(0),1;PTBP2,missense_variant,p.L460V,ENST00000676096,,c.1378C>G,MODERATE,,deleterious(0.04),benign(0.079),1;PTBP2,non_coding_transcript_exon_variant,,ENST00000476783,,n.687C>G,MODIFIER,,,,1;PTBP2,non_coding_transcript_exon_variant,,ENST00000492905,,n.684C>G,MODIFIER,,,,1;PTBP2,3_prime_UTR_variant,,ENST00000482253,,c.*1338C>G,MODIFIER,,,,1;PTBP2,3_prime_UTR_variant,,ENST00000674579,,c.*444C>G,MODIFIER,,,,1;PTBP2,3_prime_UTR_variant,,ENST00000675365,,c.*444C>G,MODIFIER,,,,1;PTBP2,3_prime_UTR_variant,,ENST00000476419,,c.*444C>G,MODIFIER,,,,1;PTBP2,non_coding_transcript_exon_variant,,ENST00000675080,,n.3106C>G,MODIFIER,,,,1;PTBP2,downstream_gene_variant,,ENST00000459735,,,MODIFIER,,,,1;PTBP2,downstream_gene_variant,,ENST00000462433,,,MODIFIER,,,,1 1650/3153 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 59 87a1660e-0b6f-486a-a768-e99cd8b7841a 92 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS PTBP2,non_coding_transcript_exon_variant,,ENST00000706599.1,n.2030C>G,MODIFIER,;PTBP2,non_coding_transcript_exon_variant,,ENST00000706598.1,n.1453C>G,MODIFIER,;PTBP2,non_coding_transcript_exon_variant,,ENST00000706597.1,n.1728C>G,MODIFIER,;PTBP2,non_coding_transcript_exon_variant,,ENST00000706596.1,n.1964C>G,MODIFIER,;PTBP2,non_coding_transcript_exon_variant,,ENST00000492905.5,n.684C>G,MODIFIER,;PTBP2,non_coding_transcript_exon_variant,,ENST00000476783.5,n.687C>G,MODIFIER,;PTBP2,missense_variant,p.L334V,ENST00000675401.1,c.1000C>G,MODERATE,;PTBP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000674579.1,c.*444C>G,MODIFIER,;PTBP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675365.1,c.*444C>G,MODIFIER,;PTBP2,missense_variant,p.L460V,ENST00000676096.1,c.1378C>G,MODERATE,;PTBP2,missense_variant,p.L490V,ENST00000676292.1,c.1468C>G,MODERATE,;PTBP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000476419.5,c.*444C>G,MODIFIER,;PTBP2,missense_variant,p.L521V,ENST00000370198.5,c.1561C>G,MODERATE,;PTBP2,missense_variant,p.L522V,ENST00000370197.5,c.1564C>G,MODERATE,;PTBP2,missense_variant,p.L525V,ENST00000426398.3,c.1573C>G,MODERATE,;PTBP2,missense_variant,p.L516V,ENST00000674951.1,c.1546C>G,MODERATE,YES;PTBP2,non_coding_transcript_exon_variant,,ENST00000675080.1,n.3106C>G,MODIFIER,;PTBP2,missense_variant,p.L517V,ENST00000609116.5,c.1549C>G,MODERATE,;PTBP2,missense_variant,p.L524V,ENST00000675735.1,c.1570C>G,MODERATE,;PTBP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000482253.5,c.*1338C>G,MODIFIER, +IL18R1 8809 BI GRCh38 2 102381674 102381674 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 20 14 c.680T>C p.Val227Ala p.V227A ENST00000233957.7 NM_003855.5 227 gTg/gCg 6/11 P1 C V/A protein_coding YES CCDS2060.1 680/1626 TGCAGTGGAAT PDB-ENSP_mappings:3wo3.B;PDB-ENSP_mappings:3wo3.D;PDB-ENSP_mappings:3wo3.F;PDB-ENSP_mappings:3wo3.H;PDB-ENSP_mappings:3wo3.J;PDB-ENSP_mappings:3wo3.L;PDB-ENSP_mappings:3wo4.B;PDB-ENSP_mappings:4r6u.A;PDB-ENSP_mappings:4r6u.C;Prints:PR01536;Superfamily:SSF48726;SMART:SM00409;Gene3D:2.60.40.10;PANTHER:PTHR11890;PANTHER:PTHR11890:SF6;PROSITE_profiles:PS50835 ENSP00000233957 6/11 ENST00000233957 Transcript ENSG00000115604 HGNC:5988 MODERATE missense_variant 1.0 benign(0.191) Unknown tolerated(0.26) Q13478.173 IL18R1 HGNC 1 5.0 UPI000012D871 SNV IL18R1,missense_variant,p.V227A,ENST00000233957,NM_003855.5&NM_001371418.1&NM_001371422.1&NM_001371423.1&NM_001371424.1&NM_001371421.1&NM_001371419.1&NM_001371420.1&NM_001282399.2,c.680T>C,MODERATE,YES,tolerated(0.26),benign(0.191),1;IL18R1,missense_variant,p.V227A,ENST00000409599,,c.680T>C,MODERATE,,tolerated(0.26),benign(0.191),1;IL18R1,missense_variant,p.V227A,ENST00000410040,,c.680T>C,MODERATE,,tolerated(0.26),benign(0.191),1;IL18R1,3_prime_UTR_variant,,ENST00000677287,,c.*224T>C,MODIFIER,,,,1 1313/4148 muse;mutect2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 30 87a1660e-0b6f-486a-a768-e99cd8b7841a 34 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS IL18R1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000677287.1,c.*224T>C,MODIFIER,;IL18R1,missense_variant,p.V227A,ENST00000409599.5,c.680T>C,MODERATE,;IL18R1,missense_variant,p.V227A,ENST00000233957.7,c.680T>C,MODERATE,YES;IL18R1,missense_variant,p.V227A,ENST00000410040.5,c.680T>C,MODERATE, +CCNG2 901 BI GRCh38 4 77158555 77158596 + inframe_deletion In_Frame_Del DEL ACTTGGCAGGTCATGAAGGGGTCCAACTTCTCGGGTTGTTGA ACTTGGCAGGTCATGAAGGGGTCCAACTTCTCGGGTTGTTGA - novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 71 20 c.25_66del p.Leu9_Asn22del p.L9_N22del ENST00000316355.10 NM_004354.3 8 cACTTGGCAGGTCATGAAGGGGTCCAACTTCTCGGGTTGTTGAac/cac 2/8 P1 - HLAGHEGVQLLGLLN/H protein_coding YES CCDS3581.1 23-64/1035 CAGAGCACTTGGCAGGTCATGAAGGGGTCCAACTTCTCGGGTTGTTGAACGTC PANTHER:PTHR10177:SF60;PANTHER:PTHR10177;Pfam:PF00134;Gene3D:1.10.472.10;Superfamily:SSF47954 ENSP00000315743 2/8 ENST00000316355 Transcript ENSG00000138764 HGNC:1593 2.0 MODERATE NM_004354.3 inframe_deletion 1.0 Unknown Q16589.163 CCNG2 HGNC 1 A0A024RDC7.44 1.0 UPI00001275D4 Q16589-1 deletion CCNG2,inframe_deletion,p.L9_N22del,ENST00000316355,NM_004354.3,c.25_66del,MODERATE,YES,,,1;CCNG2,inframe_deletion,p.L9_N22del,ENST00000509972,,c.25_66del,MODERATE,,,,1;CCNG2,inframe_deletion,p.L9_N22del,ENST00000502280,,c.25_66del,MODERATE,,,,1;CCNG2,inframe_deletion,p.L9_N22del,ENST00000395640,,c.25_66del,MODERATE,,,,1;CCNG2,inframe_deletion,p.L9_N22del,ENST00000512918,,c.25_66del,MODERATE,,,,1;CCNG2,non_coding_transcript_exon_variant,,ENST00000497512,,n.307_348del,MODIFIER,,,,1 323-364/5471 mutect2;pindel 22e7816d-4be9-4f84-b487-baa6ca35452d 0 99 87a1660e-0b6f-486a-a768-e99cd8b7841a 91 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS CCNG2,inframe_deletion,p.L9_N22del,ENST00000509972.1,c.25_66del,MODERATE,;CCNG2,inframe_deletion,p.L9_N22del,ENST00000512918.5,c.25_66del,MODERATE,;CCNG2,inframe_deletion,p.L9_N22del,ENST00000395640.5,c.25_66del,MODERATE,;CCNG2,non_coding_transcript_exon_variant,,ENST00000497512.5,n.305_346del,MODIFIER,;CCNG2,inframe_deletion,p.L9_N22del,ENST00000502280.5,c.25_66del,MODERATE,;CCNG2,inframe_deletion,p.L9_N22del,ENST00000316355.10,c.25_66del,MODERATE,YES +C4orf17 84103 BI GRCh38 4 99541928 99541928 + missense_variant Missense_Mutation SNP C C T rs201530498 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 19 15 c.899C>T p.Pro300Leu p.P300L ENST00000326581.9 NM_032149.3 300 cCa/cTa 9/9 P2 T P/L protein_coding YES CCDS3649.1 899/1080 GCCTCCACTAC PANTHER:PTHR33772;PANTHER:PTHR33772:SF2;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000322582 9/9 rs201530498 ENST00000326581 Transcript ENSG00000138813 HGNC:25274 MODERATE NM_032149.3 2.908e-05 gnomAD_AMR missense_variant 1.0 possibly_damaging(0.868) Unknown tolerated(0.06) Q53FE4.104 C4orf17 HGNC 1 1.0 UPI0000141987 Q53FE4-1 SNV C4orf17,missense_variant,p.P300L,ENST00000326581,NM_032149.3,c.899C>T,MODERATE,YES,tolerated(0.06),possibly_damaging(0.868),1;TRMT10A,downstream_gene_variant,,ENST00000273962,NM_001375881.1&NM_001375880.1&NM_152292.5,,MODIFIER,YES,,,-1;TRMT10A,downstream_gene_variant,,ENST00000394876,NM_001134666.3&NM_001375882.1&NM_001134665.3,,MODIFIER,,,,-1;TRMT10A,downstream_gene_variant,,ENST00000394877,,,MODIFIER,,,,-1;C4orf17,downstream_gene_variant,,ENST00000514652,,,MODIFIER,,,,1;C4orf17,3_prime_UTR_variant,,ENST00000477187,,c.*531C>T,MODIFIER,,,,1 1244/1619 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 4.007e-06 0.0 2.908e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 35 87a1660e-0b6f-486a-a768-e99cd8b7841a 34 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS C4orf17,missense_variant,p.P300L,ENST00000326581.9,c.899C>T,MODERATE,YES;C4orf17,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000477187.1,c.*531C>T,MODIFIER, +BLTP1 84162 BI GRCh38 4 122353898 122353898 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 28 18 c.14450C>G p.Ala4817Gly p.A4817G ENST00000679879.1 NM_001384125.1 4817 gCt/gGt 84/88 P1 G A/G protein_coding YES CCDS43267.1 14186/15018 TGGTGCTTTGG Pfam:PF10479;PANTHER:PTHR31640;SMART:SM01220 ENSP00000264501 82/86 ENST00000264501 Transcript 1.0 ENSG00000138688 HGNC:26953 MODERATE missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0.01) Q2LD37.118 KIAA1109 HGNC 1 5.0 UPI0000DD87B4 Q2LD37-1 SNV KIAA1109,missense_variant,p.A4729G,ENST00000264501,,c.14186C>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.996),1;KIAA1109,missense_variant,p.A4729G,ENST00000388738,NM_015312.3,c.14186C>G,MODERATE,,deleterious(0.01),probably_damaging(0.996),1;KIAA1109,missense_variant,p.A1398G,ENST00000438707,,c.4193C>G,MODERATE,,deleterious(0.02),probably_damaging(1),1;KIAA1109,missense_variant,p.A1105G,ENST00000306802,,c.3314C>G,MODERATE,,deleterious(0.01),probably_damaging(0.999),1;KIAA1109,downstream_gene_variant,,ENST00000491933,,,MODIFIER,,,,1 14559/15896 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 43 87a1660e-0b6f-486a-a768-e99cd8b7841a 46 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS BLTP1,non_coding_transcript_exon_variant,,ENST00000691302.1,n.317C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000688322.1,n.787C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000686950.1,n.1506C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000685604.1,n.2157C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000693357.1,n.1919C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000687387.1,n.2177C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000688874.1,n.4121C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000686040.1,n.3923C>G,MODIFIER,;BLTP1,missense_variant,p.L1105V,ENST00000306802.8,c.3313C>G,MODERATE,;BLTP1,missense_variant,p.A1398G,ENST00000438707.5,c.4193C>G,MODERATE,;BLTP1,missense_variant,p.A1605G,ENST00000686836.1,c.4814C>G,MODERATE,;BLTP1,missense_variant,NMD_transcript_variant,p.L1751V,ENST00000688248.1,c.5251C>G,MODERATE,;BLTP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686093.1,c.*5173C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000690536.1,n.15074C>G,MODIFIER,;BLTP1,missense_variant,p.A4614G,ENST00000388738.8,c.13841C>G,MODERATE,;BLTP1,non_coding_transcript_exon_variant,,ENST00000684987.1,n.18261C>G,MODIFIER,;BLTP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000693420.1,c.*1438C>G,MODIFIER,;BLTP1,non_coding_transcript_exon_variant,,ENST00000693334.1,n.14856C>G,MODIFIER,;BLTP1,missense_variant,p.A4729G,ENST00000264501.8,c.14186C>G,MODERATE,;BLTP1,missense_variant,p.A4817G,ENST00000679879.1,c.14450C>G,MODERATE,YES +SQSTM1 8878 BI GRCh38 5 179824203 179824203 + missense_variant Missense_Mutation SNP C C T rs753313263 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 28 23 c.553C>T p.Leu185Phe p.L185F ENST00000389805.9 NM_003900.5 185 Ctc/Ttc 4/8 P1 T L/F protein_coding YES CCDS34317.1 553/1323 GCTGGCTCCGG PANTHER:PTHR15090;PANTHER:PTHR15090:SF0 ENSP00000374455 4/8 rs753313263 ENST00000389805 Transcript 1.0 ENSG00000161011 HGNC:11280 MODERATE NM_003900.5 6.533e-05 gnomAD_SAS missense_variant 1.0 benign(0.003) Unknown tolerated(0.18) Q13501.209 SQSTM1 HGNC 1 1.0 UPI0000071099 Q13501-1 SNV SQSTM1,missense_variant,p.L185F,ENST00000389805,NM_003900.5,c.553C>T,MODERATE,YES,tolerated(0.18),benign(0.003),1;SQSTM1,missense_variant,p.L101F,ENST00000360718,NM_001142298.2&NM_001142299.2,c.301C>T,MODERATE,,tolerated(0.17),benign(0.003),1;SQSTM1,missense_variant,p.L185F,ENST00000510187,,c.553C>T,MODERATE,,tolerated(0.17),benign(0.052),1;SQSTM1,missense_variant,p.L101F,ENST00000514093,,c.301C>T,MODERATE,,tolerated(0.16),benign(0.003),1;SQSTM1,missense_variant,p.L101F,ENST00000422245,,c.301C>T,MODERATE,,tolerated(0.17),benign(0.003),1;SQSTM1,downstream_gene_variant,,ENST00000504627,,,MODIFIER,,,,1;SQSTM1,downstream_gene_variant,,ENST00000626660,,,MODIFIER,,,,1;SQSTM1,non_coding_transcript_exon_variant,,ENST00000464493,,n.448C>T,MODIFIER,,,,1;SQSTM1,downstream_gene_variant,,ENST00000481335,,,MODIFIER,,,,1;SQSTM1,3_prime_UTR_variant,,ENST00000508284,,c.*275C>T,MODIFIER,,,,1;SQSTM1,non_coding_transcript_exon_variant,,ENST00000466342,,n.252C>T,MODIFIER,,,,1;SQSTM1,non_coding_transcript_exon_variant,,ENST00000485412,,n.545C>T,MODIFIER,,,,1;SQSTM1,downstream_gene_variant,,ENST00000453046,,,MODIFIER,,,,1 585/2840 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 1.196e-05 0.0 0.0 0.0 0.0 0.0 8.823e-06 0.0 6.533e-05 0 53 87a1660e-0b6f-486a-a768-e99cd8b7841a 51 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS SQSTM1,non_coding_transcript_exon_variant,,ENST00000466342.1,n.252C>T,MODIFIER,;SQSTM1,non_coding_transcript_exon_variant,,ENST00000485412.1,n.545C>T,MODIFIER,;SQSTM1,missense_variant,p.L101F,ENST00000360718.5,c.301C>T,MODERATE,;SQSTM1,missense_variant,p.L185F,ENST00000510187.5,c.553C>T,MODERATE,;SQSTM1,missense_variant,p.L185F,ENST00000389805.9,c.553C>T,MODERATE,YES;SQSTM1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000508284.5,c.*275C>T,MODIFIER,;SQSTM1,non_coding_transcript_exon_variant,,ENST00000464493.5,n.448C>T,MODIFIER,;SQSTM1,missense_variant,p.L101F,ENST00000422245.5,c.301C>T,MODERATE,;SQSTM1,missense_variant,p.L101F,ENST00000514093.5,c.301C>T,MODERATE, +FOXF2 102466720 BI GRCh38 6 1391103 1391103 + missense_variant Missense_Mutation SNP C C T rs1345129732 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 11 11 c.1156C>T p.Arg386Cys p.R386C ENST00000645481.2 386/444 P1 T R/C protein_coding YES CCDS4472.1 1156/1335 ACGCTCGCGAG PANTHER:PTHR46262:SF3;PANTHER:PTHR46262 ENSP00000496415 1/2 rs1345129732 ENST00000645481 Transcript ENSG00000137273 HGNC:3810 MODERATE NM_001452.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.828) Unknown deleterious(0.01) Q12947.162 FOXF2 HGNC 1 UPI000012ADD6 SNV FOXF2,missense_variant,p.R386C,ENST00000645481,NM_001452.2,c.1156C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.828),1;MIR6720,upstream_gene_variant,,ENST00000611664,,,MODIFIER,YES,,,-1 1528/2451 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 18 87a1660e-0b6f-486a-a768-e99cd8b7841a 22 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS FOXF2,missense_variant,p.R386C,ENST00000645481.2,c.1156C>T,MODERATE,YES +BZW2 28969 BI GRCh38 7 16682791 16682791 + synonymous_variant Silent SNP A A G rs1441747313 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 38 7 c.351A>G p.Lys117= p.K117= ENST00000258761.8 NM_001159767.2 117 aaA/aaG 5/12 P1 G K protein_coding CCDS5362.1 351/1260 AATAAACTCAT PANTHER:PTHR14208;PANTHER:PTHR14208:SF7 ENSP00000258761 5/12 rs1441747313 ENST00000258761 Transcript ENSG00000136261 HGNC:18808 LOW NM_014038.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant Unknown Q9Y6E2.150 BZW2 HGNC 1 A0A024RA42.47 1.0 UPI000003B445 Q9Y6E2-1 SNV BZW2,synonymous_variant,p.K117=,ENST00000433922,NM_001159767.1,c.351A>G,LOW,YES,,,1;BZW2,synonymous_variant,p.K117=,ENST00000258761,NM_014038.3&NM_001362717.2,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000630952,,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K41=,ENST00000405202,,c.123A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000415365,,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000446596,,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000438834,,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000430000,,c.351A>G,LOW,,,,1;BZW2,5_prime_UTR_variant,,ENST00000452975,,c.-87A>G,MODIFIER,,,,1;BZW2,non_coding_transcript_exon_variant,,ENST00000432311,,n.503A>G,MODIFIER,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000436868,,c.351A>G,LOW,,,,1;BZW2,synonymous_variant,p.K117=,ENST00000437745,,c.351A>G,LOW,,,,1;BZW2,non_coding_transcript_exon_variant,,ENST00000480517,,n.397A>G,MODIFIER,,,,1 466/1804 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 39 87a1660e-0b6f-486a-a768-e99cd8b7841a 45 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS BZW2,synonymous_variant,p.K117=,ENST00000430000.1,c.351A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000438834.5,c.351A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000446596.5,c.351A>G,LOW,;BZW2,non_coding_transcript_exon_variant,,ENST00000480517.5,n.397A>G,MODIFIER,;BZW2,synonymous_variant,p.K41=,ENST00000405202.5,c.123A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000258761.8,c.351A>G,LOW,YES;BZW2,synonymous_variant,NMD_transcript_variant,p.K117=,ENST00000436868.5,c.351A>G,LOW,;BZW2,non_coding_transcript_exon_variant,,ENST00000432311.5,n.503A>G,MODIFIER,;BZW2,synonymous_variant,NMD_transcript_variant,p.K117=,ENST00000437745.5,c.351A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000433922.6,c.351A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000630952.2,c.351A>G,LOW,;BZW2,synonymous_variant,p.K117=,ENST00000415365.5,c.351A>G,LOW, +HOXA4 3201 BI GRCh38 7 27129240 27129240 + synonymous_variant Silent SNP A A T novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 18 8 c.948T>A p.Val316= p.V316= ENST00000360046.10 NM_002141.5 316 gtT/gtA 2/2 P1 T V protein_coding CCDS5405.1 948/963 GAGGGAACGGG PANTHER:PTHR45771;PANTHER:PTHR45771:SF2;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000353151 2/2 ENST00000360046 Transcript ENSG00000197576 HGNC:5105 LOW NM_002141.5 synonymous_variant Unknown Q00056.181 HOXA4 HGNC -1 1.0 UPI000013C810 SNV HOXA4,synonymous_variant,p.V316=,ENST00000610970,,c.948T>A,LOW,YES,,,-1;HOXA4,synonymous_variant,p.V316=,ENST00000360046,NM_002141.5,c.948T>A,LOW,,,,-1;HOXA4,synonymous_variant,p.V316=,ENST00000428284,,c.948T>A,LOW,,,,-1;HOXA4,synonymous_variant,p.V136=,ENST00000511914,,c.408T>A,LOW,,,,-1;HOXA3,intron_variant,,ENST00000317201,,c.-389-2170T>A,MODIFIER,,,,-1;HOXA3,intron_variant,,ENST00000522788,,c.-204-6598T>A,MODIFIER,,,,-1;HOXA3,upstream_gene_variant,,ENST00000612286,NM_153631.2,,MODIFIER,YES,,,-1;HOXA3,intron_variant,,ENST00000518451,,n.399-2170T>A,MODIFIER,,,,-1;HOXA3,intron_variant,,ENST00000521401,,n.144-2170T>A,MODIFIER,,,,-1;AC004080.6,non_coding_transcript_exon_variant,,ENST00000467897,,n.648T>A,MODIFIER,YES,,,-1;HOXA-AS2,intron_variant,,ENST00000521159,,n.578+4630A>T,MODIFIER,,,,1;HOXA-AS2,downstream_gene_variant,,ENST00000517550,,,MODIFIER,,,,1;HOXA-AS3,upstream_gene_variant,,ENST00000518848,,,MODIFIER,,,,1;HOXA-AS2,downstream_gene_variant,,ENST00000521687,,,MODIFIER,,,,1;HOXA-AS2,downstream_gene_variant,,ENST00000524048,,,MODIFIER,,,,1 972/1687 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 41 87a1660e-0b6f-486a-a768-e99cd8b7841a 26 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS ENSG00000273433,non_coding_transcript_exon_variant,,ENST00000467897.2,n.648T>A,MODIFIER,YES;HOXA4,missense_variant,p.S136T,ENST00000511914.1,c.406T>A,MODERATE,;HOXA4,synonymous_variant,p.V316=,ENST00000360046.10,c.948T>A,LOW,YES;HOXA4,synonymous_variant,p.V316=,ENST00000610970.1,c.948T>A,LOW,;HOXA-AS2,intron_variant,,ENST00000521159.5,n.578+4630A>T,MODIFIER,;HOXA3,intron_variant,,ENST00000521401.1,n.144-2170T>A,MODIFIER,;HOXA3,intron_variant,,ENST00000522788.5,c.-204-6598T>A,MODIFIER,;HOXA3,intron_variant,,ENST00000317201.7,c.-389-2170T>A,MODIFIER,;HOXA3,intron_variant,,ENST00000612286.5,c.-389-2170T>A,MODIFIER,YES +STYXL1 51657 BI GRCh38 7 75996567 75996567 + synonymous_variant Silent SNP G G A novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 33 36 c.843C>T p.Asn281= p.N281= ENST00000248600.5 NM_016086.3 281 aaC/aaT 9/9 P1 A N protein_coding YES CCDS5580.1 843/942 ATGTTGTTTTT Gene3D:3.90.190.10;Pfam:PF00782;PROSITE_profiles:PS50054;PANTHER:PTHR46659;SMART:SM00195;Superfamily:SSF52799;CDD:cd14517 ENSP00000248600 9/9 ENST00000248600 Transcript ENSG00000127952 HGNC:18165 LOW synonymous_variant 1.0 Unknown Q9Y6J8.162 STYXL1 HGNC -1 A0A024R4L1.43 1.0 UPI000012F694 Q9Y6J8-1 SNV STYXL1,stop_gained,p.Q199*,ENST00000454618,,c.595C>T,HIGH,,,,-1;STYXL1,synonymous_variant,p.N281=,ENST00000248600,NM_016086.2,c.843C>T,LOW,YES,,,-1;STYXL1,synonymous_variant,p.N281=,ENST00000359697,NM_001317786.2&NM_001317785.2,c.843C>T,LOW,,,,-1;STYXL1,synonymous_variant,p.N281=,ENST00000431581,,c.843C>T,LOW,,,,-1;STYXL1,synonymous_variant,p.N185=,ENST00000360591,NM_001317789.1,c.555C>T,LOW,,,,-1;STYXL1,synonymous_variant,p.N185=,ENST00000340062,NM_001317788.2&NM_001317787.2,c.555C>T,LOW,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000417509,NM_001363462.2,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000439537,NM_001317803.2,,MODIFIER,YES,,,-1;STYXL1,downstream_gene_variant,,ENST00000451157,,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000485200,,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000493111,NM_031925.3,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000431867,,,MODIFIER,,,,-1;STYXL1,3_prime_UTR_variant,,ENST00000438695,,c.*358C>T,MODIFIER,,,,-1;STYXL1,3_prime_UTR_variant,,ENST00000430497,,c.*245C>T,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000440632,,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000465494,,,MODIFIER,,,,-1;TMEM120A,upstream_gene_variant,,ENST00000480538,,,MODIFIER,,,,-1 1186/1415 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 54 87a1660e-0b6f-486a-a768-e99cd8b7841a 69 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS STYXL1,stop_gained,p.Q199*,ENST00000454618.5,c.595C>T,HIGH,;STYXL1,synonymous_variant,p.N281=,ENST00000431581.5,c.843C>T,LOW,;STYXL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000438695.5,c.*358C>T,MODIFIER,;STYXL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000430497.5,c.*245C>T,MODIFIER,;STYXL1,synonymous_variant,p.N281=,ENST00000359697.8,c.843C>T,LOW,YES;STYXL1,synonymous_variant,p.N185=,ENST00000340062.9,c.555C>T,LOW,;STYXL1,synonymous_variant,p.N185=,ENST00000360591.7,c.555C>T,LOW,;STYXL1,synonymous_variant,p.N281=,ENST00000248600.5,c.843C>T,LOW, +GNAQ 2776 BI GRCh38 9 77922339 77922339 + missense_variant Missense_Mutation SNP C C A TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 50 26 c.143G>T p.Gly48Val p.G48V ENST00000286548.9 NM_002072.5 48 gGa/gTa 2/7 P1 A G/V protein_coding YES CCDS6658.1 143/1080 TCTCTCCTGTC PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 2/7 COSV99680131 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1 1.0 probably_damaging(0.996) Unknown deleterious(0) 1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.G48V,ENST00000286548,NM_002072.5,c.143G>T,MODERATE,YES,deleterious(0),probably_damaging(0.996),-1;GNAQ,missense_variant,p.G19V,ENST00000411677,,c.56G>T,MODERATE,,deleterious(0),probably_damaging(1),-1 719/6882 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 76 87a1660e-0b6f-486a-a768-e99cd8b7841a 76 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS GNAQ,missense_variant,p.G19V,ENST00000411677.1,c.56G>T,MODERATE,;GNAQ,missense_variant,p.G48V,ENST00000286548.9,c.143G>T,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77922340 77922340 + stop_gained Nonsense_Mutation SNP C C A novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 50 25 c.142G>T p.Gly48Ter p.G48* ENST00000286548.9 NM_002072.5 48 Gga/Tga 2/7 P1 A G/* protein_coding YES CCDS6658.1 142/1080 CTCTCCTGTCC PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 2/7 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 HIGH NM_002072.5 stop_gained 1.0 Unknown P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,stop_gained,p.G48*,ENST00000286548,NM_002072.5,c.142G>T,HIGH,YES,,,-1;GNAQ,stop_gained,p.G19*,ENST00000411677,,c.55G>T,HIGH,,,,-1 718/6882 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 75 87a1660e-0b6f-486a-a768-e99cd8b7841a 75 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS GNAQ,stop_gained,p.G19*,ENST00000411677.1,c.55G>T,HIGH,;GNAQ,stop_gained,p.G48*,ENST00000286548.9,c.142G>T,HIGH,YES +NCAM1 4684 BI GRCh38 11 113232233 113232233 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 18 12 c.1304C>T p.Thr435Ile p.T435I ENST00000316851.12 NM_001400621.1 435 aCc/aTc 11/20 P3 T T/I protein_coding CCDS73385.1 1304/2577 CATCACCTGCG PDB-ENSP_mappings:3mtr.A;PDB-ENSP_mappings:3mtr.B;PROSITE_profiles:PS50835;CDD:cd00096;PANTHER:PTHR12231;PANTHER:PTHR12231:SF239;Gene3D:2.60.40.10;Pfam:PF07679;SMART:SM00409;SMART:SM00408;Superfamily:SSF48726 ENSP00000318472 11/20 ENST00000316851 Transcript ENSG00000149294 HGNC:7656 MODERATE NM_181351.5 missense_variant probably_damaging(0.977) Unknown deleterious(0) P13591.211 NCAM1 HGNC 1 5.0 UPI0000E445E3 P13591-2 SNV NCAM1,missense_variant,p.T461I,ENST00000615285,,c.1382C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;NCAM1,missense_variant,p.T435I,ENST00000615112,,c.1304C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;NCAM1,missense_variant,p.T425I,ENST00000618266,,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;NCAM1,missense_variant,p.T435I,ENST00000316851,NM_181351.5,c.1304C>T,MODERATE,,deleterious(0),probably_damaging(0.977),1;NCAM1,missense_variant,p.T425I,ENST00000621518,,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;NCAM1,missense_variant,p.T425I,ENST00000621128,NM_001242608.2,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.97),1;NCAM1,missense_variant,p.T461I,ENST00000619839,NM_001242607.2,c.1382C>T,MODERATE,,deleterious(0),probably_damaging(1),1;NCAM1,missense_variant,p.T425I,ENST00000531044,NM_000615.7,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.961),1;NCAM1,missense_variant,p.T425I,ENST00000621850,NM_001076682.4,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.984),1;NCAM1,missense_variant,p.T425I,ENST00000401611,,c.1274C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;NCAM1,intron_variant,,ENST00000620046,,c.53-23644C>T,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000526322,,,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000528590,,,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000530543,,,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000533073,,,MODIFIER,,,,1;NCAM1,downstream_gene_variant,,ENST00000613217,,,MODIFIER,,,,1;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,,n.1743C>T,MODIFIER,,,,1;NCAM1,non_coding_transcript_exon_variant,,ENST00000534046,,n.480C>T,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000525355,,,MODIFIER,,,,1;NCAM1,upstream_gene_variant,,ENST00000531817,,,MODIFIER,,,,1 1497/5819 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 23 87a1660e-0b6f-486a-a768-e99cd8b7841a 30 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS NCAM1,non_coding_transcript_exon_variant,,ENST00000534046.2,n.480C>T,MODIFIER,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284.4,n.1743C>T,MODIFIER,;NCAM1,missense_variant,p.T425I,ENST00000621850.4,c.1274C>T,MODERATE,;NCAM1,missense_variant,p.T425I,ENST00000531044.5,c.1274C>T,MODERATE,;NCAM1,intron_variant,,ENST00000620046.4,c.53-23644C>T,MODIFIER,;NCAM1,missense_variant,p.T435I,ENST00000316851.12,c.1304C>T,MODERATE,YES;NCAM1,missense_variant,p.T425I,ENST00000401611.6,c.1274C>T,MODERATE,;NCAM1,missense_variant,p.T425I,ENST00000621128.4,c.1274C>T,MODERATE,;NCAM1,missense_variant,p.T461I,ENST00000619839.4,c.1382C>T,MODERATE, +HEPN1 641654 BI GRCh38 11 124920011 124920011 + synonymous_variant Silent SNP A A G novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 35 20 c.261A>G p.Leu87= p.L87= ENST00000408930.7 NM_001037558.4 87 ttA/ttG 1/1 P1 G L protein_coding YES CCDS41729.1 261/267 ATGTTAGTGTG ENSP00000386143 1/1 ENST00000408930 Transcript ENSG00000221932 HGNC:34400 LOW synonymous_variant Unknown Q6WQI6.91 HEPN1 HGNC 1 UPI0000D6269C SNV HEPN1,synonymous_variant,p.L87=,ENST00000408930,NM_001037558.2,c.261A>G,LOW,YES,,,1;HEPACAM,3_prime_UTR_variant,,ENST00000298251,NM_152722.5,c.*1127T>C,MODIFIER,YES,,,-1;HEPACAM,downstream_gene_variant,,ENST00000526273,,,MODIFIER,,,,-1;HEPACAM,downstream_gene_variant,,ENST00000528971,,,MODIFIER,,,,-1 768/1434 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 57 87a1660e-0b6f-486a-a768-e99cd8b7841a 55 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS HEPN1,synonymous_variant,p.L87=,ENST00000408930.7,c.261A>G,LOW,YES;HEPACAM,3_prime_UTR_variant,,ENST00000703807.1,c.*1127T>C,MODIFIER,;HEPACAM,3_prime_UTR_variant,,ENST00000298251.5,c.*1127T>C,MODIFIER,YES +BRCA2 675 BI GRCh38 13 32370982 32370982 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 30 18 c.8514A>T p.Leu2838Phe p.L2838F ENST00000380152.8 NM_000059.4 2838 ttA/ttT 20/27 P1 T L/F protein_coding YES CCDS9344.1 8514/10257 GGATTATACAT Gene3D:1.10.132.40;Gene3D:2.40.50.140;Pfam:PF09121;PIRSF:PIRSF002397;PANTHER:PTHR11289;SMART:SM01341;Superfamily:SSF50249;Superfamily:SSF81878;CDD:cd04494 ENSP00000369497 20/27 ENST00000380152 Transcript 1.0 ENSG00000139618 HGNC:1101 MODERATE NM_000059.4 missense_variant 1.0 probably_damaging(0.965) Unknown tolerated(0.07) P51587.222 BRCA2 HGNC 1 5.0 UPI00001FCBCC SNV BRCA2,missense_variant,p.L2838F,ENST00000380152,NM_000059.4,c.8514A>T,MODERATE,YES,tolerated(0.07),probably_damaging(0.965),1;BRCA2,missense_variant,p.L2838F,ENST00000544455,,c.8514A>T,MODERATE,,tolerated(0.07),probably_damaging(0.965),1;BRCA2,missense_variant,p.L360F,ENST00000665585,,c.1080A>T,MODERATE,,tolerated(0.06),benign(0.038),1;BRCA2,missense_variant,p.L4F,ENST00000528762,,c.12A>T,MODERATE,,tolerated_low_confidence(0.11),benign(0.062),1 8713/11954 muse;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 42 87a1660e-0b6f-486a-a768-e99cd8b7841a 48 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000614259.2,c.*572A>T,MODIFIER,;BRCA2,missense_variant,p.L2838F,ENST00000680887.1,c.8514A>T,MODERATE,;BRCA2,missense_variant,NMD_transcript_variant,p.L2838F,ENST00000665585.2,c.8514A>T,MODERATE,;BRCA2,missense_variant,NMD_transcript_variant,p.L2838F,ENST00000666593.2,c.8514A>T,MODERATE,;BRCA2,missense_variant,NMD_transcript_variant,p.L2838F,ENST00000470094.2,c.8514A>T,MODERATE,;BRCA2,missense_variant,p.L2838F,ENST00000380152.8,c.8514A>T,MODERATE,YES;BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713679.1,c.*53A>T,MODIFIER,;BRCA2,missense_variant,p.L2838F,ENST00000700202.2,c.8514A>T,MODERATE,;BRCA2,missense_variant,NMD_transcript_variant,p.L2838F,ENST00000528762.2,c.8514A>T,MODERATE,;BRCA2,missense_variant,p.L2786F,ENST00000713680.1,c.8358A>T,MODERATE,;BRCA2,missense_variant,p.L2715F,ENST00000530893.7,c.8145A>T,MODERATE,;BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713677.1,c.*8153A>T,MODIFIER,;BRCA2,missense_variant,p.L2838F,ENST00000713678.1,c.8514A>T,MODERATE,;BRCA2,missense_variant,p.L2838F,ENST00000544455.6,c.8514A>T,MODERATE, +BRCA2 675 BI GRCh38 13 32370988 32370998 + frameshift_variant Frame_Shift_Del DEL ATTTCGCAATG ATTTCGCAATG - novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 38 16 c.8521_8531del p.Phe2841LysfsTer24 p.F2841Kfs*24 ENST00000380152.8 NM_000059.4 2840 atATTTCGCAATGaa/ataa 20/27 P1 - IFRNE/IX protein_coding YES CCDS9344.1 8520-8530/10257 ATACATATTTCGCAATGAAAGA Gene3D:1.10.132.40;Gene3D:2.40.50.140;Pfam:PF09121;PIRSF:PIRSF002397;PANTHER:PTHR11289;SMART:SM01341;Superfamily:SSF50249;Superfamily:SSF81878;CDD:cd04494;Low_complexity_(Seg):seg ENSP00000369497 20/27 ENST00000380152 Transcript 1.0 ENSG00000139618 HGNC:1101 1.0 HIGH NM_000059.4 frameshift_variant 1.0 Unknown P51587.222 BRCA2 HGNC 1 5.0 UPI00001FCBCC deletion BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000380152,NM_000059.4,c.8521_8531del,HIGH,YES,,,1;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000544455,,c.8521_8531del,HIGH,,,,1;BRCA2,frameshift_variant,p.F363Kfs*24,ENST00000665585,,c.1086_1096del,HIGH,,,,1;BRCA2,frameshift_variant,p.F7Kfs*24,ENST00000528762,,c.19_29del,HIGH,,,,1 8719-8729/11954 pindel;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 46 87a1660e-0b6f-486a-a768-e99cd8b7841a 54 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000614259.2,c.*578_*588del,MODIFIER,;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000680887.1,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,NMD_transcript_variant,p.F2841Kfs*24,ENST00000665585.2,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,NMD_transcript_variant,p.F2841Kfs*24,ENST00000666593.2,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,NMD_transcript_variant,p.F2841Kfs*24,ENST00000470094.2,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000380152.8,c.8521_8531del,HIGH,YES;BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713679.1,c.*59_*69del,MODIFIER,;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000700202.2,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,NMD_transcript_variant,p.F2841Kfs*24,ENST00000528762.2,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,p.F2789Kfs*24,ENST00000713680.1,c.8365_8375del,HIGH,;BRCA2,frameshift_variant,p.F2718Kfs*24,ENST00000530893.7,c.8152_8162del,HIGH,;BRCA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000713677.1,c.*8159_*8169del,MODIFIER,;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000713678.1,c.8521_8531del,HIGH,;BRCA2,frameshift_variant,p.F2841Kfs*24,ENST00000544455.6,c.8521_8531del,HIGH, +MAPKBP1 23005 BI GRCh38 15 41825413 41825413 + missense_variant Missense_Mutation SNP C C T rs533499391 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 4 26 c.4522C>T p.Arg1508Trp p.R1508W ENST00000456763.6 NM_001128608.2 1508 Cgg/Tgg 32/32 0.0002 0.0008 0.0 0.0 0.0 0.0 A2 T R/W protein_coding YES CCDS45239.1 4522/4545 TGGAACGGCGT PANTHER:PTHR45589;PANTHER:PTHR45589:SF5 ENSP00000393099 32/32 rs533499391 ENST00000456763 Transcript 1.0 ENSG00000137802 HGNC:29536 MODERATE 0.0008 AFR missense_variant 1.0 probably_damaging(0.969) Unknown deleterious(0) O60336.158 MAPKBP1 HGNC 1 1.0 UPI00002375CB O60336-1 SNV MAPKBP1,missense_variant,p.R1502W,ENST00000457542,NM_014994.3,c.4504C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;MAPKBP1,missense_variant,p.R1508W,ENST00000456763,NM_001128608.2,c.4522C>T,MODERATE,YES,deleterious(0),probably_damaging(0.969),1;MAPKBP1,missense_variant,p.R1225W,ENST00000514566,NM_001265611.2,c.3673C>T,MODERATE,,deleterious(0),possibly_damaging(0.636),1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000342159,NM_001198588.1,,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000382448,NM_005090.3,,MODIFIER,YES,,,1;JMJD7,upstream_gene_variant,,ENST00000397299,NM_001114632.2,,MODIFIER,YES,,,1;JMJD7,upstream_gene_variant,,ENST00000408047,,,MODIFIER,,,,1;JMJD7,upstream_gene_variant,,ENST00000431823,,,MODIFIER,,,,1;JMJD7,upstream_gene_variant,,ENST00000405106,,,MODIFIER,,,,1;MAPKBP1,3_prime_UTR_variant,,ENST00000512970,,c.*3318C>T,MODIFIER,,,,1;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,,c.*4055C>T,MODIFIER,,,,1;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,,n.5167C>T,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000490848,,,MODIFIER,,,,1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000491746,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000502695,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000506301,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000508050,,,MODIFIER,,,,1;MAPKBP1,downstream_gene_variant,,ENST00000512433,,,MODIFIER,,,,1;AC020659.2,intron_variant,,ENST00000510176,,n.311-40G>A,MODIFIER,YES,,,-1;AC020659.2,downstream_gene_variant,,ENST00000512295,,,MODIFIER,,,,-1 4718/7158 muse;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 4.011e-06 6.223e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.756939910701476e-06 2.430019958410412e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 10 87a1660e-0b6f-486a-a768-e99cd8b7841a 30 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS ENSG00000250379,intron_variant,,ENST00000510176.1,n.311-40G>A,MODIFIER,YES;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061.5,n.5167C>T,MODIFIER,;MAPKBP1,missense_variant,p.R1225W,ENST00000514566.5,c.3673C>T,MODERATE,;MAPKBP1,missense_variant,p.R1508W,ENST00000456763.6,c.4522C>T,MODERATE,;MAPKBP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000505373.5,c.*4055C>T,MODIFIER,;MAPKBP1,missense_variant,p.R1502W,ENST00000457542.7,c.4504C>T,MODERATE,YES;MAPKBP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000512970.5,c.*3318C>T,MODIFIER, +NOD2 64127 BI GRCh38 16 50723338 50723338 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 17 13 c.2836G>A p.Ala946Thr p.A946T ENST00000300589.6 NM_022162.3 946 Gcc/Acc 9/12 A2 A A/T protein_coding YES CCDS10746.1 2836/3123 CCCAAGCCTTG PROSITE_profiles:PS51450;PANTHER:PTHR24107;PANTHER:PTHR24107:SF19;Gene3D:3.80.10.10;Pfam:PF13516;SMART:SM00368;Superfamily:SSF52047 ENSP00000300589 9/12 ENST00000300589 Transcript 1.0 ENSG00000167207 HGNC:5331 MODERATE missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q9HC29.200 NOD2 HGNC 1 1.0 UPI000005027A Q9HC29-1 SNV NOD2,missense_variant,p.A946T,ENST00000300589,NM_022162.3,c.2836G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;NOD2,missense_variant,p.A919T,ENST00000647318,NM_001370466.1&NM_001293557.2,c.2755G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;NOD2,missense_variant,p.A158T,ENST00000534057,,c.472G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.475),1;NOD2,3_prime_UTR_variant,,ENST00000646677,,c.*520G>A,MODIFIER,,,,1;NOD2,3_prime_UTR_variant,,ENST00000534067,,c.*385G>A,MODIFIER,,,,1;NOD2,3_prime_UTR_variant,,ENST00000529633,,c.*233G>A,MODIFIER,,,,1;NOD2,3_prime_UTR_variant,,ENST00000524712,,c.*149G>A,MODIFIER,,,,1;NOD2,3_prime_UTR_variant,,ENST00000527052,,c.*121G>A,MODIFIER,,,,1;NOD2,intron_variant,,ENST00000641284,,c.*-6480G>A,MODIFIER,,,,1;AC007728.2,downstream_gene_variant,,ENST00000563315,,,MODIFIER,YES,,,-1 2941/4486 muse;mutect2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 23 87a1660e-0b6f-486a-a768-e99cd8b7841a 30 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS NOD2,non_coding_transcript_exon_variant,,ENST00000697428.1,n.2233G>A,MODIFIER,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000529633.5,c.*233G>A,MODIFIER,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697427.1,c.*205G>A,MODIFIER,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697425.1,c.*401G>A,MODIFIER,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000524712.5,c.*149G>A,MODIFIER,;NOD2,missense_variant,p.S157N,ENST00000697426.1,c.470G>A,MODERATE,;NOD2,missense_variant,p.S157N,ENST00000534057.1,c.470G>A,MODERATE,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000527052.5,c.*121G>A,MODIFIER,;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000534067.5,c.*385G>A,MODIFIER,;NOD2,missense_variant,p.A946T,ENST00000300589.6,c.2836G>A,MODERATE,;NOD2,intron_variant,NMD_transcript_variant,,ENST00000641284.2,c.2382-6480G>A,MODIFIER,;NOD2,missense_variant,p.A919T,ENST00000647318.2,c.2755G>A,MODERATE,YES;NOD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646677.2,c.*520G>A,MODIFIER, +FANCA 2175 BI GRCh38 16 89815970 89815970 + synonymous_variant Silent SNP C C T rs1381349863 TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 25 17 c.96G>A p.Arg32= p.R32= ENST00000389301.8 NM_000135.4 32 agG/agA 2/43 P4 T R protein_coding YES CCDS32515.1 96/4368 TTTTCCCTCTT PANTHER:PTHR12047 ENSP00000373952 2/43 rs1381349863 ENST00000389301 Transcript 1.0 ENSG00000187741 HGNC:3582 LOW NM_000135.4 synonymous_variant 1.0 Unknown O15360.188 FANCA HGNC -1 1.0 UPI0000520A1A O15360-1 SNV FANCA,synonymous_variant,p.R32=,ENST00000389301,NM_000135.4,c.96G>A,LOW,YES,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000568369,NM_001286167.3,c.96G>A,LOW,,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000563673,,c.96G>A,LOW,,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000389302,NM_001018112.3,c.96G>A,LOW,,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000534992,,c.96G>A,LOW,,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000543736,NM_001351830.2,c.96G>A,LOW,,,,-1;SPIRE2,upstream_gene_variant,,ENST00000564878,,,MODIFIER,,,,1;SPIRE2,upstream_gene_variant,,ENST00000565103,,,MODIFIER,,,,1;FANCA,synonymous_variant,p.R3=,ENST00000565582,,c.9G>A,LOW,,,,-1;FANCA,synonymous_variant,p.R32=,ENST00000563513,,c.96G>A,LOW,,,,-1;FANCA,3_prime_UTR_variant,,ENST00000567943,,c.*76G>A,MODIFIER,,,,-1;FANCA,non_coding_transcript_exon_variant,,ENST00000566889,,n.678G>A,MODIFIER,,,,-1;FANCA,non_coding_transcript_exon_variant,,ENST00000567883,,n.89G>A,MODIFIER,,,,-1 128/5452 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 6.757400115020573e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542830068501644e-05 0.0 0.0 0 53 87a1660e-0b6f-486a-a768-e99cd8b7841a 42 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS FANCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000567943.1,c.*76G>A,MODIFIER,;FANCA,non_coding_transcript_exon_variant,,ENST00000567883.5,n.89G>A,MODIFIER,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000563513.1,c.96G>A,LOW,;FANCA,synonymous_variant,NMD_transcript_variant,p.R3=,ENST00000565582.5,c.9G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000543736.5,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000534992.5,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000563673.5,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000389302.7,c.96G>A,LOW,;FANCA,non_coding_transcript_exon_variant,,ENST00000566889.5,n.678G>A,MODIFIER,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000567621.6,c.96G>A,LOW,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000696277.1,c.96G>A,LOW,;FANCA,non_coding_transcript_exon_variant,,ENST00000567284.7,n.139G>A,MODIFIER,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000567205.2,c.96G>A,LOW,;FANCA,non_coding_transcript_exon_variant,,ENST00000696276.1,n.139G>A,MODIFIER,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000696291.1,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000564475.6,c.96G>A,LOW,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000696275.1,c.96G>A,LOW,;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000696286.1,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000696287.1,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000568369.6,c.96G>A,LOW,;FANCA,synonymous_variant,p.R32=,ENST00000389301.8,c.96G>A,LOW,YES;FANCA,synonymous_variant,NMD_transcript_variant,p.R32=,ENST00000561667.2,c.96G>A,LOW, +SULF2 55959 BI GRCh38 20 47666434 47666434 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 44 30 c.1631T>A p.Val544Glu p.V544E ENST00000359930.8 NM_018837.4 544 gTg/gAg 12/21 P4 T V/E protein_coding YES CCDS13408.1 1631/2613 CGTCCACCTCG PANTHER:PTHR43108;PANTHER:PTHR43108:SF4;PIRSF:PIRSF036665;Pfam:PF12548 ENSP00000353007 12/21 ENST00000359930 Transcript ENSG00000196562 HGNC:20392 MODERATE missense_variant 1.0 benign(0.162) Unknown tolerated(0.19) Q8IWU5.156 SULF2 HGNC -1 1.0 UPI000003FFBA Q8IWU5-1 SNV SULF2,missense_variant,p.V544E,ENST00000359930,NM_018837.3,c.1631T>A,MODERATE,YES,tolerated(0.19),benign(0.162),-1;SULF2,missense_variant,p.V544E,ENST00000484875,NM_001161841.1,c.1631T>A,MODERATE,,tolerated(0.19),benign(0.162),-1;SULF2,missense_variant,p.V544E,ENST00000467815,NM_198596.2,c.1631T>A,MODERATE,,tolerated(0.22),benign(0.048),-1;SULF2,upstream_gene_variant,,ENST00000495544,,,MODIFIER,,,,-1;SULF2,upstream_gene_variant,,ENST00000433632,,,MODIFIER,,,,-1 2483/4915 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 61 87a1660e-0b6f-486a-a768-e99cd8b7841a 75 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS SULF2,missense_variant,p.V544E,ENST00000467815.5,c.1631T>A,MODERATE,;SULF2,missense_variant,p.V544E,ENST00000688720.1,c.1631T>A,MODERATE,YES;SULF2,missense_variant,p.V544E,ENST00000484875.5,c.1631T>A,MODERATE,;SULF2,missense_variant,p.V544E,ENST00000359930.8,c.1631T>A,MODERATE,;SULF2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698128.1,c.*1035T>A,MODIFIER, +ATP1B4 23439 BI GRCh38 X 120379612 120379612 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KI-01A TCGA-VD-A8KI-10A Somatic 5 42 c.1052T>C p.Phe351Ser p.F351S ENST00000218008.8 NM_001142447.3 351 tTt/tCt 8/8 P1 C F/S protein_coding YES CCDS48158.1 1052/1074 AATCTTTACCC Gene3D:2.60.40.1660;Pfam:PF00287;PANTHER:PTHR11523;PANTHER:PTHR11523:SF12;TIGRFAM:TIGR01107 ENSP00000218008 8/8 ENST00000218008 Transcript ENSG00000101892 HGNC:808 MODERATE NM_001142447.3 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q9UN42.153 ATP1B4 HGNC 1 1.0 UPI00001262A4 Q9UN42-1 SNV ATP1B4,missense_variant,p.F351S,ENST00000218008,NM_001142447.3,c.1052T>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;ATP1B4,missense_variant,p.F308S,ENST00000539306,,c.923T>C,MODERATE,,deleterious(0),probably_damaging(0.999),1;ATP1B4,missense_variant,p.F347S,ENST00000361319,NM_012069.5,c.1040T>C,MODERATE,,deleterious(0),probably_damaging(0.999),1 1132/4757 muse;mutect2;varscan2 22e7816d-4be9-4f84-b487-baa6ca35452d 0 63 87a1660e-0b6f-486a-a768-e99cd8b7841a 47 047fe9af-056f-45c3-ae39-74ae9e901ec2 SUCCESS ATP1B4,missense_variant,p.F347S,ENST00000361319.3,c.1040T>C,MODERATE,;ATP1B4,missense_variant,p.F351S,ENST00000218008.8,c.1052T>C,MODERATE,YES;ATP1B4,missense_variant,p.F308S,ENST00000539306.5,c.923T>C,MODERATE, +RTCA 8634 BI GRCh38 1 100275714 100275714 + missense_variant Missense_Mutation SNP A A G rs767927227 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 46 42 c.731A>G p.Asn244Ser p.N244S ENST00000370128.9 NM_003729.4 244 aAt/aGt 7/11 P1 G N/S protein_coding CCDS768.1 731/1101 TGGAAATGGAA Low_complexity_(Seg):seg;HAMAP:MF_00200;CDD:cd00874;PANTHER:PTHR11096;PANTHER:PTHR11096:SF0;Pfam:PF01137;Gene3D:3.30.360.20;TIGRFAM:TIGR03399;Pfam:PF05189;PIRSF:PIRSF005378;Gene3D:3.65.10.20;Superfamily:SSF52913 ENSP00000359146 7/11 rs767927227 ENST00000370128 Transcript ENSG00000137996 HGNC:17981 MODERATE NM_003729.4 6.175e-05 gnomAD_AFR missense_variant benign(0) Unknown tolerated(1) O00442.184 RTCA HGNC 1 1.0 UPI00001352BF O00442-1 SNV RTCA,missense_variant,p.N244S,ENST00000370128,NM_003729.4,c.731A>G,MODERATE,,tolerated(1),benign(0),1;RTCA,missense_variant,p.N257S,ENST00000260563,NM_001130841.1,c.770A>G,MODERATE,YES,tolerated(1),benign(0),1;RTCA,downstream_gene_variant,,ENST00000483474,,,MODIFIER,,,,1;RTCA,downstream_gene_variant,,ENST00000498617,,,MODIFIER,,,,1 891/2526 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 4.017e-06 6.175e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.756939910701476e-06 2.4306100385729223e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 97 57fa5336-6e2f-432d-95e1-66ba58816c83 88 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS RTCA,missense_variant,p.N257S,ENST00000260563.4,c.770A>G,MODERATE,;RTCA,missense_variant,p.N244S,ENST00000370128.9,c.731A>G,MODERATE,YES +ESRRG 2104 BI GRCh38 1 216519271 216519271 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 43 39 c.1013A>G p.Lys338Arg p.K338R ENST00000408911.8 NM_001438.4 338 aAa/aGa 6/7 P4 C K/R protein_coding CCDS41468.1 1013/1377 CTAATTTGGAC Gene3D:1.10.565.10;PDB-ENSP_mappings:1kv6.A;PDB-ENSP_mappings:1kv6.B;PDB-ENSP_mappings:1tfc.A;PDB-ENSP_mappings:1tfc.B;PDB-ENSP_mappings:1vjb.A;PDB-ENSP_mappings:1vjb.B;PDB-ENSP_mappings:2e2r.A;PDB-ENSP_mappings:2ewp.A;PDB-ENSP_mappings:2ewp.B;PDB-ENSP_mappings:2ewp.C;PDB-ENSP_mappings:2ewp.D;PDB-ENSP_mappings:2ewp.E;PDB-ENSP_mappings:2gp7.A;PDB-ENSP_mappings:2gp7.B;PDB-ENSP_mappings:2gp7.C;PDB-ENSP_mappings:2gp7.D;PDB-ENSP_mappings:2gpo.A;PDB-ENSP_mappings:2gpp.A;PDB-ENSP_mappings:2gpp.B;PDB-ENSP_mappings:2gpu.A;PDB-ENSP_mappings:2gpv.A;PDB-ENSP_mappings:2gpv.B;PDB-ENSP_mappings:2gpv.C;PDB-ENSP_mappings:2gpv.D;PDB-ENSP_mappings:2gpv.E;PDB-ENSP_mappings:2gpv.F;PDB-ENSP_mappings:2p7a.A;PDB-ENSP_mappings:2p7g.A;PDB-ENSP_mappings:2p7z.A;PDB-ENSP_mappings:2zas.A;PDB-ENSP_mappings:2zbs.A;PDB-ENSP_mappings:2zkc.A;PDB-ENSP_mappings:5yso.A;PDB-ENSP_mappings:5yso.B;PDB-ENSP_mappings:5yso.C;PDB-ENSP_mappings:6a6k.A;PDB-ENSP_mappings:6a6k.B;PDB-ENSP_mappings:6a6k.C;PDB-ENSP_mappings:6i61.A;PDB-ENSP_mappings:6i62.A;PDB-ENSP_mappings:6i63.A;PDB-ENSP_mappings:6i64.A;PDB-ENSP_mappings:6i65.A;PDB-ENSP_mappings:6i66.A;PDB-ENSP_mappings:6i67.A;PDB-ENSP_mappings:6k3n.A;Pfam:PF00104;PIRSF:PIRSF002527;PIRSF:PIRSF500939;PROSITE_profiles:PS51843;PANTHER:PTHR24084;PANTHER:PTHR24084:SF21;SMART:SM00430;Superfamily:SSF48508;CDD:cd06946 ENSP00000386171 6/7 ENST00000408911 Transcript ENSG00000196482 HGNC:3474 MODERATE NM_001438.4 missense_variant benign(0.006) Unknown tolerated(1) P62508.182 ESRRG HGNC -1 F1D8R5.73 1.0 UPI00000272E7 P62508-1 SNV ESRRG,missense_variant,p.K315R,ENST00000391890,NM_001243519.1&NM_001243515.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000360012,NM_001243514.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K350R,ENST00000366937,NM_001243518.2,c.1049A>G,MODERATE,YES,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000361525,NM_206594.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000366940,NM_001134285.3,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000493603,NM_001243511.3&NM_001243510.3&NM_001350124.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000366938,NM_001243513.1,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000361395,NM_001243505.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000359162,NM_001350122.2&NM_001243506.2&NM_206595.3&NM_001350123.2&NM_001350125.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K338R,ENST00000408911,NM_001438.4,c.1013A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000616180,,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K322R,ENST00000673908,,c.965A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K276R,ENST00000463665,NM_001243507.2,c.827A>G,MODERATE,,tolerated(1),benign(0.001),-1;ESRRG,missense_variant,p.K315R,ENST00000487276,NM_001243512.1,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000493748,NM_001243509.2,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1;ESRRG,missense_variant,p.K315R,ENST00000475275,,c.944A>G,MODERATE,,tolerated(1),benign(0.006),-1 1143/5195 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 69 57fa5336-6e2f-432d-95e1-66ba58816c83 82 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS ESRRG,missense_variant,p.K315R,ENST00000475275.5,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000493748.5,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000487276.5,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K276R,ENST00000463665.5,c.827A>G,MODERATE,;ESRRG,missense_variant,p.K322R,ENST00000673908.1,c.965A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000360012.7,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000361395.6,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K350R,ENST00000366937.5,c.1049A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000493603.5,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000366938.6,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000359162.6,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K338R,ENST00000408911.8,c.1013A>G,MODERATE,YES;ESRRG,missense_variant,p.K315R,ENST00000366940.6,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000391890.7,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000616180.4,c.944A>G,MODERATE,;ESRRG,missense_variant,p.K315R,ENST00000361525.7,c.944A>G,MODERATE, +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 27 20 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 56 57fa5336-6e2f-432d-95e1-66ba58816c83 48 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +GASK1B 51313 BI GRCh38 4 158155671 158155671 + synonymous_variant Silent SNP A A G rs1205717948 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 34 27 c.1065T>C p.Gly355= p.G355= ENST00000296530.12 NM_016613.7 355 ggT/ggC 3/5 P1 G G protein_coding CCDS3798.1 1065/1560 GTACAACCCGA Pfam:PF15051;PANTHER:PTHR15905;PANTHER:PTHR15905:SF1 ENSP00000296530 3/5 rs1205717948 ENST00000296530 Transcript ENSG00000164125 HGNC:25312 LOW 5.437e-05 gnomAD_EAS synonymous_variant Unknown Q6UWH4.120 GASK1B HGNC -1 1.0 UPI000004C63B Q6UWH4-1 SNV GASK1B,synonymous_variant,p.G355=,ENST00000296530,NM_016613.7,c.1065T>C,LOW,,,,-1;GASK1B,synonymous_variant,p.G355=,ENST00000585682,NM_001128424.2,c.1065T>C,LOW,,,,-1;GASK1B,synonymous_variant,p.G363=,ENST00000393807,NM_001031700.3,c.1089T>C,LOW,YES,,,-1;GASK1B,synonymous_variant,p.G61=,ENST00000590648,,c.183T>C,LOW,,,,-1;GASK1B,synonymous_variant,p.G96=,ENST00000593260,,c.288T>C,LOW,,,,-1;GASK1B,5_prime_UTR_variant,,ENST00000592586,,c.-34T>C,MODIFIER,,,,-1;GASK1B,non_coding_transcript_exon_variant,,ENST00000589306,,n.311T>C,MODIFIER,,,,-1 1687/4985 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 3.979e-06 0.0 0.0 0.0 5.437e-05 0.0 0.0 0.0 0.0 0 65 57fa5336-6e2f-432d-95e1-66ba58816c83 61 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS GASK1B,non_coding_transcript_exon_variant,,ENST00000589306.1,n.311T>C,MODIFIER,;GASK1B,missense_variant,p.V96A,ENST00000593260.1,c.287T>C,MODERATE,;GASK1B,5_prime_UTR_variant,,ENST00000592586.1,c.-34T>C,MODIFIER,;GASK1B,synonymous_variant,p.G61=,ENST00000590648.5,c.183T>C,LOW,;GASK1B,synonymous_variant,p.G363=,ENST00000393807.9,c.1089T>C,LOW,;GASK1B,synonymous_variant,p.G355=,ENST00000296530.12,c.1065T>C,LOW,;GASK1B,synonymous_variant,p.G355=,ENST00000585682.6,c.1065T>C,LOW,YES +FASTKD3 79072 BI GRCh38 5 7859462 7859462 + synonymous_variant Silent SNP T T C rs1423019770 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 24 16 c.1962A>G p.Gln654= p.Q654= ENST00000264669.10 NM_024091.4 654 caA/caG 7/7 P1 C Q protein_coding YES CCDS3873.1 1962/1989 GTGTTTTGAGA PANTHER:PTHR21228;PANTHER:PTHR21228:SF9 ENSP00000264669 7/7 rs1423019770 ENST00000264669 Transcript ENSG00000124279 HGNC:28758 LOW NM_024091.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q14CZ7.97 FASTKD3 HGNC -1 2.0 UPI000020BF43 SNV FASTKD3,synonymous_variant,p.Q654=,ENST00000264669,NM_024091.4,c.1962A>G,LOW,YES,,,-1;FASTKD3,non_coding_transcript_exon_variant,,ENST00000513658,,n.693A>G,MODIFIER,,,,-1;FASTKD3,non_coding_transcript_exon_variant,,ENST00000282110,,n.556A>G,MODIFIER,,,,-1;MTRR,intron_variant,,ENST00000502509,,n.392-2489T>C,MODIFIER,,,,1;MTRR,intron_variant,,ENST00000507837,,n.507-2489T>C,MODIFIER,,,,1;MTRR,intron_variant,,ENST00000511639,,n.493-2023T>C,MODIFIER,,,,1;FASTKD3,3_prime_UTR_variant,,ENST00000507036,,c.*256A>G,MODIFIER,,,,-1;FASTKD3,3_prime_UTR_variant,,ENST00000511261,,c.*1225A>G,MODIFIER,,,,-1;FASTKD3,downstream_gene_variant,,ENST00000513577,,,MODIFIER,,,,-1 2128/2431 muse;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 81 57fa5336-6e2f-432d-95e1-66ba58816c83 40 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS FASTKD3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000507036.1,c.*256A>G,MODIFIER,;FASTKD3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000511261.5,c.*1225A>G,MODIFIER,;FASTKD3,non_coding_transcript_exon_variant,,ENST00000282110.8,n.556A>G,MODIFIER,;FASTKD3,non_coding_transcript_exon_variant,,ENST00000513658.5,n.693A>G,MODIFIER,;FASTKD3,synonymous_variant,p.Q654=,ENST00000264669.10,c.1962A>G,LOW,YES;MTRR,intron_variant,,ENST00000511639.1,n.493-2023T>C,MODIFIER,;MTRR,intron_variant,,ENST00000502509.5,n.392-2489T>C,MODIFIER,;MTRR,intron_variant,,ENST00000507837.5,n.507-2489T>C,MODIFIER, +ATXN1 6310 BI GRCh38 6 16327027 16327027 + synonymous_variant Silent SNP G G C rs745328393 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 156 51 c.1284C>G p.Leu428= p.L428= ENST00000244769.8 NM_000332.4 428 ctC/ctG 8/9 P1 C L protein_coding YES CCDS34342.1 1284/2448 GGTGAGAGCGC COSM5357838 PANTHER:PTHR13392;PANTHER:PTHR13392:SF5 ENSP00000244769 8/9 rs745328393;COSV55208829;COSV55216723 ENST00000244769 Transcript 1.0 ENSG00000124788 HGNC:10548 LOW 0.0003077 gnomAD_AFR synonymous_variant 0;1;1 1.0 Unknown 0;1;1 P54253.195 ATXN1 HGNC -1 1.0 UPI000013CB8B P54253-1 SNV ATXN1,synonymous_variant,p.L428=,ENST00000244769,NM_000332.3,c.1284C>G,LOW,YES,,,-1;ATXN1,synonymous_variant,p.L428=,ENST00000436367,NM_001128164.2,c.1284C>G,LOW,,,,-1;ATXN1,downstream_gene_variant,,ENST00000642969,NM_001357857.2,,MODIFIER,,,,-1 2221/10602 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 3.182e-05 0.0003077 5.782e-05 0.0 0.0 0.0 8.793e-06 0.0 0.0 9.462909656576812e-05 0.0003161939966958 0.0 6.622519867960364e-05 0.0 0.0 0.0 afr 0.0003161939966958 0.0 0.0 0.0 0.0 0 158 57fa5336-6e2f-432d-95e1-66ba58816c83 207 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS ATXN1,synonymous_variant,p.L428=,ENST00000244769.8,c.1284C>G,LOW,;ATXN1,synonymous_variant,p.L428=,ENST00000436367.6,c.1284C>G,LOW,YES +TRIM15 89870 BI GRCh38 6 30167265 30167265 + synonymous_variant Silent SNP G G A novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 48 106 c.471G>A p.Val157= p.V157= ENST00000376694.9 NM_033229.3 157 gtG/gtA 2/7 P1 A V protein_coding YES CCDS4677.1 471/1398 CAAGTGCTGCT PANTHER:PTHR24103;PANTHER:PTHR24103:SF259 ENSP00000365884 2/7 ENST00000376694 Transcript ENSG00000204610 HGNC:16284 LOW NM_033229.3 synonymous_variant 1.0 Unknown Q9C019.172 TRIM15 HGNC 1 Q5SRL0.162 1.0 UPI0000137066 Q9C019-1 SNV TRIM15,synonymous_variant,p.V88=,ENST00000619857,,c.264G>A,LOW,,,,1;TRIM15,synonymous_variant,p.V157=,ENST00000376694,NM_033229.3,c.471G>A,LOW,YES,,,1;TRIM15,intron_variant,,ENST00000376688,,c.304+3277G>A,MODIFIER,,,,1;TRIM15,upstream_gene_variant,,ENST00000433744,,,MODIFIER,,,,1;TRIM15,upstream_gene_variant,,ENST00000477944,,,MODIFIER,,,,1 610/1881 muse;mutect2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 72 57fa5336-6e2f-432d-95e1-66ba58816c83 154 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS TRIM15,synonymous_variant,p.V157=,ENST00000376694.9,c.471G>A,LOW,YES;TRIM15,synonymous_variant,p.V88=,ENST00000619857.4,c.264G>A,LOW, +TRERF1 55809 BI GRCh38 6 42228458 42228458 + missense_variant Missense_Mutation SNP C C T rs762778385 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 174 59 c.3490G>A p.Asp1164Asn p.D1164N ENST00000372922.8 NM_033502.4 1164 Gac/Aac 18/18 A2 T D/N protein_coding CCDS4867.1 3490/3603 GTCGTCGTCGA COSM4947548;COSM4947549;COSM76808 PANTHER:PTHR16089;PANTHER:PTHR16089:SF19;Low_complexity_(Seg):seg ENSP00000362013 18/18 rs762778385;COSV61671651 ENST00000372922 Transcript ENSG00000124496 HGNC:18273 MODERATE 6.533e-05 gnomAD_SAS missense_variant 0;1 benign(0) Unknown tolerated_low_confidence(0.14) 0;1 Q96PN7.159 TRERF1 HGNC -1 1.0 UPI0000052952 Q96PN7-1 SNV TRERF1,missense_variant,p.D1184N,ENST00000541110,NM_001297573.1,c.3550G>A,MODERATE,YES,tolerated_low_confidence(0.14),benign(0),-1;TRERF1,missense_variant,p.D1164N,ENST00000372922,NM_033502.4,c.3490G>A,MODERATE,,tolerated_low_confidence(0.14),benign(0),-1;TRERF1,missense_variant,p.D1093N,ENST00000340840,,c.3277G>A,MODERATE,,tolerated_low_confidence(0.06),benign(0.003),-1;TRERF1,missense_variant,p.D1081N,ENST00000354325,,c.3241G>A,MODERATE,,tolerated_low_confidence(0.06),benign(0.003),-1;TRERF1,missense_variant,p.D920N,ENST00000372917,,c.2758G>A,MODERATE,,tolerated_low_confidence(0.06),benign(0.003),-1 4053/7286 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 1.193e-05 0.0 2.891e-05 0.0 0.0 0.0 0.0 0.0 6.533e-05 2.02784995053662e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.628919850802049e-05 0.0 4.628919850802049e-05 0.0 0.0 0 153 57fa5336-6e2f-432d-95e1-66ba58816c83 234 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS TRERF1,missense_variant,p.D1081N,ENST00000354325.2,c.3241G>A,MODERATE,;TRERF1,missense_variant,p.D1093N,ENST00000340840.6,c.3277G>A,MODERATE,;TRERF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695947.1,c.*2760G>A,MODIFIER,;TRERF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000372917.9,c.*2724G>A,MODIFIER,;TRERF1,missense_variant,p.D1164N,ENST00000372922.8,c.3490G>A,MODERATE,;TRERF1,missense_variant,p.D1176N,ENST00000695948.1,c.3526G>A,MODERATE,YES;TRERF1,missense_variant,p.D1184N,ENST00000541110.5,c.3550G>A,MODERATE,;TRERF1,missense_variant,p.D1164N,ENST00000695966.1,c.3490G>A,MODERATE, +AMZ1 155185 BI GRCh38 7 2700623 2700623 + missense_variant Missense_Mutation SNP C C G rs754107925 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 53 58 c.172C>G p.Leu58Val p.L58V ENST00000312371.8 NM_133463.4 58 Ctg/Gtg 2/7 P1 G L/V protein_coding YES CCDS34589.1 172/1497 GCACCCTGCTC PANTHER:PTHR32205:SF4;PANTHER:PTHR32205 ENSP00000308149 2/7 rs754107925 ENST00000312371 Transcript ENSG00000174945 HGNC:22231 MODERATE 6.16e-05 gnomAD_AFR missense_variant 1.0 benign(0.433) Unknown deleterious(0.01) Q400G9.116 AMZ1 HGNC 1 A4D202.105 1.0 UPI00001C1E77 Q400G9-1 SNV AMZ1,missense_variant,p.L58V,ENST00000312371,NM_133463.3&NM_001321766.1,c.172C>G,MODERATE,YES,deleterious(0.01),benign(0.433),1;AMZ1,missense_variant,p.L58V,ENST00000407112,NM_001284355.3,c.172C>G,MODERATE,,deleterious(0.02),possibly_damaging(0.763),1;AMZ1,upstream_gene_variant,,ENST00000485540,,,MODIFIER,,,,1;AMZ1,upstream_gene_variant,,ENST00000489665,,,MODIFIER,,,,1;AMZ1,upstream_gene_variant,,ENST00000480560,,,MODIFIER,,,,1 540/5516 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 4.056e-06 6.16e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.757939900126075e-06 2.4306100385729223e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 171 57fa5336-6e2f-432d-95e1-66ba58816c83 111 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS AMZ1,missense_variant,p.L58V,ENST00000407112.1,c.172C>G,MODERATE,;AMZ1,missense_variant,p.L58V,ENST00000683327.1,c.172C>G,MODERATE,YES;AMZ1,missense_variant,p.L58V,ENST00000312371.8,c.172C>G,MODERATE, +DNAJB6 10049 BI GRCh38 7 157384946 157384962 + frameshift_variant Frame_Shift_Del DEL CAACTTCAAATCGATAT CAACTTCAAATCGATAT - novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 66 24 c.567_583del p.Lys189AsnfsTer2 p.K189Nfs*2 ENST00000262177.9 NM_058246.4 186 ggCAACTTCAAATCGATATca/ggca 7/10 - GNFKSIS/GX protein_coding CCDS5946.1 558-574/981 CATGGGCAACTTCAAATCGATATCAACT PDB-ENSP_mappings:6u3r.A;PDB-ENSP_mappings:6u3s.A;PANTHER:PTHR43948;PANTHER:PTHR43948:SF6 ENSP00000262177 7/10 ENST00000262177 Transcript 1.0 ENSG00000105993 HGNC:14888 9.0 HIGH NM_058246.4 frameshift_variant Unknown O75190.194 DNAJB6 HGNC 1 1.0 UPI0000129436 O75190-1 deletion DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000262177,NM_058246.4,c.567_583del,HIGH,,,,1;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000429029,NM_005494.3,c.567_583del,HIGH,,,,1;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000634080,,c.567_583del,HIGH,YES,,,1;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000417758,,c.567_583del,HIGH,,,,1;DNAJB6,intron_variant,,ENST00000443280,NM_001363676.1,c.346+17472_346+17488del,MODIFIER,,,,1;DNAJB6,downstream_gene_variant,,ENST00000412557,,,MODIFIER,,,,1;DNAJB6,downstream_gene_variant,,ENST00000441561,,,MODIFIER,,,,1;DNAJB6,non_coding_transcript_exon_variant,,ENST00000465908,,n.363_379del,MODIFIER,,,,1;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000459889,,c.567_583del,HIGH,,,,1;DNAJB6,non_coding_transcript_exon_variant,,ENST00000487480,,n.4342_4358del,MODIFIER,,,,1;DNAJB6,non_coding_transcript_exon_variant,,ENST00000468928,,n.872_888del,MODIFIER,,,,1;DNAJB6,downstream_gene_variant,,ENST00000441291,,,MODIFIER,,,,1;DNAJB6,downstream_gene_variant,,ENST00000486247,,,MODIFIER,,,,1 725-741/2489 mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 149 57fa5336-6e2f-432d-95e1-66ba58816c83 90 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS DNAJB6,non_coding_transcript_exon_variant,,ENST00000487480.1,n.4333_4349del,MODIFIER,;DNAJB6,non_coding_transcript_exon_variant,,ENST00000465908.5,n.354_370del,MODIFIER,;DNAJB6,non_coding_transcript_exon_variant,,ENST00000468928.5,n.863_879del,MODIFIER,;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000634080.1,c.567_583del,HIGH,;DNAJB6,intron_variant,,ENST00000443280.5,c.346+17463_346+17479del,MODIFIER,;DNAJB6,frameshift_variant,NMD_transcript_variant,p.K189Nfs*2,ENST00000459889.5,c.567_583del,HIGH,;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000417758.5,c.567_583del,HIGH,;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000262177.9,c.567_583del,HIGH,YES;DNAJB6,frameshift_variant,p.K189Nfs*2,ENST00000429029.6,c.567_583del,HIGH, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 43 38 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 109 57fa5336-6e2f-432d-95e1-66ba58816c83 81 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +SLC28A3 64078 BI GRCh38 9 84279273 84279273 + synonymous_variant Silent SNP C C A rs921347526 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 34 20 c.1941G>T p.Leu647= p.L647= ENST00000376238.5 NM_022127.3 647 ctG/ctT 17/18 P1 A L protein_coding YES CCDS6670.1 1941/2076 CTCAACAGACT PANTHER:PTHR10590;PANTHER:PTHR10590:SF18 ENSP00000365413 17/18 rs921347526 ENST00000376238 Transcript ENSG00000197506 HGNC:16484 LOW NM_001199633.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q9HAS3.149 SLC28A3 HGNC -1 1.0 UPI000006F5A6 Q9HAS3-1 SNV SLC28A3,synonymous_variant,p.L647=,ENST00000376238,NM_022127.3&NM_001199633.2,c.1941G>T,LOW,YES,,,-1;AL356134.1,intron_variant,,ENST00000419815,,n.181+874C>A,MODIFIER,YES,,,1 2066/4962 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 87 57fa5336-6e2f-432d-95e1-66ba58816c83 54 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS SLC28A3-AS1,intron_variant,,ENST00000419815.1,n.181+874C>A,MODIFIER,YES;SLC28A3,synonymous_variant,p.L647=,ENST00000376238.5,c.1941G>T,LOW,YES +FGFR2 2263 BI GRCh38 10 121538712 121538712 + stop_gained Nonsense_Mutation SNP G G A TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 36 34 c.628C>T p.Arg210Ter p.R210* ENST00000358487.10 NM_000141.5 210 Cga/Tga 6/18 A2 A R/* protein_coding CCDS31298.1 628/2466 GTTTCGTACCT PDB-ENSP_mappings:1djs.A;PDB-ENSP_mappings:1e0o.B;PDB-ENSP_mappings:1e0o.D;PDB-ENSP_mappings:1ev2.E;PDB-ENSP_mappings:1ev2.F;PDB-ENSP_mappings:1ev2.G;PDB-ENSP_mappings:1ev2.H;PDB-ENSP_mappings:1ii4.E;PDB-ENSP_mappings:1ii4.F;PDB-ENSP_mappings:1ii4.G;PDB-ENSP_mappings:1ii4.H;PDB-ENSP_mappings:1iil.E;PDB-ENSP_mappings:1iil.F;PDB-ENSP_mappings:1iil.G;PDB-ENSP_mappings:1iil.H;PDB-ENSP_mappings:1nun.B;PDB-ENSP_mappings:1wvz.A;PDB-ENSP_mappings:2fdb.P;PDB-ENSP_mappings:2fdb.R;PDB-ENSP_mappings:3caf.A;PDB-ENSP_mappings:3cu1.A;PDB-ENSP_mappings:3cu1.C;PDB-ENSP_mappings:3dar.A;PDB-ENSP_mappings:3dar.B;PDB-ENSP_mappings:3euu.A;PDB-ENSP_mappings:3euu.B;PDB-ENSP_mappings:3oj2.C;PDB-ENSP_mappings:3oj2.D;PDB-ENSP_mappings:3ojm.B;PDB-ENSP_mappings:4j23.A;PDB-ENSP_mappings:4wv1.C;PDB-ENSP_mappings:4wv1.F;CDD:cd05857;PIRSF:PIRSF000628;Pfam:PF07679;Gene3D:2.60.40.10;SMART:SM00409;SMART:SM00408;Superfamily:SSF48726;PROSITE_profiles:PS50835;PANTHER:PTHR24416;PANTHER:PTHR24416:SF130 ENSP00000351276 6/18 COSV60651530 ENST00000358487 Transcript 1.0 ENSG00000066468 HGNC:3689 HIGH NM_000141.5 stop_gained 1 Unknown 1 P21802.253 FGFR2 HGNC -1 1.0 UPI000012A72A P21802-1 SNV FGFR2,stop_gained,p.R210*,ENST00000358487,NM_000141.5,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R121*,ENST00000613048,NM_023029.2,c.361C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000369061,NM_001144914.1,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R121*,ENST00000357555,NM_001144915.1,c.361C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R95*,ENST00000356226,NM_001144916.1&NM_001144918.2,c.283C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000369060,NM_001144917.2,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000457416,NM_022970.3,c.628C>T,HIGH,YES,,,-1;FGFR2,stop_gained,p.R95*,ENST00000369059,,c.283C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R121*,ENST00000360144,NM_001144919.2,c.361C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000369058,,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000369056,NM_001144913.1,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R121*,ENST00000336553,,c.361C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000351936,,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000346997,NM_001320658.2,c.628C>T,HIGH,,,,-1;FGFR2,stop_gained,p.R210*,ENST00000359354,,c.628C>T,HIGH,,,,-1;FGFR2,non_coding_transcript_exon_variant,,ENST00000490349,,n.889C>T,MODIFIER,,,,-1;FGFR2,stop_gained,p.R95*,ENST00000604236,,c.283C>T,HIGH,,,,-1 1261/4624 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 83 57fa5336-6e2f-432d-95e1-66ba58816c83 70 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS FGFR2,stop_gained,p.R210*,ENST00000359354.6,c.628C>T,HIGH,;FGFR2,non_coding_transcript_exon_variant,,ENST00000490349.5,n.889C>T,MODIFIER,;FGFR2,non_coding_transcript_exon_variant,,ENST00000683678.1,n.628C>T,MODIFIER,;FGFR2,non_coding_transcript_exon_variant,,ENST00000682400.1,n.283C>T,MODIFIER,;FGFR2,stop_gained,p.R121*,ENST00000336553.10,c.361C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000369058.7,c.628C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000369056.5,c.628C>T,HIGH,;FGFR2,stop_gained,p.R121*,ENST00000360144.7,c.361C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000346997.6,c.628C>T,HIGH,;FGFR2,stop_gained,p.R95*,ENST00000369059.5,c.283C>T,HIGH,;FGFR2,stop_gained,NMD_transcript_variant,p.R95*,ENST00000604236.5,c.283C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000369060.8,c.628C>T,HIGH,;FGFR2,stop_gained,p.R95*,ENST00000356226.8,c.283C>T,HIGH,;FGFR2,stop_gained,p.R95*,ENST00000684153.1,c.283C>T,HIGH,;FGFR2,stop_gained,NMD_transcript_variant,p.R95*,ENST00000683250.1,c.283C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000683211.1,c.628C>T,HIGH,;FGFR2,non_coding_transcript_exon_variant,,ENST00000683418.1,n.2975C>T,MODIFIER,;FGFR2,stop_gained,p.R210*,ENST00000351936.11,c.628C>T,HIGH,;FGFR2,stop_gained,p.R95*,ENST00000682550.1,c.283C>T,HIGH,;FGFR2,stop_gained,p.R121*,ENST00000613048.4,c.361C>T,HIGH,;FGFR2,stop_gained,p.R121*,ENST00000357555.9,c.361C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000369061.8,c.628C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000457416.7,c.628C>T,HIGH,;FGFR2,stop_gained,p.R210*,ENST00000358487.10,c.628C>T,HIGH,YES +ALG9 79796 BI GRCh38 11 111844619 111844619 + synonymous_variant Silent SNP G G A novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 100 96 c.1000C>T p.Leu334= p.L334= ENST00000614444.4 NM_001352418.1 334 Ctg/Ttg 9/15 P1 A L protein_coding CCDS73379.1 1000/1836 CAGCAGGTATT PANTHER:PTHR22760:SF2;PANTHER:PTHR22760;Pfam:PF03901 ENSP00000484200 9/15 ENST00000614444 Transcript 1.0 ENSG00000086848 HGNC:15672 LOW synonymous_variant Unknown Q9H6U8.153 ALG9 HGNC -1 1.0 UPI0000037C0B Q9H6U8-1 SNV ALG9,synonymous_variant,p.L334=,ENST00000616540,NM_024740.2,c.1000C>T,LOW,YES,,,-1;AP001781.2,synonymous_variant,p.L567=,ENST00000622211,,c.1699C>T,LOW,YES,,,-1;ALG9,synonymous_variant,p.L163=,ENST00000398006,NM_001352409.1&NM_001352410.1&NM_001352412.2&NM_001077692.2&NM_001352420.2&NM_001352421.2&NM_001352422.2&NM_001352423.2&NM_001352411.2&NM_001352416.1&NM_001352415.1,c.487C>T,LOW,,,,-1;ALG9,synonymous_variant,p.L334=,ENST00000614444,NM_001352418.1&NM_001352417.1&NM_001077690.1,c.1000C>T,LOW,,,,-1;ALG9,synonymous_variant,p.L163=,ENST00000531154,NM_001352413.1&NM_001352414.2&NM_001077691.2&NM_001352419.1,c.487C>T,LOW,,,,-1;ALG9,non_coding_transcript_exon_variant,,ENST00000527294,,n.318C>T,MODIFIER,,,,-1;ALG9,intron_variant,,ENST00000530851,,n.537+8761C>T,MODIFIER,,,,-1;ALG9,3_prime_UTR_variant,,ENST00000619129,,c.*552C>T,MODIFIER,,,,-1;ALG9,3_prime_UTR_variant,,ENST00000613181,,c.*422C>T,MODIFIER,,,,-1;ALG9,non_coding_transcript_exon_variant,,ENST00000527714,,n.642C>T,MODIFIER,,,,-1;ALG9,downstream_gene_variant,,ENST00000618252,,,MODIFIER,,,,-1 1051/2028 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 211 57fa5336-6e2f-432d-95e1-66ba58816c83 196 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS ALG9,non_coding_transcript_exon_variant,,ENST00000527714.5,n.642C>T,MODIFIER,;ALG9,non_coding_transcript_exon_variant,,ENST00000527294.5,n.318C>T,MODIFIER,;ALG9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000613181.4,c.*422C>T,MODIFIER,;ALG9,intron_variant,,ENST00000530851.6,n.537+8761C>T,MODIFIER,;ENSG00000258529,synonymous_variant,p.L567=,ENST00000622211.4,c.1699C>T,LOW,YES;ALG9,synonymous_variant,p.L163=,ENST00000398006.6,c.487C>T,LOW,;ALG9,synonymous_variant,p.L163=,ENST00000531154.5,c.487C>T,LOW,;ALG9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000619129.4,c.*552C>T,MODIFIER,;ALG9,synonymous_variant,p.L334=,ENST00000614444.4,c.1000C>T,LOW,;ALG9,synonymous_variant,p.L334=,ENST00000616540.5,c.1000C>T,LOW,YES +SORL1 6653 BI GRCh38 11 121558763 121558763 + missense_variant Missense_Mutation SNP A A T novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 53 25 c.2836A>T p.Ile946Phe p.I946F ENST00000260197.12 NM_003105.6 946 Atc/Ttc 20/48 P1 T I/F protein_coding YES CCDS8436.1 2836/6645 AGCGGATCACG Gene3D:2.120.10.30;PROSITE_profiles:PS51120;PANTHER:PTHR24270;PANTHER:PTHR24270:SF9;SMART:SM00135;Superfamily:SSF63825 ENSP00000260197 20/48 ENST00000260197 Transcript 1.0 ENSG00000137642 HGNC:11185 MODERATE NM_003105.6 missense_variant 1.0 benign(0.047) Unknown deleterious(0.05) Q92673.204 SORL1 HGNC 1 1.0 UPI000013D0B1 SNV SORL1,missense_variant,p.I946F,ENST00000260197,NM_003105.6,c.2836A>T,MODERATE,YES,deleterious(0.05),benign(0.047),1;SORL1,non_coding_transcript_exon_variant,,ENST00000529445,,n.542A>T,MODIFIER,,,,1;SORL1,non_coding_transcript_exon_variant,,ENST00000524873,,n.564A>T,MODIFIER,,,,1 2854/10863 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 92 57fa5336-6e2f-432d-95e1-66ba58816c83 78 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS SORL1,non_coding_transcript_exon_variant,,ENST00000524873.1,n.564A>T,MODIFIER,;SORL1,non_coding_transcript_exon_variant,,ENST00000529445.1,n.542A>T,MODIFIER,;SORL1,missense_variant,p.I946F,ENST00000260197.12,c.2836A>T,MODERATE,YES +BAZ2A 11176 BI GRCh38 12 56609798 56609798 + missense_variant Missense_Mutation SNP A A C rs1254132684 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 14 9 c.2036T>G p.Val679Gly p.V679G ENST00000551812.5 NM_013449.4 679 gTc/gGc 10/29 P4 C V/G protein_coding YES CCDS44924.1 2036/5718 TTTTGACCTTA MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;SMART:SM00384;PANTHER:PTHR45915;PANTHER:PTHR45915:SF5 ENSP00000446880 10/29 rs1254132684 ENST00000551812 Transcript ENSG00000076108 HGNC:962 MODERATE 8.854e-06 gnomAD_NFE missense_variant 1.0 benign(0.368) Unknown deleterious(0) Q9UIF9.193 BAZ2A HGNC -1 1.0 UPI0000D4FED1 Q9UIF9-1 SNV BAZ2A,missense_variant,p.V677G,ENST00000549884,NM_001351156.2&NM_001300905.2,c.2030T>G,MODERATE,,deleterious(0),benign(0.368),-1;BAZ2A,missense_variant,p.V649G,ENST00000379441,,c.1946T>G,MODERATE,,deleterious(0),possibly_damaging(0.659),-1;BAZ2A,missense_variant,p.V679G,ENST00000551812,NM_013449.4,c.2036T>G,MODERATE,YES,deleterious(0),benign(0.368),-1;BAZ2A,missense_variant,p.V105G,ENST00000547650,,c.314T>G,MODERATE,,tolerated(0.06),probably_damaging(0.942),-1;BAZ2A,downstream_gene_variant,,ENST00000551996,,,MODIFIER,,,,-1;BAZ2A,downstream_gene_variant,,ENST00000547647,,,MODIFIER,,,,-1;BAZ2A,downstream_gene_variant,,ENST00000549327,,,MODIFIER,,,,-1;BAZ2A,upstream_gene_variant,,ENST00000549763,,,MODIFIER,,,,-1;BAZ2A,upstream_gene_variant,,ENST00000548578,,,MODIFIER,,,,-1;BAZ2A,upstream_gene_variant,,ENST00000551759,,,MODIFIER,,,,-1 2230/8600 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 4.014e-06 0.0 0.0 0.0 0.0 0.0 8.854e-06 0.0 0.0 0 44 57fa5336-6e2f-432d-95e1-66ba58816c83 23 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS BAZ2A,missense_variant,p.S105A,ENST00000547650.1,c.313T>G,MODERATE,;BAZ2A,missense_variant,p.V679G,ENST00000551812.5,c.2036T>G,MODERATE,;BAZ2A,missense_variant,p.V649G,ENST00000379441.7,c.1946T>G,MODERATE,;BAZ2A,missense_variant,p.V677G,ENST00000549884.6,c.2030T>G,MODERATE,YES +SSH1 54434 BI GRCh38 12 108788337 108788337 + missense_variant Missense_Mutation SNP C C T rs1478632697 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 33 34 c.2801G>A p.Arg934Gln p.R934Q ENST00000326495.10 NM_018984.4 934 cGg/cAg 15/15 P3 T R/Q protein_coding YES CCDS9121.1 2801/3150 AGCTCCGGGTC Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR45864:SF5;PANTHER:PTHR45864 ENSP00000315713 15/15 rs1478632697;COSV100425448 ENST00000326495 Transcript ENSG00000084112 HGNC:30579 MODERATE NM_018984.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.715) Unknown deleterious_low_confidence(0) 0;1 Q8WYL5.163 SSH1 HGNC -1 1.0 UPI000003E894 Q8WYL5-1 SNV SSH1,missense_variant,p.R934Q,ENST00000326495,NM_018984.4,c.2801G>A,MODERATE,YES,deleterious_low_confidence(0),possibly_damaging(0.715),-1;SSH1,downstream_gene_variant,,ENST00000326470,NM_001161331.1,,MODIFIER,,,,-1;SSH1,downstream_gene_variant,,ENST00000551165,NM_001161330.2,,MODIFIER,,,,-1;SSH1,3_prime_UTR_variant,,ENST00000546433,,c.*1794G>A,MODIFIER,,,,-1 2888/13034 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.763149940525182e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433999578817748e-05 0.0 0.0 0 78 57fa5336-6e2f-432d-95e1-66ba58816c83 67 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS SSH1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000546433.5,c.*1794G>A,MODIFIER,;SSH1,missense_variant,p.R934Q,ENST00000326495.10,c.2801G>A,MODERATE,YES +CFAP251 144406 BI GRCh38 12 121954173 121954173 + synonymous_variant Silent SNP A A G novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 43 60 c.1374A>G p.Leu458= p.L458= ENST00000288912.9 NM_144668.6 458 ttA/ttG 10/22 P4 G L protein_coding YES CCDS41853.1 1374/3450 AATTTAACACA PANTHER:PTHR13720:SF13;PANTHER:PTHR13720;Gene3D:2.130.10.10;SMART:SM00320;Superfamily:SSF50998 ENSP00000288912 10/22 ENST00000288912 Transcript 1.0 ENSG00000158023 HGNC:28506 LOW NM_144668.6 synonymous_variant 1.0 Unknown Q8TBY9.152 CFAP251 HGNC 1 1.0 UPI00001AEB2C Q8TBY9-1 SNV CFAP251,synonymous_variant,p.L458=,ENST00000288912,NM_144668.6,c.1374A>G,LOW,YES,,,1;CFAP251,synonymous_variant,p.L458=,ENST00000397454,NM_001178003.2,c.1374A>G,LOW,,,,1;CFAP251,non_coding_transcript_exon_variant,,ENST00000535257,,n.1479A>G,MODIFIER,,,,1;CFAP251,intron_variant,,ENST00000543211,,n.3863-1526A>G,MODIFIER,,,,1;CFAP251,downstream_gene_variant,,ENST00000546044,,,MODIFIER,,,,1 1498/3729 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 116 57fa5336-6e2f-432d-95e1-66ba58816c83 103 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS CFAP251,non_coding_transcript_exon_variant,,ENST00000535257.1,n.1479A>G,MODIFIER,;CFAP251,intron_variant,,ENST00000543211.5,n.3863-1526A>G,MODIFIER,;CFAP251,synonymous_variant,p.L458=,ENST00000397454.2,c.1374A>G,LOW,;CFAP251,synonymous_variant,p.L458=,ENST00000288912.9,c.1374A>G,LOW,YES +WDHD1 11169 BI GRCh38 14 54957630 54957630 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 28 19 c.2707G>A p.Val903Ile p.V903I ENST00000360586.8 NM_007086.4 903 Gtt/Att 22/26 P1 T V/I protein_coding YES CCDS9721.1 2707/3390 GGTAACTGCAC PDB-ENSP_mappings:6xty.F;PDB-ENSP_mappings:6xty.G;PDB-ENSP_mappings:6xty.H;PANTHER:PTHR19932;PANTHER:PTHR19932:SF10 ENSP00000353793 22/26 ENST00000360586 Transcript ENSG00000198554 HGNC:23170 MODERATE NM_007086.4 missense_variant 1.0 benign(0.007) Unknown tolerated(0.51) O75717.186 WDHD1 HGNC -1 1.0 UPI0000125AC6 O75717-1 SNV WDHD1,missense_variant,p.V903I,ENST00000360586,NM_007086.4,c.2707G>A,MODERATE,YES,tolerated(0.51),benign(0.007),-1;WDHD1,missense_variant,p.V780I,ENST00000420358,NM_001008396.3,c.2338G>A,MODERATE,,tolerated(0.48),benign(0.007),-1;WDHD1,3_prime_UTR_variant,,ENST00000567693,,c.*1157G>A,MODIFIER,,,,-1 2795/6019 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 89 57fa5336-6e2f-432d-95e1-66ba58816c83 47 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS WDHD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000567693.1,c.*1157G>A,MODIFIER,;WDHD1,missense_variant,p.V780I,ENST00000420358.2,c.2338G>A,MODERATE,;WDHD1,missense_variant,p.V903I,ENST00000360586.8,c.2707G>A,MODERATE,YES +LAMA1 284217 BI GRCh38 18 6985238 6985238 + missense_variant,splice_region_variant Missense_Mutation SNP T T A novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 134 86 c.5659A>T p.Ser1887Cys p.S1887C ENST00000389658.4 NM_005559.4 1887 Agt/Tgt 39/63 P1 A S/C protein_coding YES CCDS32787.1 5659/9228 CTACCTGTACA PANTHER:PTHR10574;PANTHER:PTHR10574:SF291 ENSP00000374309 39/63 ENST00000389658 Transcript 1.0 ENSG00000101680 HGNC:6481 MODERATE NM_005559.4 missense_variant 1.0 possibly_damaging(0.872) Unknown deleterious(0.02) P25391.206 LAMA1 HGNC -1 1.0 UPI00001C1FF9 SNV LAMA1,missense_variant,p.S1887C,ENST00000389658,NM_005559.4,c.5659A>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.872),-1;LAMA1,splice_region_variant,,ENST00000579014,,n.6674A>T,LOW,,,,-1 5736/9642 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 267 57fa5336-6e2f-432d-95e1-66ba58816c83 220 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS LAMA1,non_coding_transcript_exon_variant,,ENST00000579014.5,n.6674A>T,MODIFIER,;LAMA1,missense_variant,splice_region_variant,p.S1887C,ENST00000389658.4,c.5659A>T,MODERATE,YES +MRPL4 51073 BI GRCh38 19 10254602 10254602 + missense_variant Missense_Mutation SNP C C T rs1599251239 TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 89 73 c.289C>T p.His97Tyr p.H97Y ENST00000253099.11 NM_015956.3 97 Cac/Tac 4/9 P1 T H/Y protein_coding CCDS12230.1 289/936 TACTGCACCAG PDB-ENSP_mappings:3j7y.F;PDB-ENSP_mappings:3j9m.F;PDB-ENSP_mappings:5ool.F;PDB-ENSP_mappings:5oom.F;PDB-ENSP_mappings:6nu2.F;PDB-ENSP_mappings:6nu3.F;HAMAP:MF_01328_B;PANTHER:PTHR10746:SF6;PANTHER:PTHR10746;Gene3D:3.40.1370.10;Pfam:PF00573;TIGRFAM:TIGR03953;Superfamily:SSF52166 ENSP00000253099 4/9 ENST00000253099 Transcript ENSG00000105364 HGNC:14276 MODERATE NM_015956.3 missense_variant possibly_damaging(0.893) Unknown tolerated(0.06) Q9BYD3.154 MRPL4 HGNC 1 A0A024R7C5.35 1.0 UPI0000072264 Q9BYD3-1 SNV MRPL4,missense_variant,p.H97Y,ENST00000393733,,c.289C>T,MODERATE,YES,tolerated(0.1),benign(0.209),1;MRPL4,missense_variant,p.H97Y,ENST00000590669,NM_146388.2,c.289C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.828),1;MRPL4,missense_variant,p.H97Y,ENST00000307422,NM_146387.1,c.289C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.893),1;MRPL4,missense_variant,p.H97Y,ENST00000253099,NM_015956.3,c.289C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.893),1;MRPL4,missense_variant,p.H97Y,ENST00000592514,,c.289C>T,MODERATE,,tolerated(0.06),possibly_damaging(0.893),1;MRPL4,missense_variant,p.H96Y,ENST00000588502,,c.286C>T,MODERATE,,tolerated(0.07),benign(0.149),1;MRPL4,missense_variant,p.H108Y,ENST00000590150,,c.322C>T,MODERATE,,tolerated(0.05),benign(0.22),1;MRPL4,upstream_gene_variant,,ENST00000590702,,,MODIFIER,,,,1;MRPL4,missense_variant,p.H97Y,ENST00000591054,,c.289C>T,MODERATE,,tolerated(0.06),benign(0.16),1;MRPL4,non_coding_transcript_exon_variant,,ENST00000592071,,n.372C>T,MODIFIER,,,,1;MRPL4,downstream_gene_variant,,ENST00000588963,,,MODIFIER,,,,1;AC011511.2,intron_variant,,ENST00000592893,,n.359-1775G>A,MODIFIER,YES,,,-1;AC011511.3,downstream_gene_variant,,ENST00000587088,,,MODIFIER,YES,,,-1 329/1218 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 233 57fa5336-6e2f-432d-95e1-66ba58816c83 162 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS MRPL4,missense_variant,p.H96Y,ENST00000588502.5,c.286C>T,MODERATE,;LIMASI,intron_variant,,ENST00000592893.1,n.359-1775G>A,MODIFIER,YES;MRPL4,non_coding_transcript_exon_variant,,ENST00000592071.1,n.372C>T,MODIFIER,;MRPL4,missense_variant,p.H97Y,ENST00000393733.6,c.289C>T,MODERATE,;MRPL4,missense_variant,p.H97Y,ENST00000253099.11,c.289C>T,MODERATE,YES;MRPL4,missense_variant,p.H97Y,ENST00000590669.5,c.289C>T,MODERATE,;MRPL4,missense_variant,p.H108Y,ENST00000590150.5,c.322C>T,MODERATE,;MRPL4,missense_variant,p.H97Y,ENST00000307422.9,c.289C>T,MODERATE,;MRPL4,missense_variant,NMD_transcript_variant,p.H97Y,ENST00000591054.5,c.289C>T,MODERATE,;MRPL4,missense_variant,p.H97Y,ENST00000592514.5,c.289C>T,MODERATE, +FAM187B 148109 BI GRCh38 19 35228212 35228212 + missense_variant Missense_Mutation SNP G G A novel TCGA-WC-A885-01A TCGA-WC-A885-10A Somatic 24 24 c.469C>T p.Pro157Ser p.P157S ENST00000324675.4 NM_152481.2 157 Ccg/Tcg 1/2 P1 A P/S protein_coding YES CCDS12448.1 469/1110 GCCCGGCTCCT PANTHER:PTHR32178;PANTHER:PTHR32178:SF8 ENSP00000323355 1/2 ENST00000324675 Transcript ENSG00000177558 HGNC:26366 MODERATE missense_variant 1.0 possibly_damaging(0.907) Unknown deleterious(0.01) Q17R55.101 FAM187B HGNC -1 1.0 UPI0000049306 SNV FAM187B,missense_variant,p.P157S,ENST00000324675,NM_152481.1,c.469C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.907),-1;FAM187B2P,downstream_gene_variant,,ENST00000577135,,,MODIFIER,YES,,,-1 518/1184 muse;mutect2;varscan2 f78d8541-b317-4c8a-aa66-f172a8eaf14f 0 81 57fa5336-6e2f-432d-95e1-66ba58816c83 48 3bf0c8ec-6a9b-446c-9ec1-85a33a2eff00 SUCCESS FAM187B,missense_variant,p.P157S,ENST00000324675.4,c.469C>T,MODERATE,YES +SELE 6401 BI GRCh38 1 169729327 169729327 + missense_variant Missense_Mutation SNP A A T rs936834236 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 17 11 c.949T>A p.Cys317Ser p.C317S ENST00000333360.12 NM_000450.2 317 Tgc/Agc 7/14 P1 T C/S protein_coding YES CCDS1283.1 949/1833 GCTGCACCTCA Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR19325;PANTHER:PTHR19325:SF493;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000331736 7/14 rs936834236 ENST00000333360 Transcript ENSG00000007908 HGNC:10718 MODERATE NM_000450.2 missense_variant 1.0 probably_damaging(0.99) Unknown deleterious(0) P16581.223 SELE HGNC -1 1.0 UPI000012E44A SNV SELE,missense_variant,p.C317S,ENST00000333360,NM_000450.2,c.949T>A,MODERATE,YES,deleterious(0),probably_damaging(0.99),-1;SELE,missense_variant,p.C317S,ENST00000367776,,c.949T>A,MODERATE,,deleterious(0),probably_damaging(0.987),-1;SELE,missense_variant,p.C317S,ENST00000367777,,c.949T>A,MODERATE,,deleterious(0),probably_damaging(0.982),-1;SELE,missense_variant,p.C255S,ENST00000367775,,c.763T>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;SELE,missense_variant,p.C317S,ENST00000367774,,c.949T>A,MODERATE,,deleterious(0),probably_damaging(1),-1;SELE,downstream_gene_variant,,ENST00000609271,,,MODIFIER,,,,-1;C1orf112,intron_variant,,ENST00000498289,,n.851+45395A>T,MODIFIER,,,,1;SELE,downstream_gene_variant,,ENST00000461085,,,MODIFIER,,,,-1 1106/3875 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 6.760959877283312e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 31 deb611eb-9f5c-4997-9891-2194fabd6646 28 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS SELE,missense_variant,p.C317S,ENST00000367774.1,c.949T>A,MODERATE,;SELE,missense_variant,p.C317S,ENST00000367777.5,c.949T>A,MODERATE,;SELE,missense_variant,p.C317S,ENST00000367776.5,c.949T>A,MODERATE,;SELE,missense_variant,p.C255S,ENST00000367775.5,c.763T>A,MODERATE,;SELE,missense_variant,p.C317S,ENST00000333360.12,c.949T>A,MODERATE,YES;FIRRM,intron_variant,,ENST00000498289.5,n.851+45395A>T,MODIFIER, +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 27 23 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 43 deb611eb-9f5c-4997-9891-2194fabd6646 51 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +ABCA12 26154 BI GRCh38 2 215000778 215000778 + missense_variant Missense_Mutation SNP G G C novel TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 70 55 c.3106C>G p.Gln1036Glu p.Q1036E ENST00000272895.12 NM_173076.3 1036 Caa/Gaa 22/53 P1 C Q/E protein_coding YES CCDS33372.1 3106/7788 AGTTTGCAATT Pfam:PF12698;PANTHER:PTHR19229;PANTHER:PTHR19229:SF29 ENSP00000272895 22/53 ENST00000272895 Transcript 1.0 ENSG00000144452 HGNC:14637 MODERATE NM_173076.3 missense_variant 1.0 benign(0.332) Unknown deleterious(0) Q86UK0.159 ABCA12 HGNC -1 1.0 UPI000019AB7A Q86UK0-1 SNV ABCA12,missense_variant,p.Q1036E,ENST00000272895,NM_173076.3,c.3106C>G,MODERATE,YES,deleterious(0),benign(0.332),-1;ABCA12,missense_variant,p.Q718E,ENST00000389661,NM_015657.3,c.2152C>G,MODERATE,,deleterious(0),benign(0.272),-1;AC072062.1,upstream_gene_variant,,ENST00000617699,,,MODIFIER,,,,1 3524/9298 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 129 deb611eb-9f5c-4997-9891-2194fabd6646 125 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS ABCA12,missense_variant,p.Q718E,ENST00000389661.4,c.2152C>G,MODERATE,;ABCA12,missense_variant,p.Q1036E,ENST00000272895.12,c.3106C>G,MODERATE,YES +CACNA1D 776 BI GRCh38 3 53762037 53762037 + missense_variant Missense_Mutation SNP A A T novel TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 111 43 c.3826A>T p.Ile1276Phe p.I1276F ENST00000350061.11 NM_001128840.3 1276 Atc/Ttc 30/48 A2 T I/F protein_coding CCDS46848.1 3826/6486 CCCTCATCGTA Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR45628;PANTHER:PTHR45628:SF11;Superfamily:SSF81324 ENSP00000288133 30/48 ENST00000350061 Transcript 1.0 ENSG00000157388 HGNC:1391 MODERATE NM_001128840.3 missense_variant probably_damaging(0.936) Unknown deleterious(0.01) Q01668.202 CACNA1D HGNC 1 1.0 UPI000013DEF4 Q01668-1 SNV CACNA1D,missense_variant,p.I1296F,ENST00000288139,NM_000720.4,c.3886A>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.913),1;CACNA1D,missense_variant,p.I1276F,ENST00000350061,NM_001128840.3,c.3826A>T,MODERATE,,deleterious(0.01),probably_damaging(0.936),1;CACNA1D,missense_variant,p.I1276F,ENST00000422281,NM_001128839.3,c.3826A>T,MODERATE,,deleterious(0.01),probably_damaging(0.965),1;CACNA1D,missense_variant,p.I1276F,ENST00000636938,,c.3826A>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.881),1;CACNA1D,missense_variant,p.I1300F,ENST00000637424,,c.3898A>T,MODERATE,,deleterious(0),benign(0.395),1;CACNA1D,missense_variant,p.I1276F,ENST00000636570,,c.3826A>T,MODERATE,,deleterious(0.01),possibly_damaging(0.733),1;CACNA1D,missense_variant,p.I134F,ENST00000638120,,c.400A>T,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.776),1;CACNA1D,intron_variant,,ENST00000481478,,c.2866-514A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000636627,,c.3087-514A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000636723,,c.667+8355A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000638129,,c.366+8355A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000640483,,c.3820-514A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000645528,,c.975-514A>T,MODIFIER,,,,1;CACNA1D,non_coding_transcript_exon_variant,,ENST00000637081,,n.71A>T,MODIFIER,,,,1;CACNA1D,intron_variant,,ENST00000636448,,c.62-514A>T,MODIFIER,,,,1 4382/9369 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 106 deb611eb-9f5c-4997-9891-2194fabd6646 154 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS CACNA1D,non_coding_transcript_exon_variant,,ENST00000637081.1,n.71A>T,MODIFIER,;CACNA1D,intron_variant,NMD_transcript_variant,,ENST00000636448.1,c.62-514A>T,MODIFIER,;CACNA1D,intron_variant,,ENST00000638129.1,c.366+8355A>T,MODIFIER,;CACNA1D,missense_variant,p.I134F,ENST00000638120.1,c.400A>T,MODERATE,;CACNA1D,intron_variant,,ENST00000636723.1,c.667+8355A>T,MODIFIER,;CACNA1D,intron_variant,,ENST00000645528.2,c.975-514A>T,MODIFIER,;CACNA1D,intron_variant,,ENST00000640483.1,c.3820-514A>T,MODIFIER,;CACNA1D,missense_variant,p.I1276F,ENST00000422281.7,c.3826A>T,MODERATE,;CACNA1D,missense_variant,p.I1276F,ENST00000636570.1,c.3826A>T,MODERATE,;CACNA1D,missense_variant,p.I1276F,ENST00000636938.1,c.3826A>T,MODERATE,;CACNA1D,missense_variant,p.I1276F,ENST00000350061.11,c.3826A>T,MODERATE,YES;CACNA1D,intron_variant,,ENST00000481478.2,c.3847-514A>T,MODIFIER,;CACNA1D,missense_variant,p.I1296F,ENST00000288139.11,c.3886A>T,MODERATE,;CACNA1D,intron_variant,,ENST00000636627.2,c.3847-514A>T,MODIFIER,;CACNA1D,missense_variant,p.I1300F,ENST00000637424.1,c.3898A>T,MODERATE, +ADGRL3 23284 BI GRCh38 4 61733512 61733512 + missense_variant Missense_Mutation SNP G G A rs1298975938 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 25 10 c.1357G>A p.Val453Met p.V453M ENST00000683033.1 NM_001387552.1 453 Gtg/Atg 8/27 P1 A V/M protein_coding YES 1357/4743 ACGTCGTGAAA COSM1430450;COSM1430451;COSM1430452;COSM4996453 Pfam:PF02191;SMART:SM00284;PROSITE_profiles:PS51132;PANTHER:PTHR12011:SF60;PANTHER:PTHR12011 ENSP00000420931 6/25 rs1298975938;COSV72265533 ENST00000506720 Transcript ENSG00000150471 HGNC:20974 MODERATE 6.47e-05 gnomAD_AFR missense_variant 0;1 1.0 probably_damaging(0.965) Unknown deleterious(0) 0;1 ADGRL3 HGNC 1 E7EUW2.73 5.0 UPI0001D3B3AA SNV ADGRL3,missense_variant,p.V385M,ENST00000512091,NM_001322246.2,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.991),1;ADGRL3,missense_variant,p.V385M,ENST00000514591,NM_015236.6,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.999),1;ADGRL3,missense_variant,p.V453M,ENST00000509896,,c.1357G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.999),1;ADGRL3,missense_variant,p.V453M,ENST00000511324,,c.1357G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.982),1;ADGRL3,missense_variant,p.V453M,ENST00000508693,,c.1357G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.999),1;ADGRL3,missense_variant,p.V453M,ENST00000507164,,c.1357G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.99),1;ADGRL3,missense_variant,p.V453M,ENST00000506720,NM_001322402.2,c.1357G>A,MODERATE,YES,deleterious(0),probably_damaging(0.965),1;ADGRL3,missense_variant,p.V453M,ENST00000506746,,c.1357G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;ADGRL3,missense_variant,p.V453M,ENST00000507625,NM_001371343.1&NM_001371344.1&NM_001371345.1&NM_001371346.1&NM_001371342.1,c.1357G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ADGRL3,missense_variant,p.V385M,ENST00000506700,,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.99),1;ADGRL3,missense_variant,p.V385M,ENST00000504896,,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.999),1;ADGRL3,missense_variant,p.V385M,ENST00000514157,,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.99),1;ADGRL3,missense_variant,p.V385M,ENST00000508946,,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.994),1;ADGRL3,missense_variant,p.V385M,ENST00000514996,,c.1153G>A,MODERATE,,deleterious(0.01),probably_damaging(0.99),1 1357/4962 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 8.073e-06 6.47e-05 0.0 0.0 0.0 0.0 0.0 0.0 3.278e-05 1.3523000234272333e-05 2.4332099201274104e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 19 deb611eb-9f5c-4997-9891-2194fabd6646 35 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS ADGRL3,missense_variant,p.V385M,ENST00000508946.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000506720.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000506746.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000514996.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000514157.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000504896.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000507625.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000507164.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000508693.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000506700.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000511324.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000509896.5,c.1357G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000514591.5,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V385M,ENST00000512091.6,c.1153G>A,MODERATE,;ADGRL3,missense_variant,p.V453M,ENST00000683033.1,c.1357G>A,MODERATE,YES +OCLN 100506658 BI GRCh38 5 69514021 69514021 + missense_variant Missense_Mutation SNP G G A rs762992411 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 33 22 c.803G>A p.Arg268Gln p.R268Q ENST00000355237.6 NM_002538.4 268 cGa/cAa 4/9 P1 A R/Q protein_coding YES CCDS4006.1 803/1569 AACTCGAAGAA COSM1218271 PROSITE_profiles:PS51225;CDD:cd13953;PANTHER:PTHR23288:SF4;PANTHER:PTHR23288;PIRSF:PIRSF005993;Superfamily:SSF103473 ENSP00000347379 4/9 rs762992411;COSV62285701 ENST00000355237 Transcript 1.0 ENSG00000197822 HGNC:8104 MODERATE 4.397e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q16625.181 OCLN HGNC 1 1.0 UPI00000341F0 Q16625-1 SNV OCLN,missense_variant,p.R268Q,ENST00000355237,NM_002538.4,c.803G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;OCLN,missense_variant,p.R268Q,ENST00000396442,NM_001205254.2,c.803G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;OCLN,missense_variant,p.R17Q,ENST00000538151,NM_001205255.1,c.50G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1 1239/6438 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 2.386e-05 0.0 0.0 0.0 0.0 0.0 4.397e-05 0.0 3.266e-05 2.705959923332557e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.173030124045908e-05 0.0 6.173030124045908e-05 0.0 0.0 0 67 deb611eb-9f5c-4997-9891-2194fabd6646 55 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS OCLN,missense_variant,p.R17Q,ENST00000538151.2,c.50G>A,MODERATE,;OCLN,intron_variant,,ENST00000680496.1,c.729+4202G>A,MODIFIER,;OCLN,missense_variant,p.R268Q,ENST00000680027.1,c.803G>A,MODERATE,;OCLN,missense_variant,p.R268Q,ENST00000681586.1,c.803G>A,MODERATE,;OCLN,synonymous_variant,NMD_transcript_variant,p.S124=,ENST00000681588.1,c.372G>A,LOW,;OCLN,missense_variant,p.R268Q,ENST00000681895.1,c.803G>A,MODERATE,;OCLN,intron_variant,,ENST00000680784.1,c.729+4202G>A,MODIFIER,;OCLN,missense_variant,p.R268Q,ENST00000396442.7,c.803G>A,MODERATE,YES;OCLN,missense_variant,p.R268Q,ENST00000680098.1,c.803G>A,MODERATE,;OCLN,missense_variant,p.R268Q,ENST00000681041.1,c.803G>A,MODERATE,;OCLN,missense_variant,p.R268Q,ENST00000355237.6,c.803G>A,MODERATE, +MGAT4B 11282 BI GRCh38 5 179799505 179799505 + splice_donor_variant Splice_Site SNP C C T rs112845536 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 25 18 c.1041+1G>A p.X347_splice p.X347_splice ENST00000292591.12 NM_014275.5 347 P1 T protein_coding CCDS4448.1 GCTCACCGCAT ENSP00000292591 rs112845536 ENST00000292591 Transcript NonExonic ENSG00000161013 HGNC:7048 HIGH 9/14 NM_014275.5 splice_donor_variant Unknown Q9UQ53.142 MGAT4B HGNC -1 1.0 UPI000006FDB8 Q9UQ53-1 SNV MGAT4B,splice_donor_variant,p.X347_splice,ENST00000292591,NM_014275.5,c.1041+1G>A,HIGH,,,,-1;MGAT4B,splice_donor_variant,p.X362_splice,ENST00000337755,NM_054013.3,c.1086+1G>A,HIGH,YES,,,-1;MGAT4B,splice_donor_variant,p.X173_splice,ENST00000518778,,c.517+1G>A,HIGH,,,,-1;MGAT4B,splice_donor_variant,p.X159_splice,ENST00000518867,,c.475+1G>A,HIGH,,,,-1;MGAT4B,splice_donor_variant,p.X146_splice,ENST00000520875,,c.436+1G>A,HIGH,,,,-1;MGAT4B,splice_donor_variant,p.X44_splice,ENST00000520969,,c.131+1G>A,HIGH,,,,-1;MGAT4B,intron_variant,,ENST00000518980,,c.339-255G>A,MODIFIER,,,,-1;MGAT4B,intron_variant,,ENST00000519836,,c.754-384G>A,MODIFIER,,,,-1;LTC4S,downstream_gene_variant,,ENST00000292596,NM_145867.2,,MODIFIER,YES,,,1;LTC4S,downstream_gene_variant,,ENST00000401985,,,MODIFIER,,,,1;LTC4S,downstream_gene_variant,,ENST00000486713,,,MODIFIER,,,,1;MGAT4B,downstream_gene_variant,,ENST00000523108,,,MODIFIER,,,,-1;MIR1229,upstream_gene_variant,,ENST00000408467,,,MODIFIER,YES,,,-1;MGAT4B,splice_donor_variant,,ENST00000522293,,n.71+1G>A,HIGH,,,,-1;MGAT4B,intron_variant,,ENST00000523382,,n.409-255G>A,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000519616,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000519965,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000520019,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000520134,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000521305,,,MODIFIER,,,,-1;MGAT4B,splice_donor_variant,,ENST00000518702,,n.527+1G>A,HIGH,,,,-1;LTC4S,downstream_gene_variant,,ENST00000465572,,,MODIFIER,,,,1;LTC4S,downstream_gene_variant,,ENST00000466071,,,MODIFIER,,,,1;LTC4S,downstream_gene_variant,,ENST00000505170,,,MODIFIER,,,,1;LTC4S,downstream_gene_variant,,ENST00000509898,,,MODIFIER,,,,1;LTC4S,downstream_gene_variant,,ENST00000510544,,,MODIFIER,,,,1;MGAT4B,downstream_gene_variant,,ENST00000518168,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000520822,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000520918,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000521855,,,MODIFIER,,,,-1;MGAT4B,upstream_gene_variant,,ENST00000522451,,,MODIFIER,,,,-1;MGAT4B,downstream_gene_variant,,ENST00000523329,,,MODIFIER,,,,-1 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 59 deb611eb-9f5c-4997-9891-2194fabd6646 43 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS MGAT4B,splice_donor_variant,,ENST00000518702.5,n.527+1G>A,HIGH,;MGAT4B,splice_donor_variant,p.X159_splice,ENST00000518867.5,c.475+1G>A,HIGH,;MGAT4B,intron_variant,,ENST00000523382.5,n.409-255G>A,MODIFIER,;MGAT4B,splice_donor_variant,p.X146_splice,ENST00000520875.5,c.436+1G>A,HIGH,;MGAT4B,intron_variant,,ENST00000518980.5,c.339-255G>A,MODIFIER,;MGAT4B,splice_donor_variant,,ENST00000522293.5,n.71+1G>A,HIGH,;MGAT4B,splice_donor_variant,p.X44_splice,ENST00000520969.5,c.131+1G>A,HIGH,;MGAT4B,intron_variant,,ENST00000519836.5,c.754-384G>A,MODIFIER,;MGAT4B,splice_donor_variant,p.X347_splice,ENST00000292591.12,c.1041+1G>A,HIGH,YES;MGAT4B,splice_donor_variant,p.X173_splice,ENST00000518778.5,c.517+1G>A,HIGH,;MGAT4B,splice_donor_variant,p.X362_splice,ENST00000337755.9,c.1086+1G>A,HIGH, +CSMD3 114788 BI GRCh38 8 112573632 112573632 + missense_variant Missense_Mutation SNP G G C rs143652338 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 134 21 c.3911C>G p.Thr1304Ser p.T1304S ENST00000297405.10 NM_001363185.1 1304 aCt/aGt 24/71 P1 C T/S protein_coding YES CCDS6315.1 3911/11124 GATGAGTCGTT Gene3D:2.60.120.290;Pfam:PF00431;PROSITE_profiles:PS01180;PANTHER:PTHR45656;PANTHER:PTHR45656:SF9;SMART:SM00042;Superfamily:SSF49854;CDD:cd00041 ENSP00000297405 0.0 0.0001163 24/71 rs143652338;COSV52217443 ENST00000297405 Transcript 1.0 ENSG00000164796 HGNC:19291 MODERATE NM_198123.2 0.0001163 EA missense_variant 0;1 1.0 benign(0.043) Unknown tolerated(0.72) 0;1 Q7Z407.139 CSMD3 HGNC -1 1.0 UPI00001E0584 Q7Z407-1 SNV CSMD3,missense_variant,p.T1304S,ENST00000297405,NM_001363185.1&NM_198123.2,c.3911C>G,MODERATE,YES,tolerated(0.72),benign(0.043),-1;CSMD3,missense_variant,p.T1264S,ENST00000343508,NM_198124.2,c.3791C>G,MODERATE,,tolerated(0.77),benign(0.001),-1;CSMD3,missense_variant,p.T1200S,ENST00000455883,NM_052900.3,c.3599C>G,MODERATE,,tolerated(0.75),benign(0.042),-1;CSMD3,missense_variant,p.T644S,ENST00000339701,,c.1931C>G,MODERATE,,tolerated(1),benign(0.295),-1 3996/13052 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 3.99e-06 0.0 0.0 0.0 0.0 0.0 8.844e-06 0.0 0.0 0 87 deb611eb-9f5c-4997-9891-2194fabd6646 155 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS CSMD3,missense_variant,p.T1200S,ENST00000455883.2,c.3599C>G,MODERATE,;CSMD3,missense_variant,p.T644S,ENST00000339701.7,c.1931C>G,MODERATE,;CSMD3,missense_variant,p.T1264S,ENST00000343508.7,c.3791C>G,MODERATE,;CSMD3,missense_variant,p.T1304S,ENST00000297405.10,c.3911C>G,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 58 43 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 115 deb611eb-9f5c-4997-9891-2194fabd6646 102 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +ARHGEF17 9828 BI GRCh38 11 73362538 73362538 + synonymous_variant Silent SNP G G A rs748441561 TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 21 11 c.4800G>A p.Ala1600= p.A1600= ENST00000263674.4 NM_014786.4 1600 gcG/gcA 14/21 P3 A A protein_coding YES CCDS8221.1 4800/6192 CTCGCGGAGCC Low_complexity_(Seg):seg;PANTHER:PTHR12877:SF15;PANTHER:PTHR12877 ENSP00000263674 14/21 rs748441561 ENST00000263674 Transcript ENSG00000110237 HGNC:21726 LOW NM_014786.4 7.035e-05 gnomAD_AFR synonymous_variant 1.0 Unknown Q96PE2.148 ARHGEF17 HGNC 1 1.0 UPI000004980B SNV ARHGEF17,synonymous_variant,p.A1600=,ENST00000263674,NM_014786.4,c.4800G>A,LOW,YES,,,1;ARHGEF17,synonymous_variant,p.A581=,ENST00000643371,,c.1743G>A,LOW,,,,1;ARHGEF17,upstream_gene_variant,,ENST00000536481,,,MODIFIER,,,,1;ARHGEF17,upstream_gene_variant,,ENST00000543530,,,MODIFIER,,,,1 5163/8163 muse;mutect2 4480d290-5e8a-4289-8e3c-de087e0de412 4.269e-06 7.035e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 24 deb611eb-9f5c-4997-9891-2194fabd6646 32 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS ARHGEF17,synonymous_variant,p.A581=,ENST00000643371.1,c.1743G>A,LOW,;ARHGEF17,synonymous_variant,p.A1600=,ENST00000263674.4,c.4800G>A,LOW,YES +MCRS1 10445 BI GRCh38 12 49565618 49565618 + frameshift_variant Frame_Shift_Del DEL C C - TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 113 57 c.199del p.Ala67GlnfsTer53 p.A67Qfs*53 ENST00000343810.9 NM_006337.5 67 Gca/ca 4/15 P1 - A/X protein_coding CCDS8787.1 199/1389 ATTTTGCCAGGC MobiDB_lite:mobidb-lite ENSP00000345358 4/15 COSV59459776 ENST00000343810 Transcript ENSG00000187778 HGNC:6960 HIGH NM_006337.5 frameshift_variant 1 Unknown 1 Q96EZ8.175 MCRS1 HGNC -1 1.0 UPI000012EDE9 Q96EZ8-1 deletion MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000343810,NM_006337.5,c.199del,HIGH,,,,-1;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000550165,,c.199del,HIGH,,,,-1;MCRS1,frameshift_variant,p.A80Qfs*53,ENST00000357123,NM_001012300.1,c.238del,HIGH,YES,,,-1;MCRS1,frameshift_variant,p.A54Qfs*53,ENST00000553173,,c.160del,HIGH,,,,-1;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000548596,,c.199del,HIGH,,,,-1;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000548334,,c.199del,HIGH,,,,-1;MCRS1,frameshift_variant,p.A71Qfs*53,ENST00000549528,,c.211del,HIGH,,,,-1;MCRS1,5_prime_UTR_variant,,ENST00000546244,NM_001278341.1,c.-375del,MODIFIER,,,,-1;PRPF40B,upstream_gene_variant,,ENST00000551063,,,MODIFIER,,,,1;MCRS1,upstream_gene_variant,,ENST00000547182,,,MODIFIER,,,,-1;PRPF40B,upstream_gene_variant,,ENST00000547764,,,MODIFIER,,,,1;PRPF40B,upstream_gene_variant,,ENST00000552301,,,MODIFIER,,,,1;MCRS1,frameshift_variant,p.W9Cfs*22,ENST00000548602,,c.27del,HIGH,,,,-1;MCRS1,non_coding_transcript_exon_variant,,ENST00000551625,,n.919del,MODIFIER,,,,-1;MCRS1,non_coding_transcript_exon_variant,,ENST00000552206,,n.896del,MODIFIER,,,,-1;MCRS1,intron_variant,,ENST00000549000,,n.664+645del,MODIFIER,,,,-1 404/1938 mutect2;pindel;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 165 deb611eb-9f5c-4997-9891-2194fabd6646 170 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS MCRS1,non_coding_transcript_exon_variant,,ENST00000552206.1,n.896del,MODIFIER,;MCRS1,frameshift_variant,p.A71Qfs*53,ENST00000549528.1,c.211del,HIGH,;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000548596.5,c.199del,HIGH,;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000548334.5,c.199del,HIGH,;MCRS1,frameshift_variant,p.A54Qfs*53,ENST00000553173.5,c.160del,HIGH,;MCRS1,intron_variant,,ENST00000549000.1,n.664+645del,MODIFIER,;MCRS1,frameshift_variant,p.A80Qfs*53,ENST00000357123.8,c.238del,HIGH,;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000550165.5,c.199del,HIGH,;MCRS1,non_coding_transcript_exon_variant,,ENST00000551625.5,n.919del,MODIFIER,;MCRS1,frameshift_variant,NMD_transcript_variant,p.W9Cfs*22,ENST00000548602.5,c.27del,HIGH,;MCRS1,frameshift_variant,p.A67Qfs*53,ENST00000343810.9,c.199del,HIGH,YES;MCRS1,5_prime_UTR_variant,,ENST00000546244.5,c.-375del,MODIFIER, +SAP30BP 29115 BI GRCh38 17 75699801 75699801 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 164 9 c.326T>C p.Val109Ala p.V109A ENST00000584667.6 NM_013260.8 109 gTt/gCt 5/11 P4 C V/A protein_coding CCDS11726.1 326/927 AAGAGTTCGGA PANTHER:PTHR13464 ENSP00000462116 5/11 ENST00000584667 Transcript ENSG00000161526 HGNC:30785 MODERATE NM_013260.8 missense_variant benign(0.104) Unknown deleterious(0.03) Q9UHR5.147 SAP30BP HGNC 1 A0A024R8R0.30 1.0 UPI0000072715 Q9UHR5-1 SNV SAP30BP,missense_variant,p.V109A,ENST00000584667,NM_013260.8,c.326T>C,MODERATE,,deleterious(0.03),benign(0.104),1;SAP30BP,missense_variant,p.V93A,ENST00000355423,NM_001301839.1,c.278T>C,MODERATE,,deleterious(0.04),benign(0.288),1;SAP30BP,missense_variant,p.V126A,ENST00000583536,NM_001301855.1,c.377T>C,MODERATE,YES,deleterious(0.03),benign(0.029),1;SAP30BP,missense_variant,p.V74A,ENST00000578909,,c.221T>C,MODERATE,,deleterious(0.04),probably_damaging(0.989),1;SAP30BP,5_prime_UTR_variant,,ENST00000584240,,c.-8T>C,MODIFIER,,,,1;SAP30BP,5_prime_UTR_variant,,ENST00000583063,,c.-8T>C,MODIFIER,,,,1;SAP30BP,non_coding_transcript_exon_variant,,ENST00000579864,,n.333T>C,MODIFIER,,,,1;SAP30BP,missense_variant,p.V109A,ENST00000582022,,c.326T>C,MODERATE,,deleterious(0.03),possibly_damaging(0.753),1;SAP30BP,missense_variant,p.V109A,ENST00000580322,,c.326T>C,MODERATE,,deleterious(0.03),benign(0.162),1;SAP30BP,missense_variant,p.V93A,ENST00000293208,,c.278T>C,MODERATE,,deleterious(0.02),benign(0.073),1;SAP30BP,missense_variant,p.V109A,ENST00000542343,,c.326T>C,MODERATE,,deleterious(0.03),benign(0.4),1;SAP30BP,3_prime_UTR_variant,,ENST00000579877,,c.*102T>C,MODIFIER,,,,1;SAP30BP,3_prime_UTR_variant,,ENST00000583737,,c.*336T>C,MODIFIER,,,,1;SAP30BP,non_coding_transcript_exon_variant,,ENST00000580601,,n.1932T>C,MODIFIER,,,,1;SAP30BP,non_coding_transcript_exon_variant,,ENST00000577292,,n.348T>C,MODIFIER,,,,1;SAP30BP,non_coding_transcript_exon_variant,,ENST00000580484,,n.329T>C,MODIFIER,,,,1;SAP30BP,upstream_gene_variant,,ENST00000578756,,,MODIFIER,,,,1;SAP30BP,upstream_gene_variant,,ENST00000581207,,,MODIFIER,,,,1;SAP30BP,upstream_gene_variant,,ENST00000581385,,,MODIFIER,,,,1;SAP30BP,upstream_gene_variant,,ENST00000583329,,,MODIFIER,,,,1;SAP30BP,upstream_gene_variant,,ENST00000584557,,,MODIFIER,,,,1 361/2500 muse;mutect2 4480d290-5e8a-4289-8e3c-de087e0de412 0 140 deb611eb-9f5c-4997-9891-2194fabd6646 173 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS SAP30BP,5_prime_UTR_variant,,ENST00000583063.1,c.-8T>C,MODIFIER,;SAP30BP,5_prime_UTR_variant,,ENST00000584240.5,c.-8T>C,MODIFIER,;SAP30BP,non_coding_transcript_exon_variant,,ENST00000580601.5,n.1932T>C,MODIFIER,;SAP30BP,missense_variant,p.F74L,ENST00000578909.1,c.220T>C,MODERATE,;SAP30BP,synonymous_variant,p.S125=,ENST00000583536.5,c.375T>C,LOW,;SAP30BP,missense_variant,NMD_transcript_variant,p.F109L,ENST00000580322.5,c.325T>C,MODERATE,;SAP30BP,missense_variant,NMD_transcript_variant,p.V109A,ENST00000582022.5,c.326T>C,MODERATE,;SAP30BP,non_coding_transcript_exon_variant,,ENST00000580484.5,n.329T>C,MODIFIER,;SAP30BP,missense_variant,NMD_transcript_variant,p.V93A,ENST00000293208.13,c.278T>C,MODERATE,;SAP30BP,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000583737.5,c.*336T>C,MODIFIER,;SAP30BP,non_coding_transcript_exon_variant,,ENST00000579864.5,n.333T>C,MODIFIER,;SAP30BP,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000579877.5,c.*102T>C,MODIFIER,;SAP30BP,missense_variant,NMD_transcript_variant,p.V109A,ENST00000542343.5,c.326T>C,MODERATE,;SAP30BP,non_coding_transcript_exon_variant,,ENST00000577292.5,n.348T>C,MODIFIER,;SAP30BP,missense_variant,p.V93A,ENST00000355423.7,c.278T>C,MODERATE,;SAP30BP,missense_variant,p.V109A,ENST00000584667.6,c.326T>C,MODERATE,YES +WDR7 23335 BI GRCh38 18 56935836 56935836 + synonymous_variant Silent SNP T T A novel TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 45 53 c.3762T>A p.Ser1254= p.S1254= ENST00000254442.8 NM_015285.3 1254 tcT/tcA 23/28 P4 A S protein_coding YES CCDS11962.1 3762/4473 CGCTCTGCGAG PANTHER:PTHR44099;PANTHER:PTHR44099:SF3 ENSP00000254442 23/28 ENST00000254442 Transcript ENSG00000091157 HGNC:13490 LOW NM_015285.3 synonymous_variant 1.0 Unknown Q9Y4E6.150 WDR7 HGNC 1 1.0 UPI000013CE33 Q9Y4E6-1 SNV WDR7,synonymous_variant,p.S1254=,ENST00000254442,NM_015285.3&NM_001382487.1,c.3762T>A,LOW,YES,,,1;WDR7,synonymous_variant,p.S1221=,ENST00000357574,NM_052834.3&NM_001382485.1,c.3663T>A,LOW,,,,1;WDR7,synonymous_variant,p.S579=,ENST00000615645,,c.1737T>A,LOW,,,,1;WDR7,intron_variant,,ENST00000589935,,c.1-91168T>A,MODIFIER,,,,1;WDR7,non_coding_transcript_exon_variant,,ENST00000586124,,n.352T>A,MODIFIER,,,,1;WDR7,upstream_gene_variant,,ENST00000591449,,,MODIFIER,,,,1 3999/7295 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 96 deb611eb-9f5c-4997-9891-2194fabd6646 98 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS WDR7,non_coding_transcript_exon_variant,,ENST00000586124.2,n.352T>A,MODIFIER,;WDR7,synonymous_variant,p.S1221=,ENST00000357574.7,c.3663T>A,LOW,;WDR7,synonymous_variant,p.S1254=,ENST00000254442.8,c.3762T>A,LOW,YES;WDR7,intron_variant,,ENST00000589935.1,c.1-91168T>A,MODIFIER, +ZNF304 57343 BI GRCh38 19 57356745 57356745 + synonymous_variant Silent SNP C C T novel TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 43 15 c.876C>T p.His292= p.H292= ENST00000282286.6 NM_001329456.2 292 caC/caT 3/3 P4 T H protein_coding CCDS12950.1 876/1980 TTGCACCACCT Gene3D:3.30.160.60;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR23226;PANTHER:PTHR23226;PANTHER:PTHR23226;SMART:SM00355;Superfamily:SSF57667 ENSP00000282286 3/3 ENST00000282286 Transcript ENSG00000131845 HGNC:13505 LOW NM_020657.4 synonymous_variant Unknown Q9HCX3.162 ZNF304 HGNC 1 2.0 UPI000013CAB8 SNV ZNF304,synonymous_variant,p.H292=,ENST00000282286,NM_020657.4&NM_001329456.1,c.876C>T,LOW,,,,1;ZNF304,synonymous_variant,p.H292=,ENST00000391705,,c.876C>T,LOW,,,,1;ZNF304,synonymous_variant,p.H339=,ENST00000443917,NM_001290318.1,c.1017C>T,LOW,YES,,,1;ZNF304,synonymous_variant,p.H250=,ENST00000598744,NM_001290319.1,c.750C>T,LOW,,,,1;AC005261.2,upstream_gene_variant,,ENST00000597973,,,MODIFIER,YES,,,-1 1270/4423 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 75 deb611eb-9f5c-4997-9891-2194fabd6646 59 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS ZNF304,synonymous_variant,p.H250=,ENST00000598744.1,c.750C>T,LOW,;ZNF304,synonymous_variant,p.H339=,ENST00000443917.6,c.1017C>T,LOW,;ZNF304,synonymous_variant,p.H292=,ENST00000391705.7,c.876C>T,LOW,;ZNF304,synonymous_variant,p.H292=,ENST00000282286.6,c.876C>T,LOW,YES +RSPH14 27156 BI GRCh38 22 23064059 23064059 + missense_variant Missense_Mutation SNP C C T TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 25 18 c.496G>A p.Glu166Lys p.E166K ENST00000216036.9 NM_014433.3 166 Gag/Aag 5/7 P1 T E/K protein_coding YES CCDS13803.1 496/1047 GAACTCCTCCT Gene3D:1.25.10.10;PANTHER:PTHR15599;PANTHER:PTHR15599:SF1;Superfamily:SSF48371;Low_complexity_(Seg):seg ENSP00000216036 5/7 COSV53267094 ENST00000216036 Transcript ENSG00000100218 HGNC:13437 MODERATE NM_014433.3 missense_variant 1 1.0 benign(0.417) Unknown tolerated(0.15) 1 Q9UHP6.136 RSPH14 HGNC -1 1.0 UPI000004A0CE SNV RSPH14,missense_variant,p.E166K,ENST00000216036,NM_014433.3,c.496G>A,MODERATE,YES,tolerated(0.15),benign(0.417),-1 590/1188 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 37 deb611eb-9f5c-4997-9891-2194fabd6646 43 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS RSPH14,missense_variant,p.E166K,ENST00000216036.9,c.496G>A,MODERATE,YES +GAB3 139716 BI GRCh38 X 154680243 154680243 + synonymous_variant Silent SNP C C T TCGA-WC-AA9E-01A TCGA-WC-AA9E-10A Somatic 4 64 c.1533G>A p.Glu511= p.E511= ENST00000369575.7 NM_080612.4 511 gaG/gaA 9/10 A2 T E protein_coding CCDS14760.1 1533/1761 CGGTGCTCCTC PANTHER:PTHR45960;PANTHER:PTHR45960:SF3 ENSP00000358588 9/10 COSV100850443 ENST00000369575 Transcript ENSG00000160219 HGNC:17515 LOW synonymous_variant 1 Unknown 1 Q8WWW8.132 GAB3 HGNC -1 1.0 UPI000006F752 Q8WWW8-1 SNV GAB3,synonymous_variant,p.E512=,ENST00000424127,NM_001081573.3,c.1536G>A,LOW,YES,,,-1;GAB3,synonymous_variant,p.E511=,ENST00000369575,NM_080612.4,c.1533G>A,LOW,,,,-1;GAB3,intron_variant,,ENST00000369568,NM_001282283.2,c.1531-1949G>A,MODIFIER,,,,-1;GAB3,upstream_gene_variant,,ENST00000454973,,,MODIFIER,,,,-1;GAB3,non_coding_transcript_exon_variant,,ENST00000496390,,n.1083G>A,MODIFIER,,,,-1;GAB3,non_coding_transcript_exon_variant,,ENST00000475685,,n.182G>A,MODIFIER,,,,-1 1565/4718 muse;mutect2;varscan2 4480d290-5e8a-4289-8e3c-de087e0de412 0 48 deb611eb-9f5c-4997-9891-2194fabd6646 68 c6c4b99f-c9ad-4558-9707-fdb937c72e3e SUCCESS GAB3,non_coding_transcript_exon_variant,,ENST00000475685.1,n.182G>A,MODIFIER,;GAB3,intron_variant,,ENST00000369568.8,c.1531-1949G>A,MODIFIER,;GAB3,synonymous_variant,p.E511=,ENST00000369575.7,c.1533G>A,LOW,;GAB3,non_coding_transcript_exon_variant,,ENST00000496390.5,n.1083G>A,MODIFIER,;GAB3,synonymous_variant,p.E512=,ENST00000424127.3,c.1536G>A,LOW,YES +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 34 24 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 42 a64daaad-f089-42ce-80a6-35c8e3e6c783 58 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +SLC12A9 56996 BI GRCh38 7 100862719 100862720 + frameshift_variant Frame_Shift_Ins INS - - T novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 46 16 c.1750_1751insT p.Ala584CysfsTer51 p.A584Cfs*51 ENST00000354161.8 NM_001363494.1 584 gca/gTca 13/14 P1 T A/VX protein_coding YES CCDS5707.1 1750-1751/2745 ATGGGGCATGG Pfam:PF03522;PANTHER:PTHR11827;PANTHER:PTHR11827:SF98 ENSP00000275730 13/14 ENST00000354161 Transcript ENSG00000146828 HGNC:17435 HIGH NM_020246.4 frameshift_variant 1.0 Unknown Q9BXP2.143 SLC12A9 HGNC 1 1.0 UPI000006CD28 Q9BXP2-1 insertion SLC12A9,frameshift_variant,p.A584Vfs*51,ENST00000354161,NM_001363494.1&NM_001363493.2&NM_020246.4,c.1750_1751insT,HIGH,YES,,,1;SLC12A9,frameshift_variant,p.A584Vfs*109,ENST00000540482,NM_001267812.1,c.1750_1751insT,HIGH,,,,1;SLC12A9,frameshift_variant,p.A495Vfs*51,ENST00000415287,NM_001267814.2,c.1483_1484insT,HIGH,,,,1;TRIP6,upstream_gene_variant,,ENST00000200457,NM_003302.3,,MODIFIER,YES,,,1;SLC12A9,downstream_gene_variant,,ENST00000416675,,,MODIFIER,,,,1;SLC12A9,downstream_gene_variant,,ENST00000418037,,,MODIFIER,,,,1;TRIP6,upstream_gene_variant,,ENST00000619988,,,MODIFIER,,,,1;SLC12A9,non_coding_transcript_exon_variant,,ENST00000482184,,n.279_280insT,MODIFIER,,,,1;SLC12A9,downstream_gene_variant,,ENST00000461016,,,MODIFIER,,,,1;SLC12A9,downstream_gene_variant,,ENST00000475623,,,MODIFIER,,,,1;SLC12A9,non_coding_transcript_exon_variant,,ENST00000487651,,n.3063_3064insT,MODIFIER,,,,1;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972,,n.3034_3035insT,MODIFIER,,,,1;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687,,n.2729_2730insT,MODIFIER,,,,1;TRIP6,upstream_gene_variant,,ENST00000417475,,,MODIFIER,,,,1;TRIP6,upstream_gene_variant,,ENST00000437505,,,MODIFIER,,,,1;SLC12A9,downstream_gene_variant,,ENST00000448342,,,MODIFIER,,,,1;TRIP6,upstream_gene_variant,,ENST00000476870,,,MODIFIER,,,,1;TRIP6,upstream_gene_variant,,ENST00000496260,,,MODIFIER,,,,1;SLC12A9,downstream_gene_variant,,ENST00000497958,,,MODIFIER,,,,1 1915-1916/3315 mutect2;pindel;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 65 a64daaad-f089-42ce-80a6-35c8e3e6c783 63 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS SLC12A9,non_coding_transcript_exon_variant,,ENST00000482184.1,n.279_280insT,MODIFIER,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000487651.5,n.3063_3064insT,MODIFIER,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972.5,n.3034_3035insT,MODIFIER,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687.5,n.2729_2730insT,MODIFIER,;SLC12A9,frameshift_variant,p.A495Cfs*51,ENST00000415287.5,c.1483_1484insT,HIGH,;SLC12A9,frameshift_variant,p.A584Cfs*109,ENST00000540482.5,c.1750_1751insT,HIGH,;SLC12A9,frameshift_variant,p.A584Cfs*51,ENST00000354161.8,c.1750_1751insT,HIGH,YES +PPP1R3B 79660 BI GRCh38 8 9141079 9141079 + synonymous_variant Silent SNP C C T rs758018996 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 46 37 c.573G>A p.Thr191= p.T191= ENST00000310455.4 NM_024607.4 191 acG/acA 2/2 P1 T T protein_coding YES CCDS5973.1 573/858 GAGAACGTGTC PDB-ENSP_mappings:2eef.A;PIRSF:PIRSF500814;Gene3D:2.60.40.2440;PIRSF:PIRSF038207;Pfam:PF03370;PANTHER:PTHR12307:SF13;PANTHER:PTHR12307;PROSITE_profiles:PS51159 ENSP00000308318 2/2 rs758018996 ENST00000310455 Transcript ENSG00000173281 HGNC:14942 LOW NM_024607.4 0.0002602 gnomAD_AMR synonymous_variant 1.0 Unknown Q86XI6.130 PPP1R3B HGNC -1 1.0 UPI000000DA40 SNV PPP1R3B,synonymous_variant,p.T191=,ENST00000310455,NM_024607.4,c.573G>A,LOW,YES,,,-1;PPP1R3B,synonymous_variant,p.T191=,ENST00000519699,NM_001201329.2,c.573G>A,LOW,,,,-1;AC022784.5,upstream_gene_variant,,ENST00000520017,,,MODIFIER,YES,,,1;AC022784.5,upstream_gene_variant,,ENST00000522057,,,MODIFIER,,,,1;AC022784.5,upstream_gene_variant,,ENST00000666082,,,MODIFIER,,,,1 686/5510 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 4.772e-05 0.0 0.0002602 0.0 0.0 0.0 1.758e-05 0.0 3.266e-05 2.027990012720693e-05 0.0 0.0 0.0001987279974855 0.0 0.0 0.0 amr 0.0001987279974855 0.0 0.0 0.0 0.0 0 60 a64daaad-f089-42ce-80a6-35c8e3e6c783 83 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS PPP1R3B,synonymous_variant,p.T191=,ENST00000519699.1,c.573G>A,LOW,;PPP1R3B,synonymous_variant,p.T191=,ENST00000310455.4,c.573G>A,LOW,YES +NCOA2 10499 BI GRCh38 8 70138212 70138212 + missense_variant Missense_Mutation SNP C C T rs1426956925 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 18 21 c.3149G>A p.Ser1050Asn p.S1050N ENST00000452400.7 NM_001321703.2 1050 aGc/aAc 15/23 P1 T S/N protein_coding YES CCDS47872.1 3149/4395 TTTGGCTGGCA PIRSF:PIRSF038181;PANTHER:PTHR10684;PANTHER:PTHR10684:SF2 ENSP00000399968 15/23 rs1426956925 ENST00000452400 Transcript 1.0 ENSG00000140396 HGNC:7669 MODERATE NM_006540.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(1) Q15596.221 NCOA2 HGNC -1 1.0 UPI000012FE42 SNV NCOA2,missense_variant,p.S1050N,ENST00000452400,NM_001321703.2&NM_001321711.2&NM_006540.4&NM_001321707.2&NM_001321713.2&NM_001321712.2,c.3149G>A,MODERATE,YES,tolerated(1),benign(0),-1;NCOA2,missense_variant,p.S176N,ENST00000518363,,c.527G>A,MODERATE,,tolerated(1),benign(0.001),-1;NCOA2,3_prime_UTR_variant,,ENST00000518287,,c.*106G>A,MODIFIER,,,,-1;NCOA2,non_coding_transcript_exon_variant,,ENST00000522054,,n.180G>A,MODIFIER,,,,-1 3334/8430 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 24 a64daaad-f089-42ce-80a6-35c8e3e6c783 39 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS NCOA2,non_coding_transcript_exon_variant,,ENST00000522054.1,n.180G>A,MODIFIER,;NCOA2,synonymous_variant,p.Q175=,ENST00000518363.2,c.525G>A,LOW,;NCOA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000518287.6,c.*106G>A,MODIFIER,;NCOA2,missense_variant,p.S1050N,ENST00000452400.7,c.3149G>A,MODERATE,YES +MMP20 9313 BI GRCh38 11 102616841 102616841 + synonymous_variant Silent SNP G G C novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 25 19 c.345C>G p.Pro115= p.P115= ENST00000260228.3 NM_004771.4 115 ccC/ccG 2/10 P1 C P protein_coding YES CCDS8318.1 345/1452 CATTTGGGTTC PDB-ENSP_mappings:2jsd.A;PANTHER:PTHR10201:SF125;PANTHER:PTHR10201;Superfamily:SSF55486;SMART:SM00235;Gene3D:3.40.390.10;PIRSF:PIRSF001191 ENSP00000260228 2/10 ENST00000260228 Transcript 1.0 ENSG00000137674 HGNC:7167 LOW NM_004771.4 synonymous_variant 1.0 Unknown O60882.179 MMP20 HGNC -1 1.0 UPI000013D0B3 SNV MMP20,synonymous_variant,p.P115=,ENST00000260228,NM_004771.4,c.345C>G,LOW,YES,,,-1;AP000851.1,intron_variant,,ENST00000542119,,n.86+9389G>C,MODIFIER,YES,,,1 358/1959 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 34 a64daaad-f089-42ce-80a6-35c8e3e6c783 44 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS MMP20-AS1,intron_variant,,ENST00000542119.1,n.86+9389G>C,MODIFIER,YES;MMP20,synonymous_variant,p.P115=,ENST00000260228.3,c.345C>G,LOW,YES +SKA3 221150 BI GRCh38 13 21172654 21172654 + stop_gained Nonsense_Mutation SNP A A T novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 15 8 c.131T>A p.Leu44Ter p.L44* ENST00000314759.6 NM_145061.6 44 tTa/tAa 2/9 P2 T L/* protein_coding YES CCDS31946.1 131/1239 CATATAAAATT PDB-ENSP_mappings:4aj5.1;PDB-ENSP_mappings:4aj5.2;PDB-ENSP_mappings:4aj5.3;PDB-ENSP_mappings:4aj5.4;PDB-ENSP_mappings:4aj5.U;PDB-ENSP_mappings:4aj5.V;PDB-ENSP_mappings:4aj5.W;PDB-ENSP_mappings:4aj5.X;PDB-ENSP_mappings:4aj5.Y;PDB-ENSP_mappings:4aj5.Z;PANTHER:PTHR28543;CDD:cd12957 ENSP00000319417 2/9 ENST00000314759 Transcript ENSG00000165480 HGNC:20262 HIGH NM_145061.6 stop_gained 1.0 Unknown Q8IX90.138 SKA3 HGNC -1 1.0 UPI00001AEC75 Q8IX90-1 SNV SKA3,stop_gained,p.L44*,ENST00000314759,NM_145061.6,c.131T>A,HIGH,YES,,,-1;SKA3,stop_gained,p.L44*,ENST00000400018,NM_001166017.2,c.131T>A,HIGH,,,,-1;MRPL57,upstream_gene_variant,,ENST00000309594,NM_024026.5,,MODIFIER,YES,,,1;SKA3,3_prime_UTR_variant,,ENST00000465471,,c.*47T>A,MODIFIER,,,,-1;SKA3,non_coding_transcript_exon_variant,,ENST00000536239,,n.60T>A,MODIFIER,,,,-1;SKA3,non_coding_transcript_exon_variant,,ENST00000475251,,n.127T>A,MODIFIER,,,,-1;SKA3,intron_variant,,ENST00000298260,,c.104-150T>A,MODIFIER,,,,-1;SKA3,intron_variant,,ENST00000462482,,c.103+3721T>A,MODIFIER,,,,-1 206/2869 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 16 a64daaad-f089-42ce-80a6-35c8e3e6c783 23 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS SKA3,non_coding_transcript_exon_variant,,ENST00000475251.1,n.127T>A,MODIFIER,;SKA3,non_coding_transcript_exon_variant,,ENST00000536239.1,n.60T>A,MODIFIER,;SKA3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000465471.5,c.*47T>A,MODIFIER,;SKA3,intron_variant,NMD_transcript_variant,,ENST00000462482.1,c.103+3721T>A,MODIFIER,;SKA3,intron_variant,NMD_transcript_variant,,ENST00000298260.8,c.104-150T>A,MODIFIER,;SKA3,stop_gained,p.L44*,ENST00000314759.6,c.131T>A,HIGH,YES;SKA3,stop_gained,p.L44*,ENST00000400018.7,c.131T>A,HIGH, +URAD 646625 BI GRCh38 13 27988620 27988620 + synonymous_variant Silent SNP G G A rs1249035096 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 58 39 c.18C>T p.Val6= p.V6= ENST00000332715.6 NM_001105577.2 6 gtC/gtT 1/2 P1 A V protein_coding YES CCDS45020.1 18/522 GAGTTGACCTT PANTHER:PTHR43466;Gene3D:1.10.3330.10;Superfamily:SSF158694 ENSP00000333490 1/2 rs1249035096 ENST00000332715 Transcript ENSG00000183463 HGNC:17785 LOW NM_001105577.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown A6NGE7.90 URAD HGNC -1 5.0 UPI000016154A SNV URAD,synonymous_variant,p.V6=,ENST00000332715,NM_001105577.2,c.18C>T,LOW,YES,,,-1;RN7SL272P,downstream_gene_variant,,ENST00000487762,,,MODIFIER,YES,,,-1 74/967 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 67 a64daaad-f089-42ce-80a6-35c8e3e6c783 97 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS URAD,synonymous_variant,p.V6=,ENST00000332715.6,c.18C>T,LOW,YES +RND2 8153 BI GRCh38 17 43028464 43028464 + synonymous_variant Silent SNP G G T novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 47 33 c.468G>T p.Val156= p.V156= ENST00000587250.4 NM_005440.5 156 gtG/gtT 5/5 P1 T V protein_coding YES CCDS11452.1 468/684 GCTGTGTCCTA Gene3D:3.40.50.300;Pfam:PF00071;PROSITE_profiles:PS51420;PANTHER:PTHR24072;PANTHER:PTHR24072:SF21;SMART:SM00173;SMART:SM00174;SMART:SM00175;Superfamily:SSF52540;CDD:cd04173;Low_complexity_(Seg):seg ENSP00000466680 5/5 ENST00000587250 Transcript ENSG00000108830 HGNC:18315 LOW NM_005440.5 synonymous_variant 1.0 Unknown P52198.166 RND2 HGNC 1 1.0 UPI0000133895 SNV RND2,synonymous_variant,p.V156=,ENST00000587250,NM_005440.5,c.468G>T,LOW,YES,,,1;VAT1,upstream_gene_variant,,ENST00000587062,,,MODIFIER,,,,-1;VAT1,upstream_gene_variant,,ENST00000590924,,,MODIFIER,,,,-1;RND2,downstream_gene_variant,,ENST00000587117,,,MODIFIER,,,,1 585/4162 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 62 a64daaad-f089-42ce-80a6-35c8e3e6c783 80 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS RND2,non_coding_transcript_exon_variant,,ENST00000710494.1,n.396G>T,MODIFIER,;RND2,synonymous_variant,p.V156=,ENST00000587250.4,c.468G>T,LOW,YES +SOST 50964 BI GRCh38 17 43758600 43758600 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 54 37 c.142C>T p.Pro48Ser p.P48S ENST00000301691.3 NM_025237.3 48 Ccg/Tcg 1/2 P1 A P/S protein_coding YES CCDS11468.1 142/642 CTCCGGTGGAG PDB-ENSP_mappings:2k8p.A;Pfam:PF05463;PANTHER:PTHR14903;PANTHER:PTHR14903:SF4;Low_complexity_(Seg):seg ENSP00000301691 1/2 ENST00000301691 Transcript 1.0 ENSG00000167941 HGNC:13771 MODERATE NM_025237.3 missense_variant 1.0 benign(0.007) Unknown tolerated(0.62) Q9BQB4.160 SOST HGNC -1 1.0 UPI0000035BBE Q9BQB4-1 SNV SOST,missense_variant,p.P48S,ENST00000301691,NM_025237.3,c.142C>T,MODERATE,YES,tolerated(0.62),benign(0.007),-1 192/2296 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 62 a64daaad-f089-42ce-80a6-35c8e3e6c783 91 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS SOST,missense_variant,p.P48S,ENST00000301691.3,c.142C>T,MODERATE,YES +GPATCH8 23131 BI GRCh38 17 44400028 44400028 + synonymous_variant Silent SNP T T C novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 100 76 c.2049A>G p.Lys683= p.K683= ENST00000591680.6 NM_001304939.2 683 aaA/aaG 8/8 P1 C K protein_coding YES CCDS32666.1 2049/4509 CTGGATTTTTT PANTHER:PTHR17614;PANTHER:PTHR17614:SF11;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000467556 8/8 ENST00000591680 Transcript ENSG00000186566 HGNC:29066 LOW NM_001002909.4 synonymous_variant 1.0 Unknown Q9UKJ3.148 GPATCH8 HGNC -1 2.0 UPI0000237985 Q9UKJ3-1 SNV GPATCH8,synonymous_variant,p.K683=,ENST00000591680,NM_001304939.2&NM_001304942.2&NM_001002909.4&NM_001304941.2&NM_001304940.2,c.2049A>G,LOW,YES,,,-1;GPATCH8,downstream_gene_variant,,ENST00000585614,,,MODIFIER,,,,-1;GPATCH8,3_prime_UTR_variant,,ENST00000587228,,c.*1935A>G,MODIFIER,,,,-1;GPATCH8,non_coding_transcript_exon_variant,,ENST00000335500,,n.3365A>G,MODIFIER,,,,-1;GPATCH8,non_coding_transcript_exon_variant,,ENST00000635257,NM_001304943.1,n.2148A>G,MODIFIER,,,,-1;GPATCH8,downstream_gene_variant,,ENST00000590041,,,MODIFIER,,,,-1 2085/6832 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 163 a64daaad-f089-42ce-80a6-35c8e3e6c783 177 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS GPATCH8,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000587228.5,c.*1935A>G,MODIFIER,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000635257.1,n.2148A>G,MODIFIER,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000335500.8,n.3365A>G,MODIFIER,;GPATCH8,synonymous_variant,p.K683=,ENST00000591680.6,c.2049A>G,LOW,YES +NXPH3 11248 BI GRCh38 17 49578691 49578691 + synonymous_variant Silent SNP G G A novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 33 49 c.150G>A p.Arg50= p.R50= ENST00000328741.6 NM_007225.4 50 cgG/cgA 2/2 P1 A R protein_coding CCDS11550.1 150/759 AAGCGGGGCCA PIRSF:PIRSF038019;PANTHER:PTHR17103;PANTHER:PTHR17103:SF14;MobiDB_lite:mobidb-lite ENSP00000329295 2/2 ENST00000328741 Transcript ENSG00000182575 HGNC:8077 LOW NM_007225.4 synonymous_variant Unknown O95157.144 NXPH3 HGNC 1 1.0 UPI00000389F1 SNV NXPH3,synonymous_variant,p.R50=,ENST00000328741,NM_007225.4,c.150G>A,LOW,,,,1;NXPH3,synonymous_variant,p.R50=,ENST00000513748,,c.150G>A,LOW,YES,,,1;NXPH3,non_coding_transcript_exon_variant,,ENST00000570453,,n.58G>A,MODIFIER,,,,1;AC006487.2,upstream_gene_variant,,ENST00000503624,,,MODIFIER,,,,-1;AC006487.1,upstream_gene_variant,,ENST00000514506,,,MODIFIER,YES,,,-1 499/5635 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 55 a64daaad-f089-42ce-80a6-35c8e3e6c783 82 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS NXPH3,non_coding_transcript_exon_variant,,ENST00000570453.1,n.58G>A,MODIFIER,;NXPH3,synonymous_variant,p.R50=,ENST00000513748.1,c.150G>A,LOW,;NXPH3,synonymous_variant,p.R50=,ENST00000328741.6,c.150G>A,LOW,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 27 29 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 65 a64daaad-f089-42ce-80a6-35c8e3e6c783 56 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +RBM12 10137 BI GRCh38 20 35653351 35653351 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 41 22 c.1972C>A p.Pro658Thr p.P658T ENST00000359646.1 NM_001198840.2 658 Ccc/Acc 2/2 P1 T P/T protein_coding CCDS13261.1 1972/2799 ACCGGGCAGTC PANTHER:PTHR13976;PANTHER:PTHR13976:SF31;Superfamily:SSF54928;Low_complexity_(Seg):seg ENSP00000352668 2/2 ENST00000359646 Transcript 1.0 ENSG00000244462 HGNC:9898 MODERATE missense_variant benign(0.005) Unknown deleterious_low_confidence(0.04) Q9NTZ6.179 RBM12 HGNC -1 1.0 UPI0000073D24 SNV RBM12,missense_variant,p.P658T,ENST00000374114,NM_001198838.2&NM_006047.6,c.1972C>A,MODERATE,YES,deleterious_low_confidence(0.04),benign(0.005),-1;RBM12,missense_variant,p.P658T,ENST00000359646,NM_001198840.2,c.1972C>A,MODERATE,,deleterious_low_confidence(0.04),benign(0.005),-1;RBM12,missense_variant,p.P658T,ENST00000374104,NM_152838.4,c.1972C>A,MODERATE,,deleterious_low_confidence(0.04),benign(0.005),-1;CPNE1,intron_variant,,ENST00000317677,NM_003915.5,c.15+177C>A,MODIFIER,YES,,,-1;CPNE1,intron_variant,,ENST00000352393,,c.-1+1851C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000397442,,c.-1+11451C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000397443,NM_001198863.2&NM_152926.3&NM_152925.3&NM_152928.3&NM_152927.3,c.-1+11409C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000412056,,c.-1+11451C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000414664,,c.-1+11409C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000414711,,c.-1+1851C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000416778,,c.-1+11409C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000420363,,c.-1+5579C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000430570,,c.-1+11409C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000434795,,c.-1+5579C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000435747,,c.-1+11008C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000437100,,c.-1+1851C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000437340,,c.-1+11451C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000439806,,c.-1+11528C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000440240,,c.-1+1851C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000458038,,c.-1+5579C>A,MODIFIER,,,,-1;RBM12,downstream_gene_variant,,ENST00000424458,,,MODIFIER,,,,-1;RBM12,downstream_gene_variant,,ENST00000431148,,,MODIFIER,,,,-1;RBM12,downstream_gene_variant,,ENST00000435161,,,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000401607,,c.-1+11451C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000439669,,c.-1+11409C>A,MODIFIER,,,,-1;AL109827.1,intron_variant,,ENST00000441563,,c.*210+1851C>A,MODIFIER,,,,-1;AL109827.1,intron_variant,,ENST00000454607,,c.*32+1851C>A,MODIFIER,,,,-1;CPNE1,intron_variant,,ENST00000483359,,n.102+11409C>A,MODIFIER,,,,-1;AL109827.1,intron_variant,,ENST00000541176,,c.*32+1851C>A,MODIFIER,YES,,,-1 2123/5332 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 64 a64daaad-f089-42ce-80a6-35c8e3e6c783 63 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS RBM12,missense_variant,p.P658T,ENST00000374104.7,c.1972C>A,MODERATE,;RBM12,missense_variant,p.P658T,ENST00000359646.1,c.1972C>A,MODERATE,;RBM12,missense_variant,p.P658T,ENST00000374114.8,c.1972C>A,MODERATE,YES;CPNE1,intron_variant,,ENST00000435747.2,c.-1+11008C>A,MODIFIER,;ENSG00000272897,intron_variant,NMD_transcript_variant,,ENST00000454607.5,c.*32+1851C>A,MODIFIER,;ENSG00000272897,intron_variant,NMD_transcript_variant,,ENST00000541176.2,c.*32+1851C>A,MODIFIER,YES;ENSG00000272897,intron_variant,NMD_transcript_variant,,ENST00000441563.5,c.*210+1851C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000414711.5,c.-1+1851C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000437100.5,c.-1+1851C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000458038.5,c.-1+5579C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000440240.5,c.-1+1851C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000434795.5,c.-1+5579C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000420363.5,c.-1+5579C>A,MODIFIER,;CPNE1,intron_variant,NMD_transcript_variant,,ENST00000439669.5,c.-1+11409C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000439806.6,c.-1+11528C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000416778.5,c.-1+11409C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000414664.5,c.-1+11409C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000412056.5,c.-1+11451C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000430570.5,c.-1+11409C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000437340.5,c.-1+11451C>A,MODIFIER,;CPNE1,intron_variant,NMD_transcript_variant,,ENST00000401607.6,c.-1+11451C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000397442.5,c.-1+11451C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000483359.5,n.102+11409C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000317677.9,c.15+177C>A,MODIFIER,;CPNE1,intron_variant,,ENST00000397443.7,c.-1+11409C>A,MODIFIER,YES;CPNE1,intron_variant,,ENST00000352393.8,c.-1+1851C>A,MODIFIER, +MAPK8IP2 23542 BI GRCh38 22 50601827 50601827 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 57 22 c.104A>C p.Glu35Ala p.E35A ENST00000329492.6 NM_012324.6 35 gAa/gCa 2/12 P1 C E/A protein_coding YES CCDS74886.1 104/2475 CGACGAAGATC PANTHER:PTHR47437;PANTHER:PTHR47437:SF2;Low_complexity_(Seg):seg ENSP00000330572 2/12 ENST00000329492 Transcript ENSG00000008735 HGNC:6883 MODERATE NM_012324.6 missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0) Q13387.173 MAPK8IP2 HGNC 1 1.0 UPI000012DAB7 Q13387-1 SNV MAPK8IP2,missense_variant,p.E35A,ENST00000329492,NM_012324.6,c.104A>C,MODERATE,YES,deleterious(0),probably_damaging(0.994),1;CHKB,upstream_gene_variant,,ENST00000463053,,,MODIFIER,,,,-1;MAPK8IP2,upstream_gene_variant,,ENST00000008876,,,MODIFIER,,,,1;U62317.2,downstream_gene_variant,,ENST00000609758,,,MODIFIER,YES,,,1 130/5700 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0 62 a64daaad-f089-42ce-80a6-35c8e3e6c783 79 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS MAPK8IP2,missense_variant,p.E35A,ENST00000329492.6,c.104A>C,MODERATE,YES +ANOS1 3730 BI GRCh38 X 8731866 8731866 + missense_variant Missense_Mutation SNP C C A rs1411018904 TCGA-VD-A8KH-01A TCGA-VD-A8KH-10A Somatic 2 22 c.171G>T p.Gln57His p.Q57H ENST00000262648.8 NM_000216.4 57 caG/caT 1/14 P1 A Q/H protein_coding YES CCDS14130.1 171/2043 GTGATCTGCAG PDB-ENSP_mappings:1zlg.A;PANTHER:PTHR14131:SF6;PANTHER:PTHR14131;Pfam:PF17869 ENSP00000262648 1/14 rs1411018904 ENST00000262648 Transcript 1.0 ENSG00000011201 HGNC:6211 MODERATE NM_000216.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(1) P23352.199 ANOS1 HGNC -1 1.0 UPI00001AE843 SNV ANOS1,missense_variant,p.Q57H,ENST00000262648,NM_000216.4,c.171G>T,MODERATE,YES,tolerated(1),benign(0),-1 272/6265 muse;mutect2;varscan2 39af6e0f-908c-4b2b-97b8-a4d1966e47e1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 14 a64daaad-f089-42ce-80a6-35c8e3e6c783 24 32d98156-6ada-4019-b3b4-72e5d3fa7078 SUCCESS ANOS1,missense_variant,p.Q57H,ENST00000262648.8,c.171G>T,MODERATE,YES +NBEAL2 23218 BI GRCh38 3 47000254 47000254 + synonymous_variant Silent SNP G G A novel TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 13 17 c.4155G>A p.Gln1385= p.Q1385= ENST00000450053.8 NM_015175.3 1385 caG/caA 27/54 P4 A Q protein_coding YES CCDS46817.1 4155/8265 AGCCAGCCCGG MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR13743:SF111;PANTHER:PTHR13743 ENSP00000415034 27/54 ENST00000450053 Transcript 1.0 ENSG00000160796 HGNC:31928 LOW NM_015175.3 synonymous_variant 1.0 Unknown Q6ZNJ1.144 NBEAL2 HGNC 1 2.0 UPI000022C020 Q6ZNJ1-1 SNV NBEAL2,synonymous_variant,p.Q1385=,ENST00000450053,NM_015175.3,c.4155G>A,LOW,YES,,,1;NBEAL2,synonymous_variant,p.Q1351=,ENST00000651747,NM_001365116.2,c.4053G>A,LOW,,,,1;NBEAL2,synonymous_variant,p.Q673=,ENST00000416683,,c.2019G>A,LOW,,,,1;NBEAL2,upstream_gene_variant,,ENST00000443829,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000441027,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000475689,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000486870,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000651450,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000651453,,,MODIFIER,,,,1;NBEAL2,downstream_gene_variant,,ENST00000652242,,,MODIFIER,,,,1;NBEAL2,downstream_gene_variant,,ENST00000652744,,,MODIFIER,,,,1 4351/8842 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 74 ca070df2-4342-4a09-b989-0cc323831f95 31 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS NBEAL2,missense_variant,p.S673N,ENST00000416683.5,c.2018G>A,MODERATE,;NBEAL2,synonymous_variant,p.Q1351=,ENST00000651747.1,c.4053G>A,LOW,;NBEAL2,synonymous_variant,p.Q1385=,ENST00000450053.8,c.4155G>A,LOW,YES +GPR87 53836 BI GRCh38 3 151294943 151294943 + missense_variant Missense_Mutation SNP A A C novel TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 30 20 c.303T>G p.Asp101Glu p.D101E ENST00000260843.5 NM_023915.4 101 gaT/gaG 3/3 P1 C D/E protein_coding YES CCDS3157.1 303/1077 CCTGCATCATG PROSITE_profiles:PS50262;CDD:cd15969;PANTHER:PTHR24233;PANTHER:PTHR24233:SF8;Pfam:PF00001;Gene3D:1.20.1070.10;Superfamily:SSF81321;Prints:PR01157 ENSP00000260843 3/3 ENST00000260843 Transcript ENSG00000138271 HGNC:4538 MODERATE NM_023915.4 missense_variant 1.0 possibly_damaging(0.559) Unknown deleterious(0.05) Q9BY21.156 GPR87 HGNC -1 1.0 UPI000003C9FF SNV GPR87,missense_variant,p.D101E,ENST00000260843,NM_023915.4,c.303T>G,MODERATE,YES,deleterious(0.05),possibly_damaging(0.559),-1;MED12L,intron_variant,,ENST00000273432,,c.1726-55116A>C,MODIFIER,,,,1;MED12L,intron_variant,,ENST00000474524,NM_053002.5,c.2146-55116A>C,MODIFIER,YES,,,1;MED12L,intron_variant,,ENST00000480026,,c.194-41564A>C,MODIFIER,,,,1;MED12L,intron_variant,,ENST00000491549,,n.73+53075A>C,MODIFIER,,,,1;GPR87,non_coding_transcript_exon_variant,,ENST00000629077,,n.342T>G,MODIFIER,,,,-1;AC078816.1,non_coding_transcript_exon_variant,,ENST00000666451,,n.781A>C,MODIFIER,YES,,,1 636/1493 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 99 ca070df2-4342-4a09-b989-0cc323831f95 50 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS GPR87,missense_variant,p.D101E,ENST00000260843.5,c.303T>G,MODERATE,YES;GPR87,non_coding_transcript_exon_variant,,ENST00000629077.1,n.342T>G,MODIFIER,;ENSG00000286273,non_coding_transcript_exon_variant,,ENST00000666451.1,n.781A>C,MODIFIER,YES;MED12L,intron_variant,,ENST00000491549.5,n.73+53075A>C,MODIFIER,;MED12L,intron_variant,,ENST00000480026.1,c.194-41564A>C,MODIFIER,;MED12L,intron_variant,,ENST00000273432.8,c.1726-55116A>C,MODIFIER,;MED12L,intron_variant,,ENST00000474524.5,c.2146-55116A>C,MODIFIER,;MED12L,intron_variant,,ENST00000688234.1,c.2251-41564A>C,MODIFIER,;MED12L,intron_variant,,ENST00000686666.1,c.1864-55116A>C,MODIFIER,;MED12L,intron_variant,,ENST00000693531.1,n.2326-55116A>C,MODIFIER,;MED12L,intron_variant,,ENST00000687756.1,c.2251-55116A>C,MODIFIER,YES;MED12L,intron_variant,,ENST00000685357.1,n.2509-55116A>C,MODIFIER, +FKBP9 11328 BI GRCh38 7 32988633 32988633 + synonymous_variant Silent SNP G G A rs1784621896 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 17 14 c.1020G>A p.Gly340= p.G340= ENST00000242209.9 NM_007270.5 340 ggG/ggA 6/10 P1 A G protein_coding CCDS5439.1 1020/1713 CTGGGGTATGG Gene3D:3.10.50.40;Pfam:PF00254;PROSITE_profiles:PS50059;PANTHER:PTHR46046;PANTHER:PTHR46046:SF2;Superfamily:SSF54534 ENSP00000242209 6/10 ENST00000242209 Transcript 1.0 ENSG00000122642 HGNC:3725 LOW NM_007270.5 synonymous_variant Unknown O95302.177 FKBP9 HGNC 1 1.0 UPI00001B6B0A O95302-1 SNV FKBP9,synonymous_variant,p.G393=,ENST00000538336,NM_001284341.1,c.1179G>A,LOW,YES,,,1;FKBP9,synonymous_variant,p.G340=,ENST00000242209,NM_007270.5,c.1020G>A,LOW,,,,1;FKBP9,synonymous_variant,p.G108=,ENST00000490776,NM_001284343.1,c.324G>A,LOW,,,,1;FKBP9,synonymous_variant,p.G108=,ENST00000418354,,c.324G>A,LOW,,,,1;FKBP9,non_coding_transcript_exon_variant,,ENST00000489038,,n.409G>A,MODIFIER,,,,1;FKBP9,non_coding_transcript_exon_variant,,ENST00000472007,,n.594G>A,MODIFIER,,,,1;FKBP9,non_coding_transcript_exon_variant,,ENST00000463443,,n.243G>A,MODIFIER,,,,1;FKBP9,non_coding_transcript_exon_variant,,ENST00000494374,,n.1156G>A,MODIFIER,,,,1;FKBP9,non_coding_transcript_exon_variant,,ENST00000468510,,n.48G>A,MODIFIER,,,,1 1154/3424 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 49 ca070df2-4342-4a09-b989-0cc323831f95 32 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS FKBP9,non_coding_transcript_exon_variant,,ENST00000468510.5,n.48G>A,MODIFIER,;FKBP9,non_coding_transcript_exon_variant,,ENST00000463443.1,n.243G>A,MODIFIER,;FKBP9,synonymous_variant,p.G108=,ENST00000418354.5,c.324G>A,LOW,;FKBP9,synonymous_variant,p.G108=,ENST00000490776.3,c.324G>A,LOW,;FKBP9,non_coding_transcript_exon_variant,,ENST00000489038.5,n.409G>A,MODIFIER,;FKBP9,non_coding_transcript_exon_variant,,ENST00000472007.5,n.594G>A,MODIFIER,;FKBP9,synonymous_variant,p.G340=,ENST00000242209.9,c.1020G>A,LOW,YES;FKBP9,non_coding_transcript_exon_variant,,ENST00000494374.5,n.1156G>A,MODIFIER,;FKBP9,synonymous_variant,p.G393=,ENST00000538336.5,c.1179G>A,LOW, +SLC26A5 375611 BI GRCh38 7 103410488 103410488 + missense_variant Missense_Mutation SNP C C T rs773574721 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 12 11 c.632G>A p.Arg211His p.R211H ENST00000306312.8 NM_198999.3 211 cGt/cAt 7/20 P4 T R/H protein_coding CCDS5733.1 632/2235 ACCCACGGACC Transmembrane_helices:TMhelix;PANTHER:PTHR11814;PANTHER:PTHR11814:SF32;TIGRFAM:TIGR00815;Pfam:PF00916 ENSP00000304783 7/20 rs773574721;COSV59702635 ENST00000306312 Transcript 1.0 ENSG00000170615 HGNC:9359 MODERATE NM_198999.3 5.446e-05 gnomAD_EAS missense_variant 0;1 possibly_damaging(0.634) Unknown deleterious(0.01) 0;1 P58743.150 SLC26A5 HGNC -1 1.0 UPI0000132195 P58743-1 SNV SLC26A5,missense_variant,p.R211H,ENST00000306312,NM_198999.3,c.632G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.634),-1;SLC26A5,missense_variant,p.R211H,ENST00000354356,,c.632G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.965),-1;SLC26A5,missense_variant,p.R211H,ENST00000432958,NM_001167962.1,c.632G>A,MODERATE,,deleterious(0),probably_damaging(0.944),-1;SLC26A5,missense_variant,p.R211H,ENST00000393730,,c.632G>A,MODERATE,,deleterious(0),probably_damaging(0.944),-1;SLC26A5,missense_variant,p.R211H,ENST00000339444,NM_001321787.2&NM_206883.3,c.632G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.907),-1;SLC26A5,missense_variant,p.R174H,ENST00000393729,,c.521G>A,MODERATE,,deleterious(0),probably_damaging(0.965),-1;SLC26A5,missense_variant,p.R211H,ENST00000393727,,c.632G>A,MODERATE,,deleterious(0.01),probably_damaging(0.965),-1;SLC26A5,missense_variant,p.R211H,ENST00000393723,,c.632G>A,MODERATE,,deleterious(0.01),probably_damaging(0.944),-1;SLC26A5,missense_variant,p.R211H,ENST00000393735,NM_206884.3,c.632G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.839),-1;SLC26A5,missense_variant,p.R211H,ENST00000356767,NM_206885.3,c.632G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.501),-1;SLC26A5,missense_variant,p.R211H,ENST00000423416,,c.632G>A,MODERATE,,deleterious(0),possibly_damaging(0.864),-1;SLC26A5,missense_variant,p.R174H,ENST00000456463,,c.521G>A,MODERATE,,deleterious(0.01),probably_damaging(0.972),-1;SLC26A5,missense_variant,p.R211H,ENST00000445809,,c.632G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.546),-1;SLC26A5,missense_variant,p.R211H,ENST00000454864,,c.632G>A,MODERATE,,deleterious(0),possibly_damaging(0.629),-1;SLC26A5,non_coding_transcript_exon_variant,,ENST00000487407,,n.783G>A,MODIFIER,,,,-1 924/2719 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 3.981e-06 0.0 0.0 0.0 5.446e-05 0.0 0.0 0.0 0.0 6.7646201387105975e-06 0.0 0.0 0.0 0.0 0.0 9.435739775653929e-05 0.0 0.0 0.0 0.0 0 59 ca070df2-4342-4a09-b989-0cc323831f95 23 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS SLC26A5,non_coding_transcript_exon_variant,,ENST00000487407.1,n.783G>A,MODIFIER,;SLC26A5,missense_variant,p.R211H,ENST00000393723.2,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000393727.5,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R174H,ENST00000393729.5,c.521G>A,MODERATE,;SLC26A5,missense_variant,NMD_transcript_variant,p.R174H,ENST00000456463.5,c.521G>A,MODERATE,;SLC26A5,missense_variant,NMD_transcript_variant,p.R211H,ENST00000423416.5,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000432958.6,c.632G>A,MODERATE,;SLC26A5,missense_variant,NMD_transcript_variant,p.R211H,ENST00000454864.5,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000306312.8,c.632G>A,MODERATE,YES;SLC26A5,missense_variant,p.R211H,ENST00000393730.5,c.632G>A,MODERATE,;SLC26A5,missense_variant,NMD_transcript_variant,p.R211H,ENST00000445809.5,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000393735.6,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000339444.10,c.632G>A,MODERATE,;SLC26A5,missense_variant,p.R211H,ENST00000356767.8,c.632G>A,MODERATE, +PPP1R3A 5506 BI GRCh38 7 113879435 113879435 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 37 22 c.1657G>A p.Ala553Thr p.A553T ENST00000284601.4 NM_002711.4 553 Gca/Aca 4/4 P1 T A/T protein_coding YES CCDS5759.1 1657/3369 CCCTGCCACAC PANTHER:PTHR12307;PANTHER:PTHR12307:SF2 ENSP00000284601 4/4 ENST00000284601 Transcript 1.0 ENSG00000154415 HGNC:9291 MODERATE NM_002711.4 missense_variant 1.0 benign(0.007) Unknown tolerated(0.27) Q16821.147 PPP1R3A HGNC -1 1.0 UPI000013DDAA Q16821-1 SNV PPP1R3A,missense_variant,p.A553T,ENST00000284601,NM_002711.4,c.1657G>A,MODERATE,YES,tolerated(0.27),benign(0.007),-1;PPP1R3A,downstream_gene_variant,,ENST00000449795,,,MODIFIER,,,,-1;PPP1R3A,downstream_gene_variant,,ENST00000284602,,,MODIFIER,,,,-1 1670/4328 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 134 ca070df2-4342-4a09-b989-0cc323831f95 59 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS PPP1R3A,missense_variant,p.A553T,ENST00000284601.4,c.1657G>A,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 46 40 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 141 ca070df2-4342-4a09-b989-0cc323831f95 86 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +SLC2A8 29988 BI GRCh38 9 127407229 127407229 + missense_variant Missense_Mutation SNP G G A rs1461206142 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 29 26 c.1414G>A p.Ala472Thr p.A472T ENST00000373371.8 NM_014580.5 472 Gcc/Acc 10/10 P1 A A/T protein_coding YES CCDS6870.1 1414/1434 TCACAGCCCAT Gene3D:1.20.1250.20;Pfam:PF00083;PANTHER:PTHR23500;PANTHER:PTHR23500:SF157 ENSP00000362469 10/10 rs1461206142 ENST00000373371 Transcript ENSG00000136856 HGNC:13812 MODERATE NM_014580.5 8.834e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.999) Unknown tolerated(0.09) Q9NY64.165 SLC2A8 HGNC 1 A0A024R871.42 1.0 UPI000003E7A8 SNV SLC2A8,missense_variant,p.A472T,ENST00000373371,NM_014580.5,c.1414G>A,MODERATE,YES,tolerated(0.09),probably_damaging(0.999),1;SLC2A8,missense_variant,p.A309T,ENST00000610552,NM_001271712.1,c.925G>A,MODERATE,,tolerated(0.07),probably_damaging(0.999),1;SLC2A8,missense_variant,p.A209T,ENST00000373352,,c.625G>A,MODERATE,,tolerated(0.18),probably_damaging(0.999),1;SLC2A8,3_prime_UTR_variant,,ENST00000373360,NM_001271711.1,c.*32G>A,MODIFIER,,,,1;SLC2A8,intron_variant,,ENST00000430147,,c.814-207G>A,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000419132,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000419917,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000423934,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000439597,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000451404,,,MODIFIER,,,,1;SLC2A8,intron_variant,,ENST00000477027,,n.366-207G>A,MODIFIER,,,,1;SLC2A8,upstream_gene_variant,,ENST00000484208,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000484617,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000485806,,,MODIFIER,,,,1;SLC2A8,downstream_gene_variant,,ENST00000489239,,,MODIFIER,,,,1 1476/2145 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 3.988e-06 0.0 0.0 0.0 0.0 0.0 8.834e-06 0.0 0.0 1.3518099876819178e-05 2.4320199372596107e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.542919926578179e-05 0.0 0.0 0 98 ca070df2-4342-4a09-b989-0cc323831f95 56 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS SLC2A8,intron_variant,,ENST00000477027.1,n.366-207G>A,MODIFIER,;SLC2A8,intron_variant,,ENST00000430147.1,c.814-207G>A,MODIFIER,;SLC2A8,3_prime_UTR_variant,,ENST00000373360.7,c.*32G>A,MODIFIER,;SLC2A8,missense_variant,p.A209T,ENST00000373352.5,c.625G>A,MODERATE,;SLC2A8,missense_variant,p.A472T,ENST00000373371.8,c.1414G>A,MODERATE,YES;SLC2A8,missense_variant,p.A309T,ENST00000610552.4,c.925G>A,MODERATE, +SETX 23064 BI GRCh38 9 132288559 132288559 + missense_variant Missense_Mutation SNP G G A novel TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 12 18 c.6199C>T p.His2067Tyr p.H2067Y ENST00000224140.6 NM_015046.7 2067 Cac/Tac 16/26 P1 A H/Y protein_coding YES CCDS6947.1 6199/8034 TCTGTGGTTTA Gene3D:3.40.50.300;Pfam:PF13086;PANTHER:PTHR10887;PANTHER:PTHR10887:SF382;Superfamily:SSF52540;CDD:cd18042 ENSP00000224140 16/26 ENST00000224140 Transcript 1.0 ENSG00000107290 HGNC:445 MODERATE NM_015046.7 missense_variant 1.0 probably_damaging(0.998) Unknown tolerated(0.05) Q7Z333.169 SETX HGNC -1 1.0 UPI0000210D28 Q7Z333-1 SNV SETX,missense_variant,p.H2067Y,ENST00000224140,NM_015046.7&NM_001351528.2&NM_001351527.1,c.6199C>T,MODERATE,YES,tolerated(0.05),probably_damaging(0.998),-1;SETX,missense_variant,p.H309Y,ENST00000436441,,c.925C>T,MODERATE,,tolerated(0.06),probably_damaging(0.994),-1;SETX,upstream_gene_variant,,ENST00000474172,,,MODIFIER,,,,-1 6383/11101 mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 103 ca070df2-4342-4a09-b989-0cc323831f95 30 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS SETX,missense_variant,p.H2067Y,ENST00000224140.6,c.6199C>T,MODERATE,YES;SETX,missense_variant,p.H309Y,ENST00000436441.5,c.925C>T,MODERATE, +PLD2 5338 BI GRCh38 17 4819482 4819482 + missense_variant Missense_Mutation SNP G G A rs779094449 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 5 9 c.2362G>A p.Ala788Thr p.A788T ENST00000263088.11 NM_002663.5 788 Gcc/Acc 23/25 P1 A A/T protein_coding YES CCDS11057.1 2362/2802 AGCTGGCCGTG Gene3D:3.30.870.10;PDB-ENSP_mappings:6ohm.A;PDB-ENSP_mappings:6ohm.B;PDB-ENSP_mappings:6oho.A;PDB-ENSP_mappings:6oho.B;PDB-ENSP_mappings:6ohp.A;PDB-ENSP_mappings:6ohp.B;PDB-ENSP_mappings:6ohp.C;PDB-ENSP_mappings:6ohp.D;PDB-ENSP_mappings:6ohq.A;PDB-ENSP_mappings:6ohq.B;PDB-ENSP_mappings:6ohs.A;PDB-ENSP_mappings:6ohs.B;PDB-ENSP_mappings:6ohs.C;PDB-ENSP_mappings:6ohs.D;Pfam:PF13091;PIRSF:PIRSF009376;PANTHER:PTHR18896;PANTHER:PTHR18896:SF121;Superfamily:SSF56024;CDD:cd09845 ENSP00000263088 23/25 rs779094449 ENST00000263088 Transcript ENSG00000129219 HGNC:9068 MODERATE NM_002663.5 missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) O14939.188 PLD2 HGNC 1 1.0 UPI0000131BDE O14939-1 SNV PLD2,missense_variant,p.A788T,ENST00000263088,NM_002663.5,c.2362G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;PLD2,missense_variant,p.A788T,ENST00000572940,NM_001243108.2,c.2362G>A,MODERATE,,deleterious(0),probably_damaging(0.944),1;PLD2,missense_variant,p.A86T,ENST00000576864,,c.256G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;PLD2,missense_variant,p.A186T,ENST00000576983,,c.556G>A,MODERATE,,deleterious(0),probably_damaging(0.992),1;PLD2,downstream_gene_variant,,ENST00000571273,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000572127,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000572199,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000573258,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000574796,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000575246,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000575813,,,MODIFIER,,,,1;PLD2,upstream_gene_variant,,ENST00000575945,,,MODIFIER,,,,1;PLD2,downstream_gene_variant,,ENST00000576329,,,MODIFIER,,,,1 2437/3443 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 29 ca070df2-4342-4a09-b989-0cc323831f95 14 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS PLD2,missense_variant,p.G85D,ENST00000576864.1,c.254G>A,MODERATE,;PLD2,missense_variant,p.A186T,ENST00000576983.5,c.556G>A,MODERATE,;PLD2,missense_variant,p.A788T,ENST00000572940.5,c.2362G>A,MODERATE,;PLD2,missense_variant,p.A788T,ENST00000263088.11,c.2362G>A,MODERATE,YES +DHRS7B 25979 BI GRCh38 17 21188790 21188790 + synonymous_variant Silent SNP C C T rs577733383 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 43 35 c.699C>T p.Thr233= p.T233= ENST00000395511.8 NM_015510.5 233 acC/acT 6/7 P4 T T protein_coding YES CCDS11215.1 699/978 GTGACCGTCAT Gene3D:3.40.50.720;Pfam:PF00106;PIRSF:PIRSF000126;Prints:PR00081;PANTHER:PTHR44196;PANTHER:PTHR44196:SF1;Superfamily:SSF51735;CDD:cd05332 ENSP00000378887 6/7 rs577733383 ENST00000395511 Transcript ENSG00000109016 HGNC:24547 LOW 0.0001634 gnomAD_SAS synonymous_variant 1.0 Unknown Q6IAN0.137 DHRS7B HGNC 1 1.0 UPI00000739CB SNV DHRS7B,synonymous_variant,p.T233=,ENST00000395511,NM_015510.4,c.699C>T,LOW,YES,,,1;DHRS7B,synonymous_variant,p.T218=,ENST00000579303,NM_001330159.2,c.654C>T,LOW,,,,1;DHRS7B,synonymous_variant,p.T53=,ENST00000581463,,c.159C>T,LOW,,,,1;DHRS7B,intron_variant,,ENST00000583388,,c.171-2158C>T,MODIFIER,,,,1;DHRS7B,3_prime_UTR_variant,,ENST00000578426,,c.*316C>T,MODIFIER,,,,1;DHRS7B,non_coding_transcript_exon_variant,,ENST00000346603,,n.1023C>T,MODIFIER,,,,1 1019/2175 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 1.99e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0001634 0 139 ca070df2-4342-4a09-b989-0cc323831f95 78 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS DHRS7B,synonymous_variant,p.T53=,ENST00000581463.1,c.159C>T,LOW,;DHRS7B,intron_variant,,ENST00000583388.1,c.171-2158C>T,MODIFIER,;DHRS7B,non_coding_transcript_exon_variant,,ENST00000346603.4,n.1023C>T,MODIFIER,;DHRS7B,synonymous_variant,p.T218=,ENST00000579303.5,c.654C>T,LOW,;DHRS7B,synonymous_variant,p.T233=,ENST00000395511.8,c.699C>T,LOW,YES;DHRS7B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000578426.5,c.*316C>T,MODIFIER, +CEP95 90799 BI GRCh38 17 64534595 64534595 + missense_variant Missense_Mutation SNP A A C rs185494775 TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 17 10 c.1928A>C p.Lys643Thr p.K643T ENST00000556440.7 NM_138363.3 643 aAg/aCg 17/20 P2 C K/T protein_coding YES CCDS45763.1 1928/2466 CTTCAAGGACT PANTHER:PTHR22545 ENSP00000450461 17/20 rs185494775 ENST00000556440 Transcript ENSG00000258890 HGNC:25141 MODERATE NM_138363.3 5.567e-05 gnomAD_EAS missense_variant 1.0 possibly_damaging(0.676) Unknown deleterious(0) Q96GE4.130 CEP95 HGNC 1 1.0 UPI000006F4B3 Q96GE4-1 SNV CEP95,missense_variant,p.K643T,ENST00000556440,NM_138363.3,c.1928A>C,MODERATE,YES,deleterious(0),possibly_damaging(0.676),1;CEP95,missense_variant,p.K578T,ENST00000553412,NM_001316990.2,c.1733A>C,MODERATE,,deleterious(0),possibly_damaging(0.676),1;CEP95,downstream_gene_variant,,ENST00000583457,,,MODIFIER,,,,1;CEP95,upstream_gene_variant,,ENST00000583676,,,MODIFIER,,,,1;CEP95,downstream_gene_variant,,ENST00000577476,,,MODIFIER,,,,1;CEP95,3_prime_UTR_variant,,ENST00000553956,,c.*1651A>C,MODIFIER,,,,1;CEP95,non_coding_transcript_exon_variant,,ENST00000581885,,n.580A>C,MODIFIER,,,,1;CEP95,non_coding_transcript_exon_variant,,ENST00000580285,,n.107A>C,MODIFIER,,,,1;CEP95,non_coding_transcript_exon_variant,,ENST00000582698,,n.394A>C,MODIFIER,,,,1;CEP95,downstream_gene_variant,,ENST00000579117,,,MODIFIER,,,,1;CEP95,downstream_gene_variant,,ENST00000579478,,,MODIFIER,,,,1;CEP95,downstream_gene_variant,,ENST00000579637,,,MODIFIER,,,,1;CEP95,upstream_gene_variant,,ENST00000581980,,,MODIFIER,,,,1;CEP95,downstream_gene_variant,,ENST00000584857,,,MODIFIER,,,,1 2049/2754 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 4.018e-06 0.0 0.0 0.0 5.567e-05 0.0 0.0 0.0 0.0 0 59 ca070df2-4342-4a09-b989-0cc323831f95 27 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS CEP95,non_coding_transcript_exon_variant,,ENST00000581885.1,n.580A>C,MODIFIER,;CEP95,non_coding_transcript_exon_variant,,ENST00000580285.1,n.107A>C,MODIFIER,;CEP95,non_coding_transcript_exon_variant,,ENST00000582698.5,n.394A>C,MODIFIER,;CEP95,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000553956.6,c.*1651A>C,MODIFIER,;CEP95,missense_variant,p.K643T,ENST00000556440.7,c.1928A>C,MODERATE,YES +ASXL3 80816 BI GRCh38 18 33743366 33743366 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 12 10 c.3518C>T p.Ala1173Val p.A1173V ENST00000269197.12 NM_030632.3 1173 gCc/gTc 12/12 P1 T A/V protein_coding YES CCDS45847.1 3518/6747 GTCTGCCCACC PANTHER:PTHR13578;PANTHER:PTHR13578:SF18 ENSP00000269197 12/12 ENST00000269197 Transcript 1.0 ENSG00000141431 HGNC:29357 MODERATE NM_030632.3 missense_variant 1.0 benign(0.001) Unknown tolerated_low_confidence(0.19) Q9C0F0.118 ASXL3 HGNC 1 5.0 UPI000156D0F3 Q9C0F0-1 SNV ASXL3,missense_variant,p.A1173V,ENST00000269197,NM_030632.3,c.3518C>T,MODERATE,YES,tolerated_low_confidence(0.19),benign(0.001),1;ASXL3,missense_variant,p.A1117V,ENST00000642541,,c.3350C>T,MODERATE,,tolerated_low_confidence(0.2),benign(0.001),1;ASXL3,3_prime_UTR_variant,,ENST00000593195,,c.*3544C>T,MODIFIER,,,,1;ASXL3,3_prime_UTR_variant,,ENST00000592288,,c.*2642C>T,MODIFIER,,,,1;ASXL3,3_prime_UTR_variant,,ENST00000592541,,c.*3177C>T,MODIFIER,,,,1 3931/11760 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 45 ca070df2-4342-4a09-b989-0cc323831f95 22 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS ASXL3,missense_variant,p.A1117V,ENST00000642541.1,c.3350C>T,MODERATE,;ASXL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000593195.6,c.*3544C>T,MODIFIER,;ASXL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000592541.6,c.*3177C>T,MODIFIER,;ASXL3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000592288.6,c.*2642C>T,MODIFIER,;ASXL3,missense_variant,p.A1133V,ENST00000681521.1,c.3398C>T,MODERATE,;ASXL3,missense_variant,p.A1174V,ENST00000696964.1,c.3521C>T,MODERATE,;ASXL3,missense_variant,p.A1173V,ENST00000269197.12,c.3518C>T,MODERATE,YES +EIF1AX 1964 BI GRCh38 X 20138595 20138595 + missense_variant Missense_Mutation SNP C C T TCGA-WC-A87U-01A TCGA-WC-A87U-10A Somatic 0 13 c.44G>A p.Gly15Asp p.G15D ENST00000379607.10 NM_001412.4 15 gGt/gAt 2/7 P1 T G/D protein_coding YES CCDS14196.1 44/435 TCTTACCCCTG COSM3973544 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;TIGRFAM:TIGR00523;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309310;COSV63309316 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1;1 1.0 probably_damaging(0.977) Unknown deleterious(0) 1;1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G15D,ENST00000379607,NM_001412.4,c.44G>A,MODERATE,YES,deleterious(0),probably_damaging(0.977),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2754G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 242/4414 muse;mutect2;varscan2 4498044c-1607-403e-867e-befd7fad275a 0 108 ca070df2-4342-4a09-b989-0cc323831f95 13 f1af28e8-a4d3-40ef-8a54-73966ff7ea62 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2754G>A,MODIFIER,;EIF1AX,missense_variant,p.G15D,ENST00000379607.10,c.44G>A,MODERATE,YES +F5 2153 BI GRCh38 1 169540390 169540390 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 25 36 c.4700T>C p.Ile1567Thr p.I1567T ENST00000367797.9 NM_000130.5 1567 aTt/aCt 13/25 P4 G I/T protein_coding CCDS1281.1 4700/6675 CTGCAATGTTG PDB-ENSP_mappings:3s9c.B;PIRSF:PIRSF000354 ENSP00000356771 13/25 ENST00000367797 Transcript 1.0 ENSG00000198734 HGNC:3542 MODERATE NM_000130.5 missense_variant benign(0.39) Unknown tolerated(0.1) P12259.232 F5 HGNC -1 1.0 UPI000016A8CE SNV F5,missense_variant,p.I1567T,ENST00000367797,NM_000130.5,c.4700T>C,MODERATE,,tolerated(0.1),benign(0.39),-1;F5,missense_variant,p.I1572T,ENST00000367796,,c.4715T>C,MODERATE,YES,tolerated(0.1),possibly_damaging(0.646),-1 4795/9132 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 103 66677130-d390-4759-a443-1fc82a3689c5 61 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS F5,missense_variant,p.I1572T,ENST00000367796.3,c.4715T>C,MODERATE,;F5,missense_variant,p.I1567T,ENST00000367797.9,c.4700T>C,MODERATE,YES +AMER3 205147 BI GRCh38 2 130762079 130762079 + synonymous_variant Silent SNP C C T rs1381188924 TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 9 4 c.7C>T p.Leu3= p.L3= ENST00000321420.5 NM_001105193.2 3 Ctg/Ttg 2/2 P1 T L protein_coding YES CCDS2164.1 7/2586 TGGAGCTGAAG MobiDB_lite:mobidb-lite;PANTHER:PTHR22237:SF2;PANTHER:PTHR22237 ENSP00000314914 2/2 rs1381188924 ENST00000321420 Transcript ENSG00000178171 HGNC:26771 LOW NM_152698.3 1.874e-05 gnomAD_NFE synonymous_variant 1.0 Unknown Q8N944.116 AMER3 HGNC 1 1.0 UPI0000D61239 SNV AMER3,synonymous_variant,p.L3=,ENST00000321420,NM_001105193.2&NM_152698.3,c.7C>T,LOW,YES,,,1;AMER3,synonymous_variant,p.L3=,ENST00000423981,NM_001105194.1&NM_001105195.2,c.7C>T,LOW,,,,1;AMER3,synonymous_variant,p.L3=,ENST00000458606,,c.7C>T,LOW,,,,1;AMER3,synonymous_variant,p.L3=,ENST00000431758,,c.7C>T,LOW,,,,1 161/6216 mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 8.321e-06 0.0 0.0 0.0 0.0 0.0 1.874e-05 0.0 0.0 0 18 66677130-d390-4759-a443-1fc82a3689c5 13 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS AMER3,synonymous_variant,p.L3=,ENST00000458606.6,c.7C>T,LOW,;AMER3,synonymous_variant,p.L3=,ENST00000431758.2,c.7C>T,LOW,;AMER3,synonymous_variant,p.L3=,ENST00000321420.5,c.7C>T,LOW,YES +BAP1 8314 BI GRCh38 3 52402604 52402604 + missense_variant,splice_region_variant Missense_Mutation SNP T T A TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 1 41 c.2054A>T p.Glu685Val p.E685V ENST00000460680.6 NM_004656.4 685 gAa/gTa 16/17 P1 A E/V protein_coding YES CCDS2853.1 2054/2190 CACCTTCCTGA COSM96377 PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Pfam:PF18031 ENSP00000417132 16/17 COSV56241355;COSV56242357 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 MODERATE NM_004656.4 missense_variant 1;1 1.0 possibly_damaging(0.879) Unknown deleterious(0) 1;1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,missense_variant,p.E685V,ENST00000460680,NM_004656.4,c.2054A>T,MODERATE,YES,deleterious(0),possibly_damaging(0.879),-1;BAP1,missense_variant,p.E667V,ENST00000296288,,c.2000A>T,MODERATE,,deleterious(0),probably_damaging(0.943),-1;BAP1,missense_variant,p.E85V,ENST00000469613,,c.254A>T,MODERATE,,deleterious(0),possibly_damaging(0.646),-1;BAP1,missense_variant,p.E209V,ENST00000478368,,c.626A>T,MODERATE,,deleterious(0),probably_damaging(0.964),-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,splice_region_variant,,ENST00000466093,,n.727A>T,LOW,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 2184/3600 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 71 66677130-d390-4759-a443-1fc82a3689c5 42 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000466093.1,n.727A>T,MODIFIER,;BAP1,missense_variant,splice_region_variant,p.E209V,ENST00000478368.1,c.626A>T,MODERATE,;BAP1,missense_variant,splice_region_variant,p.E667V,ENST00000296288.9,c.2000A>T,MODERATE,;BAP1,stop_gained,splice_region_variant,p.K85*,ENST00000469613.5,c.253A>T,HIGH,;BAP1,missense_variant,splice_region_variant,p.E685V,ENST00000460680.6,c.2054A>T,MODERATE,YES +SNX4 8723 BI GRCh38 3 125504688 125504688 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 1 22 c.198A>C p.Glu66Asp p.E66D ENST00000251775.9 NM_003794.4 66 gaA/gaC 2/14 P1 G E/D protein_coding YES CCDS3032.1 198/1353 CGTTTTTCTGC PROSITE_profiles:PS50195;CDD:cd06864;PANTHER:PTHR46596;Gene3D:3.30.1520.10;SMART:SM00312;Superfamily:SSF64268 ENSP00000251775 2/14 ENST00000251775 Transcript ENSG00000114520 HGNC:11175 MODERATE NM_003794.4 missense_variant 1.0 possibly_damaging(0.896) Unknown deleterious(0.01) O95219.162 SNX4 HGNC -1 1.0 UPI000003586D O95219-1 SNV SNX4,missense_variant,p.E66D,ENST00000251775,NM_003794.4,c.198A>C,MODERATE,YES,deleterious(0.01),possibly_damaging(0.896),-1;SNX4,non_coding_transcript_exon_variant,,ENST00000473417,,n.217A>C,MODIFIER,,,,-1;SNX4,missense_variant,p.E19D,ENST00000465505,,c.57A>C,MODERATE,,deleterious(0.04),possibly_damaging(0.895),-1;SNX4,intron_variant,,ENST00000471751,,c.142-6494A>C,MODIFIER,,,,-1 228/2512 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 55 66677130-d390-4759-a443-1fc82a3689c5 23 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS SNX4,missense_variant,NMD_transcript_variant,p.E19D,ENST00000465505.2,c.57A>C,MODERATE,;SNX4,non_coding_transcript_exon_variant,,ENST00000473417.5,n.217A>C,MODIFIER,;SNX4,intron_variant,NMD_transcript_variant,,ENST00000471751.5,c.142-6494A>C,MODIFIER,;SNX4,missense_variant,p.E66D,ENST00000251775.9,c.198A>C,MODERATE,YES +PREX2 80243 BI GRCh38 8 68087794 68087794 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 122 48 c.2098C>T p.His700Tyr p.H700Y ENST00000288368.5 NM_024870.4 700 Cat/Tat 19/40 P1 T H/Y protein_coding YES CCDS6201.1 2098/4821 TTGTGCATGCT Low_complexity_(Seg):seg;PROSITE_profiles:PS50106;CDD:cd00992;PANTHER:PTHR22829:SF1;PANTHER:PTHR22829;Gene3D:2.30.42.10;SMART:SM00228;Superfamily:SSF50156 ENSP00000288368 19/40 ENST00000288368 Transcript 1.0 ENSG00000046889 HGNC:22950 MODERATE NM_024870.4 missense_variant 1.0 benign(0.123) Unknown tolerated(0.3) Q70Z35.139 PREX2 HGNC 1 1.0 UPI0000375435 Q70Z35-1 SNV PREX2,missense_variant,p.H700Y,ENST00000288368,NM_024870.4,c.2098C>T,MODERATE,YES,tolerated(0.3),benign(0.123),1;PREX2,non_coding_transcript_exon_variant,,ENST00000529398,NM_025170.6,n.2125C>T,MODIFIER,,,,1;PREX2,non_coding_transcript_exon_variant,,ENST00000517617,,n.1809C>T,MODIFIER,,,,1;AC011853.2,intron_variant,,ENST00000526901,,n.94-4910G>A,MODIFIER,YES,,,-1 2447/10824 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 116 66677130-d390-4759-a443-1fc82a3689c5 170 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS ENSG00000255206,intron_variant,,ENST00000526901.1,n.94-4910G>A,MODIFIER,YES;PREX2,non_coding_transcript_exon_variant,,ENST00000517617.1,n.1809C>T,MODIFIER,;PREX2,non_coding_transcript_exon_variant,,ENST00000529398.5,n.2125C>T,MODIFIER,;PREX2,missense_variant,p.H700Y,ENST00000288368.5,c.2098C>T,MODERATE,YES +WASHC5 9897 BI GRCh38 8 125082453 125082453 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 70 70 c.347T>C p.Leu116Pro p.L116P ENST00000318410.12 NM_014846.4 116 cTc/cCc 4/29 P1 G L/P protein_coding YES CCDS6355.1 347/3480 CATTGAGATCA Pfam:PF10266;PANTHER:PTHR15691 ENSP00000318016 4/29 ENST00000318410 Transcript 1.0 ENSG00000164961 HGNC:28984 MODERATE NM_014846.4 missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0) Q12768.147 WASHC5 HGNC -1 1.0 UPI000013943B SNV WASHC5,missense_variant,p.L116P,ENST00000318410,NM_014846.4,c.347T>C,MODERATE,YES,deleterious(0),probably_damaging(0.996),-1;WASHC5,5_prime_UTR_variant,,ENST00000517845,NM_001330609.1,c.-98T>C,MODIFIER,,,,-1;WASHC5,5_prime_UTR_variant,,ENST00000523297,,c.-98T>C,MODIFIER,,,,-1;WASHC5,non_coding_transcript_exon_variant,,ENST00000521109,,n.525T>C,MODIFIER,,,,-1;WASHC5,non_coding_transcript_exon_variant,,ENST00000519340,,n.430T>C,MODIFIER,,,,-1;WASHC5,downstream_gene_variant,,ENST00000523397,,,MODIFIER,,,,-1 649/4139 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 111 66677130-d390-4759-a443-1fc82a3689c5 140 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS WASHC5,non_coding_transcript_exon_variant,,ENST00000521109.1,n.525T>C,MODIFIER,;WASHC5,non_coding_transcript_exon_variant,,ENST00000519340.5,n.430T>C,MODIFIER,;WASHC5,5_prime_UTR_variant,,ENST00000523297.5,c.-98T>C,MODIFIER,;WASHC5,5_prime_UTR_variant,,ENST00000517845.5,c.-98T>C,MODIFIER,;WASHC5,missense_variant,p.L116P,ENST00000318410.12,c.347T>C,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 48 23 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 96 66677130-d390-4759-a443-1fc82a3689c5 71 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +PARPBP 55010 BI GRCh38 12 102182553 102182553 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 29 21 c.1189C>G p.Pro397Ala p.P397A ENST00000327680.7 NM_017915.5 397 Ccc/Gcc 9/11 P4 G P/A protein_coding CCDS9090.2 1189/1740 GGTCTCCCACA PANTHER:PTHR32121 ENSP00000332915 9/11 ENST00000327680 Transcript ENSG00000185480 HGNC:26074 MODERATE NM_017915.5 missense_variant probably_damaging(0.998) Unknown deleterious(0.01) Q9NWS1.121 PARPBP HGNC 1 2.0 UPI000004A06B Q9NWS1-1 SNV PARPBP,missense_variant,p.P397A,ENST00000327680,NM_017915.5&NM_001382725.1&NM_001382723.1&NM_001382724.1&NM_001382721.1&NM_001382722.1&NM_001382726.1,c.1189C>G,MODERATE,,deleterious(0.01),probably_damaging(0.998),1;PARPBP,missense_variant,p.P474A,ENST00000541394,NM_001319988.2,c.1420C>G,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;PARPBP,missense_variant,p.P243A,ENST00000417507,NM_001382729.1&NM_001382731.1,c.727C>G,MODERATE,,tolerated_low_confidence(1),probably_damaging(0.996),1;PARPBP,missense_variant,p.P316A,ENST00000392911,NM_001319993.2&NM_001319994.2&NM_001382728.1,c.946C>G,MODERATE,,deleterious(0),probably_damaging(0.998),1;PARPBP,intron_variant,,ENST00000412715,NM_001382732.1,c.723-13398C>G,MODIFIER,,,,1;PARPBP,intron_variant,,ENST00000543784,NM_001382735.1,c.480-13398C>G,MODIFIER,,,,1;PARPBP,intron_variant,,ENST00000535811,,n.55-13398C>G,MODIFIER,,,,1;PARPBP,3_prime_UTR_variant,,ENST00000457614,,c.*503C>G,MODIFIER,,,,1 1296/3076 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 51 66677130-d390-4759-a443-1fc82a3689c5 50 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS PARPBP,intron_variant,,ENST00000535811.1,n.55-13398C>G,MODIFIER,;PARPBP,intron_variant,,ENST00000412715.3,c.723-13398C>G,MODIFIER,;PARPBP,missense_variant,p.P243A,ENST00000417507.6,c.727C>G,MODERATE,;PARPBP,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000457614.6,c.*503C>G,MODIFIER,;PARPBP,missense_variant,p.P316A,ENST00000392911.6,c.946C>G,MODERATE,;PARPBP,intron_variant,,ENST00000543784.5,c.480-13398C>G,MODIFIER,;PARPBP,missense_variant,p.P474A,ENST00000541394.5,c.1420C>G,MODERATE,;PARPBP,missense_variant,p.P397A,ENST00000327680.7,c.1189C>G,MODERATE,YES +TBX5 6910 BI GRCh38 12 114385488 114385488 + stop_gained Nonsense_Mutation SNP G G C novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 55 45 c.743C>G p.Ser248Ter p.S248* ENST00000310346.8 NM_000192.3 248 tCa/tGa 7/9 P1 C S/* protein_coding YES CCDS9173.1 743/1557 TTCTTGACATT PDB-ENSP_mappings:2x6u.A;PDB-ENSP_mappings:2x6v.A;PDB-ENSP_mappings:2x6v.B;PANTHER:PTHR11267:SF28;PANTHER:PTHR11267 ENSP00000309913 7/9 ENST00000310346 Transcript 1.0 ENSG00000089225 HGNC:11604 HIGH stop_gained 1.0 Unknown Q99593.195 TBX5 HGNC -1 1.0 UPI0000136AA2 Q99593-1 SNV TBX5,stop_gained,p.S248*,ENST00000310346,NM_000192.3,c.743C>G,HIGH,YES,,,-1;TBX5,stop_gained,p.S248*,ENST00000405440,NM_181486.4,c.743C>G,HIGH,,,,-1;TBX5,stop_gained,p.S198*,ENST00000349716,NM_080717.3,c.593C>G,HIGH,,,,-1;TBX5,stop_gained,p.S248*,ENST00000526441,,c.743C>G,HIGH,,,,-1 1410/3825 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 110 66677130-d390-4759-a443-1fc82a3689c5 100 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS TBX5,stop_gained,p.S248*,ENST00000526441.1,c.743C>G,HIGH,;TBX5,stop_gained,p.S248*,ENST00000310346.8,c.743C>G,HIGH,;TBX5,stop_gained,p.S198*,ENST00000349716.9,c.593C>G,HIGH,;TBX5,stop_gained,p.S248*,ENST00000405440.7,c.743C>G,HIGH,YES +KCTD19 146212 BI GRCh38 16 67293637 67293637 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 75 31 c.2125G>A p.Asp709Asn p.D709N ENST00000304372.6 NM_001100915.3 709 Gac/Aac 12/16 P1 T D/N protein_coding YES CCDS42179.1 2125/2781 CTTGTCTTTCG Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR14499;PANTHER:PTHR14499:SF20 ENSP00000305702 12/16 ENST00000304372 Transcript ENSG00000168676 HGNC:24753 MODERATE NM_001100915.3 missense_variant 1.0 benign(0.054) Unknown tolerated(0.05) Q17RG1.103 KCTD19 HGNC -1 1.0 UPI00001D7875 SNV KCTD19,missense_variant,p.D709N,ENST00000304372,NM_001100915.3,c.2125G>A,MODERATE,YES,tolerated(0.05),benign(0.054),-1;KCTD19,missense_variant,p.D63N,ENST00000562841,,c.187G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.995),-1;PLEKHG4,downstream_gene_variant,,ENST00000360461,NM_001129727.3,,MODIFIER,YES,,,1;PLEKHG4,downstream_gene_variant,,ENST00000379344,NM_001129729.3,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000427155,NM_001129728.1,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000450733,NM_001129731.3,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000569875,,,MODIFIER,,,,1;KCTD19,non_coding_transcript_exon_variant,,ENST00000569333,,n.4123G>A,MODIFIER,,,,-1;KCTD19,non_coding_transcript_exon_variant,,ENST00000570049,,n.3957G>A,MODIFIER,,,,-1;KCTD19,non_coding_transcript_exon_variant,,ENST00000566392,,n.3394G>A,MODIFIER,,,,-1;PLEKHG4,downstream_gene_variant,,ENST00000393966,,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000562289,,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000563969,,,MODIFIER,,,,1;PLEKHG4,downstream_gene_variant,,ENST00000567136,,,MODIFIER,,,,1 2159/2952 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 93 66677130-d390-4759-a443-1fc82a3689c5 106 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS KCTD19,non_coding_transcript_exon_variant,,ENST00000569333.5,n.4123G>A,MODIFIER,;KCTD19,non_coding_transcript_exon_variant,,ENST00000566392.5,n.3394G>A,MODIFIER,;KCTD19,missense_variant,p.D63N,ENST00000562841.1,c.187G>A,MODERATE,;KCTD19,missense_variant,p.D709N,ENST00000304372.6,c.2125G>A,MODERATE,YES;KCTD19,non_coding_transcript_exon_variant,,ENST00000570049.5,n.3957G>A,MODIFIER, +FANCA 2175 BI GRCh38 16 89764983 89764983 + synonymous_variant Silent SNP G G C novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 43 5 c.2685C>G p.Pro895= p.P895= ENST00000389301.8 NM_000135.4 895 ccC/ccG 28/43 P4 C P protein_coding YES CCDS32515.1 2685/4368 TGCAAGGGTCT PANTHER:PTHR12047 ENSP00000373952 28/43 ENST00000389301 Transcript 1.0 ENSG00000187741 HGNC:3582 LOW NM_000135.4 synonymous_variant 1.0 Unknown O15360.188 FANCA HGNC -1 1.0 UPI0000520A1A O15360-1 SNV FANCA,synonymous_variant,p.P895=,ENST00000389301,NM_000135.4,c.2685C>G,LOW,YES,,,-1;FANCA,synonymous_variant,p.P895=,ENST00000568369,NM_001286167.3,c.2685C>G,LOW,,,,-1;FANCA,synonymous_variant,p.P8=,ENST00000567988,,c.24C>G,LOW,,,,-1;FANCA,synonymous_variant,p.P21=,ENST00000561660,,c.63C>G,LOW,,,,-1;FANCA,synonymous_variant,p.P31=,ENST00000563318,,c.93C>G,LOW,,,,-1;FANCA,non_coding_transcript_exon_variant,,ENST00000305699,,n.57C>G,MODIFIER,,,,-1;FANCA,downstream_gene_variant,,ENST00000561667,,,MODIFIER,,,,-1;FANCA,upstream_gene_variant,,ENST00000563510,,,MODIFIER,,,,-1;FANCA,downstream_gene_variant,,ENST00000567205,,,MODIFIER,,,,-1 2717/5452 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 64 66677130-d390-4759-a443-1fc82a3689c5 48 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS FANCA,non_coding_transcript_exon_variant,,ENST00000696276.1,n.2728C>G,MODIFIER,;FANCA,missense_variant,NMD_transcript_variant,p.L31V,ENST00000563318.1,c.91C>G,MODERATE,;FANCA,missense_variant,NMD_transcript_variant,p.P21R,ENST00000561660.1,c.62C>G,MODERATE,;FANCA,missense_variant,NMD_transcript_variant,p.L8V,ENST00000567988.5,c.22C>G,MODERATE,;FANCA,non_coding_transcript_exon_variant,,ENST00000305699.15,n.57C>G,MODIFIER,;FANCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696291.1,c.*2405C>G,MODIFIER,;FANCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000567510.2,c.*1078C>G,MODIFIER,;FANCA,synonymous_variant,p.P895=,ENST00000564475.6,c.2685C>G,LOW,;FANCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696275.1,c.*1920C>G,MODIFIER,;FANCA,synonymous_variant,NMD_transcript_variant,p.P895=,ENST00000696286.1,c.2685C>G,LOW,;FANCA,synonymous_variant,p.P895=,ENST00000696287.1,c.2685C>G,LOW,;FANCA,non_coding_transcript_exon_variant,,ENST00000696274.1,n.2646C>G,MODIFIER,;FANCA,synonymous_variant,p.P895=,ENST00000568369.6,c.2685C>G,LOW,;FANCA,synonymous_variant,p.P895=,ENST00000389301.8,c.2685C>G,LOW,YES;FANCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000561667.2,c.*1179C>G,MODIFIER, +MYO15A 51168 BI GRCh38 17 18121670 18121670 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 11 7 c.2870C>G p.Pro957Arg p.P957R ENST00000647165.2 NM_016239.4 957 cCc/cGc 2/66 A2 G P/R protein_coding YES 2870/10593 GCCACCCCCTG MobiDB_lite:mobidb-lite ENSP00000481642 2/65 ENST00000615845 Transcript 1.0 ENSG00000091536 HGNC:7594 MODERATE missense_variant 1.0 benign(0.24) Unknown tolerated_low_confidence(0.13) MYO15A HGNC 1 A0A087WYA1.41 5.0 UPI0004E4C894 SNV MYO15A,missense_variant,p.P957R,ENST00000615845,,c.2870C>G,MODERATE,YES,tolerated_low_confidence(0.13),benign(0.24),1;MYO15A,missense_variant,p.P957R,ENST00000647165,NM_016239.4,c.2870C>G,MODERATE,,tolerated_low_confidence(0.13),benign(0.121),1;MYO15A,upstream_gene_variant,,ENST00000651088,,,MODIFIER,,,,1;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,,n.2503C>G,MODIFIER,,,,1 3208/11860 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 21 66677130-d390-4759-a443-1fc82a3689c5 18 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS MYO15A,non_coding_transcript_exon_variant,,ENST00000583079.1,n.2503C>G,MODIFIER,;MYO15A,missense_variant,p.P957R,ENST00000647165.2,c.2870C>G,MODERATE,YES +FHOD3 80206 BI GRCh38 18 36372681 36372681 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs759696197 TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 14 14 c.274C>T p.Arg92Trp p.R92W ENST00000359247.8 NM_001281739.3 92 Cgg/Tgg 3/24 A2 T R/W protein_coding CCDS62419.1 274/4269 TTAGGCGGGGC Gene3D:1.25.10.10;Pfam:PF18382;PROSITE_profiles:PS51232;PANTHER:PTHR45920;PANTHER:PTHR45920:SF3 ENSP00000352186 3/24 rs759696197 ENST00000359247 Transcript ENSG00000134775 HGNC:26178 MODERATE 0.0002292 gnomAD_SAS missense_variant probably_damaging(0.967) Unknown deleterious(0) Q2V2M9.123 FHOD3 HGNC 1 1.0 UPI0000EE543D Q2V2M9-1 SNV FHOD3,missense_variant,p.R92W,ENST00000257209,NM_025135.5,c.274C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;FHOD3,missense_variant,p.R92W,ENST00000590592,NM_001281740.3,c.274C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;FHOD3,missense_variant,p.R92W,ENST00000359247,NM_001281739.3,c.274C>T,MODERATE,,deleterious(0),probably_damaging(0.967),1;FHOD3,splice_region_variant,,ENST00000589114,,n.393C>T,LOW,,,,1 274/4518 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 6.38e-05 0.0001233 5.794e-05 0.0 0.0 4.628e-05 3.528e-05 0.0 0.0002292 4.0585498936707154e-05 7.302110316231847e-05 0.0 0.0 0.0 0.0 0.0 afr 7.302110316231847e-05 0.0 3.086610013269819e-05 0.0 0.0002088549954351 0 36 66677130-d390-4759-a443-1fc82a3689c5 28 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS FHOD3,missense_variant,splice_region_variant,p.R92W,ENST00000359247.8,c.274C>T,MODERATE,;FHOD3,non_coding_transcript_exon_variant,,ENST00000589114.5,n.393C>T,MODIFIER,;FHOD3,missense_variant,splice_region_variant,p.R92W,ENST00000257209.8,c.274C>T,MODERATE,;FHOD3,missense_variant,splice_region_variant,p.R92W,ENST00000590592.6,c.274C>T,MODERATE,YES +PLEKHG2 64857 BI GRCh38 19 39424416 39424416 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 38 3 c.3283C>T p.Pro1095Ser p.P1095S ENST00000425673.6 NM_022835.3 1095 Cca/Tca 19/19 P4 T P/S protein_coding YES CCDS33022.2 3283/4161 CCCTACCACCC PANTHER:PTHR45924;PANTHER:PTHR45924:SF3 ENSP00000392906 19/19 ENST00000425673 Transcript 1.0 ENSG00000090924 HGNC:29515 MODERATE NM_022835.3 missense_variant 1.0 benign(0.046) Unknown deleterious_low_confidence(0.01) Q9H7P9.138 PLEKHG2 HGNC 1 2.0 UPI00001C2028 Q9H7P9-1 SNV PLEKHG2,missense_variant,p.P1095S,ENST00000425673,NM_022835.3,c.3283C>T,MODERATE,YES,deleterious_low_confidence(0.01),benign(0.046),1;PLEKHG2,missense_variant,p.P963S,ENST00000205135,,c.2887C>T,MODERATE,,tolerated_low_confidence(0.05),benign(0.149),1;PLEKHG2,missense_variant,p.P1036S,ENST00000458508,NM_001351693.2,c.3106C>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.142),1;PLEKHG2,missense_variant,p.T36I,ENST00000598238,,c.107C>T,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.711),1;PLEKHG2,synonymous_variant,p.Y10=,ENST00000594161,,c.30C>T,LOW,,,,1;PLEKHG2,intron_variant,,ENST00000409797,NM_001351694.2,c.1678-822C>T,MODIFIER,,,,1;PLEKHG2,intron_variant,,ENST00000596443,,c.292-822C>T,MODIFIER,,,,1;PLEKHG2,intron_variant,,ENST00000600210,,c.255+655C>T,MODIFIER,,,,1;PLEKHG2,upstream_gene_variant,,ENST00000594124,,,MODIFIER,,,,1;PLEKHG2,upstream_gene_variant,,ENST00000596339,,,MODIFIER,,,,1;PLEKHG2,downstream_gene_variant,,ENST00000474449,,,MODIFIER,,,,1;PLEKHG2,downstream_gene_variant,,ENST00000478523,,,MODIFIER,,,,1;PLEKHG2,downstream_gene_variant,,ENST00000594307,,,MODIFIER,,,,1 4049/8048 muse;mutect2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 68 66677130-d390-4759-a443-1fc82a3689c5 41 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS PLEKHG2,missense_variant,p.T10I,ENST00000594161.1,c.29C>T,MODERATE,;PLEKHG2,missense_variant,p.P36S,ENST00000598238.1,c.106C>T,MODERATE,;PLEKHG2,intron_variant,,ENST00000600210.1,c.255+655C>T,MODIFIER,;PLEKHG2,intron_variant,,ENST00000596443.1,c.292-822C>T,MODIFIER,;PLEKHG2,synonymous_variant,p.Y962=,ENST00000205135.8,c.2886C>T,LOW,;PLEKHG2,intron_variant,,ENST00000409797.6,c.1678-822C>T,MODIFIER,;PLEKHG2,missense_variant,p.P1036S,ENST00000458508.6,c.3106C>T,MODERATE,;PLEKHG2,missense_variant,p.P1095S,ENST00000425673.6,c.3283C>T,MODERATE,YES +NLRP2 55655 BI GRCh38 19 54982772 54982772 + synonymous_variant Silent SNP C C T rs756888601 TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 23 8 c.1074C>T p.Gly358= p.G358= ENST00000448584.7 NM_017852.5 358 ggC/ggT 6/13 P4 T G protein_coding CCDS12913.1 1074/3189 GAGGGCTTCCT COSM3893506 Superfamily:SSF52540;Pfam:PF05729;PANTHER:PTHR45690;PANTHER:PTHR45690:SF18;PROSITE_profiles:PS50837 ENSP00000409370 6/13 rs756888601;COSV54755493 ENST00000448584 Transcript ENSG00000022556 HGNC:22948 LOW NM_017852.5 6.168e-05 gnomAD_AFR synonymous_variant 0;1 Unknown 0;1 Q9NX02.195 NLRP2 HGNC 1 1.0 UPI000004C0CC Q9NX02-1 SNV NLRP2,synonymous_variant,p.G358=,ENST00000543010,NM_001174081.3,c.1074C>T,LOW,YES,,,1;NLRP2,synonymous_variant,p.G358=,ENST00000448584,NM_017852.5,c.1074C>T,LOW,,,,1;NLRP2,synonymous_variant,p.G336=,ENST00000537859,NM_001174082.2,c.1008C>T,LOW,,,,1;NLRP2,synonymous_variant,p.G355=,ENST00000263437,NM_001348003.2,c.1065C>T,LOW,,,,1;NLRP2,synonymous_variant,p.G336=,ENST00000339757,,c.1008C>T,LOW,,,,1;NLRP2,synonymous_variant,p.G334=,ENST00000391721,,c.1002C>T,LOW,,,,1;NLRP2,synonymous_variant,p.G335=,ENST00000427260,NM_001174083.2,c.1005C>T,LOW,,,,1;NLRP2,downstream_gene_variant,,ENST00000397169,,,MODIFIER,,,,1;NLRP2,downstream_gene_variant,,ENST00000433772,,,MODIFIER,,,,1;NLRP2,upstream_gene_variant,,ENST00000540005,,,MODIFIER,,,,1;NLRP2,downstream_gene_variant,,ENST00000585500,,,MODIFIER,,,,1;NLRP2,downstream_gene_variant,,ENST00000588107,,,MODIFIER,,,,1;NLRP2,downstream_gene_variant,,ENST00000588619,,,MODIFIER,,,,1;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,,n.1184C>T,MODIFIER,,,,1;NLRP2,upstream_gene_variant,,ENST00000381637,,,MODIFIER,,,,1;NLRP2,downstream_gene_variant,,ENST00000539848,,,MODIFIER,,,,1;NLRP2,upstream_gene_variant,,ENST00000543277,,,MODIFIER,,,,1 1185/3540 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 7.965e-06 6.168e-05 0.0 0.0 5.441e-05 0.0 0.0 0.0 0.0 6.759590178262442e-06 2.4308399588335305e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 30 66677130-d390-4759-a443-1fc82a3689c5 31 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS NLRP2,synonymous_variant,p.G355=,ENST00000263437.10,c.1065C>T,LOW,;NLRP2,synonymous_variant,p.G358=,ENST00000448584.7,c.1074C>T,LOW,YES;NLRP2,synonymous_variant,p.G335=,ENST00000427260.6,c.1005C>T,LOW,;NLRP2,synonymous_variant,p.G336=,ENST00000537859.5,c.1008C>T,LOW,;NLRP2,synonymous_variant,p.G336=,ENST00000339757.11,c.1008C>T,LOW,;NLRP2,synonymous_variant,p.G334=,ENST00000391721.8,c.1002C>T,LOW,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597.5,n.1184C>T,MODIFIER,;NLRP2,synonymous_variant,p.G358=,ENST00000543010.5,c.1074C>T,LOW, +MTCL2 140710 BI GRCh38 20 36815381 36815381 + synonymous_variant Silent SNP G G A rs528805804 TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 13 12 c.2061C>T p.Asn687= p.N687= ENST00000237536.9 NM_080627.4 687 aaC/aaT 5/15 P3 A N protein_coding YES CCDS54459.1 2061/4986 CACTCGTTGTC PANTHER:PTHR15742;PANTHER:PTHR15742:SF1 ENSP00000237536 5/15 rs528805804 ENST00000237536 Transcript ENSG00000149639 HGNC:16111 LOW NM_080627.4 1.779e-05 gnomAD_NFE synonymous_variant 1.0 Unknown O94964.147 SOGA1 HGNC -1 5.0 UPI0000E5A319 O94964-2 SNV SOGA1,synonymous_variant,p.N687=,ENST00000237536,NM_080627.4,c.2061C>T,LOW,YES,,,-1;SOGA1,synonymous_variant,p.N449=,ENST00000279034,NM_199181.2,c.1347C>T,LOW,,,,-1;SOGA1,synonymous_variant,p.N301=,ENST00000465671,,c.903C>T,LOW,,,,-1 2255/14218 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 8.048e-06 0.0 0.0 0.0 0.0 0.0 1.779e-05 0.0 0.0 0 28 66677130-d390-4759-a443-1fc82a3689c5 25 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS MTCL2,stop_gained,NMD_transcript_variant,p.R301*,ENST00000465671.1,c.901C>T,HIGH,;MTCL2,synonymous_variant,p.N449=,ENST00000279034.10,c.1347C>T,LOW,;MTCL2,synonymous_variant,p.N687=,ENST00000237536.9,c.2061C>T,LOW,YES +GMEB2 26205 BI GRCh38 20 63604754 63604754 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9EO-01A TCGA-V4-A9EO-10A Somatic 57 32 c.218A>G p.Glu73Gly p.E73G ENST00000266068.5 73 gAa/gGa 2/9 P1 C E/G protein_coding YES CCDS13528.1 218/1593 CGGCTTCCTTG PANTHER:PTHR10417:SF2;PANTHER:PTHR10417 ENSP00000266068 2/9 ENST00000266068 Transcript ENSG00000101216 HGNC:4371 MODERATE missense_variant 1.0 benign(0.122) Unknown deleterious(0) Q9UKD1.161 GMEB2 HGNC -1 2.0 UPI000012B8AD SNV GMEB2,missense_variant,p.E73G,ENST00000266068,,c.218A>G,MODERATE,YES,deleterious(0),benign(0.122),-1;GMEB2,missense_variant,p.E73G,ENST00000370077,NM_012384.5,c.218A>G,MODERATE,,deleterious(0),benign(0.122),-1;GMEB2,missense_variant,p.E22G,ENST00000370069,,c.65A>G,MODERATE,,deleterious(0),benign(0.122),-1 697/4559 muse;mutect2;varscan2 bcb87378-9f43-45e4-bdf2-f6dfa6ac5b8c 0 82 66677130-d390-4759-a443-1fc82a3689c5 89 a8f2166f-d753-4e0e-8a11-d1b90dfeef21 SUCCESS GMEB2,missense_variant,p.E73G,ENST00000370077.2,c.218A>G,MODERATE,YES;GMEB2,missense_variant,p.E73G,ENST00000266068.5,c.218A>G,MODERATE,;GMEB2,missense_variant,p.E22G,ENST00000370069.5,c.65A>G,MODERATE, +IL24 11009 BI GRCh38 1 206900346 206900346 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 28 25 c.292C>T p.Gln98Ter p.Q98* ENST00000294984.7 NM_006850.3 98 Cag/Tag 4/7 A2 T Q/* protein_coding CCDS1471.1 292/621 TTCTGCAGAAC Gene3D:1.20.1250.10;PDB-ENSP_mappings:6df3.C;Superfamily:SSF47266 ENSP00000294984 4/7 ENST00000294984 Transcript ENSG00000162892 HGNC:11346 HIGH NM_006850.3 stop_gained Unknown Q13007.190 IL24 HGNC 1 1.0 UPI0000037343 Q13007-1 SNV IL24,stop_gained,p.Q98*,ENST00000294984,NM_006850.3,c.292C>T,HIGH,,,,1;IL24,stop_gained,p.Q99*,ENST00000367093,NM_001185157.1,c.295C>T,HIGH,,,,1;IL24,stop_gained,p.Q99*,ENST00000391929,NM_001185156.1,c.295C>T,HIGH,YES,,,1;IL24,synonymous_variant,p.C32=,ENST00000611909,NM_001185158.1,c.96C>T,LOW,,,,1;IL24,synonymous_variant,p.C32=,ENST00000480741,,c.96C>T,LOW,,,,1;FCMR,downstream_gene_variant,,ENST00000367091,NM_005449.5,,MODIFIER,YES,,,-1;FCMR,downstream_gene_variant,,ENST00000442471,NM_001142473.2,,MODIFIER,,,,-1;FCMR,downstream_gene_variant,,ENST00000628511,NM_001193338.2,,MODIFIER,,,,-1;IL24,non_coding_transcript_exon_variant,,ENST00000491169,,n.203C>T,MODIFIER,,,,1;FCMR,downstream_gene_variant,,ENST00000528654,,,MODIFIER,,,,-1;IL24,synonymous_variant,p.C32=,ENST00000367095,,c.96C>T,LOW,,,,1;FCMR,downstream_gene_variant,,ENST00000463473,,,MODIFIER,,,,-1;FCMR,downstream_gene_variant,,ENST00000474041,,,MODIFIER,,,,-1 567/1976 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 93 dafcde63-69aa-4654-aadd-b00c046551cf 53 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS IL24,synonymous_variant,p.C32=,ENST00000480741.1,c.96C>T,LOW,;IL24,non_coding_transcript_exon_variant,,ENST00000491169.1,n.203C>T,MODIFIER,;IL24,synonymous_variant,NMD_transcript_variant,p.C32=,ENST00000367095.7,c.96C>T,LOW,;IL24,stop_gained,p.Q99*,ENST00000367093.3,c.295C>T,HIGH,;IL24,stop_gained,p.Q98*,ENST00000294984.7,c.292C>T,HIGH,YES;IL24,synonymous_variant,p.C32=,ENST00000611909.4,c.96C>T,LOW,;IL24,stop_gained,p.Q99*,ENST00000391929.7,c.295C>T,HIGH, +BAP1 8314 BI GRCh38 3 52403653 52403654 + stop_gained Nonsense_Mutation INS - - A novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 1 10 c.1491dup p.Glu498Ter p.E498* ENST00000460680.6 NM_004656.4 497 -/T 13/17 P1 A -/X protein_coding YES CCDS2853.1 1491-1492/2190 GATCTCAGAGG MobiDB_lite:mobidb-lite;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 13/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D insertion BAP1,frameshift_variant,p.E498*,ENST00000460680,NM_004656.4,c.1491dup,HIGH,YES,,,-1;BAP1,frameshift_variant,p.E480*,ENST00000296288,,c.1437dup,HIGH,,,,-1;BAP1,intron_variant,,ENST00000469613,,c.119+147dup,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1621-1622/3600 mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 24 dafcde63-69aa-4654-aadd-b00c046551cf 11 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS BAP1,stop_gained,p.E480*,ENST00000296288.9,c.1437dup,HIGH,;BAP1,intron_variant,,ENST00000469613.5,c.119+147_119+148insT,MODIFIER,;BAP1,stop_gained,p.E498*,ENST00000460680.6,c.1491dup,HIGH,YES +GRM6 2916 BI GRCh38 5 178983054 178983054 + synonymous_variant Silent SNP C C T rs781607214 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 30 29 c.2292G>A p.Thr764= p.T764= ENST00000231188.9 764 acG/acA 9/10 P1 T T protein_coding CCDS4442.1 2292/2634 GTGCACGTGAC Transmembrane_helices:TMhelix;PROSITE_profiles:PS50259;CDD:cd15453;PANTHER:PTHR24060;PANTHER:PTHR24060:SF24;Pfam:PF00003;Prints:PR00248 ENSP00000231188 9/10 rs781607214 ENST00000231188 Transcript 1.0 ENSG00000113262 HGNC:4598 LOW 2.638e-05 gnomAD_NFE synonymous_variant Unknown O15303.161 GRM6 HGNC -1 2.0 UPI000013C947 SNV GRM6,synonymous_variant,p.T764=,ENST00000650031,,c.2292G>A,LOW,YES,,,-1;GRM6,synonymous_variant,p.T764=,ENST00000231188,,c.2292G>A,LOW,,,,-1;GRM6,synonymous_variant,p.T764=,ENST00000517717,NM_000843.4,c.2292G>A,LOW,,,,-1;GRM6,non_coding_transcript_exon_variant,,ENST00000650488,,n.1015G>A,MODIFIER,,,,-1;GRM6,non_coding_transcript_exon_variant,,ENST00000519003,,n.291G>A,MODIFIER,,,,-1;GRM6,downstream_gene_variant,,ENST00000518082,,,MODIFIER,,,,-1;AC104117.3,intron_variant,,ENST00000519491,,n.305-6693C>T,MODIFIER,YES,,,1 2471/6143 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 1.193e-05 0.0 0.0 0.0 0.0 0.0 2.638e-05 0.0 0.0 6.760779797332361e-06 2.4314300389960408e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 75 dafcde63-69aa-4654-aadd-b00c046551cf 59 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS GRM6,non_coding_transcript_exon_variant,,ENST00000519003.1,n.291G>A,MODIFIER,;GRM6,synonymous_variant,p.T764=,ENST00000231188.9,c.2292G>A,LOW,;GRM6,synonymous_variant,p.T764=,ENST00000650031.1,c.2292G>A,LOW,;GRM6,synonymous_variant,p.T764=,ENST00000517717.3,c.2292G>A,LOW,YES;GRM6,non_coding_transcript_exon_variant,,ENST00000650488.1,n.1015G>A,MODIFIER,;ENSG00000254035,intron_variant,,ENST00000519491.1,n.305-6693C>T,MODIFIER,YES +DOP1A 23033 BI GRCh38 6 83158619 83158619 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 17 15 c.6794C>T p.Ser2265Leu p.S2265L ENST00000349129.7 NM_015018.4 2265 tCa/tTa 36/39 A1 T S/L protein_coding CCDS4996.1 6794/7398 TATTTCACGGT PANTHER:PTHR14042:SF22;PANTHER:PTHR14042 ENSP00000195654 36/39 ENST00000349129 Transcript ENSG00000083097 HGNC:21194 MODERATE missense_variant benign(0.162) Unknown tolerated(0.44) Q5JWR5.92 DOP1A HGNC 1 1.0 UPI00001C1574 SNV DOP1A,missense_variant,p.S2265L,ENST00000349129,NM_015018.3,c.6794C>T,MODERATE,,tolerated(0.44),benign(0.162),1;DOP1A,missense_variant,p.S2256L,ENST00000237163,NM_001199942.1,c.6767C>T,MODERATE,YES,tolerated(0.44),benign(0.018),1;DOP1A,missense_variant,p.S2256L,ENST00000369739,,c.6767C>T,MODERATE,,tolerated(0.44),benign(0.018),1;DOP1A,non_coding_transcript_exon_variant,,ENST00000484282,,n.3161C>T,MODIFIER,,,,1;DOP1A,downstream_gene_variant,,ENST00000481979,,,MODIFIER,,,,1;PGM3,downstream_gene_variant,,ENST00000504780,,,MODIFIER,,,,-1 7054/8210 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 25 dafcde63-69aa-4654-aadd-b00c046551cf 32 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS PGM3,intron_variant,NMD_transcript_variant,,ENST00000698603.1,c.*1658+2494G>A,MODIFIER,;PGM3,intron_variant,NMD_transcript_variant,,ENST00000698601.1,c.*1330+2494G>A,MODIFIER,;PGM3,intron_variant,NMD_transcript_variant,,ENST00000698602.1,c.*98+2494G>A,MODIFIER,;PGM3,intron_variant,NMD_transcript_variant,,ENST00000698600.1,c.*702+2494G>A,MODIFIER,;PGM3,intron_variant,NMD_transcript_variant,,ENST00000698599.1,c.*98+2494G>A,MODIFIER,;DOP1A,non_coding_transcript_exon_variant,,ENST00000484282.1,n.3161C>T,MODIFIER,;DOP1A,missense_variant,p.S2256L,ENST00000369739.7,c.6767C>T,MODERATE,;DOP1A,missense_variant,p.S2265L,ENST00000349129.7,c.6794C>T,MODERATE,YES;DOP1A,missense_variant,p.S2256L,ENST00000237163.9,c.6767C>T,MODERATE, +PPP2R2A 5520 BI GRCh38 8 26354572 26354572 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 81 29 c.285G>C p.Lys95Asn p.K95N ENST00000380737.8 NM_002717.4 95 aaG/aaC 4/10 P4 C K/N protein_coding CCDS34867.1 285/1344 GAAAAGATCAA PDB-ENSP_mappings:3dw8.B;PDB-ENSP_mappings:3dw8.E;PANTHER:PTHR11871:SF2;PANTHER:PTHR11871;PROSITE_patterns:PS01024;Gene3D:2.130.10.10;PIRSF:PIRSF037309;SMART:SM00320;Superfamily:SSF50978;Prints:PR00600 ENSP00000370113 4/10 ENST00000380737 Transcript ENSG00000221914 HGNC:9304 MODERATE NM_002717.4 missense_variant probably_damaging(0.999) Unknown deleterious(0) P63151.165 PPP2R2A HGNC 1 A0A140VJT0.20 1.0 UPI000000D997 P63151-1 SNV PPP2R2A,missense_variant,p.K95N,ENST00000380737,NM_002717.4,c.285G>C,MODERATE,,deleterious(0),probably_damaging(0.999),1;PPP2R2A,missense_variant,p.K105N,ENST00000315985,NM_001177591.2,c.315G>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;PPP2R2A,5_prime_UTR_variant,,ENST00000665949,,c.-158G>C,MODIFIER,,,,1;PPP2R2A,5_prime_UTR_variant,,ENST00000660435,,c.-193G>C,MODIFIER,,,,1;PPP2R2A,5_prime_UTR_variant,,ENST00000522535,,c.-193G>C,MODIFIER,,,,1;PPP2R2A,5_prime_UTR_variant,,ENST00000521557,,c.-193G>C,MODIFIER,,,,1;PPP2R2A,5_prime_UTR_variant,,ENST00000523925,,c.-193G>C,MODIFIER,,,,1;PPP2R2A,intron_variant,,ENST00000524169,,c.-77-6529G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000667651,,n.291G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000657943,,n.338G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000522482,,n.511G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000519636,,n.500G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000524099,,n.439G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000523964,,n.322G>C,MODIFIER,,,,1;PPP2R2A,downstream_gene_variant,,ENST00000521095,,,MODIFIER,,,,1;PPP2R2A,missense_variant,p.K95N,ENST00000518397,,c.285G>C,MODERATE,,deleterious(0),probably_damaging(1),1;PPP2R2A,3_prime_UTR_variant,,ENST00000520329,,c.*268G>C,MODIFIER,,,,1;PPP2R2A,3_prime_UTR_variant,,ENST00000518254,,c.*249G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000666129,,n.762G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000518215,,n.154G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000519439,,n.372G>C,MODIFIER,,,,1;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000521484,,n.425G>C,MODIFIER,,,,1 597/3923 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 86 dafcde63-69aa-4654-aadd-b00c046551cf 110 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS PPP2R2A,non_coding_transcript_exon_variant,,ENST00000518215.5,n.154G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000666129.1,n.762G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000657943.1,n.338G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000667651.1,n.291G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000523964.5,n.322G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000521484.5,n.425G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000519439.5,n.372G>C,MODIFIER,;PPP2R2A,5_prime_UTR_variant,,ENST00000521557.5,c.-193G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000522482.5,n.511G>C,MODIFIER,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000519636.5,n.500G>C,MODIFIER,;PPP2R2A,missense_variant,p.K105N,ENST00000315985.7,c.315G>C,MODERATE,;PPP2R2A,non_coding_transcript_exon_variant,,ENST00000524099.5,n.439G>C,MODIFIER,;PPP2R2A,5_prime_UTR_variant,,ENST00000523925.5,c.-193G>C,MODIFIER,;PPP2R2A,5_prime_UTR_variant,,ENST00000660435.1,c.-193G>C,MODIFIER,;PPP2R2A,5_prime_UTR_variant,,ENST00000665949.1,c.-158G>C,MODIFIER,;PPP2R2A,5_prime_UTR_variant,,ENST00000522535.5,c.-193G>C,MODIFIER,;PPP2R2A,missense_variant,NMD_transcript_variant,p.K95N,ENST00000518397.5,c.285G>C,MODERATE,;PPP2R2A,intron_variant,,ENST00000524169.5,c.-77-6529G>C,MODIFIER,;PPP2R2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000518254.5,c.*249G>C,MODIFIER,;PPP2R2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000520329.5,c.*268G>C,MODIFIER,;PPP2R2A,missense_variant,p.K95N,ENST00000380737.8,c.285G>C,MODERATE,YES +GALT 2592 BI GRCh38 9 34647672 34647672 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 10 9 c.344C>T p.Pro115Leu p.P115L ENST00000378842.8 NM_000155.4 115 cCc/cTc 4/11 P1 T P/L protein_coding YES CCDS6565.1 344/1140 TCATCCCCTTT PDB-ENSP_mappings:5in3.A;PDB-ENSP_mappings:5in3.B;PDB-ENSP_mappings:6gqd.A;CDD:cd00608;PANTHER:PTHR11943;PANTHER:PTHR11943:SF1;Gene3D:3.30.428.10;Pfam:PF01087;TIGRFAM:TIGR00209;PIRSF:PIRSF000808;Superfamily:SSF54197 ENSP00000368119 4/11 ENST00000378842 Transcript 1.0 ENSG00000213930 HGNC:4135 MODERATE NM_000155.4 missense_variant 1.0 probably_damaging(0.93) Unknown deleterious(0.04) P07902.223 GALT HGNC 1 A0A0S2Z3Y7.26 1.0 UPI000012B073 P07902-1 SNV GALT,missense_variant,p.P115L,ENST00000378842,NM_000155.4,c.344C>T,MODERATE,YES,deleterious(0.04),probably_damaging(0.93),1;GALT,intron_variant,,ENST00000450095,NM_001258332.1,c.51-160C>T,MODIFIER,,,,1;AL162231.3,intron_variant,,ENST00000556278,,c.252+414C>T,MODIFIER,YES,,,1;IL11RA,upstream_gene_variant,,ENST00000441545,NM_001142784.3,,MODIFIER,,,,1;IL11RA,upstream_gene_variant,,ENST00000553620,,,MODIFIER,,,,1;IL11RA,upstream_gene_variant,,ENST00000555003,,,MODIFIER,YES,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000557541,,n.488C>T,MODIFIER,,,,1;GALT,upstream_gene_variant,,ENST00000488412,,,MODIFIER,,,,1;GALT,missense_variant,p.P99S,ENST00000473506,,c.295C>T,MODERATE,,tolerated_low_confidence(0.43),benign(0),1;GALT,3_prime_UTR_variant,,ENST00000554085,,c.*88C>T,MODIFIER,,,,1;GALT,3_prime_UTR_variant,,ENST00000556244,,c.*153C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000555020,,n.374C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000557706,,n.780C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000554638,,n.690C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000487381,,n.603C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000485531,,n.659C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000555086,,n.348C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000472111,,n.474C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000554944,,n.414C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000473529,,n.480C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000465543,,n.683C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000556494,,n.465C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000554139,,n.397C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000556403,,n.446C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000554330,,n.381C>T,MODIFIER,,,,1;GALT,non_coding_transcript_exon_variant,,ENST00000556157,,n.468C>T,MODIFIER,,,,1;GALT,intron_variant,,ENST00000489643,,n.282+414C>T,MODIFIER,,,,1;GALT,intron_variant,,ENST00000554550,,c.253-160C>T,MODIFIER,,,,1;GALT,intron_variant,,ENST00000554897,,c.253-160C>T,MODIFIER,,,,1;GALT,intron_variant,,ENST00000555214,,n.262-376C>T,MODIFIER,,,,1;GALT,downstream_gene_variant,,ENST00000468099,,,MODIFIER,,,,1;IL11RA,upstream_gene_variant,,ENST00000555247,,,MODIFIER,,,,1;GALT,upstream_gene_variant,,ENST00000555754,,,MODIFIER,,,,1;GALT,downstream_gene_variant,,ENST00000605275,,,MODIFIER,,,,1 374/1756 muse;mutect2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 40 dafcde63-69aa-4654-aadd-b00c046551cf 19 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS GALT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000556244.1,c.*153C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000556157.1,n.468C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000557706.5,n.780C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000485531.1,n.659C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000556494.5,n.465C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000554330.5,n.381C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000555086.5,n.348C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000556403.5,n.446C>T,MODIFIER,;GALT,intron_variant,,ENST00000555214.5,n.262-376C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000554638.5,n.690C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000487381.5,n.603C>T,MODIFIER,;GALT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000554085.5,c.*88C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000555020.5,n.374C>T,MODIFIER,;GALT,missense_variant,p.P115L,ENST00000378842.8,c.344C>T,MODERATE,YES;GALT,intron_variant,,ENST00000489643.6,n.282+414C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000554944.5,n.414C>T,MODIFIER,;GALT,intron_variant,NMD_transcript_variant,,ENST00000554897.5,c.253-160C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000465543.6,n.683C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000472111.5,n.474C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000473529.5,n.480C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000554139.5,n.397C>T,MODIFIER,;GALT,non_coding_transcript_exon_variant,,ENST00000557541.5,n.488C>T,MODIFIER,;ENSG00000258728,intron_variant,,ENST00000556278.1,c.252+414C>T,MODIFIER,YES;GALT,missense_variant,NMD_transcript_variant,p.P99S,ENST00000473506.6,c.295C>T,MODERATE,;GALT,intron_variant,NMD_transcript_variant,,ENST00000554550.5,c.253-160C>T,MODIFIER,;ENSG00000258728,intron_variant,NMD_transcript_variant,,ENST00000691183.1,c.328+105C>T,MODIFIER,;GALT,intron_variant,,ENST00000450095.6,c.51-160C>T,MODIFIER, +JAML 120425 BI GRCh38 11 118200599 118200599 + synonymous_variant Silent SNP C C T rs377621403 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 21 17 c.786G>A p.Pro262= p.P262= ENST00000356289.10 NM_001098526.2 262 ccG/ccA 7/10 P4 T P protein_coding YES CCDS41723.1 786/1185 GCTGCCGGGGT PANTHER:PTHR13869;PANTHER:PTHR13869:SF22 ENSP00000348635 0.0 0.0001164 7/10 rs377621403 ENST00000356289 Transcript ENSG00000160593 HGNC:19084 LOW NM_001098526.2 0.0001164 EA synonymous_variant 1.0 Unknown Q86YT9.145 JAML HGNC -1 1.0 UPI000000D82D Q86YT9-1 SNV JAML,synonymous_variant,p.P252=,ENST00000292067,NM_153206.3,c.756G>A,LOW,,,,-1;JAML,synonymous_variant,p.P262=,ENST00000356289,NM_001098526.2,c.786G>A,LOW,YES,,,-1;JAML,synonymous_variant,p.P251=,ENST00000533261,,c.753G>A,LOW,,,,-1;JAML,synonymous_variant,p.P223=,ENST00000526620,NM_001286570.2&NM_001286571.2,c.669G>A,LOW,,,,-1;JAML,downstream_gene_variant,,ENST00000640745,,,MODIFIER,,,,-1;JAML,synonymous_variant,p.P223=,ENST00000526595,,c.669G>A,LOW,,,,-1;JAML,non_coding_transcript_exon_variant,,ENST00000534294,,n.3675G>A,MODIFIER,,,,-1;JAML,non_coding_transcript_exon_variant,,ENST00000531530,,n.1977G>A,MODIFIER,,,,-1;JAML,non_coding_transcript_exon_variant,,ENST00000529164,,n.877G>A,MODIFIER,,,,-1 877/1876 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 3.581e-05 0.0 0.0 0.0 0.0 0.0 5.279e-05 0.0 9.799e-05 3.382630166015588e-05 2.435220085317269e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.17397963651456e-05 0.0 6.17397963651456e-05 0.0 0.0 0 56 dafcde63-69aa-4654-aadd-b00c046551cf 38 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS JAML,non_coding_transcript_exon_variant,,ENST00000529164.5,n.877G>A,MODIFIER,;JAML,synonymous_variant,p.P223=,ENST00000526620.5,c.669G>A,LOW,;JAML,non_coding_transcript_exon_variant,,ENST00000531530.5,n.1977G>A,MODIFIER,;JAML,synonymous_variant,NMD_transcript_variant,p.P223=,ENST00000526595.5,c.669G>A,LOW,;JAML,synonymous_variant,p.P251=,ENST00000533261.5,c.753G>A,LOW,;JAML,non_coding_transcript_exon_variant,,ENST00000534294.5,n.3675G>A,MODIFIER,;JAML,synonymous_variant,p.P252=,ENST00000292067.11,c.756G>A,LOW,;JAML,synonymous_variant,p.P262=,ENST00000356289.10,c.786G>A,LOW,YES +TPCN1 53373 BI GRCh38 12 113226922 113226922 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 21 9 c.70G>T p.Ala24Ser p.A24S ENST00000335509.11 NM_017901.6 24 Gct/Tct 2/28 P1 T A/S protein_coding CCDS31908.1 70/2451 CACTGGCTCCC MobiDB_lite:mobidb-lite ENSP00000335300 2/28 ENST00000335509 Transcript ENSG00000186815 HGNC:18182 MODERATE NM_017901.6 missense_variant benign(0) Unknown tolerated(0.41) Q9ULQ1.152 TPCN1 HGNC 1 1.0 UPI0000041252 Q9ULQ1-1 SNV TPCN1,missense_variant,p.A96S,ENST00000550785,NM_001143819.3,c.286G>T,MODERATE,YES,tolerated(0.2),benign(0.006),1;TPCN1,missense_variant,p.A24S,ENST00000335509,NM_017901.6,c.70G>T,MODERATE,,tolerated(0.41),benign(0),1;TPCN1,missense_variant,p.A96S,ENST00000541517,,c.286G>T,MODERATE,,tolerated(0.2),benign(0.006),1;TPCN1,missense_variant,p.A110S,ENST00000552985,,c.328G>T,MODERATE,,tolerated_low_confidence(0.06),benign(0.301),1;TPCN1,missense_variant,p.A24S,ENST00000551099,,c.70G>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.06),1;TPCN1,missense_variant,p.A79S,ENST00000547275,,c.235G>T,MODERATE,,tolerated_low_confidence(0.1),benign(0.233),1;TPCN1,missense_variant,p.A24S,ENST00000549279,,c.70G>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.06),1;TPCN1,missense_variant,p.A96S,ENST00000551096,,c.286G>T,MODERATE,,deleterious_low_confidence(0.02),benign(0.383),1;TPCN1,missense_variant,p.A24S,ENST00000550873,,c.70G>T,MODERATE,,tolerated(0.24),benign(0),1;TPCN1,intron_variant,,ENST00000552642,,c.40+5686G>T,MODIFIER,,,,1;TPCN1,intron_variant,,ENST00000552897,,c.-93+5296G>T,MODIFIER,,,,1;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077,,n.336G>T,MODIFIER,,,,1 358/5248 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 37 dafcde63-69aa-4654-aadd-b00c046551cf 31 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS TPCN1,missense_variant,p.A96S,ENST00000541517.5,c.286G>T,MODERATE,;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077.5,n.336G>T,MODIFIER,;TPCN1,missense_variant,p.A24S,ENST00000549279.1,c.70G>T,MODERATE,;TPCN1,missense_variant,p.A24S,ENST00000335509.11,c.70G>T,MODERATE,YES;TPCN1,missense_variant,p.A96S,ENST00000550785.5,c.286G>T,MODERATE,;TPCN1,intron_variant,,ENST00000552897.5,c.-93+5296G>T,MODIFIER,;TPCN1,missense_variant,p.A24S,ENST00000551099.5,c.70G>T,MODERATE,;TPCN1,missense_variant,p.A96S,ENST00000551096.5,c.286G>T,MODERATE,;TPCN1,missense_variant,p.A24S,ENST00000550873.5,c.70G>T,MODERATE,;TPCN1,missense_variant,p.A110S,ENST00000552985.5,c.328G>T,MODERATE,;TPCN1,missense_variant,p.A79S,ENST00000547275.5,c.235G>T,MODERATE,;TPCN1,intron_variant,,ENST00000552642.5,c.40+5686G>T,MODIFIER, +ADAM21 8747 BI GRCh38 14 70459167 70459167 + synonymous_variant Silent SNP T T C novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 41 31 c.1668T>C p.Ser556= p.S556= ENST00000603540.2 NM_003813.4 556 tcT/tcC 2/2 P1 C S protein_coding YES CCDS9804.1 1668/2169 ATCTCTGATGT Pfam:PF08516;SMART:SM00608;PANTHER:PTHR11905:SF116;PANTHER:PTHR11905 ENSP00000474385 2/2 ENST00000603540 Transcript ENSG00000139985 HGNC:200 LOW NM_003813.4 synonymous_variant 1.0 Unknown Q9UKJ8.178 ADAM21 HGNC 1 3.0 UPI000013D756 SNV ADAM21,synonymous_variant,p.S556=,ENST00000603540,NM_003813.4,c.1668T>C,LOW,YES,,,1;ADAM20P1,intron_variant,,ENST00000649019,,n.506+1283A>G,MODIFIER,,,,-1;AL357153.2,intron_variant,,ENST00000556646,,n.184-5658A>G,MODIFIER,YES,,,-1 1909/2647 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 112 dafcde63-69aa-4654-aadd-b00c046551cf 73 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS ADAM20P1,intron_variant,,ENST00000649019.1,n.506+1283A>G,MODIFIER,YES;ADAM21,synonymous_variant,p.S556=,ENST00000603540.2,c.1668T>C,LOW,YES;ENSG00000257759,intron_variant,,ENST00000556646.1,n.184-5658A>G,MODIFIER,YES;ADAM21,synonymous_variant,p.S556=,ENST00000679631.1,c.1668T>C,LOW, +MYH11 4629 BI GRCh38 16 15721001 15721003 + inframe_deletion In_Frame_Del DEL CTC CTC - novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 60 22 c.4627_4629del p.Met1544del p.M1544del ENST00000300036.6 NM_002474.3 1543 GAG/- 33/41 P3 - E/- protein_coding CCDS10565.1 4627-4629/5919 CTTCATCTCCTCCA Coiled-coils_(Ncoils):Coil;PANTHER:PTHR45615:SF23;PANTHER:PTHR45615;Pfam:PF01576;Superfamily:SSF90257 ENSP00000300036 33/41 ENST00000300036 Transcript 1.0 ENSG00000133392 HGNC:7569 MODERATE NM_002474.3 inframe_deletion Unknown P35749.208 MYH11 HGNC -1 A0A024QZJ4.50 1.0 UPI000012FB86 P35749-1 deletion MYH11,inframe_deletion,p.E1550del,ENST00000452625,NM_001040113.2,c.4648_4650del,MODERATE,,,,-1;MYH11,inframe_deletion,p.E1543del,ENST00000300036,NM_002474.3,c.4627_4629del,MODERATE,,,,-1;MYH11,inframe_deletion,p.E1550del,ENST00000396324,NM_001040114.1,c.4648_4650del,MODERATE,YES,,,-1;MYH11,inframe_deletion,p.E1543del,ENST00000576790,NM_022844.2,c.4627_4629del,MODERATE,,,,-1;NDE1,intron_variant,,ENST00000396354,NM_017668.3,c.948-3186_948-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000396355,NM_001143979.2,c.948-3186_948-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000572756,,c.796-3186_796-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000572967,,c.*33-3186_*33-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000573694,,c.380-3186_380-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000577101,,c.1031-3186_1031-3184del,MODIFIER,YES,,,1;NDE1,intron_variant,,ENST00000674581,,c.*7-3186_*7-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000674995,,c.796-3270_796-3268del,MODIFIER,,,,1;NDE1,upstream_gene_variant,,ENST00000572503,,,MODIFIER,,,,1;MYH11,3_prime_UTR_variant,,ENST00000652121,,c.*2810_*2812del,MODIFIER,,,,-1;MYH11,non_coding_transcript_exon_variant,,ENST00000576164,,n.800_802del,MODIFIER,,,,-1;MYH11,non_coding_transcript_exon_variant,,ENST00000571275,,n.915_917del,MODIFIER,,,,-1;NDE1,intron_variant,,ENST00000674538,,c.796-3186_796-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000674554,,c.948-3186_948-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000674588,,c.796-3186_796-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000674888,,c.948-3186_948-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000674900,,c.*349-3186_*349-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000675171,,c.*700-3186_*700-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000675926,,c.948-3186_948-3184del,MODIFIER,,,,1;NDE1,intron_variant,,ENST00000675951,,c.948-3186_948-3184del,MODIFIER,,,,1 4732-4734/6880 pindel;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 106 dafcde63-69aa-4654-aadd-b00c046551cf 83 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS MYH11,non_coding_transcript_exon_variant,,ENST00000571275.1,n.915_917del,MODIFIER,;MYH11,non_coding_transcript_exon_variant,,ENST00000576164.6,n.800_802del,MODIFIER,;MYH11,inframe_deletion,p.M1544del,ENST00000576790.7,c.4627_4629del,MODERATE,;MYH11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652121.1,c.*2810_*2812del,MODIFIER,;MYH11,inframe_deletion,p.M1551del,ENST00000396324.7,c.4648_4650del,MODERATE,;MYH11,inframe_deletion,p.M1544del,ENST00000713757.1,c.4627_4629del,MODERATE,;MYH11,inframe_deletion,p.M1551del,ENST00000452625.7,c.4648_4650del,MODERATE,;MYH11,inframe_deletion,p.M1544del,ENST00000300036.6,c.4627_4629del,MODERATE,YES;NDE1,intron_variant,,ENST00000572967.1,c.*33-3190_*33-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000573694.5,c.380-3190_380-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000577101.6,c.1031-3190_1031-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000572756.6,c.796-3190_796-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000674554.1,c.948-3190_948-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000674581.1,c.*7-3190_*7-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000674995.1,c.796-3274_796-3272del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000675926.1,c.948-3190_948-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000396354.6,c.948-3190_948-3188del,MODIFIER,YES;NDE1,intron_variant,NMD_transcript_variant,,ENST00000674588.1,c.796-3190_796-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000674538.1,c.796-3190_796-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000674900.1,c.*349-3190_*349-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000675951.1,c.948-3190_948-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000675171.1,c.*700-3190_*700-3188del,MODIFIER,;NDE1,intron_variant,NMD_transcript_variant,,ENST00000674888.1,c.948-3190_948-3188del,MODIFIER,;NDE1,intron_variant,,ENST00000396355.5,c.948-3190_948-3188del,MODIFIER, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 36 24 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 81 dafcde63-69aa-4654-aadd-b00c046551cf 60 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +FCGRT 2217 BI GRCh38 19 49525517 49525517 + missense_variant Missense_Mutation SNP C C T rs778656931 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 39 19 c.932C>T p.Thr311Met p.T311M ENST00000221466.10 NM_001136019.3 311 aCg/aTg 6/7 P1 T T/M protein_coding CCDS12770.1 932/1098 ACTCACGGCAG PDB-ENSP_mappings:6fgb.A;Low_complexity_(Seg):seg;PANTHER:PTHR16675;PANTHER:PTHR16675:SF3;Transmembrane_helices:TMhelix ENSP00000221466 6/7 rs778656931 ENST00000221466 Transcript ENSG00000104870 HGNC:3621 MODERATE NM_001136019.3 0.000123 gnomAD_AFR missense_variant benign(0.006) Unknown tolerated(0.31) P55899.177 FCGRT HGNC 1 A0A024QZI2.54 1.0 UPI0000119C21 SNV FCGRT,missense_variant,p.T311M,ENST00000426395,NM_004107.5,c.932C>T,MODERATE,YES,tolerated(0.31),benign(0.006),1;FCGRT,missense_variant,p.T311M,ENST00000221466,NM_001136019.3,c.932C>T,MODERATE,,tolerated(0.31),benign(0.006),1;FCGRT,missense_variant,p.T219M,ENST00000596975,,c.656C>T,MODERATE,,tolerated(0.3),benign(0.04),1;FCGRT,missense_variant,p.T45M,ENST00000599988,,c.134C>T,MODERATE,,tolerated_low_confidence(0.25),benign(0.003),1;FCGRT,intron_variant,,ENST00000598076,,c.353-493C>T,MODIFIER,,,,1;RCN3,upstream_gene_variant,,ENST00000270645,NM_020650.3,,MODIFIER,YES,,,1;FCGRT,downstream_gene_variant,,ENST00000593381,,,MODIFIER,,,,1;RCN3,upstream_gene_variant,,ENST00000597801,,,MODIFIER,,,,1;RCN3,upstream_gene_variant,,ENST00000598833,,,MODIFIER,,,,1;RCN3,upstream_gene_variant,,ENST00000593644,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000594823,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000595677,,,MODIFIER,,,,1;FCGRT,3_prime_UTR_variant,,ENST00000598927,,c.*466C>T,MODIFIER,,,,1;FCGRT,non_coding_transcript_exon_variant,,ENST00000595881,,n.2303C>T,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000452439,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000593431,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000596147,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000598319,,,MODIFIER,,,,1;FCGRT,downstream_gene_variant,,ENST00000598936,,,MODIFIER,,,,1 1036/1511 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 1.989e-05 0.000123 8.673e-05 0.0 0.0 0.0 0.0 0.0 0.0 2.0289500753278844e-05 4.866419840254821e-05 0.0 0.0 0.0 0.0 0.0 afr 4.866419840254821e-05 0.0 1.5433099179062992e-05 0.0 0.0 0 82 dafcde63-69aa-4654-aadd-b00c046551cf 58 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS FCGRT,intron_variant,,ENST00000598076.1,c.353-493C>T,MODIFIER,;FCGRT,missense_variant,p.T219M,ENST00000596975.5,c.656C>T,MODERATE,;FCGRT,missense_variant,p.T45M,ENST00000599988.5,c.134C>T,MODERATE,;FCGRT,non_coding_transcript_exon_variant,,ENST00000595881.1,n.2303C>T,MODIFIER,;FCGRT,missense_variant,p.T311M,ENST00000426395.7,c.932C>T,MODERATE,;FCGRT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000598927.5,c.*466C>T,MODIFIER,;FCGRT,missense_variant,p.T311M,ENST00000221466.10,c.932C>T,MODERATE,YES +ZNF836 162962 BI GRCh38 19 52156003 52156003 + synonymous_variant Silent SNP G G C novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 116 55 c.1680C>G p.Gly560= p.G560= ENST00000597252.5 560 ggC/ggG 5/5 P1 C G protein_coding YES CCDS46162.1 1680/2811 ACCTTGCCACA Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR23226;PANTHER:PTHR23226;PANTHER:PTHR23226;PANTHER:PTHR23226:SF133;PANTHER:PTHR23226:SF133;PANTHER:PTHR23226:SF133;SMART:SM00355;Superfamily:SSF57667 ENSP00000470239 5/5 ENST00000597252 Transcript ENSG00000196267 HGNC:34333 LOW synonymous_variant 1.0 Unknown Q6ZNA1.140 ZNF836 HGNC -1 2.0 UPI00001D818C SNV ZNF836,synonymous_variant,p.G560=,ENST00000597252,NM_001102657.3,c.1680C>G,LOW,YES,,,-1;ZNF836,synonymous_variant,p.G560=,ENST00000322146,,c.1680C>G,LOW,,,,-1;ZNF836,downstream_gene_variant,,ENST00000596428,,,MODIFIER,,,,-1;ZNF836,downstream_gene_variant,,ENST00000597065,,,MODIFIER,,,,-1;ZNF836,upstream_gene_variant,,ENST00000599618,,,MODIFIER,,,,-1;AC011468.2,intron_variant,,ENST00000594362,,n.554+4462C>G,MODIFIER,YES,,,-1;AC011468.2,intron_variant,,ENST00000598982,,n.494+4462C>G,MODIFIER,,,,-1 2054/3209 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 190 dafcde63-69aa-4654-aadd-b00c046551cf 171 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS ZNF836,synonymous_variant,p.G560=,ENST00000597252.5,c.1680C>G,LOW,;ZNF836,synonymous_variant,p.G560=,ENST00000682614.1,c.1680C>G,LOW,YES;ENSG00000267827,intron_variant,,ENST00000594362.1,n.554+4462C>G,MODIFIER,YES;ENSG00000267827,intron_variant,,ENST00000598982.5,n.494+4462C>G,MODIFIER, +RRBP1 6238 BI GRCh38 20 17658650 17658650 + missense_variant Missense_Mutation SNP T T C rs758259417 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 77 50 c.1858A>G p.Lys620Glu p.K620E ENST00000377813.6 NM_001365613.2 620 Aag/Gag 3/25 P3 C K/E protein_coding YES 1858/4233 TTGCTTTGGTG PANTHER:PTHR18939;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000367044 3/25 rs758259417 ENST00000377813 Transcript ENSG00000125844 HGNC:10448 MODERATE NM_001365613.2 0.0001164 gnomAD_AMR missense_variant 1.0 probably_damaging(0.984) Unknown deleterious(0.01) Q9P2E9.177 RRBP1 HGNC -1 1.0 UPI0004620C9C Q9P2E9-1 SNV RRBP1,missense_variant,p.K620E,ENST00000377813,NM_001365613.2,c.1858A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.984),-1;RRBP1,missense_variant,p.K620E,ENST00000246043,,c.1858A>G,MODERATE,,deleterious(0.01),probably_damaging(0.984),-1;RRBP1,missense_variant,p.K190E,ENST00000377807,NM_001042576.2,c.568A>G,MODERATE,,deleterious(0.03),benign(0.05),-1;RRBP1,missense_variant,p.K190E,ENST00000360807,NM_004587.3,c.568A>G,MODERATE,,deleterious(0.03),benign(0.05),-1;RRBP1,missense_variant,p.K144E,ENST00000610403,,c.430A>G,MODERATE,,deleterious(0),probably_damaging(0.911),-1;RRBP1,intron_variant,,ENST00000455029,,c.-65-15523A>G,MODIFIER,,,,-1;RRBP1,downstream_gene_variant,,ENST00000398782,,,MODIFIER,,,,-1;RRBP1,missense_variant,p.K95E,ENST00000495501,,c.283A>G,MODERATE,,deleterious_low_confidence(0),unknown(0),-1 2171/5049 muse;mutect2;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 1.595e-05 0.0 0.0001164 0.0 0.0 0.0 0.0 0.0 0.0 6.75803994454327e-06 0.0 0.0 6.621640204684809e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 128 dafcde63-69aa-4654-aadd-b00c046551cf 127 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS RRBP1,missense_variant,NMD_transcript_variant,p.K95E,ENST00000495501.2,c.283A>G,MODERATE,;RRBP1,intron_variant,,ENST00000455029.3,c.-65-15523A>G,MODIFIER,;RRBP1,missense_variant,p.K620E,ENST00000377813.6,c.1858A>G,MODERATE,YES;RRBP1,missense_variant,p.K620E,ENST00000246043.8,c.1858A>G,MODERATE,;RRBP1,missense_variant,p.K190E,ENST00000377807.6,c.568A>G,MODERATE,;RRBP1,missense_variant,p.K190E,ENST00000360807.8,c.568A>G,MODERATE, +HELZ2 85441 BI GRCh38 20 63562121 63562121 + synonymous_variant Silent SNP C C T rs949392781 TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 5 6 c.6480G>A p.Ala2160= p.A2160= ENST00000467148.2 NM_001037335.2 2160 gcG/gcA 10/19 P1 T A protein_coding YES CCDS33508.1 6480/7950 CTGACCGCCAC CDD:cd18040;PANTHER:PTHR10887:SF428;PANTHER:PTHR10887;Pfam:PF13086;Gene3D:3.40.50.300;Superfamily:SSF52540 ENSP00000417401 10/19 rs949392781 ENST00000467148 Transcript ENSG00000130589 HGNC:30021 LOW 2.91e-05 gnomAD_AMR synonymous_variant 1.0 Unknown Q9BYK8.187 HELZ2 HGNC -1 1.0 UPI0000246BF7 Q9BYK8-1 SNV HELZ2,synonymous_variant,p.A2160=,ENST00000467148,NM_001037335.2,c.6480G>A,LOW,YES,,,-1;HELZ2,synonymous_variant,p.A1591=,ENST00000427522,NM_033405.3,c.4773G>A,LOW,,,,-1;HELZ2,upstream_gene_variant,,ENST00000478861,,,MODIFIER,,,,-1 6550/8064 muse;mutect2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 4.088e-06 0.0 2.91e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.3517200386559123e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086320066358894e-05 0.0 3.086320066358894e-05 0.0 0.0 0 23 dafcde63-69aa-4654-aadd-b00c046551cf 11 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS HELZ2,synonymous_variant,p.A1591=,ENST00000427522.6,c.4773G>A,LOW,;HELZ2,synonymous_variant,p.A2160=,ENST00000467148.2,c.6480G>A,LOW,YES +PAXBP1 94104 BI GRCh38 21 32744843 32744843 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-VD-AA8T-01A TCGA-VD-AA8T-10A Somatic 68 34 c.2139del p.Lys713AsnfsTer2 p.K713Nfs*2 ENST00000331923.9 NM_016631.4 713 aaA/aa 13/18 P1 - K/X protein_coding YES CCDS13619.1 2139/2754 GATTAATTTTAG Pfam:PF07842;PANTHER:PTHR12214;PANTHER:PTHR12214:SF2 ENSP00000328992 13/18 ENST00000331923 Transcript ENSG00000159086 HGNC:13579 HIGH NM_016631.4 frameshift_variant 1.0 Unknown Q9Y5B6.167 PAXBP1 HGNC -1 1.0 UPI000012B294 Q9Y5B6-1 deletion PAXBP1,frameshift_variant,p.K713Nfs*2,ENST00000331923,NM_016631.4,c.2139del,HIGH,YES,,,-1;PAXBP1,frameshift_variant,p.K713Nfs*2,ENST00000290178,NM_013329.4,c.2139del,HIGH,,,,-1;PAXBP1,3_prime_UTR_variant,,ENST00000443785,,c.*620del,MODIFIER,,,,-1;PAXBP1,non_coding_transcript_exon_variant,,ENST00000466846,,n.2214del,MODIFIER,,,,-1;PAXBP1,non_coding_transcript_exon_variant,,ENST00000497873,,n.1538del,MODIFIER,,,,-1;PAXBP1,downstream_gene_variant,,ENST00000421049,,,MODIFIER,,,,-1;PAXBP1,upstream_gene_variant,,ENST00000445049,,,MODIFIER,,,,-1;PAXBP1-AS1,intron_variant,,ENST00000653345,,n.2692-931del,MODIFIER,,,,1;PAXBP1-AS1,intron_variant,,ENST00000655758,,n.5051-931del,MODIFIER,YES,,,1;PAXBP1-AS1,intron_variant,,ENST00000655910,,n.1866-931del,MODIFIER,,,,1;PAXBP1-AS1,intron_variant,,ENST00000665598,,n.1526-931del,MODIFIER,,,,1;PAXBP1-AS1,downstream_gene_variant,,ENST00000440052,,,MODIFIER,,,,1;PAXBP1-AS1,downstream_gene_variant,,ENST00000660366,,,MODIFIER,,,,1;PAXBP1-AS1,downstream_gene_variant,,ENST00000662524,,,MODIFIER,,,,1;PAXBP1-AS1,downstream_gene_variant,,ENST00000665120,,,MODIFIER,,,,1;PAXBP1-AS1,downstream_gene_variant,,ENST00000665654,,,MODIFIER,,,,1 2226/3892 mutect2;pindel;varscan2 9e35ef82-55b0-460b-8ab9-8cd708efa3b1 0 122 dafcde63-69aa-4654-aadd-b00c046551cf 102 e7cded99-5c1f-4d81-8fa4-8f65d2c05901 SUCCESS PAXBP1,frameshift_variant,p.K713Nfs*2,ENST00000290178.4,c.2139del,HIGH,;PAXBP1-AS1,intron_variant,,ENST00000665598.1,n.1526-934del,MODIFIER,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000497873.1,n.1538del,MODIFIER,;PAXBP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000443785.5,c.*620del,MODIFIER,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000466846.5,n.2214del,MODIFIER,;PAXBP1,frameshift_variant,p.K713Nfs*2,ENST00000331923.9,c.2139del,HIGH,YES;PAXBP1-AS1,intron_variant,,ENST00000655910.1,n.1866-934del,MODIFIER,;PAXBP1-AS1,intron_variant,,ENST00000653345.1,n.2692-934del,MODIFIER,YES;PAXBP1-AS1,intron_variant,,ENST00000655758.1,n.5051-934del,MODIFIER, +FSHR 2492 BI GRCh38 2 49154277 49154277 + synonymous_variant Silent SNP A A G novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 35 12 c.141T>C p.Asn47= p.N47= ENST00000406846.7 NM_000145.4 47 aaT/aaC 1/10 P1 G N protein_coding YES CCDS1843.1 141/2088 ATGGCATTCCT SMART:SM00013;Superfamily:SSF52058;PANTHER:PTHR24372:SF5;PANTHER:PTHR24372;Prints:PR01143 ENSP00000384708 1/10 ENST00000406846 Transcript 1.0 ENSG00000170820 HGNC:3969 LOW NM_000145.4 synonymous_variant 1.0 Unknown FSHR HGNC -1 A0A1D5RMN4.23 1.0 UPI000013E97A SNV FSHR,synonymous_variant,p.N47=,ENST00000406846,NM_000145.4,c.141T>C,LOW,YES,,,-1;FSHR,synonymous_variant,p.N47=,ENST00000304421,NM_181446.3,c.141T>C,LOW,,,,-1;FSHR,synonymous_variant,p.N47=,ENST00000454032,,c.141T>C,LOW,,,,-1;FSHR,synonymous_variant,p.N47=,ENST00000419927,,c.141T>C,LOW,,,,-1;AC009975.1,intron_variant,,ENST00000634588,,n.492+207872A>G,MODIFIER,YES,,,1 239/2762 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 33 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 48 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS FSHR,synonymous_variant,NMD_transcript_variant,p.N47=,ENST00000419927.1,c.141T>C,LOW,;FSHR,synonymous_variant,p.N47=,ENST00000454032.5,c.141T>C,LOW,;FSHR,synonymous_variant,p.N47=,ENST00000304421.8,c.141T>C,LOW,;FSHR,synonymous_variant,p.N47=,ENST00000406846.7,c.141T>C,LOW,YES;ENSG00000282890,intron_variant,,ENST00000634588.1,n.492+207872A>G,MODIFIER,YES +EIF1B 10289 BI GRCh38 3 40311518 40311519 + frameshift_variant Frame_Shift_Ins INS - - T novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 42 9 c.246dup p.Val82CysfsTer7 p.V82Cfs*7 ENST00000232905.4 NM_005875.3 82 gtt/gTtt 3/4 P1 T V/VX protein_coding YES CCDS2690.1 244-245/342 GAGAGGTTATT Gene3D:3.30.780.10;Pfam:PF01253;PIRSF:PIRSF004499;PROSITE_profiles:PS50296;PANTHER:PTHR10388;PANTHER:PTHR10388:SF51;Superfamily:SSF55159;TIGRFAM:TIGR01160;CDD:cd11566 ENSP00000232905 3/4 ENST00000232905 Transcript ENSG00000114784 HGNC:30792 2.0 HIGH NM_005875.3 frameshift_variant 1.0 Unknown O60739.159 EIF1B HGNC 1 Q6FG85.121 1.0 UPI0000003EA1 insertion EIF1B,frameshift_variant,p.I83Yfs*6,ENST00000232905,NM_005875.3,c.246dup,HIGH,YES,,,1;EIF1B,non_coding_transcript_exon_variant,,ENST00000488260,,n.362dup,MODIFIER,,,,1;EIF1B,non_coding_transcript_exon_variant,,ENST00000487151,,n.480dup,MODIFIER,,,,1;EIF1B,downstream_gene_variant,,ENST00000462088,,,MODIFIER,,,,1;EIF1B-AS1,upstream_gene_variant,,ENST00000626073,,,MODIFIER,,,,-1;ENTPD3-AS1,downstream_gene_variant,,ENST00000439293,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000625390,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000628298,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000629217,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000629723,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000631175,,,MODIFIER,YES,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000655651,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000657144,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000661550,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000663881,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000663919,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000668232,,,MODIFIER,,,,-1 479-480/987 mutect2;pindel;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 60 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 51 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS EIF1B,non_coding_transcript_exon_variant,,ENST00000487151.1,n.478_479insT,MODIFIER,;EIF1B,non_coding_transcript_exon_variant,,ENST00000488260.1,n.360_361insT,MODIFIER,;EIF1B,frameshift_variant,p.V82Cfs*7,ENST00000232905.4,c.246dup,HIGH,YES;EIF1B-AS1,intron_variant,,ENST00000715680.1,n.307-10123_307-10122insA,MODIFIER, +BAP1 8314 BI GRCh38 3 52405213 52405213 + frameshift_variant Frame_Shift_Del DEL G G - novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 61 22 c.1013del p.Pro338LeufsTer24 p.P338Lfs*24 ENST00000460680.6 NM_004656.4 338 cCt/ct 11/17 P1 - P/X protein_coding YES CCDS2853.1 1013/2190 CCTGGAGGCTTC Low_complexity_(Seg):seg;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 11/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D deletion BAP1,frameshift_variant,p.P338Lfs*24,ENST00000460680,NM_004656.4,c.1013del,HIGH,YES,,,-1;BAP1,frameshift_variant,p.P320Lfs*24,ENST00000296288,,c.959del,HIGH,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000490804,,n.441del,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1143/3600 mutect2;pindel;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 145 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 83 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000490804.1,n.441del,MODIFIER,;BAP1,frameshift_variant,p.P320Lfs*24,ENST00000296288.9,c.959del,HIGH,;BAP1,frameshift_variant,p.P338Lfs*24,ENST00000460680.6,c.1013del,HIGH,YES +EIF2B5 105374249 BI GRCh38 3 184138231 184138231 + synonymous_variant Silent SNP C C T TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 34 12 c.750C>T p.Ser250= p.S250= ENST00000648915.2 258/729 A2 T S protein_coding YES 774/2190 ATCAGCATCTG COSM3373107 CDD:cd04197;PANTHER:PTHR45887;Gene3D:3.90.550.10;Superfamily:SSF53448 ENSP00000498164 5/16 COSV56606336 ENST00000647909 Transcript 1.0 ENSG00000145191 HGNC:3261 LOW synonymous_variant 1 Unknown 1 EIF2B5 HGNC 1 A0A3B3IUB1.8 UPI000E6E6605 SNV EIF2B5,synonymous_variant,p.S250=,ENST00000648915,NM_003907.3,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S258=,ENST00000647909,,c.774C>T,LOW,YES,,,1;EIF2B5,downstream_gene_variant,,ENST00000432569,,,MODIFIER,,,,1;EIF2B5,downstream_gene_variant,,ENST00000498831,,,MODIFIER,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000649688,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000648314,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S248=,ENST00000648630,,c.744C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000648682,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000648599,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000647636,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S250=,ENST00000648890,,c.750C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S233=,ENST00000648256,,c.699C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S206=,ENST00000650270,,c.618C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S167=,ENST00000648189,,c.501C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S173=,ENST00000648145,,c.519C>T,LOW,,,,1;EIF2B5,synonymous_variant,p.S162=,ENST00000649545,,c.486C>T,LOW,,,,1;EIF2B5,3_prime_UTR_variant,,ENST00000648882,,c.*576C>T,MODIFIER,,,,1;EIF2B5,3_prime_UTR_variant,,ENST00000492773,,c.*79C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000468748,,n.733C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000484154,,n.1371C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000492226,,n.747C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000481054,,n.751C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491008,,n.1498C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000649814,,n.799C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491144,,n.1190C>T,MODIFIER,,,,1;EIF2B5,non_coding_transcript_exon_variant,,ENST00000465218,,n.773C>T,MODIFIER,,,,1;EIF2B5,intron_variant,,ENST00000432982,,c.245+1556C>T,MODIFIER,,,,1;EIF2B5,downstream_gene_variant,,ENST00000471832,,,MODIFIER,,,,1;EIF2B5,upstream_gene_variant,,ENST00000479250,,,MODIFIER,,,,1;EIF2B5,upstream_gene_variant,,ENST00000493740,,,MODIFIER,,,,1;EIF2B5,downstream_gene_variant,,ENST00000650244,,,MODIFIER,,,,1;AC131235.2,upstream_gene_variant,,ENST00000608135,,,MODIFIER,YES,,,-1;AC131235.2,upstream_gene_variant,,ENST00000608232,,,MODIFIER,,,,-1;AC131235.3,upstream_gene_variant,,ENST00000609288,,,MODIFIER,YES,,,-1 783/2222 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 73 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 46 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS EIF2B5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000492773.6,c.*79C>T,MODIFIER,;EIF2B5,missense_variant,NMD_transcript_variant,p.H162Y,ENST00000649545.1,c.484C>T,MODERATE,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000484154.2,n.1371C>T,MODIFIER,;EIF2B5,missense_variant,NMD_transcript_variant,p.A167V,ENST00000648189.1,c.500C>T,MODERATE,;EIF2B5,missense_variant,NMD_transcript_variant,p.A173V,ENST00000648145.1,c.518C>T,MODERATE,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491008.6,n.1498C>T,MODIFIER,;EIF2B5,missense_variant,NMD_transcript_variant,p.A206V,ENST00000650270.1,c.617C>T,MODERATE,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S233=,ENST00000648256.1,c.699C>T,LOW,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000468748.7,n.733C>T,MODIFIER,;EIF2B5,intron_variant,NMD_transcript_variant,,ENST00000432982.5,c.245+1556C>T,MODIFIER,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S248=,ENST00000648630.1,c.744C>T,LOW,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000492226.2,n.747C>T,MODIFIER,;EIF2B5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000648882.1,c.*576C>T,MODIFIER,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000481054.5,n.751C>T,MODIFIER,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000649688.1,c.750C>T,LOW,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000648599.1,c.750C>T,LOW,;EIF2B5,synonymous_variant,p.S258=,ENST00000647909.1,c.774C>T,LOW,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000648682.1,c.750C>T,LOW,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000648890.1,c.750C>T,LOW,;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000647636.1,c.750C>T,LOW,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000465218.3,n.773C>T,MODIFIER,;EIF2B5,synonymous_variant,p.S250=,ENST00000648915.2,c.750C>T,LOW,YES;EIF2B5,synonymous_variant,NMD_transcript_variant,p.S250=,ENST00000648314.1,c.750C>T,LOW,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000649814.1,n.799C>T,MODIFIER,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491144.5,n.1190C>T,MODIFIER, +TRIML1 339976 BI GRCh38 4 188147171 188147171 + synonymous_variant Silent SNP G G A rs376744139 TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 81 27 c.1206G>A p.Glu402= p.E402= ENST00000332517.4 NM_178556.5 402 gaG/gaA 6/6 P1 A E protein_coding YES CCDS3851.1 1206/1407 AGAGAGCCTGT CDD:cd13733;Gene3D:2.60.120.920;Pfam:PF00622;SMART:SM00449;Superfamily:SSF49899;PROSITE_profiles:PS50188;PANTHER:PTHR24103;PANTHER:PTHR24103:SF560;Prints:PR01407 ENSP00000327738 0.0 0.0001163 6/6 rs376744139 ENST00000332517 Transcript ENSG00000184108 HGNC:26698 LOW NM_178556.5 0.0001163 EA synonymous_variant 1.0 Unknown Q8N9V2.134 TRIML1 HGNC 1 1.0 UPI000006FC8A SNV TRIML1,synonymous_variant,p.E402=,ENST00000332517,NM_178556.5,c.1206G>A,LOW,YES,,,1;TRIML1,non_coding_transcript_exon_variant,,ENST00000507581,,n.666G>A,MODIFIER,,,,1;TRIML1,non_coding_transcript_exon_variant,,ENST00000512233,,n.556G>A,MODIFIER,,,,1;AC138781.1,upstream_gene_variant,,ENST00000501322,,,MODIFIER,YES,,,-1 1324/1896 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 1.989e-05 0.0 0.0 0.0 0.0 0.0 4.397e-05 0.0 0.0 1.3519899766833989e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085939897573553e-05 0.0 3.085939897573553e-05 0.0 0.0 0 113 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 108 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS TRIML1,non_coding_transcript_exon_variant,,ENST00000512233.1,n.556G>A,MODIFIER,;TRIML1,non_coding_transcript_exon_variant,,ENST00000507581.5,n.666G>A,MODIFIER,;TRIML1,synonymous_variant,p.E402=,ENST00000332517.4,c.1206G>A,LOW,YES +PPARD 5467 BI GRCh38 6 35426028 35426028 + synonymous_variant Silent SNP C C G rs764302707 TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 30 5 c.1275C>G p.Thr425= p.T425= ENST00000311565.4 NM_001171818.2 425 acC/acG 9/9 P2 G T protein_coding YES CCDS4803.1 1275/1326 GAAACCGAGAC PDB-ENSP_mappings:1gwx.A;PDB-ENSP_mappings:1gwx.B;PDB-ENSP_mappings:1y0s.A;PDB-ENSP_mappings:1y0s.B;PDB-ENSP_mappings:2awh.A;PDB-ENSP_mappings:2awh.B;PDB-ENSP_mappings:2b50.A;PDB-ENSP_mappings:2b50.B;PDB-ENSP_mappings:2baw.A;PDB-ENSP_mappings:2baw.B;PDB-ENSP_mappings:2gwx.A;PDB-ENSP_mappings:2gwx.B;PDB-ENSP_mappings:2j14.A;PDB-ENSP_mappings:2j14.B;PDB-ENSP_mappings:2q5g.A;PDB-ENSP_mappings:2q5g.B;PDB-ENSP_mappings:2xyj.A;PDB-ENSP_mappings:2xyj.B;PDB-ENSP_mappings:2xyw.A;PDB-ENSP_mappings:2xyw.B;PDB-ENSP_mappings:2xyx.A;PDB-ENSP_mappings:2xyx.B;PDB-ENSP_mappings:2znp.A;PDB-ENSP_mappings:2znp.B;PDB-ENSP_mappings:2znq.A;PDB-ENSP_mappings:2znq.B;PDB-ENSP_mappings:3d5f.A;PDB-ENSP_mappings:3d5f.B;PDB-ENSP_mappings:3dy6.A;PDB-ENSP_mappings:3dy6.B;PDB-ENSP_mappings:3et2.A;PDB-ENSP_mappings:3et2.B;PDB-ENSP_mappings:3gwx.A;PDB-ENSP_mappings:3gwx.B;PDB-ENSP_mappings:3gz9.A;PDB-ENSP_mappings:3oz0.A;PDB-ENSP_mappings:3peq.A;PDB-ENSP_mappings:3peq.B;PDB-ENSP_mappings:3sp9.A;PDB-ENSP_mappings:3sp9.B;PDB-ENSP_mappings:3tkm.A;PDB-ENSP_mappings:5u3q.A;PDB-ENSP_mappings:5u3q.B;PDB-ENSP_mappings:5u3r.A;PDB-ENSP_mappings:5u3r.B;PDB-ENSP_mappings:5u3s.A;PDB-ENSP_mappings:5u3s.B;PDB-ENSP_mappings:5u3t.A;PDB-ENSP_mappings:5u3t.B;PDB-ENSP_mappings:5u3u.A;PDB-ENSP_mappings:5u3u.B;PDB-ENSP_mappings:5u3v.A;PDB-ENSP_mappings:5u3v.B;PDB-ENSP_mappings:5u3w.A;PDB-ENSP_mappings:5u3w.B;PDB-ENSP_mappings:5u3x.A;PDB-ENSP_mappings:5u3x.B;PDB-ENSP_mappings:5u3y.A;PDB-ENSP_mappings:5u3y.B;PDB-ENSP_mappings:5u3z.A;PDB-ENSP_mappings:5u3z.B;PDB-ENSP_mappings:5u40.A;PDB-ENSP_mappings:5u40.B;PDB-ENSP_mappings:5u41.A;PDB-ENSP_mappings:5u41.B;PDB-ENSP_mappings:5u42.A;PDB-ENSP_mappings:5u42.B;PDB-ENSP_mappings:5u43.A;PDB-ENSP_mappings:5u43.B;PDB-ENSP_mappings:5u44.A;PDB-ENSP_mappings:5u44.B;PDB-ENSP_mappings:5u45.A;PDB-ENSP_mappings:5u45.B;PDB-ENSP_mappings:5u46.A;PDB-ENSP_mappings:5u46.B;PDB-ENSP_mappings:5xmx.A;PDB-ENSP_mappings:5xmx.B;PDB-ENSP_mappings:5y7x.A;PDB-ENSP_mappings:5y7x.B;PDB-ENSP_mappings:5zxi.A;PDB-ENSP_mappings:5zxi.B;PDB-ENSP_mappings:6a6p.A;PDB-ENSP_mappings:6a6p.B;Coiled-coils_(Ncoils):Coil;Prints:PR01288;PROSITE_profiles:PS51843;PANTHER:PTHR24082;PANTHER:PTHR24082:SF15;Superfamily:SSF48508;CDD:cd06932 ENSP00000310928 9/9 rs764302707 ENST00000311565 Transcript ENSG00000112033 HGNC:9235 LOW 0.000123 gnomAD_AFR synonymous_variant 1.0 Unknown Q03181.233 PPARD HGNC 1 A0A024RCW6.54 5.0 UPI000004EF98 Q03181-1 SNV PPARD,synonymous_variant,p.T425=,ENST00000311565,NM_001171818.2,c.1275C>G,LOW,YES,,,1;PPARD,synonymous_variant,p.T425=,ENST00000360694,NM_006238.5,c.1275C>G,LOW,,,,1;PPARD,synonymous_variant,p.T386=,ENST00000448077,NM_001171819.1,c.1158C>G,LOW,,,,1;PPARD,synonymous_variant,p.T327=,ENST00000418635,NM_001171820.1,c.981C>G,LOW,,,,1;PPARD,downstream_gene_variant,,ENST00000337400,NM_177435.3,,MODIFIER,,,,1 1624/3774 muse;mutect2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 1.991e-05 0.000123 0.0 0.0 0.0 0.0 2.639e-05 0.0 0.0 3.380619818926789e-05 9.733779734233394e-05 0.0 0.0 0.0 0.0 0.0 afr 9.733779734233394e-05 0.0 1.543160033179447e-05 0.0 0.0 0 32 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 36 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS PPARD,synonymous_variant,p.T425=,ENST00000311565.4,c.1275C>G,LOW,;PPARD,synonymous_variant,p.T327=,ENST00000418635.6,c.981C>G,LOW,;PPARD,synonymous_variant,p.T386=,ENST00000448077.6,c.1158C>G,LOW,;PPARD,synonymous_variant,p.T425=,ENST00000360694.8,c.1275C>G,LOW,YES +CCAR2 57805 BI GRCh38 8 22618449 22618450 + frameshift_variant Frame_Shift_Ins INS - - A novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 54 16 c.2175dup p.Leu725TyrfsTer87 p.L725Yfs*87 ENST00000308511.9 NM_001363069.2 725 tta/ttAa 17/21 P1 A L/LX protein_coding YES CCDS34863.1 2174-2175/2772 AGACTTAGAGA PANTHER:PTHR14304:SF12;PANTHER:PTHR14304;Superfamily:SSF47473 ENSP00000310670 17/21 ENST00000308511 Transcript ENSG00000158941 HGNC:23360 1.0 HIGH frameshift_variant 1.0 Unknown Q8N163.173 CCAR2 HGNC 1 1.0 UPI0000070A46 Q8N163-1 insertion CCAR2,frameshift_variant,p.E726Rfs*86,ENST00000308511,NM_001363069.2,c.2175dup,HIGH,YES,,,1;CCAR2,frameshift_variant,p.E726Rfs*86,ENST00000389279,NM_021174.6&NM_001363068.2,c.2175dup,HIGH,,,,1;CCAR2,frameshift_variant,p.E401Rfs*86,ENST00000520861,,c.1200dup,HIGH,,,,1;CCAR2,frameshift_variant,p.E418Rfs*86,ENST00000520738,,c.1250dup,HIGH,,,,1;CCAR2,frameshift_variant,p.E189Rfs*84,ENST00000613179,,c.564dup,HIGH,,,,1;BIN3,downstream_gene_variant,,ENST00000276416,NM_018688.6,,MODIFIER,YES,,,-1;BIN3,downstream_gene_variant,,ENST00000399977,NM_001363046.1,,MODIFIER,,,,-1;BIN3,downstream_gene_variant,,ENST00000519513,,,MODIFIER,,,,-1;CCAR2,downstream_gene_variant,,ENST00000522599,,,MODIFIER,,,,1;BIN3,downstream_gene_variant,,ENST00000519335,,,MODIFIER,,,,-1;BIN3,downstream_gene_variant,,ENST00000519863,,,MODIFIER,,,,-1;CCAR2,non_coding_transcript_exon_variant,,ENST00000520536,,n.294dup,MODIFIER,,,,1;CCAR2,non_coding_transcript_exon_variant,,ENST00000521436,,n.359dup,MODIFIER,,,,1;BIN3,downstream_gene_variant,,ENST00000520489,,,MODIFIER,,,,-1;CCAR2,downstream_gene_variant,,ENST00000521020,,,MODIFIER,,,,1;AC037459.2,upstream_gene_variant,,ENST00000521025,,,MODIFIER,YES,,,-1 2423-2424/4853 mutect2;pindel;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 99 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 70 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS CCAR2,non_coding_transcript_exon_variant,,ENST00000520536.1,n.293_294insA,MODIFIER,;CCAR2,non_coding_transcript_exon_variant,,ENST00000521436.5,n.358_359insA,MODIFIER,;CCAR2,frameshift_variant,p.*417Ifs*200,ENST00000520738.5,c.1250dup,HIGH,;CCAR2,frameshift_variant,p.L400Yfs*87,ENST00000520861.5,c.1200dup,HIGH,;CCAR2,frameshift_variant,p.L725Yfs*87,ENST00000389279.7,c.2175dup,HIGH,;CCAR2,frameshift_variant,p.L725Yfs*87,ENST00000308511.9,c.2175dup,HIGH,YES +PSAP 5660 BI GRCh38 10 71829046 71829046 + missense_variant Missense_Mutation SNP T T C rs374177795 TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 78 13 c.407A>G p.Asn136Ser p.N136S ENST00000394936.8 NM_002778.4 136 aAc/aGc 5/14 P3 C N/S protein_coding CCDS7311.1 407/1575 AGAGGTTGAGA Gene3D:1.10.225.10;PDB-ENSP_mappings:2dob.A;PDB-ENSP_mappings:4ddj.A;PDB-ENSP_mappings:4uex.A;PDB-ENSP_mappings:4uex.B;Pfam:PF03489;PIRSF:PIRSF002431;Prints:PR01797;PROSITE_profiles:PS50015;PANTHER:PTHR11480;PANTHER:PTHR11480:SF36;SMART:SM00741;Superfamily:SSF47862 ENSP00000378394 0.000227 0.0 5/14 rs374177795 ENST00000394936 Transcript 1.0 ENSG00000197746 HGNC:9498 MODERATE NM_002778.4 0.000227 AA missense_variant benign(0.006) Unknown tolerated(0.69) P07602.240 PSAP HGNC -1 A0A024QZQ2.44 1.0 UPI0000000DBF P07602-1 SNV PSAP,missense_variant,p.N136S,ENST00000394934,,c.407A>G,MODERATE,YES,tolerated(0.69),benign(0.009),-1;PSAP,missense_variant,p.N136S,ENST00000394936,NM_002778.4&NM_001042466.3&NM_001042465.3,c.407A>G,MODERATE,,tolerated(0.69),benign(0.006),-1;PSAP,intron_variant,,ENST00000610929,,c.270+2185A>G,MODIFIER,,,,-1;PSAP,upstream_gene_variant,,ENST00000633965,,,MODIFIER,,,,-1 437/2748 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 7.958e-06 0.0001233 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0302399207139388e-05 7.306029874598607e-05 0.0 0.0 0.0 0.0 0.0 afr 7.306029874598607e-05 0.0 0.0 0.0 0.0 0 85 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 91 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS PSAP,missense_variant,p.N136S,ENST00000394936.8,c.407A>G,MODERATE,YES +KCNH5 27133 BI GRCh38 14 62802473 62802473 + missense_variant Missense_Mutation SNP G G A rs899330305 TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 42 7 c.1678C>T p.Arg560Cys p.R560C ENST00000322893.12 NM_139318.5 560 Cgc/Tgc 9/11 P1 A R/C protein_coding YES CCDS9756.1 1678/2967 GGCGCGCAGAC COSM5054028;COSM5054029 Gene3D:2.60.120.10;PROSITE_profiles:PS50042;PANTHER:PTHR10217;PANTHER:PTHR10217:SF533;SMART:SM00100;Superfamily:SSF51206;CDD:cd00038 ENSP00000321427 9/11 rs899330305;COSV59760144;COSV99063064 ENST00000322893 Transcript 1.0 ENSG00000140015 HGNC:6254 MODERATE NM_139318.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1;1 Q8NCM2.170 KCNH5 HGNC -1 1.0 UPI0000039E2D Q8NCM2-1 SNV KCNH5,missense_variant,p.R560C,ENST00000322893,NM_139318.5,c.1678C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;KCNH5,missense_variant,p.R560C,ENST00000420622,NM_172375.3,c.1678C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;KCNH5,missense_variant,p.R502C,ENST00000394968,,c.1504C>T,MODERATE,,deleterious(0),probably_damaging(1),-1 1950/11283 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 65 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 49 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS KCNH5,missense_variant,p.R502C,ENST00000394968.2,c.1504C>T,MODERATE,;KCNH5,missense_variant,p.R560C,ENST00000420622.6,c.1678C>T,MODERATE,;KCNH5,missense_variant,p.R560C,ENST00000322893.12,c.1678C>T,MODERATE,YES +RNF167 26001 BI GRCh38 17 4943253 4943253 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 27 7 c.545G>A p.Gly182Glu p.G182E ENST00000262482.11 NM_001375485.1 182 gGa/gAa 7/10 P2 A G/E protein_coding YES CCDS11060.1 545/1053 TGTGGGACTGC PANTHER:PTHR22765;PANTHER:PTHR22765:SF35;Transmembrane_helices:TMhelix ENSP00000262482 7/10 ENST00000262482 Transcript ENSG00000108523 HGNC:24544 MODERATE NM_015528.3 missense_variant probably_damaging(0.917) Unknown deleterious(0) Q9H6Y7.156 RNF167 HGNC 1 2.0 UPI000006DFEF SNV RNF167,missense_variant,p.G182E,ENST00000262482,NM_001375485.1&NM_015528.3&NM_001370307.1&NM_001370313.1&NM_001370304.1&NM_001320361.2&NM_001320357.2,c.545G>A,MODERATE,YES,deleterious(0),probably_damaging(0.917),1;RNF167,missense_variant,p.G182E,ENST00000575111,,c.545G>A,MODERATE,,deleterious(0),probably_damaging(0.917),1;RNF167,missense_variant,p.G182E,ENST00000571816,NM_001370303.1&NM_001320360.2&NM_001370306.1&NM_001320356.2,c.545G>A,MODERATE,,deleterious(0),probably_damaging(0.917),1;RNF167,missense_variant,p.G182E,ENST00000572430,NM_001370305.1&NM_001320359.2&NM_001320358.2,c.545G>A,MODERATE,,deleterious(0),probably_damaging(0.917),1;RNF167,missense_variant,p.G147E,ENST00000576229,NM_001320362.2&NM_001370311.1&NM_001370308.1&NM_001320365.2&NM_001320363.2&NM_001320364.2,c.440G>A,MODERATE,,deleterious(0),probably_damaging(0.917),1;RNF167,missense_variant,p.G71E,ENST00000572382,,c.212G>A,MODERATE,,deleterious(0),probably_damaging(0.948),1;RNF167,intron_variant,,ENST00000576965,,c.91+312G>A,MODIFIER,,,,1;PFN1,downstream_gene_variant,,ENST00000225655,NM_005022.4&NM_001375991.1,,MODIFIER,,,,-1;SLC25A11,upstream_gene_variant,,ENST00000225665,NM_003562.5,,MODIFIER,YES,,,-1;ENO3,upstream_gene_variant,,ENST00000519266,,,MODIFIER,,,,1;ENO3,upstream_gene_variant,,ENST00000520221,,,MODIFIER,,,,1;SLC25A11,upstream_gene_variant,,ENST00000544061,NM_001165418.1,,MODIFIER,,,,-1;RNF167,downstream_gene_variant,,ENST00000570328,,,MODIFIER,,,,1;PFN1,downstream_gene_variant,,ENST00000572383,,,MODIFIER,YES,,,-1;RNF167,downstream_gene_variant,,ENST00000573404,,,MODIFIER,,,,1;PFN1,downstream_gene_variant,,ENST00000574872,,,MODIFIER,,,,-1;RNF167,downstream_gene_variant,,ENST00000576452,,,MODIFIER,,,,1;SLC25A11,upstream_gene_variant,,ENST00000576951,NM_001165417.1,,MODIFIER,,,,-1;RNF167,intron_variant,,ENST00000570492,,n.722+312G>A,MODIFIER,,,,1;RNF167,downstream_gene_variant,,ENST00000571365,,,MODIFIER,,,,1;RNF167,non_coding_transcript_exon_variant,,ENST00000575524,,n.186G>A,MODIFIER,,,,1;RNF167,intron_variant,,ENST00000575400,,c.389+312G>A,MODIFIER,,,,1;SLC25A11,upstream_gene_variant,,ENST00000570543,,,MODIFIER,,,,-1;RNF167,downstream_gene_variant,,ENST00000572554,,,MODIFIER,,,,1;RNF167,upstream_gene_variant,,ENST00000574548,,,MODIFIER,,,,1;SLC25A11,upstream_gene_variant,,ENST00000574710,,,MODIFIER,,,,-1 1061/1775 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 47 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 34 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS RNF167,non_coding_transcript_exon_variant,,ENST00000575524.1,n.186G>A,MODIFIER,;RNF167,intron_variant,,ENST00000576965.1,c.91+312G>A,MODIFIER,;RNF167,missense_variant,p.G71E,ENST00000572382.5,c.212G>A,MODERATE,;RNF167,intron_variant,NMD_transcript_variant,,ENST00000575400.5,c.389+312G>A,MODIFIER,;RNF167,intron_variant,,ENST00000570492.5,n.722+312G>A,MODIFIER,;RNF167,missense_variant,p.G147E,ENST00000576229.5,c.440G>A,MODERATE,;RNF167,missense_variant,p.G182E,ENST00000575111.5,c.545G>A,MODERATE,;RNF167,missense_variant,p.G182E,ENST00000262482.11,c.545G>A,MODERATE,YES;RNF167,missense_variant,p.G182E,ENST00000572430.5,c.545G>A,MODERATE,;RNF167,missense_variant,p.G182E,ENST00000571816.5,c.545G>A,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 25 7 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 61 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 32 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +STK4 6789 BI GRCh38 20 45025112 45025112 + synonymous_variant Silent SNP G G A novel TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 42 7 c.1287G>A p.Gln429= p.Q429= ENST00000372806.8 NM_006282.5 429 caG/caA 10/11 P1 A Q protein_coding YES CCDS13341.1 1287/1464 CCACAGGATGG PANTHER:PTHR24361:SF425;PANTHER:PTHR24361 ENSP00000361892 10/11 ENST00000372806 Transcript 1.0 ENSG00000101109 HGNC:11408 LOW NM_006282.5 synonymous_variant 1.0 Unknown Q13043.209 STK4 HGNC 1 1.0 UPI00001360FF Q13043-1 SNV STK4,synonymous_variant,p.Q429=,ENST00000372806,NM_006282.5,c.1287G>A,LOW,YES,,,1;STK4,synonymous_variant,p.Q374=,ENST00000499879,,c.1122G>A,LOW,,,,1;STK4,synonymous_variant,p.Q429=,ENST00000372801,NM_001352385.2,c.1287G>A,LOW,,,,1 1344/6366 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 6.758310064469697e-06 0.0 0.0 0.0 0.0 0.0 9.41620019148104e-05 0.0 0.0 0.0 0.0 0 58 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 49 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS STK4,non_coding_transcript_exon_variant,,ENST00000698225.1,n.1662G>A,MODIFIER,;STK4,synonymous_variant,p.Q353=,ENST00000474717.3,c.1059G>A,LOW,;STK4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698222.1,c.*1248G>A,MODIFIER,;STK4,synonymous_variant,p.Q374=,ENST00000499879.7,c.1122G>A,LOW,;STK4,synonymous_variant,p.Q429=,ENST00000372801.5,c.1287G>A,LOW,;STK4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698221.1,c.*339G>A,MODIFIER,;STK4,synonymous_variant,p.Q429=,ENST00000372806.8,c.1287G>A,LOW,YES +DRG1 4733 BI GRCh38 22 31420324 31420324 + missense_variant Missense_Mutation SNP A A G TCGA-YZ-A980-01A TCGA-YZ-A980-10A Somatic 46 14 c.481A>G p.Ile161Val p.I161V ENST00000331457.9 NM_004147.4 161 Att/Gtt 5/9 P1 G I/V protein_coding YES CCDS13897.1 481/1104 AGATAATTGAA PROSITE_profiles:PS51710;CDD:cd01896;PANTHER:PTHR43127;PANTHER:PTHR43127:SF1;Pfam:PF01926;TIGRFAM:TIGR00231;Superfamily:SSF52540 ENSP00000329715 5/9 COSV100513780 ENST00000331457 Transcript ENSG00000185721 HGNC:3029 MODERATE NM_004147.4 missense_variant 1 1.0 possibly_damaging(0.644) Unknown deleterious(0) 1 Q9Y295.185 DRG1 HGNC 1 1.0 UPI0000129879 SNV DRG1,missense_variant,p.I161V,ENST00000331457,NM_004147.4,c.481A>G,MODERATE,YES,deleterious(0),possibly_damaging(0.644),1;DRG1,non_coding_transcript_exon_variant,,ENST00000433341,,n.548A>G,MODIFIER,,,,1;DRG1,3_prime_UTR_variant,,ENST00000416465,,c.*113A>G,MODIFIER,,,,1 561/1665 muse;mutect2;varscan2 e00ce846-9a0e-48b5-be9f-84d443a0f78a 0 87 bc4f893e-2ed1-4fc6-91b4-47a9c92c9660 60 87d244a0-3c3b-478d-8f4a-0096ef449857 SUCCESS DRG1,non_coding_transcript_exon_variant,,ENST00000433341.5,n.548A>G,MODIFIER,;DRG1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000416465.5,c.*113A>G,MODIFIER,;DRG1,missense_variant,p.I161V,ENST00000331457.9,c.481A>G,MODERATE,YES +LRRC42 115353 BI GRCh38 1 53960365 53960365 + synonymous_variant Silent SNP G G A novel TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 39 30 c.615G>A p.Gln205= p.Q205= ENST00000319223.8 NM_052940.5 205 caG/caA 4/8 P1 A Q protein_coding CCDS585.1 615/1287 ACTCAGCTCCA PANTHER:PTHR31994;Gene3D:3.80.10.10;Pfam:PF13516;Superfamily:SSF52047 ENSP00000318185 4/8 ENST00000319223 Transcript ENSG00000116212 HGNC:28792 LOW synonymous_variant Unknown Q9Y546.133 LRRC42 HGNC 1 1.0 UPI0000073684 SNV LRRC42,synonymous_variant,p.Q205=,ENST00000371370,NM_001256409.2,c.615G>A,LOW,YES,,,1;LRRC42,synonymous_variant,p.Q205=,ENST00000319223,NM_052940.5,c.615G>A,LOW,,,,1;LRRC42,synonymous_variant,p.Q205=,ENST00000444987,,c.615G>A,LOW,,,,1;LRRC42,downstream_gene_variant,,ENST00000371368,,,MODIFIER,,,,1;LRRC42,upstream_gene_variant,,ENST00000477905,,,MODIFIER,,,,1 826/1727 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 0 72 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 70 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS LRRC42,synonymous_variant,p.Q205=,ENST00000444987.1,c.615G>A,LOW,;LRRC42,synonymous_variant,p.Q205=,ENST00000319223.8,c.615G>A,LOW,;LRRC42,synonymous_variant,p.Q205=,ENST00000371370.8,c.615G>A,LOW,YES;LRRC42,synonymous_variant,p.Q205=,ENST00000713564.1,c.615G>A,LOW, +IVL 3713 BI GRCh38 1 152911420 152911420 + missense_variant Missense_Mutation SNP G G C rs1297610112 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 5 8 c.1623G>C p.Glu541Asp p.E541D ENST00000368764.4 NM_005547.4 541 gaG/gaC 2/2 P1 C E/D protein_coding YES CCDS1030.1 1623/1758 CTGGAGCAGCC Coiled-coils_(Ncoils):Coil;Pfam:PF00904 ENSP00000357753 2/2 rs1297610112 ENST00000368764 Transcript ENSG00000163207 HGNC:6187 MODERATE 0.0001849 gnomAD_AFR missense_variant 1.0 probably_damaging(0.963) Unknown deleterious_low_confidence(0.03) P07476.180 IVL HGNC 1 2.0 UPI000013E24A SNV IVL,missense_variant,p.E541D,ENST00000368764,NM_005547.3,c.1623G>C,MODERATE,YES,deleterious_low_confidence(0.03),probably_damaging(0.963),1 1686/2152 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 1.195e-05 0.0001849 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 36 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 13 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS IVL,missense_variant,p.E541D,ENST00000368764.4,c.1623G>C,MODERATE,YES;ENSG00000289062,intron_variant,,ENST00000702923.1,n.238+1453C>G,MODIFIER,;ENSG00000289062,intron_variant,,ENST00000686895.2,n.94+1621C>G,MODIFIER,YES +GARIN4 149647 BI GRCh38 1 212625400 212625400 + missense_variant Missense_Mutation SNP C C T rs528047581 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 95 67 c.523C>T p.Arg175Trp p.R175W ENST00000294829.5 NM_153606.4 175 Cgg/Tgg 1/1 0.0002 0.0 0.0 0.0 0.0 0.001 P1 T R/W protein_coding YES CCDS1507.1 523/1785 TCTTGCGGCCA Pfam:PF12480;PANTHER:PTHR22574;PANTHER:PTHR22574:SF15 ENSP00000294829 1/1 rs528047581;COSV54236822 ENST00000294829 Transcript ENSG00000162771 HGNC:26541 MODERATE NM_153606.4 0.001 SAS missense_variant 0;1 probably_damaging(0.923) Unknown deleterious(0) 0;1 Q8IYT1.106 FAM71A HGNC 1 UPI000013E1C2 SNV FAM71A,missense_variant,p.R175W,ENST00000294829,NM_153606.4,c.523C>T,MODERATE,YES,deleterious(0),probably_damaging(0.923),1;ATF3,downstream_gene_variant,,ENST00000341491,NM_001674.4,,MODIFIER,YES,,,1;ATF3,downstream_gene_variant,,ENST00000366987,NM_001030287.3,,MODIFIER,,,,1;ATF3,downstream_gene_variant,,ENST00000613954,NM_001206484.3&NM_001206488.3,,MODIFIER,,,,1;ATF3,downstream_gene_variant,,ENST00000492118,,,MODIFIER,,,,1;AL590648.2,non_coding_transcript_exon_variant,,ENST00000427949,,n.1372G>A,MODIFIER,YES,,,-1 927/2302 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 4.774e-05 0.0 2.891e-05 0.0 0.0001631 0.0 0.0 0.0 0.0002613 2.70413001999259e-05 0.0 0.0 0.0 0.0 0.0002017759979935 0.0 nfe 3.085660137003288e-05 0.0 3.085660137003288e-05 0.0 0.0002088549954351 0 165 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 162 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS GARIN4,missense_variant,p.R175W,ENST00000294829.5,c.523C>T,MODERATE,YES;ENSG00000235862,non_coding_transcript_exon_variant,,ENST00000427949.1,n.1372G>A,MODIFIER,YES +OR2L2 26246 BI GRCh38 1 248038474 248038474 + missense_variant Missense_Mutation SNP C C G TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 85 37 c.207C>G p.Asp69Glu p.D69E ENST00000366479.4 69 gaC/gaG 1/1 P1 G D/E protein_coding CCDS31103.1 207/939 ATTGACCTAAA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR26453;PANTHER:PTHR26453:SF645;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15421 ENSP00000355435 1/1 COSV63558123 ENST00000366479 Transcript ENSG00000203663 HGNC:8266 MODERATE missense_variant 1 benign(0.32) Unknown deleterious(0.01) 1 Q8NH16.147 OR2L2 HGNC 1 A0A126GW34.33 UPI0000061EAA SNV OR2L2,missense_variant,p.D69E,ENST00000641771,,c.207C>G,MODERATE,YES,deleterious(0.01),benign(0.32),1;OR2L2,missense_variant,p.D69E,ENST00000642011,,c.207C>G,MODERATE,,deleterious(0.01),benign(0.32),1;OR2L2,missense_variant,p.D69E,ENST00000366479,NM_001004686.2,c.207C>G,MODERATE,,deleterious(0.01),benign(0.32),1 303/1134 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 0 184 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 122 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS OR2L2,missense_variant,p.D69E,ENST00000366479.4,c.207C>G,MODERATE,;OR2L2,missense_variant,p.D69E,ENST00000641771.1,c.207C>G,MODERATE,YES;OR2L2,missense_variant,p.D69E,ENST00000642011.1,c.207C>G,MODERATE, +OBSL1 23363 BI GRCh38 2 219568076 219568076 + missense_variant Missense_Mutation SNP C C T rs371966827 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 57 37 c.1261G>A p.Val421Met p.V421M ENST00000404537.6 NM_015311.3 421 Gtg/Atg 2/21 P1 T V/M protein_coding YES CCDS46520.1 1261/5691 GGCCACGGTGC Gene3D:2.60.40.10;PROSITE_profiles:PS50835;PANTHER:PTHR13817;PANTHER:PTHR13817:SF30;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096 ENSP00000385636 2/21 rs371966827;COSV54722843 ENST00000404537 Transcript 1.0 ENSG00000124006 HGNC:29092 MODERATE NM_015311.3 6.539e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 O75147.164 OBSL1 HGNC -1 1.0 UPI0000E07EA0 O75147-3 SNV OBSL1,missense_variant,p.V421M,ENST00000404537,NM_015311.3,c.1261G>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;OBSL1,missense_variant,p.V421M,ENST00000603926,NM_001173431.2,c.1261G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;OBSL1,missense_variant,p.V421M,ENST00000373876,,c.1261G>A,MODERATE,,deleterious(0),probably_damaging(0.995),-1;OBSL1,missense_variant,p.V421M,ENST00000373873,NM_001173408.2,c.1261G>A,MODERATE,,deleterious(0),probably_damaging(0.984),-1;OBSL1,missense_variant,p.V8M,ENST00000289656,,c.22G>A,MODERATE,,deleterious(0),probably_damaging(0.945),-1;INHA,upstream_gene_variant,,ENST00000243786,NM_002191.4,,MODIFIER,YES,,,1;OBSL1,downstream_gene_variant,,ENST00000465589,,,MODIFIER,,,,-1;INHA,upstream_gene_variant,,ENST00000489456,,,MODIFIER,,,,1;OBSL1,downstream_gene_variant,,ENST00000491370,,,MODIFIER,,,,-1;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,,n.768G>A,MODIFIER,,,,-1;OBSL1,upstream_gene_variant,,ENST00000462385,,,MODIFIER,,,,-1 1568/6105 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 2.427e-05 6.461e-05 0.0 0.0 5.568e-05 0.0 1.801e-05 0.0 6.539e-05 1.3517200386559123e-05 2.4315499103977345e-05 0.0 6.622519867960364e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 107 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 94 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS OBSL1,missense_variant,p.V8M,ENST00000289656.3,c.22G>A,MODERATE,;OBSL1,missense_variant,p.V421M,ENST00000373873.8,c.1261G>A,MODERATE,;OBSL1,missense_variant,p.V421M,ENST00000603926.5,c.1261G>A,MODERATE,;OBSL1,missense_variant,p.V421M,ENST00000373876.5,c.1261G>A,MODERATE,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149.1,n.768G>A,MODIFIER,;OBSL1,missense_variant,p.V421M,ENST00000404537.6,c.1261G>A,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 56 31 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 0 78 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 87 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +OR4E2 26686 BI GRCh38 14 21666008 21666008 + missense_variant Missense_Mutation SNP C C T rs376029887 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 13 5 c.926C>T p.Thr309Met p.T309M ENST00000641524.1 309 aCg/aTg 1/1 P1 T T/M protein_coding CCDS41916.1 926/942 TTTCACGAAAT COSM3401232 ENSP00000386195 1/1 rs376029887;COSV57731883 ENST00000408935 Transcript ENSG00000221977 HGNC:8297 MODERATE 0.0001245 gnomAD_NFE missense_variant 0;1 benign(0.006) Unknown tolerated(0.13) 0;1 Q8NGC2.135 OR4E2 HGNC 1 UPI0000EE498D SNV OR4E2,missense_variant,p.T309M,ENST00000641524,,c.926C>T,MODERATE,YES,tolerated(0.13),benign(0.006),1;OR4E2,missense_variant,p.T309M,ENST00000408935,NM_001001912.2,c.926C>T,MODERATE,,tolerated(0.13),benign(0.006),1;OR4E1,downstream_gene_variant,,ENST00000610316,,,MODIFIER,,,,-1;OR4E1,downstream_gene_variant,,ENST00000641792,NM_001317107.1,,MODIFIER,YES,,,-1 926/942 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 6.046e-05 0.0 0.0 0.0 0.0 0.0 0.0001245 0.0 3.289e-05 4.739459836855531e-05 4.872820136370137e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.177029717946425e-05 0.0 6.177029717946425e-05 0.0 0.0002088549954351 0 25 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 18 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS OR4E2,missense_variant,p.T309M,ENST00000641524.1,c.926C>T,MODERATE,YES +MEAK7 57707 BI GRCh38 16 84486748 84486748 + stop_gained Nonsense_Mutation SNP G G A rs755637814 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 29 16 c.841C>T p.Gln281Ter p.Q281* ENST00000343629.11 NM_020947.4 281 Cag/Tag 5/8 P1 A Q/* protein_coding YES CCDS32498.1 841/1371 GAGCTGGGAGA Pfam:PF07534;PROSITE_profiles:PS51886;PANTHER:PTHR23354;PANTHER:PTHR23354:SF97;SMART:SM00584 ENSP00000343635 5/8 rs755637814;COSV100640392 ENST00000343629 Transcript ENSG00000140950 HGNC:29325 HIGH NM_020947.4 3.267e-05 gnomAD_SAS stop_gained 0;1 1.0 Unknown 0;1 Q6P9B6.125 MEAK7 HGNC -1 1.0 UPI00001BBB2E SNV MEAK7,stop_gained,p.Q281*,ENST00000343629,NM_020947.4,c.841C>T,HIGH,YES,,,-1;MEAK7,downstream_gene_variant,,ENST00000565079,,,MODIFIER,,,,-1;MEAK7,downstream_gene_variant,,ENST00000561807,,,MODIFIER,,,,-1;MEAK7,3_prime_UTR_variant,,ENST00000566995,,c.*255C>T,MODIFIER,,,,-1;MEAK7,3_prime_UTR_variant,,ENST00000570036,,c.*896C>T,MODIFIER,,,,-1;MEAK7,non_coding_transcript_exon_variant,,ENST00000567321,,n.1689C>T,MODIFIER,,,,-1 925/5013 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 7.967e-06 0.0 0.0 0.0 0.0 0.0 8.817e-06 0.0 3.267e-05 0 49 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 45 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS MEAK7,non_coding_transcript_exon_variant,,ENST00000567321.1,n.1689C>T,MODIFIER,;MEAK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000570036.5,c.*896C>T,MODIFIER,;MEAK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000566995.5,c.*255C>T,MODIFIER,;MEAK7,stop_gained,p.Q281*,ENST00000343629.11,c.841C>T,HIGH,YES +MINK1 50488 BI GRCh38 17 4895104 4895104 + missense_variant Missense_Mutation SNP G G A rs755386461 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 83 55 c.2947G>A p.Asp983Asn p.D983N ENST00000355280.11 NM_001321236.2 983 Gac/Aac 25/32 P3 A D/N protein_coding YES CCDS45588.1 2947/3999 GGCTCGACCAG PANTHER:PTHR24361;PANTHER:PTHR24361:SF225 ENSP00000347427 25/32 rs755386461 ENST00000355280 Transcript ENSG00000141503 HGNC:17565 MODERATE NM_153827.5 0.0001961 gnomAD_SAS missense_variant 1.0 benign(0.015) Unknown deleterious(0.02) Q8N4C8.181 MINK1 HGNC 1 1.0 UPI00001678BB SNV MINK1,missense_variant,p.D983N,ENST00000355280,NM_001321236.2&NM_153827.5&NM_015716.5,c.2947G>A,MODERATE,YES,deleterious(0.02),benign(0.015),1;MINK1,missense_variant,p.D954N,ENST00000347992,NM_170663.5,c.2860G>A,MODERATE,,deleterious(0.02),benign(0.034),1;MINK1,missense_variant,p.D963N,ENST00000453408,NM_001024937.4,c.2887G>A,MODERATE,,deleterious(0.02),benign(0.034),1;C17orf107,upstream_gene_variant,,ENST00000381365,NM_001145536.2,,MODIFIER,YES,,,1;C17orf107,upstream_gene_variant,,ENST00000521575,,,MODIFIER,,,,1;MINK1,upstream_gene_variant,,ENST00000576037,,,MODIFIER,,,,1;CHRNE,downstream_gene_variant,,ENST00000649488,NM_000080.4,,MODIFIER,YES,,,-1;CHRNE,downstream_gene_variant,,ENST00000649830,,,MODIFIER,,,,-1;MINK1,downstream_gene_variant,,ENST00000664602,,,MODIFIER,,,,1;MINK1,3_prime_UTR_variant,,ENST00000574453,,c.*2616G>A,MODIFIER,,,,1;MINK1,3_prime_UTR_variant,,ENST00000571207,,c.*1598G>A,MODIFIER,,,,1;MINK1,non_coding_transcript_exon_variant,,ENST00000572330,,n.3729G>A,MODIFIER,,,,1;MINK1,non_coding_transcript_exon_variant,,ENST00000574871,,n.561G>A,MODIFIER,,,,1;MINK1,non_coding_transcript_exon_variant,,ENST00000575511,,n.247G>A,MODIFIER,,,,1;MINK1,downstream_gene_variant,,ENST00000571526,,,MODIFIER,,,,1;MINK1,downstream_gene_variant,,ENST00000572304,,,MODIFIER,,,,1;CHRNE,downstream_gene_variant,,ENST00000572438,,,MODIFIER,,,,-1;MINK1,downstream_gene_variant,,ENST00000572629,,,MODIFIER,,,,1;CHRNE,downstream_gene_variant,,ENST00000652550,,,MODIFIER,,,,-1 3191/5017 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 3.613e-05 0.0001294 2.9e-05 0.0 0.0 0.0 0.0 0.0 0.0001961 0 178 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 139 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS MINK1,non_coding_transcript_exon_variant,,ENST00000575511.1,n.247G>A,MODIFIER,;MINK1,non_coding_transcript_exon_variant,,ENST00000574871.1,n.561G>A,MODIFIER,;MINK1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000571207.5,c.*1598G>A,MODIFIER,;MINK1,missense_variant,p.D963N,ENST00000453408.7,c.2887G>A,MODERATE,;MINK1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000574453.5,c.*2616G>A,MODIFIER,;MINK1,missense_variant,p.D954N,ENST00000347992.11,c.2860G>A,MODERATE,;MINK1,non_coding_transcript_exon_variant,,ENST00000572330.5,n.3729G>A,MODIFIER,;MINK1,missense_variant,p.D983N,ENST00000355280.11,c.2947G>A,MODERATE,YES +MYO15A 51168 BI GRCh38 17 18143881 18143881 + missense_variant Missense_Mutation SNP G G T rs1173298214 TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 3 12 c.6058G>T p.Ala2020Ser p.A2020S ENST00000647165.2 NM_016239.4 2020 Gcc/Tcc 28/66 A2 T A/S protein_coding YES 6058/10593 GGCTGGCCCAG PANTHER:PTHR22692;PANTHER:PTHR22692:SF21;Low_complexity_(Seg):seg ENSP00000481642 27/65 rs1173298214 ENST00000615845 Transcript 1.0 ENSG00000091536 HGNC:7594 MODERATE 1.151e-05 gnomAD_NFE missense_variant 1.0 benign(0) Unknown tolerated(0.54) MYO15A HGNC 1 A0A087WYA1.41 5.0 UPI0004E4C894 SNV MYO15A,missense_variant,p.A2020S,ENST00000615845,,c.6058G>T,MODERATE,YES,tolerated(0.54),benign(0),1;MYO15A,missense_variant,p.A2020S,ENST00000647165,NM_016239.4,c.6058G>T,MODERATE,,tolerated(0.55),benign(0),1;MYO15A,downstream_gene_variant,,ENST00000412324,,,MODIFIER,,,,1;MYO15A,downstream_gene_variant,,ENST00000646238,,,MODIFIER,,,,1;MYO15A,upstream_gene_variant,,ENST00000578999,,,MODIFIER,,,,1 6396/11860 muse;mutect2;varscan2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 4.949e-06 0.0 0.0 0.0 0.0 0.0 1.151e-05 0.0 0.0 0 17 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 15 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS MYO15A,missense_variant,p.A2020S,ENST00000647165.2,c.6058G>T,MODERATE,YES +PPIL2 23759 BI GRCh38 22 21684812 21684812 + synonymous_variant Silent SNP C C A TCGA-VD-A8KN-01A TCGA-VD-A8KN-10B Somatic 44 3 c.613C>A p.Arg205= p.R205= ENST00000335025.12 NM_148175.3 205 Cga/Aga 10/21 P1 A R protein_coding CCDS13793.1 613/1563 AGACCCGAGAG PANTHER:PTHR45625;PANTHER:PTHR45625:SF1 ENSP00000334553 10/21 COSV58605579 ENST00000335025 Transcript ENSG00000100023 HGNC:9261 LOW synonymous_variant 1 Unknown 1 Q13356.182 PPIL2 HGNC 1 A0A024R1C1.53 1.0 UPI0000128C6F Q13356-1 SNV PPIL2,synonymous_variant,p.R205=,ENST00000335025,NM_148175.3,c.613C>A,LOW,,,,1;PPIL2,synonymous_variant,p.R205=,ENST00000398831,NM_001317996.1&NM_014337.4,c.613C>A,LOW,,,,1;PPIL2,synonymous_variant,p.R205=,ENST00000406385,,c.613C>A,LOW,,,,1;PPIL2,synonymous_variant,p.R205=,ENST00000626352,NM_148176.2,c.613C>A,LOW,YES,,,1;PPIL2,downstream_gene_variant,,ENST00000458567,,,MODIFIER,,,,1;PPIL2,non_coding_transcript_exon_variant,,ENST00000484439,,n.797C>A,MODIFIER,,,,1;PPIL2,upstream_gene_variant,,ENST00000446951,,,MODIFIER,,,,1;PPIL2,3_prime_UTR_variant,,ENST00000417788,,c.*549C>A,MODIFIER,,,,1 704/4929 muse;mutect2 b26cb5f2-4ff0-4476-8d02-7256ace7d8a3 0 60 2c1e4c96-7664-41e3-9297-ccfaaf48eb34 48 c41572b9-6b12-4df8-848d-e6fe843f4ccd SUCCESS PPIL2,non_coding_transcript_exon_variant,,ENST00000680183.1,n.757C>A,MODIFIER,;PPIL2,synonymous_variant,p.R27=,ENST00000680860.1,c.79C>A,LOW,;PPIL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681137.1,c.*255C>A,MODIFIER,;PPIL2,non_coding_transcript_exon_variant,,ENST00000680022.1,n.666C>A,MODIFIER,;PPIL2,synonymous_variant,p.R205=,ENST00000406385.1,c.613C>A,LOW,;PPIL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680434.1,c.*723C>A,MODIFIER,;PPIL2,synonymous_variant,p.R184=,ENST00000680109.1,c.550C>A,LOW,;PPIL2,non_coding_transcript_exon_variant,,ENST00000484439.5,n.797C>A,MODIFIER,;PPIL2,synonymous_variant,p.R205=,ENST00000680094.1,c.613C>A,LOW,;PPIL2,synonymous_variant,NMD_transcript_variant,p.R205=,ENST00000679692.1,c.613C>A,LOW,;PPIL2,non_coding_transcript_exon_variant,,ENST00000679586.1,n.688C>A,MODIFIER,;PPIL2,synonymous_variant,NMD_transcript_variant,p.R205=,ENST00000681791.1,c.613C>A,LOW,;PPIL2,synonymous_variant,NMD_transcript_variant,p.R205=,ENST00000680962.1,c.613C>A,LOW,;PPIL2,non_coding_transcript_exon_variant,,ENST00000679857.1,n.688C>A,MODIFIER,;PPIL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000417788.5,c.*549C>A,MODIFIER,;PPIL2,synonymous_variant,p.R205=,ENST00000626352.2,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000679477.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000398831.8,c.613C>A,LOW,YES;PPIL2,synonymous_variant,NMD_transcript_variant,p.R205=,ENST00000681394.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000335025.12,c.613C>A,LOW,;PPIL2,non_coding_transcript_exon_variant,,ENST00000498109.2,n.1692C>A,MODIFIER,;PPIL2,non_coding_transcript_exon_variant,,ENST00000496819.2,n.1307C>A,MODIFIER,;PPIL2,non_coding_transcript_exon_variant,,ENST00000680426.1,n.1096C>A,MODIFIER,;PPIL2,synonymous_variant,p.R205=,ENST00000681956.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000680393.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000679534.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000679540.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000679827.1,c.613C>A,LOW,;PPIL2,non_coding_transcript_exon_variant,,ENST00000680463.1,n.713C>A,MODIFIER,;PPIL2,non_coding_transcript_exon_variant,,ENST00000681286.1,n.713C>A,MODIFIER,;PPIL2,non_coding_transcript_exon_variant,,ENST00000679479.1,n.713C>A,MODIFIER,;PPIL2,synonymous_variant,NMD_transcript_variant,p.R205=,ENST00000679580.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000681338.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000680061.1,c.613C>A,LOW,;PPIL2,synonymous_variant,p.R205=,ENST00000679795.1,c.613C>A,LOW, +MACF1 23499 BI GRCh38 1 39387411 39387411 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 59 48 c.14584G>A p.Gly4862Arg p.G4862R ENST00000372915.8 4862 Ggg/Agg 57/96 A2 A G/R protein_coding 14584/22158 CTGAAGGGGAA Gene3D:1.20.58.60;Pfam:PF00435;PANTHER:PTHR23169;PANTHER:PTHR23169:SF24;SMART:SM00150;Superfamily:SSF46966;Superfamily:SSF46966;CDD:cd00176 ENSP00000362006 57/96 ENST00000372915 Transcript 1.0 ENSG00000127603 HGNC:13664 MODERATE missense_variant Unknown Q9UPN3.196 MACF1 HGNC 1 5.0 Q9UPN3-1 SNV MACF1,missense_variant,p.G4857R,ENST00000564288,,c.14569G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;MACF1,missense_variant,p.G4894R,ENST00000567887,,c.14680G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;MACF1,missense_variant,p.G4862R,ENST00000372915,,c.14584G>A,MODERATE,,,,1;MACF1,missense_variant,p.G2795R,ENST00000361689,NM_012090.5,c.8383G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;MACF1,missense_variant,p.G2744R,ENST00000671089,,c.8230G>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;MACF1,missense_variant,p.G1908R,ENST00000372925,,c.5722G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;MACF1,missense_variant,p.G76R,ENST00000673980,,c.226G>A,MODERATE,,deleterious(0),probably_damaging(1),1;MACF1,non_coding_transcript_exon_variant,,ENST00000289893,,n.10020G>A,MODIFIER,,,,1 14671/23431 muse;mutect2;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 0 141 323ac618-cea2-416e-a584-77e83fbd6e72 107 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS MACF1,synonymous_variant,NMD_transcript_variant,p.K75=,ENST00000673980.1,c.225G>A,LOW,;MACF1,non_coding_transcript_exon_variant,,ENST00000686067.1,n.569G>A,MODIFIER,;MACF1,non_coding_transcript_exon_variant,,ENST00000687997.1,n.569G>A,MODIFIER,;MACF1,non_coding_transcript_exon_variant,,ENST00000289893.8,n.10020G>A,MODIFIER,;MACF1,missense_variant,p.R1907K,ENST00000372925.6,c.5720G>A,MODERATE,;MACF1,missense_variant,p.G2744R,ENST00000671089.2,c.8230G>A,MODERATE,;MACF1,missense_variant,p.G4857R,ENST00000564288.6,c.14569G>A,MODERATE,YES;MACF1,missense_variant,p.G4862R,ENST00000372915.8,c.14584G>A,MODERATE,;MACF1,missense_variant,p.G4894R,ENST00000567887.5,c.14680G>A,MODERATE,;MACF1,missense_variant,p.G2795R,ENST00000361689.7,c.8383G>A,MODERATE, +COA7 65260 BI GRCh38 1 52687998 52687998 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 47 27 c.418del p.Arg140GlyfsTer37 p.R140Gfs*37 ENST00000371538.5 NM_023077.3 140 Agg/gg 3/3 P1 - R/X protein_coding YES CCDS570.1 418/696 AGGCCCTTGTGT Gene3D:1.25.40.10;Pfam:PF08238;PANTHER:PTHR13891;SMART:SM00671;Superfamily:SSF81901 ENSP00000360593 3/3 ENST00000371538 Transcript 1.0 ENSG00000162377 HGNC:25716 HIGH NM_023077.3 frameshift_variant 1.0 Unknown Q96BR5.132 COA7 HGNC -1 1.0 UPI0000034E0F deletion COA7,frameshift_variant,p.R140Gfs*37,ENST00000371538,NM_023077.3,c.418del,HIGH,YES,,,-1;COA7,non_coding_transcript_exon_variant,,ENST00000486918,,n.472del,MODIFIER,,,,-1 439/3988 mutect2;pindel;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 0 73 323ac618-cea2-416e-a584-77e83fbd6e72 74 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS COA7,non_coding_transcript_exon_variant,,ENST00000486918.1,n.472del,MODIFIER,;COA7,frameshift_variant,p.R140Gfs*37,ENST00000371538.5,c.418del,HIGH,YES +ITPR1 3708 BI GRCh38 3 4683725 4683725 + stop_gained Nonsense_Mutation SNP G G A TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 12 16 c.3398G>A p.Trp1133Ter p.W1133* ENST00000354582.12 1133 tGg/tAg 28/62 A1 A W/* protein_coding 3398/8253 GCTTTGGGTGT PANTHER:PTHR45816;PANTHER:PTHR45816:SF2;Superfamily:SSF100909 ENSP00000346595 28/62 COSV56970516 ENST00000354582 Transcript 1.0 ENSG00000150995 HGNC:6180 HIGH stop_gained 1 Unknown 1 ITPR1 HGNC 1 A0A3F2YNW8.10 5.0 UPI0005D007F7 SNV ITPR1,stop_gained,p.W1127*,ENST00000302640,NM_001168272.2,c.3380G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1142*,ENST00000649015,NM_001378452.1,c.3425G>A,HIGH,YES,,,1;ITPR1,stop_gained,p.W1133*,ENST00000354582,,c.3398G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1133*,ENST00000357086,NM_001099952.4,c.3398G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1133*,ENST00000648266,,c.3398G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1118*,ENST00000456211,NM_002222.7,c.3353G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1127*,ENST00000443694,,c.3380G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1127*,ENST00000650294,,c.3380G>A,HIGH,,,,1;ITPR1,stop_gained,p.W1118*,ENST00000648309,,c.3353G>A,HIGH,,,,1;ITPR1,stop_gained,p.W412*,ENST00000648038,,c.1235G>A,HIGH,,,,1;ITPR1,stop_gained,p.W243*,ENST00000648431,,c.728G>A,HIGH,,,,1;ITPR1,stop_gained,p.W112*,ENST00000648212,,c.335G>A,HIGH,,,,1;ITPR1,intron_variant,,ENST00000544951,,c.996+29839G>A,MODIFIER,,,,1;ITPR1,upstream_gene_variant,,ENST00000648016,,,MODIFIER,,,,1;ITPR1,non_coding_transcript_exon_variant,,ENST00000647717,,n.926G>A,MODIFIER,,,,1;ITPR1,non_coding_transcript_exon_variant,,ENST00000647624,,n.137G>A,MODIFIER,,,,1 3726/9853 muse;mutect2;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 0 33 323ac618-cea2-416e-a584-77e83fbd6e72 28 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS ITPR1,non_coding_transcript_exon_variant,,ENST00000647624.1,n.137G>A,MODIFIER,;ITPR1,synonymous_variant,p.L111=,ENST00000648212.1,c.333G>A,LOW,;ITPR1,missense_variant,p.G243R,ENST00000648431.1,c.727G>A,MODERATE,;ITPR1,non_coding_transcript_exon_variant,,ENST00000647717.1,n.926G>A,MODIFIER,;ITPR1,stop_gained,p.W412*,ENST00000648038.1,c.1235G>A,HIGH,;ITPR1,stop_gained,NMD_transcript_variant,p.W1133*,ENST00000302640.13,c.3398G>A,HIGH,;ITPR1,stop_gained,p.W1118*,ENST00000648309.1,c.3353G>A,HIGH,;ITPR1,stop_gained,p.W1127*,ENST00000650294.1,c.3380G>A,HIGH,;ITPR1,intron_variant,,ENST00000544951.6,c.996+29839G>A,MODIFIER,;ITPR1,stop_gained,p.W1133*,ENST00000648266.1,c.3398G>A,HIGH,;ITPR1,stop_gained,p.W1127*,ENST00000443694.5,c.3380G>A,HIGH,;ITPR1,stop_gained,p.W1118*,ENST00000456211.8,c.3353G>A,HIGH,;ITPR1,stop_gained,p.W1142*,ENST00000649015.2,c.3425G>A,HIGH,YES;ITPR1,stop_gained,p.W1133*,ENST00000354582.12,c.3398G>A,HIGH,;ITPR1,stop_gained,p.W1133*,ENST00000357086.10,c.3398G>A,HIGH, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 29 51 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 0 67 323ac618-cea2-416e-a584-77e83fbd6e72 80 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +KCNK13 56659 BI GRCh38 14 90184798 90184798 + missense_variant Missense_Mutation SNP G G A rs538269862 TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 28 13 c.1022G>A p.Arg341Gln p.R341Q ENST00000282146.5 NM_022054.4 341 cGg/cAg 2/2 P1 A R/Q protein_coding YES CCDS9889.1 1022/1227 GCGCCGGCTCT PANTHER:PTHR11003:SF57;PANTHER:PTHR11003 ENSP00000282146 2/2 rs538269862 ENST00000282146 Transcript ENSG00000152315 HGNC:6275 MODERATE NM_022054.4 0.0004248 gnomAD_SAS missense_variant 1.0 probably_damaging(0.957) Unknown deleterious(0) Q9HB14.158 KCNK13 HGNC 1 1.0 UPI0000127A55 SNV KCNK13,missense_variant,p.R341Q,ENST00000282146,NM_022054.4,c.1022G>A,MODERATE,YES,deleterious(0),probably_damaging(0.957),1 1234/2289 muse;mutect2;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 6.383e-05 0.0 0.0 0.0 5.441e-05 4.621e-05 0.0 0.0001635 0.0004248 3.379469853825867e-05 2.4308399588335305e-05 0.0 0.0 0.0 0.0 0.0 sas 0.0004164930141996 0.0 3.085850039497018e-05 0.0 0.0004164930141996 0 62 323ac618-cea2-416e-a584-77e83fbd6e72 41 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS KCNK13,missense_variant,p.R341Q,ENST00000282146.5,c.1022G>A,MODERATE,YES +SERPINA9 327657 BI GRCh38 14 94469614 94469614 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8S-01B TCGA-VD-AA8S-10A Somatic 25 22 c.227C>T p.Ser76Phe p.S76F ENST00000380365.7 76 tCc/tTc 2/5 A2 A S/F protein_coding 227/1254 AAGTGGAGACA Gene3D:3.30.497.10;Pfam:PF00079;PANTHER:PTHR11461;PANTHER:PTHR11461:SF40;SMART:SM00093;Superfamily:SSF56574;CDD:cd02056 ENSP00000369723 2/5 ENST00000380365 Transcript ENSG00000170054 HGNC:15995 MODERATE missense_variant probably_damaging(0.999) Unknown deleterious(0) Q86WD7.137 SERPINA9 HGNC -1 5.0 UPI000003B052 Q86WD7-1 SNV SERPINA9,missense_variant,p.S94F,ENST00000337425,,c.281C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;SERPINA9,missense_variant,p.S76F,ENST00000674397,NM_175739.4,c.227C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;SERPINA9,missense_variant,p.S76F,ENST00000380365,,c.227C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;SERPINA9,5_prime_UTR_variant,,ENST00000448305,NM_001284275.2,c.-14C>T,MODIFIER,,,,-1;SERPINA9,5_prime_UTR_variant,,ENST00000546329,,c.-14C>T,MODIFIER,,,,-1;SERPINA9,intron_variant,,ENST00000298845,NM_001042518.2,c.216+11C>T,MODIFIER,,,,-1;SERPINA9,intron_variant,,ENST00000424550,NM_001284276.2,c.-19-148C>T,MODIFIER,,,,-1;SERPINA9,intron_variant,,ENST00000674164,,c.270+11C>T,MODIFIER,,,,-1;SERPINA9,downstream_gene_variant,,ENST00000539349,,,MODIFIER,,,,-1;SERPINA9,synonymous_variant,p.L121=,ENST00000538527,,c.363C>T,LOW,,,,-1;AL132708.1,downstream_gene_variant,,ENST00000536735,,,MODIFIER,YES,,,1 306/1333 muse;mutect2;varscan2 9752c320-79eb-49ea-aa1f-d7a79bead901 0 44 323ac618-cea2-416e-a584-77e83fbd6e72 47 de8fc4d3-b57e-41c7-a930-b4eaabee604d SUCCESS SERPINA9,synonymous_variant,NMD_transcript_variant,p.L121=,ENST00000538527.5,c.363C>T,LOW,;SERPINA9,5_prime_UTR_variant,,ENST00000546329.2,c.-14C>T,MODIFIER,;SERPINA9,missense_variant,p.S76F,ENST00000380365.7,c.227C>T,MODERATE,;SERPINA9,missense_variant,p.S94F,ENST00000337425.10,c.281C>T,MODERATE,;SERPINA9,intron_variant,,ENST00000674164.1,c.270+11C>T,MODIFIER,;SERPINA9,missense_variant,p.S76F,ENST00000674397.2,c.227C>T,MODERATE,YES;SERPINA9,5_prime_UTR_variant,,ENST00000448305.6,c.-14C>T,MODIFIER,;SERPINA9,intron_variant,,ENST00000298845.12,c.216+11C>T,MODIFIER,;SERPINA9,intron_variant,,ENST00000424550.6,c.-19-148C>T,MODIFIER, +DR1 1810 BI GRCh38 1 93346665 93346665 + missense_variant Missense_Mutation SNP A A G novel TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 58 60 c.20A>G p.Asn7Ser p.N7S ENST00000370267.1 7 aAc/aGc 2/4 P1 G N/S protein_coding CCDS744.1 20/531 TGGCAACGATG PDB-ENSP_mappings:1jfi.B;PANTHER:PTHR46138;Gene3D:1.10.20.10 ENSP00000359290 2/4 ENST00000370267 Transcript ENSG00000117505 HGNC:3017 MODERATE missense_variant benign(0.06) Unknown tolerated(0.42) Q01658.187 DR1 HGNC 1 Q658N3.140 2.0 UPI0000136997 SNV DR1,missense_variant,p.N7S,ENST00000370272,NM_001938.3,c.20A>G,MODERATE,YES,tolerated(0.42),benign(0.06),1;DR1,missense_variant,p.N7S,ENST00000370267,,c.20A>G,MODERATE,,tolerated(0.42),benign(0.06),1;CCDC18-AS1,upstream_gene_variant,,ENST00000411670,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000413606,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000421202,,,MODIFIER,YES,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000438777,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000445076,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000449305,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000451302,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000452347,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000457387,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000653362,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000655606,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000657560,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000659026,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000661111,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000668257,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000669506,,,MODIFIER,,,,-1;CCDC18-AS1,upstream_gene_variant,,ENST00000670231,,,MODIFIER,,,,-1 607/1647 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 108 9e6d04ed-96fe-4e02-adfd-bf0b54676009 118 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS DR1,missense_variant,p.N7S,ENST00000370267.1,c.20A>G,MODERATE,;DR1,missense_variant,p.N7S,ENST00000370272.9,c.20A>G,MODERATE,YES +ZSCAN16 80345 BI GRCh38 6 28129562 28129562 + missense_variant Missense_Mutation SNP T T C rs773429225 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 41 57 c.659T>C p.Ile220Thr p.I220T ENST00000340487.5 NM_001320555.2 220 aTt/aCt 4/4 P1 C I/T protein_coding YES CCDS4644.1 659/1047 TATTATTGAAA PANTHER:PTHR23226;PANTHER:PTHR23226:SF52 ENSP00000366527 4/4 rs773429225 ENST00000340487 Transcript ENSG00000196812 HGNC:20813 MODERATE NM_025231.3 6.534e-05 gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated(0.27) Q9H4T2.166 ZSCAN16 HGNC 1 1.0 UPI000013A46E SNV ZSCAN16,missense_variant,p.I220T,ENST00000340487,NM_001320558.1&NM_001320555.2&NM_001320557.2&NM_025231.3&NM_001320556.2,c.659T>C,MODERATE,YES,tolerated(0.27),benign(0),1;ZSCAN16-AS1,intron_variant,,ENST00000600652,,n.550-3743A>G,MODIFIER,,,,-1;ZSCAN16-AS1,intron_variant,,ENST00000602810,,n.123-6351A>G,MODIFIER,,,,-1;ZSCAN16-AS1,intron_variant,,ENST00000660873,,n.77+7183A>G,MODIFIER,,,,-1;ZSCAN16-AS1,intron_variant,,ENST00000667674,,n.104-6351A>G,MODIFIER,YES,,,-1 759/1279 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 7.961e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.534e-05 0 41 9e6d04ed-96fe-4e02-adfd-bf0b54676009 98 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS ZSCAN16,missense_variant,p.I220T,ENST00000340487.5,c.659T>C,MODERATE,YES;ZSCAN16-AS1,intron_variant,,ENST00000602810.2,n.570-6351A>G,MODIFIER,;ZSCAN16-AS1,intron_variant,,ENST00000600652.1,n.550-3743A>G,MODIFIER,;ZSCAN16-AS1,intron_variant,,ENST00000667674.1,n.104-6351A>G,MODIFIER,;ZSCAN16,missense_variant,p.I220T,ENST00000685330.1,c.659T>C,MODERATE,;ZSCAN16-AS1,intron_variant,,ENST00000660873.1,n.77+7183A>G,MODIFIER,YES +GAL3ST4 79690 BI GRCh38 7 100160808 100160808 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 61 30 c.581G>A p.Gly194Asp p.G194D ENST00000360039.9 NM_024637.5 194 gGc/gAc 4/4 P1 T G/D protein_coding YES CCDS5688.1 581/1461 AGAAGCCTCGA Pfam:PF06990;PANTHER:PTHR14647;PANTHER:PTHR14647:SF78;Superfamily:SSF52540 ENSP00000353142 4/4 ENST00000360039 Transcript ENSG00000197093 HGNC:24145 MODERATE NM_024637.5 missense_variant 1.0 benign(0.055) Unknown tolerated(0.19) Q96RP7.141 GAL3ST4 HGNC -1 1.0 UPI0000070C68 Q96RP7-1 SNV GAL3ST4,missense_variant,p.G194D,ENST00000360039,NM_024637.5,c.581G>A,MODERATE,YES,tolerated(0.19),benign(0.055),-1;GAL3ST4,missense_variant,p.G194D,ENST00000413800,,c.581G>A,MODERATE,,tolerated(0.19),benign(0.055),-1;GAL3ST4,missense_variant,p.A93T,ENST00000423751,,c.277G>A,MODERATE,,,unknown(0),-1;GAL3ST4,missense_variant,p.A93T,ENST00000411994,,c.277G>A,MODERATE,,,unknown(0),-1;GAL3ST4,missense_variant,p.A93T,ENST00000498000,,c.277G>A,MODERATE,,,unknown(0),-1;MAP11,upstream_gene_variant,,ENST00000316937,NM_018275.5,,MODIFIER,YES,,,-1;MAP11,upstream_gene_variant,,ENST00000456769,NM_001303470.2,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000457641,,,MODIFIER,,,,-1;LAMTOR4,downstream_gene_variant,,ENST00000490633,,,MODIFIER,,,,1;MIR4658,upstream_gene_variant,,ENST00000584344,,,MODIFIER,YES,,,-1;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000495882,,n.1598G>A,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000394035,,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000419037,,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000419841,,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000448720,,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000472061,,,MODIFIER,,,,-1;MAP11,upstream_gene_variant,,ENST00000498638,,,MODIFIER,,,,-1 841/2405 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 52 9e6d04ed-96fe-4e02-adfd-bf0b54676009 91 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS GAL3ST4,missense_variant,p.A93T,ENST00000498000.5,c.277G>A,MODERATE,;GAL3ST4,missense_variant,p.A93T,ENST00000411994.1,c.277G>A,MODERATE,;GAL3ST4,missense_variant,p.A93T,ENST00000423751.2,c.277G>A,MODERATE,;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000495882.1,n.1598G>A,MODIFIER,;GAL3ST4,missense_variant,p.G194D,ENST00000413800.5,c.581G>A,MODERATE,;GAL3ST4,missense_variant,p.G194D,ENST00000360039.9,c.581G>A,MODERATE,YES +SVEP1 79987 BI GRCh38 9 110503130 110503130 + missense_variant Missense_Mutation SNP A A G novel TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 49 43 c.1391T>C p.Val464Ala p.V464A ENST00000374469.6 NM_153366.4 464 gTt/gCt 6/48 P4 G V/A protein_coding CCDS48004.1 1391/10716 AGGCAACCAAA Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR19325;PANTHER:PTHR19325:SF43;SMART:SM00032;Superfamily:SSF57535;CDD:cd00033 ENSP00000363593 6/48 ENST00000374469 Transcript ENSG00000165124 HGNC:15985 MODERATE NM_153366.4 missense_variant benign(0.029) Unknown tolerated(0.18) Q4LDE5.143 SVEP1 HGNC -1 5.0 UPI000153DA74 Q4LDE5-1 SNV SVEP1,missense_variant,p.V464A,ENST00000401783,,c.1391T>C,MODERATE,YES,tolerated(0.18),benign(0.003),-1;SVEP1,missense_variant,p.V464A,ENST00000374469,NM_153366.4,c.1391T>C,MODERATE,,tolerated(0.18),benign(0.029),-1;SVEP1,missense_variant,p.V464A,ENST00000374461,,c.1391T>C,MODERATE,,tolerated(0.18),benign(0.069),-1;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,,n.810T>C,MODIFIER,,,,-1 1589/12205 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 59 9e6d04ed-96fe-4e02-adfd-bf0b54676009 92 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS SVEP1,missense_variant,p.V464A,ENST00000374461.1,c.1391T>C,MODERATE,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821.1,n.810T>C,MODIFIER,;SVEP1,missense_variant,p.V464A,ENST00000374469.6,c.1391T>C,MODERATE,YES +PRDM11 56981 BI GRCh38 11 45182963 45182963 + missense_variant Missense_Mutation SNP C C G TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 33 29 c.326C>G p.Ala109Gly p.A109G ENST00000530656.5 NM_001359633.2 109 gCg/gGg 4/7 G A/G protein_coding CCDS7912.1 428/1536 CCGGGCGGCGC PDB-ENSP_mappings:3ray.A;PANTHER:PTHR16515:SF11;PANTHER:PTHR16515;Gene3D:2.170.270.10 ENSP00000435976 4/7 COSV55440423 ENST00000530656 Transcript ENSG00000019485 HGNC:13996 MODERATE missense_variant 1 probably_damaging(0.975) Unknown deleterious(0) 1 Q9NQV5.131 PRDM11 HGNC 1 2.0 UPI000013D45B Q9NQV5-1 SNV PRDM11,missense_variant,p.A109G,ENST00000622142,NM_001256695.1,c.326C>G,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.991),1;PRDM11,missense_variant,p.A73G,ENST00000534751,,c.218C>G,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.933),1;PRDM11,missense_variant,p.A109G,ENST00000424263,NM_001256696.1,c.326C>G,MODERATE,,deleterious(0),probably_damaging(0.975),1;PRDM11,missense_variant,p.A143G,ENST00000530656,NM_001359633.1,c.428C>G,MODERATE,,deleterious(0),probably_damaging(0.975),1;PRDM11,missense_variant,p.A109G,ENST00000526442,,c.326C>G,MODERATE,,deleterious(0.01),probably_damaging(0.975),1;PRDM11,non_coding_transcript_exon_variant,,ENST00000528980,,n.47C>G,MODIFIER,,,,1 428/1536 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 30 9e6d04ed-96fe-4e02-adfd-bf0b54676009 62 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS PRDM11,non_coding_transcript_exon_variant,,ENST00000528980.1,n.47C>G,MODIFIER,;PRDM11,missense_variant,p.A109G,ENST00000622142.5,c.326C>G,MODERATE,;PRDM11,missense_variant,p.A109G,ENST00000424263.6,c.326C>G,MODERATE,;PRDM11,missense_variant,p.A109G,ENST00000534751.3,c.326C>G,MODERATE,;PRDM11,missense_variant,p.A109G,ENST00000683152.1,c.326C>G,MODERATE,YES;PRDM11,missense_variant,p.A109G,ENST00000530656.5,c.326C>G,MODERATE, +SCARB1 949 BI GRCh38 12 124814302 124814302 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 68 5 c.530G>A p.Gly177Asp p.G177D ENST00000415380.6 NM_001367981.1 177 gGt/gAt 4/12 T G/D protein_coding YES 530/1659 TCTCACCCACA PANTHER:PTHR11923;PANTHER:PTHR11923:SF96;Pfam:PF01130 ENSP00000414979 4/12 ENST00000415380 Transcript 1.0 ENSG00000073060 HGNC:1664 MODERATE missense_variant 1.0 benign(0.284) Unknown tolerated(0.06) Q8WTV0.179 SCARB1 HGNC -1 2.0 UPI000006E977 Q8WTV0-1 SNV SCARB1,missense_variant,p.G177D,ENST00000261693,NM_001367988.1&NM_001367985.1&NM_001367984.1&NM_005505.5&NM_001367989.1&NM_001367983.1,c.530G>A,MODERATE,,tolerated(0.1),benign(0.052),-1;SCARB1,missense_variant,p.G177D,ENST00000339570,NM_001367987.1&NM_001082959.2,c.530G>A,MODERATE,,tolerated(0.09),benign(0.127),-1;SCARB1,missense_variant,p.G177D,ENST00000415380,NM_001367981.1,c.530G>A,MODERATE,YES,tolerated(0.06),benign(0.284),-1;SCARB1,missense_variant,p.G123D,ENST00000544327,NM_001367982.1,c.368G>A,MODERATE,,tolerated(0.11),benign(0.132),-1;SCARB1,missense_variant,p.G177D,ENST00000546215,NM_001367986.1,c.530G>A,MODERATE,,tolerated(0.1),benign(0.093),-1;SCARB1,downstream_gene_variant,,ENST00000545493,,,MODIFIER,,,,-1;SCARB1,non_coding_transcript_exon_variant,,ENST00000535005,,n.845G>A,MODIFIER,,,,-1;SCARB1,downstream_gene_variant,,ENST00000539320,,,MODIFIER,,,,-1;SCARB1,downstream_gene_variant,,ENST00000541661,,,MODIFIER,,,,-1;SCARB1,non_coding_transcript_exon_variant,,ENST00000538291,,n.673G>A,MODIFIER,,,,-1 656/2731 muse;mutect2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 34 9e6d04ed-96fe-4e02-adfd-bf0b54676009 73 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS SCARB1,non_coding_transcript_exon_variant,,ENST00000539320.3,n.763G>A,MODIFIER,;SCARB1,missense_variant,p.G123D,ENST00000544327.1,c.368G>A,MODERATE,;SCARB1,non_coding_transcript_exon_variant,,ENST00000535005.5,n.845G>A,MODIFIER,;SCARB1,missense_variant,p.G177D,ENST00000546215.5,c.530G>A,MODERATE,;SCARB1,non_coding_transcript_exon_variant,,ENST00000538291.5,n.673G>A,MODIFIER,;SCARB1,non_coding_transcript_exon_variant,,ENST00000681499.1,n.403G>A,MODIFIER,;SCARB1,missense_variant,NMD_transcript_variant,p.G177D,ENST00000681117.1,c.530G>A,MODERATE,;SCARB1,missense_variant,p.G177D,ENST00000415380.6,c.530G>A,MODERATE,;SCARB1,missense_variant,NMD_transcript_variant,p.G177D,ENST00000681686.1,c.530G>A,MODERATE,;SCARB1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680982.1,c.*513G>A,MODIFIER,;SCARB1,missense_variant,p.G177D,ENST00000680556.1,c.530G>A,MODERATE,;SCARB1,missense_variant,NMD_transcript_variant,p.G177D,ENST00000679605.1,c.530G>A,MODERATE,;SCARB1,non_coding_transcript_exon_variant,,ENST00000681555.1,n.220G>A,MODIFIER,;SCARB1,missense_variant,p.G177D,ENST00000680596.1,c.530G>A,MODERATE,;SCARB1,missense_variant,NMD_transcript_variant,p.G177D,ENST00000680926.1,c.530G>A,MODERATE,;SCARB1,missense_variant,p.G177D,ENST00000261693.11,c.530G>A,MODERATE,YES;SCARB1,missense_variant,p.G177D,ENST00000339570.9,c.530G>A,MODERATE, +NOC4L 79050 BI GRCh38 12 132148852 132148852 + missense_variant Missense_Mutation SNP G G T rs529616528 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 9 4 c.858G>T p.Gln286His p.Q286H ENST00000330579.6 NM_024078.3 286 caG/caT 9/15 P1 T Q/H protein_coding YES CCDS9277.1 858/1551 GCGCAGCCCAC COSM1605817 PANTHER:PTHR12455;Superfamily:SSF48371 ENSP00000328854 9/15 rs529616528;COSV57958444 ENST00000330579 Transcript ENSG00000184967 HGNC:28461 MODERATE NM_024078.3 missense_variant 0;1 1.0 benign(0.079) Unknown deleterious(0.04) 0;1 Q9BVI4.156 NOC4L HGNC 1 1.0 UPI00000723C4 SNV NOC4L,missense_variant,p.Q286H,ENST00000330579,NM_024078.3,c.858G>T,MODERATE,YES,deleterious(0.04),benign(0.079),1;NOC4L,missense_variant,p.Q253H,ENST00000541954,,c.759G>T,MODERATE,,deleterious(0.03),benign(0.026),1;DDX51,upstream_gene_variant,,ENST00000397333,NM_175066.4,,MODIFIER,YES,,,-1;NOC4L,non_coding_transcript_exon_variant,,ENST00000535343,,n.381G>T,MODIFIER,,,,1;NOC4L,upstream_gene_variant,,ENST00000538784,,,MODIFIER,,,,1 890/1650 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 24 9e6d04ed-96fe-4e02-adfd-bf0b54676009 13 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS NOC4L,non_coding_transcript_exon_variant,,ENST00000535343.5,n.381G>T,MODIFIER,;NOC4L,missense_variant,p.Q253H,ENST00000541954.1,c.759G>T,MODERATE,;NOC4L,missense_variant,p.Q286H,ENST00000330579.6,c.858G>T,MODERATE,YES +PLCB2 5330 BI GRCh38 15 40298938 40298938 + missense_variant Missense_Mutation SNP G G A rs1242886355 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 48 43 c.710C>T p.Thr237Met p.T237M ENST00000260402.8 NM_004573.3 237 aCg/aTg 9/32 P4 A T/M protein_coding YES CCDS42020.1 710/3558 CCTTCGTCATG Gene3D:1.10.238.10;PDB-ENSP_mappings:2fju.B;PDB-ENSP_mappings:2zkm.X;Pfam:PF09279;PIRSF:PIRSF000956;PANTHER:PTHR10336;PANTHER:PTHR10336:SF10;Superfamily:SSF47473;CDD:cd16209 ENSP00000260402 9/32 rs1242886355 ENST00000260402 Transcript ENSG00000137841 HGNC:9055 MODERATE NM_004573.3 8.867e-06 gnomAD_NFE missense_variant 1.0 possibly_damaging(0.888) Unknown deleterious(0) Q00722.190 PLCB2 HGNC -1 2.0 UPI0000D79B75 Q00722-1 SNV PLCB2,missense_variant,p.T237M,ENST00000260402,NM_004573.3,c.710C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.888),-1;PLCB2,missense_variant,p.T237M,ENST00000557821,NM_001284297.2,c.710C>T,MODERATE,,deleterious(0),possibly_damaging(0.777),-1;PLCB2,missense_variant,p.T237M,ENST00000456256,NM_001284298.2,c.710C>T,MODERATE,,deleterious(0),possibly_damaging(0.88),-1;PLCB2,downstream_gene_variant,,ENST00000543785,NM_001284299.2,,MODIFIER,,,,-1;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588,,n.731C>T,MODIFIER,,,,-1;PLCB2,non_coding_transcript_exon_variant,,ENST00000560093,,n.189C>T,MODIFIER,,,,-1;PLCB2,upstream_gene_variant,,ENST00000558409,,,MODIFIER,,,,-1;PLCB2,downstream_gene_variant,,ENST00000559634,,,MODIFIER,,,,-1;PLCB2-AS1,upstream_gene_variant,,ENST00000559520,,,MODIFIER,YES,,,1 973/4627 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 4.102e-06 0.0 0.0 0.0 0.0 0.0 8.867e-06 0.0 0.0 1.3521400433091912e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5433099179062992e-05 0.0 0.0002084199950331 0 86 9e6d04ed-96fe-4e02-adfd-bf0b54676009 91 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS PLCB2,non_coding_transcript_exon_variant,,ENST00000560093.1,n.189C>T,MODIFIER,;PLCB2,missense_variant,p.T237M,ENST00000456256.6,c.710C>T,MODERATE,;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588.5,n.731C>T,MODIFIER,;PLCB2,missense_variant,p.T237M,ENST00000260402.8,c.710C>T,MODERATE,YES;PLCB2,missense_variant,p.T237M,ENST00000557821.5,c.710C>T,MODERATE, +CPEB1 64506 BI GRCh38 15 82549515 82549515 + synonymous_variant Silent SNP T T C rs368407272 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 36 18 c.1425A>G p.Leu475= p.L475= ENST00000684509.1 NM_001387064.1 475 ctA/ctG 10/13 0.0002 0.0008 0.0 0.0 0.0 0.0 C L protein_coding YES 1539/1881 CCAAATAGGTC PROSITE_profiles:PS50102;CDD:cd12725;PANTHER:PTHR12566;PANTHER:PTHR12566:SF9;Gene3D:3.30.70.330;Superfamily:SSF54928 ENSP00000478598 0.0 0.0001196 9/12 rs368407272 ENST00000617958 Transcript ENSG00000214575 HGNC:21744 LOW 0.0008 AFR synonymous_variant 1.0 Unknown CPEB1 HGNC -1 A0A024R214.52 1.0 UPI0000D48C42 SNV CPEB1,synonymous_variant,p.L475=,ENST00000614918,NM_001365241.1&NM_001365242.1&NM_001365240.1,c.1425A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L448=,ENST00000611031,,c.1344A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L513=,ENST00000617958,,c.1539A>G,LOW,YES,,,-1;CPEB1,synonymous_variant,p.L378=,ENST00000618449,NM_001365250.1&NM_001079533.2,c.1134A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L373=,ENST00000620182,NM_001365244.1&NM_001288819.1&NM_001365247.1&NM_001365245.1&NM_001365246.1,c.1119A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L373=,ENST00000617522,,c.1119A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L448=,ENST00000615198,NM_030594.5&NM_001365243.1,c.1344A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L373=,ENST00000617462,NM_001365248.1&NM_001365249.1&NM_001079535.2,c.1119A>G,LOW,,,,-1;AC245033.1,synonymous_variant,p.L373=,ENST00000562833,,c.1119A>G,LOW,YES,,,-1;CPEB1,synonymous_variant,p.L451=,ENST00000616959,,c.1353A>G,LOW,,,,-1;CPEB1,synonymous_variant,p.L373=,ENST00000611163,NM_001288820.2&NM_001079534.2,c.1119A>G,LOW,,,,-1;AC245033.1,3_prime_UTR_variant,,ENST00000642270,,c.*475A>G,MODIFIER,,,,-1;CPEB1,3_prime_UTR_variant,,ENST00000614977,,c.*475A>G,MODIFIER,,,,-1;CPEB1,non_coding_transcript_exon_variant,,ENST00000618698,,n.1152A>G,MODIFIER,,,,-1;AC245033.2,intron_variant,,ENST00000621893,,n.226+744T>C,MODIFIER,YES,,,1 1676/2776 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 4.408e-05 6.458e-05 2.896e-05 0.0 0.0 0.0 0.0 0.0 0.0002941 3.38079989887774e-05 4.865229857387021e-05 0.0 0.0 0.0 0.0 0.0 afr 4.865229857387021e-05 0.0 3.0867100576870143e-05 0.0 0.0002086809981847 0 42 9e6d04ed-96fe-4e02-adfd-bf0b54676009 54 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS CPEB1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000614977.4,c.*475A>G,MODIFIER,;CPEB1,synonymous_variant,p.L373=,ENST00000617522.4,c.1119A>G,LOW,;CPEB1,synonymous_variant,p.L373=,ENST00000620182.4,c.1119A>G,LOW,;CPEB1,synonymous_variant,p.L373=,ENST00000617462.4,c.1119A>G,LOW,;CPEB1,synonymous_variant,p.L451=,ENST00000616959.4,c.1353A>G,LOW,;CPEB1,synonymous_variant,p.L373=,ENST00000611163.4,c.1119A>G,LOW,;CPEB1,synonymous_variant,p.L448=,ENST00000615198.4,c.1344A>G,LOW,;CPEB1,synonymous_variant,p.L513=,ENST00000617958.4,c.1539A>G,LOW,;CPEB1,synonymous_variant,p.L378=,ENST00000618449.4,c.1134A>G,LOW,;CPEB1,synonymous_variant,p.L448=,ENST00000611031.4,c.1344A>G,LOW,;CPEB1,synonymous_variant,p.L475=,ENST00000614918.4,c.1425A>G,LOW,;CPEB1,synonymous_variant,p.L475=,ENST00000684509.1,c.1425A>G,LOW,YES;CPEB1,non_coding_transcript_exon_variant,,ENST00000618698.4,n.1152A>G,MODIFIER,;ENSG00000278013,intron_variant,,ENST00000621893.1,n.226+744T>C,MODIFIER,YES;ENSG00000260836,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642270.1,c.*475A>G,MODIFIER,;ENSG00000260836,synonymous_variant,p.L373=,ENST00000562833.2,c.1119A>G,LOW,YES +BNC1 646 BI GRCh38 15 83268171 83268171 + missense_variant Missense_Mutation SNP C C T rs1396582148 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 36 35 c.161G>A p.Arg54His p.R54H ENST00000345382.7 NM_001717.4 54 cGt/cAt 2/5 A2 T R/H protein_coding YES CCDS10324.1 161/2985 ACTGACGGTGG PANTHER:PTHR15021;PANTHER:PTHR15021:SF1 ENSP00000307041 2/5 rs1396582148 ENST00000345382 Transcript 1.0 ENSG00000169594 HGNC:1081 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) Q01954.162 BNC1 HGNC -1 1.0 UPI0000126796 SNV BNC1,missense_variant,p.R54H,ENST00000345382,NM_001717.4,c.161G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;BNC1,missense_variant,p.R47H,ENST00000569704,NM_001301206.2,c.140G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;AC103876.1,intron_variant,,ENST00000565495,,n.264+83103C>T,MODIFIER,,,,1 247/4610 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.763149940525182e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 61 9e6d04ed-96fe-4e02-adfd-bf0b54676009 71 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS BNC1,missense_variant,p.R54H,ENST00000345382.7,c.161G>A,MODERATE,YES;BNC1,missense_variant,p.R47H,ENST00000569704.2,c.140G>A,MODERATE,;ENSG00000259986,intron_variant,,ENST00000565495.1,n.264+83103C>T,MODIFIER,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 40 27 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 0 51 9e6d04ed-96fe-4e02-adfd-bf0b54676009 68 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +PPARA 5465 BI GRCh38 22 46219826 46219826 + stop_gained Nonsense_Mutation SNP C C T rs764930526 TCGA-WC-A88A-01A TCGA-WC-A88A-10A Somatic 55 13 c.523C>T p.Arg175Ter p.R175* ENST00000407236.6 NM_005036.6 175 Cga/Tga 7/9 P1 T R/* protein_coding CCDS33669.1 523/1407 TTGGACGAATG COSM1736297 CDD:cd06965;Gene3D:3.30.50.10;Superfamily:SSF57716;PANTHER:PTHR24082;PANTHER:PTHR24082:SF197 ENSP00000262735 6/8 rs764930526;COSV53077323 ENST00000262735 Transcript 1.0 ENSG00000186951 HGNC:9232 HIGH 0.0001629 gnomAD_OTH stop_gained 0;1 Unknown 0;1 Q07869.231 PPARA HGNC 1 F1D8S4.87 5.0 UPI000000D8E0 Q07869-1 SNV PPARA,stop_gained,p.R175*,ENST00000407236,NM_005036.6&NM_001362872.2&NM_001362873.1,c.523C>T,HIGH,YES,,,1;PPARA,stop_gained,p.R175*,ENST00000262735,NM_001001928.3,c.523C>T,HIGH,,,,1;PPARA,stop_gained,p.R175*,ENST00000402126,,c.523C>T,HIGH,,,,1;PPARA,downstream_gene_variant,,ENST00000420804,,,MODIFIER,,,,1;PPARA,non_coding_transcript_exon_variant,,ENST00000493286,,n.733C>T,MODIFIER,,,,1 705/9965 muse;mutect2;varscan2 4e531546-56f1-4165-94a2-ee45abd5e0f7 2.784e-05 0.0 2.891e-05 0.0 0.0 0.0 3.517e-05 0.0001629 3.266e-05 1.3521400433091912e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086039941990748e-05 0.0 3.086039941990748e-05 0.0 0.0 0 55 9e6d04ed-96fe-4e02-adfd-bf0b54676009 68 f6127eb8-8474-416e-ac97-21096502d920 SUCCESS PPARA,non_coding_transcript_exon_variant,,ENST00000493286.1,n.733C>T,MODIFIER,;PPARA,stop_gained,p.R175*,ENST00000402126.2,c.523C>T,HIGH,;PPARA,stop_gained,p.R175*,ENST00000407236.6,c.523C>T,HIGH,YES +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 26 18 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 49 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 44 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +SEL1L3 23231 BI GRCh38 4 25835273 25835273 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 45 32 c.784G>A p.Gly262Ser p.G262S ENST00000399878.8 NM_015187.5 262 Ggc/Agc 3/24 P4 T G/S protein_coding YES CCDS47037.1 784/3399 AATGCCTGTGT PANTHER:PTHR44444;PANTHER:PTHR44444:SF1 ENSP00000382767 3/24 ENST00000399878 Transcript ENSG00000091490 HGNC:29108 MODERATE NM_015187.5 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0.01) Q68CR1.121 SEL1L3 HGNC -1 1.0 UPI00001D7736 Q68CR1-1 SNV SEL1L3,missense_variant,p.G262S,ENST00000399878,NM_015187.5,c.784G>A,MODERATE,YES,deleterious(0.01),probably_damaging(1),-1;SEL1L3,missense_variant,p.G227S,ENST00000264868,NM_001297592.2,c.679G>A,MODERATE,,deleterious(0.01),probably_damaging(1),-1;SEL1L3,missense_variant,p.G109S,ENST00000502949,NM_001297594.2,c.325G>A,MODERATE,,deleterious(0.01),probably_damaging(1),-1;SEL1L3,non_coding_transcript_exon_variant,,ENST00000513364,,n.365G>A,MODIFIER,,,,-1 936/4543 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 73 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 78 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS SEL1L3,non_coding_transcript_exon_variant,,ENST00000513364.1,n.365G>A,MODIFIER,;SEL1L3,missense_variant,p.G109S,ENST00000502949.5,c.325G>A,MODERATE,;SEL1L3,missense_variant,p.G262S,ENST00000399878.8,c.784G>A,MODERATE,YES;SEL1L3,missense_variant,p.G227S,ENST00000264868.9,c.679G>A,MODERATE, +PDE8B 8622 BI GRCh38 5 77312031 77312031 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 42 35 c.377G>A p.Arg126Lys p.R126K ENST00000264917.10 NM_001349749.3 126 aGa/aAa 2/22 P1 A R/K protein_coding YES CCDS4037.1 377/2658 CATGAGACTGA PANTHER:PTHR11347;PANTHER:PTHR11347:SF98 ENSP00000264917 2/22 ENST00000264917 Transcript 1.0 ENSG00000113231 HGNC:8794 MODERATE NM_003719.5 missense_variant 1.0 benign(0.05) Unknown tolerated(0.37) O95263.188 PDE8B HGNC 1 1.0 UPI0000001BBE O95263-1 SNV PDE8B,missense_variant,p.R126K,ENST00000264917,NM_001349749.3&NM_003719.5&NM_001376063.1&NM_001349748.3&NM_001349751.3,c.377G>A,MODERATE,YES,tolerated(0.37),benign(0.05),1;PDE8B,missense_variant,p.R126K,ENST00000340978,NM_001376069.1&NM_001376070.1&NM_001376071.1&NM_001029854.4,c.377G>A,MODERATE,,tolerated(0.38),benign(0.019),1;AC022414.1,missense_variant,p.R2K,ENST00000646262,NM_001349750.3&NM_001376062.1&NM_001376072.1&NM_001349752.3&NM_001349753.2&NM_001376067.1&NM_001376068.1,c.5G>A,MODERATE,YES,tolerated(0.37),benign(0.05),1;PDE8B,missense_variant,p.R126K,ENST00000346042,NM_001376073.1&NM_001376074.1&NM_001376075.1&NM_001376064.1&NM_001029851.4&NM_001376065.1,c.377G>A,MODERATE,,tolerated(0.41),benign(0.097),1;PDE8B,missense_variant,p.R126K,ENST00000333194,NM_001029852.4,c.377G>A,MODERATE,,tolerated(0.28),benign(0.029),1;PDE8B,missense_variant,p.R2K,ENST00000505926,,c.5G>A,MODERATE,,tolerated(0.35),benign(0.005),1;PDE8B,missense_variant,p.R2K,ENST00000502945,,c.5G>A,MODERATE,,tolerated(0.36),benign(0.05),1;PDE8B,intron_variant,,ENST00000342343,NM_001376066.1&NM_001029853.4,c.340-13508G>A,MODIFIER,,,,1 623/4606 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 94 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 77 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS PDE8B,missense_variant,p.R2K,ENST00000502945.1,c.5G>A,MODERATE,;PDE8B,missense_variant,p.R126K,ENST00000333194.8,c.377G>A,MODERATE,;PDE8B,intron_variant,,ENST00000342343.8,c.340-13508G>A,MODIFIER,;PDE8B,missense_variant,p.R126K,ENST00000340978.7,c.377G>A,MODERATE,;PDE8B,missense_variant,p.R126K,ENST00000346042.7,c.377G>A,MODERATE,;PDE8B,missense_variant,p.R126K,ENST00000264917.10,c.377G>A,MODERATE,YES;PDE8B,missense_variant,p.R2K,ENST00000505926.5,c.5G>A,MODERATE,;PDE8B,missense_variant,p.R2K,ENST00000646262.1,c.5G>A,MODERATE,YES +RASGRF2 5924 BI GRCh38 5 81112636 81112636 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 50 40 c.1865A>G p.Asp622Gly p.D622G ENST00000265080.9 NM_006909.3 622 gAc/gGc 14/27 P1 G D/G protein_coding YES CCDS4052.1 1865/3714 AGACGACACTG Gene3D:1.20.870.10;PANTHER:PTHR23113;PANTHER:PTHR23113:SF187 ENSP00000265080 14/27 ENST00000265080 Transcript ENSG00000113319 HGNC:9876 MODERATE NM_006909.3 missense_variant 1.0 benign(0.242) Unknown deleterious(0.01) O14827.168 RASGRF2 HGNC 1 A0A2X0SFL3.11 1.0 UPI0000047ABF SNV RASGRF2,missense_variant,p.D622G,ENST00000265080,NM_006909.3,c.1865A>G,MODERATE,YES,deleterious(0.01),benign(0.242),1;RASGRF2,missense_variant,p.D622G,ENST00000503795,,c.1865A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.488),1;AC026427.1,downstream_gene_variant,,ENST00000508993,,,MODIFIER,YES,,,-1 2241/8482 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 99 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 90 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS RASGRF2,missense_variant,NMD_transcript_variant,p.D622G,ENST00000503795.1,c.1865A>G,MODERATE,;RASGRF2,missense_variant,p.D622G,ENST00000265080.9,c.1865A>G,MODERATE,YES +PKHD1L1 93035 BI GRCh38 8 109400234 109400234 + missense_variant Missense_Mutation SNP C C T rs751058194 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 235 62 c.1171C>T p.Arg391Cys p.R391C ENST00000378402.10 NM_177531.6 391 Cgc/Tgc 13/78 P1 T R/C protein_coding YES CCDS47911.1 1171/12732 TTGCACGCTTT Gene3D:3.90.182.10;Pfam:PF07691;PROSITE_profiles:PS51820;PANTHER:PTHR46769;PANTHER:PTHR46769:SF2;SMART:SM00758;Superfamily:SSF56988 ENSP00000367655 13/78 rs751058194 ENST00000378402 Transcript ENSG00000205038 HGNC:20313 MODERATE NM_177531.6 0.0006536 gnomAD_SAS missense_variant 1.0 probably_damaging(0.991) Unknown deleterious(0) Q86WI1.128 PKHD1L1 HGNC 1 1.0 UPI0000E5B020 SNV PKHD1L1,missense_variant,p.R391C,ENST00000378402,NM_177531.6,c.1171C>T,MODERATE,YES,deleterious(0),probably_damaging(0.991),1 1291/19969 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0.0001084 6.46e-05 0.0001158 0.0 5.564e-05 0.0 8.861e-06 0.0 0.0006536 4.060089850099757e-05 4.867129973717965e-05 0.0 0.0 0.0 0.0 0.0 sas 0.0006257820059545 0.0 1.543729922559578e-05 0.0 0.0006257820059545 0 247 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 297 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS PKHD1L1,missense_variant,p.R391C,ENST00000378402.10,c.1171C>T,MODERATE,YES +PIP4K2A 5305 BI GRCh38 10 22609645 22609645 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 31 35 c.217A>C p.Lys73Gln p.K73Q ENST00000376573.9 NM_005028.5 73 Aag/Cag 2/10 P1 G K/Q protein_coding YES CCDS7141.1 217/1221 CACCTTTATTT PDB-ENSP_mappings:2ybx.A;PDB-ENSP_mappings:2ybx.B;PDB-ENSP_mappings:6osp.A;PDB-ENSP_mappings:6osp.B;PROSITE_profiles:PS51455;CDD:cd17309;PANTHER:PTHR23086;PANTHER:PTHR23086:SF21;Gene3D:3.30.800.10;SMART:SM00330;Superfamily:SSF56104 ENSP00000365757 2/10 ENST00000376573 Transcript 1.0 ENSG00000150867 HGNC:8997 MODERATE NM_005028.5 missense_variant 1.0 probably_damaging(0.927) Unknown deleterious(0.04) P48426.174 PIP4K2A HGNC -1 1.0 UPI0000001052 P48426-1 SNV PIP4K2A,missense_variant,p.K73Q,ENST00000376573,NM_005028.5,c.217A>C,MODERATE,YES,deleterious(0.04),probably_damaging(0.927),-1;PIP4K2A,missense_variant,p.K14Q,ENST00000545335,NM_001330062.1,c.40A>C,MODERATE,,deleterious(0.04),probably_damaging(0.927),-1;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000422321,,n.73A>C,MODIFIER,,,,-1;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000432610,,n.73A>C,MODIFIER,,,,-1 469/3820 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 61 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 66 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS PIP4K2A,non_coding_transcript_exon_variant,,ENST00000432610.1,n.73A>C,MODIFIER,;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000422321.5,n.73A>C,MODIFIER,;PIP4K2A,missense_variant,p.K14Q,ENST00000545335.5,c.40A>C,MODERATE,;PIP4K2A,missense_variant,p.K73Q,ENST00000376573.9,c.217A>C,MODERATE,YES +MUC2 4583 BI GRCh38 11 1107208 1107208 + synonymous_variant Silent SNP C C A novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 37 17 c.2019C>A p.Thr673= p.T673= ENST00000674892.1 673 acC/acA 12/20 A2 A T protein_coding 2019/2958 GGCACCTACCT SMART:SM00214;PROSITE_profiles:PS50184;PANTHER:PTHR11339;PANTHER:PTHR11339:SF261 ENSP00000501871 12/20 cds_start_NF ENST00000674892 Transcript ENSG00000198788 HGNC:7512 LOW synonymous_variant Unknown MUC2 HGNC 1 SNV MUC2,synonymous_variant,p.T673=,ENST00000674892,,c.2019C>A,LOW,,,,1;MUC2,non_coding_transcript_exon_variant,,ENST00000361558,NM_002457.4,n.11572C>A,MODIFIER,,,,1 2019/3111 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 73 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 54 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS MUC2,synonymous_variant,p.T673=,ENST00000674892.1,c.2019C>A,LOW,;MUC2,non_coding_transcript_exon_variant,,ENST00000361558.7,n.11572C>A,MODIFIER, +TKFC 26007 BI GRCh38 11 61343345 61343345 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 58 52 c.869G>A p.Gly290Asp p.G290D ENST00000394900.8 NM_001351978.2 290 gGc/gAc 11/18 P1 A G/D protein_coding YES CCDS8003.1 869/1728 AGAGGGCCGCG PROSITE_profiles:PS51481;PANTHER:PTHR28629:SF4;PANTHER:PTHR28629;Pfam:PF02733;TIGRFAM:TIGR02361;Gene3D:3.30.1180.20;Superfamily:SSF82549 ENSP00000378360 11/18 ENST00000394900 Transcript 1.0 ENSG00000149476 HGNC:24552 MODERATE NM_015533.4 missense_variant 1.0 benign(0.023) Unknown tolerated(0.53) Q3LXA3.136 TKFC HGNC 1 A0A140VJH7.21 1.0 UPI00000718B9 Q3LXA3-1 SNV TKFC,missense_variant,p.G290D,ENST00000394900,NM_001351978.1&NM_001351977.2&NM_001351976.2&NM_015533.4,c.869G>A,MODERATE,YES,tolerated(0.53),benign(0.023),1;TKFC,missense_variant,p.G289D,ENST00000529479,NM_001351980.2&NM_001351979.2,c.866G>A,MODERATE,,tolerated(0.5),benign(0.003),1;TKFC,downstream_gene_variant,,ENST00000532173,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000534084,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000530456,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000533393,,,MODIFIER,,,,1;TKFC,non_coding_transcript_exon_variant,,ENST00000534370,,n.136G>A,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000524440,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000524953,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000525366,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000528061,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000529092,,,MODIFIER,,,,1;TKFC,upstream_gene_variant,,ENST00000530329,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000533853,,,MODIFIER,,,,1;TKFC,downstream_gene_variant,,ENST00000534134,,,MODIFIER,,,,1;DDB1,upstream_gene_variant,,ENST00000540166,,,MODIFIER,,,,-1 1080/4678 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 113 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 110 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS TKFC,non_coding_transcript_exon_variant,,ENST00000534370.1,n.136G>A,MODIFIER,;TKFC,missense_variant,p.G289D,ENST00000529479.5,c.866G>A,MODERATE,;TKFC,missense_variant,p.G290D,ENST00000394900.8,c.869G>A,MODERATE,YES +PHLDB1 23187 BI GRCh38 11 118628471 118628471 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 10 4 c.1648G>A p.Ala550Thr p.A550T ENST00000361417.6 NM_015157.4 550 Gct/Act 7/24 A A/T protein_coding YES CCDS8401.1 1648/4134 CTGGGGCTTCA PANTHER:PTHR12156;PANTHER:PTHR12156:SF23 ENSP00000354498 7/24 ENST00000361417 Transcript ENSG00000019144 HGNC:23697 MODERATE missense_variant 1.0 benign(0.366) Unknown tolerated(0.44) Q86UU1.142 PHLDB1 HGNC 1 A0A024R3H6.51 1.0 UPI0000192101 Q86UU1-1 SNV PHLDB1,missense_variant,p.A550T,ENST00000361417,NM_015157.4,c.1648G>A,MODERATE,YES,tolerated(0.44),benign(0.366),1;PHLDB1,missense_variant,p.A550T,ENST00000600882,NM_001144758.3,c.1648G>A,MODERATE,,tolerated(0.44),benign(0.366),1;PHLDB1,missense_variant,p.A550T,ENST00000356063,NM_001144759.3,c.1648G>A,MODERATE,,tolerated(0.38),benign(0.137),1;PHLDB1,downstream_gene_variant,,ENST00000530708,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000532639,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000534140,,,MODIFIER,,,,1;PHLDB1,intron_variant,,ENST00000621027,,n.1193+540G>A,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000526374,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000527259,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000527898,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000614369,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000617208,,,MODIFIER,,,,1;PHLDB1,missense_variant,p.A550T,ENST00000530994,,c.1648G>A,MODERATE,,tolerated(0.15),benign(0.39),1;PHLDB1,missense_variant,p.A550T,ENST00000528594,,c.1648G>A,MODERATE,,tolerated(0.15),benign(0.39),1;PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517,,n.1542G>A,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000612681,,,MODIFIER,,,,1 2059/5753 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 21 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 14 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517.5,n.1542G>A,MODIFIER,;PHLDB1,missense_variant,p.A550T,ENST00000356063.9,c.1648G>A,MODERATE,;PHLDB1,intron_variant,,ENST00000621027.4,n.1193+540G>A,MODIFIER,;PHLDB1,missense_variant,NMD_transcript_variant,p.A550T,ENST00000528594.5,c.1648G>A,MODERATE,;PHLDB1,missense_variant,p.A550T,ENST00000600882.6,c.1648G>A,MODERATE,YES;PHLDB1,missense_variant,NMD_transcript_variant,p.A550T,ENST00000530994.5,c.1648G>A,MODERATE,;PHLDB1,missense_variant,p.A550T,ENST00000361417.6,c.1648G>A,MODERATE, +PHLDB1 23187 BI GRCh38 11 118628472 118628472 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 10 4 c.1649C>T p.Ala550Val p.A550V ENST00000361417.6 NM_015157.4 550 gCt/gTt 7/24 T A/V protein_coding YES CCDS8401.1 1649/4134 TGGGGCTTCAC PANTHER:PTHR12156;PANTHER:PTHR12156:SF23 ENSP00000354498 7/24 ENST00000361417 Transcript ENSG00000019144 HGNC:23697 MODERATE missense_variant 1.0 possibly_damaging(0.549) Unknown tolerated(0.22) Q86UU1.142 PHLDB1 HGNC 1 A0A024R3H6.51 1.0 UPI0000192101 Q86UU1-1 SNV PHLDB1,missense_variant,p.A550V,ENST00000361417,NM_015157.4,c.1649C>T,MODERATE,YES,tolerated(0.22),possibly_damaging(0.549),1;PHLDB1,missense_variant,p.A550V,ENST00000600882,NM_001144758.3,c.1649C>T,MODERATE,,tolerated(0.22),possibly_damaging(0.549),1;PHLDB1,missense_variant,p.A550V,ENST00000356063,NM_001144759.3,c.1649C>T,MODERATE,,tolerated(0.2),benign(0.037),1;PHLDB1,downstream_gene_variant,,ENST00000530708,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000532639,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000534140,,,MODIFIER,,,,1;PHLDB1,intron_variant,,ENST00000621027,,n.1193+541C>T,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000526374,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000527259,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000527898,,,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000614369,,,MODIFIER,,,,1;PHLDB1,downstream_gene_variant,,ENST00000617208,,,MODIFIER,,,,1;PHLDB1,missense_variant,p.A550V,ENST00000530994,,c.1649C>T,MODERATE,,tolerated(0.14),benign(0.135),1;PHLDB1,missense_variant,p.A550V,ENST00000528594,,c.1649C>T,MODERATE,,tolerated(0.14),benign(0.135),1;PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517,,n.1543C>T,MODIFIER,,,,1;PHLDB1,upstream_gene_variant,,ENST00000612681,,,MODIFIER,,,,1 2060/5753 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 21 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 14 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517.5,n.1543C>T,MODIFIER,;PHLDB1,missense_variant,p.A550V,ENST00000356063.9,c.1649C>T,MODERATE,;PHLDB1,intron_variant,,ENST00000621027.4,n.1193+541C>T,MODIFIER,;PHLDB1,missense_variant,NMD_transcript_variant,p.A550V,ENST00000528594.5,c.1649C>T,MODERATE,;PHLDB1,missense_variant,p.A550V,ENST00000600882.6,c.1649C>T,MODERATE,YES;PHLDB1,missense_variant,NMD_transcript_variant,p.A550V,ENST00000530994.5,c.1649C>T,MODERATE,;PHLDB1,missense_variant,p.A550V,ENST00000361417.6,c.1649C>T,MODERATE, +GARIN2 161142 BI GRCh38 14 67204771 67204771 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 33 28 c.594C>T p.Asp198= p.D198= ENST00000696955.1 NM_001395907.1 198 gaC/gaT 5/8 T D nonsense_mediated_decay CCDS9778.1 594/1269 ACAGACATCAC ENSP00000431905 5/9 ENST00000311864 Transcript ENSG00000172717 HGNC:20101 LOW synonymous_variant Unknown Q8N9W8.132 FAM71D HGNC 1 2.0 UPI000013F210 Q8N9W8-1 SNV FAM71D,synonymous_variant,p.D198=,ENST00000612183,NM_173526.4,c.594C>T,LOW,YES,,,1;FAM71D,downstream_gene_variant,,ENST00000524532,,,MODIFIER,,,,1;FAM71D,downstream_gene_variant,,ENST00000530728,,,MODIFIER,,,,1;FAM71D,upstream_gene_variant,,ENST00000556117,,,MODIFIER,,,,1;FAM71D,downstream_gene_variant,,ENST00000531566,,,MODIFIER,,,,1;FAM71D,synonymous_variant,p.D198=,ENST00000311864,,c.594C>T,LOW,,,,1;FAM71D,synonymous_variant,p.D198=,ENST00000534174,,c.594C>T,LOW,,,,1;FAM71D,3_prime_UTR_variant,,ENST00000556046,,c.*650C>T,MODIFIER,,,,1;FAM71D,intron_variant,,ENST00000557671,,c.*414+165C>T,MODIFIER,,,,1;FAM71D,downstream_gene_variant,,ENST00000524914,,,MODIFIER,,,,1;SF3B4P1,downstream_gene_variant,,ENST00000553618,,,MODIFIER,YES,,,1 848/1754 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 61 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 62 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS GARIN2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000556046.5,c.*650C>T,MODIFIER,;GARIN2,synonymous_variant,p.D198=,ENST00000534174.5,c.594C>T,LOW,;GARIN2,synonymous_variant,p.D198=,ENST00000696961.1,c.594C>T,LOW,;GARIN2,intron_variant,NMD_transcript_variant,,ENST00000557671.2,c.*414+165C>T,MODIFIER,;GARIN2,synonymous_variant,p.D198=,ENST00000696955.1,c.594C>T,LOW,YES;GARIN2,intron_variant,,ENST00000696960.1,c.429+165C>T,MODIFIER,;GARIN2,synonymous_variant,p.D198=,ENST00000696958.1,c.594C>T,LOW,;GARIN2,intron_variant,,ENST00000696959.1,c.429+165C>T,MODIFIER,;GARIN2,synonymous_variant,p.D198=,ENST00000696956.1,c.594C>T,LOW,;GARIN2,synonymous_variant,p.D198=,ENST00000696957.1,c.594C>T,LOW,;GARIN2,synonymous_variant,p.D198=,ENST00000612183.4,c.594C>T,LOW, +GPR68 8111 BI GRCh38 14 91234976 91234976 + synonymous_variant Silent SNP C C T rs199863841 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 19 13 c.75G>A p.Pro25= p.P25= ENST00000531499.2 NM_003485.3 25 ccG/ccA 2/2 P1 T P protein_coding CCDS9894.2 75/1098 ACCACCGGGGC Gene3D:1.20.1070.10;Prints:PR00237;Prints:PR01564;PANTHER:PTHR24234;PANTHER:PTHR24234:SF5;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15367 ENSP00000434045 2/2 rs199863841 ENST00000531499 Transcript 1.0 ENSG00000119714 HGNC:4519 LOW 5.795e-05 gnomAD_AMR synonymous_variant Unknown Q15743.165 GPR68 HGNC -1 1.0 UPI000005042A SNV GPR68,synonymous_variant,p.P25=,ENST00000650645,NM_001177676.2,c.75G>A,LOW,YES,,,-1;GPR68,synonymous_variant,p.P25=,ENST00000531499,NM_003485.3&NM_001348437.1,c.75G>A,LOW,,,,-1;GPR68,synonymous_variant,p.P25=,ENST00000535815,,c.75G>A,LOW,,,,-1;GPR68,synonymous_variant,p.P25=,ENST00000529102,,c.75G>A,LOW,,,,-1;GPR68,downstream_gene_variant,,ENST00000529300,,,MODIFIER,,,,-1 415/2859 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 7.977e-06 0.0 5.795e-05 0.0 0.0 0.0 0.0 0.0 0.0 6.7616001615533605e-06 0.0 0.0 0.0 0.0 0.0002017759979935 0.0 0.0 0.0 0.0 0.0 0 31 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 32 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS GPR68,synonymous_variant,p.P25=,ENST00000529102.1,c.75G>A,LOW,;GPR68,synonymous_variant,p.P25=,ENST00000535815.5,c.75G>A,LOW,;GPR68,synonymous_variant,p.P25=,ENST00000531499.2,c.75G>A,LOW,;GPR68,synonymous_variant,p.P25=,ENST00000650645.1,c.75G>A,LOW,YES +ARNT2 9915 BI GRCh38 15 80470243 80470243 + missense_variant Missense_Mutation SNP C C T rs1211454281 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 11 14 c.220C>T p.Arg74Cys p.R74C ENST00000303329.9 NM_014862.4 74 Cgc/Tgc 4/19 P4 T R/C protein_coding YES CCDS32307.1 220/2154 AAAGGCGCAGA Gene3D:4.10.280.10;Pfam:PF00010;PROSITE_profiles:PS50888;PANTHER:PTHR23042;PANTHER:PTHR23042:SF6;SMART:SM00353;Superfamily:SSF47459;CDD:cd00083;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000307479 4/19 rs1211454281;COSV100308950 ENST00000303329 Transcript 1.0 ENSG00000172379 HGNC:16876 MODERATE NM_014862.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q9HBZ2.179 ARNT2 HGNC 1 X5DQN9.47 1.0 UPI00001FEA05 Q9HBZ2-1 SNV ARNT2,missense_variant,p.R63C,ENST00000533983,,c.187C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ARNT2,missense_variant,p.R74C,ENST00000303329,NM_014862.4,c.220C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;ARNT2,missense_variant,p.R74C,ENST00000622346,,c.220C>T,MODERATE,,deleterious(0),probably_damaging(1),1;ARNT2,missense_variant,p.R63C,ENST00000527771,,c.187C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;ARNT2,intron_variant,,ENST00000525103,,c.-57+28865C>T,MODIFIER,,,,1;ARNT2,non_coding_transcript_exon_variant,,ENST00000531595,,n.1C>T,MODIFIER,,,,1;ARNT2,non_coding_transcript_exon_variant,,ENST00000529181,,n.386C>T,MODIFIER,,,,1 354/6523 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 17 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 25 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS ARNT2,non_coding_transcript_exon_variant,,ENST00000531595.3,n.1C>T,MODIFIER,;ARNT2,intron_variant,,ENST00000525103.1,c.-57+28865C>T,MODIFIER,;ARNT2,missense_variant,p.R63C,ENST00000527771.5,c.187C>T,MODERATE,;ARNT2,missense_variant,p.R63C,ENST00000533983.5,c.187C>T,MODERATE,;ARNT2,missense_variant,p.R74C,ENST00000303329.9,c.220C>T,MODERATE,YES;ARNT2,non_coding_transcript_exon_variant,,ENST00000529181.1,n.386C>T,MODIFIER, +ADAMTS18 170692 BI GRCh38 16 77431464 77431464 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 67 68 c.326A>C p.His109Pro p.H109P ENST00000282849.10 NM_199355.4 109 cAc/cCc 3/23 P1 G H/P protein_coding YES CCDS10926.1 326/3666 CTAAGTGCAGT PANTHER:PTHR13723:SF167;PANTHER:PTHR13723;Pfam:PF01562 ENSP00000282849 3/23 ENST00000282849 Transcript 1.0 ENSG00000140873 HGNC:17110 MODERATE NM_199355.4 missense_variant 1.0 probably_damaging(0.99) Unknown deleterious(0) Q8TE60.162 ADAMTS18 HGNC -1 1.0 UPI0000233610 Q8TE60-1 SNV ADAMTS18,missense_variant,p.H109P,ENST00000282849,NM_199355.4&NM_001326358.2,c.326A>C,MODERATE,YES,deleterious(0),probably_damaging(0.99),-1;ADAMTS18,missense_variant,p.H42P,ENST00000562345,,c.125A>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567121,,n.183A>C,MODIFIER,,,,-1;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000564369,,n.252A>C,MODIFIER,,,,-1;ADAMTS18,missense_variant,p.H109P,ENST00000449265,,c.326A>C,MODERATE,,deleterious(0),probably_damaging(0.958),-1;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000569309,,n.283A>C,MODIFIER,,,,-1;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567914,,n.170A>C,MODIFIER,,,,-1;AC025284.1,upstream_gene_variant,,ENST00000564358,,,MODIFIER,,,,1;AC025284.1,upstream_gene_variant,,ENST00000659510,,,MODIFIER,YES,,,1;AC025284.1,upstream_gene_variant,,ENST00000670344,,,MODIFIER,,,,1 665/5833 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 165 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 135 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS ADAMTS18,non_coding_transcript_exon_variant,,ENST00000569309.1,n.283A>C,MODIFIER,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000564369.1,n.252A>C,MODIFIER,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567121.5,n.183A>C,MODIFIER,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567914.1,n.170A>C,MODIFIER,;ADAMTS18,missense_variant,p.T42P,ENST00000562345.1,c.124A>C,MODERATE,;ADAMTS18,missense_variant,NMD_transcript_variant,p.H109P,ENST00000449265.2,c.326A>C,MODERATE,;ADAMTS18,missense_variant,p.H109P,ENST00000282849.10,c.326A>C,MODERATE,YES +NAA38 84316 BI GRCh38 17 7856779 7856779 + synonymous_variant Silent SNP A A G novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 38 20 c.330T>C p.Val110= p.V110= ENST00000575771.6 NM_001320925.4 110 gtT/gtC 3/3 P1 G V protein_coding CCDS82060.1 330/378 ATGGAAACGAT Gene3D:2.30.30.100;Pfam:PF01423;PANTHER:PTHR10701;PANTHER:PTHR10701:SF11;SMART:SM00651;Superfamily:SSF50182;CDD:cd06168 ENSP00000460172 3/3 ENST00000575771 Transcript ENSG00000183011 HGNC:28212 LOW synonymous_variant Unknown Q9BRA0.134 NAA38 HGNC -1 1.0 UPI0000070016 Q9BRA0-1 SNV NAA38,synonymous_variant,p.V158=,ENST00000333775,NM_032356.5,c.474T>C,LOW,YES,,,-1;NAA38,synonymous_variant,p.V110=,ENST00000575771,NM_001320925.2,c.330T>C,LOW,,,,-1;NAA38,synonymous_variant,p.V84=,ENST00000576861,NM_001330111.2,c.252T>C,LOW,,,,-1;NAA38,synonymous_variant,p.V120=,ENST00000575071,NM_001320924.2,c.360T>C,LOW,,,,-1;NAA38,synonymous_variant,p.V58=,ENST00000575208,,c.174T>C,LOW,,,,-1;NAA38,synonymous_variant,p.V68=,ENST00000576384,,c.204T>C,LOW,,,,-1;KDM6B,downstream_gene_variant,,ENST00000254846,NM_001080424.2,,MODIFIER,YES,,,1;TMEM88,downstream_gene_variant,,ENST00000301599,NM_203411.2,,MODIFIER,YES,,,1;CYB5D1,upstream_gene_variant,,ENST00000332439,NM_144607.6,,MODIFIER,YES,,,1;KDM6B,downstream_gene_variant,,ENST00000448097,NM_001348716.1,,MODIFIER,,,,1;CYB5D1,upstream_gene_variant,,ENST00000570446,,,MODIFIER,,,,1;CYB5D1,upstream_gene_variant,,ENST00000571846,NM_001330110.2,,MODIFIER,,,,1;TMEM88,downstream_gene_variant,,ENST00000574668,NM_001319941.1,,MODIFIER,,,,1;NAA38,downstream_gene_variant,,ENST00000570555,,,MODIFIER,,,,-1;AC104581.4,upstream_gene_variant,,ENST00000624171,,,MODIFIER,YES,,,1;CYB5D1,upstream_gene_variant,,ENST00000573940,,,MODIFIER,,,,1;CYB5D1,upstream_gene_variant,,ENST00000574196,,,MODIFIER,,,,1;CYB5D1,upstream_gene_variant,,ENST00000574357,,,MODIFIER,,,,1 758/852 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 64 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 58 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS NAA38,synonymous_variant,p.V68=,ENST00000576384.1,c.204T>C,LOW,;NAA38,synonymous_variant,p.V84=,ENST00000576861.5,c.252T>C,LOW,;NAA38,synonymous_variant,p.V110=,ENST00000575771.6,c.330T>C,LOW,YES;NAA38,synonymous_variant,p.V58=,ENST00000575208.2,c.174T>C,LOW,;NAA38,synonymous_variant,p.V120=,ENST00000575071.5,c.360T>C,LOW,;NAA38,synonymous_variant,p.V158=,ENST00000333775.9,c.474T>C,LOW, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 27 25 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 67 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 52 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +TNFSF14 8740 BI GRCh38 19 6665000 6665000 + missense_variant Missense_Mutation SNP C C T rs202048657 TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 47 20 c.649G>A p.Val217Ile p.V217I ENST00000599359.1 NM_003807.5 217 Gtc/Atc 5/5 0.0002 0.0 0.0 0.001 0.0 0.0 P1 T V/I protein_coding CCDS12171.1 649/723 ACGGACGACCA COSM4082593 Gene3D:2.60.120.40;PDB-ENSP_mappings:4en0.A;PDB-ENSP_mappings:4en0.B;PDB-ENSP_mappings:4en0.C;PDB-ENSP_mappings:4j6g.A;PDB-ENSP_mappings:4j6g.B;PDB-ENSP_mappings:4kg8.A;PDB-ENSP_mappings:4kg8.B;PDB-ENSP_mappings:4kg8.C;PDB-ENSP_mappings:4kgg.A;PDB-ENSP_mappings:4kgg.B;PDB-ENSP_mappings:4kgq.A;PDB-ENSP_mappings:4kgq.B;PDB-ENSP_mappings:4rsu.A;PDB-ENSP_mappings:4rsu.B;PDB-ENSP_mappings:4rsu.C;PDB-ENSP_mappings:4rsu.G;PDB-ENSP_mappings:4rsu.H;PDB-ENSP_mappings:4rsu.I;Pfam:PF00229;Prints:PR01234;PROSITE_profiles:PS50049;PANTHER:PTHR11471;PANTHER:PTHR11471:SF34;SMART:SM00207;Superfamily:SSF49842;CDD:cd00184;Low_complexity_(Seg):seg ENSP00000469049 5/5 rs202048657;COSV55591291 ENST00000599359 Transcript ENSG00000125735 HGNC:11930 MODERATE 0.001 EAS missense_variant 0;1 benign(0.325) Unknown deleterious(0.04) 0;1 O43557.185 TNFSF14 HGNC -1 1.0 UPI000013CBC2 O43557-1 SNV TNFSF14,missense_variant,p.V217I,ENST00000675206,NM_001376887.1,c.649G>A,MODERATE,YES,deleterious(0.04),benign(0.325),-1;TNFSF14,missense_variant,p.V181I,ENST00000245912,NM_172014.3,c.541G>A,MODERATE,,deleterious(0.04),benign(0.075),-1;TNFSF14,missense_variant,p.V217I,ENST00000599359,NM_003807.4,c.649G>A,MODERATE,,deleterious(0.04),benign(0.325),-1 1031/1476 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 1.99e-05 0.0 0.0 0.0 0.0002175 0.0 8.802e-06 0.0 0.0 2.703619975363836e-05 2.4317900169990025e-05 0.0 0.0 0.0 0.0004025759990327 0.0 eas 0.0004025759990327 0.0 0.0 0.0004945599939674 0.0 0 64 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 67 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS TNFSF14,missense_variant,p.V217I,ENST00000599359.1,c.649G>A,MODERATE,;TNFSF14,missense_variant,p.V217I,ENST00000675206.1,c.649G>A,MODERATE,YES;TNFSF14,missense_variant,p.V181I,ENST00000245912.7,c.541G>A,MODERATE, +ZNF599 148103 BI GRCh38 19 34759870 34759870 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 53 31 c.931T>G p.Phe311Val p.F311V ENST00000329285.13 NM_001007248.3 311 Ttt/Gtt 4/4 P1 C F/V protein_coding YES CCDS32991.1 931/1767 TAAAAAGGGTT Gene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF20;SMART:SM00355;Superfamily:SSF57667 ENSP00000333802 4/4 ENST00000329285 Transcript 1.0 ENSG00000153896 HGNC:26408 MODERATE NM_001007248.3 missense_variant 1.0 benign(0.444) Unknown deleterious(0) Q96NL3.152 ZNF599 HGNC -1 2.0 UPI0000071186 Q96NL3-1 SNV ZNF599,missense_variant,p.F311V,ENST00000329285,NM_001007248.3,c.931T>G,MODERATE,YES,deleterious(0),benign(0.444),-1;ZNF599,downstream_gene_variant,,ENST00000587354,,,MODIFIER,,,,-1;ZNF599,3_prime_UTR_variant,,ENST00000673678,,c.*931T>G,MODIFIER,,,,-1 1305/3102 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 84 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 84 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS ZNF599,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673678.1,c.*931T>G,MODIFIER,;ZNF599,missense_variant,p.F311V,ENST00000329285.13,c.931T>G,MODERATE,YES +OR11H1 81061 BI GRCh38 22 15528243 15528243 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 104 28 c.52C>T p.Leu18Phe p.L18F ENST00000643195.1 NM_001005239.1 18 Ctc/Ttc 1/1 P1 T L/F protein_coding YES 52/948 TTATACTCCAA PANTHER:PTHR24242;PANTHER:PTHR24242:SF201;Superfamily:SSF81321 ENSP00000495403 1/1 ENST00000643195 Transcript ENSG00000130538 HGNC:15404 MODERATE missense_variant 1.0 possibly_damaging(0.484) Unknown deleterious(0.01) OR11H1 HGNC 1 A0A126GWF9.12 UPI0000041E0A SNV OR11H1,missense_variant,p.L18F,ENST00000643195,NM_001005239.1,c.52C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.484),1 52/948 mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 1.3514800230041146e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085749995079823e-05 0.0 3.085749995079823e-05 0.0 0.0 0 262 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 132 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS OR11H1,missense_variant,p.L18F,ENST00000643195.1,c.52C>T,MODERATE,YES +ADGRG4 139378 BI GRCh38 X 136387739 136387739 + splice_acceptor_variant Splice_Site SNP G G T TCGA-V4-A9EJ-01A TCGA-V4-A9EJ-10A Somatic 2 43 c.7777-1G>T p.X2593_splice p.X2593_splice ENST00000394143.6 NM_153834.4 2593 P1 T protein_coding CCDS35409.1 TGGCAGATTTT ENSP00000359686 COSV54959562;COSV54961749 ENST00000370652 Transcript NonExonic ENSG00000156920 HGNC:18992 HIGH 13/23 splice_acceptor_variant 1;1 Unknown 1;1 Q8IZF6.145 ADGRG4 HGNC 1 5.0 UPI00004CEC5B Q8IZF6-1 SNV ADGRG4,splice_acceptor_variant,p.X2593_splice,ENST00000370652,,c.7777-1G>T,HIGH,,,,1;ADGRG4,splice_acceptor_variant,p.X2388_splice,ENST00000394141,,c.7162-1G>T,HIGH,,,,1;ADGRG4,splice_acceptor_variant,p.X2593_splice,ENST00000394143,NM_153834.4,c.7777-1G>T,HIGH,YES,,,1 muse;mutect2;varscan2 d9ccba9b-6bf0-44d9-8097-a97ab747f0bd 0 72 cc7f302e-abe0-4866-bab5-82a8dcd05d5d 45 cc4d4642-7d5a-4b42-9122-7afac12075b0 SUCCESS ADGRG4,splice_acceptor_variant,p.X2388_splice,ENST00000394141.1,c.7162-1G>T,HIGH,;ADGRG4,splice_acceptor_variant,p.X2593_splice,ENST00000370652.5,c.7777-1G>T,HIGH,;ADGRG4,splice_acceptor_variant,p.X2593_splice,ENST00000394143.6,c.7777-1G>T,HIGH,YES +FAM161A 84140 BI GRCh38 2 61839722 61839722 + missense_variant Missense_Mutation SNP T T C rs911408597 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 71 40 c.1282A>G p.Thr428Ala p.T428A ENST00000405894.3 NM_032180.3 428 Act/Gct 3/6 C T/A protein_coding CCDS42687.2 1282/1983 AGGAGTTGGGC COSM1666723;COSM1666724;COSM1666725 Pfam:PF10595;PANTHER:PTHR21501;PANTHER:PTHR21501:SF3 ENSP00000385893 3/6 rs911408597;COSV56764701 ENST00000405894 Transcript 1.0 ENSG00000170264 HGNC:25808 MODERATE missense_variant 0;1 benign(0.015) Unknown tolerated(0.11) 0;1 Q3B820.119 FAM161A HGNC -1 1.0 UPI0000160B77 Q3B820-1 SNV FAM161A,missense_variant,p.T428A,ENST00000404929,NM_001201543.2,c.1282A>G,MODERATE,YES,tolerated(0.14),benign(0.005),-1;FAM161A,missense_variant,p.T428A,ENST00000405894,NM_032180.3,c.1282A>G,MODERATE,,tolerated(0.11),benign(0.015),-1;FAM161A,missense_variant,p.T424A,ENST00000418113,,c.1270A>G,MODERATE,,tolerated(0.15),benign(0.017),-1;FAM161A,3_prime_UTR_variant,,ENST00000456262,,c.*797A>G,MODIFIER,,,,-1;FAM161A,3_prime_UTR_variant,,ENST00000307507,,c.*1292A>G,MODIFIER,,,,-1;FAM161A,upstream_gene_variant,,ENST00000478494,,,MODIFIER,,,,-1;FAM161A,upstream_gene_variant,,ENST00000496369,,,MODIFIER,,,,-1 1384/3684 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 123 14348583-4e8e-494f-8f71-470aeacfcd40 111 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS FAM161A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000307507.3,c.*1292A>G,MODIFIER,;FAM161A,synonymous_variant,NMD_transcript_variant,p.Q423=,ENST00000418113.5,c.1269A>G,LOW,;FAM161A,missense_variant,p.T428A,ENST00000405894.3,c.1282A>G,MODERATE,;FAM161A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000456262.5,c.*797A>G,MODIFIER,;FAM161A,missense_variant,p.T428A,ENST00000404929.6,c.1282A>G,MODERATE,YES +NPHP3 27031 BI GRCh38 3 132692775 132692775 + missense_variant Missense_Mutation SNP G G A TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 1 15 c.2354C>T p.Ser785Leu p.S785L ENST00000337331.10 NM_153240.5 785 tCa/tTa 17/27 P1 A S/L protein_coding YES CCDS3078.1 2354/3993 GTTCTGATTCA COSM1666728 PANTHER:PTHR19871:SF30;PANTHER:PTHR19871 ENSP00000338766 17/27 COSV58628737 ENST00000337331 Transcript 1.0 ENSG00000113971 HGNC:7907 MODERATE NM_153240.5 missense_variant 1 1.0 benign(0.122) Unknown tolerated(0.13) 1 Q7Z494.155 NPHP3 HGNC -1 1.0 UPI00001B6B30 Q7Z494-1 SNV NPHP3,missense_variant,p.S785L,ENST00000337331,NM_153240.5,c.2354C>T,MODERATE,YES,tolerated(0.13),benign(0.122),-1;NPHP3-ACAD11,3_prime_UTR_variant,,ENST00000471702,,c.*345C>T,MODIFIER,,,,-1;NPHP3,3_prime_UTR_variant,,ENST00000465756,,c.*262C>T,MODIFIER,,,,-1;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,,n.3079C>T,MODIFIER,,,,-1;NPHP3,non_coding_transcript_exon_variant,,ENST00000474871,,n.88C>T,MODIFIER,,,,-1;NPHP3,non_coding_transcript_exon_variant,,ENST00000515289,,n.374C>T,MODIFIER,,,,-1 2408/5348 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 43 14348583-4e8e-494f-8f71-470aeacfcd40 16 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS NPHP3,non_coding_transcript_exon_variant,,ENST00000515289.2,n.374C>T,MODIFIER,;NPHP3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000465756.5,c.*262C>T,MODIFIER,;NPHP3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000684294.1,c.*262C>T,MODIFIER,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993.5,n.3079C>T,MODIFIER,;NPHP3,non_coding_transcript_exon_variant,,ENST00000474871.5,n.88C>T,MODIFIER,;NPHP3,missense_variant,p.S785L,ENST00000337331.10,c.2354C>T,MODERATE,YES;NPHP3-ACAD11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000471702.2,c.*345C>T,MODIFIER, +SH3RF2 153769 BI GRCh38 5 146047819 146047819 + synonymous_variant Silent SNP C C T rs770613982 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 23 26 c.1107C>T p.Ala369= p.A369= ENST00000359120.9 NM_152550.4 369 gcC/gcT 6/10 P1 T A protein_coding CCDS4280.1 1107/2190 ACAGCCGTGGT PANTHER:PTHR14167;PANTHER:PTHR14167:SF60 ENSP00000352028 6/10 rs770613982 ENST00000359120 Transcript ENSG00000156463 HGNC:26299 LOW NM_152550.4 4.625e-05 gnomAD_FIN synonymous_variant Unknown Q8TEC5.144 SH3RF2 HGNC 1 1.0 UPI0000457366 Q8TEC5-1 SNV SH3RF2,synonymous_variant,p.A369=,ENST00000511217,,c.1107C>T,LOW,YES,,,1;SH3RF2,synonymous_variant,p.A369=,ENST00000359120,NM_152550.4,c.1107C>T,LOW,,,,1;SH3RF2,non_coding_transcript_exon_variant,,ENST00000509286,,n.234C>T,MODIFIER,,,,1;SH3RF2,upstream_gene_variant,,ENST00000503848,,,MODIFIER,,,,1;SH3RF2,upstream_gene_variant,,ENST00000511705,,,MODIFIER,,,,1 1330/3004 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 1.591e-05 0.0 0.0 0.0 0.0 4.625e-05 1.759e-05 0.0 3.266e-05 0 49 14348583-4e8e-494f-8f71-470aeacfcd40 49 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS SH3RF2,non_coding_transcript_exon_variant,,ENST00000509286.1,n.234C>T,MODIFIER,;SH3RF2,synonymous_variant,p.A369=,ENST00000511217.1,c.1107C>T,LOW,;SH3RF2,synonymous_variant,p.A369=,ENST00000359120.9,c.1107C>T,LOW,YES +BTNL3 10917 BI GRCh38 5 181005727 181005727 + missense_variant Missense_Mutation SNP C C T rs1468570079 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 24 24 c.1256C>T p.Ser419Phe p.S419F ENST00000342868.7 NM_197975.3 419 tCc/tTc 8/8 P1 T S/F protein_coding YES CCDS47358.1 1256/1401 CATCTCCTTCT COSM1666729 PROSITE_profiles:PS50188;CDD:cd13733;PANTHER:PTHR24100:SF109;PANTHER:PTHR24100;Pfam:PF00622;Gene3D:2.60.120.920;SMART:SM00449;Superfamily:SSF49899;Prints:PR01407 ENSP00000341787 8/8 rs1468570079;COSV61564583 ENST00000342868 Transcript ENSG00000168903 HGNC:1143 MODERATE NM_197975.3 3.268e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.995) Unknown deleterious(0.02) 0;1 Q6UXE8.139 BTNL3 HGNC 1 1.0 UPI00001D69EF Q6UXE8-1 SNV BTNL3,missense_variant,p.S419F,ENST00000342868,NM_197975.3,c.1256C>T,MODERATE,YES,deleterious(0.02),probably_damaging(0.995),1;RNU6-1036P,upstream_gene_variant,,ENST00000383959,,,MODIFIER,YES,,,1 1439/2439 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 4.007e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.268e-05 6.762420071027009e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5436400644830428e-05 0.0 0.0 0 85 14348583-4e8e-494f-8f71-470aeacfcd40 49 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS BTNL3,missense_variant,p.S419F,ENST00000342868.7,c.1256C>T,MODERATE,YES +NEDD9 4739 BI GRCh38 6 11213485 11213485 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 36 22 c.255C>T p.Thr85= p.T85= ENST00000379446.10 NM_006403.4 85 acC/acT 2/7 P4 A T protein_coding YES CCDS4520.1 255/2505 CCAAAGGTCTG PANTHER:PTHR10654;PANTHER:PTHR10654:SF20 ENSP00000368759 2/7 ENST00000379446 Transcript ENSG00000111859 HGNC:7733 LOW NM_006403.4 synonymous_variant 1.0 Unknown Q14511.207 NEDD9 HGNC -1 1.0 UPI000000D981 Q14511-1 SNV NEDD9,synonymous_variant,p.T85=,ENST00000379446,NM_006403.4,c.255C>T,LOW,YES,,,-1;NEDD9,synonymous_variant,p.T85=,ENST00000379433,NM_182966.4,c.255C>T,LOW,,,,-1;NEDD9,synonymous_variant,p.T85=,ENST00000504387,NM_001142393.1,c.255C>T,LOW,,,,-1;NEDD9,intron_variant,,ENST00000620854,NM_001271033.1,c.12+19019C>T,MODIFIER,,,,-1;NEDD9,downstream_gene_variant,,ENST00000397378,,,MODIFIER,,,,-1;NEDD9,downstream_gene_variant,,ENST00000508546,,,MODIFIER,,,,-1;NEDD9,downstream_gene_variant,,ENST00000513989,,,MODIFIER,,,,-1;NEDD9,3_prime_UTR_variant,,ENST00000448183,,c.*217C>T,MODIFIER,,,,-1;AL139807.1,intron_variant,,ENST00000500636,,n.250+5950G>A,MODIFIER,YES,,,1 408/4522 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 97 14348583-4e8e-494f-8f71-470aeacfcd40 58 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS NEDD9,synonymous_variant,p.T85=,ENST00000379433.5,c.255C>T,LOW,;NEDD9,synonymous_variant,p.T85=,ENST00000504387.5,c.255C>T,LOW,;NEDD9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000448183.6,c.*217C>T,MODIFIER,;NEDD9,intron_variant,,ENST00000620854.4,c.12+19019C>T,MODIFIER,;NEDD9,synonymous_variant,p.T85=,ENST00000379446.10,c.255C>T,LOW,YES;ENSG00000247925,intron_variant,,ENST00000500636.2,n.250+5950G>A,MODIFIER,YES +GSTA4 2941 BI GRCh38 6 52984555 52984555 + missense_variant Missense_Mutation SNP A A T TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 57 43 c.323T>A p.Met108Lys p.M108K ENST00000370959.1 108 aTg/aAg 5/7 P1 T M/K protein_coding CCDS4948.1 323/669 GATGCATGATA COSM1666730 PDB-ENSP_mappings:1gul.A;PDB-ENSP_mappings:1gul.B;PDB-ENSP_mappings:1gul.C;PDB-ENSP_mappings:1gul.D;PDB-ENSP_mappings:1gul.E;PDB-ENSP_mappings:1gul.F;PDB-ENSP_mappings:1gul.G;PDB-ENSP_mappings:1gul.H;PDB-ENSP_mappings:1gum.A;PDB-ENSP_mappings:1gum.B;PDB-ENSP_mappings:1gum.C;PDB-ENSP_mappings:1gum.D;PDB-ENSP_mappings:1gum.E;PDB-ENSP_mappings:1gum.F;PDB-ENSP_mappings:1gum.G;PDB-ENSP_mappings:1gum.H;PDB-ENSP_mappings:3ik7.A;PDB-ENSP_mappings:3ik7.B;PDB-ENSP_mappings:3ik7.C;PDB-ENSP_mappings:3ik7.D;PROSITE_profiles:PS50405;SFLD:SFLDS00019;SFLD:SFLDG01205;CDD:cd03208;PANTHER:PTHR11571;PANTHER:PTHR11571:SF123;Gene3D:1.20.1050.10;Gene3D:3.40.30.10;Superfamily:SSF47616 ENSP00000359998 5/7 COSV63955304 ENST00000370959 Transcript ENSG00000170899 HGNC:4629 MODERATE missense_variant 1 benign(0.006) Unknown tolerated(0.19) 1 O15217.190 GSTA4 HGNC -1 A0A024RD58.38 5.0 UPI00001119FD O15217-1 SNV GSTA4,missense_variant,p.M108K,ENST00000370963,NM_001512.4,c.323T>A,MODERATE,YES,tolerated(0.19),benign(0.006),-1;GSTA4,missense_variant,p.M15K,ENST00000370960,,c.44T>A,MODERATE,,tolerated(0.24),benign(0.006),-1;GSTA4,missense_variant,p.M108K,ENST00000370959,,c.323T>A,MODERATE,,tolerated(0.19),benign(0.006),-1;GSTA4,missense_variant,p.M15K,ENST00000457564,,c.44T>A,MODERATE,,tolerated(0.2),benign(0.006),-1;GSTA4,non_coding_transcript_exon_variant,,ENST00000486559,,n.830T>A,MODIFIER,,,,-1;GSTA4,non_coding_transcript_exon_variant,,ENST00000477599,,n.264T>A,MODIFIER,,,,-1 441/793 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 110 14348583-4e8e-494f-8f71-470aeacfcd40 100 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS GSTA4,missense_variant,p.M15K,ENST00000457564.1,c.44T>A,MODERATE,;GSTA4,missense_variant,p.M108K,ENST00000370959.1,c.323T>A,MODERATE,;GSTA4,missense_variant,p.M15K,ENST00000370960.5,c.44T>A,MODERATE,;GSTA4,missense_variant,p.M108K,ENST00000370963.9,c.323T>A,MODERATE,YES;GSTA4,non_coding_transcript_exon_variant,,ENST00000477599.5,n.264T>A,MODIFIER,;GSTA4,non_coding_transcript_exon_variant,,ENST00000486559.5,n.830T>A,MODIFIER, +VWA5A 4013 BI GRCh38 11 124117792 124117792 + missense_variant Missense_Mutation SNP A A G rs767909087 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 44 34 c.163A>G p.Met55Val p.M55V ENST00000392748.5 55 Atg/Gtg 3/18 P1 G M/V protein_coding CCDS8444.1 163/2361 TCCCCATGGAT COSM1666732 Pfam:PF08487;PROSITE_profiles:PS51468;PANTHER:PTHR45737;PANTHER:PTHR45737:SF3;SMART:SM00609 ENSP00000376504 3/18 rs767909087;COSV63707332 ENST00000392748 Transcript ENSG00000110002 HGNC:6658 MODERATE 8.673e-05 gnomAD_AMR missense_variant 0;1 benign(0.088) Unknown tolerated(0.11) 0;1 O00534.144 VWA5A HGNC 1 A0A024R3H3.49 1.0 UPI0000158B80 O00534-1 SNV VWA5A,missense_variant,p.M55V,ENST00000456829,NM_001130142.2,c.163A>G,MODERATE,YES,tolerated(0.11),benign(0.088),1;VWA5A,missense_variant,p.M55V,ENST00000392748,NM_014622.4,c.163A>G,MODERATE,,tolerated(0.11),benign(0.088),1;VWA5A,missense_variant,p.M71V,ENST00000392744,,c.211A>G,MODERATE,,tolerated(0.15),benign(0.015),1;VWA5A,missense_variant,p.M55V,ENST00000449321,,c.163A>G,MODERATE,,tolerated(0.15),benign(0.088),1;VWA5A,missense_variant,p.M55V,ENST00000361352,NM_198315.2,c.163A>G,MODERATE,,tolerated(0.15),benign(0.088),1;VWA5A,non_coding_transcript_exon_variant,,ENST00000533623,,n.180A>G,MODIFIER,,,,1 257/3419 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 2.783e-05 0.0 8.673e-05 0.0 5.437e-05 0.0 2.637e-05 0.0 0.0 6.759129973943345e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 123 14348583-4e8e-494f-8f71-470aeacfcd40 78 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS VWA5A,non_coding_transcript_exon_variant,,ENST00000533623.1,n.180A>G,MODIFIER,;VWA5A,missense_variant,p.M71V,ENST00000392744.4,c.211A>G,MODERATE,;VWA5A,missense_variant,p.M55V,ENST00000456829.7,c.163A>G,MODERATE,YES;VWA5A,missense_variant,p.M55V,ENST00000449321.5,c.163A>G,MODERATE,;VWA5A,missense_variant,p.M55V,ENST00000361352.9,c.163A>G,MODERATE,;VWA5A,missense_variant,p.M55V,ENST00000392748.5,c.163A>G,MODERATE, +TRAV8-2 28684 BI GRCh38 14 21846770 21846770 + synonymous_variant Silent SNP G G C novel TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 30 20 c.9G>C p.Leu3= p.L3= ENST00000390434.3 3 ctG/ctC 1/2 P1 C L TR_V_gene YES 9/341 CTCCTGCTGCT ENSP00000439323 1/2 cds_end_NF ENST00000390434 Transcript ENSG00000211786 HGNC:12147 LOW synonymous_variant 1.0 Unknown A0A0B4J237.33 TRAV8-2 HGNC 1 UPI000011C709 SNV TRAV8-2,synonymous_variant,p.L3=,ENST00000390434,,c.9G>C,LOW,YES,,,1;TRAV12-1,downstream_gene_variant,,ENST00000390433,,,MODIFIER,YES,,,1 234/566 muse;mutect2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 74 14348583-4e8e-494f-8f71-470aeacfcd40 50 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS TRAV8-2,synonymous_variant,p.L3=,ENST00000390434.3,c.9G>C,LOW,YES +SLC4A1 6521 BI GRCh38 17 44258562 44258562 + missense_variant Missense_Mutation SNP C C A TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 15 13 c.938G>T p.Gly313Val p.G313V ENST00000262418.12 NM_000342.4 313 gGc/gTc 10/20 P1 A G/V protein_coding YES CCDS11481.1 938/2736 GGAAGCCCTCT COSM1666733 PDB-ENSP_mappings:1hyn.P;PDB-ENSP_mappings:1hyn.Q;PDB-ENSP_mappings:1hyn.R;PDB-ENSP_mappings:1hyn.S;Gene3D:3.40.930.10;PDB-ENSP_mappings:4ky9.A;PDB-ENSP_mappings:4ky9.P;PDB-ENSP_mappings:4yzf.A;PDB-ENSP_mappings:4yzf.B;PDB-ENSP_mappings:4yzf.C;PDB-ENSP_mappings:4yzf.D;Pfam:PF07565;PANTHER:PTHR11453;PANTHER:PTHR11453:SF12;Superfamily:SSF55804;TIGRFAM:TIGR00834 ENSP00000262418 10/20 COSV52258880;COSV99293214 ENST00000262418 Transcript 1.0 ENSG00000004939 HGNC:11027 MODERATE NM_000342.4 missense_variant 1;1 1.0 benign(0.151) Unknown deleterious(0.03) 1;1 P02730.254 SLC4A1 HGNC -1 1.0 UPI00000375B8 P02730-1 SNV SLC4A1,missense_variant,p.G313V,ENST00000262418,NM_000342.4,c.938G>T,MODERATE,YES,deleterious(0.03),benign(0.151),-1;SLC4A1,intron_variant,,ENST00000399246,,c.777+700G>T,MODIFIER,,,,-1;SLC4A1,downstream_gene_variant,,ENST00000471005,,,MODIFIER,,,,-1;SLC4A1,downstream_gene_variant,,ENST00000498270,,,MODIFIER,,,,-1 1088/4954 mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 22 14348583-4e8e-494f-8f71-470aeacfcd40 28 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS SLC4A1,intron_variant,,ENST00000399246.3,c.777+700G>T,MODIFIER,;SLC4A1,missense_variant,p.G313V,ENST00000262418.12,c.938G>T,MODERATE,YES +ABCA6 23460 BI GRCh38 17 69123334 69123334 + synonymous_variant Silent SNP A A G novel TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 31 15 c.1341T>C p.Asn447= p.N447= ENST00000284425.7 NM_080284.3 447 aaT/aaC 10/39 P1 G N protein_coding YES CCDS11683.1 1341/4854 TTAGCATTAGT PANTHER:PTHR19229;PANTHER:PTHR19229:SF13 ENSP00000284425 10/39 ENST00000284425 Transcript ENSG00000154262 HGNC:36 LOW NM_080284.3 synonymous_variant 1.0 Unknown Q8N139.140 ABCA6 HGNC -1 1.0 UPI000013DD9D Q8N139-1 SNV ABCA6,synonymous_variant,p.N447=,ENST00000284425,NM_080284.3,c.1341T>C,LOW,YES,,,-1 1537/5321 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 52 14348583-4e8e-494f-8f71-470aeacfcd40 46 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS ABCA6,synonymous_variant,p.N447=,ENST00000284425.7,c.1341T>C,LOW,YES +MC2R 4158 BI GRCh38 18 13885068 13885068 + missense_variant Missense_Mutation SNP G G A rs1383119237 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 19 19 c.451C>T p.Leu151Phe p.L151F ENST00000327606.4 NM_001291911.1 151 Ctt/Ttt 2/2 P1 A L/F protein_coding YES CCDS11869.1 451/894 CGTAAGCACCA COSM1666734 Gene3D:1.20.1070.10;Pfam:PF00001;PROSITE_profiles:PS50262;PANTHER:PTHR22750;PANTHER:PTHR22750:SF3;SMART:SM01381;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15350;Low_complexity_(Seg):seg ENSP00000333821 2/2 rs1383119237;COSV59617328 ENST00000327606 Transcript 1.0 ENSG00000185231 HGNC:6930 MODERATE NM_000529.2 missense_variant 0;1 1.0 probably_damaging(0.997) Unknown deleterious(0) 0;1 Q01718.182 MC2R HGNC -1 1.0 UPI00000503E5 SNV MC2R,missense_variant,p.L151F,ENST00000327606,NM_001291911.1&NM_000529.2,c.451C>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;MC2R,downstream_gene_variant,,ENST00000399821,,,MODIFIER,,,,-1 628/3652 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 6.760590167687042e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 54 14348583-4e8e-494f-8f71-470aeacfcd40 38 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS MC2R,missense_variant,p.L151F,ENST00000327606.4,c.451C>T,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EQ-01A TCGA-V4-A9EQ-10A Somatic 38 22 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 a6ff0b7a-1d04-4a64-af43-5011a4487cb2 0 86 14348583-4e8e-494f-8f71-470aeacfcd40 60 ba56671c-3ec2-487c-ae76-edbdeb912cc2 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +SCN11A 11280 BI GRCh38 3 38897036 38897036 + missense_variant Missense_Mutation SNP G G T novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 31 18 c.2212C>A p.Pro738Thr p.P738T ENST00000302328.9 NM_001349253.2 738 Ccg/Acg 18/30 P4 T P/T protein_coding CCDS33737.1 2212/5376 TGTCGGGTTAC Gene3D:1.10.287.70;Pfam:PF00520;PANTHER:PTHR10037;PANTHER:PTHR10037:SF210;Superfamily:SSF81324 ENSP00000307599 18/30 ENST00000302328 Transcript 1.0 ENSG00000168356 HGNC:10583 MODERATE NM_001349253.2 missense_variant benign(0.007) Unknown tolerated(0.41) Q9UI33.156 SCN11A HGNC -1 5.0 UPI000006CCD7 Q9UI33-1 SNV SCN11A,missense_variant,p.P738T,ENST00000668754,,c.2212C>A,MODERATE,YES,tolerated(0.41),benign(0.007),-1;SCN11A,missense_variant,p.P738T,ENST00000302328,NM_001349253.2&NM_014139.3,c.2212C>A,MODERATE,,tolerated(0.41),benign(0.007),-1;SCN11A,missense_variant,p.P738T,ENST00000444237,,c.2212C>A,MODERATE,,tolerated(0.45),benign(0.037),-1;SCN11A,missense_variant,p.P738T,ENST00000456224,,c.2212C>A,MODERATE,,tolerated(0.25),benign(0.003),-1;SCN11A,missense_variant,p.P678T,ENST00000675892,,c.2032C>A,MODERATE,,tolerated(0.36),benign(0.006),-1;SCN11A,intron_variant,,ENST00000676176,,c.2023-2072C>A,MODIFIER,,,,-1;SCN11A,missense_variant,p.P738T,ENST00000675223,,c.2212C>A,MODERATE,,tolerated(0.44),benign(0.006),-1;SCN11A,missense_variant,p.P738T,ENST00000675672,,c.2212C>A,MODERATE,,tolerated(0.42),benign(0.01),-1;SCN11A,3_prime_UTR_variant,,ENST00000676045,,c.*1929C>A,MODIFIER,,,,-1 2699/6793 muse;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 46 e4711e43-ee7e-4b57-873a-fc4a954c5216 50 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS SCN11A,missense_variant,p.P738T,ENST00000444237.2,c.2212C>A,MODERATE,;SCN11A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676045.1,c.*1929C>A,MODIFIER,;SCN11A,missense_variant,p.P678T,ENST00000675892.1,c.2032C>A,MODERATE,;SCN11A,missense_variant,NMD_transcript_variant,p.P738T,ENST00000675223.1,c.2212C>A,MODERATE,;SCN11A,missense_variant,NMD_transcript_variant,p.P738T,ENST00000675672.1,c.2212C>A,MODERATE,;SCN11A,intron_variant,,ENST00000676176.1,c.2023-2072C>A,MODIFIER,;SCN11A,missense_variant,p.P738T,ENST00000456224.7,c.2212C>A,MODERATE,;SCN11A,missense_variant,p.P738T,ENST00000668754.1,c.2212C>A,MODERATE,;SCN11A,missense_variant,p.P738T,ENST00000302328.9,c.2212C>A,MODERATE,YES +NBEAL2 23218 BI GRCh38 3 46991945 46991945 + missense_variant,splice_region_variant Missense_Mutation SNP A A T rs903364181 TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 4 5 c.1031A>T p.Lys344Met p.K344M ENST00000450053.8 NM_015175.3 344 aAg/aTg 9/54 P4 T K/M protein_coding YES CCDS46817.1 1031/8265 CAGCAAGGTGG PANTHER:PTHR13743:SF111;PANTHER:PTHR13743;Superfamily:SSF48371 ENSP00000415034 9/54 rs903364181 ENST00000450053 Transcript 1.0 ENSG00000160796 HGNC:31928 MODERATE NM_015175.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.733) Unknown deleterious(0) Q6ZNJ1.144 NBEAL2 HGNC 1 2.0 UPI000022C020 Q6ZNJ1-1 SNV NBEAL2,missense_variant,p.K344M,ENST00000450053,NM_015175.3,c.1031A>T,MODERATE,YES,deleterious(0),possibly_damaging(0.733),1;NBEAL2,missense_variant,p.K337M,ENST00000651747,NM_001365116.2,c.1010A>T,MODERATE,,deleterious(0),probably_damaging(0.975),1;NBEAL2,upstream_gene_variant,,ENST00000416683,,,MODIFIER,,,,1;NBEAL2,upstream_gene_variant,,ENST00000652242,,,MODIFIER,,,,1 1227/8842 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 12 e4711e43-ee7e-4b57-873a-fc4a954c5216 9 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS NBEAL2,missense_variant,splice_region_variant,p.K337M,ENST00000651747.1,c.1010A>T,MODERATE,;NBEAL2,missense_variant,splice_region_variant,p.K344M,ENST00000450053.8,c.1031A>T,MODERATE,YES +PTPRG 5793 BI GRCh38 3 61562368 61562380 + splice_donor_variant Splice_Site DEL CCCCGGTGAGTGC CCCCGGTGAGTGC - novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 140 16 c.81_85+8del p.Phe27LeufsTer59 p.F27Lfs*59 ENST00000474889.6 NM_002841.4 28 1/30 P4 - protein_coding YES CCDS2895.1 81-?/4338 GTGCTTCCCCGGTGAGTGCCGGCC ENSP00000418112 1/30 ENST00000474889 Transcript ENSG00000144724 HGNC:9671 HIGH 1/29 NM_002841.4 splice_donor_variant 1.0 Unknown P23470.209 PTPRG HGNC 1 1.0 UPI00001AEBFB P23470-1 deletion PTPRG,splice_donor_variant,p.X28_splice,ENST00000474889,NM_002841.4,c.82_85+9del,HIGH,YES,,,1;PTPRG,splice_donor_variant,p.X28_splice,ENST00000295874,NM_001375471.1,c.82_85+9del,HIGH,,,,1;PTPRG,splice_donor_variant,,ENST00000495879,,n.801_804+9del,HIGH,,,,1;PTPRG,splice_donor_variant,,ENST00000475527,,n.519_522+9del,HIGH,,,,1 798-?/9357 mutect2;pindel 60d7b6cf-d605-4837-9061-612f6bbb7393 0 190 e4711e43-ee7e-4b57-873a-fc4a954c5216 156 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS PTPRG,splice_donor_variant,p.F27Lfs*59,ENST00000295874.14,c.81_85+8del,HIGH,;PTPRG,non_coding_transcript_exon_variant,,ENST00000475527.1,n.518_522+8del,MODIFIER,;PTPRG,splice_donor_variant,p.F27Lfs*59,ENST00000474889.6,c.81_85+8del,HIGH,YES;PTPRG,non_coding_transcript_exon_variant,,ENST00000495879.1,n.800_804+8del,MODIFIER, +IGSF11 152404 BI GRCh38 3 119105178 119105178 + synonymous_variant Silent SNP T T C novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 16 13 c.15A>G p.Glu5= p.E5= ENST00000354673.6 5 gaA/gaG 1/7 A2 C E protein_coding CCDS2983.1 15/1293 AAAAGTTCCAC Cleavage_site_(Signalp):SignalP-TM ENSP00000406092 2/8 ENST00000425327 Transcript ENSG00000144847 HGNC:16669 LOW synonymous_variant Unknown Q5DX21.132 IGSF11 HGNC -1 2.0 UPI0000140923 Q5DX21-2 SNV IGSF11,synonymous_variant,p.E5=,ENST00000425327,NM_001353320.2&NM_152538.4,c.15A>G,LOW,,,,-1;IGSF11,synonymous_variant,p.E5=,ENST00000354673,,c.15A>G,LOW,,,,-1;IGSF11,synonymous_variant,p.E5=,ENST00000441144,NM_001353322.2,c.15A>G,LOW,,,,-1;IGSF11,non_coding_transcript_exon_variant,,ENST00000494802,,n.314A>G,MODIFIER,,,,-1 284/3525 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 35 e4711e43-ee7e-4b57-873a-fc4a954c5216 29 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS IGSF11,non_coding_transcript_exon_variant,,ENST00000494802.1,n.314A>G,MODIFIER,;IGSF11,synonymous_variant,p.E5=,ENST00000441144.6,c.15A>G,LOW,;IGSF11,synonymous_variant,p.E5=,ENST00000354673.6,c.15A>G,LOW,;IGSF11,synonymous_variant,p.E5=,ENST00000425327.6,c.15A>G,LOW, +KIAA1549 57670 BI GRCh38 7 138868085 138868085 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 16 9 c.4819G>A p.Val1607Ile p.V1607I ENST00000422774.2 NM_001164665.2 1607 Gtc/Atc 15/20 P4 T V/I protein_coding YES CCDS56513.1 4819/5853 GTTGACCTGGT PANTHER:PTHR21590:SF4;PANTHER:PTHR21590;Pfam:PF12877 ENSP00000416040 15/20 ENST00000422774 Transcript 1.0 ENSG00000122778 HGNC:22219 MODERATE NM_001164665.2 missense_variant 1.0 benign(0.063) Unknown tolerated(0.65) Q9HCM3.123 KIAA1549 HGNC -1 1.0 UPI0001837EBD Q9HCM3-1 SNV KIAA1549,missense_variant,p.V1607I,ENST00000422774,NM_001164665.2,c.4819G>A,MODERATE,YES,tolerated(0.65),benign(0.063),-1;KIAA1549,missense_variant,p.V1607I,ENST00000440172,NM_020910.3,c.4819G>A,MODERATE,,tolerated(0.65),benign(0.038),-1 4939/12498 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 32 e4711e43-ee7e-4b57-873a-fc4a954c5216 25 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS KIAA1549,missense_variant,p.V1607I,ENST00000422774.2,c.4819G>A,MODERATE,YES;KIAA1549,missense_variant,p.V1607I,ENST00000440172.5,c.4819G>A,MODERATE, +TRPM7 54822 BI GRCh38 15 50574717 50574717 + missense_variant,splice_region_variant Missense_Mutation SNP T T A rs1230531821 TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 47 24 c.5022A>T p.Glu1674Asp p.E1674D ENST00000646667.1 NM_017672.6 1674 gaA/gaT 35/39 A1 A E/D protein_coding YES CCDS42035.1 5022/5598 TGAATTTCCTA PROSITE_profiles:PS51158;CDD:cd16971;PANTHER:PTHR13800:SF8;PANTHER:PTHR13800;Pfam:PF02816;Gene3D:3.30.200.20;SMART:SM00811;Superfamily:SSF56112 ENSP00000495860 35/39 rs1230531821 ENST00000646667 Transcript 1.0 ENSG00000092439 HGNC:17994 MODERATE NM_017672.6 8.855e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.997) Unknown deleterious(0) Q96QT4.161 TRPM7 HGNC -1 A0A024R5V1.53 UPI0000071CBA SNV TRPM7,missense_variant,p.E1674D,ENST00000646667,NM_017672.6,c.5022A>T,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;TRPM7,missense_variant,p.E1673D,ENST00000560955,NM_001301212.2,c.5019A>T,MODERATE,,deleterious(0),probably_damaging(0.994),-1;TRPM7,missense_variant,p.E54D,ENST00000561267,,c.162A>T,MODERATE,,tolerated(0.25),probably_damaging(0.91),-1;TRPM7,downstream_gene_variant,,ENST00000558444,,,MODIFIER,,,,-1;TRPM7,splice_region_variant,,ENST00000561443,,n.579A>T,LOW,,,,-1;TRPM7,non_coding_transcript_exon_variant,,ENST00000560516,,n.369A>T,MODIFIER,,,,-1;TRPM7,downstream_gene_variant,,ENST00000560849,,,MODIFIER,,,,-1 5286/10382 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 4.027e-06 0.0 0.0 0.0 0.0 0.0 8.855e-06 0.0 0.0 0 84 e4711e43-ee7e-4b57-873a-fc4a954c5216 71 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS TRPM7,non_coding_transcript_exon_variant,,ENST00000560516.1,n.369A>T,MODIFIER,;TRPM7,non_coding_transcript_exon_variant,,ENST00000561443.5,n.579A>T,MODIFIER,;TRPM7,missense_variant,splice_region_variant,p.E1673D,ENST00000560955.5,c.5019A>T,MODERATE,;TRPM7,missense_variant,splice_region_variant,p.E1674D,ENST00000646667.1,c.5022A>T,MODERATE,YES;TRPM7,missense_variant,splice_region_variant,p.N54Y,ENST00000561267.5,c.160A>T,MODERATE, +RNF213 57674 BI GRCh38 17 80358309 80358309 + synonymous_variant Silent SNP C C T novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 26 13 c.10884C>T p.Val3628= p.V3628= ENST00000582970.6 NM_001256071.3 3628 gtC/gtT 37/68 P4 T V protein_coding CCDS58606.1 10884/15624 CGGGTCCAAGG PANTHER:PTHR22605;PANTHER:PTHR22605:SF18 ENSP00000464087 37/68 ENST00000582970 Transcript 1.0 ENSG00000173821 HGNC:14539 LOW synonymous_variant Unknown RNF213 HGNC 1 A0A0A0MTR7.48 1.0 UPI00043788D6 SNV RNF213,synonymous_variant,p.V3628=,ENST00000582970,NM_001256071.3,c.10884C>T,LOW,,,,1;RNF213,synonymous_variant,p.V3677=,ENST00000508628,,c.11031C>T,LOW,YES,,,1;RNF213,non_coding_transcript_exon_variant,,ENST00000558116,,n.213C>T,MODIFIER,,,,1;RNF213,non_coding_transcript_exon_variant,,ENST00000560694,,n.140C>T,MODIFIER,,,,1;RNF213-AS1,intron_variant,,ENST00000572151,,n.191-3494G>A,MODIFIER,,,,-1;RNF213-AS1,intron_variant,,ENST00000575034,,n.191-3021G>A,MODIFIER,YES,,,-1;RNF213-AS1,upstream_gene_variant,,ENST00000613190,,,MODIFIER,,,,-1;RNF213-AS1,downstream_gene_variant,,ENST00000667202,,,MODIFIER,,,,-1 11027/21055 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 44 e4711e43-ee7e-4b57-873a-fc4a954c5216 39 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS RNF213,non_coding_transcript_exon_variant,,ENST00000560694.1,n.140C>T,MODIFIER,;RNF213-AS1,intron_variant,,ENST00000572151.1,n.191-3494G>A,MODIFIER,;RNF213,non_coding_transcript_exon_variant,,ENST00000558116.5,n.213C>T,MODIFIER,;RNF213-AS1,intron_variant,,ENST00000575034.5,n.191-3021G>A,MODIFIER,YES;RNF213,synonymous_variant,p.V3677=,ENST00000508628.6,c.11031C>T,LOW,;RNF213,synonymous_variant,p.V3628=,ENST00000582970.6,c.10884C>T,LOW,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 43 27 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 77 e4711e43-ee7e-4b57-873a-fc4a954c5216 70 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +PPP1R15A 23645 BI GRCh38 19 48874424 48874425 + frameshift_variant Frame_Shift_Ins INS - - G novel TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 61 31 c.1192dup p.Glu398ArgfsTer6 p.E398Rfs*6 ENST00000200453.6 NM_014330.5 397 -/G 2/3 P1 G -/X protein_coding YES CCDS12738.1 1191-1192/2025 GACACAGAGGA PANTHER:PTHR16489;PANTHER:PTHR16489:SF14;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000200453 2/3 ENST00000200453 Transcript ENSG00000087074 HGNC:14375 1.0 HIGH frameshift_variant 1.0 Unknown O75807.141 PPP1R15A HGNC 1 1.0 UPI000006F652 O75807-1 insertion PPP1R15A,frameshift_variant,p.E398Gfs*6,ENST00000200453,NM_014330.3,c.1192dup,HIGH,YES,,,1;PPP1R15A,frameshift_variant,p.E37Gfs*6,ENST00000600406,,c.108dup,HIGH,,,,1 1431-1432/2350 mutect2;pindel;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 0 120 e4711e43-ee7e-4b57-873a-fc4a954c5216 92 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS PPP1R15A,frameshift_variant,p.E414Rfs*6,ENST00000704027.1,c.1240dup,HIGH,;PPP1R15A,frameshift_variant,p.E303Rfs*6,ENST00000704026.1,c.907dup,HIGH,;PPP1R15A,frameshift_variant,p.E398Rfs*6,ENST00000200453.6,c.1192dup,HIGH,YES;PPP1R15A,frameshift_variant,p.E398Rfs*6,ENST00000600406.2,c.1192dup,HIGH, +MAGED1 9500 BI GRCh38 X 51897809 51897809 + synonymous_variant Silent SNP A A G rs1928827600 TCGA-WC-A87W-01A TCGA-WC-A87W-10A Somatic 16 9 c.1581A>G p.Gln527= p.Q527= ENST00000326587.12 NM_006986.4 527 caA/caG 7/13 A2 G Q protein_coding CCDS14337.1 1581/2337 ATTCAACTGAA Gene3D:1.10.10.1200;Pfam:PF01454;PROSITE_profiles:PS50838;PANTHER:PTHR11736;PANTHER:PTHR11736:SF28;SMART:SM01373 ENSP00000325333 7/13 ENST00000326587 Transcript ENSG00000179222 HGNC:6813 LOW NM_006986.4 synonymous_variant Unknown Q9Y5V3.191 MAGED1 HGNC 1 1.0 UPI000006CD3E Q9Y5V3-1 SNV MAGED1,synonymous_variant,p.Q583=,ENST00000375695,NM_001005333.2,c.1749A>G,LOW,YES,,,1;MAGED1,synonymous_variant,p.Q527=,ENST00000375722,,c.1581A>G,LOW,,,,1;MAGED1,synonymous_variant,p.Q527=,ENST00000326587,NM_006986.4,c.1581A>G,LOW,,,,1;MAGED1,synonymous_variant,p.Q527=,ENST00000375772,NM_001005332.2,c.1581A>G,LOW,,,,1;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,,n.2129A>G,MODIFIER,,,,1;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,,n.1708A>G,MODIFIER,,,,1;MAGED1,downstream_gene_variant,,ENST00000470461,,,MODIFIER,,,,1;MAGED1,upstream_gene_variant,,ENST00000473931,,,MODIFIER,,,,1;MAGED1,downstream_gene_variant,,ENST00000482188,,,MODIFIER,,,,1;MAGED1,downstream_gene_variant,,ENST00000482599,,,MODIFIER,,,,1 1750/2723 muse;mutect2;varscan2 60d7b6cf-d605-4837-9061-612f6bbb7393 2.786550066957716e-05 9.97241004370153e-05 0.0 0.0 0.0 0.0 0.0 afr 9.97241004370153e-05 0.0 0.0 0.0 0.0 0 22 e4711e43-ee7e-4b57-873a-fc4a954c5216 25 db3769de-df8b-4f43-a2e7-528a3fd2d744 SUCCESS MAGED1,non_coding_transcript_exon_variant,,ENST00000485420.5,n.1708A>G,MODIFIER,;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718.5,n.2129A>G,MODIFIER,;MAGED1,synonymous_variant,p.Q583=,ENST00000375695.2,c.1749A>G,LOW,;MAGED1,synonymous_variant,p.Q527=,ENST00000326587.12,c.1581A>G,LOW,YES;MAGED1,synonymous_variant,p.Q527=,ENST00000375722.5,c.1581A>G,LOW,;MAGED1,synonymous_variant,p.Q527=,ENST00000375772.7,c.1581A>G,LOW, +CRYBG2 55057 BI GRCh38 1 26328749 26328749 + missense_variant Missense_Mutation SNP C C T rs1324289433 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 67 31 c.4439G>A p.Arg1480Gln p.R1480Q ENST00000308182.10 NM_001039775.4 1480 cGg/cAg 16/20 A2 T R/Q protein_coding 4439/4986 TGATCCGCACA Gene3D:2.60.20.10;Pfam:PF00030;PROSITE_profiles:PS50915;PANTHER:PTHR11818;PANTHER:PTHR11818:SF50;SMART:SM00247;Superfamily:SSF49695 ENSP00000310435 16/20 rs1324289433;COSV57488999 ENST00000308182 Transcript ENSG00000176092 HGNC:17295 MODERATE 6.155e-05 gnomAD_AFR missense_variant 0;1 benign(0.095) Unknown tolerated(0.15) 0;1 Q8N1P7.132 CRYBG2 HGNC -1 5.0 UPI0001DD21C3 SNV CRYBG2,missense_variant,p.R1804Q,ENST00000475866,,c.5411G>A,MODERATE,YES,tolerated(0.13),possibly_damaging(0.566),-1;CRYBG2,missense_variant,p.R1480Q,ENST00000308182,NM_001039775.3,c.4439G>A,MODERATE,,tolerated(0.15),benign(0.095),-1;CRYBG2,downstream_gene_variant,,ENST00000429942,,,MODIFIER,,,,-1;CRYBG2,upstream_gene_variant,,ENST00000374208,,,MODIFIER,,,,-1;CRYBG2,upstream_gene_variant,,ENST00000374211,,,MODIFIER,,,,-1;CRYBG2,downstream_gene_variant,,ENST00000522923,,,MODIFIER,,,,-1;CRYBG2,non_coding_transcript_exon_variant,,ENST00000520372,,n.414G>A,MODIFIER,,,,-1;AL451139.1,downstream_gene_variant,,ENST00000434718,,,MODIFIER,YES,,,1 4589/5245 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 1.195e-05 6.155e-05 0.0 0.0 0.0 4.625e-05 0.0 0.0 3.267e-05 0 97 3c53a947-143e-4671-b109-95b0b7011106 99 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS CRYBG2,non_coding_transcript_exon_variant,,ENST00000520372.5,n.414G>A,MODIFIER,;CRYBG2,missense_variant,p.R1480Q,ENST00000308182.10,c.4439G>A,MODERATE,YES;CRYBG2,missense_variant,p.R1804Q,ENST00000475866.3,c.5411G>A,MODERATE, +ATG9A 79065 BI GRCh38 2 219221302 219221302 + missense_variant,splice_region_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 12 5 c.2146C>G p.Leu716Val p.L716V ENST00000361242.9 NM_001077198.3 716 Ctc/Gtc 14/16 P2 C L/V protein_coding CCDS42820.1 2146/2520 GTGGAGCTGGA PANTHER:PTHR13038;PANTHER:PTHR13038:SF13 ENSP00000355173 14/16 ENST00000361242 Transcript ENSG00000198925 HGNC:22408 MODERATE NM_001077198.3 missense_variant benign(0.147) Unknown tolerated(0.11) Q7Z3C6.156 ATG9A HGNC -1 A0A024R438.41 2.0 UPI0000209615 Q7Z3C6-1 SNV ATG9A,missense_variant,p.L716V,ENST00000409618,,c.2146C>G,MODERATE,YES,tolerated(0.11),benign(0.147),-1;ATG9A,missense_variant,p.L716V,ENST00000396761,NM_024085.5,c.2146C>G,MODERATE,,tolerated(0.11),benign(0.147),-1;ATG9A,missense_variant,p.L716V,ENST00000361242,NM_001077198.3,c.2146C>G,MODERATE,,tolerated(0.11),benign(0.147),-1;ATG9A,missense_variant,p.L655V,ENST00000409422,,c.1963C>G,MODERATE,,tolerated(0.12),benign(0.147),-1;ATG9A,splice_region_variant,p.G235=,ENST00000429920,,c.705C>G,LOW,,,,-1;ABCB6,upstream_gene_variant,,ENST00000265316,NM_005689.4,,MODIFIER,YES,,,-1;ABCB6,upstream_gene_variant,,ENST00000295750,NM_001349828.2,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000428226,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000431715,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000432520,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000434939,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000436856,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000439812,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000443140,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000457841,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000455079,,,MODIFIER,,,,-1;AC068946.2,missense_variant,p.L132V,ENST00000446716,,c.394C>G,MODERATE,YES,tolerated(0.06),benign(0.328),-1;ATG9A,splice_region_variant,,ENST00000409033,,c.*500C>G,LOW,,,,-1;ATG9A,splice_region_variant,,ENST00000475339,,n.200C>G,LOW,,,,-1;ATG9A,downstream_gene_variant,,ENST00000412355,,,MODIFIER,,,,-1;ABCB6,upstream_gene_variant,,ENST00000417678,,,MODIFIER,,,,-1;ABCB6,upstream_gene_variant,,ENST00000448398,,,MODIFIER,,,,-1;ABCB6,upstream_gene_variant,,ENST00000452545,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000456708,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000466217,,,MODIFIER,,,,-1;ATG9A,downstream_gene_variant,,ENST00000486766,,,MODIFIER,,,,-1 2329/3770 mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 18 3c53a947-143e-4671-b109-95b0b7011106 17 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS ATG9A,synonymous_variant,splice_region_variant,p.G235=,ENST00000429920.1,c.705C>G,LOW,;ATG9A,missense_variant,splice_region_variant,p.L655V,ENST00000409422.5,c.1963C>G,MODERATE,;ATG9A,non_coding_transcript_exon_variant,,ENST00000475339.1,n.200C>G,MODIFIER,;ATG9A,missense_variant,splice_region_variant,p.L716V,ENST00000409618.5,c.2146C>G,MODERATE,;ATG9A,missense_variant,splice_region_variant,p.L716V,ENST00000361242.9,c.2146C>G,MODERATE,YES;ATG9A,missense_variant,splice_region_variant,p.L716V,ENST00000396761.6,c.2146C>G,MODERATE,;ATG9A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000409033.7,c.*500C>G,MODIFIER,;ENSG00000284820,missense_variant,splice_region_variant,NMD_transcript_variant,p.A131G,ENST00000446716.5,c.392C>G,MODERATE,YES +PTPN23 25930 BI GRCh38 3 47412576 47412576 + synonymous_variant Silent SNP T T C novel TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 3 11 c.4380T>C p.His1460= p.H1460= ENST00000265562.5 NM_015466.4 1460 caT/caC 24/25 P1 C H protein_coding YES CCDS2754.1 4380/4911 CGCCATGGTGT Gene3D:3.90.190.10 ENSP00000265562 24/25 ENST00000265562 Transcript 1.0 ENSG00000076201 HGNC:14406 LOW NM_015466.4 synonymous_variant 1.0 Unknown Q9H3S7.166 PTPN23 HGNC 1 1.0 UPI000006EBC4 SNV PTPN23,synonymous_variant,p.H1460=,ENST00000265562,NM_015466.4&NM_001304482.2,c.4380T>C,LOW,YES,,,1;SCAP,downstream_gene_variant,,ENST00000265565,NM_001320044.2&NM_012235.4,,MODIFIER,YES,,,-1;SCAP,downstream_gene_variant,,ENST00000428413,,,MODIFIER,,,,-1;SCAP,downstream_gene_variant,,ENST00000545718,,,MODIFIER,,,,-1;SCAP,downstream_gene_variant,,ENST00000648151,,,MODIFIER,,,,-1;PTPN23,3_prime_UTR_variant,,ENST00000602307,,c.*4057T>C,MODIFIER,,,,1;SCAP,downstream_gene_variant,,ENST00000320017,,,MODIFIER,,,,-1;SCAP,downstream_gene_variant,,ENST00000441517,,,MODIFIER,,,,-1;PTPN23,downstream_gene_variant,,ENST00000495653,,,MODIFIER,,,,1 4456/5237 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 52 3c53a947-143e-4671-b109-95b0b7011106 14 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS PTPN23,non_coding_transcript_exon_variant,,ENST00000683708.1,n.1140T>C,MODIFIER,;PTPN23,synonymous_variant,p.H1460=,ENST00000265562.5,c.4380T>C,LOW,YES;PTPN23,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000602307.5,c.*4057T>C,MODIFIER, +BAP1 8314 BI GRCh38 3 52409558 52409558 + stop_gained Nonsense_Mutation SNP G G A rs1553646284 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 24 101 c.118C>T p.Gln40Ter p.Q40* ENST00000460680.6 NM_004656.4 40 Cag/Tag 3/17 P1 A Q/* protein_coding YES CCDS2853.1 118/2190 pathogenic CCCCTGACATT COSM96361 CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 3/17 rs1553646284;COSV56230759 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 stop_gained 1;1 1.0 Unknown 0;1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D SNV BAP1,stop_gained,p.Q40*,ENST00000460680,NM_004656.4,c.118C>T,HIGH,YES,,,-1;BAP1,stop_gained,p.Q40*,ENST00000296288,,c.118C>T,HIGH,,,,-1;BAP1,5_prime_UTR_variant,,ENST00000470173,,c.-120C>T,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000461861,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000614886,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000615126,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000472337,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,stop_gained,p.Q40*,ENST00000490917,,c.118C>T,HIGH,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,,n.118C>T,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 248/3600 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 219 3c53a947-143e-4671-b109-95b0b7011106 125 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS BAP1,5_prime_UTR_variant,,ENST00000470173.1,c.-120C>T,MODIFIER,;BAP1,stop_gained,NMD_transcript_variant,p.Q40*,ENST00000490917.1,c.118C>T,HIGH,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984.5,n.118C>T,MODIFIER,;BAP1,stop_gained,p.Q40*,ENST00000296288.9,c.118C>T,HIGH,;BAP1,stop_gained,p.Q40*,ENST00000460680.6,c.118C>T,HIGH,YES +SLC18B1 116843 BI GRCh38 6 132784027 132784027 + synonymous_variant Silent SNP C C T rs1227055671 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 61 15 c.564G>A p.Leu188= p.L188= ENST00000275227.9 NM_052831.3 188 ttG/ttA 6/14 P2 T L protein_coding YES CCDS5163.1 564/1371 TGATACAAAAA Low_complexity_(Seg):seg;PROSITE_profiles:PS50850;CDD:cd17385;PANTHER:PTHR23506;PANTHER:PTHR23506:SF26;Gene3D:1.20.1250.20;Pfam:PF07690;Superfamily:SSF103473 ENSP00000275227 6/14 rs1227055671 ENST00000275227 Transcript ENSG00000146409 HGNC:21573 LOW NM_052831.3 2.971e-05 gnomAD_AMR synonymous_variant 1.0 Unknown Q6NT16.133 SLC18B1 HGNC -1 1.0 UPI000013DA50 SNV SLC18B1,synonymous_variant,p.L188=,ENST00000275227,NM_052831.3,c.564G>A,LOW,YES,,,-1;SLC18B1,synonymous_variant,p.L141=,ENST00000650278,,c.423G>A,LOW,,,,-1;SLC18B1,synonymous_variant,p.L115=,ENST00000647932,,c.345G>A,LOW,,,,-1;SLC18B1,intron_variant,,ENST00000367918,,n.298+6197G>A,MODIFIER,,,,-1;SLC18B1,downstream_gene_variant,,ENST00000460518,,,MODIFIER,,,,-1;SLC18B1,synonymous_variant,p.L141=,ENST00000650298,,c.423G>A,LOW,,,,-1;SLC18B1,3_prime_UTR_variant,,ENST00000650136,,c.*417G>A,MODIFIER,,,,-1 745/2452 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 4.029e-06 0.0 2.971e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 89 3c53a947-143e-4671-b109-95b0b7011106 76 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS SLC18B1,intron_variant,,ENST00000367918.1,n.298+6197G>A,MODIFIER,;SLC18B1,synonymous_variant,NMD_transcript_variant,p.L141=,ENST00000650298.1,c.423G>A,LOW,;SLC18B1,synonymous_variant,p.L115=,ENST00000647932.1,c.345G>A,LOW,;SLC18B1,synonymous_variant,p.L141=,ENST00000650278.1,c.423G>A,LOW,;SLC18B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000650136.1,c.*417G>A,MODIFIER,;SLC18B1,synonymous_variant,p.L188=,ENST00000275227.9,c.564G>A,LOW,YES +ARFGEF3 57221 BI GRCh38 6 138286913 138286913 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 6 5 c.2782C>G p.Leu928Val p.L928V ENST00000251691.5 NM_020340.5 928 Cta/Gta 16/34 P1 G L/V protein_coding YES CCDS5189.2 2782/6534 GCGCTCTAGGT PANTHER:PTHR10663;PANTHER:PTHR10663:SF344;Superfamily:SSF48371 ENSP00000251691 16/34 ENST00000251691 Transcript ENSG00000112379 HGNC:21213 MODERATE NM_020340.5 missense_variant 1.0 probably_damaging(0.991) Unknown deleterious(0) Q5TH69.122 ARFGEF3 HGNC 1 1.0 UPI000150AF4A SNV ARFGEF3,missense_variant,p.L928V,ENST00000251691,NM_020340.5,c.2782C>G,MODERATE,YES,deleterious(0),probably_damaging(0.991),1 2930/14859 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 26 3c53a947-143e-4671-b109-95b0b7011106 11 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS ARFGEF3,missense_variant,p.L928V,ENST00000251691.5,c.2782C>G,MODERATE,YES +GLIS3 169792 BI GRCh38 9 3856041 3856041 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 57 51 c.1976C>T p.Ser659Phe p.S659F ENST00000324333.14 NM_152629.4 659 tCt/tTt 8/10 A2 A S/F protein_coding CCDS6451.1 1976/2328 AAGAAGAGTTT PANTHER:PTHR45718;PANTHER:PTHR45718:SF1 ENSP00000325494 8/10 ENST00000324333 Transcript 1.0 ENSG00000107249 HGNC:28510 MODERATE missense_variant possibly_damaging(0.459) Unknown tolerated(0.19) Q8NEA6.149 GLIS3 HGNC -1 A0A0S2Z689.24 1.0 UPI00003675FE Q8NEA6-1 SNV GLIS3,missense_variant,p.S814F,ENST00000381971,NM_001042413.2,c.2441C>T,MODERATE,YES,tolerated(0.42),possibly_damaging(0.742),-1;GLIS3,missense_variant,p.S659F,ENST00000324333,NM_152629.3,c.1976C>T,MODERATE,,tolerated(0.19),possibly_damaging(0.459),-1;GLIS3,non_coding_transcript_exon_variant,,ENST00000461870,,n.797C>T,MODIFIER,,,,-1;GLIS3,non_coding_transcript_exon_variant,,ENST00000645252,,n.883C>T,MODIFIER,,,,-1;GLIS3,non_coding_transcript_exon_variant,,ENST00000467497,,n.981C>T,MODIFIER,,,,-1 2170/6667 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 91 3c53a947-143e-4671-b109-95b0b7011106 108 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS GLIS3,non_coding_transcript_exon_variant,,ENST00000464391.2,n.999C>T,MODIFIER,;GLIS3,non_coding_transcript_exon_variant,,ENST00000467497.6,n.981C>T,MODIFIER,;GLIS3,non_coding_transcript_exon_variant,,ENST00000645252.2,n.883C>T,MODIFIER,;GLIS3,intron_variant,NMD_transcript_variant,,ENST00000682846.1,c.132-26549C>T,MODIFIER,;GLIS3,non_coding_transcript_exon_variant,,ENST00000461870.5,n.797C>T,MODIFIER,;GLIS3,non_coding_transcript_exon_variant,,ENST00000682864.1,n.940C>T,MODIFIER,;GLIS3,missense_variant,p.S659F,ENST00000682749.1,c.1976C>T,MODERATE,;GLIS3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000491889.6,c.*1804C>T,MODIFIER,;GLIS3,missense_variant,p.S659F,ENST00000324333.14,c.1976C>T,MODERATE,;GLIS3,missense_variant,p.S814F,ENST00000381971.8,c.2441C>T,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 42 39 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 99 3c53a947-143e-4671-b109-95b0b7011106 81 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +TNFRSF1A 7132 BI GRCh38 12 6329932 6329932 + synonymous_variant Silent SNP G G A rs1338450773 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 3 6 c.903C>T p.Pro301= p.P301= ENST00000162749.7 NM_001065.4 301 ccC/ccT 9/10 P1 A P protein_coding YES CCDS8542.1 903/1368 TCACCGGGGGT Low_complexity_(Seg):seg;PANTHER:PTHR46861 ENSP00000162749 9/10 rs1338450773 ENST00000162749 Transcript 1.0 ENSG00000067182 HGNC:11916 LOW NM_001065.4 9.232e-05 gnomAD_AFR synonymous_variant 1.0 Unknown P19438.243 TNFRSF1A HGNC -1 1.0 UPI000002CE11 P19438-1 SNV TNFRSF1A,synonymous_variant,p.P301=,ENST00000162749,NM_001065.4,c.903C>T,LOW,YES,,,-1;TNFRSF1A,synonymous_variant,p.P258=,ENST00000540022,NM_001346091.2&NM_001346092.2,c.774C>T,LOW,,,,-1;PLEKHG6,downstream_gene_variant,,ENST00000011684,NM_018173.3,,MODIFIER,,,,1;PLEKHG6,downstream_gene_variant,,ENST00000304581,,,MODIFIER,,,,1;TNFRSF1A,downstream_gene_variant,,ENST00000366159,,,MODIFIER,,,,-1;PLEKHG6,downstream_gene_variant,,ENST00000396988,NM_001144856.1,,MODIFIER,YES,,,1;TNFRSF1A,downstream_gene_variant,,ENST00000440083,,,MODIFIER,,,,-1;PLEKHG6,downstream_gene_variant,,ENST00000449001,NM_001144857.1,,MODIFIER,,,,1;TNFRSF1A,downstream_gene_variant,,ENST00000536194,,,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000539372,,,MODIFIER,,,,-1;TNFRSF1A,non_coding_transcript_exon_variant,,ENST00000543359,,n.315C>T,MODIFIER,,,,-1;TNFRSF1A,intron_variant,,ENST00000537842,,n.373-33C>T,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000437813,,,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000535038,,,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000535958,,,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000538363,,,MODIFIER,,,,-1;TNFRSF1A,3_prime_UTR_variant,,ENST00000534885,,c.*380C>T,MODIFIER,,,,-1;TNFRSF1A,3_prime_UTR_variant,,ENST00000543995,,c.*490C>T,MODIFIER,,,,-1;TNFRSF1A,non_coding_transcript_exon_variant,,ENST00000536717,,n.807C>T,MODIFIER,,,,-1;TNFRSF1A,downstream_gene_variant,,ENST00000543048,,,MODIFIER,,,,-1 1165/2171 muse;varscan2 892e7630-b11e-47bd-987c-327d33258e11 5.511e-06 9.232e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.757210030627903e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542919926578179e-05 0.0 0.0 0 10 3c53a947-143e-4671-b109-95b0b7011106 9 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS TNFRSF1A,intron_variant,,ENST00000537842.5,n.373-33C>T,MODIFIER,;TNFRSF1A,synonymous_variant,p.P258=,ENST00000540022.5,c.774C>T,LOW,;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000543995.5,c.*490C>T,MODIFIER,;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000535958.2,c.*730C>T,MODIFIER,;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698339.1,c.*398C>T,MODIFIER,;TNFRSF1A,non_coding_transcript_exon_variant,,ENST00000366159.9,n.2004C>T,MODIFIER,;TNFRSF1A,non_coding_transcript_exon_variant,,ENST00000698338.1,n.1517C>T,MODIFIER,;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000437813.8,c.*364C>T,MODIFIER,;TNFRSF1A,non_coding_transcript_exon_variant,,ENST00000698337.1,n.864C>T,MODIFIER,;TNFRSF1A,synonymous_variant,p.P374=,ENST00000440083.7,c.1122C>T,LOW,;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000698340.1,c.*142C>T,MODIFIER,;TNFRSF1A,synonymous_variant,p.P301=,ENST00000162749.7,c.903C>T,LOW,YES;TNFRSF1A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000534885.5,c.*380C>T,MODIFIER, +RESF1 55196 BI GRCh38 12 31984714 31984714 + synonymous_variant Silent SNP C C T rs150095870 TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 39 26 c.3759C>T p.Asp1253= p.D1253= ENST00000312561.9 NM_018169.4 1253 gaC/gaT 4/6 P1 T D protein_coding YES CCDS8725.2 3759/5244 CAAGACGACAG Pfam:PF15395;PANTHER:PTHR21604;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000310338 0.0 0.0001163 4/6 rs150095870 ENST00000312561 Transcript ENSG00000174718 HGNC:25559 LOW NM_018169.4 0.000187 gnomAD_FIN synonymous_variant 1.0 Unknown Q9HCM1.116 RESF1 HGNC 1 1.0 UPI0000577B2F SNV RESF1,synonymous_variant,p.D1253=,ENST00000312561,NM_018169.4,c.3759C>T,LOW,YES,,,1;RESF1,downstream_gene_variant,,ENST00000381054,,,MODIFIER,,,,1;RESF1,downstream_gene_variant,,ENST00000540924,,,MODIFIER,,,,1;RESF1,intron_variant,,ENST00000397578,,n.139-2525C>T,MODIFIER,,,,1;RESF1,intron_variant,,ENST00000535596,,n.318-2525C>T,MODIFIER,,,,1;RESF1,intron_variant,,ENST00000541981,,n.218-7664C>T,MODIFIER,,,,1;RESF1,upstream_gene_variant,,ENST00000543763,,,MODIFIER,,,,1 4177/6234 muse;mutect2;varscan2 892e7630-b11e-47bd-987c-327d33258e11 7.581e-05 0.0 6.496e-05 0.0 0.0 0.000187 8.214e-05 0.0 0.00011 4.735169932246208e-05 0.0 0.0 0.0 0.0 0.0 0.0001888929982669 fin 0.0001888929982669 0.0 7.715810352237895e-05 0.0 0.0 0 50 3c53a947-143e-4671-b109-95b0b7011106 65 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS RESF1,intron_variant,,ENST00000397578.7,n.139-2525C>T,MODIFIER,;RESF1,intron_variant,,ENST00000535596.5,n.318-2525C>T,MODIFIER,;RESF1,synonymous_variant,p.D1253=,ENST00000312561.9,c.3759C>T,LOW,YES;RESF1,intron_variant,,ENST00000541981.5,n.218-7664C>T,MODIFIER, +DMXL2 23312 BI GRCh38 15 51499021 51499022 + frameshift_variant Frame_Shift_Ins INS - - A novel TCGA-V4-A9EX-01A TCGA-V4-A9EX-10A Somatic 127 69 c.4202dup p.Ser1402LysfsTer21 p.S1402Kfs*21 ENST00000251076.9 NM_015263.5 1401 gta/gtTa 18/43 A2 A V/VX protein_coding CCDS10141.1 4202-4203/9111 CCACTTACACT PANTHER:PTHR13950;PANTHER:PTHR13950:SF13 ENSP00000251076 18/43 ENST00000251076 Transcript 1.0 ENSG00000104093 HGNC:2938 HIGH frameshift_variant Unknown Q8TDJ6.153 DMXL2 HGNC -1 A0A024R5V2.44 1.0 UPI000013CCDD Q8TDJ6-1 insertion DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000251076,NM_015263.5&NM_001378464.1&NM_001378462.1,c.4202dup,HIGH,,,,-1;DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000560891,NM_001378458.1&NM_001378459.1&NM_001378457.1,c.4202dup,HIGH,YES,,,-1;DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000543779,NM_001174116.3&NM_001378463.1&NM_001378461.1,c.4202dup,HIGH,,,,-1;DMXL2,intron_variant,,ENST00000449909,NM_001378460.1&NM_001174117.3,c.2765-3888dup,MODIFIER,,,,-1;AC066613.2,downstream_gene_variant,,ENST00000561007,,,MODIFIER,YES,,,1 4490-4491/10672 mutect2;pindel;varscan2 892e7630-b11e-47bd-987c-327d33258e11 0 168 3c53a947-143e-4671-b109-95b0b7011106 196 423d56b2-46c1-43e9-9d81-4562189e5475 SUCCESS DMXL2,intron_variant,,ENST00000449909.7,c.2765-3888_2765-3887insT,MODIFIER,;DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000560891.6,c.4202dup,HIGH,YES;DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000543779.6,c.4202dup,HIGH,;DMXL2,frameshift_variant,p.S1402Kfs*21,ENST00000251076.9,c.4202dup,HIGH, +AHCTF1 25909 BI GRCh38 1 246842770 246842770 + missense_variant Missense_Mutation SNP C C T rs1013821654 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 47 25 c.6532G>A p.Asp2178Asn p.D2178N ENST00000648844.2 NM_001323343.2 2178 Gat/Aat 35/36 A2 T D/N protein_coding YES 6637/6906 TGCATCATCTT PANTHER:PTHR21583;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000355464 35/36 rs1013821654 ENST00000366508 Transcript ENSG00000153207 HGNC:24618 MODERATE 0.0003269 gnomAD_OTH missense_variant 1.0 benign(0.021) Unknown tolerated(0.09) Q8WYP5.154 AHCTF1 HGNC -1 5.0 UPI000059D0E4 Q8WYP5-2 SNV AHCTF1,missense_variant,p.D2178N,ENST00000648844,NM_001323343.2&NM_001323342.2,c.6532G>A,MODERATE,,tolerated(0.09),benign(0.018),-1;AHCTF1,missense_variant,p.D2213N,ENST00000366508,,c.6637G>A,MODERATE,YES,tolerated(0.09),benign(0.021),-1;AHCTF1,missense_variant,p.D2187N,ENST00000326225,NM_015446.5,c.6559G>A,MODERATE,,tolerated(0.09),benign(0.059),-1;AHCTF1,intron_variant,,ENST00000470300,,n.5140+1025G>A,MODIFIER,,,,-1;AHCTF1,stop_retained_variant,p.*81=,ENST00000498601,,c.242G>A,LOW,,,,-1;KIF28P,upstream_gene_variant,,ENST00000504864,,,MODIFIER,YES,,,-1 6774/8751 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 7.976e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0003269 0.0 2.028860035352409e-05 0.0 0.0 0.0001326079946011 0.0 0.0 0.0 amr 0.0001326079946011 0.0 0.0 0.0004945599939674 0.0 0 108 43c0e262-1510-4418-b0b0-df3c9ed75b94 72 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS AHCTF1,stop_retained_variant,NMD_transcript_variant,p.*81=,ENST00000498601.1,c.242G>A,LOW,;AHCTF1,missense_variant,p.D2187N,ENST00000326225.3,c.6559G>A,MODERATE,;AHCTF1,missense_variant,p.D2213N,ENST00000366508.5,c.6637G>A,MODERATE,;AHCTF1,intron_variant,,ENST00000470300.5,n.5140+1025G>A,MODIFIER,;AHCTF1,missense_variant,p.D2178N,ENST00000648844.2,c.6532G>A,MODERATE,YES +SNTG2 54221 BI GRCh38 2 1259375 1259375 + synonymous_variant Silent SNP C C T rs1405891115 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 38 8 c.1011C>T p.Ser337= p.S337= ENST00000308624.10 NM_018968.4 337 agC/agT 13/17 P1 T S protein_coding YES CCDS46220.1 1011/1620 GTGAGCACATT PANTHER:PTHR10554;PANTHER:PTHR10554:SF3;Superfamily:SSF50729 ENSP00000311837 13/17 rs1405891115 ENST00000308624 Transcript ENSG00000172554 HGNC:13741 LOW NM_018968.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q9NY99.146 SNTG2 HGNC 1 1.0 UPI0000456D73 Q9NY99-1 SNV SNTG2,synonymous_variant,p.S337=,ENST00000308624,NM_018968.4,c.1011C>T,LOW,YES,,,1;SNTG2,synonymous_variant,p.S210=,ENST00000407292,,c.630C>T,LOW,,,,1;SNTG2,upstream_gene_variant,,ENST00000471239,,,MODIFIER,,,,1;SNTG2,downstream_gene_variant,,ENST00000489646,,,MODIFIER,,,,1 1159/1907 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 46 43c0e262-1510-4418-b0b0-df3c9ed75b94 46 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS SNTG2,synonymous_variant,p.S210=,ENST00000407292.1,c.630C>T,LOW,;SNTG2,synonymous_variant,p.S337=,ENST00000308624.10,c.1011C>T,LOW,YES +CASTOR3P 352954 BI GRCh38 7 100271928 100271944 + non_coding_transcript_exon_variant RNA DEL GTGCTCCAGGATGTGGA GTGCTCCAGGATGTGGA - novel TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 18 4 n.40_56del ENST00000647868.1 1/5 - processed_transcript YES CAGCCGGTGCTCCAGGATGTGGAGTTCC 1/8 ENST00000328453 Transcript ENSG00000239521 HGNC:29954 MODIFIER non_coding_transcript_exon_variant 1.0 Unknown CASTOR3 HGNC -1 1.0 deletion CASTOR3,non_coding_transcript_exon_variant,,ENST00000328453,,n.263_279del,MODIFIER,YES,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000543273,,n.265_281del,MODIFIER,,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000649671,,n.275_291del,MODIFIER,,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000414739,,n.271_287del,MODIFIER,,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000435519,,n.271_287del,MODIFIER,,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000454084,,n.244_260del,MODIFIER,,,,-1;CASTOR3,non_coding_transcript_exon_variant,,ENST00000647868,,n.40_56del,MODIFIER,,,,-1 263-279/3526 mutect2;pindel 3a161c85-2544-4283-a10d-e332c9dd1692 0 35 43c0e262-1510-4418-b0b0-df3c9ed75b94 22 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS CASTOR3P,non_coding_transcript_exon_variant,,ENST00000701563.1,n.22_38del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000689058.1,n.81_97del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000647868.1,n.40_56del,MODIFIER,YES;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000702747.1,n.28_44del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000701477.1,n.24_40del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000700967.1,n.17_33del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000414739.3,n.271_287del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000435519.6,n.271_287del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000454084.5,n.244_260del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000328453.9,n.263_279del,MODIFIER,;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000649671.1,n.275_291del,MODIFIER,YES;CASTOR3P,non_coding_transcript_exon_variant,,ENST00000543273.5,n.265_281del,MODIFIER, +PRRG4 79056 BI GRCh38 11 32836725 32836725 + synonymous_variant Silent SNP G G A rs1388798496 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 33 14 c.171G>A p.Leu57= p.L57= ENST00000257836.4 NM_024081.6 57 ctG/ctA 3/6 P1 A L protein_coding YES CCDS7881.1 171/681 GATCTGGAGCT PROSITE_profiles:PS50998;PANTHER:PTHR24251;PANTHER:PTHR24251:SF15;Pfam:PF00594;Gene3D:4.10.740.10;SMART:SM00069;Superfamily:SSF57630;Prints:PR00001 ENSP00000257836 3/6 rs1388798496 ENST00000257836 Transcript ENSG00000135378 HGNC:30799 LOW NM_024081.6 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q9BZD6.151 PRRG4 HGNC 1 A0A0S2Z5N9.33 1.0 UPI000013707A SNV PRRG4,synonymous_variant,p.L57=,ENST00000257836,NM_024081.6,c.171G>A,LOW,YES,,,1 440/5543 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 56 43c0e262-1510-4418-b0b0-df3c9ed75b94 47 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS PRRG4,synonymous_variant,p.L57=,ENST00000257836.4,c.171G>A,LOW,YES +ANXA2 302 BI GRCh38 15 60355986 60355986 + missense_variant Missense_Mutation SNP T T A novel TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 20 19 c.461A>T p.Asp154Val p.D154V ENST00000396024.7 NM_001136015.3 154 gAt/gTt 8/14 P1 A D/V protein_coding CCDS10175.1 461/1020 CCAGATCAGTC Gene3D:1.10.220.10;PDB-ENSP_mappings:1w7b.A;PDB-ENSP_mappings:1xjl.A;PDB-ENSP_mappings:1xjl.B;PDB-ENSP_mappings:2hyu.A;PDB-ENSP_mappings:2hyv.A;PDB-ENSP_mappings:2hyw.A;PDB-ENSP_mappings:2hyw.B;PDB-ENSP_mappings:5lpu.A;PDB-ENSP_mappings:5lpu.B;PDB-ENSP_mappings:5lpx.A;PDB-ENSP_mappings:5lq0.A;PDB-ENSP_mappings:5lq0.B;PDB-ENSP_mappings:5lq2.A;PDB-ENSP_mappings:5lq2.B;PDB-ENSP_mappings:5n7d.A;PDB-ENSP_mappings:5n7d.B;PDB-ENSP_mappings:5n7f.A;PDB-ENSP_mappings:5n7f.B;PDB-ENSP_mappings:5n7g.A;PDB-ENSP_mappings:5n7g.B;PDB-ENSP_mappings:6t58.A;PDB-ENSP_mappings:6t58.B;PDB-ENSP_mappings:6twq.A;PDB-ENSP_mappings:6twq.B;PDB-ENSP_mappings:6twu.A;PDB-ENSP_mappings:6twu.B;PDB-ENSP_mappings:6twx.A;PDB-ENSP_mappings:6twx.B;PDB-ENSP_mappings:6twy.A;PDB-ENSP_mappings:6twy.B;Pfam:PF00191;PROSITE_patterns:PS00223;PROSITE_profiles:PS51897;PANTHER:PTHR10502;PANTHER:PTHR10502:SF18;SMART:SM00335;Superfamily:SSF47874 ENSP00000379342 8/14 ENST00000396024 Transcript ENSG00000182718 HGNC:537 MODERATE missense_variant possibly_damaging(0.653) Unknown tolerated(0.06) P07355.239 ANXA2 HGNC -1 A0A024R5Z7.53 1.0 UPI0000161B7A P07355-1 SNV ANXA2,missense_variant,p.D154V,ENST00000678450,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000678061,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D182V,ENST00000559780,,c.545A>T,MODERATE,YES,tolerated(0.06),benign(0.038),-1;ANXA2,missense_variant,p.D154V,ENST00000560468,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000557906,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000677968,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000678870,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000559956,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000396024,NM_001136015.3,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000558558,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000559818,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000679109,,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000451270,NM_004039.3,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D37V,ENST00000559113,,c.110A>T,MODERATE,,deleterious(0),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D37V,ENST00000558985,,c.110A>T,MODERATE,,deleterious(0),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D172V,ENST00000332680,NM_001002858.3,c.515A>T,MODERATE,,tolerated(0.05),benign(0.267),-1;ANXA2,missense_variant,p.D154V,ENST00000421017,NM_001002857.2,c.461A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000560367,,c.461A>T,MODERATE,,deleterious(0.03),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D123V,ENST00000559176,,c.368A>T,MODERATE,,deleterious(0),benign(0.019),-1;ANXA2,missense_variant,p.D154V,ENST00000560165,,c.461A>T,MODERATE,,deleterious(0.05),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D37V,ENST00000560466,,c.110A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D154V,ENST00000560389,,c.461A>T,MODERATE,,deleterious(0.05),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D89V,ENST00000558132,,c.266A>T,MODERATE,,deleterious(0),benign(0.029),-1;ANXA2,missense_variant,p.D37V,ENST00000559725,,c.110A>T,MODERATE,,deleterious(0),possibly_damaging(0.653),-1;ANXA2,missense_variant,p.D37V,ENST00000558998,,c.110A>T,MODERATE,,deleterious(0),possibly_damaging(0.653),-1;ANXA2,downstream_gene_variant,,ENST00000558986,,,MODIFIER,,,,-1;ANXA2,downstream_gene_variant,,ENST00000559350,,,MODIFIER,,,,-1;ANXA2,downstream_gene_variant,,ENST00000559467,,,MODIFIER,,,,-1;ANXA2,stop_lost,p.*156Cext*12,ENST00000676687,,c.468A>T,HIGH,,,,-1;ANXA2,missense_variant,p.D154V,ENST00000560014,,c.461A>T,MODERATE,,deleterious(0.03),benign(0.019),-1;ANXA2,missense_variant,p.D154V,ENST00000558169,,c.461A>T,MODERATE,,deleterious(0.03),benign(0.011),-1;ANXA2,3_prime_UTR_variant,,ENST00000561022,,c.*315A>T,MODIFIER,,,,-1;ANXA2,3_prime_UTR_variant,,ENST00000558503,,c.*72A>T,MODIFIER,,,,-1;ANXA2,non_coding_transcript_exon_variant,,ENST00000504475,,n.2799A>T,MODIFIER,,,,-1;ANXA2,non_coding_transcript_exon_variant,,ENST00000678796,,n.607A>T,MODIFIER,,,,-1;ANXA2,non_coding_transcript_exon_variant,,ENST00000559647,,n.416A>T,MODIFIER,,,,-1;ANXA2,non_coding_transcript_exon_variant,,ENST00000559559,,n.518A>T,MODIFIER,,,,-1;ANXA2,downstream_gene_variant,,ENST00000677258,,,MODIFIER,,,,-1 621/1676 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0 49 43c0e262-1510-4418-b0b0-df3c9ed75b94 39 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS ANXA2,missense_variant,p.D37V,ENST00000559725.5,c.110A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000560389.5,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000560165.5,c.461A>T,MODERATE,;ANXA2,non_coding_transcript_exon_variant,,ENST00000559559.5,n.518A>T,MODIFIER,;ANXA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000558503.6,c.*72A>T,MODIFIER,;ANXA2,missense_variant,p.D37V,ENST00000558998.5,c.110A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000560367.6,c.461A>T,MODERATE,;ANXA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000561022.5,c.*315A>T,MODIFIER,;ANXA2,missense_variant,p.D89V,ENST00000558132.5,c.266A>T,MODERATE,;ANXA2,missense_variant,p.D37V,ENST00000560466.5,c.110A>T,MODERATE,;ANXA2,missense_variant,p.I123F,ENST00000559176.5,c.367A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000421017.6,c.461A>T,MODERATE,;ANXA2,non_coding_transcript_exon_variant,,ENST00000504475.6,n.2799A>T,MODIFIER,;ANXA2,missense_variant,NMD_transcript_variant,p.D154V,ENST00000560014.5,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D172V,ENST00000332680.8,c.515A>T,MODERATE,;ANXA2,non_coding_transcript_exon_variant,,ENST00000559647.2,n.416A>T,MODIFIER,;ANXA2,non_coding_transcript_exon_variant,,ENST00000678796.1,n.607A>T,MODIFIER,;ANXA2,missense_variant,p.D37V,ENST00000558985.6,c.110A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000451270.7,c.461A>T,MODERATE,YES;ANXA2,missense_variant,p.D182V,ENST00000559780.6,c.545A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000677968.1,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000678061.1,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000678450.1,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000560468.6,c.461A>T,MODERATE,;ANXA2,missense_variant,NMD_transcript_variant,p.D154V,ENST00000558169.6,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000559956.6,c.461A>T,MODERATE,;ANXA2,stop_lost,NMD_transcript_variant,p.*156Cext*12,ENST00000676687.1,c.468A>T,HIGH,;ANXA2,missense_variant,p.D37V,ENST00000559113.6,c.110A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000678870.1,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000559818.6,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000558558.6,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000679109.1,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000557906.6,c.461A>T,MODERATE,;ANXA2,missense_variant,p.D154V,ENST00000396024.7,c.461A>T,MODERATE, +ABHD2 11057 BI GRCh38 15 89151693 89151693 + missense_variant Missense_Mutation SNP A A G novel TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 76 39 c.211A>G p.Ile71Val p.I71V ENST00000352732.10 NM_001416423.1 71 Atc/Gtc 4/11 P1 G I/V protein_coding YES CCDS10348.1 211/1278 CGTTGATCTGG PIRSF:PIRSF005211;PANTHER:PTHR10794;PANTHER:PTHR10794:SF80 ENSP00000268129 4/11 ENST00000352732 Transcript ENSG00000140526 HGNC:18717 MODERATE NM_152924.5 missense_variant 1.0 benign(0.027) Unknown deleterious(0.01) P08910.165 ABHD2 HGNC 1 A0A024RC89.43 1.0 UPI000012E24E SNV ABHD2,missense_variant,p.I71V,ENST00000352732,NM_152924.5,c.211A>G,MODERATE,YES,deleterious(0.01),benign(0.027),1;ABHD2,missense_variant,p.I71V,ENST00000565973,NM_007011.8,c.211A>G,MODERATE,,deleterious(0.01),benign(0.027),1;ABHD2,missense_variant,p.I71V,ENST00000565066,,c.211A>G,MODERATE,,deleterious(0.01),benign(0.027),1;ABHD2,missense_variant,p.I71V,ENST00000569411,,c.211A>G,MODERATE,,deleterious(0.01),benign(0.027),1;ABHD2,non_coding_transcript_exon_variant,,ENST00000562073,,n.35A>G,MODIFIER,,,,1 425/8424 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0 85 43c0e262-1510-4418-b0b0-df3c9ed75b94 115 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS ABHD2,non_coding_transcript_exon_variant,,ENST00000562073.1,n.35A>G,MODIFIER,;ABHD2,missense_variant,p.I71V,ENST00000352732.10,c.211A>G,MODERATE,YES;ABHD2,missense_variant,p.I71V,ENST00000565973.5,c.211A>G,MODERATE,;ABHD2,missense_variant,p.I71V,ENST00000565066.5,c.211A>G,MODERATE,;ABHD2,missense_variant,p.I71V,ENST00000569411.5,c.211A>G,MODERATE, +RGS11 8786 BI GRCh38 16 271228 271228 + synonymous_variant Silent SNP G G A rs370941756 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 12 9 c.837C>T p.Asp279= p.D279= ENST00000397770.8 NM_183337.3 279 gaC/gaT 12/17 P4 A D protein_coding YES CCDS42088.1 837/1404 TAGGCGTCATT COSM5448860 SMART:SM01224;SMART:SM00224;Pfam:PF00631;Gene3D:1.20.58.1850;PANTHER:PTHR45746:SF3;PANTHER:PTHR45746 ENSP00000380876 0.0 0.0001163 12/17 rs370941756;COSV51451845 ENST00000397770 Transcript ENSG00000076344 HGNC:9993 LOW NM_183337.3 0.0004249 gnomAD_SAS synonymous_variant 0;1 1.0 Unknown 0;1 O94810.168 RGS11 HGNC -1 Q4TT70.140 1.0 UPI000013382E O94810-1 SNV RGS11,synonymous_variant,p.D279=,ENST00000397770,NM_183337.3,c.837C>T,LOW,YES,,,-1;RGS11,synonymous_variant,p.D258=,ENST00000316163,NM_001286486.2&NM_003834.3,c.774C>T,LOW,,,,-1;RGS11,synonymous_variant,p.D268=,ENST00000359740,NM_001286485.2,c.804C>T,LOW,,,,-1;FAM234A,downstream_gene_variant,,ENST00000301679,,,MODIFIER,,,,1;RGS11,3_prime_UTR_variant,,ENST00000168869,,c.*343C>T,MODIFIER,,,,-1;RGS11,non_coding_transcript_exon_variant,,ENST00000477143,,n.2777C>T,MODIFIER,,,,-1;RGS11,non_coding_transcript_exon_variant,,ENST00000481672,,n.527C>T,MODIFIER,,,,-1;FAM234A,intron_variant,,ENST00000659283,,c.*153-654G>A,MODIFIER,,,,1;RGS11,downstream_gene_variant,,ENST00000472466,,,MODIFIER,,,,-1;RGS11,downstream_gene_variant,,ENST00000493449,,,MODIFIER,,,,-1;FAM234A,downstream_gene_variant,,ENST00000600536,,,MODIFIER,,,,1;FAM234A,downstream_gene_variant,,ENST00000653392,,,MODIFIER,,,,1;FAM234A,downstream_gene_variant,,ENST00000654053,,,MODIFIER,,,,1;FAM234A,downstream_gene_variant,,ENST00000666018,,,MODIFIER,,,,1;Z69667.1,intron_variant,,ENST00000412541,,n.279+2223G>A,MODIFIER,,,,1;Z69667.1,intron_variant,,ENST00000435035,,n.279+2223G>A,MODIFIER,YES,,,1 870/2399 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0.0001047 0.0001899 5.797e-05 0.0 5.452e-05 0.0 6.259e-05 0.0 0.0004249 0.0001013899964164 9.72479028860107e-05 0.0 0.0001324500044574 0.0 0.0 0.0 amr 0.0001324500044574 0.0 0.0001080310030374 0.000494070991408 0.0002082470018649 0 23 43c0e262-1510-4418-b0b0-df3c9ed75b94 21 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS RGS11,non_coding_transcript_exon_variant,,ENST00000481672.5,n.527C>T,MODIFIER,;RGS11,synonymous_variant,p.D268=,ENST00000359740.6,c.804C>T,LOW,;ENSG00000286901,intron_variant,,ENST00000435035.5,n.279+2223G>A,MODIFIER,YES;ENSG00000286901,intron_variant,,ENST00000412541.5,n.279+2223G>A,MODIFIER,;RGS11,non_coding_transcript_exon_variant,,ENST00000477143.5,n.2777C>T,MODIFIER,;RGS11,synonymous_variant,p.D258=,ENST00000316163.9,c.774C>T,LOW,;RGS11,synonymous_variant,p.D279=,ENST00000397770.8,c.837C>T,LOW,YES;RGS11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000168869.12,c.*343C>T,MODIFIER,;FAM234A,intron_variant,NMD_transcript_variant,,ENST00000659283.1,c.*153-654G>A,MODIFIER, +PRR14 78994 BI GRCh38 16 30654856 30654856 + missense_variant Missense_Mutation SNP G G A novel TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 22 16 c.886G>A p.Ala296Thr p.A296T ENST00000300835.9 NM_024031.5 296 Gct/Act 8/12 P1 A A/T protein_coding CCDS10687.1 886/1758 CTGGGGCTGCT PANTHER:PTHR14522;PANTHER:PTHR14522:SF2;MobiDB_lite:mobidb-lite ENSP00000300835 8/12 ENST00000300835 Transcript ENSG00000156858 HGNC:28458 MODERATE NM_024031.5 missense_variant possibly_damaging(0.503) Unknown deleterious(0.02) Q9BWN1.121 PRR14 HGNC 1 A0A024QZB5.43 1.0 UPI000006F1D0 SNV PRR14,missense_variant,p.A296T,ENST00000542965,NM_001320464.2,c.886G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.503),1;PRR14,missense_variant,p.A296T,ENST00000300835,NM_024031.5,c.886G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.503),1;FBRS,upstream_gene_variant,,ENST00000356166,NM_001105079.3,,MODIFIER,YES,,,1;PRR14,downstream_gene_variant,,ENST00000568754,,,MODIFIER,,,,1;PRR14,downstream_gene_variant,,ENST00000569864,,,MODIFIER,,,,1;PRR14,non_coding_transcript_exon_variant,,ENST00000571654,,n.36G>A,MODIFIER,,,,1;PRR14,non_coding_transcript_exon_variant,,ENST00000287463,,n.1150G>A,MODIFIER,,,,1;PRR14,non_coding_transcript_exon_variant,,ENST00000564946,,n.1161G>A,MODIFIER,,,,1;PRR14,non_coding_transcript_exon_variant,,ENST00000567322,,n.459G>A,MODIFIER,,,,1;PRR14,downstream_gene_variant,,ENST00000563211,,,MODIFIER,,,,1;PRR14,downstream_gene_variant,,ENST00000563399,,,MODIFIER,,,,1;PRR14,downstream_gene_variant,,ENST00000565410,,,MODIFIER,,,,1;PRR14,upstream_gene_variant,,ENST00000565977,,,MODIFIER,,,,1;PRR14,upstream_gene_variant,,ENST00000567989,,,MODIFIER,,,,1 1104/2078 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0 36 43c0e262-1510-4418-b0b0-df3c9ed75b94 38 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS PRR14,non_coding_transcript_exon_variant,,ENST00000571654.1,n.36G>A,MODIFIER,;PRR14,non_coding_transcript_exon_variant,,ENST00000567322.1,n.459G>A,MODIFIER,;PRR14,missense_variant,p.A296T,ENST00000542965.2,c.886G>A,MODERATE,;PRR14,non_coding_transcript_exon_variant,,ENST00000287463.8,n.1150G>A,MODIFIER,;PRR14,missense_variant,p.A296T,ENST00000300835.9,c.886G>A,MODERATE,YES;PRR14,non_coding_transcript_exon_variant,,ENST00000564946.5,n.1161G>A,MODIFIER, +CHST4 10164 BI GRCh38 16 71537215 71537215 + missense_variant Missense_Mutation SNP C C T rs768338660 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 20 7 c.538C>T p.Arg180Cys p.R180C ENST00000338482.5 NM_005769.2 180 Cgc/Tgc 3/3 P1 T R/C protein_coding YES CCDS10902.1 538/1161 AGGTGCGCTTC COSM272031 PANTHER:PTHR10704;PANTHER:PTHR10704:SF40;PIRSF:PIRSF005883;Pfam:PF00685;Gene3D:3.40.50.300;Superfamily:SSF52540 ENSP00000341206 3/3 rs768338660;COSV58296873 ENST00000338482 Transcript ENSG00000140835 HGNC:1972 MODERATE 5.437e-05 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q8NCG5.136 CHST4 HGNC 1 4.0 UPI000006F41D SNV CHST4,missense_variant,p.R180C,ENST00000338482,NM_005769.2,c.538C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;CHST4,missense_variant,p.R180C,ENST00000539698,NM_001166395.2,c.538C>T,MODERATE,,deleterious(0),probably_damaging(1),1;ZNF19,intron_variant,,ENST00000564225,,c.-255+9062G>A,MODIFIER,,,,-1;ZNF19,intron_variant,,ENST00000566202,,c.-190+8987G>A,MODIFIER,,,,-1;ZNF19,intron_variant,,ENST00000568446,,n.105+9062G>A,MODIFIER,,,,-1;CHST4,non_coding_transcript_exon_variant,,ENST00000572693,,n.630C>T,MODIFIER,,,,1;AC010547.2,downstream_gene_variant,,ENST00000568523,,,MODIFIER,YES,,,-1 881/2412 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 1.591e-05 0.0 0.0 0.0 5.437e-05 0.0 1.76e-05 0.0 3.266e-05 1.3526099792215971e-05 0.0 0.0 0.0 0.0 0.0002021840045927 0.0 0.0 0.0 0.0 0.0002085940068354 0 55 43c0e262-1510-4418-b0b0-df3c9ed75b94 27 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS CHST4,non_coding_transcript_exon_variant,,ENST00000572693.1,n.630C>T,MODIFIER,;CHST4,missense_variant,p.R180C,ENST00000539698.4,c.538C>T,MODERATE,YES;CHST4,missense_variant,p.R180C,ENST00000338482.5,c.538C>T,MODERATE,;ZNF19,intron_variant,,ENST00000568446.1,n.105+9062G>A,MODIFIER,;ZNF19,intron_variant,,ENST00000566202.5,c.-190+8987G>A,MODIFIER,;ZNF19,intron_variant,,ENST00000564225.5,c.-255+9062G>A,MODIFIER, +MYH4 4622 BI GRCh38 17 10452207 10452207 + missense_variant Missense_Mutation SNP C C T rs764056557 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 109 58 c.3472G>A p.Gly1158Ser p.G1158S ENST00000255381.2 NM_017533.2 1158 Ggt/Agt 27/40 P1 T G/S protein_coding YES CCDS11154.1 3472/5820 CCCACCGGCTT COSM4063819 Coiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR45615;PANTHER:PTHR45615:SF3;Superfamily:SSF90257 ENSP00000255381 27/40 rs764056557;COSV55113103 ENST00000255381 Transcript ENSG00000264424 HGNC:7574 MODERATE NM_017533.2 6.533e-05 gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.7) Unknown deleterious(0.04) 0;1 Q9Y623.171 MYH4 HGNC -1 1.0 UPI000013CEAB SNV MYH4,missense_variant,p.G1158S,ENST00000255381,NM_017533.2,c.3472G>A,MODERATE,YES,deleterious(0.04),possibly_damaging(0.7),-1;AC005323.2,intron_variant,,ENST00000399342,,n.206+45930C>T,MODIFIER,YES,,,1;AC005323.2,intron_variant,,ENST00000581304,,n.143+45969C>T,MODIFIER,,,,1;MYHAS,intron_variant,,ENST00000587182,,n.155+45969C>T,MODIFIER,YES,,,1 3583/6016 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 7.967e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.533e-05 6.760959877283312e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 141 43c0e262-1510-4418-b0b0-df3c9ed75b94 167 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS MYH4,missense_variant,p.G1158S,ENST00000255381.2,c.3472G>A,MODERATE,YES;MYHAS,intron_variant,,ENST00000581304.2,n.143+45969C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000587182.3,n.155+45969C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000399342.6,n.206+45930C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000715727.1,n.169+45969C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000584139.2,n.530+45969C>T,MODIFIER,YES;MYHAS,intron_variant,,ENST00000715356.1,n.306+45969C>T,MODIFIER, +TNS4 84951 BI GRCh38 17 40488805 40488805 + missense_variant Missense_Mutation SNP T T C rs372464786 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 53 25 c.604A>G p.Ile202Val p.I202V ENST00000254051.11 NM_032865.6 202 Atc/Gtc 3/13 P1 C I/V protein_coding YES CCDS11368.1 604/2148 GAAGATGAGGC PANTHER:PTHR45734;PANTHER:PTHR45734:SF6;MobiDB_lite:mobidb-lite ENSP00000254051 0.0 0.0001166 3/13 rs372464786 ENST00000254051 Transcript ENSG00000131746 HGNC:24352 MODERATE NM_032865.6 0.0001166 EA missense_variant 1.0 possibly_damaging(0.6) Unknown tolerated(0.68) Q8IZW8.139 TNS4 HGNC -1 1.0 UPI000013CE0F SNV TNS4,missense_variant,p.I202V,ENST00000254051,NM_032865.6,c.604A>G,MODERATE,YES,tolerated(0.68),possibly_damaging(0.6),-1 789/4087 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 8.044e-06 0.0 0.0 0.0 0.0 0.0 1.783e-05 0.0 0.0 2.055470031336881e-05 4.964260006090626e-05 0.0 0.0 0.0 0.0 0.0 afr 4.964260006090626e-05 0.0 1.5514500773861073e-05 0.0 0.0 0 77 43c0e262-1510-4418-b0b0-df3c9ed75b94 78 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS TNS4,missense_variant,p.I202V,ENST00000254051.11,c.604A>G,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A87Y-01A TCGA-WC-A87Y-10A Somatic 48 17 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 3a161c85-2544-4283-a10d-e332c9dd1692 0 70 43c0e262-1510-4418-b0b0-df3c9ed75b94 65 95c20c25-e9ae-43b3-862c-9f60e65d525f SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +LIMS1 3987 BI GRCh38 2 108680747 108680747 + synonymous_variant Silent SNP C C G novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 58 16 c.840C>G p.Thr280= p.T280= ENST00000332345.10 NM_004987.6 280 acC/acG 9/10 G T protein_coding CCDS2078.1 840/978 TCTACCTGCAA PDB-ENSP_mappings:6mif.A;PROSITE_profiles:PS50023;CDD:cd09335;PANTHER:PTHR24210:SF11;PANTHER:PTHR24210;Pfam:PF00412;Gene3D:2.10.110.10;PIRSF:PIRSF038003;SMART:SM00132;Superfamily:SSF57716 ENSP00000331775 9/10 ENST00000332345 Transcript ENSG00000169756 HGNC:6616 LOW synonymous_variant Unknown P48059.202 LIMS1 HGNC 1 1.0 UPI0000131AF3 P48059-1 SNV LIMS1,synonymous_variant,p.T292=,ENST00000544547,NM_001371495.1&NM_001193483.3,c.876C>G,LOW,,,,1;LIMS1,synonymous_variant,p.T280=,ENST00000393310,NM_001371496.1&NM_001371498.1&NM_001371497.1&NM_001193488.2,c.840C>G,LOW,,,,1;LIMS1,synonymous_variant,p.T342=,ENST00000338045,NM_001371494.1&NM_001193485.3,c.1026C>G,LOW,YES,,,1;LIMS1,synonymous_variant,p.T317=,ENST00000409441,NM_001193484.2,c.951C>G,LOW,,,,1;LIMS1,synonymous_variant,p.T284=,ENST00000410093,NM_001193482.2,c.852C>G,LOW,,,,1;LIMS1,synonymous_variant,p.T280=,ENST00000332345,NM_004987.6,c.840C>G,LOW,,,,1;LIMS1,synonymous_variant,p.T116=,ENST00000542845,,c.348C>G,LOW,,,,1;LIMS1-AS1,upstream_gene_variant,,ENST00000411710,,,MODIFIER,YES,,,-1 959/1235 muse;mutect2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 166 a90c725c-d79a-416c-b090-fa9a5d533381 74 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS LIMS1,missense_variant,p.L116V,ENST00000542845.3,c.346C>G,MODERATE,;LIMS1,synonymous_variant,p.T216=,ENST00000695523.1,c.648C>G,LOW,;LIMS1,synonymous_variant,p.T342=,ENST00000695522.1,c.1026C>G,LOW,;LIMS1,synonymous_variant,p.T342=,ENST00000338045.7,c.1026C>G,LOW,;LIMS1,synonymous_variant,p.T317=,ENST00000409441.5,c.951C>G,LOW,;LIMS1,synonymous_variant,p.T284=,ENST00000410093.5,c.852C>G,LOW,;LIMS1,synonymous_variant,p.T280=,ENST00000695521.1,c.840C>G,LOW,;LIMS1,synonymous_variant,p.T280=,ENST00000393310.5,c.840C>G,LOW,;LIMS1,synonymous_variant,p.T216=,ENST00000695520.1,c.648C>G,LOW,;LIMS1,synonymous_variant,p.T280=,ENST00000332345.10,c.840C>G,LOW,;LIMS1,synonymous_variant,p.T287=,ENST00000695519.1,c.861C>G,LOW,;LIMS1,synonymous_variant,p.T280=,ENST00000695518.1,c.840C>G,LOW,;LIMS1,synonymous_variant,p.T292=,ENST00000695517.1,c.876C>G,LOW,;LIMS1,synonymous_variant,p.T292=,ENST00000544547.6,c.876C>G,LOW,YES;LIMS1,synonymous_variant,p.T301=,ENST00000695516.1,c.903C>G,LOW, +ERBB4 2066 BI GRCh38 2 211619275 211619275 + missense_variant,splice_region_variant Missense_Mutation SNP C C A rs1369649105 TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 40 10 c.2203G>T p.Gly735Cys p.G735C ENST00000342788.9 NM_005235.3 735 Ggt/Tgt 19/28 P1 A G/C protein_coding YES CCDS2394.1 2203/3927 AATACCCTTTG PDB-ENSP_mappings:2r4b.A;PDB-ENSP_mappings:2r4b.B;Gene3D:3.30.200.20;PDB-ENSP_mappings:3bbt.B;PDB-ENSP_mappings:3bbt.D;PDB-ENSP_mappings:3bbw.A;PDB-ENSP_mappings:3bbw.B;PDB-ENSP_mappings:3bce.A;PDB-ENSP_mappings:3bce.B;PDB-ENSP_mappings:3bce.C;Pfam:PF07714;PIRSF:PIRSF000619;PROSITE_patterns:PS00107;PROSITE_profiles:PS50011;PANTHER:PTHR24416;PANTHER:PTHR24416:SF90;SMART:SM00219;Superfamily:SSF56112;CDD:cd05110 ENSP00000342235 19/28 rs1369649105;COSV53506429;COSV53551915 ENST00000342788 Transcript 1.0 ENSG00000178568 HGNC:3432 MODERATE NM_005235.3 missense_variant 0;1;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1;1 Q15303.223 ERBB4 HGNC -1 1.0 UPI00000499DF Q15303-1 SNV ERBB4,missense_variant,p.G735C,ENST00000342788,NM_005235.3,c.2203G>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;ERBB4,missense_variant,p.G735C,ENST00000436443,NM_001042599.1,c.2203G>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;ERBB4,missense_variant,p.G709C,ENST00000402597,,c.2125G>T,MODERATE,,deleterious(0),probably_damaging(1),-1;ERBB4,missense_variant,p.G725C,ENST00000260943,,c.2173G>T,MODERATE,,deleterious(0),probably_damaging(1),-1;ERBB4,splice_region_variant,,ENST00000484594,,n.2255G>T,LOW,,,,-1 2475/12097 muse;mutect2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 46 a90c725c-d79a-416c-b090-fa9a5d533381 51 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS ERBB4,non_coding_transcript_exon_variant,,ENST00000484594.5,n.2255G>T,MODIFIER,;ERBB4,missense_variant,splice_region_variant,p.G725C,ENST00000260943.11,c.2173G>T,MODERATE,;ERBB4,missense_variant,splice_region_variant,p.G735C,ENST00000436443.5,c.2203G>T,MODERATE,;ERBB4,missense_variant,splice_region_variant,p.G735C,ENST00000342788.9,c.2203G>T,MODERATE,YES +SNTN 132203 BI GRCh38 3 63652787 63652787 + missense_variant Missense_Mutation SNP A A T novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 25 13 c.100A>T p.Met34Leu p.M34L ENST00000343837.8 NM_001080537.2 34 Atg/Ttg 1/4 P1 T M/L protein_coding CCDS33779.1 100/444 GGAAAATGCCC PANTHER:PTHR11639;PANTHER:PTHR11639:SF24 ENSP00000341442 1/4 ENST00000343837 Transcript ENSG00000188817 HGNC:33706 MODERATE NM_001080537.2 missense_variant probably_damaging(0.95) Unknown tolerated(0.05) A6NMZ2.87 SNTN HGNC 1 2.0 UPI000015D697 SNV SNTN,missense_variant,p.M30L,ENST00000496807,,c.88A>T,MODERATE,,tolerated(0.06),probably_damaging(0.95),1;SNTN,missense_variant,p.M34L,ENST00000343837,NM_001080537.2,c.100A>T,MODERATE,,tolerated(0.05),probably_damaging(0.95),1;SNTN,missense_variant,p.M34L,ENST00000469440,NM_001348756.2,c.100A>T,MODERATE,YES,tolerated_low_confidence(0.05),probably_damaging(0.95),1 113/1574 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 44 a90c725c-d79a-416c-b090-fa9a5d533381 39 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS SNTN,missense_variant,p.M30L,ENST00000496807.1,c.88A>T,MODERATE,;SNTN,missense_variant,p.M34L,ENST00000469440.5,c.100A>T,MODERATE,;SNTN,missense_variant,p.M34L,ENST00000343837.8,c.100A>T,MODERATE,YES +ZNF518B 85460 BI GRCh38 4 10443228 10443228 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 42 17 c.3101G>A p.Cys1034Tyr p.C1034Y ENST00000326756.4 NM_001375817.1 1034 tGt/tAt 3/3 P1 T C/Y protein_coding YES CCDS33960.1 3101/3225 ATACACACTGT PANTHER:PTHR24403;PANTHER:PTHR24403:SF57 ENSP00000317614 3/3 ENST00000326756 Transcript ENSG00000178163 HGNC:29365 MODERATE NM_053042.3 missense_variant 1.0 possibly_damaging(0.706) Unknown deleterious(0) Q9C0D4.128 ZNF518B HGNC -1 3.0 UPI0000160B97 SNV ZNF518B,missense_variant,p.C1034Y,ENST00000326756,NM_001375817.1&NM_053042.3&NM_001375816.1,c.3101G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.706),-1;ZNF518B,downstream_gene_variant,,ENST00000507515,,,MODIFIER,,,,-1 3606/6954 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 87 a90c725c-d79a-416c-b090-fa9a5d533381 59 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS ZNF518B,missense_variant,p.C1034Y,ENST00000326756.4,c.3101G>A,MODERATE,YES +PCDHGB4 8641 BI GRCh38 5 141389751 141389751 + missense_variant Missense_Mutation SNP G G A rs755499740 TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 45 24 c.1867G>A p.Glu623Lys p.E623K ENST00000519479.2 NM_003736.4 623 Gaa/Aaa 1/4 P1 A E/K protein_coding YES CCDS54928.1 1867/2772 CGGGCGAAGTG COSM3851931 Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF117;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000428288 1/4 COSV53919987 ENST00000519479 Transcript ENSG00000253953 HGNC:8711 MODERATE NM_003736.4 missense_variant 1 1.0 probably_damaging(0.997) Unknown deleterious(0.01) 1 Q9UN71.150 PCDHGB4 HGNC 1 1.0 UPI000006F773 Q9UN71-1 SNV PCDHGB4,missense_variant,p.E623K,ENST00000519479,NM_003736.4,c.1867G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.997),1;PCDHGB4,missense_variant,p.E623K,ENST00000615384,NM_032098.1,c.1867G>A,MODERATE,,deleterious(0.01),probably_damaging(0.995),1;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.4,c.2424+43294G>A,MODIFIER,YES,,,1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.4,c.2424+48356G>A,MODIFIER,YES,,,1;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2,c.2421+56646G>A,MODIFIER,YES,,,1;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.3,c.2424+13244G>A,MODIFIER,YES,,,1;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2,c.2421+23000G>A,MODIFIER,YES,,,1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.4,c.2424+4428G>A,MODIFIER,YES,,,1;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2,c.2421+27195G>A,MODIFIER,YES,,,1;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2,c.2409+37082G>A,MODIFIER,YES,,,1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.4,c.2514+32130G>A,MODIFIER,YES,,,1;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.5,c.2415+16942G>A,MODIFIER,YES,,,1;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1,,MODIFIER,YES,,,1;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2,,MODIFIER,,,,1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.3,,MODIFIER,,,,1;PCDHGA3,intron_variant,,ENST00000612467,,c.*2003+43294G>A,MODIFIER,,,,1 2054/4761 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 65 a90c725c-d79a-416c-b090-fa9a5d533381 69 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS PCDHGB4,missense_variant,p.E623K,ENST00000519479.2,c.1867G>A,MODERATE,YES;PCDHGB4,missense_variant,p.E623K,ENST00000615384.1,c.1867G>A,MODERATE,;PCDHGA7,intron_variant,,ENST00000518325.2,c.2424+4428G>A,MODIFIER,YES;PCDHGA6,intron_variant,,ENST00000517434.3,c.2424+13244G>A,MODIFIER,YES;PCDHGB3,intron_variant,,ENST00000576222.2,c.2415+16942G>A,MODIFIER,YES;PCDHGA5,intron_variant,,ENST00000518069.2,c.2421+23000G>A,MODIFIER,YES;PCDHGB2,intron_variant,,ENST00000522605.2,c.2421+27195G>A,MODIFIER,YES;PCDHGA4,intron_variant,,ENST00000571252.3,c.2514+32130G>A,MODIFIER,YES;PCDHGB1,intron_variant,,ENST00000523390.2,c.2409+37082G>A,MODIFIER,YES;PCDHGA3,intron_variant,NMD_transcript_variant,,ENST00000612467.1,c.*2003+43294G>A,MODIFIER,;PCDHGA3,intron_variant,,ENST00000253812.8,c.2424+43294G>A,MODIFIER,YES;PCDHGA2,intron_variant,,ENST00000394576.3,c.2424+48356G>A,MODIFIER,YES;PCDHGA1,intron_variant,,ENST00000517417.3,c.2421+56646G>A,MODIFIER,YES +LAMA2 3908 BI GRCh38 6 129342394 129342394 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 63 24 c.4363T>C p.Tyr1455His p.Y1455H ENST00000421865.3 NM_000426.4 1455 Tac/Cac 30/65 P3 C Y/H protein_coding YES CCDS5138.1 4363/9369 TTGGATACTAT Gene3D:2.170.300.10;Pfam:PF00053;PROSITE_profiles:PS50027;PANTHER:PTHR10574;PANTHER:PTHR10574:SF291;SMART:SM00180;SMART:SM00181;Superfamily:SSF57196;CDD:cd00055 ENSP00000400365 30/65 ENST00000421865 Transcript 1.0 ENSG00000196569 HGNC:6482 MODERATE NM_000426.4 missense_variant 1.0 probably_damaging(0.942) Unknown deleterious(0.01) P24043.212 LAMA2 HGNC 1 5.0 UPI00003673E0 SNV LAMA2,missense_variant,p.Y1455H,ENST00000421865,NM_000426.4&NM_001079823.2,c.4363T>C,MODERATE,YES,deleterious(0.01),probably_damaging(0.942),1;LAMA2,missense_variant,p.Y1455H,ENST00000618192,,c.4363T>C,MODERATE,,deleterious(0.01),probably_damaging(0.986),1;LAMA2,missense_variant,p.Y1455H,ENST00000617695,,c.4363T>C,MODERATE,,deleterious(0.01),probably_damaging(0.951),1 4471/9696 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 106 a90c725c-d79a-416c-b090-fa9a5d533381 87 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS LAMA2,non_coding_transcript_exon_variant,,ENST00000692206.1,n.12T>C,MODIFIER,;LAMA2,missense_variant,p.Y1543H,ENST00000618192.5,c.4627T>C,MODERATE,;LAMA2,missense_variant,p.Y1455H,ENST00000617695.5,c.4363T>C,MODERATE,;LAMA2,missense_variant,p.Y1455H,ENST00000421865.3,c.4363T>C,MODERATE,YES +ZNF511 118472 BI GRCh38 10 133309856 133309856 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 32 20 c.308C>T p.Thr103Met p.T103M ENST00000359035.4 103 aCg/aTg 3/5 A2 T T/M protein_coding YES 308/789 CCACACGCTGC PANTHER:PTHR21354;PANTHER:PTHR21354:SF2;PROSITE_patterns:PS00028;SMART:SM00355 ENSP00000351929 3/5 ENST00000359035 Transcript ENSG00000198546 HGNC:28445 MODERATE missense_variant benign(0.079) Unknown tolerated(0.14) Q8NB15.145 ZNF511 HGNC 1 2.0 UPI00000729D2 Q8NB15-1 SNV ZNF511,missense_variant,p.T103M,ENST00000359035,,c.308C>T,MODERATE,YES,tolerated(0.14),benign(0.079),1;ZNF511,missense_variant,p.T103M,ENST00000361518,NM_145806.4,c.308C>T,MODERATE,,tolerated(0.22),benign(0.071),1;ZNF511-PRAP1,missense_variant,p.T46M,ENST00000368554,,c.137C>T,MODERATE,YES,tolerated_low_confidence(0.17),benign(0.023),1;TUBGCP2,upstream_gene_variant,,ENST00000368563,NM_006659.4,,MODIFIER,,,,-1;TUBGCP2,upstream_gene_variant,,ENST00000417178,NM_001256618.1,,MODIFIER,,,,-1;TUBGCP2,upstream_gene_variant,,ENST00000543663,NM_001256617.1,,MODIFIER,YES,,,-1;ZNF511,intron_variant,,ENST00000463816,,n.25-308C>T,MODIFIER,,,,1;TUBGCP2,upstream_gene_variant,,ENST00000470829,,,MODIFIER,,,,-1;ZNF511,non_coding_transcript_exon_variant,,ENST00000482153,,n.303C>T,MODIFIER,,,,1;TUBGCP2,intron_variant,,ENST00000482278,,c.-40+1764G>A,MODIFIER,,,,-1;TUBGCP2,upstream_gene_variant,,ENST00000480198,,,MODIFIER,,,,-1;TUBGCP2,upstream_gene_variant,,ENST00000487796,,,MODIFIER,,,,-1 311/2004 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 55 a90c725c-d79a-416c-b090-fa9a5d533381 52 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS ZNF511,intron_variant,,ENST00000463816.2,n.25-308C>T,MODIFIER,;ZNF511-PRAP1,synonymous_variant,p.H45=,ENST00000368554.8,c.135C>T,LOW,YES;ZNF511,non_coding_transcript_exon_variant,,ENST00000482153.1,n.303C>T,MODIFIER,;ZNF511,missense_variant,p.T103M,ENST00000359035.4,c.308C>T,MODERATE,;ZNF511,missense_variant,p.T103M,ENST00000361518.10,c.308C>T,MODERATE,YES;TUBGCP2,intron_variant,NMD_transcript_variant,,ENST00000482278.5,c.-40+1764G>A,MODIFIER,;TUBGCP2,intron_variant,,ENST00000682123.1,c.-39-6876G>A,MODIFIER, +SHF 90525 BI GRCh38 15 45171924 45171924 + synonymous_variant Silent SNP G G A rs1427750273 TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 15 15 c.1044C>T p.Arg348= p.R348= ENST00000290894.12 NM_138356.3 348 cgC/cgT 7/8 A2 A R protein_coding YES CCDS10120.2 1044/1272 CTGTTGCGCAC Gene3D:3.30.505.10;Pfam:PF00017;Prints:PR00401;PROSITE_profiles:PS50001;PANTHER:PTHR15127;PANTHER:PTHR15127:SF28;SMART:SM00252;Superfamily:SSF55550;CDD:cd10392 ENSP00000290894 7/8 rs1427750273 ENST00000290894 Transcript ENSG00000138606 HGNC:25116 LOW 8.814e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q7M4L6.117 SHF HGNC -1 2.0 UPI00001402D9 Q7M4L6-1 SNV SHF,stop_gained,p.Q413*,ENST00000560471,,c.1237C>T,HIGH,,,,-1;SHF,stop_gained,p.Q366*,ENST00000560540,NM_001301169.2&NM_001301168.2,c.1096C>T,HIGH,,,,-1;SHF,splice_region_variant,,ENST00000561239,,c.328+6C>T,LOW,,,,-1;SHF,synonymous_variant,p.R348=,ENST00000290894,NM_138356.3,c.1044C>T,LOW,YES,,,-1;SHF,synonymous_variant,p.R164=,ENST00000458022,NM_001301171.1,c.492C>T,LOW,,,,-1;SHF,synonymous_variant,p.R185=,ENST00000559566,,c.555C>T,LOW,,,,-1;SHF,synonymous_variant,p.R88=,ENST00000558294,,c.264C>T,LOW,,,,-1;SHF,3_prime_UTR_variant,,ENST00000558685,,c.*79C>T,MODIFIER,,,,-1;SHF,intron_variant,,ENST00000560734,NM_001301170.2,c.847+3295C>T,MODIFIER,,,,-1;SHF,downstream_gene_variant,,ENST00000561278,,,MODIFIER,,,,-1;SHF,downstream_gene_variant,,ENST00000561091,,,MODIFIER,,,,-1;AC051619.3,intron_variant,,ENST00000560034,,n.191+1390G>A,MODIFIER,YES,,,1;AC051619.5,upstream_gene_variant,,ENST00000558039,,,MODIFIER,YES,,,-1 1539/2500 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.814e-06 0.0 0.0 0 38 a90c725c-d79a-416c-b090-fa9a5d533381 30 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS SHF,3_prime_UTR_variant,,ENST00000558685.1,c.*79C>T,MODIFIER,;SHF,missense_variant,p.A185V,ENST00000559566.5,c.554C>T,MODERATE,;SHF,stop_gained,p.Q413*,ENST00000560471.5,c.1237C>T,HIGH,;ENSG00000259519,intron_variant,,ENST00000560034.1,n.191+1390G>A,MODIFIER,YES;SHF,splice_region_variant,intron_variant,,ENST00000561239.6,c.328+6C>T,LOW,;SHF,missense_variant,p.A88V,ENST00000558294.1,c.263C>T,MODERATE,;SHF,synonymous_variant,p.R164=,ENST00000458022.6,c.492C>T,LOW,;SHF,intron_variant,,ENST00000560734.5,c.847+3295C>T,MODIFIER,;SHF,stop_gained,p.Q366*,ENST00000560540.5,c.1096C>T,HIGH,;SHF,synonymous_variant,p.R348=,ENST00000290894.12,c.1044C>T,LOW,;SHF,synonymous_variant,p.R413=,ENST00000690270.1,c.1239C>T,LOW,YES +SRSF2 6427 BI GRCh38 17 76736861 76736887 + inframe_deletion In_Frame_Del DEL GTGGTGTGAGTCCGGGGGGCGGCCGTA GTGGTGTGAGTCCGGGGGGCGGCCGTA - novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 34 10 c.274_300del p.His100_Arg109delinsGln p.H100_R109delinsQ ENST00000359995.10 NM_001195427.2 92 TACGGCCGCCCCCCGGACTCACACCAC/- 1/3 P1 - YGRPPDSHH/- protein_coding CCDS11749.1 274-300/666 GCGGCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCG PDB-ENSP_mappings:2kn4.A;PDB-ENSP_mappings:2lea.A;PDB-ENSP_mappings:2leb.A;PDB-ENSP_mappings:2lec.A;Gene3D:3.30.70.330;PROSITE_profiles:PS50102;PANTHER:PTHR23147;PANTHER:PTHR23147:SF119;Superfamily:SSF54928;MobiDB_lite:mobidb-lite ENSP00000353089 1/3 ENST00000359995 Transcript 1.0 ENSG00000161547 HGNC:10783 MODERATE NM_001195427.2 inframe_deletion Unknown Q01130.232 SRSF2 HGNC -1 A0A024R8U5.53 1.0 UPI0000000C2A Q01130-1 deletion SRSF2,inframe_deletion,p.Y92_H100del,ENST00000392485,NM_003016.4,c.274_300del,MODERATE,YES,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000359995,NM_001195427.2,c.274_300del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000508921,,c.274_300del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000358156,,c.274_300del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000583836,,c.274_300del,MODERATE,,,,-1;MFSD11,5_prime_UTR_variant,,ENST00000588460,NM_001353018.1,c.-1491_-1465del,MODIFIER,YES,,,1;MFSD11,5_prime_UTR_variant,,ENST00000586622,,c.-301_-275del,MODIFIER,,,,1;MFSD11,5_prime_UTR_variant,,ENST00000621483,NM_001242534.2&NM_001353017.1,c.-301_-275del,MODIFIER,,,,1;MFSD11,5_prime_UTR_variant,,ENST00000591864,,c.-301_-275del,MODIFIER,,,,1;AC005837.2,intron_variant,,ENST00000587459,,c.239-1420_239-1394del,MODIFIER,YES,,,1;MFSD11,upstream_gene_variant,,ENST00000336509,NM_001353019.1&NM_001242535.2&NM_024311.4&NM_001242532.4,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000341249,NM_001378349.1&NM_001378351.1&NM_001080510.5&NM_001378352.1,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000355954,NM_001242536.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586200,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000586689,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586738,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586752,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000587661,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588302,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588563,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588783,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588822,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588964,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589977,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590393,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590514,NM_001242533.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000590964,NM_001206987.2&NM_001206986.2&NM_001206985.2&NM_001302704.1&NM_001378354.1,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000591571,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000592849,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000593181,NM_001242537.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000615984,NM_001206983.2&NM_001302703.1&NM_001206984.2&NM_001302705.1&NM_001378348.1&NM_001378353.1&NM_001378350.1,,MODIFIER,YES,,,1;MIR636,upstream_gene_variant,,ENST00000384825,,,MODIFIER,YES,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000585202,,c.274_300del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H100del,ENST00000452355,,c.274_300del,MODERATE,,,,-1;SRSF2,upstream_gene_variant,,ENST00000582449,,,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000586778,,,MODIFIER,,,,-1;MFSD11,upstream_gene_variant,,ENST00000588031,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588670,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588768,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589581,,,MODIFIER,,,,1;SRSF2,upstream_gene_variant,,ENST00000589919,,,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000592676,,,MODIFIER,,,,-1 445-471/1888 mutect2;pindel 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 44 a90c725c-d79a-416c-b090-fa9a5d533381 44 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS MFSD11,5_prime_UTR_variant,,ENST00000591864.1,c.-302_-276del,MODIFIER,;MFSD11,5_prime_UTR_variant,,ENST00000621483.4,c.-302_-276del,MODIFIER,;SRSF2,inframe_deletion,p.S101_S109del,ENST00000583836.1,c.274_300del,MODERATE,;MFSD11,5_prime_UTR_variant,,ENST00000586622.5,c.-302_-276del,MODIFIER,;SRSF2,inframe_deletion,p.S101_S109del,ENST00000508921.7,c.274_300del,MODERATE,;SRSF2,inframe_deletion,NMD_transcript_variant,p.H100_R109delinsQ,ENST00000452355.7,c.274_300del,MODERATE,;SRSF2,inframe_deletion,NMD_transcript_variant,p.H100_R109delinsQ,ENST00000585202.5,c.274_300del,MODERATE,;SRSF2,inframe_deletion,p.H100_R109delinsQ,ENST00000359995.10,c.274_300del,MODERATE,YES;SRSF2,inframe_deletion,p.H100_R109delinsQ,ENST00000392485.2,c.274_300del,MODERATE,;SRSF2,inframe_deletion,p.H100_R109delinsQ,ENST00000358156.7,c.274_300del,MODERATE,;ENSG00000267168,intron_variant,,ENST00000587459.1,c.239-1421_239-1395del,MODIFIER,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 24 15 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 69 a90c725c-d79a-416c-b090-fa9a5d533381 39 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +DGKK 139189 BI GRCh38 X 50470125 50470125 + missense_variant Missense_Mutation SNP G G A rs985368837 TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 46 3 c.554C>T p.Pro185Leu p.P185L ENST00000611977.2 NM_001013742.4 185 cCg/cTg 1/28 P1 A P/L protein_coding YES CCDS75980.1 554/3816 CCACCGGACAT PANTHER:PTHR11255;PANTHER:PTHR11255:SF33 ENSP00000477515 1/28 rs985368837 ENST00000611977 Transcript ENSG00000274588 HGNC:32395 MODERATE NM_001013742.4 1.237e-05 gnomAD_NFE missense_variant 1.0 benign(0.003) Unknown deleterious_low_confidence(0) Q5KSL6.127 DGKK HGNC -1 1.0 UPI00004BA922 SNV DGKK,missense_variant,p.P185L,ENST00000611977,NM_001013742.4,c.554C>T,MODERATE,YES,deleterious_low_confidence(0),benign(0.003),-1 701/7494 muse;mutect2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 5.533e-06 0.0 0.0 0.0 0.0 0.0 1.237e-05 0.0 0.0 9.089750165003352e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.956219966814388e-05 0.0 0.0 0 56 a90c725c-d79a-416c-b090-fa9a5d533381 49 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS DGKK,missense_variant,p.P185L,ENST00000611977.2,c.554C>T,MODERATE,YES +MIR224 407009 BI GRCh38 X 151958595 151958595 + mature_miRNA_variant mature_miRNA_variant SNP G G T novel TCGA-WC-A882-01A TCGA-WC-A882-10A Somatic 60 10 n.64C>A ENST00000384889.1 1/1 P1 T protein_coding YES CCDS14703.1 CACTAGGGCAC ENSP00000359353 ENST00000370328 Transcript ENSG00000102287 HGNC:4085 MODIFIER 6/8 NM_004961.4 intron_variant 1.0 Unknown P78334.175 GABRE HGNC -1 1.0 UPI00000307E6 P78334-1 SNV GABRE,intron_variant,,ENST00000370328,NM_004961.4,c.784+1244C>A,MODIFIER,YES,,,-1;MIR224,mature_miRNA_variant,,ENST00000384889,,n.64C>A,MODIFIER,YES,,,-1;MIR452,downstream_gene_variant,,ENST00000385020,,,MODIFIER,YES,,,-1;GABRE,upstream_gene_variant,,ENST00000462018,,,MODIFIER,,,,-1;GABRE,upstream_gene_variant,,ENST00000483564,,,MODIFIER,,,,-1;GABRE,non_coding_transcript_exon_variant,,ENST00000486255,,n.1129C>A,MODIFIER,,,,-1;GABRE,intron_variant,,ENST00000441219,,c.*933+369C>A,MODIFIER,,,,-1;GABRE,downstream_gene_variant,,ENST00000474932,,,MODIFIER,,,,-1;GABRE,downstream_gene_variant,,ENST00000476016,,,MODIFIER,,,,-1;GABRE,upstream_gene_variant,,ENST00000489333,,,MODIFIER,,,,-1;GABRE,upstream_gene_variant,,ENST00000495862,,,MODIFIER,,,,-1 muse;mutect2;varscan2 7f1e74d4-8789-4954-8a63-b0ca5f0373c3 0 86 a90c725c-d79a-416c-b090-fa9a5d533381 70 60c1316e-1daf-4f8a-8557-045387efe4bc SUCCESS MIR224,mature_miRNA_variant,,ENST00000384889.1,n.64C>A,MODIFIER,YES;GABRE,intron_variant,NMD_transcript_variant,,ENST00000441219.5,c.*933+369C>A,MODIFIER,;GABRE,non_coding_transcript_exon_variant,,ENST00000486255.1,n.1129C>A,MODIFIER,;GABRE,intron_variant,,ENST00000370328.4,c.784+1244C>A,MODIFIER,YES +GNB1 2782 BI GRCh38 1 1787390 1787390 + missense_variant Missense_Mutation SNP C C G TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 30 14 c.964G>C p.Asp322His p.D322H ENST00000378609.9 NM_002074.5 322 Gac/Cac 11/12 P1 G D/H protein_coding YES CCDS34.1 964/1023 ATCGTCAGTCA Gene3D:2.130.10.10;PDB-ENSP_mappings:4kfm.B;PDB-ENSP_mappings:4pnk.B;PDB-ENSP_mappings:5he0.B;PDB-ENSP_mappings:5he1.B;PDB-ENSP_mappings:5he2.B;PDB-ENSP_mappings:5he3.B;PDB-ENSP_mappings:5ukk.B;PDB-ENSP_mappings:5ukl.B;PDB-ENSP_mappings:5ukm.B;PDB-ENSP_mappings:5uz7.B;PDB-ENSP_mappings:6b3j.B;PDB-ENSP_mappings:6crk.B;PDB-ENSP_mappings:6d9h.B;PDB-ENSP_mappings:6dde.B;PDB-ENSP_mappings:6ddf.B;PDB-ENSP_mappings:6e3y.B;PDB-ENSP_mappings:6eg8.A;PDB-ENSP_mappings:6eg8.B;PDB-ENSP_mappings:6eg8.D;PDB-ENSP_mappings:6eg8.F;PDB-ENSP_mappings:6g79.B;PDB-ENSP_mappings:6gdg.B;PDB-ENSP_mappings:6kpf.B;PDB-ENSP_mappings:6kpg.B;PDB-ENSP_mappings:6li3.B;PDB-ENSP_mappings:6lmk.B;PDB-ENSP_mappings:6lml.B;PDB-ENSP_mappings:6m1h.E;PDB-ENSP_mappings:6m1i.E;PDB-ENSP_mappings:6m8s.C;PDB-ENSP_mappings:6m8s.D;PDB-ENSP_mappings:6m8s.G;PDB-ENSP_mappings:6m8s.H;PDB-ENSP_mappings:6m8s.K;PDB-ENSP_mappings:6n4b.B;PDB-ENSP_mappings:6ni3.B;PDB-ENSP_mappings:6niy.B;PDB-ENSP_mappings:6oij.B;PDB-ENSP_mappings:6oik.B;PDB-ENSP_mappings:6omm.B;PDB-ENSP_mappings:6orv.BP;PDB-ENSP_mappings:6os9.B;PDB-ENSP_mappings:6osa.B;PDB-ENSP_mappings:6ot0.B;PDB-ENSP_mappings:6p9x.B;PDB-ENSP_mappings:6p9y.B;PDB-ENSP_mappings:6pb0.B;PDB-ENSP_mappings:6pb1.B;PDB-ENSP_mappings:6pt0.B;PDB-ENSP_mappings:6uun.B;PDB-ENSP_mappings:6uus.B;PDB-ENSP_mappings:6uva.B;PDB-ENSP_mappings:6vms.B;PDB-ENSP_mappings:6whc.B;Pfam:PF00400;PIRSF:PIRSF002394;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR19850;PANTHER:PTHR19850:SF29;SMART:SM00320;Superfamily:SSF50978;CDD:cd00200 ENSP00000367872 11/12 COSV66100547 ENST00000378609 Transcript 1.0 ENSG00000078369 HGNC:4396 MODERATE NM_002074.5 missense_variant 1 1.0 possibly_damaging(0.686) Unknown deleterious(0.01) 1 P62873.178 GNB1 HGNC -1 A0A140VJJ8.3 1.0 UPI00000230B3 P62873-1 SNV GNB1,missense_variant,p.D322H,ENST00000378609,NM_002074.5,c.964G>C,MODERATE,YES,deleterious(0.01),possibly_damaging(0.686),-1;GNB1,missense_variant,p.D322H,ENST00000610897,NM_001282539.1,c.964G>C,MODERATE,,deleterious(0.01),possibly_damaging(0.686),-1;GNB1,missense_variant,p.D222H,ENST00000615252,NM_001282538.1,c.664G>C,MODERATE,,deleterious(0),possibly_damaging(0.686),-1;GNB1,downstream_gene_variant,,ENST00000439272,,,MODIFIER,,,,-1;GNB1,downstream_gene_variant,,ENST00000461893,,,MODIFIER,,,,-1;GNB1,downstream_gene_variant,,ENST00000471354,,,MODIFIER,,,,-1 1327/3163 muse;mutect2;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 84 183566df-0a7d-4b7f-8879-c5c89a348353 44 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS GNB1,missense_variant,p.D322H,ENST00000703711.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703710.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703709.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703708.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D309H,ENST00000703707.1,c.925G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703706.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D278H,ENST00000703705.1,c.832G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703704.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703703.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703702.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703701.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703699.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703700.1,c.964G>C,MODERATE,;GNB1,non_coding_transcript_exon_variant,,ENST00000703698.1,n.253G>C,MODIFIER,;GNB1,missense_variant,p.D322H,ENST00000703697.1,c.964G>C,MODERATE,;GNB1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000703695.1,c.*177G>C,MODIFIER,;GNB1,missense_variant,p.D322H,ENST00000703694.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703693.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703696.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000703692.1,c.964G>C,MODERATE,;GNB1,missense_variant,p.D309H,ENST00000439272.7,c.925G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000378609.9,c.964G>C,MODERATE,YES;GNB1,missense_variant,p.D222H,ENST00000615252.5,c.664G>C,MODERATE,;GNB1,missense_variant,p.D322H,ENST00000610897.4,c.964G>C,MODERATE, +TRIM67 440730 BI GRCh38 1 231163997 231163997 + missense_variant Missense_Mutation SNP T T C novel TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 8 3 c.1028T>C p.Met343Thr p.M343T ENST00000366653.6 NM_001004342.5 343 aTg/aCg 1/10 A2 C M/T protein_coding YES CCDS44333.1 1028/2352 GGCCATGTGGA Gene3D:3.30.40.200;PANTHER:PTHR24099;PANTHER:PTHR24099:SF21;Superfamily:SSF57845 ENSP00000355613 1/10 ENST00000366653 Transcript ENSG00000119283 HGNC:31859 MODERATE missense_variant 1.0 benign(0.046) Unknown tolerated(0.2) Q6ZTA4.135 TRIM67 HGNC 1 1.0 UPI0000418F23 Q6ZTA4-3 SNV TRIM67,missense_variant,p.M343T,ENST00000444294,,c.1028T>C,MODERATE,,tolerated(0.13),benign(0.099),1;TRIM67,missense_variant,p.M343T,ENST00000366653,NM_001004342.4,c.1028T>C,MODERATE,YES,tolerated(0.2),benign(0.046),1;TRIM67,missense_variant,p.M281T,ENST00000449018,NM_001300889.2,c.842T>C,MODERATE,,tolerated(0.22),benign(0.017),1 1028/3936 muse;mutect2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 14 183566df-0a7d-4b7f-8879-c5c89a348353 12 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS TRIM67,missense_variant,p.M281T,ENST00000449018.7,c.842T>C,MODERATE,;TRIM67,missense_variant,p.M343T,ENST00000444294.7,c.1028T>C,MODERATE,;TRIM67,missense_variant,p.M343T,ENST00000366653.6,c.1028T>C,MODERATE,YES +BAP1 8314 BI GRCh38 3 52403779 52403779 + frameshift_variant Frame_Shift_Del DEL G G - TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 9 12 c.1366del p.Gln456ArgfsTer115 p.Q456Rfs*115 ENST00000460680.6 NM_004656.4 456 Cag/ag 13/17 P1 - Q/X protein_coding YES CCDS2853.1 1366/2190 CCTTCTGGGACT PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 13/17 COSV56240393;COSV99964331 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1;1 1.0 Unknown 1;1 Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D deletion BAP1,frameshift_variant,p.Q456Rfs*115,ENST00000460680,NM_004656.4,c.1366del,HIGH,YES,,,-1;BAP1,frameshift_variant,p.Q438Rfs*115,ENST00000296288,,c.1312del,HIGH,,,,-1;BAP1,intron_variant,,ENST00000469613,,c.119+22del,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000490804,,n.794del,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1496/3600 pindel;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 45 183566df-0a7d-4b7f-8879-c5c89a348353 21 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000490804.1,n.794del,MODIFIER,;BAP1,frameshift_variant,p.Q438Rfs*115,ENST00000296288.9,c.1312del,HIGH,;BAP1,intron_variant,,ENST00000469613.5,c.119+22del,MODIFIER,;BAP1,frameshift_variant,p.Q456Rfs*115,ENST00000460680.6,c.1366del,HIGH,YES +TNIP1 10318 BI GRCh38 5 151032323 151032323 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 16 17 c.1840G>C p.Val614Leu p.V614L ENST00000315050.11 NM_001252391.2 614 Gtg/Ctg 17/18 P4 G V/L protein_coding CCDS34280.1 1840/1911 CATCACTTGGG PANTHER:PTHR31882;PANTHER:PTHR31882:SF3;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000317891 17/18 ENST00000315050 Transcript 1.0 ENSG00000145901 HGNC:16903 MODERATE missense_variant possibly_damaging(0.574) Unknown tolerated_low_confidence(0.06) Q15025.185 TNIP1 HGNC -1 1.0 UPI000000DCDC Q15025-1 SNV TNIP1,missense_variant,p.K619N,ENST00000389378,NM_001252385.1,c.1857G>C,MODERATE,,deleterious_low_confidence(0.05),benign(0.013),-1;TNIP1,missense_variant,p.V614L,ENST00000521591,NM_001258454.2&NM_006058.5,c.1840G>C,MODERATE,YES,tolerated_low_confidence(0.06),possibly_damaging(0.574),-1;TNIP1,missense_variant,p.V614L,ENST00000315050,NM_001252391.2,c.1840G>C,MODERATE,,tolerated_low_confidence(0.06),possibly_damaging(0.574),-1;TNIP1,missense_variant,p.V614L,ENST00000523338,NM_001252392.2,c.1840G>C,MODERATE,,tolerated_low_confidence(0.06),possibly_damaging(0.477),-1;TNIP1,missense_variant,p.V550L,ENST00000610535,NM_001258455.1&NM_001364487.2,c.1648G>C,MODERATE,,deleterious_low_confidence(0.03),benign(0.081),-1;TNIP1,missense_variant,p.V561L,ENST00000520931,NM_001252386.2,c.1681G>C,MODERATE,,tolerated_low_confidence(0.05),possibly_damaging(0.574),-1;TNIP1,missense_variant,p.V614L,ENST00000522226,NM_001252390.2,c.1840G>C,MODERATE,,tolerated_low_confidence(0.06),possibly_damaging(0.574),-1;TNIP1,missense_variant,p.V614L,ENST00000518977,NM_001364486.2&NM_001252393.2,c.1840G>C,MODERATE,,tolerated_low_confidence(0.06),possibly_damaging(0.477),-1;TNIP1,missense_variant,p.V550L,ENST00000523200,,c.1648G>C,MODERATE,,deleterious_low_confidence(0.03),benign(0.081),-1;TNIP1,intron_variant,,ENST00000517504,,c.388-2200G>C,MODIFIER,,,,-1;TNIP1,intron_variant,,ENST00000524280,,c.1588-1576G>C,MODIFIER,,,,-1;TNIP1,intron_variant,,ENST00000610874,NM_001258456.1,c.1588-1576G>C,MODIFIER,,,,-1;GPX3,downstream_gene_variant,,ENST00000388825,NM_002084.5,,MODIFIER,YES,,,1;GPX3,downstream_gene_variant,,ENST00000517973,,,MODIFIER,,,,1;GPX3,downstream_gene_variant,,ENST00000520059,,,MODIFIER,,,,1;GPX3,downstream_gene_variant,,ENST00000521632,,,MODIFIER,,,,1;GPX3,downstream_gene_variant,,ENST00000521650,,,MODIFIER,,,,1;GPX3,downstream_gene_variant,,ENST00000614343,,,MODIFIER,,,,1;GPX3,downstream_gene_variant,,ENST00000622181,NM_001329790.2,,MODIFIER,,,,1;TNIP1,non_coding_transcript_exon_variant,,ENST00000521423,,n.653G>C,MODIFIER,,,,-1;TNIP1,3_prime_UTR_variant,,ENST00000519339,,c.*110G>C,MODIFIER,,,,-1;TNIP1,non_coding_transcript_exon_variant,,ENST00000522574,,n.1094G>C,MODIFIER,,,,-1;TNIP1,downstream_gene_variant,,ENST00000517329,,,MODIFIER,,,,-1;GPX3,downstream_gene_variant,,ENST00000520597,,,MODIFIER,,,,1 1950/2785 muse;mutect2;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 28 183566df-0a7d-4b7f-8879-c5c89a348353 33 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS TNIP1,non_coding_transcript_exon_variant,,ENST00000521423.1,n.653G>C,MODIFIER,;TNIP1,missense_variant,p.V550L,ENST00000523200.5,c.1648G>C,MODERATE,;TNIP1,intron_variant,,ENST00000524280.5,c.1588-1576G>C,MODIFIER,;TNIP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000519339.5,c.*110G>C,MODIFIER,;TNIP1,missense_variant,p.V614L,ENST00000518977.5,c.1840G>C,MODERATE,;TNIP1,missense_variant,p.V614L,ENST00000521001.2,c.1840G>C,MODERATE,;TNIP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000714530.1,c.*163G>C,MODIFIER,;TNIP1,missense_variant,p.V614L,ENST00000522226.5,c.1840G>C,MODERATE,;TNIP1,non_coding_transcript_exon_variant,,ENST00000522574.5,n.1094G>C,MODIFIER,;TNIP1,missense_variant,p.V550L,ENST00000610535.5,c.1648G>C,MODERATE,;TNIP1,missense_variant,p.V614L,ENST00000523338.5,c.1840G>C,MODERATE,;TNIP1,missense_variant,p.V614L,ENST00000315050.11,c.1840G>C,MODERATE,;TNIP1,missense_variant,p.K619N,ENST00000389378.6,c.1857G>C,MODERATE,;TNIP1,missense_variant,p.V614L,ENST00000520695.6,c.1840G>C,MODERATE,;TNIP1,missense_variant,p.V614L,ENST00000521591.6,c.1840G>C,MODERATE,YES;TNIP1,missense_variant,p.V561L,ENST00000520931.5,c.1681G>C,MODERATE,;TNIP1,missense_variant,p.V561L,ENST00000522100.6,c.1681G>C,MODERATE, +KCNV1 27012 BI GRCh38 8 109972517 109972517 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 54 24 c.732C>G p.Ile244Met p.I244M ENST00000297404.1 244 atC/atG 2/3 P1 C I/M protein_coding CCDS6314.1 732/1503 TCCAGGATTTC Gene3D:1.20.120.350;Pfam:PF00520;Prints:PR00169;PANTHER:PTHR11537;PANTHER:PTHR11537:SF38;Superfamily:SSF81324;Transmembrane_helices:TMhelix ENSP00000297404 2/3 ENST00000297404 Transcript ENSG00000164794 HGNC:18861 MODERATE missense_variant benign(0.291) Unknown tolerated(0.31) Q6PIU1.142 KCNV1 HGNC -1 1.0 UPI0000073DA5 SNV KCNV1,missense_variant,p.I244M,ENST00000524391,NM_014379.4,c.732C>G,MODERATE,YES,tolerated(0.31),benign(0.291),-1;KCNV1,missense_variant,p.I244M,ENST00000297404,,c.732C>G,MODERATE,,tolerated(0.31),benign(0.291),-1;AC027451.1,upstream_gene_variant,,ENST00000530667,,,MODIFIER,YES,,,1 1074/2927 muse;mutect2;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 45 183566df-0a7d-4b7f-8879-c5c89a348353 78 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS KCNV1,missense_variant,p.I244M,ENST00000297404.1,c.732C>G,MODERATE,;KCNV1,missense_variant,p.I244M,ENST00000524391.6,c.732C>G,MODERATE,YES +TYRP1 7306 BI GRCh38 9 12704605 12704606 + frameshift_variant Frame_Shift_Ins INS - - GG novel TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 74 19 c.1165_1166dup p.Gly388GlufsTer29 p.G388Efs*29 ENST00000388918.10 NM_000550.3 387 -/GG 6/8 P1 GG -/X protein_coding YES CCDS34990.1 1161-1162/1614 GGAACAGGGGG Gene3D:1.10.1280.10;PDB-ENSP_mappings:5m8l.A;PDB-ENSP_mappings:5m8l.B;PDB-ENSP_mappings:5m8l.C;PDB-ENSP_mappings:5m8l.D;PDB-ENSP_mappings:5m8m.A;PDB-ENSP_mappings:5m8m.B;PDB-ENSP_mappings:5m8m.C;PDB-ENSP_mappings:5m8m.D;PDB-ENSP_mappings:5m8n.A;PDB-ENSP_mappings:5m8n.B;PDB-ENSP_mappings:5m8n.C;PDB-ENSP_mappings:5m8n.D;PDB-ENSP_mappings:5m8o.A;PDB-ENSP_mappings:5m8o.B;PDB-ENSP_mappings:5m8o.C;PDB-ENSP_mappings:5m8o.D;PDB-ENSP_mappings:5m8p.A;PDB-ENSP_mappings:5m8p.B;PDB-ENSP_mappings:5m8p.C;PDB-ENSP_mappings:5m8p.D;PDB-ENSP_mappings:5m8q.A;PDB-ENSP_mappings:5m8q.B;PDB-ENSP_mappings:5m8q.C;PDB-ENSP_mappings:5m8q.D;PDB-ENSP_mappings:5m8r.A;PDB-ENSP_mappings:5m8r.B;PDB-ENSP_mappings:5m8r.C;PDB-ENSP_mappings:5m8r.D;PDB-ENSP_mappings:5m8s.A;PDB-ENSP_mappings:5m8s.B;PDB-ENSP_mappings:5m8s.C;PDB-ENSP_mappings:5m8s.D;PDB-ENSP_mappings:5m8t.A;PDB-ENSP_mappings:5m8t.B;PDB-ENSP_mappings:5m8t.C;PDB-ENSP_mappings:5m8t.D;Pfam:PF00264;PANTHER:PTHR11474;PANTHER:PTHR11474:SF3;Superfamily:SSF48056 ENSP00000373570 6/8 ENST00000388918 Transcript 1.0 ENSG00000107165 HGNC:12450 5.0 HIGH NM_000550.3 frameshift_variant 1.0 Unknown P17643.195 TYRP1 HGNC 1 1.0 UPI0000039DCA insertion TYRP1,frameshift_variant,p.Q390Dfs*27,ENST00000388918,NM_000550.3,c.1165_1166dup,HIGH,YES,,,1;TYRP1,frameshift_variant,p.Q100Dfs*27,ENST00000381136,,c.295_296dup,HIGH,,,,1;TYRP1,non_coding_transcript_exon_variant,,ENST00000381142,,n.402_403dup,MODIFIER,,,,1;TYRP1,downstream_gene_variant,,ENST00000470909,,,MODIFIER,,,,1;TYRP1,upstream_gene_variant,,ENST00000473504,,,MODIFIER,,,,1;LURAP1L-AS1,intron_variant,,ENST00000417638,,n.273-3981_273-3980dup,MODIFIER,,,,-1;LURAP1L-AS1,intron_variant,,ENST00000650458,,n.193-5252_193-5251dup,MODIFIER,,,,-1;LURAP1L-AS1,intron_variant,,ENST00000654076,,n.159-3981_159-3980dup,MODIFIER,,,,-1 1340-1341/2896 mutect2;pindel;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 89 183566df-0a7d-4b7f-8879-c5c89a348353 93 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS LURAP1L-AS1,intron_variant,,ENST00000417638.1,n.273-3980_273-3979insCC,MODIFIER,YES;LURAP1L-AS1,intron_variant,,ENST00000654076.1,n.159-3980_159-3979insCC,MODIFIER,;LURAP1L-AS1,intron_variant,,ENST00000650458.1,n.193-5251_193-5250insCC,MODIFIER,;TYRP1,non_coding_transcript_exon_variant,,ENST00000381142.3,n.398_399insGG,MODIFIER,;TYRP1,frameshift_variant,p.G98Efs*29,ENST00000381136.2,c.295_296dup,HIGH,;TYRP1,frameshift_variant,p.G388Efs*29,ENST00000388918.10,c.1165_1166dup,HIGH,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 49 42 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 115 183566df-0a7d-4b7f-8879-c5c89a348353 91 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +PITPNM2 57605 BI GRCh38 12 122991797 122991797 + intron_variant Intron SNP C C T TCGA-V4-A9F0-01A TCGA-V4-A9F0-10A Somatic 13 8 c.2404+702G>A ENST00000320201.10 NM_001384661.1 P3 T protein_coding YES CCDS9242.1 GGGCGCGGGAA COSM4420050 ENSP00000322218 COSV54902835 ENST00000320201 Transcript ENSG00000090975 HGNC:21044 MODIFIER 15/24 intron_variant 1 1.0 Unknown 1 Q9BZ72.133 PITPNM2 HGNC -1 5.0 UPI0000070D27 Q9BZ72-1 SNV PITPNM2,missense_variant,p.A836T,ENST00000280562,NM_001300801.1,c.2506G>A,MODERATE,,tolerated(0.63),benign(0.003),-1;PITPNM2,intron_variant,,ENST00000320201,NM_020845.2,c.2404+702G>A,MODIFIER,YES,,,-1 muse;mutect2;varscan2 92fca97d-6123-46a7-9c34-7a6f877fe612 0 27 183566df-0a7d-4b7f-8879-c5c89a348353 21 c8a688ea-b483-4c7a-9b0c-cdba0f9ccece SUCCESS PITPNM2,missense_variant,p.A836T,ENST00000280562.9,c.2506G>A,MODERATE,;PITPNM2,intron_variant,,ENST00000320201.10,c.2404+702G>A,MODIFIER,YES +HSD17B7 51478 BI GRCh38 1 162803453 162803453 + missense_variant Missense_Mutation SNP G G C rs1436565170 TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 49 24 c.665G>C p.Cys222Ser p.C222S ENST00000254521.8 NM_016371.4 222 tGt/tCt 6/9 P1 C C/S protein_coding YES CCDS1242.1 665/1026 GGCCTGTCCAG Pfam:PF00106;Prints:PR00081;PANTHER:PTHR44442;Superfamily:SSF51735;CDD:cd08941 ENSP00000254521 6/9 rs1436565170 ENST00000254521 Transcript ENSG00000132196 HGNC:5215 MODERATE 8.804e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.989) Unknown deleterious(0.02) P56937.188 HSD17B7 HGNC 1 A0A024R913.36 1.0 UPI000004C64C P56937-1 SNV HSD17B7,missense_variant,p.C222S,ENST00000254521,NM_016371.3,c.665G>C,MODERATE,YES,deleterious(0.02),probably_damaging(0.989),1;HSD17B7,non_coding_transcript_exon_variant,,ENST00000485405,,n.1783G>C,MODIFIER,,,,1;HSD17B7,downstream_gene_variant,,ENST00000463037,,,MODIFIER,,,,1;HSD17B7,downstream_gene_variant,,ENST00000484251,,,MODIFIER,,,,1;HSD17B7,non_coding_transcript_exon_variant,,ENST00000649629,,n.2595G>C,MODIFIER,,,,1;HSD17B7,non_coding_transcript_exon_variant,,ENST00000488656,,n.536G>C,MODIFIER,,,,1;HSD17B7,non_coding_transcript_exon_variant,,ENST00000494450,,n.457G>C,MODIFIER,,,,1;HSD17B7,intron_variant,,ENST00000470195,,c.*22-814G>C,MODIFIER,,,,1;HSD17B7,downstream_gene_variant,,ENST00000466176,,,MODIFIER,,,,1 720/1190 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.804e-06 0.0 0.0 0 71 73506437-4ce8-4ff2-82e3-dbad9af4496a 73 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS HSD17B7,non_coding_transcript_exon_variant,,ENST00000488656.1,n.536G>C,MODIFIER,;HSD17B7,intron_variant,NMD_transcript_variant,,ENST00000470195.2,c.*22-814G>C,MODIFIER,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000494450.1,n.457G>C,MODIFIER,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000649629.1,n.2595G>C,MODIFIER,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000485405.5,n.1783G>C,MODIFIER,;HSD17B7,missense_variant,p.C222S,ENST00000254521.8,c.665G>C,MODERATE,YES +AMER3 205147 BI GRCh38 2 130762600 130762600 + synonymous_variant Silent SNP G G A rs776935592 TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 45 25 c.528G>A p.Ser176= p.S176= ENST00000321420.5 NM_001105193.2 176 tcG/tcA 2/2 P1 A S protein_coding YES CCDS2164.1 528/2586 GCCTCGCTGGC PANTHER:PTHR22237:SF2;PANTHER:PTHR22237 ENSP00000314914 2/2 rs776935592;COSV58467357;COSV58469465 ENST00000321420 Transcript ENSG00000178171 HGNC:26771 LOW NM_152698.3 0.0003921 gnomAD_SAS synonymous_variant 0;1;1 1.0 Unknown 0;1;1 Q8N944.116 AMER3 HGNC 1 1.0 UPI0000D61239 SNV AMER3,synonymous_variant,p.S176=,ENST00000321420,NM_001105193.2&NM_152698.3,c.528G>A,LOW,YES,,,1;AMER3,synonymous_variant,p.S176=,ENST00000423981,NM_001105194.1&NM_001105195.2,c.528G>A,LOW,,,,1;AMER3,synonymous_variant,p.S176=,ENST00000458606,,c.528G>A,LOW,,,,1;AMER3,downstream_gene_variant,,ENST00000431758,,,MODIFIER,,,,1 682/6216 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 6.811e-05 0.0 2.893e-05 0.0 0.0 0.0 2.665e-05 0.0001636 0.0003921 4.731009903480299e-05 4.862390051130205e-05 0.0 0.0 0.0 0.0004040400090161 0.0 eas 0.0004040400090161 0.0 1.5429699487867765e-05 0.000494070991408 0.0002084199950331 0 73 73506437-4ce8-4ff2-82e3-dbad9af4496a 71 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS AMER3,synonymous_variant,p.S176=,ENST00000458606.6,c.528G>A,LOW,;AMER3,synonymous_variant,p.S176=,ENST00000431758.2,c.528G>A,LOW,;AMER3,synonymous_variant,p.S176=,ENST00000321420.5,c.528G>A,LOW,YES +ETS1 2113 BI GRCh38 11 128490475 128490475 + stop_gained Nonsense_Mutation SNP G G A TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 96 18 c.184C>T p.Arg62Ter p.R62* ENST00000319397.7 NM_005238.4 62 Cga/Tga 2/8 P3 A R/* protein_coding CCDS8475.1 184/1326 CAGTCGTTGCT COSM6067954;COSM6067955;COSM6067956 Gene3D:1.10.150.50;Pfam:PF02198;PIRSF:PIRSF001698;PROSITE_profiles:PS51433;PANTHER:PTHR11849;PANTHER:PTHR11849:SF209;SMART:SM00251;Superfamily:SSF47769;CDD:cd08542 ENSP00000324578 2/8 COSV60091588;COSV60094331 ENST00000319397 Transcript 1.0 ENSG00000134954 HGNC:3488 HIGH stop_gained 1;1 Unknown 1;1 P14921.218 ETS1 HGNC -1 1.0 UPI000012A268 P14921-1 SNV ETS1,stop_gained,p.R106*,ENST00000392668,NM_001143820.2,c.316C>T,HIGH,YES,,,-1;ETS1,stop_gained,p.R62*,ENST00000526145,NM_001330451.2,c.184C>T,HIGH,,,,-1;ETS1,stop_gained,p.R62*,ENST00000319397,NM_005238.4,c.184C>T,HIGH,,,,-1;ETS1,stop_gained,p.R62*,ENST00000531611,,c.184C>T,HIGH,,,,-1;ETS1,stop_gained,p.R34*,ENST00000608978,,c.100C>T,HIGH,,,,-1;ETS1,intron_variant,,ENST00000535549,NM_001162422.1,c.83-10024C>T,MODIFIER,,,,-1 494/2231 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 0 121 73506437-4ce8-4ff2-82e3-dbad9af4496a 114 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS ETS1,stop_gained,p.R34*,ENST00000608978.1,c.100C>T,HIGH,;ETS1,stop_gained,p.R62*,ENST00000531611.5,c.184C>T,HIGH,;ETS1,stop_gained,p.R62*,ENST00000526145.6,c.184C>T,HIGH,;ETS1,stop_gained,p.R106*,ENST00000392668.8,c.316C>T,HIGH,YES;ETS1,stop_gained,p.R62*,ENST00000319397.7,c.184C>T,HIGH,;ETS1,intron_variant,,ENST00000535549.5,c.83-10024C>T,MODIFIER, +NACA 4666 BI GRCh38 12 56719365 56719365 + intron_variant Intron SNP G G A novel TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 8 10 c.71-4678C>T ENST00000356769.7 NM_001113202.2 P1 A protein_coding CCDS31837.1 AGGTAGCCAGA ENSP00000349212 ENST00000356769 Transcript 1.0 ENSG00000196531 HGNC:7629 MODIFIER 2/7 intron_variant Unknown Q13765.180 NACA HGNC -1 A0A024RB41.36 1.0 UPI0000073EC7 Q13765-1 SNV NACA,missense_variant,p.A722V,ENST00000454682,NM_001365896.1,c.2165C>T,MODERATE,YES,tolerated(0.27),benign(0.059),-1;NACA,intron_variant,,ENST00000356769,NM_001113202.2&NM_001320193.2,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000393891,NM_005594.6,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000546392,,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000546862,,c.-183-4662C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000548563,,c.-183-4662C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000549259,NM_001320194.2,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000549855,,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000550920,,c.130+172C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000550952,NM_001113203.3,c.1864+172C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000552055,,c.71-4690C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000552540,NM_001113201.3,c.71-4678C>T,MODIFIER,,,,-1;AC117378.1,intron_variant,,ENST00000647707,,c.513-4678C>T,MODIFIER,YES,,,-1;NACA,intron_variant,,ENST00000678047,,c.71-3255C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678066,,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678376,,c.-167-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678416,,c.-167-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000679092,,c.71-4690C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551775,,n.115-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551793,,n.112-4678C>T,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000550343,,,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000547914,,c.71-4678C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000548084,,c.71-4662C>T,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551520,,n.106-4678C>T,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000548386,,,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000676873,,,MODIFIER,,,,-1 mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 0 18 73506437-4ce8-4ff2-82e3-dbad9af4496a 18 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS ENSG00000285625,intron_variant,,ENST00000647707.1,c.513-4678C>T,MODIFIER,YES;NACA,intron_variant,NMD_transcript_variant,,ENST00000548084.1,c.71-4662C>T,MODIFIER,;NACA,intron_variant,,ENST00000551520.1,n.106-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000551793.5,n.112-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000549855.5,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000552055.5,c.71-4690C>T,MODIFIER,;NACA,intron_variant,,ENST00000551775.5,n.115-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000549259.5,c.71-4678C>T,MODIFIER,;NACA,intron_variant,NMD_transcript_variant,,ENST00000547914.5,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000546392.6,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000548563.5,c.-183-4662C>T,MODIFIER,;NACA,intron_variant,,ENST00000393891.8,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000552540.5,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000356769.7,c.71-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000678376.1,c.-167-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000550920.6,c.130+172C>T,MODIFIER,;NACA,missense_variant,p.A722V,ENST00000454682.6,c.2165C>T,MODERATE,YES;NACA,intron_variant,,ENST00000550952.6,c.1864+172C>T,MODIFIER,;NACA,intron_variant,,ENST00000546862.6,c.-183-4662C>T,MODIFIER,;NACA,intron_variant,,ENST00000678416.1,c.-167-4678C>T,MODIFIER,;NACA,intron_variant,,ENST00000679092.1,c.71-4690C>T,MODIFIER,;NACA,intron_variant,,ENST00000678047.1,c.71-3255C>T,MODIFIER,;NACA,intron_variant,,ENST00000678066.1,c.71-4678C>T,MODIFIER, +CYSLTR2 57105 BI GRCh38 13 48707203 48707203 + missense_variant Missense_Mutation SNP T T A TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 124 90 c.386T>A p.Leu129Gln p.L129Q ENST00000282018.4 NM_001308471.3 129 cTg/cAg 1/1 P1 A L/Q protein_coding YES CCDS9412.1 386/1041 TTTCCTGACCG COSM1666392 Gene3D:1.20.1070.10;PDB-ENSP_mappings:6rz6.A;PDB-ENSP_mappings:6rz7.A;PDB-ENSP_mappings:6rz8.A;PDB-ENSP_mappings:6rz9.A;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24230;PANTHER:PTHR24230:SF10;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15157 ENSP00000282018 1/1 COSV56166671 ENST00000282018 Transcript 1.0 ENSG00000152207 HGNC:18274 MODERATE missense_variant 1 1.0 probably_damaging(0.997) Unknown deleterious(0) 1 Q9NS75.162 CYSLTR2 HGNC 1 Q5KU17.121 UPI000003BCCC SNV CYSLTR2,missense_variant,p.L129Q,ENST00000282018,NM_001308471.3,c.386T>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;CYSLTR2,missense_variant,p.L129Q,ENST00000614739,NM_001308465.3&NM_001308476.3&NM_001308468.3&NM_001308467.3&NM_020377.5&NM_001308469.3&NM_001308470.3,c.386T>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;CYSLTR2,downstream_gene_variant,,ENST00000617562,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000621321,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000622559,,,MODIFIER,,,,1 649/4672 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 0 184 73506437-4ce8-4ff2-82e3-dbad9af4496a 214 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS CYSLTR2,missense_variant,p.L129Q,ENST00000282018.4,c.386T>A,MODERATE,;CYSLTR2,missense_variant,p.L129Q,ENST00000682523.1,c.386T>A,MODERATE,YES;CYSLTR2,missense_variant,p.L129Q,ENST00000614739.4,c.386T>A,MODERATE, +ASIC2 40 BI GRCh38 17 34156161 34156161 + synonymous_variant Silent SNP C C T rs770764384 TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 49 32 c.372G>A p.Pro124= p.P124= ENST00000359872.6 NM_001094.5 124 ccG/ccA 1/10 P1 T P protein_coding CCDS42296.1 372/1539 GGGTCCGGGAT COSM1244077 Gene3D:1.10.287.770;Gene3D:1.10.3590.10;Gene3D:2.60.470.10;Pfam:PF00858;PANTHER:PTHR11690;PANTHER:PTHR11690:SF128 ENSP00000352934 1/10 rs770764384;COSV63332185 ENST00000359872 Transcript ENSG00000108684 HGNC:99 LOW 6.536e-05 gnomAD_SAS synonymous_variant 0;1 Unknown 0;1 Q16515.183 ASIC2 HGNC -1 1.0 UPI00000441F0 Q16515-1 SNV ASIC2,synonymous_variant,p.P124=,ENST00000359872,NM_001094.4,c.372G>A,LOW,,,,-1;ASIC2,downstream_gene_variant,,ENST00000583395,,,MODIFIER,,,,-1;AC004147.2,non_coding_transcript_exon_variant,,ENST00000583224,,n.596C>T,MODIFIER,YES,,,1;AC004147.2,non_coding_transcript_exon_variant,,ENST00000667899,,n.548C>T,MODIFIER,,,,1;AC004147.4,upstream_gene_variant,,ENST00000636421,,,MODIFIER,YES,,,-1 1134/3179 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 3.607e-05 0.0 0.0 0.0 0.0 0.0 6.182e-05 0.0 6.536e-05 7.443300273735076e-05 0.0 0.0 6.628660048590973e-05 0.0 0.0 9.439310088055208e-05 nfe 0.0001389450044371 0.0 0.0001389450044371 0.0 0.0 0 84 73506437-4ce8-4ff2-82e3-dbad9af4496a 81 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS ENSG00000263571,non_coding_transcript_exon_variant,,ENST00000667899.1,n.548C>T,MODIFIER,;ENSG00000263571,non_coding_transcript_exon_variant,,ENST00000583224.3,n.596C>T,MODIFIER,YES;ASIC2,synonymous_variant,p.P124=,ENST00000359872.6,c.372G>A,LOW, +BCAS1 8537 BI GRCh38 20 53953606 53953606 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9ED-01A TCGA-V4-A9ED-10A Somatic 47 34 c.1506C>G p.Asp502Glu p.D502E ENST00000395961.7 NM_001366295.2 502 gaC/gaG 11/12 P3 C D/E protein_coding YES CCDS13444.1 1506/1755 TTCTTGTCCTT PANTHER:PTHR15016;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000379290 11/12 ENST00000395961 Transcript ENSG00000064787 HGNC:974 MODERATE missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0.02) O75363.147 BCAS1 HGNC -1 1.0 UPI000013D2E2 O75363-1 SNV BCAS1,missense_variant,p.D373E,ENST00000448484,,c.1119C>G,MODERATE,,deleterious(0.02),benign(0.242),-1;BCAS1,missense_variant,p.D502E,ENST00000395961,NM_003657.3&NM_001366295.1&NM_001366296.1&NM_001366298.1,c.1506C>G,MODERATE,YES,deleterious(0.02),probably_damaging(0.996),-1;BCAS1,missense_variant,p.D424E,ENST00000371435,NM_001316361.2&NM_001366297.1&NM_001323347.1,c.1272C>G,MODERATE,,deleterious(0.04),probably_damaging(0.99),-1;BCAS1,missense_variant,p.D165E,ENST00000422805,,c.495C>G,MODERATE,,deleterious(0),possibly_damaging(0.779),-1 1673/3303 muse;mutect2;varscan2 367869f9-bbe7-4e57-a16f-f2b63f2de697 0 68 73506437-4ce8-4ff2-82e3-dbad9af4496a 82 3e13a977-c19c-445b-b0c9-60fc3badd304 SUCCESS BCAS1,missense_variant,p.D159E,ENST00000422805.2,c.477C>G,MODERATE,;BCAS1,missense_variant,p.D455E,ENST00000686565.1,c.1365C>G,MODERATE,;BCAS1,missense_variant,p.D168E,ENST00000689476.1,c.504C>G,MODERATE,;BCAS1,missense_variant,p.D238E,ENST00000688711.1,c.714C>G,MODERATE,;BCAS1,missense_variant,p.D224E,ENST00000690125.1,c.672C>G,MODERATE,;BCAS1,missense_variant,p.D424E,ENST00000371435.6,c.1272C>G,MODERATE,;BCAS1,missense_variant,p.D547E,ENST00000688948.1,c.1641C>G,MODERATE,YES;BCAS1,missense_variant,p.D502E,ENST00000395961.7,c.1506C>G,MODERATE,;BCAS1,missense_variant,p.D413E,ENST00000685429.1,c.1239C>G,MODERATE,;BCAS1,missense_variant,p.D373E,ENST00000448484.5,c.1119C>G,MODERATE, +PRAMEF20 645425 BI GRCh38 1 13421178 13421178 + missense_variant Missense_Mutation SNP A A T rs900978963 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 127 62 c.1348A>T p.Ile450Phe p.I450F ENST00000602960.2 NM_001099852.2 450 Atc/Ttc 3/3 P1 T I/F protein_coding YES CCDS41265.1 1348/1428 AGAGGATCTTG PIRSF:PIRSF038286;PANTHER:PTHR14224;PANTHER:PTHR14224:SF19 ENSP00000473584 3/3 rs900978963 ENST00000602960 Transcript ENSG00000204478 HGNC:25224 MODERATE missense_variant 1.0 possibly_damaging(0.877) Unknown deleterious(0.01) Q5VT98.123 PRAMEF20 HGNC 1 5.0 UPI0004423C14 SNV PRAMEF20,missense_variant,p.I450F,ENST00000602960,NM_001099852.2,c.1348A>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.877),1 1352/1502 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 1.3534499885281548e-05 2.435220085317269e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.543970029160846e-05 0.0 0.0 0 286 2ead8e38-8e26-473c-b589-e29eb03839ad 189 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS PRAMEF20,missense_variant,p.I450F,ENST00000602960.2,c.1348A>T,MODERATE,YES +CNST 163882 BI GRCh38 1 246660285 246660285 + synonymous_variant Silent SNP A A G rs1001635740 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 90 51 c.1923A>G p.Pro641= p.P641= ENST00000366513.9 NM_152609.3 641 ccA/ccG 10/11 P1 G P protein_coding YES CCDS1628.1 1923/2178 AAACCATCTAA Pfam:PF15281;PANTHER:PTHR28581 ENSP00000355470 10/11 rs1001635740 ENST00000366513 Transcript ENSG00000162852 HGNC:26486 LOW NM_152609.3 synonymous_variant 1.0 Unknown Q6PJW8.126 CNST HGNC 1 1.0 UPI000013E1DF Q6PJW8-1 SNV CNST,synonymous_variant,p.P641=,ENST00000366513,NM_152609.3,c.1923A>G,LOW,YES,,,1 2182/5127 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 0 91 2ead8e38-8e26-473c-b589-e29eb03839ad 141 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS CNST,synonymous_variant,p.P641=,ENST00000366513.9,c.1923A>G,LOW,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 34 25 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 58 2ead8e38-8e26-473c-b589-e29eb03839ad 59 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +PKHD1L1 93035 BI GRCh38 8 109491043 109491057 + inframe_deletion In_Frame_Del DEL ATTTGGGACAGATGG ATTTGGGACAGATGG - novel TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 65 8 c.10059_10073del p.Phe3353_Gly3357del p.F3353_G3357del ENST00000378402.10 NM_177531.6 3352 gtATTTGGGACAGATGGa/gta 61/78 P1 - VFGTDG/V protein_coding YES CCDS47911.1 10056-10070/12732 TGGTGTATTTGGGACAGATGGATTGG Gene3D:2.160.20.10;PANTHER:PTHR46769;PANTHER:PTHR46769:SF2;SMART:SM00710;Superfamily:SSF51126 ENSP00000367655 61/78 ENST00000378402 Transcript ENSG00000205038 HGNC:20313 3.0 MODERATE NM_177531.6 inframe_deletion 1.0 Unknown Q86WI1.128 PKHD1L1 HGNC 1 1.0 UPI0000E5B020 deletion PKHD1L1,inframe_deletion,p.F3353_G3357del,ENST00000378402,NM_177531.6,c.10059_10073del,MODERATE,YES,,,1;PKHD1L1,inframe_deletion,p.F281_G285del,ENST00000526472,,c.843_857del,MODERATE,,,,1 10176-10190/19969 mutect2;pindel 6be5176c-4980-4663-adff-d04f05737da0 0 85 2ead8e38-8e26-473c-b589-e29eb03839ad 73 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS PKHD1L1,inframe_deletion,p.F281_G285del,ENST00000526472.1,c.843_857del,MODERATE,;PKHD1L1,inframe_deletion,p.F3353_G3357del,ENST00000378402.10,c.10059_10073del,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 53 35 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 0 107 2ead8e38-8e26-473c-b589-e29eb03839ad 88 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +SLC5A12 159963 BI GRCh38 11 26703916 26703916 + missense_variant Missense_Mutation SNP G G A rs1291728602 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 72 73 c.557C>T p.Ala186Val p.A186V ENST00000396005.8 NM_178498.4 186 gCa/gTa 5/15 P1 A A/V protein_coding YES CCDS7860.2 557/1857 GAAATGCATCT PROSITE_profiles:PS50283;CDD:cd11520;PANTHER:PTHR42985;PANTHER:PTHR42985:SF15;Gene3D:1.20.1730.10;Pfam:PF00474;TIGRFAM:TIGR00813 ENSP00000379326 5/15 rs1291728602 ENST00000396005 Transcript ENSG00000148942 HGNC:28750 MODERATE NM_178498.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.23) Unknown tolerated(1) Q1EHB4.114 SLC5A12 HGNC -1 1.0 UPI000003ED2C Q1EHB4-1 SNV SLC5A12,missense_variant,p.A186V,ENST00000396005,NM_178498.4,c.557C>T,MODERATE,YES,tolerated(1),benign(0.23),-1;SLC5A12,missense_variant,p.A186V,ENST00000280467,,c.557C>T,MODERATE,,tolerated(1),benign(0.023),-1;SLC5A12,5_prime_UTR_variant,,ENST00000533617,,c.-8C>T,MODIFIER,,,,-1;SLC5A12,5_prime_UTR_variant,,ENST00000527405,,c.-8C>T,MODIFIER,,,,-1 903/6285 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 166 2ead8e38-8e26-473c-b589-e29eb03839ad 145 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS SLC5A12,5_prime_UTR_variant,,ENST00000533617.5,c.-8C>T,MODIFIER,;SLC5A12,missense_variant,p.A186V,ENST00000280467.10,c.557C>T,MODERATE,;SLC5A12,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000527405.5,c.-8C>T,MODIFIER,;SLC5A12,missense_variant,p.A186V,ENST00000396005.8,c.557C>T,MODERATE,YES +ACP2 53 BI GRCh38 11 47240132 47240132 + missense_variant Missense_Mutation SNP C C T rs762176748 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 55 6 c.1256G>A p.Gly419Glu p.G419E ENST00000256997.9 419 gGg/gAg 11/11 P1 T G/E protein_coding CCDS7928.1 1256/1272 CCTCCCCATCT ENSP00000256997 11/11 rs762176748 ENST00000256997 Transcript 1.0 ENSG00000134575 HGNC:123 MODERATE 5.439e-05 gnomAD_EAS missense_variant benign(0.007) Unknown tolerated_low_confidence(0.06) P11117.183 ACP2 HGNC -1 1.0 UPI0000131FE1 P11117-1 SNV ACP2,missense_variant,p.G419E,ENST00000256997,,c.1256G>A,MODERATE,,tolerated_low_confidence(0.06),benign(0.007),-1;ACP2,missense_variant,p.G419E,ENST00000672073,NM_001357016.1&NM_001610.4,c.1256G>A,MODERATE,,tolerated_low_confidence(0.06),benign(0.007),-1;ACP2,missense_variant,p.G419E,ENST00000672636,,c.1256G>A,MODERATE,YES,tolerated_low_confidence(0.05),benign(0.065),-1;ACP2,missense_variant,p.G356E,ENST00000529444,NM_001302491.1,c.1067G>A,MODERATE,,tolerated_low_confidence(0.09),benign(0.009),-1;ACP2,missense_variant,p.G387E,ENST00000527256,NM_001302490.1&NM_001302492.1,c.1160G>A,MODERATE,,tolerated_low_confidence(0.05),benign(0.009),-1;ACP2,missense_variant,p.G391E,ENST00000533929,NM_001302489.1,c.1172G>A,MODERATE,,tolerated_low_confidence(0.07),benign(0.005),-1;DDB2,downstream_gene_variant,,ENST00000256996,NM_000107.3,,MODIFIER,YES,,,1;DDB2,downstream_gene_variant,,ENST00000378600,NM_001300734.1,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000378603,,,MODIFIER,,,,1;ACP2,downstream_gene_variant,,ENST00000672787,,,MODIFIER,,,,-1;ACP2,downstream_gene_variant,,ENST00000673604,,,MODIFIER,,,,-1;ACP2,non_coding_transcript_exon_variant,,ENST00000672728,,n.710G>A,MODIFIER,,,,-1;ACP2,intron_variant,,ENST00000672351,,n.194-743G>A,MODIFIER,,,,-1;DDB2,downstream_gene_variant,,ENST00000620515,,,MODIFIER,,,,1;ACP2,downstream_gene_variant,,ENST00000671941,,,MODIFIER,,,,-1;ACP2,3_prime_UTR_variant,,ENST00000672075,,c.*729G>A,MODIFIER,,,,-1;ACP2,non_coding_transcript_exon_variant,,ENST00000673184,,n.1593G>A,MODIFIER,,,,-1;DDB2,downstream_gene_variant,,ENST00000378601,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000612309,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000614394,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000614884,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000616278,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000617022,,,MODIFIER,,,,1;DDB2,downstream_gene_variant,,ENST00000617847,,,MODIFIER,,,,1;ACP2,downstream_gene_variant,,ENST00000673511,,,MODIFIER,,,,-1 1373/2200 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 3.989e-06 0.0 0.0 0.0 5.439e-05 0.0 0.0 0.0 0.0 0 56 2ead8e38-8e26-473c-b589-e29eb03839ad 62 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS ACP2,non_coding_transcript_exon_variant,,ENST00000672728.1,n.710G>A,MODIFIER,;ACP2,missense_variant,p.G391E,ENST00000533929.7,c.1172G>A,MODERATE,;ACP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000672075.1,c.*729G>A,MODIFIER,;ACP2,missense_variant,p.G387E,ENST00000527256.7,c.1160G>A,MODERATE,;ACP2,non_coding_transcript_exon_variant,,ENST00000673184.1,n.1593G>A,MODIFIER,;ACP2,missense_variant,p.G356E,ENST00000529444.7,c.1067G>A,MODERATE,;ACP2,intron_variant,,ENST00000672351.1,n.194-743G>A,MODIFIER,;ACP2,missense_variant,p.G419E,ENST00000256997.9,c.1256G>A,MODERATE,;ACP2,missense_variant,p.G419E,ENST00000672636.2,c.1256G>A,MODERATE,;ACP2,missense_variant,p.G419E,ENST00000672073.1,c.1256G>A,MODERATE,YES +CNTN5 53942 BI GRCh38 11 100271226 100271226 + missense_variant Missense_Mutation SNP C C T rs370172429 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 19 13 c.2299C>T p.Arg767Cys p.R767C ENST00000524871.6 NM_014361.4 767 Cgc/Tgc 18/25 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 T R/C protein_coding YES CCDS53696.1 2299/3303 TGATCCGCACA PDB-ENSP_mappings:5e52.A;PROSITE_profiles:PS50853;CDD:cd00063;PANTHER:PTHR44170;PANTHER:PTHR44170:SF17;Gene3D:2.60.40.10;Superfamily:SSF49265 ENSP00000435637 0.0002607 0.0 18/25 rs370172429 ENST00000524871 Transcript ENSG00000149972 HGNC:2175 MODERATE NM_014361.4 0.0008 AFR missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0) O94779.152 CNTN5 HGNC 1 1.0 UPI000006DAB0 O94779-1 SNV CNTN5,missense_variant,p.R767C,ENST00000524871,NM_014361.4&NM_001243270.2,c.2299C>T,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;CNTN5,missense_variant,p.R751C,ENST00000279463,,c.2251C>T,MODERATE,,deleterious(0),probably_damaging(0.95),1;CNTN5,missense_variant,p.R689C,ENST00000619298,,c.2065C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;CNTN5,missense_variant,p.R767C,ENST00000527185,NM_001243271.2,c.2299C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;CNTN5,missense_variant,p.R767C,ENST00000528682,,c.2299C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;CNTN5,missense_variant,p.R693C,ENST00000418526,NM_175566.2,c.2077C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,,n.547C>T,MODIFIER,,,,1 2830/6499 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 1.684e-05 0.0001308 3.216e-05 0.0 0.0 0.0 9.138e-06 0.0 0.0 4.7357498260680586e-05 0.0001217140015796 0.0 6.636579928454012e-05 0.0 0.0 9.450010111322626e-05 afr 0.0001217140015796 0.0 0.0 0.0 0.0 0 34 2ead8e38-8e26-473c-b589-e29eb03839ad 32 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS CNTN5,non_coding_transcript_exon_variant,,ENST00000524560.1,n.547C>T,MODIFIER,;CNTN5,missense_variant,p.R751C,ENST00000279463.7,c.2251C>T,MODERATE,;CNTN5,missense_variant,p.R693C,ENST00000418526.6,c.2077C>T,MODERATE,;CNTN5,missense_variant,p.R767C,ENST00000528682.5,c.2299C>T,MODERATE,;CNTN5,missense_variant,p.R767C,ENST00000527185.5,c.2299C>T,MODERATE,;CNTN5,missense_variant,p.R767C,ENST00000524871.6,c.2299C>T,MODERATE,YES +DCAF11 80344 BI GRCh38 14 24119843 24119843 + missense_variant Missense_Mutation SNP C C T rs777653791 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 10 7 c.1039C>T p.Pro347Ser p.P347S ENST00000446197.8 NM_025230.5 347 Cct/Tct 11/15 P1 T P/S protein_coding YES CCDS9610.1 1039/1641 CCAAGCCTGTG Gene3D:2.130.10.10;Pfam:PF00400;PIRSF:PIRSF038135;PROSITE_profiles:PS50294;PANTHER:PTHR19847;PANTHER:PTHR19847:SF7;SMART:SM00320;Superfamily:SSF50978 ENSP00000415556 11/15 rs777653791 ENST00000446197 Transcript ENSG00000100897 HGNC:20258 MODERATE NM_025230.5 4.636e-05 gnomAD_FIN missense_variant 1.0 probably_damaging(0.976) Unknown deleterious(0.01) Q8TEB1.163 DCAF11 HGNC 1 1.0 UPI0000073AB2 Q8TEB1-1 SNV DCAF11,missense_variant,p.P347S,ENST00000446197,NM_025230.5,c.1039C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.976),1;DCAF11,missense_variant,p.P347S,ENST00000559115,NM_001163484.1,c.1039C>T,MODERATE,,deleterious(0.01),probably_damaging(0.976),1;DCAF11,missense_variant,p.P247S,ENST00000396936,,c.739C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.793),1;DCAF11,missense_variant,p.P321S,ENST00000396941,NM_181357.2,c.961C>T,MODERATE,,deleterious(0.01),probably_damaging(0.932),1;DCAF11,missense_variant,p.P87S,ENST00000559144,,c.259C>T,MODERATE,,tolerated(0.06),probably_damaging(0.953),1;DCAF11,downstream_gene_variant,,ENST00000557810,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000558215,,,MODIFIER,,,,1;NRL,upstream_gene_variant,,ENST00000558280,,,MODIFIER,,,,-1;AL136295.3,upstream_gene_variant,,ENST00000558325,,,MODIFIER,YES,,,1;DCAF11,downstream_gene_variant,,ENST00000558408,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000558638,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559017,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559288,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559354,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559382,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559396,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559593,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559796,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560459,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560713,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560901,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000561001,,,MODIFIER,,,,1;NRL,upstream_gene_variant,,ENST00000561028,NM_001354768.3&NM_001354770.2&NM_006177.5,,MODIFIER,YES,,,-1;DCAF11,downstream_gene_variant,,ENST00000561041,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000561375,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000557809,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000557952,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560171,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000561016,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000561056,,,MODIFIER,,,,1;DCAF11,3_prime_UTR_variant,,ENST00000557802,,c.*735C>T,MODIFIER,,,,1;DCAF11,3_prime_UTR_variant,,ENST00000326009,,c.*800C>T,MODIFIER,,,,1;DCAF11,3_prime_UTR_variant,,ENST00000558914,,c.*570C>T,MODIFIER,,,,1;DCAF11,non_coding_transcript_exon_variant,,ENST00000558624,,n.1207C>T,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000557888,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000558706,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000559451,,,MODIFIER,,,,1;DCAF11,upstream_gene_variant,,ENST00000559472,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560046,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560457,,,MODIFIER,,,,1;DCAF11,downstream_gene_variant,,ENST00000560614,,,MODIFIER,,,,1 1769/4304 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 3.984e-06 0.0 0.0 0.0 0.0 4.636e-05 0.0 0.0 0.0 6.7600499278341886e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542919926578179e-05 0.0 0.0 0 26 2ead8e38-8e26-473c-b589-e29eb03839ad 17 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS DCAF11,missense_variant,p.P87S,ENST00000559144.1,c.259C>T,MODERATE,;DCAF11,non_coding_transcript_exon_variant,,ENST00000558624.1,n.1207C>T,MODIFIER,;DCAF11,missense_variant,p.P247S,ENST00000396936.5,c.739C>T,MODERATE,;DCAF11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000558914.5,c.*570C>T,MODIFIER,;DCAF11,missense_variant,p.P321S,ENST00000396941.8,c.961C>T,MODERATE,;DCAF11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000326009.9,c.*800C>T,MODIFIER,;DCAF11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000557802.5,c.*735C>T,MODIFIER,;DCAF11,missense_variant,p.P347S,ENST00000446197.8,c.1039C>T,MODERATE,YES;DCAF11,missense_variant,p.P347S,ENST00000559115.5,c.1039C>T,MODERATE, +ZFYVE19 84936 BI GRCh38 15 40807760 40807760 + synonymous_variant Silent SNP A A G rs1193218587 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 20 11 c.171A>G p.Pro57= p.P57= ENST00000355341.8 NM_001077268.2 57 ccA/ccG 1/11 P4 G P protein_coding YES CCDS42025.1 171/1416 GGCCCAGGACT MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000347498 1/11 rs1193218587 ENST00000355341 Transcript ENSG00000166140 HGNC:20758 LOW NM_001077268.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q96K21.157 ZFYVE19 HGNC 1 1.0 UPI0000E5924A Q96K21-1 SNV ZFYVE19,synonymous_variant,p.P57=,ENST00000355341,NM_001077268.2,c.171A>G,LOW,YES,,,1;ZFYVE19,synonymous_variant,p.P57=,ENST00000299173,NM_001258420.2,c.171A>G,LOW,,,,1;ZFYVE19,synonymous_variant,p.P28=,ENST00000566407,,c.84A>G,LOW,,,,1;ZFYVE19,synonymous_variant,p.P2=,ENST00000561617,,c.6A>G,LOW,,,,1;ZFYVE19,intron_variant,,ENST00000336455,NM_032850.5,c.125+347A>G,MODIFIER,,,,1;ZFYVE19,intron_variant,,ENST00000564258,NM_001258421.2,c.-247+89A>G,MODIFIER,,,,1;ZFYVE19,intron_variant,,ENST00000570108,,c.134-32A>G,MODIFIER,,,,1;DNAJC17,upstream_gene_variant,,ENST00000220496,NM_018163.3,,MODIFIER,YES,,,-1;ZFYVE19,upstream_gene_variant,,ENST00000566767,,,MODIFIER,,,,1;DNAJC17,upstream_gene_variant,,ENST00000627802,,,MODIFIER,,,,-1;ZFYVE19,non_coding_transcript_exon_variant,,ENST00000563530,,n.101A>G,MODIFIER,,,,1;ZFYVE19,synonymous_variant,p.P40=,ENST00000568062,,c.120A>G,LOW,,,,1;ZFYVE19,synonymous_variant,p.P9=,ENST00000567756,,c.27A>G,LOW,,,,1;DNAJC17,upstream_gene_variant,,ENST00000559238,,,MODIFIER,,,,-1;DNAJC17,upstream_gene_variant,,ENST00000559310,,,MODIFIER,,,,-1;DNAJC17,upstream_gene_variant,,ENST00000560065,,,MODIFIER,,,,-1;ZFYVE19,upstream_gene_variant,,ENST00000560078,,,MODIFIER,,,,1;DNAJC17,upstream_gene_variant,,ENST00000560301,,,MODIFIER,,,,-1;DNAJC17,upstream_gene_variant,,ENST00000560645,,,MODIFIER,,,,-1;DNAJC17,upstream_gene_variant,,ENST00000561018,,,MODIFIER,,,,-1;ZFYVE19,upstream_gene_variant,,ENST00000561768,,,MODIFIER,,,,1;ZFYVE19,upstream_gene_variant,,ENST00000569057,,,MODIFIER,,,,1;ZFYVE19,upstream_gene_variant,,ENST00000570162,,,MODIFIER,,,,1 672/2775 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 22 2ead8e38-8e26-473c-b589-e29eb03839ad 31 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS ZFYVE19,missense_variant,p.R2G,ENST00000561617.1,c.4A>G,MODERATE,;ZFYVE19,synonymous_variant,NMD_transcript_variant,p.P9=,ENST00000567756.5,c.27A>G,LOW,;ZFYVE19,synonymous_variant,p.P28=,ENST00000566407.5,c.84A>G,LOW,;ZFYVE19,non_coding_transcript_exon_variant,,ENST00000563530.1,n.101A>G,MODIFIER,;ZFYVE19,missense_variant,NMD_transcript_variant,p.Q40R,ENST00000568062.5,c.119A>G,MODERATE,;ZFYVE19,synonymous_variant,p.P57=,ENST00000299173.14,c.171A>G,LOW,;ZFYVE19,intron_variant,,ENST00000336455.9,c.125+347A>G,MODIFIER,;ZFYVE19,synonymous_variant,p.P57=,ENST00000355341.8,c.171A>G,LOW,YES;ZFYVE19,intron_variant,,ENST00000564258.5,c.-247+89A>G,MODIFIER,;ZFYVE19,intron_variant,,ENST00000570108.5,c.134-32A>G,MODIFIER, +LCAT 3931 BI GRCh38 16 67942388 67942388 + synonymous_variant Silent SNP G G A novel TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 26 4 c.723C>T p.Ile241= p.I241= ENST00000264005.10 NM_000229.2 241 atC/atT 5/6 P1 A I protein_coding YES CCDS10854.1 723/1323 GGCTTGATGGA PDB-ENSP_mappings:4x96.A;PDB-ENSP_mappings:4x96.B;PDB-ENSP_mappings:4x96.C;PDB-ENSP_mappings:4x96.D;PDB-ENSP_mappings:4xwg.A;PDB-ENSP_mappings:4xx1.A;PDB-ENSP_mappings:4xx1.B;PDB-ENSP_mappings:4xx1.J;PDB-ENSP_mappings:5bv7.A;PDB-ENSP_mappings:5txf.A;PDB-ENSP_mappings:5txf.B;PDB-ENSP_mappings:5txf.C;PDB-ENSP_mappings:5txf.D;PDB-ENSP_mappings:6mvd.A;PDB-ENSP_mappings:6mvd.B;Pfam:PF02450;PANTHER:PTHR11440;PANTHER:PTHR11440:SF18;Superfamily:SSF53474 ENSP00000264005 5/6 ENST00000264005 Transcript 1.0 ENSG00000213398 HGNC:6522 LOW NM_000229.2 synonymous_variant 1.0 Unknown P04180.205 LCAT HGNC -1 A0A140VK24.17 1.0 UPI0000000DE7 SNV LCAT,missense_variant,p.S24L,ENST00000570396,,c.71C>T,MODERATE,,,unknown(0),-1;LCAT,synonymous_variant,p.I241=,ENST00000264005,NM_000229.2,c.723C>T,LOW,YES,,,-1;LCAT,synonymous_variant,p.I169=,ENST00000570980,,c.507C>T,LOW,,,,-1;LCAT,synonymous_variant,p.I64=,ENST00000576450,,c.192C>T,LOW,,,,-1;LCAT,intron_variant,,ENST00000570369,,c.155+473C>T,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000316341,NM_001145961.2&NM_005072.5,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000422611,NM_001145962.1,,MODIFIER,YES,,,-1;SLC12A4,downstream_gene_variant,,ENST00000537830,NM_001145963.2,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000541864,NM_001145964.2,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000572037,,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000576616,,,MODIFIER,,,,-1;LCAT,synonymous_variant,p.I122=,ENST00000573538,,c.366C>T,LOW,,,,-1;LCAT,3_prime_UTR_variant,,ENST00000575467,,c.*418C>T,MODIFIER,,,,-1;LCAT,non_coding_transcript_exon_variant,,ENST00000573846,,n.337C>T,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000570616,,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000570802,,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000573023,,,MODIFIER,,,,-1;LCAT,downstream_gene_variant,,ENST00000575277,,,MODIFIER,,,,-1;SLC12A4,downstream_gene_variant,,ENST00000575857,,,MODIFIER,,,,-1 742/1496 muse;mutect2 6be5176c-4980-4663-adff-d04f05737da0 0 28 2ead8e38-8e26-473c-b589-e29eb03839ad 30 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS LCAT,non_coding_transcript_exon_variant,,ENST00000573846.1,n.337C>T,MODIFIER,;LCAT,missense_variant,p.S24L,ENST00000570396.1,c.71C>T,MODERATE,;LCAT,stop_gained,p.Q64*,ENST00000576450.1,c.190C>T,HIGH,;LCAT,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000575467.5,c.*418C>T,MODIFIER,;LCAT,synonymous_variant,p.I169=,ENST00000570980.1,c.507C>T,LOW,;LCAT,intron_variant,,ENST00000570369.5,c.155+473C>T,MODIFIER,;LCAT,synonymous_variant,NMD_transcript_variant,p.I122=,ENST00000573538.5,c.366C>T,LOW,;LCAT,synonymous_variant,p.I241=,ENST00000264005.10,c.723C>T,LOW,YES +RUNDC1 146923 BI GRCh38 17 42991290 42991290 + synonymous_variant Silent SNP G G A rs749457403 TCGA-V4-A9EW-01A TCGA-V4-A9EW-10A Somatic 57 12 c.1416G>A p.Pro472= p.P472= ENST00000361677.6 NM_001321381.3 472 ccG/ccA 5/5 P1 A P protein_coding YES CCDS11448.1 1416/1842 CACCCGTGGGA Gene3D:1.20.58.900;Pfam:PF02759;PROSITE_profiles:PS50826;PANTHER:PTHR22957;PANTHER:PTHR22957:SF2 ENSP00000354622 5/5 rs749457403 ENST00000361677 Transcript ENSG00000198863 HGNC:25418 LOW 0.0003971 gnomAD_ASJ synonymous_variant 1.0 Unknown Q96C34.111 RUNDC1 HGNC 1 1.0 UPI00001AED0E Q96C34-1 SNV RUNDC1,synonymous_variant,p.P472=,ENST00000361677,NM_001321381.3&NM_173079.5,c.1416G>A,LOW,YES,,,1;RUNDC1,downstream_gene_variant,,ENST00000589705,,,MODIFIER,,,,1 1428/3828 muse;mutect2;varscan2 6be5176c-4980-4663-adff-d04f05737da0 6.761e-05 0.0 5.782e-05 0.0003971 0.0 0.0 7.913e-05 0.0 6.533e-05 0.0001014419976854 2.4338000002899207e-05 0.0 0.0001989129959838 0.0003028470091521 0.0 0.0 amr 0.0001989129959838 0.0 0.0001543069956824 0.0 0.0 0 65 2ead8e38-8e26-473c-b589-e29eb03839ad 69 20163d4a-6116-469e-8c60-05d973da5c23 SUCCESS RUNDC1,synonymous_variant,p.P472=,ENST00000361677.6,c.1416G>A,LOW,YES +CELSR2 1952 BI GRCh38 1 109261166 109261166 + synonymous_variant Silent SNP G G A novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 44 38 c.4083G>A p.Glu1361= p.E1361= ENST00000271332.4 NM_001408.3 1361 gaG/gaA 3/34 P1 A E protein_coding YES CCDS796.1 4083/8772 TTCGAGAAGCC CDD:cd00054;Gene3D:2.10.25.10;SMART:SM00181;SMART:SM00179;Superfamily:SSF57184;Superfamily:SSF49899;PROSITE_profiles:PS50026;PANTHER:PTHR24026:SF32;PANTHER:PTHR24026 ENSP00000271332 3/34 ENST00000271332 Transcript ENSG00000143126 HGNC:3231 LOW NM_001408.3 synonymous_variant 1.0 Unknown Q9HCU4.180 CELSR2 HGNC 1 1.0 UPI00000015B6 SNV CELSR2,synonymous_variant,p.E1361=,ENST00000271332,NM_001408.3,c.4083G>A,LOW,YES,,,1;CELSR2,upstream_gene_variant,,ENST00000459940,,,MODIFIER,,,,1 4624/11015 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 88 9de08711-9c83-42ff-ad12-f18facf0432b 83 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS CELSR2,synonymous_variant,p.E1361=,ENST00000271332.4,c.4083G>A,LOW,YES +ATAD2B 54454 BI GRCh38 2 23823287 23823290 + frameshift_variant Frame_Shift_Del DEL GCAT GCAT - novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 9 12 c.2099_2102del p.Ala701GlufsTer11 p.A701Efs*11 ENST00000238789.10 NM_001242338.3 700 cATGCt/ct 16/28 P1 - HA/X protein_coding YES CCDS46227.1 2099-2102/4377 ATTTCAGCATGAGGA PANTHER:PTHR23069;PANTHER:PTHR23069:SF5 ENSP00000238789 16/28 ENST00000238789 Transcript ENSG00000119778 HGNC:29230 HIGH NM_017552.4 frameshift_variant 1.0 Unknown Q9ULI0.144 ATAD2B HGNC -1 5.0 UPI00006C056C deletion ATAD2B,frameshift_variant,p.H700Lfs*12,ENST00000238789,NM_001242338.3&NM_017552.4&NM_001354107.2,c.2099_2102del,HIGH,YES,,,-1;ATAD2B,upstream_gene_variant,,ENST00000381024,,,MODIFIER,,,,-1;ATAD2B,downstream_gene_variant,,ENST00000458510,,,MODIFIER,,,,-1;ATAD2B,non_coding_transcript_exon_variant,,ENST00000474583,,n.829_832del,MODIFIER,,,,-1 2452-2455/8112 mutect2;pindel;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 27 9de08711-9c83-42ff-ad12-f18facf0432b 21 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS ATAD2B,non_coding_transcript_exon_variant,,ENST00000474583.5,n.829_832del,MODIFIER,;ATAD2B,frameshift_variant,p.A701Efs*11,ENST00000238789.10,c.2099_2102del,HIGH,YES +SF3B1 23451 BI GRCh38 2 197402648 197402648 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 31 32 c.1985A>G p.His662Arg p.H662R ENST00000335508.11 NM_012433.4 662 cAc/cGc 14/25 P1 C H/R protein_coding YES CCDS33356.1 1985/3915 CAGTGTGTCTC Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.H662R,ENST00000335508,NM_012433.4,c.1985A>G,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*3052A>G,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2244A>G,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3869A>G,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 2014/6463 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 72 9de08711-9c83-42ff-ad12-f18facf0432b 64 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3869A>G,MODIFIER,;SF3B1,missense_variant,p.H662R,ENST00000335508.11,c.1985A>G,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*3052A>G,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2244A>G,MODIFIER, +TF 7018 BI GRCh38 3 133754654 133754654 + missense_variant Missense_Mutation SNP G G A rs371174384 TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 58 57 c.485G>A p.Arg162His p.R162H ENST00000402696.9 NM_001354703.2 162 cGt/cAt 4/17 P1 A R/H protein_coding YES CCDS3080.1 485/2097 GCCACGTAAAC PDB-ENSP_mappings:1a8e.A;PDB-ENSP_mappings:1a8f.A;PDB-ENSP_mappings:1b3e.A;PDB-ENSP_mappings:1bp5.A;PDB-ENSP_mappings:1bp5.B;PDB-ENSP_mappings:1bp5.C;PDB-ENSP_mappings:1bp5.D;PDB-ENSP_mappings:1btj.A;PDB-ENSP_mappings:1btj.B;PDB-ENSP_mappings:1d3k.A;PDB-ENSP_mappings:1d4n.A;PDB-ENSP_mappings:1dtg.A;PDB-ENSP_mappings:1fqe.A;PDB-ENSP_mappings:1fqf.A;PDB-ENSP_mappings:1jqf.A;PDB-ENSP_mappings:1n7w.A;PDB-ENSP_mappings:1n7x.A;PDB-ENSP_mappings:1n84.A;PDB-ENSP_mappings:1oqg.A;PDB-ENSP_mappings:1oqh.A;PDB-ENSP_mappings:1ryo.A;PDB-ENSP_mappings:1suv.C;PDB-ENSP_mappings:1suv.D;PDB-ENSP_mappings:2hau.A;PDB-ENSP_mappings:2hau.B;PDB-ENSP_mappings:2hav.A;PDB-ENSP_mappings:2hav.B;PDB-ENSP_mappings:2o7u.A;PDB-ENSP_mappings:2o7u.B;PDB-ENSP_mappings:2o7u.C;PDB-ENSP_mappings:2o7u.D;PDB-ENSP_mappings:2o7u.E;PDB-ENSP_mappings:2o7u.F;PDB-ENSP_mappings:2o7u.G;PDB-ENSP_mappings:2o7u.H;PDB-ENSP_mappings:2o7u.I;PDB-ENSP_mappings:2o84.X;PDB-ENSP_mappings:3fgs.A;PDB-ENSP_mappings:3qyt.A;PDB-ENSP_mappings:3s9l.C;PDB-ENSP_mappings:3s9l.D;PDB-ENSP_mappings:3s9m.C;PDB-ENSP_mappings:3s9m.D;PDB-ENSP_mappings:3s9n.C;PDB-ENSP_mappings:3s9n.D;PDB-ENSP_mappings:3v83.A;PDB-ENSP_mappings:3v83.B;PDB-ENSP_mappings:3v83.C;PDB-ENSP_mappings:3v83.D;PDB-ENSP_mappings:3v83.E;PDB-ENSP_mappings:3v83.F;PDB-ENSP_mappings:3v8x.B;PDB-ENSP_mappings:3ve1.B;PDB-ENSP_mappings:3ve1.D;PDB-ENSP_mappings:4h0w.A;PDB-ENSP_mappings:4x1b.A;PDB-ENSP_mappings:4x1d.A;PDB-ENSP_mappings:4x1d.B;PDB-ENSP_mappings:5dyh.A;PDB-ENSP_mappings:5dyh.B;PDB-ENSP_mappings:5h52.A;PDB-ENSP_mappings:5wtd.A;PDB-ENSP_mappings:5x5p.A;PDB-ENSP_mappings:5y6k.A;PDB-ENSP_mappings:6ctc.A;PDB-ENSP_mappings:6d03.C;PDB-ENSP_mappings:6d03.D;PDB-ENSP_mappings:6d04.C;PDB-ENSP_mappings:6d04.D;PDB-ENSP_mappings:6d05.C;PDB-ENSP_mappings:6d05.D;PDB-ENSP_mappings:6jas.A;PDB-ENSP_mappings:6soy.C;PDB-ENSP_mappings:6soz.C;CDD:cd13618;Pfam:PF00405;PIRSF:PIRSF500682;PIRSF:PIRSF002549;Gene3D:3.40.190.10;Gene3D:3.40.190.10;SMART:SM00094;Superfamily:SSF53850;PROSITE_profiles:PS51408;PANTHER:PTHR11485;PANTHER:PTHR11485:SF31 ENSP00000385834 0.0 0.0001163 4/17 rs371174384 ENST00000402696 Transcript 1.0 ENSG00000091513 HGNC:11740 MODERATE NM_001063.4 0.0001163 EA missense_variant 1.0 benign(0.029) Unknown tolerated(0.19) P02787.241 TF HGNC 1 1.0 UPI000013D5A6 SNV TF,missense_variant,p.R162H,ENST00000402696,NM_001354703.2&NM_001063.4&NM_001354704.2,c.485G>A,MODERATE,YES,tolerated(0.19),benign(0.029),1;TF,missense_variant,p.R35H,ENST00000482271,,c.104G>A,MODERATE,,tolerated(0.16),benign(0.029),1;TF,downstream_gene_variant,,ENST00000466911,,,MODIFIER,,,,1;TF,non_coding_transcript_exon_variant,,ENST00000475382,,n.577G>A,MODIFIER,,,,1;INHCAP,downstream_gene_variant,,ENST00000460564,,,MODIFIER,,,,1;TF,3_prime_UTR_variant,,ENST00000494430,,c.*114G>A,MODIFIER,,,,1;TF,non_coding_transcript_exon_variant,,ENST00000493011,,n.533G>A,MODIFIER,,,,1;TF,non_coding_transcript_exon_variant,,ENST00000498622,,n.714G>A,MODIFIER,,,,1;TF,intron_variant,,ENST00000485977,,c.158-2278G>A,MODIFIER,,,,1;TF,downstream_gene_variant,,ENST00000414694,,,MODIFIER,,,,1;TF,downstream_gene_variant,,ENST00000460531,,,MODIFIER,,,,1;TF,downstream_gene_variant,,ENST00000474287,,,MODIFIER,,,,1 533/20166 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 1.591e-05 0.0 0.0 0.0 0.0 0.0 3.516e-05 0.0 0.0 4.73178006359376e-05 2.4326200218638405e-05 0.0 0.0001986749994102 0.0 0.0 0.0 amr 0.0001986749994102 0.0 3.085939897573553e-05 0.000494070991408 0.0 0 162 9de08711-9c83-42ff-ad12-f18facf0432b 115 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS TF,non_coding_transcript_exon_variant,,ENST00000498622.1,n.714G>A,MODIFIER,;TF,non_coding_transcript_exon_variant,,ENST00000475382.5,n.577G>A,MODIFIER,;TF,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000494430.5,c.*114G>A,MODIFIER,;TF,missense_variant,p.R35H,ENST00000482271.5,c.104G>A,MODERATE,;TF,non_coding_transcript_exon_variant,,ENST00000493011.5,n.533G>A,MODIFIER,;TF,missense_variant,p.R162H,ENST00000402696.9,c.485G>A,MODERATE,YES;TF,intron_variant,NMD_transcript_variant,,ENST00000485977.1,c.158-2278G>A,MODIFIER, +SLIT2 9353 BI GRCh38 4 20253828 20253828 + missense_variant Missense_Mutation SNP G G T rs1376555171 TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 50 41 c.13G>T p.Gly5Cys p.G5C ENST00000504154.6 NM_004787.4 5 Ggc/Tgc 1/37 A2 T G/C protein_coding CCDS3426.1 13/4590 GCGTTGGCTGG Cleavage_site_(Signalp):SignalP-noTM ENSP00000422591 1/37 rs1376555171 ENST00000504154 Transcript ENSG00000145147 HGNC:11086 MODERATE NM_004787.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant possibly_damaging(0.766) Unknown deleterious_low_confidence(0.01) O94813.199 SLIT2 HGNC 1 1.0 UPI00000747E4 SNV SLIT2,missense_variant,p.G5C,ENST00000504154,NM_004787.4,c.13G>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.766),1;SLIT2,missense_variant,p.G5C,ENST00000503823,NM_001289136.3,c.13G>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.882),1;SLIT2,missense_variant,p.G5C,ENST00000273739,,c.13G>T,MODERATE,YES,deleterious_low_confidence(0.01),possibly_damaging(0.882),1;SLIT2,missense_variant,p.G5C,ENST00000503837,NM_001289135.3,c.13G>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.882),1;SLIT2,5_prime_UTR_variant,,ENST00000622093,,c.-246G>T,MODIFIER,,,,1;SLIT2,upstream_gene_variant,,ENST00000508824,,,MODIFIER,,,,1 1924/8053 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 76 9de08711-9c83-42ff-ad12-f18facf0432b 92 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS SLIT2,missense_variant,p.G5C,ENST00000503837.5,c.13G>T,MODERATE,;SLIT2,missense_variant,p.G5C,ENST00000273739.9,c.13G>T,MODERATE,;SLIT2,5_prime_UTR_variant,,ENST00000622093.4,c.-246G>T,MODIFIER,;SLIT2,missense_variant,p.G5C,ENST00000503823.5,c.13G>T,MODERATE,;SLIT2,missense_variant,p.G5C,ENST00000504154.6,c.13G>T,MODERATE,YES +VWA7 80737 BI GRCh38 6 31769152 31769152 + missense_variant Missense_Mutation SNP G G A novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 33 13 c.1369C>T p.Arg457Cys p.R457C ENST00000375688.5 NM_025258.3 457 Cgt/Tgt 10/17 P1 A R/C protein_coding YES CCDS4721.2 1369/2676 CTCACGCCGAG PANTHER:PTHR14905:SF7;PANTHER:PTHR14905;Gene3D:3.40.50.410 ENSP00000364840 10/17 ENST00000375688 Transcript ENSG00000204396 HGNC:13939 MODERATE NM_025258.3 missense_variant probably_damaging(0.998) Unknown deleterious(0) Q9Y334.135 VWA7 HGNC -1 A0A1U9X8T7.16 5.0 UPI0000E5AD19 Q9Y334-1 SNV VWA7,missense_variant,p.R457C,ENST00000375688,NM_025258.3,c.1369C>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;SAPCD1,downstream_gene_variant,,ENST00000415669,NM_001039651.1,,MODIFIER,YES,,,1;SAPCD1,downstream_gene_variant,,ENST00000425424,,,MODIFIER,,,,1;VWA7,non_coding_transcript_exon_variant,,ENST00000467576,,n.1232C>T,MODIFIER,,,,-1;VWA7,downstream_gene_variant,,ENST00000487013,,,MODIFIER,,,,-1;MSH5-SAPCD1,downstream_gene_variant,,ENST00000476085,,,MODIFIER,,,,1;VWA7,upstream_gene_variant,,ENST00000486423,,,MODIFIER,,,,-1;MSH5-SAPCD1,downstream_gene_variant,,ENST00000493662,,,MODIFIER,YES,,,1;SAPCD1,downstream_gene_variant,,ENST00000494299,,,MODIFIER,,,,1;MSH5-SAPCD1,downstream_gene_variant,,ENST00000498473,,,MODIFIER,,,,1;SAPCD1-AS1,upstream_gene_variant,,ENST00000419679,,,MODIFIER,YES,,,-1 1604/2915 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 6.759410098311491e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002080730046145 0 63 9de08711-9c83-42ff-ad12-f18facf0432b 46 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS VWA7,non_coding_transcript_exon_variant,,ENST00000467576.1,n.1232C>T,MODIFIER,;VWA7,missense_variant,p.R457C,ENST00000375688.5,c.1369C>T,MODERATE,YES +PPP2R5D 5528 BI GRCh38 6 43010467 43010467 + splice_acceptor_variant Splice_Site SNP G G C novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 55 20 c.1380-1G>C p.X460_splice p.X460_splice ENST00000485511.6 NM_006245.4 460 P1 C protein_coding YES CCDS4878.1 TGGCAGGACAA ENSP00000417963 ENST00000485511 Transcript NonExonic 1.0 ENSG00000112640 HGNC:9312 HIGH 12/15 NM_006245.4 splice_acceptor_variant 1.0 Unknown Q14738.205 PPP2R5D HGNC 1 A0A024RD11.38 1.0 UPI0000124E92 Q14738-1 SNV PPP2R5D,splice_acceptor_variant,p.X428_splice,ENST00000394110,NM_180976.3,c.1284-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,p.X354_splice,ENST00000461010,NM_001270476.2&NM_180977.3,c.1062-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,p.X362_splice,ENST00000470467,,c.1084-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,p.X452_splice,ENST00000472118,,c.1356-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,p.X460_splice,ENST00000485511,NM_006245.4,c.1380-1G>C,HIGH,YES,,,1;PPP2R5D,splice_acceptor_variant,p.X82_splice,ENST00000486843,,c.244-1G>C,HIGH,,,,1;KLHDC3,upstream_gene_variant,,ENST00000244670,,,MODIFIER,,,,1;MEA1,downstream_gene_variant,,ENST00000244711,NM_014623.4,,MODIFIER,,,,-1;KLHDC3,upstream_gene_variant,,ENST00000326974,NM_057161.4,,MODIFIER,,,,1;KLHDC3,upstream_gene_variant,,ENST00000332245,,,MODIFIER,YES,,,1;MEA1,downstream_gene_variant,,ENST00000642555,,,MODIFIER,,,,-1;MEA1,downstream_gene_variant,,ENST00000642748,NM_001363578.1,,MODIFIER,YES,,,-1;MEA1,downstream_gene_variant,,ENST00000643776,NM_001318942.1,,MODIFIER,,,,-1;MEA1,downstream_gene_variant,,ENST00000645375,,,MODIFIER,,,,-1;MEA1,downstream_gene_variant,,ENST00000645410,NM_001318943.1,,MODIFIER,,,,-1;PPP2R5D,splice_acceptor_variant,,ENST00000230402,,c.*1061-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,,ENST00000482315,,n.551-1G>C,HIGH,,,,1;PPP2R5D,splice_acceptor_variant,,ENST00000676174,,n.1701-1G>C,HIGH,,,,1;PPP2R5D,downstream_gene_variant,,ENST00000467447,,,MODIFIER,,,,1 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 57 9de08711-9c83-42ff-ad12-f18facf0432b 75 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS PPP2R5D,splice_acceptor_variant,p.X82_splice,ENST00000486843.1,c.244-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,,ENST00000482315.1,n.551-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,,ENST00000676174.1,n.1701-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,p.X362_splice,ENST00000470467.5,c.1084-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,p.X354_splice,ENST00000461010.5,c.1062-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,NMD_transcript_variant,,ENST00000230402.10,c.*1061-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,p.X460_splice,ENST00000485511.6,c.1380-1G>C,HIGH,YES;PPP2R5D,splice_acceptor_variant,p.X452_splice,ENST00000472118.5,c.1356-1G>C,HIGH,;PPP2R5D,splice_acceptor_variant,p.X428_splice,ENST00000394110.7,c.1284-1G>C,HIGH, +TRIM29 23650 BI GRCh38 11 120125839 120125839 + synonymous_variant Silent SNP G G T TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 18 25 c.1185C>A p.Thr395= p.T395= ENST00000341846.10 NM_012101.4 395 acC/acA 4/9 P1 T T protein_coding YES CCDS8428.1 1185/1767 TGATAGGTGGG PANTHER:PTHR25465;PANTHER:PTHR25465:SF7 ENSP00000343129 4/9 COSV100531627 ENST00000341846 Transcript ENSG00000137699 HGNC:17274 LOW NM_012101.4 synonymous_variant 1 1.0 Unknown 1 Q14134.181 TRIM29 HGNC -1 A0A024R3J1.47 1.0 UPI0000073FDE Q14134-1 SNV TRIM29,synonymous_variant,p.T395=,ENST00000341846,NM_012101.4,c.1185C>A,LOW,YES,,,-1;TRIM29,synonymous_variant,p.T134=,ENST00000529044,NM_001330382.2,c.402C>A,LOW,,,,-1;TRIM29,upstream_gene_variant,,ENST00000526881,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000528870,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000533302,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000524816,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000524956,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000525327,,,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000525887,,,MODIFIER,,,,-1;TRIM29,3_prime_UTR_variant,,ENST00000475051,,c.*523C>A,MODIFIER,,,,-1;TRIM29,non_coding_transcript_exon_variant,,ENST00000530470,,n.519C>A,MODIFIER,,,,-1;TRIM29,upstream_gene_variant,,ENST00000531555,,,MODIFIER,,,,-1;TRIM29,downstream_gene_variant,,ENST00000532195,,,MODIFIER,,,,-1 1267/2977 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 58 9de08711-9c83-42ff-ad12-f18facf0432b 43 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS TRIM29,non_coding_transcript_exon_variant,,ENST00000530470.1,n.519C>A,MODIFIER,;TRIM29,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000475051.4,c.*523C>A,MODIFIER,;TRIM29,synonymous_variant,p.T134=,ENST00000529044.5,c.402C>A,LOW,;TRIM29,synonymous_variant,p.T395=,ENST00000341846.10,c.1185C>A,LOW,YES +DCUN1D2 55208 BI GRCh38 13 113461117 113461117 + synonymous_variant Silent SNP C C T rs765799407 TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 19 14 c.540G>A p.Ala180= p.A180= ENST00000478244.6 NM_001014283.2 180 gcG/gcA 5/7 P1 T A protein_coding YES CCDS32013.1 540/780 CAATACGCAAC COSM6051090 PDB-ENSP_mappings:4gao.A;PDB-ENSP_mappings:4gao.B;PDB-ENSP_mappings:4gao.D;PDB-ENSP_mappings:4gao.G;PROSITE_profiles:PS51229;PANTHER:PTHR12281:SF16;PANTHER:PTHR12281;Gene3D:1.10.238.200;Pfam:PF03556 ENSP00000417706 5/7 rs765799407;COSV60261877;COSV60262342 ENST00000478244 Transcript ENSG00000150401 HGNC:20328 LOW NM_001014283.2 6.645e-05 gnomAD_SAS synonymous_variant 0;1;1 1.0 Unknown 0;1;1 Q6PH85.133 DCUN1D2 HGNC -1 1.0 UPI00001CE006 Q6PH85-1 SNV DCUN1D2,synonymous_variant,p.A180=,ENST00000478244,NM_001014283.2,c.540G>A,LOW,YES,,,-1;DCUN1D2,synonymous_variant,p.A47=,ENST00000332592,,c.141G>A,LOW,,,,-1;DCUN1D2,3_prime_UTR_variant,,ENST00000375403,,c.*131G>A,MODIFIER,,,,-1;DCUN1D2,3_prime_UTR_variant,,ENST00000438545,,c.*131G>A,MODIFIER,,,,-1;DCUN1D2,non_coding_transcript_exon_variant,,ENST00000491647,,n.369G>A,MODIFIER,,,,-1;DCUN1D2,upstream_gene_variant,,ENST00000482038,,,MODIFIER,,,,-1 582/3032 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 4.019e-05 0.0 0.0 0.0 5.475e-05 0.0 6.193e-05 0.0 6.645e-05 1.3519499589165209e-05 2.4317900169990025e-05 0.0 6.625150126637891e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 52 9de08711-9c83-42ff-ad12-f18facf0432b 33 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS DCUN1D2,non_coding_transcript_exon_variant,,ENST00000491647.1,n.369G>A,MODIFIER,;DCUN1D2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000438545.6,c.*131G>A,MODIFIER,;DCUN1D2,synonymous_variant,p.A180=,ENST00000478244.6,c.540G>A,LOW,YES;DCUN1D2,synonymous_variant,p.A47=,ENST00000332592.7,c.141G>A,LOW,;DCUN1D2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000375403.6,c.*131G>A,MODIFIER, +PPL 5493 BI GRCh38 16 4885850 4885850 + missense_variant Missense_Mutation SNP C C G novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 41 43 c.2805G>C p.Lys935Asn p.K935N ENST00000345988.7 NM_002705.5 935 aaG/aaC 22/22 P3 G K/N protein_coding YES CCDS10526.1 2805/5271 ACCTCCTTCCT PANTHER:PTHR23169;PANTHER:PTHR23169:SF10 ENSP00000340510 22/22 ENST00000345988 Transcript ENSG00000118898 HGNC:9273 MODERATE NM_002705.5 missense_variant 1.0 benign(0.444) Unknown deleterious(0) O60437.180 PPL HGNC -1 1.0 UPI00001AE832 SNV PPL,missense_variant,p.K935N,ENST00000345988,NM_002705.5,c.2805G>C,MODERATE,YES,deleterious(0),benign(0.444),-1;PPL,missense_variant,p.K933N,ENST00000590782,,c.2799G>C,MODERATE,,deleterious(0),possibly_damaging(0.847),-1;PPL,missense_variant,p.K356N,ENST00000592772,,c.1068G>C,MODERATE,,deleterious(0),possibly_damaging(0.777),-1;UBN1,downstream_gene_variant,,ENST00000262376,NM_001079514.3,,MODIFIER,YES,,,1;UBN1,downstream_gene_variant,,ENST00000396658,,,MODIFIER,,,,1;PPL,downstream_gene_variant,,ENST00000589090,,,MODIFIER,,,,-1 2908/6251 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 118 9de08711-9c83-42ff-ad12-f18facf0432b 84 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS PPL,missense_variant,p.K356N,ENST00000592772.1,c.1068G>C,MODERATE,;PPL,missense_variant,p.K933N,ENST00000590782.6,c.2799G>C,MODERATE,;PPL,missense_variant,p.K935N,ENST00000345988.7,c.2805G>C,MODERATE,YES +CDR2L 30850 BI GRCh38 17 75001461 75001461 + missense_variant Missense_Mutation SNP A A G novel TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 6 3 c.313A>G p.Ser105Gly p.S105G ENST00000337231.5 NM_014603.3 105 Agt/Ggt 3/5 P1 G S/G protein_coding YES CCDS11710.2 313/1398 TGGAGAGTAAG Coiled-coils_(Ncoils):Coil;PANTHER:PTHR19232;PANTHER:PTHR19232:SF10 ENSP00000336587 3/5 ENST00000337231 Transcript ENSG00000109089 HGNC:29999 MODERATE NM_014603.3 missense_variant 1.0 possibly_damaging(0.488) Unknown deleterious(0.01) Q86X02.112 CDR2L HGNC 1 A0A024R8R6.35 1.0 UPI00005AE46D SNV CDR2L,missense_variant,p.S105G,ENST00000337231,NM_014603.3,c.313A>G,MODERATE,YES,deleterious(0.01),possibly_damaging(0.488),1 725/3536 muse;mutect2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 16 9de08711-9c83-42ff-ad12-f18facf0432b 9 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS CDR2L,missense_variant,p.S105G,ENST00000337231.5,c.313A>G,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 24 21 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 77 9de08711-9c83-42ff-ad12-f18facf0432b 45 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +CLEC4M 10332 BI GRCh38 19 7768866 7768866 + missense_variant Missense_Mutation SNP C C T TCGA-WC-A881-01A TCGA-WC-A881-10A Somatic 21 21 c.1078C>T p.Pro360Ser p.P360S ENST00000327325.10 NM_014257.5 360 Ccc/Tcc 7/7 P2 T P/S protein_coding YES CCDS12187.1 1078/1200 GAGAACCCAAC COSM3971375 PDB-ENSP_mappings:1k9j.A;PDB-ENSP_mappings:1k9j.B;PDB-ENSP_mappings:1sl6.A;PDB-ENSP_mappings:1sl6.B;PDB-ENSP_mappings:1sl6.C;PDB-ENSP_mappings:1sl6.D;PDB-ENSP_mappings:1sl6.E;PDB-ENSP_mappings:1sl6.F;PDB-ENSP_mappings:1xar.A;PDB-ENSP_mappings:1xar.B;PDB-ENSP_mappings:1xph.A;Gene3D:3.10.100.10;Pfam:PF00059;PROSITE_profiles:PS50041;PANTHER:PTHR22802;PANTHER:PTHR22802:SF267;SMART:SM00034;Superfamily:SSF56436;CDD:cd03590 ENSP00000316228 7/7 COSV50224280 ENST00000327325 Transcript ENSG00000104938 HGNC:13523 MODERATE NM_014257.5 missense_variant 1 1.0 probably_damaging(1) Unknown deleterious(0) 1 Q9H2X3.182 CLEC4M HGNC 1 1.0 UPI0000073C48 Q9H2X3-1 SNV CLEC4M,missense_variant,p.P360S,ENST00000327325,NM_014257.5&NM_001144909.2&NM_001144910.2&NM_001144905.2,c.1078C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;CLEC4M,missense_variant,p.P332S,ENST00000359059,NM_001144906.2&NM_001144907.2,c.994C>T,MODERATE,,deleterious(0.02),probably_damaging(0.994),1;CLEC4M,missense_variant,p.P332S,ENST00000394122,NM_001144904.2,c.994C>T,MODERATE,,deleterious(0.03),probably_damaging(0.994),1;CLEC4M,missense_variant,p.T294I,ENST00000596363,NM_001144908.2&NM_001144911.2,c.881C>T,MODERATE,,deleterious_low_confidence(0.04),benign(0.048),1;CLEC4M,non_coding_transcript_exon_variant,,ENST00000598879,,n.1413C>T,MODIFIER,,,,1;CLEC4M,non_coding_transcript_exon_variant,,ENST00000602143,,n.356C>T,MODIFIER,,,,1;CLEC4M,downstream_gene_variant,,ENST00000601089,,,MODIFIER,,,,1 1102/1841 muse;mutect2;varscan2 56ed4ea2-18ce-48d4-bf72-9ffabe576ca9 0 93 9de08711-9c83-42ff-ad12-f18facf0432b 42 8e24ccac-1b43-41c6-9657-e71aeae8d965 SUCCESS CLEC4M,non_coding_transcript_exon_variant,,ENST00000602143.1,n.356C>T,MODIFIER,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000598879.5,n.1413C>T,MODIFIER,;CLEC4M,missense_variant,p.P360S,ENST00000327325.10,c.1078C>T,MODERATE,YES;CLEC4M,missense_variant,p.P332S,ENST00000394122.7,c.994C>T,MODERATE,;CLEC4M,missense_variant,p.T294I,ENST00000596363.5,c.881C>T,MODERATE,;CLEC4M,missense_variant,p.P332S,ENST00000359059.10,c.994C>T,MODERATE, +AADACL4 343066 BI GRCh38 1 12651288 12651288 + missense_variant Missense_Mutation SNP C C T rs559695381 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 28 14 c.334C>T p.Arg112Trp p.R112W ENST00000376221.2 NM_001013630.2 112 Cgg/Tgg 2/4 P1 T R/W protein_coding YES CCDS30590.1 334/1224 GACCCCGGCGA PANTHER:PTHR23024;PANTHER:PTHR23024:SF457;PIRSF:PIRSF037251;Superfamily:SSF53474 ENSP00000365395 2/4 rs559695381 ENST00000376221 Transcript ENSG00000204518 HGNC:32038 MODERATE 4.396e-05 gnomAD_NFE missense_variant 1.0 benign(0.317) Unknown tolerated(0.06) Q5VUY2.113 AADACL4 HGNC 1 5.0 UPI0000160609 SNV AADACL4,missense_variant,p.R112W,ENST00000376221,NM_001013630.1,c.334C>T,MODERATE,YES,tolerated(0.06),benign(0.317),1 334/1575 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 2.386e-05 0.0 0.0 0.0 0.0 0.0 4.396e-05 0.0 3.266e-05 2.7040199711336758e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 6.171889981487766e-05 0.0 6.171889981487766e-05 0.0 0.0 0 82 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 42 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS AADACL4,missense_variant,p.R112W,ENST00000376221.2,c.334C>T,MODERATE,YES +USP34 9736 BI GRCh38 2 61206816 61206816 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 26 9 c.8990T>C p.Leu2997Pro p.L2997P ENST00000398571.7 NM_014709.4 2997 cTt/cCt 71/80 P1 G L/P protein_coding YES CCDS42686.1 8990/10641 ACAGAAGTTCT PANTHER:PTHR24006;PANTHER:PTHR24006:SF671;Superfamily:SSF48371 ENSP00000381577 71/80 ENST00000398571 Transcript ENSG00000115464 HGNC:20066 MODERATE NM_014709.4 missense_variant 1.0 possibly_damaging(0.77) Unknown deleterious(0) Q70CQ2.138 USP34 HGNC -1 5.0 UPI0000410E09 Q70CQ2-1 SNV USP34,missense_variant,p.L2997P,ENST00000398571,NM_014709.4,c.8990T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.77),-1;USP34,missense_variant,p.L757P,ENST00000411912,,c.2270T>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;USP34,upstream_gene_variant,,ENST00000436269,,,MODIFIER,,,,-1;USP34,non_coding_transcript_exon_variant,,ENST00000476716,,n.367T>C,MODIFIER,,,,-1;USP34,non_coding_transcript_exon_variant,,ENST00000467128,,n.503T>C,MODIFIER,,,,-1;USP34,downstream_gene_variant,,ENST00000472689,,,MODIFIER,,,,-1;USP34,non_coding_transcript_exon_variant,,ENST00000463046,,n.4430T>C,MODIFIER,,,,-1 9385/11675 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 45 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 35 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS USP34,non_coding_transcript_exon_variant,,ENST00000467128.5,n.503T>C,MODIFIER,;USP34,non_coding_transcript_exon_variant,,ENST00000476716.5,n.367T>C,MODIFIER,;USP34,non_coding_transcript_exon_variant,,ENST00000463046.5,n.4430T>C,MODIFIER,;USP34,missense_variant,p.L2997P,ENST00000398571.7,c.8990T>C,MODERATE,YES;USP34,synonymous_variant,p.T756=,ENST00000411912.5,c.2268T>C,LOW, +SPHKAP 80309 BI GRCh38 2 228016839 228016839 + missense_variant Missense_Mutation SNP C C T rs1338854193 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 81 21 c.4015G>A p.Gly1339Ser p.G1339S ENST00000392056.8 NM_001142644.2 1339 Ggc/Agc 7/12 P4 T G/S protein_coding YES CCDS46537.1 4015/5103 AGAGCCACCAG PANTHER:PTHR10226;PANTHER:PTHR10226:SF7 ENSP00000375909 7/12 rs1338854193 ENST00000392056 Transcript ENSG00000153820 HGNC:30619 MODERATE NM_001142644.2 missense_variant 1.0 benign(0.03) Unknown tolerated(0.31) Q2M3C7.118 SPHKAP HGNC -1 1.0 UPI0000411D7E Q2M3C7-1 SNV SPHKAP,missense_variant,p.G1339S,ENST00000392056,NM_001142644.2,c.4015G>A,MODERATE,YES,tolerated(0.31),benign(0.03),-1;SPHKAP,missense_variant,p.G1339S,ENST00000344657,NM_030623.3,c.4015G>A,MODERATE,,tolerated(0.29),benign(0.076),-1 4104/6954 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 6.7646201387105975e-06 2.4338000002899207e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 58 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 102 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS SPHKAP,missense_variant,p.G1339S,ENST00000344657.5,c.4015G>A,MODERATE,;SPHKAP,missense_variant,p.G1339S,ENST00000392056.8,c.4015G>A,MODERATE,YES +ABCA13 154664 BI GRCh38 7 48272290 48272290 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 58 34 c.2624A>T p.Gln875Leu p.Q875L ENST00000435803.6 NM_152701.5 875 cAg/cTg 17/62 P1 T Q/L protein_coding YES CCDS47584.1 2624/15177 TTCCCAGTTGT ENSP00000411096 17/62 ENST00000435803 Transcript ENSG00000179869 HGNC:14638 MODERATE NM_152701.5 missense_variant 1.0 possibly_damaging(0.49) Unknown deleterious(0) ABCA13 HGNC 1 A0A0A0MT16.43 1.0 UPI00043788D8 SNV ABCA13,missense_variant,p.Q875L,ENST00000435803,NM_152701.5,c.2624A>T,MODERATE,YES,deleterious(0),possibly_damaging(0.49),1;ABCA13,3_prime_UTR_variant,,ENST00000417403,,c.*1843A>T,MODIFIER,,,,1 2650/17188 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 181 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 92 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS ABCA13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000417403.5,c.*1843A>T,MODIFIER,;ABCA13,missense_variant,p.Q875L,ENST00000435803.6,c.2624A>T,MODERATE,YES +PCLO 27445 BI GRCh38 7 82955888 82955888 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 9 4 c.5065del p.Thr1689GlnfsTer16 p.T1689Qfs*16 ENST00000333891.14 NM_033026.6 1689 Aca/ca 5/25 P1 - T/X protein_coding YES CCDS47630.1 5065/15429 AACTTGTTTTTT PANTHER:PTHR14113;PANTHER:PTHR14113:SF6;MobiDB_lite:mobidb-lite ENSP00000334319 5/25 ENST00000333891 Transcript 1.0 ENSG00000186472 HGNC:13406 HIGH NM_033026.6 frameshift_variant 1.0 Unknown Q9Y6V0.188 PCLO HGNC -1 2.0 UPI0001573469 Q9Y6V0-5 deletion PCLO,frameshift_variant,p.T1689Qfs*16,ENST00000333891,NM_033026.6,c.5065del,HIGH,YES,,,-1;PCLO,frameshift_variant,p.T1689Qfs*16,ENST00000423517,NM_014510.3,c.5065del,HIGH,,,,-1 5357/20284 mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 48 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 13 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS PCLO,frameshift_variant,p.T1689Qfs*16,ENST00000423517.6,c.5065del,HIGH,;PCLO,frameshift_variant,p.T1689Qfs*16,ENST00000333891.14,c.5065del,HIGH,YES +RGS20 8601 BI GRCh38 8 53958457 53958457 + stop_lost Nonstop_Mutation SNP A A G novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 14 4 c.1166A>G p.Ter389Trpext*20 p.*389Wext*20 ENST00000297313.8 NM_170587.4 389 tAg/tGg 6/6 A2 G */W protein_coding YES CCDS6155.1 1166/1167 AGCATAGGATT ENSP00000297313 6/6 ENST00000297313 Transcript ENSG00000147509 HGNC:14600 HIGH NM_170587.4 stop_lost 1.0 Unknown O76081.186 RGS20 HGNC 1 1.0 UPI000013383C O76081-1 SNV RGS20,stop_lost,p.*389Wext*20,ENST00000297313,NM_170587.4,c.1166A>G,HIGH,YES,,,1;RGS20,stop_lost,p.*274Wext*20,ENST00000344277,NM_001286673.2&NM_001286675.2,c.821A>G,HIGH,,,,1;RGS20,stop_lost,p.*242Wext*20,ENST00000276500,NM_003702.4,c.725A>G,HIGH,,,,1;RGS20,stop_lost,p.*123Wext*20,ENST00000522225,NM_001286674.2,c.368A>G,HIGH,,,,1;RGS20,non_coding_transcript_exon_variant,,ENST00000517405,,n.553A>G,MODIFIER,,,,1;RGS20,downstream_gene_variant,,ENST00000518286,,,MODIFIER,,,,1;RGS20,downstream_gene_variant,,ENST00000523414,,,MODIFIER,,,,1;RGS20,3_prime_UTR_variant,,ENST00000517659,,c.*495A>G,MODIFIER,,,,1;RGS20,3_prime_UTR_variant,,ENST00000523280,,c.*375A>G,MODIFIER,,,,1 1271/2117 muse;mutect2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 16 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 18 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS RGS20,non_coding_transcript_exon_variant,,ENST00000517405.1,n.553A>G,MODIFIER,;RGS20,stop_lost,p.*123Wext*20,ENST00000522225.5,c.368A>G,HIGH,;RGS20,stop_lost,p.*242Wext*20,ENST00000276500.5,c.725A>G,HIGH,YES;RGS20,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000523280.1,c.*375A>G,MODIFIER,;RGS20,stop_lost,p.*274Wext*20,ENST00000344277.10,c.821A>G,HIGH,;RGS20,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000517659.5,c.*495A>G,MODIFIER,;RGS20,stop_lost,p.*389Wext*20,ENST00000297313.8,c.1166A>G,HIGH, +COL14A1 7373 BI GRCh38 8 120225188 120225188 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 70 32 c.1838A>G p.Glu613Gly p.E613G ENST00000297848.8 NM_001413490.1 613 gAg/gGg 15/48 P4 G E/G protein_coding YES CCDS34938.1 1838/5391 GTCAGAGCCTC Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR24020;PANTHER:PTHR24020:SF15;Superfamily:SSF49265;CDD:cd00063 ENSP00000297848 15/48 ENST00000297848 Transcript 1.0 ENSG00000187955 HGNC:2191 MODERATE NM_021110.4 missense_variant 1.0 possibly_damaging(0.708) Unknown tolerated(0.34) Q05707.166 COL14A1 HGNC 1 5.0 UPI000046D377 Q05707-1 SNV COL14A1,missense_variant,p.E613G,ENST00000297848,NM_021110.4,c.1838A>G,MODERATE,YES,tolerated(0.34),possibly_damaging(0.708),1;COL14A1,missense_variant,p.E613G,ENST00000309791,,c.1838A>G,MODERATE,,tolerated(0.39),possibly_damaging(0.819),1;COL14A1,missense_variant,p.E426G,ENST00000434620,,c.1277A>G,MODERATE,,tolerated(0.09),possibly_damaging(0.583),1;COL14A1,3_prime_UTR_variant,,ENST00000537875,,c.*360A>G,MODIFIER,,,,1;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,,n.2072A>G,MODIFIER,,,,1;COL14A1,3_prime_UTR_variant,,ENST00000498051,,c.*360A>G,MODIFIER,,,,1 2114/8009 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 77 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 103 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS COL14A1,missense_variant,p.E426G,ENST00000434620.5,c.1277A>G,MODERATE,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943.6,n.2072A>G,MODIFIER,;COL14A1,missense_variant,p.E613G,ENST00000309791.8,c.1838A>G,MODERATE,;COL14A1,missense_variant,p.E613G,ENST00000297848.8,c.1838A>G,MODERATE,YES;COL14A1,3_prime_UTR_variant,,ENST00000537875.2,c.*360A>G,MODIFIER,;COL14A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000498051.6,c.*360A>G,MODIFIER, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 29 20 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 116 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 50 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +DNM1 1759 BI GRCh38 9 128246405 128246405 + synonymous_variant Silent SNP G G A rs1263582663 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 10 12 c.1683G>A p.Lys561= p.K561= ENST00000372923.8 NM_004408.4 561 aaG/aaA 16/22 P4 A K protein_coding CCDS6895.1 1683/2595 GAGAAGAAATA COSM4448002;COSM4448003;COSM4448004 Gene3D:1.20.120.1240;PDB-ENSP_mappings:1dyn.A;PDB-ENSP_mappings:1dyn.B;Gene3D:2.30.29.30;PDB-ENSP_mappings:2dyn.A;PDB-ENSP_mappings:2dyn.B;Gene3D:3.40.50.300;PDB-ENSP_mappings:3snh.A;PDB-ENSP_mappings:3zys.C;PDB-ENSP_mappings:3zys.F;PDB-ENSP_mappings:4uud.A;PDB-ENSP_mappings:4uud.B;PDB-ENSP_mappings:4uud.C;PDB-ENSP_mappings:4uud.D;PDB-ENSP_mappings:4uud.E;PDB-ENSP_mappings:4uud.F;PDB-ENSP_mappings:4uud.G;PDB-ENSP_mappings:4uud.H;PDB-ENSP_mappings:4uud.I;PDB-ENSP_mappings:4uud.J;PDB-ENSP_mappings:4uud.K;PDB-ENSP_mappings:4uud.L;PDB-ENSP_mappings:4uuk.A;PDB-ENSP_mappings:4uuk.B;PDB-ENSP_mappings:4uuk.C;PDB-ENSP_mappings:4uuk.D;PDB-ENSP_mappings:4uuk.E;PDB-ENSP_mappings:4uuk.F;PDB-ENSP_mappings:4uuk.G;PDB-ENSP_mappings:4uuk.H;PDB-ENSP_mappings:4uuk.I;PDB-ENSP_mappings:4uuk.J;PDB-ENSP_mappings:4uuk.K;PDB-ENSP_mappings:4uuk.L;PDB-ENSP_mappings:6dlu.B;PDB-ENSP_mappings:6dlu.P;PDB-ENSP_mappings:6dlv.b;PDB-ENSP_mappings:6dlv.c;PDB-ENSP_mappings:6dlv.f;PDB-ENSP_mappings:6dlv.g;Pfam:PF00169;PROSITE_profiles:PS50003;PANTHER:PTHR11566;PANTHER:PTHR11566:SF32;SMART:SM00233;Superfamily:SSF50729;CDD:cd01256;Low_complexity_(Seg):seg ENSP00000362014 16/22 rs1263582663;COSV57854389 ENST00000372923 Transcript 1.0 ENSG00000106976 HGNC:2972 LOW NM_004408.4 synonymous_variant 0;1 Unknown 0;1 Q05193.198 DNM1 HGNC 1 1.0 UPI000013CA31 Q05193-1 SNV DNM1,synonymous_variant,p.K561=,ENST00000627543,,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K557=,ENST00000628346,NM_001374269.1,c.1671G>A,LOW,YES,,,1;DNM1,synonymous_variant,p.K561=,ENST00000341179,NM_001005336.3,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K561=,ENST00000393594,NM_001288738.2&NM_001288737.2,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K561=,ENST00000372923,NM_004408.4,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K561=,ENST00000486160,NM_001288739.2,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K561=,ENST00000634267,,c.1683G>A,LOW,,,,1;DNM1,synonymous_variant,p.K532=,ENST00000627061,,c.1596G>A,LOW,,,,1;DNM1,synonymous_variant,p.K561=,ENST00000475805,,c.1683G>A,LOW,,,,1;DNM1,intron_variant,,ENST00000636201,,c.41-920G>A,MODIFIER,,,,1;DNM1,upstream_gene_variant,,ENST00000625457,,,MODIFIER,,,,1;MIR199B,upstream_gene_variant,,ENST00000384849,,,MODIFIER,YES,,,-1;MIR3154,upstream_gene_variant,,ENST00000577829,,,MODIFIER,YES,,,-1;DNM1,non_coding_transcript_exon_variant,,ENST00000493925,,n.426G>A,MODIFIER,,,,1;DNM1,non_coding_transcript_exon_variant,,ENST00000631179,,n.208G>A,MODIFIER,,,,1;DNM1,non_coding_transcript_exon_variant,,ENST00000441149,,n.1484G>A,MODIFIER,,,,1;DNM1,non_coding_transcript_exon_variant,,ENST00000463998,,n.805G>A,MODIFIER,,,,1;DNM1,downstream_gene_variant,,ENST00000482638,,,MODIFIER,,,,1;DNM1,upstream_gene_variant,,ENST00000630850,,,MODIFIER,,,,1;DNM1,downstream_gene_variant,,ENST00000637999,,,MODIFIER,,,,1 1775/3217 muse;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 2.02784995053662e-05 2.4317900169990025e-05 0.0 0.0 0.0 0.0 0.0 nfe 3.086039941990748e-05 0.0 3.086039941990748e-05 0.0 0.0 0 32 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 22 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS DNM1,intron_variant,,ENST00000636201.1,c.41-920G>A,MODIFIER,;DNM1,non_coding_transcript_exon_variant,,ENST00000493925.3,n.426G>A,MODIFIER,;DNM1,non_coding_transcript_exon_variant,,ENST00000631179.2,n.208G>A,MODIFIER,;DNM1,non_coding_transcript_exon_variant,,ENST00000463998.3,n.805G>A,MODIFIER,;DNM1,missense_variant,p.E440K,ENST00000706054.1,c.1318G>A,MODERATE,;DNM1,non_coding_transcript_exon_variant,,ENST00000441149.6,n.1484G>A,MODIFIER,;DNM1,synonymous_variant,p.K561=,ENST00000634267.2,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K532=,ENST00000627061.2,c.1596G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000706053.1,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000627543.2,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000486160.3,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K557=,ENST00000628346.2,c.1671G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000393594.7,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000475805.5,c.1683G>A,LOW,;DNM1,synonymous_variant,p.K561=,ENST00000372923.8,c.1683G>A,LOW,YES;DNM1,synonymous_variant,p.K561=,ENST00000341179.11,c.1683G>A,LOW, +DNM1 1759 BI GRCh38 9 128246496 128246496 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 9 7 c.1774G>A p.Glu592Lys p.E592K ENST00000372923.8 NM_004408.4 592 Gag/Aag 16/22 P4 A E/K protein_coding CCDS6895.1 1774/2595 ACACGGAGCAG Gene3D:1.20.120.1240;PDB-ENSP_mappings:1dyn.A;PDB-ENSP_mappings:1dyn.B;Gene3D:2.30.29.30;PDB-ENSP_mappings:2dyn.A;PDB-ENSP_mappings:2dyn.B;Gene3D:3.40.50.300;PDB-ENSP_mappings:3snh.A;PDB-ENSP_mappings:3zys.C;PDB-ENSP_mappings:3zys.F;PDB-ENSP_mappings:4uud.A;PDB-ENSP_mappings:4uud.B;PDB-ENSP_mappings:4uud.C;PDB-ENSP_mappings:4uud.D;PDB-ENSP_mappings:4uud.E;PDB-ENSP_mappings:4uud.F;PDB-ENSP_mappings:4uud.G;PDB-ENSP_mappings:4uud.H;PDB-ENSP_mappings:4uud.I;PDB-ENSP_mappings:4uud.J;PDB-ENSP_mappings:4uud.K;PDB-ENSP_mappings:4uud.L;PDB-ENSP_mappings:4uuk.A;PDB-ENSP_mappings:4uuk.B;PDB-ENSP_mappings:4uuk.C;PDB-ENSP_mappings:4uuk.D;PDB-ENSP_mappings:4uuk.E;PDB-ENSP_mappings:4uuk.F;PDB-ENSP_mappings:4uuk.G;PDB-ENSP_mappings:4uuk.H;PDB-ENSP_mappings:4uuk.I;PDB-ENSP_mappings:4uuk.J;PDB-ENSP_mappings:4uuk.K;PDB-ENSP_mappings:4uuk.L;PDB-ENSP_mappings:6dlu.B;PDB-ENSP_mappings:6dlu.P;PDB-ENSP_mappings:6dlv.b;PDB-ENSP_mappings:6dlv.c;PDB-ENSP_mappings:6dlv.f;PDB-ENSP_mappings:6dlv.g;Pfam:PF00169;PROSITE_profiles:PS50003;PANTHER:PTHR11566;PANTHER:PTHR11566:SF32;SMART:SM00233;Superfamily:SSF50729;CDD:cd01256 ENSP00000362014 16/22 ENST00000372923 Transcript 1.0 ENSG00000106976 HGNC:2972 MODERATE NM_004408.4 missense_variant possibly_damaging(0.732) Unknown deleterious(0.02) Q05193.198 DNM1 HGNC 1 1.0 UPI000013CA31 Q05193-1 SNV DNM1,missense_variant,p.E592K,ENST00000627543,,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.613),1;DNM1,missense_variant,p.E588K,ENST00000628346,NM_001374269.1,c.1762G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.984),1;DNM1,missense_variant,p.E592K,ENST00000341179,NM_001005336.3,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.613),1;DNM1,missense_variant,p.E592K,ENST00000393594,NM_001288738.2&NM_001288737.2,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.613),1;DNM1,missense_variant,p.E592K,ENST00000372923,NM_004408.4,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.732),1;DNM1,missense_variant,p.E592K,ENST00000486160,NM_001288739.2,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.613),1;DNM1,missense_variant,p.E592K,ENST00000634267,,c.1774G>A,MODERATE,,deleterious(0.02),benign(0.441),1;DNM1,missense_variant,p.E563K,ENST00000627061,,c.1687G>A,MODERATE,,deleterious(0.02),probably_damaging(0.984),1;DNM1,missense_variant,p.E592K,ENST00000475805,,c.1774G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.613),1;DNM1,intron_variant,,ENST00000636201,,c.41-829G>A,MODIFIER,,,,1;DNM1,upstream_gene_variant,,ENST00000625457,,,MODIFIER,,,,1;MIR199B,upstream_gene_variant,,ENST00000384849,,,MODIFIER,YES,,,-1;MIR3154,upstream_gene_variant,,ENST00000577829,,,MODIFIER,YES,,,-1;DNM1,non_coding_transcript_exon_variant,,ENST00000493925,,n.517G>A,MODIFIER,,,,1;DNM1,non_coding_transcript_exon_variant,,ENST00000631179,,n.299G>A,MODIFIER,,,,1;DNM1,non_coding_transcript_exon_variant,,ENST00000441149,,n.1575G>A,MODIFIER,,,,1;DNM1,downstream_gene_variant,,ENST00000463998,,,MODIFIER,,,,1;DNM1,downstream_gene_variant,,ENST00000482638,,,MODIFIER,,,,1;DNM1,upstream_gene_variant,,ENST00000630850,,,MODIFIER,,,,1;DNM1,downstream_gene_variant,,ENST00000637999,,,MODIFIER,,,,1 1866/3217 muse;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 20 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 16 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS DNM1,intron_variant,,ENST00000636201.1,c.41-829G>A,MODIFIER,;DNM1,non_coding_transcript_exon_variant,,ENST00000493925.3,n.517G>A,MODIFIER,;DNM1,non_coding_transcript_exon_variant,,ENST00000631179.2,n.299G>A,MODIFIER,;DNM1,missense_variant,p.G470E,ENST00000706054.1,c.1409G>A,MODERATE,;DNM1,non_coding_transcript_exon_variant,,ENST00000441149.6,n.1575G>A,MODIFIER,;DNM1,missense_variant,p.E592K,ENST00000634267.2,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E563K,ENST00000627061.2,c.1687G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000706053.1,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000627543.2,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000486160.3,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E588K,ENST00000628346.2,c.1762G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000393594.7,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000475805.5,c.1774G>A,MODERATE,;DNM1,missense_variant,p.E592K,ENST00000372923.8,c.1774G>A,MODERATE,YES;DNM1,missense_variant,p.E592K,ENST00000341179.11,c.1774G>A,MODERATE, +AGAP7P 653268 BI GRCh38 10 46130807 46130807 + non_coding_transcript_exon_variant RNA SNP G G T rs1554941383 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 212 28 n.1511G>T ENST00000582299.2 8/8 T unprocessed_pseudogene YES GCTCAGGTATC 8/8 rs1554941383 ENST00000582299 Transcript ENSG00000264204 HGNC:23465 MODIFIER non_coding_transcript_exon_variant 1.0 Unknown AGAP7P HGNC 1 SNV AGAP7P,non_coding_transcript_exon_variant,,ENST00000582299,,n.1511G>T,MODIFIER,YES,,,1 1511/2062 muse;mutect2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 562 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 240 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS AGAP7P,non_coding_transcript_exon_variant,,ENST00000582299.2,n.1511G>T,MODIFIER,YES +PNLIP 5406 BI GRCh38 10 116555226 116555226 + missense_variant Missense_Mutation SNP G G A rs149884015 TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 42 23 c.620G>A p.Arg207Gln p.R207Q ENST00000369221.2 NM_000936.4 207 cGa/cAa 7/13 P1 A R/Q protein_coding YES CCDS7594.1 620/1398 AGTCCGATTGG COSM109426 PDB-ENSP_mappings:1lpa.B;PDB-ENSP_mappings:1lpb.B;PDB-ENSP_mappings:1n8s.A;CDD:cd00707;PANTHER:PTHR11610;PANTHER:PTHR11610:SF115;Pfam:PF00151;PIRSF:PIRSF000865;Gene3D:3.40.50.1820;Superfamily:SSF53474 ENSP00000358223 7/13 rs149884015;COSV65041649 ENST00000369221 Transcript 1.0 ENSG00000175535 HGNC:9155 MODERATE NM_000936.4 8.797e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 P16233.201 PNLIP HGNC 1 1.0 UPI000004F1A0 SNV PNLIP,missense_variant,p.R207Q,ENST00000369221,NM_000936.4,c.620G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;PNLIP,downstream_gene_variant,,ENST00000470562,,,MODIFIER,,,,1 648/1483 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 3.978e-06 0.0 0.0 0.0 0.0 0.0 8.797e-06 0.0 0.0 6.759680218237918e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5431100109708495e-05 0.0 0.0 0 72 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 65 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS PNLIP,missense_variant,p.R207Q,ENST00000369221.2,c.620G>A,MODERATE,YES +FTHL17 53940 BI GRCh38 X 31071717 31071717 + synonymous_variant Silent SNP G G T novel TCGA-V4-A9EK-01A TCGA-V4-A9EK-10A Somatic 41 8 c.237C>A p.Gly79= p.G79= ENST00000359202.5 NM_031894.3 79 ggC/ggA 1/1 P1 T G protein_coding YES CCDS14227.1 237/552 ATGTGGCCACC Gene3D:1.20.1260.10;Pfam:PF00210;PROSITE_profiles:PS50905;PANTHER:PTHR11431;PANTHER:PTHR11431:SF97;Superfamily:SSF47240;CDD:cd01056 ENSP00000368207 1/1 ENST00000359202 Transcript ENSG00000132446 HGNC:3987 LOW NM_031894.3 synonymous_variant 1.0 Unknown Q9BXU8.130 FTHL17 HGNC -1 A0A384NPV7.9 UPI00000421FF SNV FTHL17,synonymous_variant,p.G79=,ENST00000359202,NM_031894.3,c.237C>A,LOW,YES,,,-1 325/809 muse;mutect2;varscan2 4464418c-ec35-4826-b3d5-152ac2a27a04 0 55 b37ee32a-51ec-4c0a-bbf5-7e20c89e2b33 49 ce4510b7-c8c4-4d2c-8e29-93f3a1880cb7 SUCCESS FTHL17,synonymous_variant,p.G79=,ENST00000359202.5,c.237C>A,LOW,YES +OR6K3 391114 BI GRCh38 1 158717207 158717207 + synonymous_variant Silent SNP C C T rs927290143 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 39 36 c.957G>A p.Leu319= p.L319= ENST00000368146.1 319 ctG/ctA 1/1 T L protein_coding YES 957/996 CAGAACAGTTT Gene3D:1.20.1070.10;Pfam:PF13853;PANTHER:PTHR26451;PANTHER:PTHR26451:SF956;Superfamily:SSF81321 ENSP00000357128 1/1 rs927290143 ENST00000368146 Transcript ENSG00000203757 HGNC:15030 LOW 8.838e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q8NGY3.145 OR6K3 HGNC -1 UPI000004B220 SNV OR6K3,synonymous_variant,p.L303=,ENST00000368145,NM_001005327.2,c.909G>A,LOW,,,,-1;OR6K3,synonymous_variant,p.L319=,ENST00000368146,,c.957G>A,LOW,YES,,,-1 957/996 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 3.992e-06 0.0 0.0 0.0 0.0 0.0 8.838e-06 0.0 0.0 2.706320083234459e-05 2.4326200218638405e-05 0.0 0.0 0.0 0.0 0.0 nfe 4.632350101019256e-05 0.0 4.632350101019256e-05 0.0 0.0 0 108 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 76 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS OR6K3,synonymous_variant,p.L319=,ENST00000368146.1,c.957G>A,LOW,;OR6K3,synonymous_variant,p.L303=,ENST00000368145.2,c.909G>A,LOW,YES +NCF2 4688 BI GRCh38 1 183560245 183560245 + missense_variant Missense_Mutation SNP T T G rs979540396 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 64 40 c.1319A>C p.Lys440Thr p.K440T ENST00000367535.8 NM_000433.4 440 aAg/aCg 14/15 P1 G K/T protein_coding YES CCDS1356.1 1319/1581 TTTCCTTGGGT PANTHER:PTHR15175;PANTHER:PTHR15175:SF3;MobiDB_lite:mobidb-lite ENSP00000356505 14/15 rs979540396 ENST00000367535 Transcript 1.0 ENSG00000116701 HGNC:7661 MODERATE NM_000433.4 6.152e-05 gnomAD_AFR missense_variant 1.0 benign(0.021) Unknown tolerated(0.37) P19878.225 NCF2 HGNC -1 A0A0S2Z457.29 1.0 UPI0000000A07 P19878-1 SNV NCF2,missense_variant,p.K395T,ENST00000413720,NM_001190794.1,c.1184A>C,MODERATE,,tolerated(0.36),benign(0.069),-1;NCF2,missense_variant,p.K440T,ENST00000367535,NM_000433.4,c.1319A>C,MODERATE,YES,tolerated(0.37),benign(0.021),-1;NCF2,missense_variant,p.K440T,ENST00000367536,NM_001127651.3,c.1319A>C,MODERATE,,tolerated(0.37),benign(0.021),-1;NCF2,missense_variant,p.K359T,ENST00000418089,NM_001190789.1,c.1076A>C,MODERATE,,tolerated(0.29),benign(0),-1;NCF2,downstream_gene_variant,,ENST00000419402,,,MODIFIER,,,,-1;NCF2,downstream_gene_variant,,ENST00000420553,,,MODIFIER,,,,-1;SMG7,intron_variant,,ENST00000495321,,n.233+9055T>G,MODIFIER,,,,1;NCF2,downstream_gene_variant,,ENST00000469280,,,MODIFIER,,,,-1 1449/2267 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 3.977e-06 6.152e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.3519499589165209e-05 4.864290167461149e-05 0.0 0.0 0.0 0.0 0.0 afr 4.864290167461149e-05 0.0 0.0 0.0 0.0 0 160 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 104 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS NCF2,non_coding_transcript_exon_variant,,ENST00000469280.2,n.759A>C,MODIFIER,;NCF2,missense_variant,p.K404T,ENST00000697351.1,c.1211A>C,MODERATE,;NCF2,missense_variant,p.K440T,ENST00000697330.1,c.1319A>C,MODERATE,;NCF2,missense_variant,p.K359T,ENST00000418089.5,c.1076A>C,MODERATE,;NCF2,missense_variant,p.K395T,ENST00000413720.5,c.1184A>C,MODERATE,;NCF2,missense_variant,p.K440T,ENST00000367536.5,c.1319A>C,MODERATE,;NCF2,missense_variant,p.K440T,ENST00000367535.8,c.1319A>C,MODERATE,YES;NCF2,non_coding_transcript_exon_variant,,ENST00000697329.1,n.1239A>C,MODIFIER,;SMG7,intron_variant,,ENST00000495321.1,n.233+9055T>G,MODIFIER, +SPATA31H1 84226 BI GRCh38 2 27581547 27581570 + inframe_deletion In_Frame_Del DEL GAGAGAAGCCATCGCAGTTCCTCT GAGAGAAGCCATCGCAGTTCCTCT - rs1558459412 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 146 46 c.15195_15218del p.Ser5065_Arg5072del p.S5065_R5072del ENST00000447166.3 NM_032266.5 5063 GAGAGAAGCCATCGCAGTTCCTCT/- 5/5 A2 - ERSHRSSS/- protein_coding CCDS42666.1 4975-4998/5955 CCCTCAGAGAGAAGCCATCGCAGTTCCTCTGAGAG PANTHER:PTHR33888;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000386190 1/1 rs1558459412 ENST00000408964 Transcript ENSG00000221843 HGNC:25275 8.0 MODERATE 8.961e-06 gnomAD_NFE inframe_deletion Unknown Q68DN1.108 C2orf16 HGNC 1 UPI0000D61179 deletion C2orf16,inframe_deletion,p.S5065_R5072del,ENST00000447166,,c.15195_15218del,MODERATE,YES,,,1;C2orf16,inframe_deletion,p.S1661_R1668del,ENST00000408964,NM_032266.3,c.4983_5006del,MODERATE,,,,1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.4,,MODIFIER,YES,,,1;ZNF512,upstream_gene_variant,,ENST00000379717,,,MODIFIER,,,,1;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271318.1&NM_001271289.1,,MODIFIER,,,,1;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1,,MODIFIER,,,,1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1&NM_001271288.1,,MODIFIER,,,,1;ZNF512,upstream_gene_variant,,ENST00000494548,,,MODIFIER,,,,1;ZNF512,upstream_gene_variant,,ENST00000461705,,,MODIFIER,,,,1;AC074091.2,upstream_gene_variant,,ENST00000505973,,,MODIFIER,YES,,,1 5026-5049/6200 muse*;mutect2;varscan2* 31771082-c094-4749-a9c7-80b67762f4d1 4.112e-06 0.0 0.0 0.0 0.0 0.0 8.961e-06 0.0 0.0 0 348 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 192 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS SPATA31H1,inframe_deletion,p.S5065_R5072del,ENST00000447166.3,c.15195_15218del,MODERATE,YES +SAP130 79595 BI GRCh38 2 128017785 128017785 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 70 39 c.321G>T p.Leu107Phe p.L107F ENST00000259235.7 NM_024545.4 107 ttG/ttT 3/20 A L/F protein_coding CCDS2153.1 321/3147 GTCGACAACAT PANTHER:PTHR13497 ENSP00000259235 3/20 ENST00000259235 Transcript ENSG00000136715 HGNC:29813 MODERATE missense_variant probably_damaging(0.914) Unknown tolerated_low_confidence(0.11) Q9H0E3.144 SAP130 HGNC -1 1.0 UPI0000037CDA Q9H0E3-1 SNV SAP130,missense_variant,p.L107F,ENST00000357702,NM_001145928.1,c.321G>T,MODERATE,YES,tolerated_low_confidence(0.11),benign(0.189),-1;SAP130,missense_variant,p.L81F,ENST00000259234,NM_001330300.2&NM_001330302.2,c.243G>T,MODERATE,,tolerated_low_confidence(0.11),probably_damaging(0.994),-1;SAP130,missense_variant,p.L81F,ENST00000643581,NM_001330299.2&NM_001330303.2&NM_001330301.2,c.243G>T,MODERATE,,tolerated_low_confidence(0.12),benign(0.189),-1;SAP130,missense_variant,p.L107F,ENST00000259235,NM_024545.4,c.321G>T,MODERATE,,tolerated_low_confidence(0.11),probably_damaging(0.914),-1;SAP130,missense_variant,p.L81F,ENST00000424298,,c.243G>T,MODERATE,,tolerated_low_confidence(0.15),probably_damaging(0.914),-1;SAP130,missense_variant,p.L81F,ENST00000450957,,c.243G>T,MODERATE,,tolerated(0.29),probably_damaging(0.914),-1 451/4065 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 99 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 109 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS SAP130,missense_variant,p.L81F,ENST00000450957.1,c.243G>T,MODERATE,;SAP130,missense_variant,p.L81F,ENST00000424298.5,c.243G>T,MODERATE,;SAP130,missense_variant,p.L81F,ENST00000259234.10,c.243G>T,MODERATE,;SAP130,missense_variant,p.L81F,ENST00000643581.2,c.243G>T,MODERATE,YES;SAP130,missense_variant,p.L107F,ENST00000259235.7,c.321G>T,MODERATE,;SAP130,missense_variant,p.L107F,ENST00000357702.9,c.321G>T,MODERATE, +GTDC1 79712 BI GRCh38 2 144208651 144208651 + missense_variant Missense_Mutation SNP G G A rs115723847 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 42 9 c.131C>T p.Thr44Ile p.T44I ENST00000344850.8 NM_001354361.1 44 aCa/aTa 4/12 0.0002 0.0008 0.0 0.0 0.0 0.0 A2 A T/I protein_coding CCDS33300.1 131/1377 CAGATGTCCGG PANTHER:PTHR13615:SF3;PANTHER:PTHR13615;Pfam:PF12038 ENSP00000339750 4/12 rs115723847 ENST00000344850 Transcript ENSG00000121964 HGNC:20887 MODERATE 0.0008 AFR missense_variant probably_damaging(0.999) Unknown deleterious(0.02) Q4AE62.122 GTDC1 HGNC -1 5.0 UPI000022BC3B Q4AE62-1 SNV GTDC1,missense_variant,p.T44I,ENST00000392869,NM_001376308.2&NM_001376307.2&NM_001376313.2&NM_001376316.2&NM_001376312.2&NM_001376306.2&NM_001376314.2&NM_001354354.2&NM_001376309.2&NM_001376311.2&NM_001376310.2&NM_001376315.2,c.131C>T,MODERATE,YES,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,missense_variant,p.T44I,ENST00000409214,NM_001006636.5,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,missense_variant,p.T44I,ENST00000542155,NM_001164629.5,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,missense_variant,p.T44I,ENST00000344850,NM_001354361.1,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,missense_variant,p.T44I,ENST00000392867,NM_001376320.2&NM_001376321.2&NM_001376332.2&NM_001376323.2&NM_001376322.2&NM_001376324.2&NM_024659.6,c.131C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.693),-1;GTDC1,missense_variant,p.T44I,ENST00000241391,NM_001354360.2&NM_001376331.2&NM_001284233.4&NM_001376317.2&NM_001376319.2&NM_001376318.2,c.131C>T,MODERATE,,deleterious(0.01),probably_damaging(0.977),-1;GTDC1,missense_variant,p.T44I,ENST00000409298,NM_001376325.2&NM_001376327.2&NM_001376326.2&NM_001354352.2&NM_001354353.2&NM_001354362.3&NM_001376328.1,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.993),-1;GTDC1,missense_variant,p.T44I,ENST00000437114,NM_001284235.2&NM_001354356.2&NM_001376330.1&NM_001354358.1,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,missense_variant,p.T44I,ENST00000417450,,c.131C>T,MODERATE,,deleterious(0.02),probably_damaging(0.999),-1;GTDC1,intron_variant,,ENST00000463875,NM_001284234.3&NM_001354350.2&NM_001376329.2&NM_001354351.2&NM_001354355.3,c.-209+27025C>T,MODIFIER,,,,-1;GTDC1,downstream_gene_variant,,ENST00000467352,,,MODIFIER,,,,-1;GTDC1,missense_variant,p.T44I,ENST00000415569,,c.131C>T,MODERATE,,deleterious(0.03),probably_damaging(1),-1;GTDC1,missense_variant,p.T44I,ENST00000392871,,c.131C>T,MODERATE,,deleterious(0.01),probably_damaging(0.977),-1;GTDC1,missense_variant,p.T44I,ENST00000429978,,c.131C>T,MODERATE,,deleterious(0.03),probably_damaging(1),-1;GTDC1,non_coding_transcript_exon_variant,,ENST00000491448,,n.281C>T,MODIFIER,,,,-1;GTDC1,non_coding_transcript_exon_variant,,ENST00000484303,,n.283C>T,MODIFIER,,,,-1 325/2607 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 6.763149940525182e-06 2.4334500267286785e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 62 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 51 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS GTDC1,non_coding_transcript_exon_variant,,ENST00000429978.5,n.411C>T,MODIFIER,;GTDC1,non_coding_transcript_exon_variant,,ENST00000484303.5,n.283C>T,MODIFIER,;GTDC1,missense_variant,p.T44I,ENST00000417450.5,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000437114.5,c.131C>T,MODERATE,;GTDC1,non_coding_transcript_exon_variant,,ENST00000491448.5,n.281C>T,MODIFIER,;GTDC1,intron_variant,,ENST00000463875.6,c.-209+27025C>T,MODIFIER,;GTDC1,missense_variant,NMD_transcript_variant,p.T44I,ENST00000415569.5,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000392871.6,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000409298.5,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000542155.5,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000344850.8,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000241391.9,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000392867.7,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000409214.5,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000392869.6,c.131C>T,MODERATE,;GTDC1,missense_variant,p.T44I,ENST00000682281.1,c.131C>T,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 34 22 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 57 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 56 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +SCN11A 11280 BI GRCh38 3 38872217 38872217 + synonymous_variant Silent SNP C C T rs771153034 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 70 69 c.3471G>A p.Ala1157= p.A1157= ENST00000302328.9 NM_001349253.2 1157 gcG/gcA 24/30 P4 T A protein_coding CCDS33737.1 3471/5376 likely_benign GACAGCGCACG Gene3D:1.20.120.350;Pfam:PF00520;PANTHER:PTHR10037;PANTHER:PTHR10037:SF210;Superfamily:SSF81324;Low_complexity_(Seg):seg ENSP00000307599 24/30 rs771153034;COSV100181135 ENST00000302328 Transcript 1.0 ENSG00000168356 HGNC:10583 LOW NM_001349253.2 0.0001449 gnomAD_AMR synonymous_variant 1;1 Unknown 0;1 Q9UI33.156 SCN11A HGNC -1 5.0 UPI000006CCD7 Q9UI33-1 SNV SCN11A,synonymous_variant,p.A1157=,ENST00000668754,,c.3471G>A,LOW,YES,,,-1;SCN11A,synonymous_variant,p.A1157=,ENST00000302328,NM_001349253.2&NM_014139.3,c.3471G>A,LOW,,,,-1;SCN11A,synonymous_variant,p.A1157=,ENST00000444237,,c.3471G>A,LOW,,,,-1;SCN11A,synonymous_variant,p.A1119=,ENST00000456224,,c.3357G>A,LOW,,,,-1;SCN11A,synonymous_variant,p.A1097=,ENST00000675892,,c.3291G>A,LOW,,,,-1;SCN11A,synonymous_variant,p.A1030=,ENST00000676176,,c.3090G>A,LOW,,,,-1;SCN11A,synonymous_variant,p.A1157=,ENST00000675223,,c.3471G>A,LOW,,,,-1;SCN11A,3_prime_UTR_variant,,ENST00000675672,,c.*642G>A,MODIFIER,,,,-1;SCN11A,3_prime_UTR_variant,,ENST00000676045,,c.*3188G>A,MODIFIER,,,,-1 3958/6793 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 2.791e-05 0.0 0.0001449 0.0 0.0 0.0 1.766e-05 0.0 0.0 3.381169881322421e-05 4.86665012431331e-05 0.0 6.631299766013399e-05 0.0 0.0 0.0 afr 4.86665012431331e-05 0.0 3.086520155193284e-05 0.0 0.0 0 138 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 139 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS SCN11A,synonymous_variant,p.A1157=,ENST00000444237.2,c.3471G>A,LOW,;SCN11A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676045.1,c.*3188G>A,MODIFIER,;SCN11A,synonymous_variant,p.A1097=,ENST00000675892.1,c.3291G>A,LOW,;SCN11A,synonymous_variant,NMD_transcript_variant,p.A1157=,ENST00000675223.1,c.3471G>A,LOW,;SCN11A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000675672.1,c.*642G>A,MODIFIER,;SCN11A,synonymous_variant,p.A1030=,ENST00000676176.1,c.3090G>A,LOW,;SCN11A,synonymous_variant,p.A1119=,ENST00000456224.7,c.3357G>A,LOW,;SCN11A,synonymous_variant,p.A1157=,ENST00000668754.1,c.3471G>A,LOW,;SCN11A,synonymous_variant,p.A1157=,ENST00000302328.9,c.3471G>A,LOW,YES +ROS1 6098 BI GRCh38 6 117389625 117389625 + missense_variant Missense_Mutation SNP G G A rs766232395 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 1 19 c.1484C>T p.Pro495Leu p.P495L ENST00000368508.7 NM_002944.3 495 cCc/cTc 12/43 A2 A P/L protein_coding YES CCDS5116.1 1484/7044 CAAAGGGGATG Gene3D:2.120.10.30;Superfamily:SSF63825;PANTHER:PTHR24416;PANTHER:PTHR24416:SF527 ENSP00000357494 12/43 rs766232395 ENST00000368508 Transcript 1.0 ENSG00000047936 HGNC:10261 MODERATE 5.437e-05 gnomAD_EAS missense_variant 1.0 benign(0.001) Unknown tolerated(0.06) P08922.203 ROS1 HGNC -1 1.0 UPI000013D467 SNV ROS1,missense_variant,p.P504L,ENST00000368507,NM_001378902.1&NM_001378891.1,c.1511C>T,MODERATE,,tolerated(0.14),benign(0.001),-1;ROS1,missense_variant,p.P495L,ENST00000368508,NM_002944.3,c.1484C>T,MODERATE,YES,tolerated(0.06),benign(0.001),-1;AL132671.2,intron_variant,,ENST00000467125,,c.548-68231C>T,MODIFIER,YES,,,-1 1683/7435 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 3.98e-06 0.0 0.0 0.0 5.437e-05 0.0 0.0 0.0 0.0 0 54 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 20 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS ENSG00000282218,intron_variant,,ENST00000467125.1,c.548-68231C>T,MODIFIER,YES;ROS1,missense_variant,p.P495L,ENST00000368508.7,c.1484C>T,MODERATE,;ROS1,missense_variant,p.P504L,ENST00000368507.8,c.1511C>T,MODERATE,YES +FMC1 154791 BI GRCh38 7 139341388 139341388 + missense_variant Missense_Mutation SNP G G A rs75669887 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 31 22 c.4G>A p.Ala2Thr p.A2T ENST00000297534.7 NM_197964.5 2 Gcg/Acg 1/2 0.0002 0.0 0.0 0.0 0.001 0.0 P1 A A/T protein_coding YES CCDS59084.1 4/1377 CAATGGCGGCC ENSP00000440222 1/11 rs75669887 ENST00000541515 Transcript ENSG00000269955 HGNC:44671 MODERATE 0.001 EUR missense_variant benign(0.006) Unknown deleterious_low_confidence(0) FMC1-LUC7L2 HGNC 1 A0A0A6YYJ8.38 2.0 UPI0001914F36 SNV FMC1-LUC7L2,missense_variant,p.A2T,ENST00000541515,NM_001244584.2,c.4G>A,MODERATE,YES,deleterious_low_confidence(0),benign(0.006),1;FMC1,missense_variant,p.A2T,ENST00000297534,NM_197964.5,c.4G>A,MODERATE,YES,deleterious(0),benign(0.031),1;LUC7L2,intron_variant,,ENST00000541170,NM_001244585.1,c.-26+871G>A,MODIFIER,,,,1;FMC1,intron_variant,,ENST00000468383,,n.50+1882G>A,MODIFIER,,,,1;FMC1,intron_variant,,ENST00000481123,,n.170+769G>A,MODIFIER,,,,1;FMC1,intron_variant,,ENST00000482181,,n.109+789G>A,MODIFIER,,,,1;FMC1,intron_variant,,ENST00000488886,,n.43+769G>A,MODIFIER,,,,1 29/1661 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 1.601e-05 0.0 0.0 0.0 0.0 0.0 3.53e-05 0.0 0.0 2.0273300833650865e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.628629903891124e-05 0.0 4.628629903891124e-05 0.0 0.0 0 45 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 53 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS FMC1-LUC7L2,missense_variant,p.A2T,ENST00000541515.3,c.4G>A,MODERATE,YES;FMC1,missense_variant,p.A2T,ENST00000297534.7,c.4G>A,MODERATE,YES;FMC1,intron_variant,,ENST00000488886.1,n.43+769G>A,MODIFIER,;FMC1,intron_variant,,ENST00000482181.1,n.109+789G>A,MODIFIER,;FMC1,intron_variant,,ENST00000481123.1,n.170+769G>A,MODIFIER,;LUC7L2,intron_variant,,ENST00000541170.7,c.-26+871G>A,MODIFIER,;FMC1,intron_variant,,ENST00000468383.5,n.50+1882G>A,MODIFIER, +DENND3 22898 BI GRCh38 8 141151652 141151652 + missense_variant Missense_Mutation SNP G G A rs571831372 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 144 23 c.649G>A p.Val217Ile p.V217I ENST00000262585.6 NM_014957.5 217 Gtc/Atc 7/23 0.0002 0.0 0.0 0.0 0.001 0.0 A2 A V/I protein_coding CCDS34947.1 649/3597 GGATCGTCTTC COSM1096756 PROSITE_profiles:PS50211;PANTHER:PTHR12296:SF21;PANTHER:PTHR12296;Pfam:PF02141;Gene3D:3.40.50.11500;SMART:SM00799 ENSP00000262585 7/23 rs571831372;COSV52801720 ENST00000262585 Transcript ENSG00000105339 HGNC:29134 MODERATE 0.001 EUR missense_variant 0;1 probably_damaging(0.992) Unknown tolerated(0.06) 0;1 A2RUS2.118 DENND3 HGNC 1 5.0 UPI00003CEFBA A2RUS2-1 SNV DENND3,missense_variant,p.V297I,ENST00000519811,NM_001362798.2&NM_001352890.3,c.889G>A,MODERATE,YES,tolerated(0.05),probably_damaging(0.998),1;DENND3,missense_variant,p.V217I,ENST00000262585,NM_014957.5,c.649G>A,MODERATE,,tolerated(0.06),probably_damaging(0.992),1;DENND3,missense_variant,p.V274I,ENST00000518668,,c.820G>A,MODERATE,,tolerated(0.07),probably_damaging(0.993),1;DENND3,missense_variant,p.V217I,ENST00000424248,,c.649G>A,MODERATE,,tolerated(0.07),probably_damaging(0.967),1;DENND3,missense_variant,p.V219I,ENST00000520986,,c.655G>A,MODERATE,,deleterious(0),possibly_damaging(0.772),1;DENND3,downstream_gene_variant,,ENST00000523058,,,MODIFIER,,,,1;DENND3,upstream_gene_variant,,ENST00000521477,,,MODIFIER,,,,1;DENND3,downstream_gene_variant,,ENST00000523015,,,MODIFIER,,,,1 927/5438 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 1.591e-05 0.0 2.891e-05 0.0 0.0 0.0 2.637e-05 0.0 0.0 2.0317500457167625e-05 0.0 0.0 6.636579928454012e-05 0.0 0.000202020004508 0.0 0.0 1.5435900422744453e-05 0.0 0.0 0 110 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 168 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS DENND3,missense_variant,p.V217I,ENST00000424248.2,c.649G>A,MODERATE,;DENND3,missense_variant,p.R273H,ENST00000518668.5,c.818G>A,MODERATE,;DENND3,missense_variant,p.V219I,ENST00000520986.5,c.655G>A,MODERATE,;DENND3,missense_variant,p.V217I,ENST00000262585.6,c.649G>A,MODERATE,;DENND3,missense_variant,p.V297I,ENST00000519811.6,c.889G>A,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 40 46 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 88 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 86 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +TRAF2 7186 BI GRCh38 9 136925721 136925721 + synonymous_variant Silent SNP C C T rs560077345 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 38 21 c.1326C>T p.His442= p.H442= ENST00000247668.7 NM_021138.4 442 caC/caT 11/11 0.0002 0.0 0.0 0.001 0.0 0.0 P1 T H protein_coding YES CCDS7013.1 1326/1506 GAGCACGTGAT COSM1461253 PDB-ENSP_mappings:1ca4.A;PDB-ENSP_mappings:1ca4.B;PDB-ENSP_mappings:1ca4.C;PDB-ENSP_mappings:1ca4.D;PDB-ENSP_mappings:1ca4.E;PDB-ENSP_mappings:1ca4.F;PDB-ENSP_mappings:1ca9.A;PDB-ENSP_mappings:1ca9.B;PDB-ENSP_mappings:1ca9.C;PDB-ENSP_mappings:1ca9.D;PDB-ENSP_mappings:1ca9.E;PDB-ENSP_mappings:1ca9.F;PDB-ENSP_mappings:1czy.A;PDB-ENSP_mappings:1czy.B;PDB-ENSP_mappings:1czy.C;PDB-ENSP_mappings:1czz.A;PDB-ENSP_mappings:1czz.B;PDB-ENSP_mappings:1czz.C;PDB-ENSP_mappings:1d00.A;PDB-ENSP_mappings:1d00.B;PDB-ENSP_mappings:1d00.C;PDB-ENSP_mappings:1d00.D;PDB-ENSP_mappings:1d00.E;PDB-ENSP_mappings:1d00.F;PDB-ENSP_mappings:1d00.G;PDB-ENSP_mappings:1d00.H;PDB-ENSP_mappings:1d01.A;PDB-ENSP_mappings:1d01.B;PDB-ENSP_mappings:1d01.C;PDB-ENSP_mappings:1d01.D;PDB-ENSP_mappings:1d01.E;PDB-ENSP_mappings:1d01.F;PDB-ENSP_mappings:1d0a.A;PDB-ENSP_mappings:1d0a.B;PDB-ENSP_mappings:1d0a.C;PDB-ENSP_mappings:1d0a.D;PDB-ENSP_mappings:1d0a.E;PDB-ENSP_mappings:1d0a.F;PDB-ENSP_mappings:1d0j.A;PDB-ENSP_mappings:1d0j.B;PDB-ENSP_mappings:1d0j.C;PDB-ENSP_mappings:1d0j.D;PDB-ENSP_mappings:1d0j.E;PDB-ENSP_mappings:1d0j.F;PDB-ENSP_mappings:1f3v.B;PDB-ENSP_mappings:1qsc.A;PDB-ENSP_mappings:1qsc.B;PDB-ENSP_mappings:1qsc.C;Gene3D:2.60.210.10;PIRSF:PIRSF015614;PROSITE_profiles:PS50144;PANTHER:PTHR10131;PANTHER:PTHR10131:SF21;SMART:SM00061;Superfamily:SSF49599;CDD:cd03778 ENSP00000247668 11/11 rs560077345;COSV56036868 ENST00000247668 Transcript ENSG00000127191 HGNC:12032 LOW NM_021138.4 0.001 EAS synonymous_variant 0;1 1.0 Unknown 0;1 Q12933.236 TRAF2 HGNC 1 A0A024R8H5.56 1.0 UPI0000001612 Q12933-1 SNV TRAF2,synonymous_variant,p.H442=,ENST00000247668,NM_021138.4,c.1326C>T,LOW,YES,,,1;TRAF2,downstream_gene_variant,,ENST00000466107,,,MODIFIER,,,,1 1380/2266 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 5.582e-05 0.0 0.0 0.0 0.0005982 0.0 1.766e-05 0.0001632 0.0 6.757400115020573e-06 0.0 0.0 0.0 0.0 0.0002012879995163 0.0 0.0 0.0 0.0 0.0 0 63 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 60 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS TRAF2,synonymous_variant,p.H442=,ENST00000247668.7,c.1326C>T,LOW,YES +LMO3 55885 BI GRCh38 12 16600744 16600744 + synonymous_variant Silent SNP C C T novel TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 38 32 c.117G>A p.Lys39= p.K39= ENST00000320122.10 39 aaG/aaA 2/4 T K protein_coding CCDS8678.1 117/438 GCACACTTCAG Gene3D:2.10.110.10;Pfam:PF00412;PROSITE_profiles:PS50023;PANTHER:PTHR45787;PANTHER:PTHR45787:SF7;SMART:SM00132;Superfamily:SSF57716;CDD:cd09388 ENSP00000312856 2/4 ENST00000320122 Transcript ENSG00000048540 HGNC:6643 LOW synonymous_variant Unknown Q8TAP4.144 LMO3 HGNC -1 A0A024RAT1.51 1.0 UPI000006F2D4 Q8TAP4-1 SNV LMO3,synonymous_variant,p.K50=,ENST00000261169,NM_001243611.1,c.150G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000320122,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000354662,NM_001001395.2,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000441439,NM_001243609.1,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K57=,ENST00000541295,NM_001243612.1,c.171G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000537304,NM_018640.5,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000447609,NM_001243610.1,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000616247,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000540848,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000535535,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000534946,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000540445,NM_001243613.1,c.117G>A,LOW,YES,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000538020,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000546279,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000538051,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000541846,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000540590,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000539534,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000545436,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000537757,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000546281,,c.117G>A,LOW,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000537568,,n.481G>A,MODIFIER,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000536509,,n.456G>A,MODIFIER,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000332914,,n.486G>A,MODIFIER,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000544276,,n.278G>A,MODIFIER,,,,-1;MGST1,intron_variant,,ENST00000539036,,n.401-8350C>T,MODIFIER,,,,1;LMO3,synonymous_variant,p.K39=,ENST00000396205,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000453727,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000541589,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000541764,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000424192,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000536172,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000539232,,c.117G>A,LOW,,,,-1;LMO3,synonymous_variant,p.K39=,ENST00000544754,,c.117G>A,LOW,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000543721,,n.498G>A,MODIFIER,,,,-1;LMO3,non_coding_transcript_exon_variant,,ENST00000439600,,n.317G>A,MODIFIER,,,,-1 640/3759 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 72 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 70 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS LMO3,synonymous_variant,p.K39=,ENST00000538020.1,c.117G>A,LOW,;LMO3,non_coding_transcript_exon_variant,,ENST00000439600.2,n.317G>A,MODIFIER,;LMO3,non_coding_transcript_exon_variant,,ENST00000544276.1,n.278G>A,MODIFIER,;LMO3,non_coding_transcript_exon_variant,,ENST00000543721.1,n.498G>A,MODIFIER,;LMO3,non_coding_transcript_exon_variant,,ENST00000537568.1,n.481G>A,MODIFIER,;LMO3,non_coding_transcript_exon_variant,,ENST00000332914.10,n.486G>A,MODIFIER,;LMO3,synonymous_variant,p.K39=,ENST00000540590.1,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000545436.5,c.117G>A,LOW,;LMO3,non_coding_transcript_exon_variant,,ENST00000536509.5,n.456G>A,MODIFIER,;LMO3,synonymous_variant,p.K39=,ENST00000538051.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000546279.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000539232.1,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000539534.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000537757.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000546281.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000544754.1,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000536172.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000541846.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000540445.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000424192.6,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000534946.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000541764.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000535535.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000541589.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000540848.5,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000453727.6,c.117G>A,LOW,;LMO3,synonymous_variant,NMD_transcript_variant,p.K39=,ENST00000396205.6,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000320122.10,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000447609.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000441439.6,c.117G>A,LOW,;LMO3,synonymous_variant,p.K57=,ENST00000541295.5,c.171G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000354662.5,c.117G>A,LOW,;LMO3,synonymous_variant,p.K50=,ENST00000261169.10,c.150G>A,LOW,;LMO3,synonymous_variant,p.K39=,ENST00000537304.6,c.117G>A,LOW,YES;MGST1,intron_variant,,ENST00000539036.5,n.401-8350C>T,MODIFIER, +PITPNM2 57605 BI GRCh38 12 122996839 122996839 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 21 21 c.1544C>A p.Pro515His p.P515H ENST00000320201.10 NM_001384661.1 515 cCc/cAc 12/26 P3 T P/H protein_coding YES CCDS9242.1 1544/4050 GCAGGGGGAGG Low_complexity_(Seg):seg;PANTHER:PTHR10658:SF41;PANTHER:PTHR10658 ENSP00000322218 11/25 ENST00000320201 Transcript ENSG00000090975 HGNC:21044 MODERATE missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q9BZ72.133 PITPNM2 HGNC -1 5.0 UPI0000070D27 Q9BZ72-1 SNV PITPNM2,missense_variant,p.P515H,ENST00000280562,NM_001300801.1,c.1544C>A,MODERATE,,deleterious(0),probably_damaging(1),-1;PITPNM2,missense_variant,p.P515H,ENST00000320201,NM_020845.2,c.1544C>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;PITPNM2,downstream_gene_variant,,ENST00000546049,,,MODIFIER,,,,-1;PITPNM2,downstream_gene_variant,,ENST00000451868,,,MODIFIER,,,,-1;PITPNM2,downstream_gene_variant,,ENST00000436074,,,MODIFIER,,,,-1 1683/6735 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 71 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 42 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS PITPNM2,missense_variant,p.P515H,ENST00000280562.9,c.1544C>A,MODERATE,;PITPNM2,missense_variant,p.P515H,ENST00000320201.10,c.1544C>A,MODERATE,YES +MINAR1 23251 BI GRCh38 15 79468205 79468205 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 19 14 c.2572C>T p.Pro858Ser p.P858S ENST00000305428.8 NM_015206.3 858 Cca/Tca 4/4 P1 T P/S protein_coding YES CCDS32306.1 2572/2751 TAAACCCAAAT PANTHER:PTHR31530:SF2;PANTHER:PTHR31530;Pfam:PF06789 ENSP00000307461 4/4 ENST00000305428 Transcript ENSG00000169330 HGNC:29172 MODERATE NM_015206.3 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q9UPX6.120 MINAR1 HGNC 1 1.0 UPI00001B2F56 SNV MINAR1,missense_variant,p.P858S,ENST00000305428,NM_015206.3,c.2572C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;MINAR1,3_prime_UTR_variant,,ENST00000559272,,c.*73C>T,MODIFIER,,,,1 2827/6926 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 34 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 34 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS MINAR1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000559272.1,c.*73C>T,MODIFIER,;MINAR1,missense_variant,p.P858S,ENST00000305428.8,c.2572C>T,MODERATE,YES +KRT32 3882 BI GRCh38 17 41464149 41464149 + stop_gained Nonsense_Mutation SNP G G A rs1361360350 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 27 21 c.925C>T p.Gln309Ter p.Q309* ENST00000225899.4 NM_002278.3 309 Cag/Tag 5/7 P1 A Q/* protein_coding YES CCDS11393.1 925/1347 TGACTGGTAGT Gene3D:1.20.5.500;Coiled-coils_(Ncoils):Coil;Pfam:PF00038;PROSITE_profiles:PS51842;PANTHER:PTHR23239;PANTHER:PTHR23239:SF155;SMART:SM01391;Superfamily:SSF57184 ENSP00000225899 5/7 rs1361360350 ENST00000225899 Transcript ENSG00000108759 HGNC:6449 HIGH NM_002278.3 8.837e-06 gnomAD_NFE stop_gained 1.0 Unknown Q14532.152 KRT32 HGNC -1 1.0 UPI000013C883 SNV KRT32,stop_gained,p.Q309*,ENST00000225899,NM_002278.3,c.925C>T,HIGH,YES,,,-1;RNU2-32P,upstream_gene_variant,,ENST00000411193,,,MODIFIER,YES,,,1 986/2005 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 3.994e-06 0.0 0.0 0.0 0.0 0.0 8.837e-06 0.0 0.0 0 54 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 48 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS KRT32,stop_gained,p.Q309*,ENST00000225899.4,c.925C>T,HIGH,YES +RNF43 54894 BI GRCh38 17 58357971 58357971 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 78 47 c.1805A>G p.Asn602Ser p.N602S ENST00000407977.7 NM_017763.6 602 aAc/aGc 9/10 P1 C N/S protein_coding CCDS11607.1 1805/2352 CTGAGTTGGAT PANTHER:PTHR16200;PANTHER:PTHR16200:SF2;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000385328 9/10 ENST00000407977 Transcript 1.0 ENSG00000108375 HGNC:18505 MODERATE NM_017763.6 missense_variant benign(0) Unknown tolerated_low_confidence(0.66) Q68DV7.150 RNF43 HGNC -1 2.0 UPI000022A469 Q68DV7-1 SNV RNF43,missense_variant,p.N602S,ENST00000584437,,c.1805A>G,MODERATE,YES,tolerated_low_confidence(0.66),benign(0),-1;RNF43,missense_variant,p.N602S,ENST00000407977,NM_017763.6,c.1805A>G,MODERATE,,tolerated_low_confidence(0.66),benign(0),-1;RNF43,missense_variant,p.N602S,ENST00000577716,NM_001305544.2,c.1805A>G,MODERATE,,tolerated_low_confidence(0.66),benign(0),-1;RNF43,missense_variant,p.N561S,ENST00000583753,,c.1682A>G,MODERATE,,tolerated(0.65),benign(0),-1;RNF43,missense_variant,p.N475S,ENST00000581868,,c.1424A>G,MODERATE,,tolerated_low_confidence(0.29),benign(0),-1;RNF43,missense_variant,p.N475S,ENST00000577625,NM_001305545.1,c.1424A>G,MODERATE,,tolerated(0.62),benign(0),-1;SUPT4H1,upstream_gene_variant,,ENST00000580947,,,MODIFIER,,,,-1;AC004687.2,missense_variant,p.N602S,ENST00000648873,,c.1805A>G,MODERATE,YES,tolerated_low_confidence(0.51),benign(0.001),-1;TSPOAP1-AS1,intron_variant,,ENST00000583841,,n.434+20292T>C,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000578025,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000579527,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000579859,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000580022,,,MODIFIER,YES,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000585236,,,MODIFIER,,,,1;TSPOAP1-AS1,downstream_gene_variant,,ENST00000667382,,,MODIFIER,,,,1 2708/4522 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0 92 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 126 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS RNF43,missense_variant,p.N475S,ENST00000581868.1,c.1424A>G,MODERATE,;RNF43,missense_variant,p.N475S,ENST00000577625.5,c.1424A>G,MODERATE,;RNF43,missense_variant,p.N602S,ENST00000577716.5,c.1805A>G,MODERATE,;RNF43,missense_variant,p.N602S,ENST00000407977.7,c.1805A>G,MODERATE,YES;RNF43,missense_variant,p.N602S,ENST00000584437.5,c.1805A>G,MODERATE,;RNF43,missense_variant,p.N561S,ENST00000583753.5,c.1682A>G,MODERATE,;ENSG00000285897,missense_variant,NMD_transcript_variant,p.N602S,ENST00000648873.1,c.1805A>G,MODERATE,YES;TSPOAP1-AS1,intron_variant,,ENST00000583841.1,n.434+20292T>C,MODIFIER,YES +NPEPL1 79716 BI GRCh38 20 58701145 58701145 + missense_variant Missense_Mutation SNP G G A rs1420947341 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 3 6 c.809G>A p.Ser270Asn p.S270N ENST00000356091.11 NM_024663.4 270 aGc/aAc 6/12 P1 A S/N protein_coding YES CCDS46621.1 809/1572 CCTCAGCATCA Gene3D:3.40.630.10;Pfam:PF00883;Prints:PR00481;PANTHER:PTHR11963;PANTHER:PTHR11963:SF4;Superfamily:SSF53187;CDD:cd00433 ENSP00000348395 6/12 rs1420947341;COSV100622506 ENST00000356091 Transcript ENSG00000215440 HGNC:16244 MODERATE NM_024663.4 1.168e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.985) Unknown deleterious(0.01) 0;1 Q8NDH3.152 NPEPL1 HGNC 1 1.0 UPI000036789E Q8NDH3-1 SNV NPEPL1,missense_variant,p.S270N,ENST00000356091,NM_024663.4,c.809G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.985),1;NPEPL1,missense_variant,p.S242N,ENST00000525967,NM_001204872.2,c.725G>A,MODERATE,,deleterious(0.01),probably_damaging(0.995),1;NPEPL1,missense_variant,p.S222N,ENST00000525817,NM_001204873.2,c.665G>A,MODERATE,,deleterious(0.01),probably_damaging(0.975),1;NPEPL1,missense_variant,p.S159N,ENST00000533788,,c.476G>A,MODERATE,,deleterious(0.04),probably_damaging(0.927),1;STX16-NPEPL1,3_prime_UTR_variant,,ENST00000530122,,c.*792G>A,MODIFIER,YES,,,1;NPEPL1,non_coding_transcript_exon_variant,,ENST00000529976,,n.1227G>A,MODIFIER,,,,1;NPEPL1,non_coding_transcript_exon_variant,,ENST00000527587,,n.1217G>A,MODIFIER,,,,1 910/2191 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 5.176e-06 0.0 0.0 0.0 0.0 0.0 1.168e-05 0.0 0.0 0 10 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 9 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS NPEPL1,synonymous_variant,NMD_transcript_variant,p.Q158=,ENST00000533788.1,c.474G>A,LOW,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000527587.5,n.1217G>A,MODIFIER,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000529976.5,n.1227G>A,MODIFIER,;NPEPL1,missense_variant,p.S270N,ENST00000356091.11,c.809G>A,MODERATE,YES;NPEPL1,missense_variant,p.S222N,ENST00000525817.5,c.665G>A,MODERATE,;NPEPL1,missense_variant,p.S242N,ENST00000525967.5,c.725G>A,MODERATE,;STX16-NPEPL1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000530122.1,c.*792G>A,MODIFIER,YES +THOC2 57187 BI GRCh38 X 123636084 123636084 + synonymous_variant Silent SNP G G T rs1204579479 TCGA-VD-A8KB-01A TCGA-VD-A8KB-10C Somatic 39 39 c.2013C>A p.Gly671= p.G671= ENST00000245838.13 NM_001081550.2 671 ggC/ggA 19/39 P1 T G protein_coding YES CCDS43988.1 2013/4782 CTTTTGCCCGC PANTHER:PTHR21597;PANTHER:PTHR21597:SF1 ENSP00000245838 19/39 rs1204579479 ENST00000245838 Transcript 1.0 ENSG00000125676 HGNC:19073 LOW NM_001081550.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q8NI27.151 THOC2 HGNC -1 5.0 UPI00001D7C42 Q8NI27-1 SNV THOC2,synonymous_variant,p.G671=,ENST00000245838,NM_001081550.2,c.2013C>A,LOW,YES,,,-1;THOC2,synonymous_variant,p.G671=,ENST00000355725,,c.2013C>A,LOW,,,,-1;THOC2,synonymous_variant,p.G556=,ENST00000491737,,c.1668C>A,LOW,,,,-1 2043/5600 muse;mutect2;varscan2 31771082-c094-4749-a9c7-80b67762f4d1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 75 23c33bb0-50ce-4d0f-85a1-829abaf68dc6 79 4df7b038-77d7-450b-b4e0-f292a1721e8e SUCCESS THOC2,synonymous_variant,p.G556=,ENST00000491737.5,c.1668C>A,LOW,;THOC2,synonymous_variant,p.G671=,ENST00000355725.8,c.2013C>A,LOW,;THOC2,synonymous_variant,p.G671=,ENST00000245838.13,c.2013C>A,LOW,YES +CCDC126 90693 BI GRCh38 7 23611407 23611407 + missense_variant Missense_Mutation SNP A A G rs1324302686 TCGA-VD-A8K7-01B TCGA-VD-A8K7-10A Somatic 30 28 c.92A>G p.His31Arg p.H31R ENST00000307471.8 NM_138771.4 31 cAc/cGc 3/4 P1 G H/R protein_coding YES CCDS5384.1 92/423 ACTGCACTATA Pfam:PF15027;PANTHER:PTHR46941;Transmembrane_helices:TMhelix ENSP00000304355 3/4 rs1324302686 ENST00000307471 Transcript ENSG00000169193 HGNC:22398 MODERATE NM_138771.4 2.891e-05 gnomAD_AMR missense_variant 1.0 benign(0) Unknown tolerated(0.76) Q96EE4.125 CCDC126 HGNC 1 A0A024RA08.51 1.0 UPI0000048F13 SNV CCDC126,missense_variant,p.H31R,ENST00000307471,NM_138771.4,c.92A>G,MODERATE,YES,tolerated(0.76),benign(0),1;CCDC126,missense_variant,p.H31R,ENST00000409765,,c.92A>G,MODERATE,,tolerated(0.76),benign(0),1;CCDC126,missense_variant,p.H31R,ENST00000410069,,c.92A>G,MODERATE,,tolerated(0.76),benign(0),1;CCDC126,missense_variant,p.H31R,ENST00000448353,,c.92A>G,MODERATE,,tolerated(0.84),benign(0),1;CCDC126,non_coding_transcript_exon_variant,,ENST00000486109,,n.658A>G,MODIFIER,,,,1;CCDC126,non_coding_transcript_exon_variant,,ENST00000472407,,n.645A>G,MODIFIER,,,,1;CCDC126,non_coding_transcript_exon_variant,,ENST00000485233,,n.566A>G,MODIFIER,,,,1 546/2470 muse;mutect2;varscan2 6103e640-8b62-4e39-908b-b62a0debeb0e 7.957e-06 0.0 2.891e-05 0.0 0.0 0.0 8.8e-06 0.0 0.0 2.7038700864068232e-05 9.723370021674782e-05 0.0 0.0 0.0 0.0 0.0 afr 9.723370021674782e-05 0.0 0.0 0.0 0.0 0 81 32cf3aa3-e89a-4386-b66d-0a933dc2cfeb 58 3b822209-f10e-44f5-b998-e4176a9f4c98 SUCCESS CCDC126,non_coding_transcript_exon_variant,,ENST00000486109.1,n.658A>G,MODIFIER,;CCDC126,missense_variant,p.H31R,ENST00000410069.1,c.92A>G,MODERATE,;CCDC126,non_coding_transcript_exon_variant,,ENST00000472407.5,n.645A>G,MODIFIER,;CCDC126,non_coding_transcript_exon_variant,,ENST00000485233.1,n.566A>G,MODIFIER,;CCDC126,missense_variant,p.H31R,ENST00000448353.5,c.92A>G,MODERATE,;CCDC126,missense_variant,p.H31R,ENST00000409765.5,c.92A>G,MODERATE,;CCDC126,missense_variant,p.H31R,ENST00000307471.8,c.92A>G,MODERATE,YES +CCDC126 90693 BI GRCh38 7 23611408 23611408 + synonymous_variant Silent SNP C C T rs866686971 TCGA-VD-A8K7-01B TCGA-VD-A8K7-10A Somatic 30 27 c.93C>T p.His31= p.H31= ENST00000307471.8 NM_138771.4 31 caC/caT 3/4 P1 T H protein_coding YES CCDS5384.1 93/423 CTGCACTATAC Pfam:PF15027;PANTHER:PTHR46941;Transmembrane_helices:TMhelix ENSP00000304355 3/4 rs866686971 ENST00000307471 Transcript ENSG00000169193 HGNC:22398 LOW NM_138771.4 synonymous_variant 1.0 Unknown Q96EE4.125 CCDC126 HGNC 1 A0A024RA08.51 1.0 UPI0000048F13 SNV CCDC126,synonymous_variant,p.H31=,ENST00000307471,NM_138771.4,c.93C>T,LOW,YES,,,1;CCDC126,synonymous_variant,p.H31=,ENST00000409765,,c.93C>T,LOW,,,,1;CCDC126,synonymous_variant,p.H31=,ENST00000410069,,c.93C>T,LOW,,,,1;CCDC126,synonymous_variant,p.H31=,ENST00000448353,,c.93C>T,LOW,,,,1;CCDC126,non_coding_transcript_exon_variant,,ENST00000486109,,n.659C>T,MODIFIER,,,,1;CCDC126,non_coding_transcript_exon_variant,,ENST00000472407,,n.646C>T,MODIFIER,,,,1;CCDC126,non_coding_transcript_exon_variant,,ENST00000485233,,n.567C>T,MODIFIER,,,,1 547/2470 muse;mutect2;varscan2 6103e640-8b62-4e39-908b-b62a0debeb0e 0 82 32cf3aa3-e89a-4386-b66d-0a933dc2cfeb 58 3b822209-f10e-44f5-b998-e4176a9f4c98 SUCCESS CCDC126,non_coding_transcript_exon_variant,,ENST00000486109.1,n.659C>T,MODIFIER,;CCDC126,synonymous_variant,p.H31=,ENST00000410069.1,c.93C>T,LOW,;CCDC126,non_coding_transcript_exon_variant,,ENST00000472407.5,n.646C>T,MODIFIER,;CCDC126,non_coding_transcript_exon_variant,,ENST00000485233.1,n.567C>T,MODIFIER,;CCDC126,synonymous_variant,p.H31=,ENST00000448353.5,c.93C>T,LOW,;CCDC126,synonymous_variant,p.H31=,ENST00000409765.5,c.93C>T,LOW,;CCDC126,synonymous_variant,p.H31=,ENST00000307471.8,c.93C>T,LOW,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-VD-A8K7-01B TCGA-VD-A8K7-10A Somatic 45 30 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 6103e640-8b62-4e39-908b-b62a0debeb0e 0 83 32cf3aa3-e89a-4386-b66d-0a933dc2cfeb 75 3b822209-f10e-44f5-b998-e4176a9f4c98 SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +PRAMEF18 391003 BI GRCh38 1 13225895 13225895 + missense_variant Missense_Mutation SNP T T C rs2100401630 TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 204 42 c.212A>G p.Lys71Arg p.K71R ENST00000624297.3 NM_001099850.2 71 aAg/aGg 1/3 P1 C K/R protein_coding YES CCDS41258.2 212/1440 GCGTCTTCATC PIRSF:PIRSF038286;PANTHER:PTHR14224;PANTHER:PTHR14224:SF79 ENSP00000485473 1/3 ENST00000624297 Transcript ENSG00000279804 HGNC:30693 MODERATE missense_variant 1.0 benign(0.343) Unknown deleterious(0.04) Q5VWM3.103 PRAMEF18 HGNC -1 1.0 UPI0004423C16 SNV PRAMEF18,missense_variant,p.K71R,ENST00000624297,NM_001099850.2,c.212A>G,MODERATE,YES,deleterious(0.04),benign(0.343),-1 212/2067 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 296 4774e843-682e-4098-82eb-675e81205987 246 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS PRAMEF18,missense_variant,p.K71R,ENST00000624297.3,c.212A>G,MODERATE,YES +TRIM62 55223 BI GRCh38 1 33147279 33147279 + synonymous_variant Silent SNP G G A rs746662481 TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 31 21 c.1326C>T p.Arg442= p.R442= ENST00000291416.10 NM_018207.3 442 cgC/cgT 5/5 P1 A R protein_coding YES CCDS376.1 1326/1428 TTCTCGCGGAA CDD:cd13744;Pfam:PF00622;Gene3D:2.60.120.920;SMART:SM00449;Superfamily:SSF49899;PROSITE_profiles:PS50188;PANTHER:PTHR24103;PANTHER:PTHR24103:SF573 ENSP00000291416 5/5 rs746662481 ENST00000291416 Transcript ENSG00000116525 HGNC:25574 LOW NM_018207.3 0.0007228 gnomAD_AMR synonymous_variant 1.0 Unknown Q9BVG3.161 TRIM62 HGNC -1 1.0 UPI000004E050 Q9BVG3-1 SNV TRIM62,synonymous_variant,p.R442=,ENST00000291416,NM_018207.3,c.1326C>T,LOW,YES,,,-1;TRIM62,synonymous_variant,p.R321=,ENST00000543586,NM_001330483.1,c.963C>T,LOW,,,,-1;AL662907.1,upstream_gene_variant,,ENST00000622988,,,MODIFIER,YES,,,-1 1937/3817 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0.0001233 0.0 0.0007228 0.0 0.0 0.0 2.637e-05 0.0004886 0.0 1.3519200365408324e-05 2.4311999368364923e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5432100553880446e-05 0.0 0.0 0 59 4774e843-682e-4098-82eb-675e81205987 52 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS TRIM62,synonymous_variant,p.R321=,ENST00000543586.1,c.963C>T,LOW,;TRIM62,synonymous_variant,p.R442=,ENST00000291416.10,c.1326C>T,LOW,YES +NLRP3 114548 BI GRCh38 1 247418813 247418813 + missense_variant Missense_Mutation SNP C C T rs1033902069 TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 24 9 c.13C>T p.Arg5Cys p.R5C ENST00000336119.8 NM_001243133.2 5 Cgc/Tgc 2/10 P1 T R/C protein_coding YES 13/3105 GCACCCGCTGC COSM5460971 Gene3D:1.10.533.10;PDB-ENSP_mappings:2naq.A;PDB-ENSP_mappings:3qf2.A;PDB-ENSP_mappings:3qf2.B;PROSITE_profiles:PS50824;PANTHER:PTHR24107;PANTHER:PTHR24107:SF10;SMART:SM01289;Superfamily:SSF47986 ENSP00000337383 2/10 rs1033902069;COSV60222719 ENST00000336119 Transcript 1.0 ENSG00000162711 HGNC:16400 MODERATE NM_001243133.2 missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q96P20.204 NLRP3 HGNC 1 1.0 UPI000004454C Q96P20-1 SNV NLRP3,missense_variant,p.R7C,ENST00000366497,,c.19C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;NLRP3,missense_variant,p.R5C,ENST00000391827,NM_001127462.3,c.13C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;NLRP3,missense_variant,p.R5C,ENST00000336119,NM_001243133.2&NM_004895.5&NM_001079821.3,c.13C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;NLRP3,missense_variant,p.R5C,ENST00000366496,NM_001127461.3,c.13C>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.983),1;NLRP3,missense_variant,p.R5C,ENST00000391828,,c.13C>T,MODERATE,,deleterious(0),probably_damaging(1),1;NLRP3,missense_variant,p.R5C,ENST00000348069,NM_183395.3,c.13C>T,MODERATE,,deleterious(0),probably_damaging(0.988),1;NLRP3,missense_variant,p.R5C,ENST00000643234,,c.13C>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;NLRP3,missense_variant,p.R5C,ENST00000474792,,c.13C>T,MODERATE,,deleterious(0),probably_damaging(1),1;NLRP3,upstream_gene_variant,,ENST00000642259,,,MODIFIER,,,,1 782/4187 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 6.7641599343915004e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543019970995374e-05 0.0 0.0 0 36 4774e843-682e-4098-82eb-675e81205987 34 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS NLRP3,missense_variant,p.R5C,ENST00000643234.2,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000474792.2,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000697350.1,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000366496.7,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000348069.7,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000336119.8,c.13C>T,MODERATE,YES;NLRP3,missense_variant,p.R5C,ENST00000391827.3,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000391828.8,c.13C>T,MODERATE,;NLRP3,missense_variant,p.R5C,ENST00000697408.2,c.13C>T,MODERATE, +FANCD2 2177 BI GRCh38 3 10098878 10098878 + intron_variant Intron SNP T T C novel TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 41 33 c.4281+63T>C ENST00000675286.1 NM_001018115.3 1448/1471 A2 C S protein_coding YES CCDS2595.1 4344/4416 CTAAGTTGGTG ENSP00000287647 43/43 ENST00000287647 Transcript 1.0 ENSG00000144554 HGNC:3585 LOW synonymous_variant 1.0 Unknown Q9BXW9.176 FANCD2 HGNC 1 1.0 UPI000006F678 Q9BXW9-1 SNV FANCD2,synonymous_variant,p.S1448=,ENST00000287647,NM_033084.6&NM_001374254.1,c.4344T>C,LOW,YES,,,1;FANCD2,intron_variant,,ENST00000419585,NM_001319984.2,c.4281+63T>C,MODIFIER,,,,1;FANCD2OS,intron_variant,,ENST00000524279,NM_173472.2,c.*43+5320A>G,MODIFIER,,,,-1;FANCD2,intron_variant,,ENST00000675286,NM_001018115.3,c.4281+63T>C,MODIFIER,,,,1;FANCD2,intron_variant,,ENST00000676013,NM_001374253.1,c.4170+63T>C,MODIFIER,,,,1;FANCD2OS,downstream_gene_variant,,ENST00000453223,,,MODIFIER,,,,-1;FANCD2OS,intron_variant,,ENST00000431315,,n.71-3988A>G,MODIFIER,,,,-1;FANCD2,intron_variant,,ENST00000470028,,n.354+63T>C,MODIFIER,,,,1;FANCD2OS,upstream_gene_variant,,ENST00000436517,,,MODIFIER,,,,-1;FANCD2,intron_variant,,ENST00000421731,,c.*437+63T>C,MODIFIER,,,,1 4437/5219 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 96 4774e843-682e-4098-82eb-675e81205987 74 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS FANCD2,intron_variant,,ENST00000470028.1,n.354+63T>C,MODIFIER,;FANCD2,non_coding_transcript_exon_variant,,ENST00000683312.1,n.3895T>C,MODIFIER,;FANCD2OS,intron_variant,,ENST00000524279.1,c.*43+5320A>G,MODIFIER,;FANCD2OS,intron_variant,,ENST00000431315.5,n.71-3988A>G,MODIFIER,;FANCD2,intron_variant,NMD_transcript_variant,,ENST00000421731.5,c.*437+63T>C,MODIFIER,;FANCD2,non_coding_transcript_exon_variant,,ENST00000683263.1,n.3343T>C,MODIFIER,;FANCD2,non_coding_transcript_exon_variant,,ENST00000681997.1,n.3428T>C,MODIFIER,;FANCD2,intron_variant,,ENST00000419585.5,c.4281+63T>C,MODIFIER,;FANCD2,intron_variant,,ENST00000675286.1,c.4281+63T>C,MODIFIER,YES;FANCD2,intron_variant,,ENST00000676013.1,c.4170+63T>C,MODIFIER,;FANCD2,synonymous_variant,p.S1448=,ENST00000287647.7,c.4344T>C,LOW, +CCN4 8840 BI GRCh38 8 133227643 133227643 + missense_variant Missense_Mutation SNP G G A TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 47 22 c.1037G>A p.Cys346Tyr p.C346Y ENST00000250160.11 NM_003882.4 346 tGt/tAt 5/5 P1 A C/Y protein_coding YES CCDS6371.1 1037/1104 GAGCTGTAGGA COSM5884654;COSM5884655 PROSITE_profiles:PS01225;PANTHER:PTHR11348:SF4;PANTHER:PTHR11348;PROSITE_patterns:PS01185;Pfam:PF00007;PIRSF:PIRSF036495;SMART:SM00041 ENSP00000250160 5/5 COSV51532731 ENST00000250160 Transcript ENSG00000104415 HGNC:12769 MODERATE NM_003882.4 missense_variant 1 1.0 probably_damaging(1) Unknown deleterious(0) 1 O95388.172 CCN4 HGNC 1 1.0 UPI00000359FE O95388-1 SNV CCN4,missense_variant,p.C346Y,ENST00000250160,NM_003882.4,c.1037G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;CCN4,missense_variant,p.C259Y,ENST00000220856,NM_080838.3,c.776G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;CCN4,missense_variant,p.C101Y,ENST00000519433,NM_001204870.2,c.302G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;CCN4,3_prime_UTR_variant,,ENST00000517423,NM_001204869.2,c.*114G>A,MODIFIER,,,,1;CCN4,3_prime_UTR_variant,,ENST00000377862,,c.*385G>A,MODIFIER,,,,1 1143/5190 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 55 4774e843-682e-4098-82eb-675e81205987 69 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS CCN4,missense_variant,p.C259Y,ENST00000220856.6,c.776G>A,MODERATE,;CCN4,3_prime_UTR_variant,,ENST00000517423.5,c.*114G>A,MODIFIER,;CCN4,missense_variant,p.C101Y,ENST00000519433.1,c.302G>A,MODERATE,;CCN4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000377862.6,c.*385G>A,MODIFIER,;CCN4,missense_variant,p.C346Y,ENST00000250160.11,c.1037G>A,MODERATE,YES +MSS51 118490 BI GRCh38 10 73426684 73426684 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 57 42 c.425G>A p.Trp142Ter p.W142* ENST00000299432.7 NM_001024593.2 142 tGg/tAg 4/7 P1 T W/* protein_coding YES CCDS31221.1 425/1383 CGGGCCAGTCT PROSITE_profiles:PS50865;PANTHER:PTHR46920:SF1;PANTHER:PTHR46920;PROSITE_patterns:PS01360;Gene3D:3.30.60.180;Pfam:PF01753;Superfamily:SSF144232 ENSP00000299432 4/7 ENST00000299432 Transcript ENSG00000166343 HGNC:21000 HIGH NM_001024593.2 stop_gained 1.0 Unknown Q4VC12.106 MSS51 HGNC -1 1.0 UPI00004CA0F2 Q4VC12-1 SNV MSS51,stop_gained,p.W142*,ENST00000299432,NM_001024593.2,c.425G>A,HIGH,YES,,,-1;MSS51,stop_gained,p.W142*,ENST00000372912,,c.425G>A,HIGH,,,,-1;MSS51,stop_gained,p.W142*,ENST00000487126,,c.425G>A,HIGH,,,,-1;RPL26P6,upstream_gene_variant,,ENST00000440913,,,MODIFIER,YES,,,-1 491/2423 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 95 4774e843-682e-4098-82eb-675e81205987 100 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS MSS51,stop_gained,p.W142*,ENST00000372912.1,c.425G>A,HIGH,;MSS51,stop_gained,NMD_transcript_variant,p.W142*,ENST00000487126.5,c.425G>A,HIGH,;MSS51,stop_gained,p.W142*,ENST00000299432.7,c.425G>A,HIGH,YES +ALDH2 217 BI GRCh38 12 111792646 111792646 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 10 6 c.947G>C p.Gly316Ala p.G316A ENST00000261733.7 NM_000690.4 316 gGc/gCc 9/13 P1 C G/A protein_coding YES CCDS9155.1 947/1554 CCAGGGCCAGT PDB-ENSP_mappings:1cw3.A;PDB-ENSP_mappings:1cw3.B;PDB-ENSP_mappings:1cw3.C;PDB-ENSP_mappings:1cw3.D;PDB-ENSP_mappings:1cw3.E;PDB-ENSP_mappings:1cw3.F;PDB-ENSP_mappings:1cw3.G;PDB-ENSP_mappings:1cw3.H;PDB-ENSP_mappings:1nzw.A;PDB-ENSP_mappings:1nzw.B;PDB-ENSP_mappings:1nzw.C;PDB-ENSP_mappings:1nzw.D;PDB-ENSP_mappings:1nzw.E;PDB-ENSP_mappings:1nzw.F;PDB-ENSP_mappings:1nzw.G;PDB-ENSP_mappings:1nzw.H;PDB-ENSP_mappings:1nzx.A;PDB-ENSP_mappings:1nzx.B;PDB-ENSP_mappings:1nzx.C;PDB-ENSP_mappings:1nzx.D;PDB-ENSP_mappings:1nzx.E;PDB-ENSP_mappings:1nzx.F;PDB-ENSP_mappings:1nzx.G;PDB-ENSP_mappings:1nzx.H;PDB-ENSP_mappings:1nzz.A;PDB-ENSP_mappings:1nzz.B;PDB-ENSP_mappings:1nzz.C;PDB-ENSP_mappings:1nzz.D;PDB-ENSP_mappings:1nzz.E;PDB-ENSP_mappings:1nzz.F;PDB-ENSP_mappings:1nzz.G;PDB-ENSP_mappings:1nzz.H;PDB-ENSP_mappings:1o00.A;PDB-ENSP_mappings:1o00.B;PDB-ENSP_mappings:1o00.C;PDB-ENSP_mappings:1o00.D;PDB-ENSP_mappings:1o00.E;PDB-ENSP_mappings:1o00.F;PDB-ENSP_mappings:1o00.G;PDB-ENSP_mappings:1o00.H;PDB-ENSP_mappings:1o01.A;PDB-ENSP_mappings:1o01.B;PDB-ENSP_mappings:1o01.C;PDB-ENSP_mappings:1o01.D;PDB-ENSP_mappings:1o01.E;PDB-ENSP_mappings:1o01.F;PDB-ENSP_mappings:1o01.G;PDB-ENSP_mappings:1o01.H;PDB-ENSP_mappings:1o02.A;PDB-ENSP_mappings:1o02.B;PDB-ENSP_mappings:1o02.C;PDB-ENSP_mappings:1o02.D;PDB-ENSP_mappings:1o02.E;PDB-ENSP_mappings:1o02.F;PDB-ENSP_mappings:1o02.G;PDB-ENSP_mappings:1o02.H;PDB-ENSP_mappings:1o04.A;PDB-ENSP_mappings:1o04.B;PDB-ENSP_mappings:1o04.C;PDB-ENSP_mappings:1o04.D;PDB-ENSP_mappings:1o04.E;PDB-ENSP_mappings:1o04.F;PDB-ENSP_mappings:1o04.G;PDB-ENSP_mappings:1o04.H;PDB-ENSP_mappings:1o05.A;PDB-ENSP_mappings:1o05.B;PDB-ENSP_mappings:1o05.C;PDB-ENSP_mappings:1o05.D;PDB-ENSP_mappings:1o05.E;PDB-ENSP_mappings:1o05.F;PDB-ENSP_mappings:1o05.G;PDB-ENSP_mappings:1o05.H;PDB-ENSP_mappings:1zum.A;PDB-ENSP_mappings:1zum.B;PDB-ENSP_mappings:1zum.C;PDB-ENSP_mappings:1zum.D;PDB-ENSP_mappings:1zum.E;PDB-ENSP_mappings:1zum.F;PDB-ENSP_mappings:1zum.G;PDB-ENSP_mappings:1zum.H;PDB-ENSP_mappings:1zum.I;PDB-ENSP_mappings:1zum.J;PDB-ENSP_mappings:1zum.K;PDB-ENSP_mappings:1zum.L;PDB-ENSP_mappings:2onm.A;PDB-ENSP_mappings:2onm.B;PDB-ENSP_mappings:2onm.C;PDB-ENSP_mappings:2onm.D;PDB-ENSP_mappings:2onm.E;PDB-ENSP_mappings:2onm.F;PDB-ENSP_mappings:2onm.G;PDB-ENSP_mappings:2onm.H;PDB-ENSP_mappings:2onm.I;PDB-ENSP_mappings:2onm.J;PDB-ENSP_mappings:2onm.K;PDB-ENSP_mappings:2onm.L;PDB-ENSP_mappings:2onn.A;PDB-ENSP_mappings:2onn.B;PDB-ENSP_mappings:2onn.C;PDB-ENSP_mappings:2onn.D;PDB-ENSP_mappings:2onn.E;PDB-ENSP_mappings:2onn.F;PDB-ENSP_mappings:2onn.G;PDB-ENSP_mappings:2onn.H;PDB-ENSP_mappings:2ono.A;PDB-ENSP_mappings:2ono.B;PDB-ENSP_mappings:2ono.C;PDB-ENSP_mappings:2ono.D;PDB-ENSP_mappings:2ono.E;PDB-ENSP_mappings:2ono.F;PDB-ENSP_mappings:2ono.G;PDB-ENSP_mappings:2ono.H;PDB-ENSP_mappings:2onp.A;PDB-ENSP_mappings:2onp.B;PDB-ENSP_mappings:2onp.C;PDB-ENSP_mappings:2onp.D;PDB-ENSP_mappings:2onp.E;PDB-ENSP_mappings:2onp.F;PDB-ENSP_mappings:2onp.G;PDB-ENSP_mappings:2onp.H;PDB-ENSP_mappings:2vle.A;PDB-ENSP_mappings:2vle.B;PDB-ENSP_mappings:2vle.C;PDB-ENSP_mappings:2vle.D;PDB-ENSP_mappings:2vle.E;PDB-ENSP_mappings:2vle.F;PDB-ENSP_mappings:2vle.G;PDB-ENSP_mappings:2vle.H;PDB-ENSP_mappings:3inj.A;PDB-ENSP_mappings:3inj.B;PDB-ENSP_mappings:3inj.C;PDB-ENSP_mappings:3inj.D;PDB-ENSP_mappings:3inj.E;PDB-ENSP_mappings:3inj.F;PDB-ENSP_mappings:3inj.G;PDB-ENSP_mappings:3inj.H;PDB-ENSP_mappings:3inl.A;PDB-ENSP_mappings:3inl.B;PDB-ENSP_mappings:3inl.C;PDB-ENSP_mappings:3inl.D;PDB-ENSP_mappings:3inl.E;PDB-ENSP_mappings:3inl.F;PDB-ENSP_mappings:3inl.G;PDB-ENSP_mappings:3inl.H;PDB-ENSP_mappings:3n80.A;PDB-ENSP_mappings:3n80.B;PDB-ENSP_mappings:3n80.C;PDB-ENSP_mappings:3n80.D;PDB-ENSP_mappings:3n80.E;PDB-ENSP_mappings:3n80.F;PDB-ENSP_mappings:3n80.G;PDB-ENSP_mappings:3n80.H;PDB-ENSP_mappings:3n81.A;PDB-ENSP_mappings:3n81.B;PDB-ENSP_mappings:3n81.C;PDB-ENSP_mappings:3n81.D;PDB-ENSP_mappings:3n81.E;PDB-ENSP_mappings:3n81.F;PDB-ENSP_mappings:3n81.G;PDB-ENSP_mappings:3n81.H;PDB-ENSP_mappings:3n82.A;PDB-ENSP_mappings:3n82.B;PDB-ENSP_mappings:3n82.C;PDB-ENSP_mappings:3n82.D;PDB-ENSP_mappings:3n82.E;PDB-ENSP_mappings:3n82.F;PDB-ENSP_mappings:3n82.G;PDB-ENSP_mappings:3n82.H;PDB-ENSP_mappings:3n83.A;PDB-ENSP_mappings:3n83.B;PDB-ENSP_mappings:3n83.C;PDB-ENSP_mappings:3n83.D;PDB-ENSP_mappings:3n83.E;PDB-ENSP_mappings:3n83.F;PDB-ENSP_mappings:3n83.G;PDB-ENSP_mappings:3n83.H;PDB-ENSP_mappings:3sz9.A;PDB-ENSP_mappings:3sz9.B;PDB-ENSP_mappings:3sz9.C;PDB-ENSP_mappings:3sz9.D;PDB-ENSP_mappings:3sz9.E;PDB-ENSP_mappings:3sz9.F;PDB-ENSP_mappings:3sz9.G;PDB-ENSP_mappings:3sz9.H;PDB-ENSP_mappings:4fqf.A;PDB-ENSP_mappings:4fqf.B;PDB-ENSP_mappings:4fqf.C;PDB-ENSP_mappings:4fqf.D;PDB-ENSP_mappings:4fr8.A;PDB-ENSP_mappings:4fr8.B;PDB-ENSP_mappings:4fr8.C;PDB-ENSP_mappings:4fr8.D;PDB-ENSP_mappings:4fr8.E;PDB-ENSP_mappings:4fr8.F;PDB-ENSP_mappings:4fr8.G;PDB-ENSP_mappings:4fr8.H;PDB-ENSP_mappings:4kwf.A;PDB-ENSP_mappings:4kwf.B;PDB-ENSP_mappings:4kwf.C;PDB-ENSP_mappings:4kwf.D;PDB-ENSP_mappings:4kwf.E;PDB-ENSP_mappings:4kwf.F;PDB-ENSP_mappings:4kwf.G;PDB-ENSP_mappings:4kwf.H;PDB-ENSP_mappings:4kwg.A;PDB-ENSP_mappings:4kwg.B;PDB-ENSP_mappings:4kwg.C;PDB-ENSP_mappings:4kwg.D;PDB-ENSP_mappings:4kwg.E;PDB-ENSP_mappings:4kwg.F;PDB-ENSP_mappings:4kwg.G;PDB-ENSP_mappings:4kwg.H;PDB-ENSP_mappings:5l13.A;PDB-ENSP_mappings:5l13.B;PDB-ENSP_mappings:5l13.C;PDB-ENSP_mappings:5l13.D;PDB-ENSP_mappings:5l13.E;PDB-ENSP_mappings:5l13.F;PDB-ENSP_mappings:5l13.G;PDB-ENSP_mappings:5l13.H;CDD:cd07141;PANTHER:PTHR11699:SF233;PANTHER:PTHR11699;PROSITE_patterns:PS00070;Gene3D:3.40.309.10;Pfam:PF00171;Gene3D:3.40.605.10;Superfamily:SSF53720 ENSP00000261733 9/13 ENST00000261733 Transcript 1.0 ENSG00000111275 HGNC:404 MODERATE NM_000690.4 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0.01) P05091.237 ALDH2 HGNC 1 A0A384NPN7.9 1.0 UPI0000129293 P05091-1 SNV ALDH2,missense_variant,p.G316A,ENST00000261733,NM_000690.4,c.947G>C,MODERATE,YES,deleterious(0.01),probably_damaging(1),1;ALDH2,missense_variant,p.G269A,ENST00000416293,NM_001204889.2,c.806G>C,MODERATE,,deleterious(0.01),probably_damaging(0.998),1;AC002996.1,downstream_gene_variant,,ENST00000546840,,,MODIFIER,YES,,,1;ALDH2,missense_variant,p.G13A,ENST00000549106,,c.38G>C,MODERATE,,deleterious(0.02),probably_damaging(1),1;ALDH2,3_prime_UTR_variant,,ENST00000548536,,c.*823G>C,MODIFIER,,,,1 997/9561 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 16 4774e843-682e-4098-82eb-675e81205987 16 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS ALDH2,synonymous_variant,NMD_transcript_variant,p.G12=,ENST00000549106.1,c.36G>C,LOW,;ALDH2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000548536.1,c.*823G>C,MODIFIER,;ALDH2,missense_variant,p.G316A,ENST00000261733.7,c.947G>C,MODERATE,YES;ALDH2,missense_variant,p.G269A,ENST00000416293.7,c.806G>C,MODERATE, +SYNE2 23224 BI GRCh38 14 64219303 64219304 + frameshift_variant Frame_Shift_Ins INS - - C novel TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 31 19 c.19686dup p.Ala6562ArgfsTer10 p.A6562Rfs*10 ENST00000344113.8 NM_015180.6 6562 gcc/gCcc 109/115 P4 C A/AX protein_coding CCDS41963.1 19684-19685/20658 TCAGCGCCATC Gene3D:1.20.58.1940;Pfam:PF00435;PANTHER:PTHR14514;PANTHER:PTHR14514:SF4;SMART:SM00150;Superfamily:SSF46966;CDD:cd00176 ENSP00000341781 109/115 ENST00000344113 Transcript 1.0 ENSG00000054654 HGNC:17084 2.0 HIGH frameshift_variant Unknown Q8WXH0.188 SYNE2 HGNC 1 1.0 UPI00001B0452 Q8WXH0-1 insertion SYNE2,frameshift_variant,p.I6586Hfs*9,ENST00000358025,,c.19755dup,HIGH,YES,,,1;SYNE2,frameshift_variant,p.I6586Hfs*9,ENST00000555002,NM_182914.3,c.19755dup,HIGH,,,,1;SYNE2,frameshift_variant,p.I6563Hfs*9,ENST00000344113,NM_015180.5,c.19686dup,HIGH,,,,1;SYNE2,frameshift_variant,p.I6485Hfs*9,ENST00000357395,,c.19452dup,HIGH,,,,1;SYNE2,frameshift_variant,p.I6479Hfs*9,ENST00000554584,,c.19434dup,HIGH,,,,1;SYNE2,frameshift_variant,p.I220Hfs*9,ENST00000458046,NM_182913.3&NM_182910.2,c.657dup,HIGH,,,,1;SYNE2,frameshift_variant,p.I197Hfs*?,ENST00000557084,,c.588dup,HIGH,,,,1;ESR2,intron_variant,,ENST00000556275,,c.1406+15666dup,MODIFIER,,,,-1;SYNE2,non_coding_transcript_exon_variant,,ENST00000555022,,n.1520dup,MODIFIER,,,,1;SYNE2,3_prime_UTR_variant,,ENST00000555612,,c.*1465dup,MODIFIER,,,,1;SYNE2,3_prime_UTR_variant,,ENST00000553289,,c.*1561dup,MODIFIER,,,,1;SYNE2,non_coding_transcript_exon_variant,,ENST00000394768,,n.9219dup,MODIFIER,,,,1;SYNE2,non_coding_transcript_exon_variant,,ENST00000554805,,n.1605dup,MODIFIER,,,,1;SYNE2,non_coding_transcript_exon_variant,,ENST00000441438,,n.1169dup,MODIFIER,,,,1;SYNE2,non_coding_transcript_exon_variant,,ENST00000554928,,n.379dup,MODIFIER,,,,1;SYNE2,downstream_gene_variant,,ENST00000557307,,,MODIFIER,,,,1 19896-19897/21777 mutect2;pindel;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 69 4774e843-682e-4098-82eb-675e81205987 50 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS SYNE2,non_coding_transcript_exon_variant,,ENST00000554928.1,n.377_378insC,MODIFIER,;SYNE2,non_coding_transcript_exon_variant,,ENST00000441438.2,n.1167_1168insC,MODIFIER,;SYNE2,frameshift_variant,p.A219Rfs*10,ENST00000458046.6,c.657dup,HIGH,;SYNE2,frameshift_variant,p.A196Rfs,ENST00000557084.1,c.588dup,HIGH,;SYNE2,non_coding_transcript_exon_variant,,ENST00000554805.6,n.1603_1604insC,MODIFIER,;SYNE2,non_coding_transcript_exon_variant,,ENST00000555022.5,n.1518_1519insC,MODIFIER,;SYNE2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000553289.5,c.*1559_*1560insC,MODIFIER,;SYNE2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000555612.5,c.*1463_*1464insC,MODIFIER,;ESR2,intron_variant,,ENST00000556275.5,c.1406+15666_1406+15667insG,MODIFIER,;SYNE2,non_coding_transcript_exon_variant,,ENST00000394768.6,n.9217_9218insC,MODIFIER,;SYNE2,frameshift_variant,p.A6478Rfs*10,ENST00000554584.5,c.19434dup,HIGH,;SYNE2,frameshift_variant,p.A6585Rfs*10,ENST00000555002.6,c.19755dup,HIGH,YES;SYNE2,frameshift_variant,p.A6585Rfs*10,ENST00000358025.7,c.19755dup,HIGH,;SYNE2,frameshift_variant,p.A6562Rfs*10,ENST00000344113.8,c.19686dup,HIGH, +SNX20 124460 BI GRCh38 16 50673468 50673468 + missense_variant Missense_Mutation SNP G G A rs757162450 TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 34 29 c.889C>T p.Arg297Trp p.R297W ENST00000330943.9 NM_182854.4 297 Cgg/Tgg 4/4 P1 A R/W protein_coding YES CCDS10745.1 889/951 CCTCCGGAGCT COSM4728815 PANTHER:PTHR20939:SF1;PANTHER:PTHR20939;Gene3D:1.25.40.10 ENSP00000332062 4/4 rs757162450;COSV56056827 ENST00000330943 Transcript ENSG00000167208 HGNC:30390 MODERATE NM_182854.4 3.437e-05 gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.826) Unknown deleterious(0.01) 0;1 Q7Z614.131 SNX20 HGNC -1 1.0 UPI000004348D Q7Z614-1 SNV SNX20,missense_variant,p.R297W,ENST00000330943,NM_182854.4,c.889C>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.826),-1;SNX20,missense_variant,p.R133W,ENST00000610485,,c.397C>T,MODERATE,,deleterious(0.02),possibly_damaging(0.644),-1;SNX20,intron_variant,,ENST00000300590,NM_153337.3,c.282+2302C>T,MODIFIER,,,,-1;SNX20,intron_variant,,ENST00000423026,NM_001144972.2,c.282+2302C>T,MODIFIER,,,,-1;SNX20,intron_variant,,ENST00000568993,,c.282+2302C>T,MODIFIER,,,,-1;AC007608.3,downstream_gene_variant,,ENST00000570167,,,MODIFIER,YES,,,1;AC007608.3,downstream_gene_variant,,ENST00000570241,,,MODIFIER,,,,1 1021/2860 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 4.248e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.437e-05 6.758859854016919e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 75 4774e843-682e-4098-82eb-675e81205987 63 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS SNX20,missense_variant,p.R297W,ENST00000330943.9,c.889C>T,MODERATE,YES;SNX20,intron_variant,NMD_transcript_variant,,ENST00000568993.5,c.282+2302C>T,MODIFIER,;SNX20,intron_variant,,ENST00000423026.6,c.282+2302C>T,MODIFIER,;SNX20,intron_variant,,ENST00000300590.7,c.282+2302C>T,MODIFIER, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EH-01A TCGA-V4-A9EH-10A Somatic 20 25 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 5e54122f-1c4d-45cc-8842-cd1c1df0eed8 0 59 4774e843-682e-4098-82eb-675e81205987 46 053ccb20-48a8-49d6-8da2-5a0d567e84fc SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +LRRIQ3 127255 BI GRCh38 1 74041481 74041481 + stop_gained Nonsense_Mutation SNP G G A rs750155109 TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 53 33 c.1450C>T p.Arg484Ter p.R484* ENST00000354431.9 NM_001322315.2 484 Cga/Tga 7/8 P4 A R/* protein_coding YES CCDS41350.1 1450/1875 TTGTCGTAAAC PANTHER:PTHR46723 ENSP00000346414 7/8 rs750155109;COSV63048740 ENST00000354431 Transcript ENSG00000162620 HGNC:28318 HIGH NM_001105659.2 0.0001293 gnomAD_AFR stop_gained 0;1 1.0 Unknown 0;1 A6PVS8.101 LRRIQ3 HGNC -1 5.0 UPI000155D493 A6PVS8-1 SNV LRRIQ3,stop_gained,p.R484*,ENST00000354431,NM_001322315.2&NM_001105659.2,c.1450C>T,HIGH,YES,,,-1;LRRIQ3,stop_gained,p.R484*,ENST00000395089,,c.1450C>T,HIGH,,,,-1;LRRIQ3,intron_variant,,ENST00000417067,,c.131-14512C>T,MODIFIER,,,,-1;LRRIQ3,intron_variant,,ENST00000415760,,c.*2703+210C>T,MODIFIER,,,,-1 1631/2854 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 2.825e-05 0.0001293 0.0 0.0 0.0 0.0 1.786e-05 0.0 9.837e-05 2.7066900656791404e-05 9.736150241224097e-05 0.0 0.0 0.0 0.0 0.0 afr 9.736150241224097e-05 0.0 0.0 0.0 0.0 0 92 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 86 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS LRRIQ3,intron_variant,NMD_transcript_variant,,ENST00000415760.5,c.*2703+210C>T,MODIFIER,;LRRIQ3,stop_gained,p.R484*,ENST00000354431.9,c.1450C>T,HIGH,YES;LRRIQ3,intron_variant,,ENST00000417067.5,c.131-14512C>T,MODIFIER,;LRRIQ3,stop_gained,p.R484*,ENST00000395089.5,c.1450C>T,HIGH, +SPTA1 6708 BI GRCh38 1 158635968 158635968 + missense_variant Missense_Mutation SNP G G A rs375618954 TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 93 55 c.5377C>T p.Arg1793Trp p.R1793W ENST00000643759.2 NM_003126.4 1793 Cgg/Tgg 38/52 P1 A R/W protein_coding YES CCDS41423.1 5377/7260 CAGCCGCAACT Gene3D:1.20.58.60;PDB-ENSP_mappings:5j4o.A;Pfam:PF00435;PANTHER:PTHR11915;PANTHER:PTHR11915:SF431;SMART:SM00150;Superfamily:SSF46966;Superfamily:SSF46966;CDD:cd00176;CDD:cd00176 ENSP00000495214 0.0 0.0001202 38/52 rs375618954 ENST00000643759 Transcript 1.0 ENSG00000163554 HGNC:11272 MODERATE NM_003126.4 0.0001202 EA missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) P02549.231 SPTA1 HGNC -1 UPI0000458906 P02549-1 SNV SPTA1,missense_variant,p.R1793W,ENST00000643759,NM_003126.4,c.5377C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;SPTA1,upstream_gene_variant,,ENST00000461624,,,MODIFIER,,,,-1;SPTA1,downstream_gene_variant,,ENST00000465741,,,MODIFIER,,,,-1 5575/8018 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 3.609e-05 0.0 0.0 0.0 0.0001113 0.0 5.302e-05 0.0 3.268e-05 3.381349961273372e-05 4.866889867116697e-05 0.0 0.0 0.0 0.0002018569939536 0.0 afr 4.866889867116697e-05 0.0 3.086229844484478e-05 0.0 0.0 0 103 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 148 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS SPTA1,missense_variant,p.R1793W,ENST00000643759.2,c.5377C>T,MODERATE,YES +STK36 27148 BI GRCh38 2 218696848 218696848 + intron_variant Intron SNP G G A TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 52 41 c.2587-191G>A ENST00000295709.8 NM_015690.5 P1 A protein_coding YES CCDS2421.1 CACATGAGTTG ENSP00000295709 COSV99830988 ENST00000295709 Transcript 1.0 ENSG00000163482 HGNC:17209 MODIFIER 22/26 NM_015690.5 intron_variant 1 1.0 Unknown 1 Q9NRP7.175 STK36 HGNC 1 A0A140VJW1.25 1.0 UPI00000342FC Q9NRP7-1 SNV STK36,intron_variant,,ENST00000295709,NM_015690.5,c.2587-191G>A,MODIFIER,YES,,,1;STK36,intron_variant,,ENST00000392105,NM_001243313.2,c.2524-191G>A,MODIFIER,,,,1;STK36,intron_variant,,ENST00000440309,NM_001369423.1,c.2587-191G>A,MODIFIER,,,,1;STK36,non_coding_transcript_exon_variant,,ENST00000473681,,n.434G>A,MODIFIER,,,,1;STK36,intron_variant,,ENST00000419433,,c.74-191G>A,MODIFIER,,,,1;STK36,intron_variant,,ENST00000486644,,n.578+93G>A,MODIFIER,,,,1;STK36,upstream_gene_variant,,ENST00000462031,,,MODIFIER,,,,1;STK36,downstream_gene_variant,,ENST00000480709,,,MODIFIER,,,,1;STK36,downstream_gene_variant,,ENST00000492486,,,MODIFIER,,,,1 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 65 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 93 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS STK36,intron_variant,NMD_transcript_variant,,ENST00000419433.1,c.74-191G>A,MODIFIER,;STK36,non_coding_transcript_exon_variant,,ENST00000473681.1,n.434G>A,MODIFIER,;STK36,intron_variant,,ENST00000486644.1,n.578+93G>A,MODIFIER,;STK36,intron_variant,,ENST00000440309.5,c.2587-191G>A,MODIFIER,;STK36,intron_variant,,ENST00000295709.8,c.2587-191G>A,MODIFIER,YES;STK36,intron_variant,,ENST00000392105.7,c.2524-191G>A,MODIFIER, +PREX2 80243 BI GRCh38 8 68080495 68080495 + synonymous_variant Silent SNP G G T TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 63 47 c.1695G>T p.Ser565= p.S565= ENST00000288368.5 NM_024870.4 565 tcG/tcT 16/40 P1 T S protein_coding YES CCDS6201.1 1695/4821 TTTTCGGATGA PROSITE_profiles:PS50186;CDD:cd04440;PANTHER:PTHR22829:SF1;PANTHER:PTHR22829;Gene3D:1.10.10.10;SMART:SM00049;Superfamily:SSF46785 ENSP00000288368 16/40 COSV55752115 ENST00000288368 Transcript 1.0 ENSG00000046889 HGNC:22950 LOW NM_024870.4 synonymous_variant 1 1.0 Unknown 1 Q70Z35.139 PREX2 HGNC 1 1.0 UPI0000375435 Q70Z35-1 SNV PREX2,synonymous_variant,p.S565=,ENST00000288368,NM_024870.4,c.1695G>T,LOW,YES,,,1;PREX2,non_coding_transcript_exon_variant,,ENST00000529398,NM_025170.6,n.1722G>T,MODIFIER,,,,1;PREX2,non_coding_transcript_exon_variant,,ENST00000517617,,n.1406G>T,MODIFIER,,,,1;AC011853.2,downstream_gene_variant,,ENST00000526901,,,MODIFIER,YES,,,-1 2044/10824 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 42 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 110 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS PREX2,non_coding_transcript_exon_variant,,ENST00000517617.1,n.1406G>T,MODIFIER,;PREX2,non_coding_transcript_exon_variant,,ENST00000529398.5,n.1722G>T,MODIFIER,;PREX2,synonymous_variant,p.S565=,ENST00000288368.5,c.1695G>T,LOW,YES +MYH6 4624 BI GRCh38 14 23393729 23393746 + inframe_deletion In_Frame_Del DEL GTCCTTCTTGAGCTCTGA GTCCTTCTTGAGCTCTGA - novel TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 70 28 c.2848_2865del p.Asp955_Leu961delinsGlu p.D955_L961delinsE ENST00000405093.9 NM_002471.4 950 TCAGAGCTCAAGAAGGAC/- 22/39 P1 - SELKKD/- protein_coding YES CCDS9600.1 2848-2865/5820 ATCAATGTCCTTCTTGAGCTCTGAGCACT Gene3D:1.20.5.1050;Coiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR45615;PANTHER:PTHR45615:SF11;Superfamily:SSF90257 ENSP00000386041 22/39 ENST00000405093 Transcript 1.0 ENSG00000197616 HGNC:7576 MODERATE NM_002471.4 inframe_deletion 1.0 Unknown P13533.210 MYH6 HGNC -1 5.0 UPI0000160969 deletion MYH6,inframe_deletion,p.S950_D955del,ENST00000405093,NM_002471.4,c.2848_2865del,MODERATE,YES,,,-1 2915-2932/5940 mutect2;pindel;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 79 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 98 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS MYH6,inframe_deletion,p.D955_L961delinsE,ENST00000405093.9,c.2848_2865del,MODERATE,YES +SEC14L1 6397 BI GRCh38 17 77212108 77212108 + synonymous_variant Silent SNP C C T novel TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 148 79 c.1770C>T p.Asn590= p.N590= ENST00000430767.8 NM_001204410.2 590 aaC/aaT 16/18 T N protein_coding CCDS11752.1 1770/2148 GGGAACAATGT PROSITE_profiles:PS50866;PANTHER:PTHR23324;PANTHER:PTHR23324:SF51;Superfamily:SSF101576 ENSP00000408169 16/18 ENST00000430767 Transcript ENSG00000129657 HGNC:10698 LOW synonymous_variant Unknown Q92503.156 SEC14L1 HGNC 1 2.0 UPI000013D328 Q92503-1 SNV SEC14L1,splice_region_variant,,ENST00000588488,,c.334+8C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N590=,ENST00000436233,NM_001143998.2&NM_001143999.2&NM_003003.4,c.1770C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N590=,ENST00000430767,NM_001204410.2,c.1770C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N590=,ENST00000392476,NM_001204408.2,c.1770C>T,LOW,YES,,,1;SEC14L1,synonymous_variant,p.N590=,ENST00000443798,NM_001039573.3,c.1770C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N556=,ENST00000591437,,c.1668C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N590=,ENST00000585618,,c.1770C>T,LOW,,,,1;SEC14L1,synonymous_variant,p.N556=,ENST00000431431,NM_001144001.2,c.1668C>T,LOW,,,,1;SEC14L1,upstream_gene_variant,,ENST00000588721,,,MODIFIER,,,,1;SEC14L1,non_coding_transcript_exon_variant,,ENST00000587491,,n.2248C>T,MODIFIER,,,,1;SEC14L1,non_coding_transcript_exon_variant,,ENST00000591413,,n.372C>T,MODIFIER,,,,1 2126/5283 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 188 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 228 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS SEC14L1,non_coding_transcript_exon_variant,,ENST00000591413.1,n.372C>T,MODIFIER,;SEC14L1,non_coding_transcript_exon_variant,,ENST00000587491.5,n.2248C>T,MODIFIER,;SEC14L1,splice_region_variant,intron_variant,,ENST00000588488.1,c.334+8C>T,LOW,;SEC14L1,synonymous_variant,p.N556=,ENST00000431431.6,c.1668C>T,LOW,;SEC14L1,synonymous_variant,p.N556=,ENST00000591437.5,c.1668C>T,LOW,;SEC14L1,synonymous_variant,p.N590=,ENST00000443798.8,c.1770C>T,LOW,;SEC14L1,synonymous_variant,p.N590=,ENST00000436233.9,c.1770C>T,LOW,YES;SEC14L1,synonymous_variant,p.N590=,ENST00000585618.5,c.1770C>T,LOW,;SEC14L1,synonymous_variant,p.N590=,ENST00000430767.8,c.1770C>T,LOW,;SEC14L1,synonymous_variant,p.N590=,ENST00000392476.6,c.1770C>T,LOW, +EPG5 57724 BI GRCh38 18 45954996 45954996 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 42 46 c.406A>G p.Lys136Glu p.K136E ENST00000282041.11 NM_020964.3 136 Aag/Gag 2/44 P1 C K/E protein_coding YES CCDS11926.2 406/7740 GTTCTTGGGGG PANTHER:PTHR31139;PANTHER:PTHR31139:SF4 ENSP00000282041 2/44 ENST00000282041 Transcript 1.0 ENSG00000152223 HGNC:29331 MODERATE NM_020964.3 missense_variant 1.0 benign(0.001) Unknown tolerated_low_confidence(0.41) Q9HCE0.120 EPG5 HGNC -1 1.0 UPI00004F6F8A Q9HCE0-1 SNV EPG5,missense_variant,p.K136E,ENST00000282041,NM_020964.3,c.406A>G,MODERATE,YES,tolerated_low_confidence(0.41),benign(0.001),-1;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,,n.441A>G,MODIFIER,,,,-1 496/12688 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 70 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 88 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS EPG5,non_coding_transcript_exon_variant,,ENST00000587974.1,n.441A>G,MODIFIER,;EPG5,missense_variant,p.K136E,ENST00000696490.1,c.406A>G,MODERATE,;EPG5,missense_variant,NMD_transcript_variant,p.K136E,ENST00000696482.1,c.406A>G,MODERATE,;EPG5,missense_variant,NMD_transcript_variant,p.K136E,ENST00000696485.1,c.406A>G,MODERATE,;EPG5,missense_variant,p.K136E,ENST00000696489.1,c.406A>G,MODERATE,;EPG5,missense_variant,p.K136E,ENST00000282041.11,c.406A>G,MODERATE,YES;EPG5,missense_variant,NMD_transcript_variant,p.K136E,ENST00000587884.2,c.406A>G,MODERATE,;EPG5,missense_variant,NMD_transcript_variant,p.K136E,ENST00000590884.6,c.406A>G,MODERATE,;EPG5,missense_variant,NMD_transcript_variant,p.K136E,ENST00000592272.6,c.406A>G,MODERATE,;EPG5,missense_variant,p.K136E,ENST00000696484.1,c.406A>G,MODERATE,;EPG5,missense_variant,p.K136E,ENST00000696483.1,c.406A>G,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 45 26 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 90 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 71 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +MORC3 23515 BI GRCh38 21 36360005 36360005 + missense_variant Missense_Mutation SNP G G A TCGA-VD-AA8N-01A TCGA-VD-AA8N-10A Somatic 83 65 c.1259G>A p.Arg420Gln p.R420Q ENST00000400485.6 NM_001320446.2 420 cGg/cAg 11/17 P1 A R/Q protein_coding YES CCDS42924.1 1259/2820 GTGGCGGAAAT COSM245749 PDB-ENSP_mappings:4qq4.A;PDB-ENSP_mappings:4qq4.B;PDB-ENSP_mappings:5svi.A;PDB-ENSP_mappings:5svi.B;PDB-ENSP_mappings:5svx.A;PDB-ENSP_mappings:5svy.A;PDB-ENSP_mappings:6o1e.A;PDB-ENSP_mappings:6o5w.A;Gene3D:3.30.40.100;Pfam:PF07496;PANTHER:PTHR23336:SF17;PANTHER:PTHR23336;PROSITE_profiles:PS51050 ENSP00000383333 11/17 COSV68203612 ENST00000400485 Transcript ENSG00000159256 HGNC:23572 MODERATE NM_015358.3 missense_variant 1 1.0 probably_damaging(0.985) Unknown deleterious(0) 1 Q14149.150 MORC3 HGNC 1 1.0 UPI0000167F94 SNV MORC3,missense_variant,p.R420Q,ENST00000400485,NM_001320446.1&NM_001320445.1&NM_015358.3,c.1259G>A,MODERATE,YES,deleterious(0),probably_damaging(0.985),1;MORC3,non_coding_transcript_exon_variant,,ENST00000487909,,n.1220G>A,MODIFIER,,,,1;MORC3,non_coding_transcript_exon_variant,,ENST00000485299,,n.643G>A,MODIFIER,,,,1;MORC3,upstream_gene_variant,,ENST00000484028,,,MODIFIER,,,,1;AP000692.1,upstream_gene_variant,,ENST00000397184,,,MODIFIER,YES,,,1 1327/4224 muse;mutect2;varscan2 1dbd7b0e-9234-47d9-bdca-5b17f5af619b 0 109 8e1cd1dc-3484-49fa-a696-92d0fbd97f25 149 bfec0266-51ce-481d-8a65-43b605fe5c01 SUCCESS MORC3,non_coding_transcript_exon_variant,,ENST00000485299.1,n.643G>A,MODIFIER,;MORC3,non_coding_transcript_exon_variant,,ENST00000487909.5,n.1220G>A,MODIFIER,;MORC3,missense_variant,p.R420Q,ENST00000400485.6,c.1259G>A,MODERATE,YES +ACTRT2 140625 BI GRCh38 1 3022628 3022628 + synonymous_variant Silent SNP G G A rs771094841 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 29 26 c.942G>A p.Arg314= p.R314= ENST00000378404.4 NM_080431.5 314 cgG/cgA 1/1 P1 A R protein_coding YES CCDS45.1 942/1134 GACCGGCTTCT PANTHER:PTHR11937:SF38;PANTHER:PTHR11937;Gene3D:3.30.420.40;Pfam:PF00022;Gene3D:3.30.420.40;SMART:SM00268;Superfamily:SSF53067 ENSP00000367658 1/1 rs771094841 ENST00000378404 Transcript ENSG00000169717 HGNC:24026 LOW NM_080431.5 synonymous_variant 1.0 Unknown Q8TDY3.125 ACTRT2 HGNC 1 UPI0000070494 SNV ACTRT2,synonymous_variant,p.R314=,ENST00000378404,NM_080431.5,c.942G>A,LOW,YES,,,1 1162/1437 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 78 84a213d6-6138-4e86-98cf-c2748e3c99ed 55 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS ACTRT2,synonymous_variant,p.R314=,ENST00000378404.4,c.942G>A,LOW,YES +GAP43 2596 BI GRCh38 3 115676218 115676218 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 25 20 c.236A>C p.Glu79Ala p.E79A ENST00000305124.11 NM_002045.4 79 gAg/gCg 2/3 P1 C E/A protein_coding CCDS33830.1 236/717 GGTGGAGAAGA Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR10699:SF15;PANTHER:PTHR10699;Pfam:PF06614 ENSP00000305010 2/3 ENST00000305124 Transcript ENSG00000172020 HGNC:4140 MODERATE NM_002045.4 missense_variant benign(0.011) Unknown tolerated(0.1) P17677.198 GAP43 HGNC 1 Q5U058.117 1.0 UPI000012FF84 P17677-1 SNV GAP43,missense_variant,p.E115A,ENST00000393780,NM_001130064.2,c.344A>C,MODERATE,YES,tolerated(0.08),benign(0.031),1;GAP43,missense_variant,p.E79A,ENST00000305124,NM_002045.4,c.236A>C,MODERATE,,tolerated(0.1),benign(0.011),1 416/1498 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 45 84a213d6-6138-4e86-98cf-c2748e3c99ed 45 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS GAP43,missense_variant,p.E115A,ENST00000393780.3,c.344A>C,MODERATE,;GAP43,missense_variant,p.E79A,ENST00000305124.11,c.236A>C,MODERATE,YES +RASA2 5922 BI GRCh38 3 141512270 141512270 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 21 19 c.241A>C p.Lys81Gln p.K81Q ENST00000286364.9 NM_001303245.3 81 Aaa/Caa 2/24 P4 C K/Q protein_coding CCDS3117.1 241/2550 TGGAAAAATCT CDD:cd08401;Gene3D:2.60.40.150;Pfam:PF00168;SMART:SM00239;Superfamily:SSF49562;PROSITE_profiles:PS50004;PANTHER:PTHR10194;PANTHER:PTHR10194:SF21 ENSP00000286364 2/24 ENST00000286364 Transcript 1.0 ENSG00000155903 HGNC:9872 MODERATE NM_006506.5 missense_variant probably_damaging(0.982) Unknown deleterious(0.03) Q15283.173 RASA2 HGNC 1 1.0 UPI00001351F5 Q15283-2 SNV RASA2,missense_variant,p.K81Q,ENST00000286364,NM_001303245.2&NM_001303246.2&NM_006506.5,c.241A>C,MODERATE,,deleterious(0.03),probably_damaging(0.982),1;RASA2,missense_variant,p.K81Q,ENST00000452898,,c.241A>C,MODERATE,YES,deleterious(0.03),probably_damaging(0.986),1;RASA2,3_prime_UTR_variant,,ENST00000515549,,c.*63A>C,MODIFIER,,,,1 298/5638 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 68 84a213d6-6138-4e86-98cf-c2748e3c99ed 40 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS RASA2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000515549.1,c.*63A>C,MODIFIER,;RASA2,missense_variant,p.K81Q,ENST00000286364.9,c.241A>C,MODERATE,YES +EXOC2 55770 BI GRCh38 6 610103 610103 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 26 19 c.737T>C p.Leu246Pro p.L246P ENST00000230449.9 NM_018303.6 246 cTg/cCg 7/28 P1 G L/P protein_coding YES CCDS34327.1 737/2775 TGTTCAGAACA PANTHER:PTHR13043;PANTHER:PTHR13043:SF1;Pfam:PF15469 ENSP00000230449 7/28 ENST00000230449 Transcript ENSG00000112685 HGNC:24968 MODERATE NM_018303.6 missense_variant 1.0 probably_damaging(0.98) Unknown deleterious(0) Q96KP1.174 EXOC2 HGNC -1 A0A024QZT2.50 1.0 UPI000003E7E3 SNV EXOC2,missense_variant,p.L246P,ENST00000230449,NM_018303.6,c.737T>C,MODERATE,YES,deleterious(0),probably_damaging(0.98),-1 901/4456 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 63 84a213d6-6138-4e86-98cf-c2748e3c99ed 45 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS EXOC2,missense_variant,p.L246P,ENST00000230449.9,c.737T>C,MODERATE,YES +FASTK 10922 BI GRCh38 7 151078941 151078941 + missense_variant Missense_Mutation SNP A A C rs1461067885 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 7 5 c.586T>G p.Leu196Val p.L196V ENST00000297532.11 NM_006712.5 196 Ttg/Gtg 3/10 P1 C L/V protein_coding YES CCDS5918.1 586/1650 CTGCAAAGGGG Low_complexity_(Seg):seg;PANTHER:PTHR21228;PANTHER:PTHR21228:SF4 ENSP00000297532 3/10 rs1461067885 ENST00000297532 Transcript ENSG00000164896 HGNC:24676 MODERATE NM_006712.5 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 benign(0.021) Unknown tolerated(0.28) Q14296.168 FASTK HGNC -1 A0A090N8Z7.36 1.0 UPI0000000CBA Q14296-1 SNV FASTK,missense_variant,p.L196V,ENST00000297532,NM_006712.5,c.586T>G,MODERATE,YES,tolerated(0.28),benign(0.021),-1;FASTK,missense_variant,p.L196V,ENST00000482571,NM_001258461.1,c.586T>G,MODERATE,,tolerated(0.41),benign(0.099),-1;FASTK,missense_variant,p.L196V,ENST00000540185,,c.586T>G,MODERATE,,tolerated(0.16),benign(0.068),-1;FASTK,missense_variant,p.L55V,ENST00000353841,NM_033015.3,c.163T>G,MODERATE,,tolerated(0.45),benign(0.034),-1;TMUB1,downstream_gene_variant,,ENST00000297533,NM_001136044.2,,MODIFIER,,,,-1;TMUB1,downstream_gene_variant,,ENST00000392818,NM_031434.4,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000392826,NM_001199693.1,,MODIFIER,,,,1;SLC4A2,downstream_gene_variant,,ENST00000413384,NM_003040.4,,MODIFIER,,,,1;SLC4A2,downstream_gene_variant,,ENST00000461735,NM_001199694.2,,MODIFIER,,,,1;TMUB1,downstream_gene_variant,,ENST00000462940,,,MODIFIER,,,,-1;TMUB1,downstream_gene_variant,,ENST00000476627,,,MODIFIER,,,,-1;TMUB1,downstream_gene_variant,,ENST00000482202,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000485713,NM_001199692.2,,MODIFIER,YES,,,1;TMUB1,downstream_gene_variant,,ENST00000488752,,,MODIFIER,,,,-1;TMUB1,downstream_gene_variant,,ENST00000492838,,,MODIFIER,,,,-1;TMUB1,downstream_gene_variant,,ENST00000653405,,,MODIFIER,YES,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000489884,,n.667T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000461979,,n.243T>G,MODIFIER,,,,-1;FASTK,intron_variant,,ENST00000478477,,n.432+559T>G,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000482697,,,MODIFIER,,,,1;FASTK,downstream_gene_variant,,ENST00000496663,,,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000467237,,n.1556T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000469237,,n.388T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000466855,,n.439T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000482806,,n.610T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000460980,,n.263T>G,MODIFIER,,,,-1;FASTK,non_coding_transcript_exon_variant,,ENST00000478883,,n.109T>G,MODIFIER,,,,-1;FASTK,upstream_gene_variant,,ENST00000459800,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000460010,,,MODIFIER,,,,1;FASTK,upstream_gene_variant,,ENST00000465272,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000469467,,,MODIFIER,,,,1;SLC4A2,downstream_gene_variant,,ENST00000472204,,,MODIFIER,,,,1;FASTK,upstream_gene_variant,,ENST00000483953,,,MODIFIER,,,,-1;SLC4A2,downstream_gene_variant,,ENST00000677246,,,MODIFIER,,,,1;AC010973.2,upstream_gene_variant,,ENST00000485974,,,MODIFIER,YES,,,-1 629/1794 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 28 84a213d6-6138-4e86-98cf-c2748e3c99ed 12 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS FASTK,non_coding_transcript_exon_variant,,ENST00000478883.1,n.109T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000461979.1,n.243T>G,MODIFIER,;FASTK,intron_variant,,ENST00000478477.1,n.432+559T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000466855.1,n.439T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000482806.5,n.610T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000469237.5,n.388T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000460980.5,n.263T>G,MODIFIER,;FASTK,non_coding_transcript_exon_variant,,ENST00000467237.5,n.1556T>G,MODIFIER,;FASTK,missense_variant,p.L196V,ENST00000482571.2,c.586T>G,MODERATE,;FASTK,missense_variant,p.L55V,ENST00000353841.6,c.163T>G,MODERATE,;FASTK,missense_variant,p.L196V,ENST00000297532.11,c.586T>G,MODERATE,YES;FASTK,non_coding_transcript_exon_variant,,ENST00000489884.5,n.667T>G,MODIFIER, +LMBR1 64327 BI GRCh38 7 156826682 156826682 + stop_gained Nonsense_Mutation SNP G G C rs1233438390 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 16 10 c.242C>G p.Ser81Ter p.S81* ENST00000353442.10 NM_001363412.2 81 tCa/tGa 4/17 P1 C S/* protein_coding CCDS5945.1 242/1473 TGATTGAGAAG Pfam:PF04791;Prints:PR01692;PANTHER:PTHR12625;PANTHER:PTHR12625:SF1;Transmembrane_helices:TMhelix ENSP00000326604 4/17 rs1233438390 ENST00000353442 Transcript 1.0 ENSG00000105983 HGNC:13243 HIGH NM_022458.4 stop_gained Unknown Q8WVP7.125 LMBR1 HGNC -1 1.0 UPI000005340E Q8WVP7-1 SNV LMBR1,stop_gained,p.S81*,ENST00000353442,NM_001363412.2&NM_001363410.2&NM_022458.4,c.242C>G,HIGH,,,,-1;LMBR1,stop_gained,p.S79*,ENST00000415428,NM_001363409.2&NM_001350953.2,c.236C>G,HIGH,YES,,,-1;LMBR1,5_prime_UTR_variant,,ENST00000359422,NM_001350954.2&NM_001350958.2&NM_001350956.2&NM_001350957.2&NM_001363411.2&NM_001350955.2&NM_001363413.2,c.-215C>G,MODIFIER,,,,-1;LMBR1,non_coding_transcript_exon_variant,,ENST00000433968,,n.530C>G,MODIFIER,,,,-1;LMBR1,non_coding_transcript_exon_variant,,ENST00000461469,,n.286C>G,MODIFIER,,,,-1;LMBR1,non_coding_transcript_exon_variant,,ENST00000498034,,n.395C>G,MODIFIER,,,,-1;LMBR1,intron_variant,,ENST00000430278,,n.329+10131C>G,MODIFIER,,,,-1;LMBR1,synonymous_variant,p.L43=,ENST00000434278,,c.129C>G,LOW,,,,-1;LMBR1,3_prime_UTR_variant,,ENST00000454132,,c.*201C>G,MODIFIER,,,,-1;LMBR1,3_prime_UTR_variant,,ENST00000434453,,c.*99C>G,MODIFIER,,,,-1;LMBR1,3_prime_UTR_variant,,ENST00000444719,,c.*64C>G,MODIFIER,,,,-1;LMBR1,3_prime_UTR_variant,,ENST00000414218,,c.*52C>G,MODIFIER,,,,-1;LMBR1,intron_variant,,ENST00000434503,,c.139+10131C>G,MODIFIER,,,,-1 432/7950 muse;mutect2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 32 84a213d6-6138-4e86-98cf-c2748e3c99ed 26 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS LMBR1,non_coding_transcript_exon_variant,,ENST00000433968.5,n.530C>G,MODIFIER,;LMBR1,non_coding_transcript_exon_variant,,ENST00000498034.5,n.395C>G,MODIFIER,;LMBR1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000434453.1,c.*99C>G,MODIFIER,;LMBR1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000414218.1,c.*52C>G,MODIFIER,;LMBR1,non_coding_transcript_exon_variant,,ENST00000461469.5,n.286C>G,MODIFIER,;LMBR1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000444719.5,c.*64C>G,MODIFIER,;LMBR1,synonymous_variant,NMD_transcript_variant,p.L43=,ENST00000434278.5,c.129C>G,LOW,;LMBR1,intron_variant,,ENST00000430278.5,n.329+10131C>G,MODIFIER,;LMBR1,intron_variant,NMD_transcript_variant,,ENST00000434503.5,c.139+10131C>G,MODIFIER,;LMBR1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000454132.5,c.*201C>G,MODIFIER,;LMBR1,stop_gained,p.S79*,ENST00000415428.5,c.236C>G,HIGH,;LMBR1,stop_gained,p.S81*,ENST00000353442.10,c.242C>G,HIGH,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 58 25 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 80 84a213d6-6138-4e86-98cf-c2748e3c99ed 83 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +TTF1 7270 BI GRCh38 9 132376139 132376139 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 28 18 c.2494C>G p.Leu832Val p.L832V ENST00000334270.3 NM_007344.4 832 Cta/Gta 11/11 P4 C L/V protein_coding YES CCDS6948.1 2494/2718 AGGTAGAGTCG Low_complexity_(Seg):seg;PANTHER:PTHR46760 ENSP00000333920 11/11 ENST00000334270 Transcript ENSG00000125482 HGNC:12397 MODERATE NM_007344.4 missense_variant 1.0 possibly_damaging(0.824) Unknown deleterious(0.03) Q15361.170 TTF1 HGNC -1 A0A024R8C1.49 1.0 UPI00001B55A7 SNV TTF1,missense_variant,p.L832V,ENST00000334270,NM_007344.4,c.2494C>G,MODERATE,YES,deleterious(0.03),possibly_damaging(0.824),-1;TTF1,missense_variant,p.L317V,ENST00000612514,NM_001205296.1,c.949C>G,MODERATE,,tolerated(0.14),possibly_damaging(0.824),-1;TTF1,non_coding_transcript_exon_variant,,ENST00000461970,,n.177C>G,MODIFIER,,,,-1 2552/3143 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 63 84a213d6-6138-4e86-98cf-c2748e3c99ed 46 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS TTF1,non_coding_transcript_exon_variant,,ENST00000461970.1,n.177C>G,MODIFIER,;TTF1,missense_variant,p.L317V,ENST00000612514.4,c.949C>G,MODERATE,;TTF1,missense_variant,p.L832V,ENST00000334270.3,c.2494C>G,MODERATE,YES +DEAF1 10522 BI GRCh38 11 679783 679783 + missense_variant Missense_Mutation SNP G G A rs1166736149 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 15 7 c.1031C>T p.Ser344Leu p.S344L ENST00000382409.4 NM_001293634.1 344 tCg/tTg 8/12 P1 A S/L protein_coding YES CCDS31327.1 1031/1698 CCCCCGAGGTC COSM3452415 PANTHER:PTHR10237;PANTHER:PTHR10237:SF1 ENSP00000371846 8/12 rs1166736149;COSV58607924 ENST00000382409 Transcript 1.0 ENSG00000177030 HGNC:14677 MODERATE NM_021008.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 possibly_damaging(0.487) Unknown deleterious(0) 0;1 O75398.198 DEAF1 HGNC -1 1.0 UPI00001290E6 O75398-1 SNV DEAF1,missense_variant,p.S344L,ENST00000382409,NM_001293634.1&NM_001367390.1&NM_021008.4,c.1031C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.487),-1;DEAF1,non_coding_transcript_exon_variant,,ENST00000525904,,n.214C>T,MODIFIER,,,,-1;DEAF1,non_coding_transcript_exon_variant,,ENST00000530813,,n.235C>T,MODIFIER,,,,-1;DEAF1,missense_variant,p.S132L,ENST00000527170,,c.395C>T,MODERATE,,deleterious(0),probably_damaging(0.935),-1;DEAF1,upstream_gene_variant,,ENST00000526790,,,MODIFIER,,,,-1;AC131934.1,downstream_gene_variant,,ENST00000527799,,,MODIFIER,YES,,,1 1206/2190 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 39 84a213d6-6138-4e86-98cf-c2748e3c99ed 22 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS DEAF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000530813.2,c.*654C>T,MODIFIER,;DEAF1,non_coding_transcript_exon_variant,,ENST00000525904.5,n.214C>T,MODIFIER,;DEAF1,missense_variant,p.S276L,ENST00000689835.1,c.827C>T,MODERATE,;DEAF1,missense_variant,p.S276L,ENST00000686001.1,c.827C>T,MODERATE,;DEAF1,missense_variant,NMD_transcript_variant,p.S276L,ENST00000687329.1,c.827C>T,MODERATE,;DEAF1,missense_variant,p.S276L,ENST00000690068.1,c.827C>T,MODERATE,;DEAF1,intron_variant,NMD_transcript_variant,,ENST00000692634.1,c.667-961C>T,MODIFIER,;DEAF1,non_coding_transcript_exon_variant,,ENST00000525626.6,n.916C>T,MODIFIER,;DEAF1,non_coding_transcript_exon_variant,,ENST00000528864.6,n.917C>T,MODIFIER,;DEAF1,non_coding_transcript_exon_variant,,ENST00000682936.1,n.791C>T,MODIFIER,;DEAF1,missense_variant,p.S102L,ENST00000683307.1,c.305C>T,MODERATE,;DEAF1,missense_variant,p.S276L,ENST00000685854.1,c.827C>T,MODERATE,;DEAF1,synonymous_variant,NMD_transcript_variant,p.L131=,ENST00000527170.5,c.393C>T,LOW,;DEAF1,missense_variant,p.S344L,ENST00000382409.4,c.1031C>T,MODERATE,YES +RARG 5916 BI GRCh38 12 53213161 53213161 + synonymous_variant Silent SNP G G C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 26 25 c.1101C>G p.Arg367= p.R367= ENST00000425354.7 NM_000966.6 367 cgC/cgG 9/10 P1 C R protein_coding YES CCDS8850.1 1101/1365 CGCCGGCGCCG Gene3D:1.10.565.10;PDB-ENSP_mappings:1exa.A;PDB-ENSP_mappings:1exx.A;PDB-ENSP_mappings:1fcx.A;PDB-ENSP_mappings:1fcy.A;PDB-ENSP_mappings:1fcz.A;PDB-ENSP_mappings:1fd0.A;PDB-ENSP_mappings:2lbd.A;PDB-ENSP_mappings:3lbd.A;PDB-ENSP_mappings:4lbd.A;PDB-ENSP_mappings:5m24.A;PDB-ENSP_mappings:6fx0.A;Pfam:PF00104;PROSITE_profiles:PS51843;PANTHER:PTHR24082;PANTHER:PTHR24082:SF116;SMART:SM00430;Superfamily:SSF48508;CDD:cd06937;Low_complexity_(Seg):seg ENSP00000388510 9/10 ENST00000425354 Transcript ENSG00000172819 HGNC:9866 LOW NM_000966.6 synonymous_variant 1.0 Unknown P13631.231 RARG HGNC -1 A8K3H3.122 1.0 UPI000000105D P13631-1 SNV RARG,synonymous_variant,p.R367=,ENST00000425354,NM_000966.6,c.1101C>G,LOW,YES,,,-1;RARG,synonymous_variant,p.R295=,ENST00000394426,NM_001243730.1&NM_001243731.2,c.885C>G,LOW,,,,-1;RARG,synonymous_variant,p.R356=,ENST00000338561,NM_001042728.3,c.1068C>G,LOW,,,,-1;RARG,synonymous_variant,p.R345=,ENST00000543726,NM_001243732.2,c.1035C>G,LOW,,,,-1;RARG,non_coding_transcript_exon_variant,,ENST00000543762,,n.1094C>G,MODIFIER,,,,-1;RARG,downstream_gene_variant,,ENST00000548284,,,MODIFIER,,,,-1;RARG,downstream_gene_variant,,ENST00000548317,,,MODIFIER,,,,-1;RARG,downstream_gene_variant,,ENST00000550265,,,MODIFIER,,,,-1;RARG,downstream_gene_variant,,ENST00000551580,,,MODIFIER,,,,-1 1546/2917 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 67 84a213d6-6138-4e86-98cf-c2748e3c99ed 51 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS RARG,non_coding_transcript_exon_variant,,ENST00000543762.5,n.1094C>G,MODIFIER,;RARG,synonymous_variant,p.R345=,ENST00000543726.1,c.1035C>G,LOW,;RARG,synonymous_variant,p.R356=,ENST00000338561.9,c.1068C>G,LOW,;RARG,synonymous_variant,p.R367=,ENST00000425354.7,c.1101C>G,LOW,YES;RARG,synonymous_variant,p.R295=,ENST00000394426.5,c.885C>G,LOW, +CDH24 64403 BI GRCh38 14 23053531 23053531 + synonymous_variant Silent SNP G G A rs780138714 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 10 15 c.1191C>T p.Ser397= p.S397= ENST00000267383.5 397 tcC/tcT 6/12 A S protein_coding CCDS9585.1 1191/2460 GCCGCGGAGAT Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24027;PANTHER:PTHR24027:SF272;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000267383 6/12 rs780138714 ENST00000267383 Transcript ENSG00000139880 HGNC:14265 LOW 2.913e-05 gnomAD_AMR synonymous_variant Unknown Q86UP0.150 CDH24 HGNC -1 1.0 UPI0000190F86 Q86UP0-1 SNV CDH24,synonymous_variant,p.S397=,ENST00000397359,NM_022478.3,c.1191C>T,LOW,YES,,,-1;CDH24,synonymous_variant,p.S397=,ENST00000487137,NM_144985.3,c.1191C>T,LOW,,,,-1;CDH24,synonymous_variant,p.S397=,ENST00000267383,,c.1191C>T,LOW,,,,-1;CDH24,synonymous_variant,p.S397=,ENST00000554034,,c.1191C>T,LOW,,,,-1;CDH24,intron_variant,,ENST00000610348,,c.417+1607C>T,MODIFIER,,,,-1;CDH24,upstream_gene_variant,,ENST00000485922,,,MODIFIER,,,,-1 1284/2873 muse;mutect2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 8.085e-06 0.0 2.913e-05 0.0 0.0 0.0 8.985e-06 0.0 0.0 6.758220024494221e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 31 84a213d6-6138-4e86-98cf-c2748e3c99ed 25 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS CDH24,synonymous_variant,p.S397=,ENST00000554034.5,c.1191C>T,LOW,;CDH24,synonymous_variant,p.S397=,ENST00000267383.5,c.1191C>T,LOW,;CDH24,synonymous_variant,p.S397=,ENST00000487137.7,c.1191C>T,LOW,YES;CDH24,synonymous_variant,p.S397=,ENST00000397359.7,c.1191C>T,LOW, +SRRM2 23524 BI GRCh38 16 2768117 2768117 + missense_variant Missense_Mutation SNP G G A rs1307066107 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 16 14 c.7589G>A p.Arg2530Gln p.R2530Q ENST00000301740.13 NM_016333.4 2530 cGg/cAg 11/15 P1 A R/Q protein_coding YES CCDS32373.1 7589/8259 GGAGCGGCGGA COSM84326 PDB-ENSP_mappings:5mqf.S;PDB-ENSP_mappings:5xjc.U;PDB-ENSP_mappings:5yzg.U;PDB-ENSP_mappings:5z56.U;PDB-ENSP_mappings:5z57.U;PDB-ENSP_mappings:6ff4.S;PDB-ENSP_mappings:6ff7.S;PDB-ENSP_mappings:6icz.U;PANTHER:PTHR34755;PANTHER:PTHR34755:SF3;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000301740 11/15 rs1307066107;COSV51940226 ENST00000301740 Transcript 1.0 ENSG00000167978 HGNC:16639 MODERATE NM_016333.4 8.905e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.968) Unknown deleterious_low_confidence(0) 0;1 Q9UQ35.170 SRRM2 HGNC 1 A0A140VK53.20 1.0 UPI000049DDFC Q9UQ35-1 SNV SRRM2,missense_variant,p.R2530Q,ENST00000301740,NM_016333.4,c.7589G>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.968),1;SRRM2,intron_variant,,ENST00000630499,,c.883-3187G>A,MODIFIER,,,,1;ELOB,downstream_gene_variant,,ENST00000262306,NM_207013.3,,MODIFIER,YES,,,-1;ELOB,downstream_gene_variant,,ENST00000409477,,,MODIFIER,,,,-1;ELOB,downstream_gene_variant,,ENST00000409906,NM_007108.4,,MODIFIER,,,,-1;ELOB,downstream_gene_variant,,ENST00000494946,,,MODIFIER,,,,-1;SRRM2,upstream_gene_variant,,ENST00000570539,,,MODIFIER,,,,1;SRRM2,downstream_gene_variant,,ENST00000571378,,,MODIFIER,,,,1;ELOB,downstream_gene_variant,,ENST00000572954,,,MODIFIER,,,,-1;SRRM2,downstream_gene_variant,,ENST00000576924,,,MODIFIER,,,,1;SRRM2,non_coding_transcript_exon_variant,,ENST00000574593,,n.611G>A,MODIFIER,,,,1;SRRM2,non_coding_transcript_exon_variant,,ENST00000572721,,n.262G>A,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000573583,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000574866,,,MODIFIER,,,,1;SRRM2,downstream_gene_variant,,ENST00000576674,,,MODIFIER,,,,1;SRRM2,missense_variant,p.R133Q,ENST00000572883,,c.398G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.997),1;SRRM2,non_coding_transcript_exon_variant,,ENST00000573311,,n.37G>A,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000570705,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000571041,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000573692,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000574331,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000576878,,,MODIFIER,,,,1 7829/9044 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 4.003e-06 0.0 0.0 0.0 0.0 0.0 8.905e-06 0.0 0.0 6.759129973943345e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 41 84a213d6-6138-4e86-98cf-c2748e3c99ed 30 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS SRRM2,non_coding_transcript_exon_variant,,ENST00000573311.1,n.37G>A,MODIFIER,;SRRM2,non_coding_transcript_exon_variant,,ENST00000572721.1,n.262G>A,MODIFIER,;SRRM2,non_coding_transcript_exon_variant,,ENST00000574593.1,n.611G>A,MODIFIER,;SRRM2,missense_variant,NMD_transcript_variant,p.R1136Q,ENST00000572883.2,c.3407G>A,MODERATE,;SRRM2,missense_variant,p.R2530Q,ENST00000301740.13,c.7589G>A,MODERATE,YES;SRRM2,missense_variant,p.R2530Q,ENST00000576924.6,c.7589G>A,MODERATE, +KRTAP9-3 83900 BI GRCh38 17 41232891 41232891 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 18 32 c.390C>G p.Cys130Trp p.C130W ENST00000411528.4 NM_031962.3 130 tgC/tgG 1/1 P1 G C/W protein_coding YES CCDS11385.1 390/480 TGCTGCCGCCC Pfam:PF13885;PANTHER:PTHR23262;PANTHER:PTHR23262:SF185;Low_complexity_(Seg):seg ENSP00000392189 1/1 ENST00000411528 Transcript ENSG00000204873 HGNC:16927 MODERATE NM_031962.3 missense_variant 1.0 possibly_damaging(0.896) Unknown deleterious(0) Q9BYQ3.124 KRTAP9-3 HGNC 1 UPI0000071C07 SNV KRTAP9-3,missense_variant,p.C130W,ENST00000411528,NM_031962.3,c.390C>G,MODERATE,YES,deleterious(0),possibly_damaging(0.896),1 443/1006 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 131 84a213d6-6138-4e86-98cf-c2748e3c99ed 50 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS KRTAP9-3,missense_variant,p.C130W,ENST00000411528.4,c.390C>G,MODERATE,YES +HOXB5 3215 BI GRCh38 17 48593152 48593152 + missense_variant Missense_Mutation SNP G G T rs1442101132 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 32 8 c.531C>A p.Phe177Leu p.F177L ENST00000239151.6 NM_002147.4 177 ttC/ttA 1/2 P1 T F/L protein_coding YES CCDS11530.1 531/810 CAGGGGAATAT Gene3D:1.10.10.60;Prints:PR00025;PROSITE_patterns:PS00032;PANTHER:PTHR45659;PANTHER:PTHR45659:SF2 ENSP00000239151 1/2 rs1442101132 ENST00000239151 Transcript ENSG00000120075 HGNC:5116 MODERATE missense_variant 1.0 possibly_damaging(0.477) Unknown deleterious(0.02) P09067.192 HOXB5 HGNC -1 1.0 UPI000012CF58 SNV HOXB5,missense_variant,p.F177L,ENST00000239151,NM_002147.3,c.531C>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.477),-1;HOXB6,downstream_gene_variant,,ENST00000225648,NM_018952.5,,MODIFIER,,,,-1;HOXB3,upstream_gene_variant,,ENST00000460160,NM_001330323.1,,MODIFIER,,,,-1;HOXB3,upstream_gene_variant,,ENST00000472863,,,MODIFIER,,,,-1;HOXB3,upstream_gene_variant,,ENST00000476342,,,MODIFIER,,,,-1;HOXB6,downstream_gene_variant,,ENST00000484302,NM_001369397.2,,MODIFIER,YES,,,-1;HOXB3,upstream_gene_variant,,ENST00000498678,,,MODIFIER,,,,-1;HOXB3,intron_variant,,ENST00000552000,,n.433+11328C>A,MODIFIER,,,,-1;HOXB6,downstream_gene_variant,,ENST00000470193,,,MODIFIER,,,,-1;HOXB-AS3,intron_variant,,ENST00000429755,,n.73+788G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000465846,,n.78-7295G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000467155,,n.113+2563G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000474040,,n.148+2563G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000476204,,n.170+2563G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000480872,,n.109+2563G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000487849,,n.45+788G>T,MODIFIER,,,,1;HOXB-AS3,intron_variant,,ENST00000492897,,n.52+788G>T,MODIFIER,,,,1;HOXB-AS3,upstream_gene_variant,,ENST00000460041,,,MODIFIER,,,,1;HOXB-AS3,upstream_gene_variant,,ENST00000466037,,,MODIFIER,,,,1;HOXB-AS3,upstream_gene_variant,,ENST00000474324,,,MODIFIER,,,,1;HOXB-AS3,upstream_gene_variant,,ENST00000477144,,,MODIFIER,YES,,,1;HOXB-AS3,upstream_gene_variant,,ENST00000481995,,,MODIFIER,,,,1 810/2041 muse;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 74 84a213d6-6138-4e86-98cf-c2748e3c99ed 40 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS HOXB-AS3,intron_variant,,ENST00000487849.7,n.45+788G>T,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000492897.3,n.52+788G>T,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000429755.8,n.73+788G>T,MODIFIER,;HOXB5,missense_variant,p.F177L,ENST00000239151.6,c.531C>A,MODERATE,YES;HOXB-AS3,intron_variant,,ENST00000480872.5,n.109+2563G>T,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000467155.6,n.113+2563G>T,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000474040.5,n.148+2563G>T,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000476204.5,n.170+2563G>T,MODIFIER,;HOXB3,intron_variant,,ENST00000552000.2,n.433+11328C>A,MODIFIER,;HOXB-AS3,intron_variant,,ENST00000465846.6,n.78-7295G>T,MODIFIER,YES +HOXB8 3218 BI GRCh38 17 48614542 48614542 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 11 6 c.163C>G p.Gln55Glu p.Q55E ENST00000239144.5 NM_024016.4 55 Cag/Gag 1/2 P4 C Q/E protein_coding YES CCDS11533.1 163/732 CTCCTGGATTT PANTHER:PTHR46166;PANTHER:PTHR46166:SF2 ENSP00000239144 1/2 ENST00000239144 Transcript ENSG00000120068 HGNC:5119 MODERATE NM_024016.4 missense_variant possibly_damaging(0.759) Unknown tolerated(0.05) P17481.177 HOXB8 HGNC -1 2.0 UPI000012CF63 SNV HOXB8,missense_variant,p.Q55E,ENST00000239144,NM_024016.4,c.163C>G,MODERATE,YES,tolerated(0.05),possibly_damaging(0.759),-1;HOXB8,missense_variant,p.Q55E,ENST00000576562,,c.163C>G,MODERATE,,tolerated(0.19),possibly_damaging(0.709),-1;HOXB7,upstream_gene_variant,,ENST00000239165,NM_004502.4,,MODIFIER,YES,,,-1;HOXB8,upstream_gene_variant,,ENST00000498634,,,MODIFIER,,,,-1;HOXB7,intron_variant,,ENST00000567101,,n.60-6447C>G,MODIFIER,,,,-1 751/2176 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 24 84a213d6-6138-4e86-98cf-c2748e3c99ed 17 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS HOXB8,missense_variant,p.Q55E,ENST00000576562.1,c.163C>G,MODERATE,;HOXB8,missense_variant,p.Q55E,ENST00000239144.5,c.163C>G,MODERATE,YES;HOXB7,intron_variant,,ENST00000567101.2,n.60-6447C>G,MODIFIER, +DNAH17 8632 BI GRCh38 17 78425352 78425352 + missense_variant Missense_Mutation SNP T T G novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 49 34 c.13135A>C p.Met4379Leu p.M4379L ENST00000389840.7 NM_173628.4 4379 Atg/Ctg 80/81 P1 G M/L protein_coding YES CCDS11757.2 13135/13389 TTCCATGAAGA Gene3D:3.10.490.20;Pfam:PF18199;PANTHER:PTHR10676;PANTHER:PTHR10676:SF284 ENSP00000374490 80/81 ENST00000389840 Transcript 1.0 ENSG00000187775 HGNC:2946 MODERATE NM_173628.4 missense_variant probably_damaging(0.988) Unknown tolerated(0.2) Q9UFH2.131 DNAH17 HGNC -1 5.0 UPI0001B25601 Q9UFH2-1 SNV DNAH17,missense_variant,p.M4379L,ENST00000389840,NM_173628.4,c.13135A>C,MODERATE,YES,tolerated(0.2),probably_damaging(0.988),-1;PGS1,downstream_gene_variant,,ENST00000262764,NM_024419.5,,MODIFIER,YES,,,1;DNAH17,non_coding_transcript_exon_variant,,ENST00000586052,,n.6296A>C,MODIFIER,,,,-1;DNAH17,downstream_gene_variant,,ENST00000586850,,,MODIFIER,,,,-1;PGS1,downstream_gene_variant,,ENST00000586880,,,MODIFIER,,,,1;PGS1,downstream_gene_variant,,ENST00000588281,,,MODIFIER,,,,1;DNAH17,downstream_gene_variant,,ENST00000592192,,,MODIFIER,,,,-1;DNAH17,3_prime_UTR_variant,,ENST00000591369,,c.*66A>C,MODIFIER,,,,-1;DNAH17,non_coding_transcript_exon_variant,,ENST00000590227,,n.2809A>C,MODIFIER,,,,-1;PGS1,downstream_gene_variant,,ENST00000588169,,,MODIFIER,,,,1;PGS1,downstream_gene_variant,,ENST00000589425,,,MODIFIER,,,,1;PGS1,downstream_gene_variant,,ENST00000589426,,,MODIFIER,,,,1;DNAH17,downstream_gene_variant,,ENST00000591647,,,MODIFIER,,,,-1;PGS1,downstream_gene_variant,,ENST00000591996,,,MODIFIER,,,,1 13262/13725 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 106 84a213d6-6138-4e86-98cf-c2748e3c99ed 83 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS DNAH17,non_coding_transcript_exon_variant,,ENST00000586052.5,n.6296A>C,MODIFIER,;DNAH17,non_coding_transcript_exon_variant,,ENST00000590227.5,n.2809A>C,MODIFIER,;DNAH17,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000591369.5,c.*66A>C,MODIFIER,;DNAH17,missense_variant,p.M4379L,ENST00000389840.7,c.13135A>C,MODERATE,YES +ZNF180 7733 BI GRCh38 19 44476850 44476850 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 42 32 c.1631C>G p.Thr544Ser p.T544S ENST00000221327.8 NM_013256.7 544 aCt/aGt 5/5 A2 C T/S protein_coding YES CCDS12639.1 1631/2079 CTCCAGTGTGA Gene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF27;Superfamily:SSF57667 ENSP00000221327 5/5 ENST00000221327 Transcript ENSG00000167384 HGNC:12970 MODERATE missense_variant 1.0 probably_damaging(0.985) Unknown tolerated(0.07) Q9UJW8.167 ZNF180 HGNC -1 1.0 UPI000013C30E SNV ZNF180,missense_variant,p.T544S,ENST00000221327,NM_013256.6&NM_001288759.3,c.1631C>G,MODERATE,YES,tolerated(0.07),probably_damaging(0.985),-1;ZNF180,missense_variant,p.T519S,ENST00000391956,NM_001278508.3,c.1556C>G,MODERATE,,tolerated(0.07),probably_damaging(0.994),-1;ZNF180,missense_variant,p.T517S,ENST00000592529,NM_001291633.2&NM_001288761.3&NM_001278509.3&NM_001288760.3&NM_001288762.3,c.1550C>G,MODERATE,,tolerated(0.07),probably_damaging(0.991),-1;ZNF180,downstream_gene_variant,,ENST00000587047,,,MODIFIER,,,,-1;ZNF180,downstream_gene_variant,,ENST00000591064,,,MODIFIER,,,,-1;ZNF180,downstream_gene_variant,,ENST00000585514,,,MODIFIER,,,,-1;ZNF180,downstream_gene_variant,,ENST00000586637,,,MODIFIER,,,,-1;ZNF180,3_prime_UTR_variant,,ENST00000592095,,c.*1642C>G,MODIFIER,,,,-1;ZNF180,3_prime_UTR_variant,,ENST00000590088,,c.*1438C>G,MODIFIER,,,,-1;ZNF285B,downstream_gene_variant,,ENST00000561698,,,MODIFIER,YES,,,1 1913/4335 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 111 84a213d6-6138-4e86-98cf-c2748e3c99ed 74 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS ZNF180,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000590088.5,c.*1438C>G,MODIFIER,;ZNF180,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000592095.5,c.*1642C>G,MODIFIER,;ZNF180,missense_variant,p.T519S,ENST00000391956.8,c.1556C>G,MODERATE,;ZNF180,missense_variant,p.T517S,ENST00000592529.6,c.1550C>G,MODERATE,YES;ZNF180,missense_variant,p.T544S,ENST00000221327.8,c.1631C>G,MODERATE, +UMODL1 89766 BI GRCh38 21 42123017 42123017 + missense_variant Missense_Mutation SNP G G A rs768514919 TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 22 12 c.3014G>A p.Arg1005His p.R1005H ENST00000408910.7 NM_001004416.3 1005 cGc/cAc 17/23 A2 A R/H protein_coding CCDS42936.1 3014/3957 GAAGCGCTTCC Gene3D:2.60.40.3210;Pfam:PF00100;PROSITE_profiles:PS51034;PANTHER:PTHR14002;PANTHER:PTHR14002:SF22;SMART:SM00241 ENSP00000386147 17/23 rs768514919 ENST00000408910 Transcript ENSG00000177398 HGNC:12560 MODERATE 6.536e-05 gnomAD_SAS missense_variant benign(0.007) Unknown tolerated(0.13) Q5DID0.131 UMODL1 HGNC 1 1.0 UPI00006C2192 Q5DID0-1 SNV UMODL1,missense_variant,p.R933H,ENST00000400424,NM_001199528.3,c.2798G>A,MODERATE,,tolerated(0.13),benign(0.007),1;UMODL1,missense_variant,p.R1061H,ENST00000400427,NM_001199527.2,c.3182G>A,MODERATE,,tolerated(0.12),benign(0.005),1;UMODL1,missense_variant,p.R1133H,ENST00000408989,NM_173568.3,c.3398G>A,MODERATE,YES,tolerated(0.12),benign(0.005),1;UMODL1,missense_variant,p.R1005H,ENST00000408910,NM_001004416.2,c.3014G>A,MODERATE,,tolerated(0.13),benign(0.007),1;UMODL1,non_coding_transcript_exon_variant,,ENST00000400423,,n.758G>A,MODIFIER,,,,1;UMODL1,intron_variant,,ENST00000484174,,n.571+1793G>A,MODIFIER,,,,1;UMODL1,upstream_gene_variant,,ENST00000484712,,,MODIFIER,,,,1 3014/4878 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 2.405e-05 0.0 2.897e-05 0.0 0.0 4.655e-05 1.766e-05 0.0 6.536e-05 3.382310023880564e-05 0.0 0.0 0.0001326610072283 0.0 0.0 0.0 amr 0.0001326610072283 0.0 3.086610013269819e-05 0.0 0.0002084199950331 0 62 84a213d6-6138-4e86-98cf-c2748e3c99ed 34 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS UMODL1,intron_variant,,ENST00000484174.5,n.571+1793G>A,MODIFIER,;UMODL1,non_coding_transcript_exon_variant,,ENST00000400423.6,n.758G>A,MODIFIER,;UMODL1,missense_variant,p.R1005H,ENST00000408910.7,c.3014G>A,MODERATE,YES;UMODL1,missense_variant,p.R1133H,ENST00000408989.6,c.3398G>A,MODERATE,;UMODL1,missense_variant,p.R933H,ENST00000400424.6,c.2798G>A,MODERATE,;UMODL1,missense_variant,p.R1061H,ENST00000400427.5,c.3182G>A,MODERATE, +ZNF182 7569 BI GRCh38 X 47977508 47977508 + synonymous_variant Silent SNP A A G novel TCGA-VD-AA8Q-01A TCGA-VD-AA8Q-10A Somatic 10 11 c.522T>C p.His174= p.H174= ENST00000376943.8 NM_001007088.2 174 caT/caC 6/6 A2 G H protein_coding YES CCDS35236.1 579/1920 TCAGTATGGAA PANTHER:PTHR24377;PANTHER:PTHR24377:SF218 ENSP00000380165 7/7 ENST00000396965 Transcript ENSG00000147118 HGNC:13001 LOW synonymous_variant 1.0 Unknown P17025.190 ZNF182 HGNC -1 2.0 UPI0000211F7D P17025-1 SNV ZNF182,synonymous_variant,p.H193=,ENST00000396965,NM_006962.2&NM_001178099.2,c.579T>C,LOW,YES,,,-1;ZNF182,synonymous_variant,p.H174=,ENST00000376943,NM_001007088.2,c.522T>C,LOW,,,,-1;ZNF81,intron_variant,,ENST00000376950,,c.278-25020A>G,MODIFIER,,,,1 930/3586 muse;mutect2;varscan2 1d00217f-28df-4d91-aeb9-0d9a83a907e6 0 25 84a213d6-6138-4e86-98cf-c2748e3c99ed 21 b359cb99-b9c0-46f3-a9a7-d0398734f3b5 SUCCESS ZNF182,synonymous_variant,p.H193=,ENST00000396965.5,c.579T>C,LOW,;ZNF182,synonymous_variant,p.H174=,ENST00000376943.8,c.522T>C,LOW,YES;ZNF81,intron_variant,,ENST00000376950.4,c.278-25020A>G,MODIFIER, +FCRL1 115350 BI GRCh38 1 157801944 157801944 + missense_variant Missense_Mutation SNP C C T rs551893022 TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 56 41 c.857G>A p.Arg286His p.R286H ENST00000368176.8 NM_052938.5 286 cGc/cAc 5/11 P4 T R/H protein_coding YES CCDS1170.1 857/1290 CACTGCGCTGG Gene3D:2.60.40.10;Pfam:PF17736;PROSITE_profiles:PS50835;PANTHER:PTHR11481;PANTHER:PTHR11481:SF92;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096 ENSP00000357158 5/11 rs551893022;COSV63824514 ENST00000368176 Transcript ENSG00000163534 HGNC:18509 MODERATE NM_052938.5 0.0001637 gnomAD_OTH missense_variant 0;1 1.0 benign(0.003) Unknown tolerated(0.45) 0;1 Q96LA6.161 FCRL1 HGNC -1 1.0 UPI000006E5BD Q96LA6-1 SNV FCRL1,missense_variant,p.R286H,ENST00000368176,NM_052938.5,c.857G>A,MODERATE,YES,tolerated(0.45),benign(0.003),-1;FCRL1,missense_variant,p.R286H,ENST00000358292,NM_001159397.2,c.857G>A,MODERATE,,tolerated(0.49),benign(0.052),-1;FCRL1,missense_variant,p.R286H,ENST00000491942,NM_001159398.2,c.857G>A,MODERATE,,tolerated(0.45),benign(0.048),-1;FCRL1,non_coding_transcript_exon_variant,,ENST00000489998,,n.1078G>A,MODIFIER,,,,-1;FCRL1,non_coding_transcript_exon_variant,,ENST00000368175,,n.623G>A,MODIFIER,,,,-1;FCRL1,non_coding_transcript_exon_variant,,ENST00000463001,,n.24G>A,MODIFIER,,,,-1;FCRL1,downstream_gene_variant,,ENST00000480310,,,MODIFIER,,,,-1;FCRL1,upstream_gene_variant,,ENST00000495126,,,MODIFIER,,,,-1 940/3069 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 2.795e-05 0.0001231 0.0 0.0 0.0 0.0 8.849e-06 0.0001637 9.814e-05 3.3784199331421405e-05 7.29075982235372e-05 0.0 6.621640204684809e-05 0.0 0.0 0.0 afr 7.29075982235372e-05 0.0 1.5428800907102413e-05 0.0 0.0 0 66 882f4a96-ba33-454e-8b4c-56b86e35ba5c 97 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS FCRL1,missense_variant,p.R286H,ENST00000491942.1,c.857G>A,MODERATE,;FCRL1,non_coding_transcript_exon_variant,,ENST00000368175.7,n.623G>A,MODIFIER,;FCRL1,non_coding_transcript_exon_variant,,ENST00000489998.5,n.1078G>A,MODIFIER,;FCRL1,missense_variant,p.R286H,ENST00000358292.7,c.857G>A,MODERATE,;FCRL1,non_coding_transcript_exon_variant,,ENST00000463001.5,n.24G>A,MODIFIER,;FCRL1,missense_variant,p.R286H,ENST00000368176.8,c.857G>A,MODERATE,YES +BAP1 8314 BI GRCh38 3 52407962 52407962 + frameshift_variant Frame_Shift_Del DEL G G - novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 9 15 c.371del p.Pro124LeufsTer63 p.P124Lfs*63 ENST00000460680.6 NM_004656.4 124 cCt/ct 5/17 P1 - P/X protein_coding YES CCDS2853.1 371/2190 ACCTCAGGGCTG CDD:cd09617;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:3.40.532.10;Pfam:PF01088;Superfamily:SSF54001 ENSP00000417132 5/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D deletion BAP1,frameshift_variant,p.P124Lfs*63,ENST00000460680,NM_004656.4,c.371del,HIGH,YES,,,-1;BAP1,frameshift_variant,p.P124Lfs*63,ENST00000296288,,c.371del,HIGH,,,,-1;BAP1,frameshift_variant,p.P45Lfs*63,ENST00000470173,,c.134del,HIGH,,,,-1;PHF7,upstream_gene_variant,,ENST00000327906,NM_001321127.2&NM_016483.7&NM_001321126.2,,MODIFIER,YES,,,1;PHF7,upstream_gene_variant,,ENST00000347025,NM_001278221.3,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000469613,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000614886,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000615126,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000472337,,,MODIFIER,,,,1;PHF7,upstream_gene_variant,,ENST00000482327,,,MODIFIER,,,,1;BAP1,3_prime_UTR_variant,,ENST00000490917,,c.*112del,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000471532,,n.86del,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,,n.371del,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;PHF7,upstream_gene_variant,,ENST00000473145,,,MODIFIER,,,,1;BAP1,upstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1 501/3600 mutect2;pindel;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 26 882f4a96-ba33-454e-8b4c-56b86e35ba5c 24 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS BAP1,frameshift_variant,p.P45Lfs*63,ENST00000470173.1,c.134del,HIGH,;BAP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000490917.1,c.*112del,MODIFIER,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984.5,n.371del,MODIFIER,;BAP1,non_coding_transcript_exon_variant,,ENST00000471532.5,n.86del,MODIFIER,;BAP1,frameshift_variant,p.P124Lfs*63,ENST00000296288.9,c.371del,HIGH,;BAP1,frameshift_variant,p.P124Lfs*63,ENST00000460680.6,c.371del,HIGH,YES +CENPE 1062 BI GRCh38 4 103153171 103153171 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 7 8 c.3113T>C p.Ile1038Thr p.I1038T ENST00000265148.9 NM_001813.3 1038 aTa/aCa 25/49 P4 G I/T protein_coding YES CCDS34042.1 3113/8106 CAATTATCTCA PANTHER:PTHR24115;PANTHER:PTHR24115:SF592 ENSP00000265148 25/49 ENST00000265148 Transcript 1.0 ENSG00000138778 HGNC:1856 MODERATE NM_001813.3 missense_variant 1.0 benign(0.01) Unknown tolerated(0.14) Q02224.202 CENPE HGNC -1 2.0 UPI000020B28A Q02224-1 SNV CENPE,missense_variant,p.I1013T,ENST00000380026,NM_001286734.2,c.3038T>C,MODERATE,,tolerated(0.24),benign(0.017),-1;CENPE,missense_variant,p.I1038T,ENST00000265148,NM_001813.3,c.3113T>C,MODERATE,YES,tolerated(0.14),benign(0.01),-1;CENPE,missense_variant,p.I1038T,ENST00000611174,,c.3113T>C,MODERATE,,tolerated(0.09),benign(0.102),-1 3137/8541 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 32 882f4a96-ba33-454e-8b4c-56b86e35ba5c 15 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS CENPE,missense_variant,p.I1038T,ENST00000265148.9,c.3113T>C,MODERATE,YES;CENPE,missense_variant,p.I1013T,ENST00000380026.8,c.3038T>C,MODERATE, +PDE4D 5144 BI GRCh38 5 58993398 58993398 + stop_gained Nonsense_Mutation SNP G G C novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 31 23 c.989C>G p.Ser330Ter p.S330* ENST00000340635.11 NM_001104631.2 330 tCa/tGa 7/15 C S/* protein_coding YES CCDS47213.1 989/2430 ACTCTGACACT PDB-ENSP_mappings:3g4g.A;PDB-ENSP_mappings:3g4g.B;PDB-ENSP_mappings:3g4g.C;PDB-ENSP_mappings:3g4g.D;PDB-ENSP_mappings:3iad.A;PDB-ENSP_mappings:3iad.B;PDB-ENSP_mappings:3iad.C;PDB-ENSP_mappings:3iad.D;PDB-ENSP_mappings:5wh6.A;PDB-ENSP_mappings:5wh6.B;PDB-ENSP_mappings:6njh.A;PDB-ENSP_mappings:6njh.B;PDB-ENSP_mappings:6njh.C;PDB-ENSP_mappings:6njh.D;PDB-ENSP_mappings:6nji.A;PDB-ENSP_mappings:6nji.B;PDB-ENSP_mappings:6njj.A;PDB-ENSP_mappings:6njj.B;PDB-ENSP_mappings:6njj.C;PDB-ENSP_mappings:6njj.D;Pfam:PF18100;PANTHER:PTHR11347;PANTHER:PTHR11347:SF91 ENSP00000345502 7/15 ENST00000340635 Transcript 1.0 ENSG00000113448 HGNC:8783 HIGH NM_001104631.2 stop_gained 1.0 Unknown Q08499.216 PDE4D HGNC -1 A0A140VJR0.35 1.0 UPI0000050EB1 Q08499-1 SNV PDE4D,stop_gained,p.S330*,ENST00000340635,NM_001104631.2,c.989C>G,HIGH,YES,,,-1;PDE4D,stop_gained,p.S199*,ENST00000546160,,c.596C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S220*,ENST00000636120,NM_001349242.1,c.659C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S266*,ENST00000507116,NM_001197218.2,c.797C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S194*,ENST00000360047,NM_006203.4,c.581C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S28*,ENST00000358923,NM_001349243.2&NM_001364603.1&NM_001364604.1&NM_001197221.2&NM_001197222.2,c.83C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S200*,ENST00000503258,NM_001197220.2,c.599C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S39*,ENST00000317118,NM_001197223.2,c.116C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S269*,ENST00000502484,NM_001364599.1&NM_001165899.2&NM_001349241.2,c.806C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S208*,ENST00000405755,NM_001197219.2,c.623C>G,HIGH,,,,-1;PDE4D,stop_gained,p.S28*,ENST00000505453,,c.83C>G,HIGH,,,,-1;PDE4D,downstream_gene_variant,,ENST00000405053,,,MODIFIER,,,,-1;PDE4D,3_prime_UTR_variant,,ENST00000309641,,c.*193C>G,MODIFIER,,,,-1;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011,,n.725C>G,MODIFIER,,,,-1 1093/8160 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 40 882f4a96-ba33-454e-8b4c-56b86e35ba5c 54 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS PDE4D,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000309641.10,c.*193C>G,MODIFIER,;PDE4D,stop_gained,p.S28*,ENST00000505453.1,c.83C>G,HIGH,;PDE4D,stop_gained,p.S269*,ENST00000502484.6,c.806C>G,HIGH,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011.5,n.725C>G,MODIFIER,;PDE4D,stop_gained,p.S208*,ENST00000405755.6,c.623C>G,HIGH,;PDE4D,stop_gained,p.S200*,ENST00000503258.5,c.599C>G,HIGH,;PDE4D,stop_gained,p.S39*,ENST00000317118.12,c.116C>G,HIGH,;PDE4D,stop_gained,p.S28*,ENST00000358923.10,c.83C>G,HIGH,;PDE4D,stop_gained,p.S194*,ENST00000360047.9,c.581C>G,HIGH,;PDE4D,stop_gained,p.S220*,ENST00000636120.1,c.659C>G,HIGH,;PDE4D,stop_gained,p.S330*,ENST00000340635.11,c.989C>G,HIGH,YES;PDE4D,stop_gained,p.S266*,ENST00000507116.6,c.797C>G,HIGH, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 88 44 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 79 882f4a96-ba33-454e-8b4c-56b86e35ba5c 132 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +OVCH1 341350 BI GRCh38 12 29444152 29444152 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 99 97 c.3010A>G p.Thr1004Ala p.T1004A ENST00000318184.9 1004 Act/Gct 24/28 P1 C T/A protein_coding YES 3010/3405 CATAGTAGTTC PANTHER:PTHR24251;PANTHER:PTHR24251:SF21;Superfamily:SSF49854 ENSP00000326708 24/28 ENST00000318184 Transcript ENSG00000187950 HGNC:23080 MODERATE missense_variant 1.0 benign(0.061) Unknown tolerated(0.27) Q7RTY7.122 OVCH1 HGNC -1 1.0 UPI000040640A SNV OVCH1,missense_variant,p.T1004A,ENST00000318184,NM_001353179.1,c.3010A>G,MODERATE,YES,tolerated(0.27),benign(0.061),-1;OVCH1,missense_variant,p.T29A,ENST00000537054,,c.85A>G,MODERATE,,tolerated(0.34),benign(0.038),-1;OVCH1,missense_variant,p.T40A,ENST00000539117,,c.118A>G,MODERATE,,tolerated(0.23),benign(0.021),-1;OVCH1-AS1,intron_variant,,ENST00000549411,,n.140+18088T>C,MODIFIER,,,,1;OVCH1-AS1,intron_variant,,ENST00000550906,,n.218-17582T>C,MODIFIER,,,,1;OVCH1-AS1,intron_variant,,ENST00000551108,,n.561-42734T>C,MODIFIER,,,,1 3010/3405 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 113 882f4a96-ba33-454e-8b4c-56b86e35ba5c 196 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS OVCH1,non_coding_transcript_exon_variant,,ENST00000696934.1,n.3298A>G,MODIFIER,;OVCH1,missense_variant,p.T1039A,ENST00000537054.2,c.3115A>G,MODERATE,YES;OVCH1,missense_variant,p.T1004A,ENST00000318184.9,c.3010A>G,MODERATE,;OVCH1-AS1,intron_variant,,ENST00000549411.1,n.140+18088T>C,MODIFIER,;OVCH1,synonymous_variant,NMD_transcript_variant,p.L39=,ENST00000539117.5,c.117A>G,LOW,;OVCH1-AS1,intron_variant,,ENST00000701302.1,n.213-17582T>C,MODIFIER,;OVCH1-AS1,intron_variant,,ENST00000550906.2,n.218-17582T>C,MODIFIER,;OVCH1-AS1,intron_variant,,ENST00000551108.2,n.561-42734T>C,MODIFIER,YES +IRAK3 11213 BI GRCh38 12 66244946 66244946 + splice_acceptor_variant Splice_Site SNP A A G TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 40 39 c.1087-2A>G p.X363_splice p.X363_splice ENST00000261233.9 NM_007199.3 363 P1 G protein_coding YES CCDS8975.1 CTTGTAGGTAA ENSP00000261233 COSV99706593 ENST00000261233 Transcript NonExonic 1.0 ENSG00000090376 HGNC:17020 HIGH 9/11 NM_007199.3 splice_acceptor_variant 1 1.0 Unknown 1 Q9Y616.173 IRAK3 HGNC 1 1.0 UPI000013D14A Q9Y616-1 SNV IRAK3,splice_acceptor_variant,p.X363_splice,ENST00000261233,NM_007199.3,c.1087-2A>G,HIGH,YES,,,1;IRAK3,splice_acceptor_variant,p.X302_splice,ENST00000457197,NM_001142523.2,c.904-2A>G,HIGH,,,,1 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 38 882f4a96-ba33-454e-8b4c-56b86e35ba5c 79 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS IRAK3,splice_acceptor_variant,p.X302_splice,ENST00000457197.2,c.904-2A>G,HIGH,;IRAK3,splice_acceptor_variant,p.X363_splice,ENST00000261233.9,c.1087-2A>G,HIGH,YES +CAND1 55832 BI GRCh38 12 67311771 67311771 + missense_variant Missense_Mutation SNP G G A rs1310639632 TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 68 59 c.3439G>A p.Glu1147Lys p.E1147K ENST00000545606.6 NM_001329674.2 1147 Gag/Aag 14/15 P1 A E/K protein_coding YES CCDS8977.1 3439/3693 TTGTTGAGCCA PDB-ENSP_mappings:1u6g.C;PDB-ENSP_mappings:4a0c.A;PDB-ENSP_mappings:4a0c.B;PANTHER:PTHR12696;PANTHER:PTHR12696:SF1;Pfam:PF08623;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000442318 14/15 rs1310639632 ENST00000545606 Transcript ENSG00000111530 HGNC:30688 MODERATE NM_018448.5 missense_variant 1.0 probably_damaging(0.975) Unknown deleterious(0) Q86VP6.173 CAND1 HGNC 1 1.0 UPI0000037CC5 Q86VP6-1 SNV CAND1,missense_variant,p.E1147K,ENST00000545606,NM_001329674.2&NM_001329675.2&NM_001329676.2&NM_018448.5,c.3439G>A,MODERATE,YES,deleterious(0),probably_damaging(0.975),1;CAND1,missense_variant,p.E687K,ENST00000544619,,c.2059G>A,MODERATE,,deleterious(0),probably_damaging(0.972),1;CAND1,downstream_gene_variant,,ENST00000540319,,,MODIFIER,,,,1 3799/11176 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 71 882f4a96-ba33-454e-8b4c-56b86e35ba5c 128 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS CAND1,missense_variant,p.E687K,ENST00000544619.1,c.2059G>A,MODERATE,;CAND1,missense_variant,p.E1147K,ENST00000545606.6,c.3439G>A,MODERATE,YES +FUS 2521 BI GRCh38 16 31182623 31182623 + missense_variant Missense_Mutation SNP A A G rs1480335769 TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 61 67 c.149A>G p.Tyr50Cys p.Y50C ENST00000254108.12 NM_001170937.1 50 tAt/tGt 3/15 P4 G Y/C protein_coding CCDS10707.1 149/1581 AGGCTATGGCC PDB-ENSP_mappings:5w3n.A;PDB-ENSP_mappings:5w3n.B;PDB-ENSP_mappings:5w3n.C;PDB-ENSP_mappings:5w3n.D;PDB-ENSP_mappings:5w3n.E;PDB-ENSP_mappings:5w3n.F;PDB-ENSP_mappings:5w3n.G;PDB-ENSP_mappings:5w3n.H;PDB-ENSP_mappings:5w3n.I;PDB-ENSP_mappings:5yvg.X;PDB-ENSP_mappings:5yvg.Y;PANTHER:PTHR23238;PANTHER:PTHR23238:SF5;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000254108 3/15 rs1480335769 ENST00000254108 Transcript 1.0 ENSG00000089280 HGNC:4010 MODERATE NM_004960.4 missense_variant probably_damaging(0.996) Unknown deleterious(0) P35637.222 FUS HGNC 1 Q6IBQ5.132 1.0 UPI000012AD9A P35637-1 SNV FUS,missense_variant,p.Y50C,ENST00000254108,NM_001170937.1&NM_004960.4,c.149A>G,MODERATE,,deleterious(0),probably_damaging(0.996),1;FUS,missense_variant,p.Y50C,ENST00000380244,NM_001170634.1,c.149A>G,MODERATE,,deleterious(0),probably_damaging(0.998),1;FUS,missense_variant,p.Y50C,ENST00000568685,,c.149A>G,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;FUS,upstream_gene_variant,,ENST00000474990,,,MODIFIER,,,,1;FUS,missense_variant,p.Y50C,ENST00000566605,,c.149A>G,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.998),1;FUS,non_coding_transcript_exon_variant,,ENST00000487509,,n.214A>G,MODIFIER,,,,1;FUS,non_coding_transcript_exon_variant,,ENST00000487045,,n.225A>G,MODIFIER,,,,1;FUS,upstream_gene_variant,,ENST00000487974,,,MODIFIER,,,,1;FUS,upstream_gene_variant,,ENST00000570090,,,MODIFIER,,,,1;AC009088.2,non_coding_transcript_exon_variant,,ENST00000564743,,n.351T>C,MODIFIER,YES,,,-1 225/1824 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 6.757300070603378e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5430699932039715e-05 0.0 0.0 0 86 882f4a96-ba33-454e-8b4c-56b86e35ba5c 128 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS ENSG00000260304,non_coding_transcript_exon_variant,,ENST00000564743.1,n.351T>C,MODIFIER,YES;FUS,missense_variant,p.Y50C,ENST00000568685.1,c.149A>G,MODERATE,;FUS,non_coding_transcript_exon_variant,,ENST00000487509.6,n.214A>G,MODIFIER,;FUS,non_coding_transcript_exon_variant,,ENST00000487045.6,n.225A>G,MODIFIER,;FUS,missense_variant,p.Y50C,ENST00000715542.1,c.149A>G,MODERATE,;FUS,missense_variant,p.Y50C,ENST00000254108.12,c.149A>G,MODERATE,YES;FUS,missense_variant,p.Y50C,ENST00000380244.8,c.149A>G,MODERATE,;FUS,missense_variant,NMD_transcript_variant,p.Y50C,ENST00000715541.1,c.149A>G,MODERATE,;FUS,missense_variant,NMD_transcript_variant,p.Y50C,ENST00000566605.5,c.149A>G,MODERATE, +OR7D4 125958 BI GRCh38 19 9214522 9214522 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 44 32 c.316A>G p.Met106Val p.M106V ENST00000308682.3 106 Atg/Gtg 1/1 P1 C M/V protein_coding CCDS32901.1 316/939 AAACATCATTA Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR26451;PANTHER:PTHR26451:SF906;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15234 ENSP00000310488 1/1 ENST00000308682 Transcript ENSG00000174667 HGNC:8380 MODERATE missense_variant benign(0) Unknown tolerated(0.36) Q8NG98.133 OR7D4 HGNC -1 A0A126GVR1.28 UPI00000472B5 SNV OR7D4,missense_variant,p.M106V,ENST00000641244,,c.316A>G,MODERATE,YES,tolerated(0.36),benign(0),-1;OR7D4,missense_variant,p.M106V,ENST00000641669,,c.316A>G,MODERATE,,tolerated(0.36),benign(0),-1;OR7D4,missense_variant,p.M106V,ENST00000308682,NM_001005191.2,c.316A>G,MODERATE,,tolerated(0.36),benign(0),-1;OR7E25P,downstream_gene_variant,,ENST00000641088,,,MODIFIER,YES,,,1 350/1022 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 65 882f4a96-ba33-454e-8b4c-56b86e35ba5c 76 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS OR7D4,missense_variant,p.M106V,ENST00000308682.3,c.316A>G,MODERATE,;OR7D4,missense_variant,p.M106V,ENST00000641244.1,c.316A>G,MODERATE,;OR7D4,missense_variant,p.M106V,ENST00000641669.1,c.316A>G,MODERATE,YES +ZNF527 84503 BI GRCh38 19 37389745 37389745 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 41 36 c.1696A>G p.Ile566Val p.I566V ENST00000436120.7 NM_032453.2 566 Atc/Gtc 5/5 P1 G I/V protein_coding YES CCDS42559.1 1696/1830 ATCAGATCTTG Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF620;SMART:SM00355;Superfamily:SSF57667 ENSP00000390179 5/5 ENST00000436120 Transcript ENSG00000189164 HGNC:29385 MODERATE NM_032453.2 missense_variant 1.0 benign(0) Unknown tolerated(0.52) Q8NB42.144 ZNF527 HGNC 1 4.0 UPI00002021F5 Q8NB42-1 SNV ZNF527,missense_variant,p.I566V,ENST00000436120,NM_032453.2,c.1696A>G,MODERATE,YES,tolerated(0.52),benign(0),1;ZNF527,intron_variant,,ENST00000587349,,c.*5-2670A>G,MODIFIER,,,,1;ZNF527,downstream_gene_variant,,ENST00000483919,,,MODIFIER,,,,1;ZNF527,downstream_gene_variant,,ENST00000588911,,,MODIFIER,,,,1;ZNF527,3_prime_UTR_variant,,ENST00000356178,,c.*1640A>G,MODIFIER,,,,1;ZNF527,downstream_gene_variant,,ENST00000588512,,,MODIFIER,,,,1 1865/5186 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 76 882f4a96-ba33-454e-8b4c-56b86e35ba5c 77 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS ZNF527,intron_variant,,ENST00000587349.1,c.*5-2670A>G,MODIFIER,;ZNF527,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000356178.8,c.*1640A>G,MODIFIER,;ZNF527,missense_variant,p.I566V,ENST00000436120.7,c.1696A>G,MODERATE,YES +NUP62 23636 BI GRCh38 19 49909169 49909169 + synonymous_variant Silent SNP G G C novel TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 57 58 c.639C>G p.Thr213= p.T213= ENST00000352066.8 NM_016553.5 213 acC/acG 3/3 P1 C T protein_coding CCDS12788.1 639/1569 GTGATGGTGGC PDB-ENSP_mappings:5ijn.H;PDB-ENSP_mappings:5ijn.N;PDB-ENSP_mappings:5ijn.T;PDB-ENSP_mappings:5ijn.Z;PDB-ENSP_mappings:5ijo.H;PDB-ENSP_mappings:5ijo.N;PDB-ENSP_mappings:5ijo.T;PDB-ENSP_mappings:5ijo.Z;Low_complexity_(Seg):seg;PANTHER:PTHR12084:SF12;PANTHER:PTHR12084 ENSP00000305503 3/3 ENST00000352066 Transcript 1.0 ENSG00000213024 HGNC:8066 LOW NM_016553.5 synonymous_variant Unknown P37198.211 NUP62 HGNC -1 A0A024QZF1.54 1.0 UPI000013EAFD SNV NUP62,synonymous_variant,p.T213=,ENST00000596217,,c.639C>G,LOW,YES,,,-1;NUP62,synonymous_variant,p.T213=,ENST00000422090,NM_001193357.2&NM_012346.5&NM_153718.4,c.639C>G,LOW,,,,-1;NUP62,synonymous_variant,p.T213=,ENST00000352066,NM_016553.5&NM_153719.4,c.639C>G,LOW,,,,-1;NUP62,synonymous_variant,p.T213=,ENST00000597029,,c.639C>G,LOW,,,,-1;NUP62,synonymous_variant,p.T213=,ENST00000597723,,c.639C>G,LOW,,,,-1;IL4I1,intron_variant,,ENST00000341114,NM_001258017.2&NM_172374.3,c.-227-4848C>G,MODIFIER,,,,-1;IL4I1,intron_variant,,ENST00000595948,NM_001258018.2,c.-285-4848C>G,MODIFIER,YES,,,-1;IL4I1,intron_variant,,ENST00000596011,,c.-328-4848C>G,MODIFIER,,,,-1;IL4I1,intron_variant,,ENST00000596022,,c.-227-4848C>G,MODIFIER,,,,-1;IL4I1,intron_variant,,ENST00000597295,,c.-145-4848C>G,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000593652,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000594673,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000595761,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000596437,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000596680,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000599567,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000599788,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000600645,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000600935,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000595373,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000595463,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000597814,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000598301,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000599186,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000599560,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000599830,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000600583,,,MODIFIER,,,,-1;NUP62,downstream_gene_variant,,ENST00000601665,,,MODIFIER,,,,-1;IL4I1,intron_variant,,ENST00000601717,,c.-227-4848C>G,MODIFIER,,,,-1;AC011452.1,downstream_gene_variant,,ENST00000451973,,,MODIFIER,YES,,,-1 1017/3361 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 0 57 882f4a96-ba33-454e-8b4c-56b86e35ba5c 115 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS NUP62,synonymous_variant,p.T213=,ENST00000596217.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000597723.5,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700478.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000599560.6,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700477.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000599788.2,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000598301.2,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700475.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700476.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000600583.6,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000597029.6,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000596437.6,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700474.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000600935.2,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000700473.1,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000422090.2,c.639C>G,LOW,;NUP62,synonymous_variant,p.T213=,ENST00000352066.8,c.639C>G,LOW,YES;IL4I1,intron_variant,,ENST00000596011.1,c.-328-4848C>G,MODIFIER,;IL4I1,intron_variant,,ENST00000597295.5,c.-145-4848C>G,MODIFIER,;IL4I1,intron_variant,,ENST00000596022.5,c.-227-4848C>G,MODIFIER,;IL4I1,intron_variant,,ENST00000595948.5,c.-285-4848C>G,MODIFIER,;IL4I1,intron_variant,,ENST00000341114.7,c.-227-4848C>G,MODIFIER,;IL4I1,intron_variant,NMD_transcript_variant,,ENST00000601717.5,c.-227-4848C>G,MODIFIER, +VPREB3 29802 BI GRCh38 22 23752959 23752959 + missense_variant Missense_Mutation SNP C C T rs1341387207 TCGA-VD-A8KK-01A TCGA-VD-A8KK-10A Somatic 27 25 c.289G>A p.Ala97Thr p.A97T ENST00000248948.4 NM_013378.3 97 Gcc/Acc 2/2 P1 T A/T protein_coding YES CCDS13813.1 289/372 ACAGGCATTGT Gene3D:2.60.40.10;Pfam:PF07686;PROSITE_profiles:PS50835;PANTHER:PTHR23267;PANTHER:PTHR23267:SF133;SMART:SM00406;SMART:SM00409;Superfamily:SSF48726 ENSP00000248948 2/2 rs1341387207 ENST00000248948 Transcript ENSG00000128218 HGNC:12710 MODERATE NM_013378.3 9.925e-05 gnomAD_ASJ missense_variant 1.0 benign(0.045) Unknown tolerated(0.13) Q9UKI3.150 VPREB3 HGNC -1 1.0 UPI0000049DEB SNV VPREB3,missense_variant,p.A97T,ENST00000248948,NM_013378.3,c.289G>A,MODERATE,YES,tolerated(0.13),benign(0.045),-1;VPREB3,missense_variant,p.A81T,ENST00000398465,,c.241G>A,MODERATE,,tolerated(0.1),benign(0.018),-1;ZNF70,upstream_gene_variant,,ENST00000341976,NM_021916.4,,MODIFIER,YES,,,-1 351/567 muse;mutect2;varscan2 8e6d3005-445a-4b7f-95ec-a988a121c628 3.977e-06 0.0 0.0 9.925e-05 0.0 0.0 0.0 0.0 0.0 0 27 882f4a96-ba33-454e-8b4c-56b86e35ba5c 52 31cb01c0-216d-48c4-97e1-d42d4b42a003 SUCCESS VPREB3,missense_variant,p.A97T,ENST00000248948.4,c.289G>A,MODERATE,YES;VPREB3,missense_variant,p.A81T,ENST00000398465.3,c.241G>A,MODERATE, +PTCH2 8643 BI GRCh38 1 44827632 44827632 + missense_variant Missense_Mutation SNP G G A rs777545138 TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 49 30 c.2141C>T p.Thr714Met p.T714M ENST00000372192.4 NM_003738.5 714 aCg/aTg 15/22 P2 A T/M protein_coding YES CCDS516.1 2141/3612 CATCCGTCAGG PANTHER:PTHR46022:SF3;PANTHER:PTHR46022;TIGRFAM:TIGR00918 ENSP00000361266 15/22 rs777545138 ENST00000372192 Transcript 1.0 ENSG00000117425 HGNC:9586 MODERATE NM_003738.5 0.0001634 gnomAD_SAS missense_variant 1.0 possibly_damaging(0.849) Unknown deleterious(0.03) Q9Y6C5.166 PTCH2 HGNC -1 1.0 UPI00001328B8 Q9Y6C5-1 SNV PTCH2,missense_variant,p.T714M,ENST00000372192,NM_003738.5,c.2141C>T,MODERATE,YES,deleterious(0.03),possibly_damaging(0.849),-1;PTCH2,missense_variant,p.T714M,ENST00000447098,NM_001166292.1,c.2141C>T,MODERATE,,deleterious(0.03),benign(0.355),-1;PTCH2,upstream_gene_variant,,ENST00000438067,,,MODIFIER,,,,-1 2462/4410 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 4.405e-05 0.0001234 5.785e-05 0.0 0.0 0.0 1.776e-05 0.0 0.0001634 1.3519899766833989e-05 4.863809954258613e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863809954258613e-05 0.0 0.0 0.0 0.0 0 67 d29cc427-c613-4a80-b958-15d922833322 79 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS PTCH2,missense_variant,p.T714M,ENST00000372192.4,c.2141C>T,MODERATE,YES;PTCH2,missense_variant,p.T714M,ENST00000447098.6,c.2141C>T,MODERATE, +BEST3 144453 BI GRCh38 12 69693761 69693761 + missense_variant Missense_Mutation SNP C C T rs117505973 TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 52 22 c.394G>A p.Val132Ile p.V132I ENST00000330891.10 NM_032735.3 132 Gtc/Atc 4/10 0.0002 0.0 0.0 0.0 0.001 0.0 P4 T V/I protein_coding YES CCDS8992.2 394/2007 ATTGACGTAGC PANTHER:PTHR10736:SF2;PANTHER:PTHR10736;Pfam:PF01062 ENSP00000332413 0.0 0.0001163 4/10 rs117505973 ENST00000330891 Transcript ENSG00000127325 HGNC:17105 MODERATE NM_032735.3 0.001 EUR missense_variant 1.0 benign(0.251) Unknown tolerated(0.13) Q8N1M1.149 BEST3 HGNC -1 5.0 UPI000006E397 Q8N1M1-2 SNV BEST3,missense_variant,p.V132I,ENST00000330891,NM_032735.3,c.394G>A,MODERATE,YES,tolerated(0.13),benign(0.251),-1;BEST3,missense_variant,p.V26I,ENST00000553096,NM_001282613.1,c.76G>A,MODERATE,,tolerated(0.12),benign(0.251),-1;BEST3,missense_variant,p.V26I,ENST00000266661,NM_001282615.2,c.76G>A,MODERATE,,tolerated(0.2),benign(0.019),-1;BEST3,missense_variant,p.V132I,ENST00000331471,NM_001282614.1,c.394G>A,MODERATE,,tolerated(0.13),benign(0.01),-1;BEST3,missense_variant,p.V26I,ENST00000551160,NM_001282616.2,c.76G>A,MODERATE,,tolerated(0.2),benign(0.019),-1;BEST3,missense_variant,p.V26I,ENST00000552295,,c.76G>A,MODERATE,,tolerated(0.33),benign(0.009),-1;BEST3,5_prime_UTR_variant,,ENST00000476098,,c.-38G>A,MODIFIER,,,,-1;BEST3,intron_variant,,ENST00000548658,,c.247+609G>A,MODIFIER,,,,-1;BEST3,upstream_gene_variant,,ENST00000488961,NM_152439.3,,MODIFIER,,,,-1;BEST3,non_coding_transcript_exon_variant,,ENST00000533674,,n.382G>A,MODIFIER,,,,-1;BEST3,upstream_gene_variant,,ENST00000529843,,,MODIFIER,,,,-1;BEST3,missense_variant,p.V4I,ENST00000547208,,c.10G>A,MODERATE,,tolerated(0.48),benign(0.006),-1 508/3419 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 3.581e-05 0.0 0.0 0.0 5.441e-05 0.0 7.041e-05 0.0 0.0 4.732930028694682e-05 2.4326200218638405e-05 0.0 0.0 0.0 0.0 0.0 nfe 9.25839995034039e-05 0.0 9.25839995034039e-05 0.0 0.0 0 60 d29cc427-c613-4a80-b958-15d922833322 74 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS BEST3,non_coding_transcript_exon_variant,,ENST00000533674.1,n.382G>A,MODIFIER,;BEST3,missense_variant,p.V26I,ENST00000551160.5,c.76G>A,MODERATE,;BEST3,missense_variant,p.V26I,ENST00000266661.8,c.76G>A,MODERATE,;BEST3,intron_variant,,ENST00000548658.1,c.247+609G>A,MODIFIER,;BEST3,missense_variant,p.V26I,ENST00000552295.5,c.76G>A,MODERATE,;BEST3,5_prime_UTR_variant,,ENST00000476098.5,c.-38G>A,MODIFIER,;BEST3,missense_variant,p.V26I,ENST00000553096.5,c.76G>A,MODERATE,;BEST3,missense_variant,p.V132I,ENST00000330891.10,c.394G>A,MODERATE,YES;BEST3,missense_variant,p.V132I,ENST00000331471.8,c.394G>A,MODERATE,;BEST3,missense_variant,NMD_transcript_variant,p.V4I,ENST00000547208.5,c.10G>A,MODERATE, +CUX2 23316 BI GRCh38 12 111310577 111310577 + missense_variant Missense_Mutation SNP C C T rs200707164 TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 80 12 c.1795C>T p.Arg599Cys p.R599C ENST00000261726.11 NM_015267.4 599 Cgc/Tgc 15/22 P1 T R/C protein_coding YES CCDS41837.1 1795/4461 CCTGGCGCAAG PDB-ENSP_mappings:1x2l.A;PROSITE_profiles:PS51042;PANTHER:PTHR14043:SF5;PANTHER:PTHR14043;Pfam:PF02376;Gene3D:1.10.260.40;SMART:SM01109;Superfamily:SSF47413 ENSP00000261726 15/22 rs200707164;COSV55652824 ENST00000261726 Transcript 1.0 ENSG00000111249 HGNC:19347 MODERATE NM_015267.4 0.0003343 gnomAD_EAS missense_variant 0;1 1.0 probably_damaging(0.98) Unknown deleterious(0) 0;1 O14529.180 CUX2 HGNC 1 1.0 UPI00001FBB07 SNV CUX2,missense_variant,p.R599C,ENST00000261726,NM_015267.4&NM_001370598.1,c.1795C>T,MODERATE,YES,deleterious(0),probably_damaging(0.98),1 1808/6703 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 2.813e-05 0.0 2.898e-05 0.0 0.0003343 0.0 0.0 0.0 0.0 0 64 d29cc427-c613-4a80-b958-15d922833322 93 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS CUX2,missense_variant,p.R599C,ENST00000261726.11,c.1795C>T,MODERATE,YES +RPL36AL 6166 BI GRCh38 14 49618915 49618915 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 156 28 c.190A>G p.Lys64Glu p.K64E ENST00000298289.7 NM_001001.5 64 Aag/Gag 2/2 P1 C K/E protein_coding YES CCDS9689.1 190/321 CTTCTTTGTGG Gene3D:3.10.450.80;Pfam:PF00935;PROSITE_patterns:PS01172;PANTHER:PTHR10369;PANTHER:PTHR10369:SF30;Superfamily:SSF57829 ENSP00000346012 2/2 ENST00000298289 Transcript ENSG00000165502 HGNC:10346 MODERATE NM_001001.5 missense_variant 1.0 benign(0.309) Unknown tolerated(0.06) Q969Q0.151 RPL36AL HGNC -1 1.0 UPI000000D720 SNV RPL36AL,missense_variant,p.K64E,ENST00000298289,NM_001001.5,c.190A>G,MODERATE,YES,tolerated(0.06),benign(0.309),-1;LRR1,downstream_gene_variant,,ENST00000298288,NM_152329.4,,MODIFIER,YES,,,1;MGAT2,upstream_gene_variant,,ENST00000305386,NM_002408.4,,MODIFIER,YES,,,1;LRR1,downstream_gene_variant,,ENST00000318317,NM_203467.1,,MODIFIER,,,,1;LRR1,downstream_gene_variant,,ENST00000540712,,,MODIFIER,,,,1;LRR1,downstream_gene_variant,,ENST00000554869,,,MODIFIER,,,,1;AL139099.1,downstream_gene_variant,,ENST00000555043,,,MODIFIER,YES,,,-1 291/676 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 0 143 d29cc427-c613-4a80-b958-15d922833322 184 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS RPL36AL,missense_variant,p.K64E,ENST00000298289.7,c.190A>G,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 31 26 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 0 60 d29cc427-c613-4a80-b958-15d922833322 58 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +EIF1AX 1964 BI GRCh38 X 20138617 20138617 + missense_variant Missense_Mutation SNP C C G TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 37 37 c.22G>C p.Gly8Arg p.G8R ENST00000379607.10 NM_001412.4 8 Gga/Cga 2/7 P1 G G/R protein_coding YES CCDS14196.1 22/435 ACCTCCTTTAC PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309305;COSV63309328 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1;1 1.0 probably_damaging(0.991) Unknown deleterious(0.03) 1;1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G8R,ENST00000379607,NM_001412.4,c.22G>C,MODERATE,YES,deleterious(0.03),probably_damaging(0.991),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2776G>C,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 220/4414 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 0 129 d29cc427-c613-4a80-b958-15d922833322 74 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2776G>C,MODIFIER,;EIF1AX,missense_variant,p.G8R,ENST00000379607.10,c.22G>C,MODERATE,YES +FAM47A 158724 BI GRCh38 X 34130460 34130460 + missense_variant Missense_Mutation SNP T T C TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 37 33 c.1819A>G p.Lys607Glu p.K607E ENST00000346193.5 NM_203408.4 607 Aaa/Gaa 1/1 P4 C K/E protein_coding YES CCDS43926.1 1819/2376 GAGTTTTTCCG PANTHER:PTHR47415;PANTHER:PTHR47415:SF4 ENSP00000345029 1/1 COSV60495284 ENST00000346193 Transcript ENSG00000185448 HGNC:29962 MODERATE missense_variant 1 1.0 possibly_damaging(0.448) Unknown tolerated(0.05) 1 Q5JRC9.109 FAM47A HGNC -1 UPI000013F1F4 SNV FAM47A,missense_variant,p.K607E,ENST00000346193,NM_203408.3,c.1819A>G,MODERATE,YES,tolerated(0.05),possibly_damaging(0.448),-1;FAM47A,missense_variant,p.K594E,ENST00000613251,,c.1780A>G,MODERATE,,tolerated(0.06),benign(0.439),-1;AL591501.1,intron_variant,,ENST00000653446,,n.390+53891T>C,MODIFIER,,,,1;AL591501.1,intron_variant,,ENST00000656777,,n.452+53891T>C,MODIFIER,,,,1;AL591501.1,intron_variant,,ENST00000656973,,n.304+53891T>C,MODIFIER,,,,1;AL591501.1,intron_variant,,ENST00000662177,,n.381+53891T>C,MODIFIER,YES,,,1;AL591501.1,intron_variant,,ENST00000665540,,n.379-27636T>C,MODIFIER,,,,1;AL591501.1,intron_variant,,ENST00000668394,,n.495+53891T>C,MODIFIER,,,,1 1852/2556 muse;mutect2;varscan2 a83802da-0219-4cf1-9560-16295363491d 0 66 d29cc427-c613-4a80-b958-15d922833322 70 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS FAM47A,missense_variant,p.K607E,ENST00000346193.5,c.1819A>G,MODERATE,YES;ENSG00000233928,intron_variant,,ENST00000656973.1,n.304+53891T>C,MODIFIER,;ENSG00000233928,intron_variant,,ENST00000665540.1,n.379-27636T>C,MODIFIER,;ENSG00000233928,intron_variant,,ENST00000662177.1,n.381+53891T>C,MODIFIER,;ENSG00000233928,intron_variant,,ENST00000653446.1,n.390+53891T>C,MODIFIER,;ENSG00000233928,intron_variant,,ENST00000656777.1,n.452+53891T>C,MODIFIER,;ENSG00000233928,intron_variant,,ENST00000668394.1,n.495+53891T>C,MODIFIER,YES +LONRF3 79836 BI GRCh38 X 118975358 118975358 + missense_variant Missense_Mutation SNP C C T novel TCGA-WC-A884-01A TCGA-WC-A884-10A Somatic 40 5 c.578C>T p.Ala193Val p.A193V ENST00000371628.8 NM_001031855.3 193 gCg/gTg 1/11 P1 T A/V protein_coding YES CCDS35374.1 578/2280 CTGTGCGCTGT PROSITE_profiles:PS50089;CDD:cd16513;PANTHER:PTHR23327:SF41;PANTHER:PTHR23327;Gene3D:3.30.40.10;SMART:SM00184;Superfamily:SSF57850 ENSP00000360690 1/11 ENST00000371628 Transcript ENSG00000175556 HGNC:21152 MODERATE NM_001031855.3 missense_variant 1.0 benign(0.044) Unknown tolerated(0.43) Q496Y0.138 LONRF3 HGNC 1 1.0 UPI0000211E03 Q496Y0-1 SNV LONRF3,missense_variant,p.A193V,ENST00000371628,NM_001031855.3,c.578C>T,MODERATE,YES,tolerated(0.43),benign(0.044),1;LONRF3,missense_variant,p.A193V,ENST00000304778,NM_024778.5,c.578C>T,MODERATE,,tolerated(0.43),benign(0.007),1;LONRF3,upstream_gene_variant,,ENST00000422289,NM_001289109.1,,MODIFIER,,,,1;LONRF3,upstream_gene_variant,,ENST00000439603,,,MODIFIER,,,,1;LONRF3,upstream_gene_variant,,ENST00000472173,,,MODIFIER,,,,1;LONRF3,missense_variant,p.A193V,ENST00000481285,,c.578C>T,MODERATE,,tolerated(0.45),benign(0.056),1 741/3108 muse;mutect2 a83802da-0219-4cf1-9560-16295363491d 0 35 d29cc427-c613-4a80-b958-15d922833322 45 4b5eb7e3-e9d9-413f-9d77-468dfeb558dd SUCCESS LONRF3,missense_variant,p.A193V,ENST00000371628.8,c.578C>T,MODERATE,YES;LONRF3,missense_variant,NMD_transcript_variant,p.A193V,ENST00000481285.5,c.578C>T,MODERATE,;LONRF3,missense_variant,p.A193V,ENST00000304778.11,c.578C>T,MODERATE, +CHML 1122 BI GRCh38 1 241634661 241634661 + missense_variant Missense_Mutation SNP C C T rs200203736 TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 39 15 c.1106G>A p.Arg369Gln p.R369Q ENST00000366553.3 NM_001381854.1 369 cGg/cAg 2/2 P1 T R/Q protein_coding YES CCDS31073.1 1106/1971 CAAACCGTCCG Gene3D:1.10.405.10;Gene3D:3.30.519.10;Gene3D:3.50.50.60;Pfam:PF00996;PIRSF:PIRSF016550;Prints:PR00891;Prints:PR00893;PANTHER:PTHR11787;PANTHER:PTHR11787:SF9;Superfamily:SSF51905 ENSP00000355511 0.000227 0.0 2/2 rs200203736 ENST00000366553 Transcript ENSG00000203668 HGNC:1941 MODERATE NM_001381853.1 0.000227 AA missense_variant possibly_damaging(0.719) Unknown deleterious(0.01) P26374.165 CHML HGNC -1 2.0 UPI0000073C74 SNV CHML,missense_variant,p.R369Q,ENST00000366553,NM_001381854.1&NM_001381853.1&NM_001821.4,c.1106G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.719),-1;OPN3,intron_variant,,ENST00000366554,NM_014322.3,c.373+5221G>A,MODIFIER,YES,,,-1;CHML,downstream_gene_variant,,ENST00000638018,,,MODIFIER,,,,-1;CHML,downstream_gene_variant,,ENST00000638121,NM_001381856.1,,MODIFIER,,,,-1;CHML,downstream_gene_variant,,ENST00000638160,NM_001381855.1,,MODIFIER,,,,-1;OPN3,intron_variant,,ENST00000463155,,n.75-36664G>A,MODIFIER,,,,-1;CHML,downstream_gene_variant,,ENST00000636025,,,MODIFIER,,,,-1;OPN3,intron_variant,,ENST00000469376,,c.373+5221G>A,MODIFIER,,,,-1;OPN3,intron_variant,,ENST00000478849,,c.329+5221G>A,MODIFIER,,,,-1;OPN3,intron_variant,,ENST00000490673,,c.373+5221G>A,MODIFIER,,,,-1 1901/7711 muse;mutect2;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 7.961e-06 6.155e-05 0.0 0.0 0.0 0.0 8.805e-06 0.0 0.0 4.0588300180388615e-05 4.8676000005798414e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.174940062919632e-05 0.0 6.174940062919632e-05 0.0 0.0 0 65 59c77c22-a720-4839-86c6-05f589e502d3 54 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS CHML,missense_variant,p.R369Q,ENST00000366553.3,c.1106G>A,MODERATE,YES;OPN3,intron_variant,NMD_transcript_variant,,ENST00000478849.1,c.329+5221G>A,MODIFIER,;OPN3,intron_variant,,ENST00000463155.5,n.75-36664G>A,MODIFIER,;OPN3,intron_variant,NMD_transcript_variant,,ENST00000490673.5,c.373+5221G>A,MODIFIER,;OPN3,intron_variant,NMD_transcript_variant,,ENST00000469376.5,c.373+5221G>A,MODIFIER,;OPN3,intron_variant,,ENST00000366554.3,c.373+5221G>A,MODIFIER,YES +BAP1 8314 BI GRCh38 3 52403883 52403883 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 21 33 c.1262del p.Lys421ArgfsTer9 p.K421Rfs*9 ENST00000460680.6 NM_004656.4 421 aAg/ag 13/17 P1 - K/X protein_coding YES CCDS2853.1 1262/2190 GTTCCCTTCCCC MobiDB_lite:mobidb-lite;PANTHER:PTHR10589:SF28;PANTHER:PTHR10589 ENSP00000417132 13/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D deletion BAP1,frameshift_variant,p.K421Rfs*9,ENST00000460680,NM_004656.4,c.1262del,HIGH,YES,,,-1;BAP1,frameshift_variant,p.K403Rfs*9,ENST00000296288,,c.1208del,HIGH,,,,-1;BAP1,frameshift_variant,p.K13Rfs*9,ENST00000469613,,c.37del,HIGH,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000478368,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000490804,,n.690del,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000466093,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 1392/3600 mutect2;pindel;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 0 73 59c77c22-a720-4839-86c6-05f589e502d3 54 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000490804.1,n.690del,MODIFIER,;BAP1,frameshift_variant,p.K403Rfs*9,ENST00000296288.9,c.1208del,HIGH,;BAP1,frameshift_variant,p.R13Gfs*13,ENST00000469613.5,c.37del,HIGH,;BAP1,frameshift_variant,p.K421Rfs*9,ENST00000460680.6,c.1262del,HIGH,YES +TMEM44 93109 BI GRCh38 3 194625907 194625907 + synonymous_variant Silent SNP C C T rs1297791553 TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 11 55 c.348G>A p.Lys116= p.K116= ENST00000392432.6 NM_001166305.2 116 aaG/aaA 3/11 A2 T K protein_coding YES CCDS54699.1 348/1428 TTAGACTTGAA PANTHER:PTHR16201;PANTHER:PTHR16201:SF41 ENSP00000376227 3/11 rs1297791553 ENST00000392432 Transcript ENSG00000145014 HGNC:25120 LOW synonymous_variant 1.0 Unknown Q2T9K0.101 TMEM44 HGNC -1 1.0 UPI00015E0940 Q2T9K0-1 SNV TMEM44,synonymous_variant,p.K116=,ENST00000392432,NM_001166305.2,c.348G>A,LOW,YES,,,-1;TMEM44,synonymous_variant,p.K116=,ENST00000347147,NM_001011655.3,c.348G>A,LOW,,,,-1;TMEM44,synonymous_variant,p.K116=,ENST00000381975,NM_001166306.2,c.348G>A,LOW,,,,-1;TMEM44,synonymous_variant,p.K116=,ENST00000473092,NM_138399.5,c.348G>A,LOW,,,,-1;TMEM44,synonymous_variant,p.K13=,ENST00000330115,,c.39G>A,LOW,,,,-1;TMEM44,synonymous_variant,p.K15=,ENST00000452358,,c.45G>A,LOW,,,,-1;TMEM44,intron_variant,,ENST00000494894,,n.211-2212G>A,MODIFIER,,,,-1;TMEM44,missense_variant,p.S95N,ENST00000430601,,c.284G>A,MODERATE,,,unknown(0),-1;TMEM44,synonymous_variant,p.K13=,ENST00000419280,,c.39G>A,LOW,,,,-1 554/2490 muse;mutect2;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 0 105 59c77c22-a720-4839-86c6-05f589e502d3 66 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS TMEM44,missense_variant,NMD_transcript_variant,p.S95N,ENST00000430601.1,c.284G>A,MODERATE,;TMEM44,synonymous_variant,p.K13=,ENST00000330115.3,c.39G>A,LOW,;TMEM44,intron_variant,,ENST00000494894.5,n.211-2212G>A,MODIFIER,;TMEM44,synonymous_variant,NMD_transcript_variant,p.K13=,ENST00000419280.5,c.39G>A,LOW,;TMEM44,synonymous_variant,p.K15=,ENST00000452358.5,c.45G>A,LOW,;TMEM44,synonymous_variant,p.K116=,ENST00000473092.5,c.348G>A,LOW,;TMEM44,synonymous_variant,p.K116=,ENST00000381975.7,c.348G>A,LOW,;TMEM44,synonymous_variant,p.K116=,ENST00000347147.9,c.348G>A,LOW,YES;TMEM44,synonymous_variant,p.K116=,ENST00000392432.6,c.348G>A,LOW, +CDC40 51362 BI GRCh38 6 110219790 110219790 + missense_variant Missense_Mutation SNP G G A rs1409140018 TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 90 27 c.1261G>A p.Val421Ile p.V421I ENST00000307731.2 NM_015891.3 421 Gtc/Atc 12/15 P1 A V/I protein_coding CCDS5081.1 1261/1740 GAGCTGTCAAC PDB-ENSP_mappings:5mqf.E;PDB-ENSP_mappings:5xjc.W;PDB-ENSP_mappings:5yzg.W;PDB-ENSP_mappings:5z56.W;PDB-ENSP_mappings:5z57.W;PDB-ENSP_mappings:6ff4.E;PDB-ENSP_mappings:6ff7.E;PDB-ENSP_mappings:6icz.W;PDB-ENSP_mappings:6id0.W;PDB-ENSP_mappings:6id1.W;PDB-ENSP_mappings:6qdv.o;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;CDD:cd00200;PANTHER:PTHR43979;Gene3D:2.130.10.10;Pfam:PF00400;SMART:SM00320;Superfamily:SSF50978 ENSP00000304370 12/15 rs1409140018;COSV57011845 ENST00000307731 Transcript ENSG00000168438 HGNC:17350 MODERATE NM_015891.3 2.891e-05 gnomAD_AMR missense_variant 0;1 possibly_damaging(0.789) Unknown tolerated(0.08) 0;1 O60508.179 CDC40 HGNC 1 1.0 UPI0000132145 SNV CDC40,missense_variant,p.V421I,ENST00000368932,,c.1261G>A,MODERATE,YES,tolerated(0.08),possibly_damaging(0.789),1;CDC40,missense_variant,p.V421I,ENST00000307731,NM_015891.3,c.1261G>A,MODERATE,,tolerated(0.08),possibly_damaging(0.789),1;CDC40,missense_variant,p.V421I,ENST00000368930,,c.1261G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.576),1;CDC40,upstream_gene_variant,,ENST00000445340,,,MODIFIER,,,,1;CDC40,non_coding_transcript_exon_variant,,ENST00000606893,,n.2691G>A,MODIFIER,,,,1 1279/3859 muse;mutect2;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 3.977e-06 0.0 2.891e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 101 59c77c22-a720-4839-86c6-05f589e502d3 117 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS CDC40,missense_variant,p.V421I,ENST00000307731.2,c.1261G>A,MODERATE,YES;CDC40,missense_variant,p.V421I,ENST00000368930.5,c.1261G>A,MODERATE,;CDC40,missense_variant,p.V421I,ENST00000368932.5,c.1261G>A,MODERATE,;CDC40,non_coding_transcript_exon_variant,,ENST00000606893.5,n.2691G>A,MODIFIER, +HERC2 8924 BI GRCh38 15 28196492 28196492 + stop_gained Nonsense_Mutation SNP C C A novel TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 55 63 c.8089G>T p.Glu2697Ter p.E2697* ENST00000261609.13 NM_004667.6 2697 Gag/Tag 51/93 P1 A E/* protein_coding YES CCDS10021.1 8089/14505 CAACTCCATTT ENSP00000261609 51/93 ENST00000261609 Transcript 1.0 ENSG00000128731 HGNC:4868 HIGH NM_004667.6 stop_gained 1.0 Unknown O95714.179 HERC2 HGNC -1 1.0 UPI00004578F7 SNV HERC2,stop_gained,p.E2697*,ENST00000261609,NM_004667.6,c.8089G>T,HIGH,YES,,,-1;HERC2,non_coding_transcript_exon_variant,,ENST00000567869,,n.2199G>T,MODIFIER,,,,-1;HERC2,upstream_gene_variant,,ENST00000650509,,,MODIFIER,,,,-1 8225/15364 muse;mutect2;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 0 112 59c77c22-a720-4839-86c6-05f589e502d3 118 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS HERC2,non_coding_transcript_exon_variant,,ENST00000567869.1,n.2199G>T,MODIFIER,;HERC2,stop_gained,p.E2697*,ENST00000261609.13,c.8089G>T,HIGH,YES +CYLD 1540 BI GRCh38 16 50754371 50754371 + missense_variant Missense_Mutation SNP G G T novel TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 62 5 c.860G>T p.Ser287Ile p.S287I ENST00000398568.6 NM_001378746.1 287 aGt/aTt 5/18 A1 T S/I protein_coding CCDS45482.1 860/2871 TTGTAGTTTTG PDB-ENSP_mappings:1whm.A;PANTHER:PTHR11830:SF15;PANTHER:PTHR11830;Gene3D:2.30.30.190;SMART:SM01052;Superfamily:SSF74924 ENSP00000308928 6/20 ENST00000311559 Transcript 1.0 ENSG00000083799 HGNC:2584 MODERATE missense_variant benign(0.265) Unknown deleterious(0.02) Q9NQC7.182 CYLD HGNC 1 5.0 UPI0000073A15 Q9NQC7-1 SNV CYLD,missense_variant,p.S287I,ENST00000427738,NM_001378743.1,c.860G>T,MODERATE,YES,deleterious(0.02),benign(0.265),1;CYLD,missense_variant,p.S287I,ENST00000311559,NM_015247.3,c.860G>T,MODERATE,,deleterious(0.02),benign(0.265),1;CYLD,missense_variant,p.S287I,ENST00000398568,NM_001378746.1&NM_001042412.3&NM_001378752.1&NM_001378747.1&NM_001378750.1&NM_001378748.1&NM_001378755.1,c.860G>T,MODERATE,,deleterious(0.02),benign(0.173),1;CYLD,missense_variant,p.S287I,ENST00000569418,NM_001378745.1&NM_001378744.1&NM_001378753.1&NM_001042355.2&NM_001378751.1&NM_001378754.1&NM_001378749.1,c.860G>T,MODERATE,,deleterious(0.02),benign(0.173),1;CYLD,missense_variant,p.S287I,ENST00000568704,,c.860G>T,MODERATE,,tolerated(0.14),possibly_damaging(0.801),1;CYLD,missense_variant,p.S287I,ENST00000564326,,c.860G>T,MODERATE,,deleterious(0.02),benign(0.173),1;CYLD,missense_variant,p.S287I,ENST00000566206,,c.860G>T,MODERATE,,deleterious(0.03),possibly_damaging(0.776),1;CYLD,missense_variant,p.S287I,ENST00000566679,,c.860G>T,MODERATE,,deleterious(0.02),benign(0.265),1;CYLD,downstream_gene_variant,,ENST00000564634,,,MODIFIER,,,,1;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,,n.1255G>T,MODIFIER,,,,1;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,,n.596G>T,MODIFIER,,,,1 1251/5371 muse;mutect2 743fc661-9ba2-4fa8-966e-508fb4b965e0 0 54 59c77c22-a720-4839-86c6-05f589e502d3 68 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS CYLD,non_coding_transcript_exon_variant,,ENST00000563629.1,n.596G>T,MODIFIER,;CYLD,missense_variant,p.S287I,ENST00000568704.2,c.860G>T,MODERATE,;CYLD,missense_variant,p.S287I,ENST00000398568.6,c.860G>T,MODERATE,;CYLD,missense_variant,p.S287I,ENST00000566679.6,c.860G>T,MODERATE,;CYLD,missense_variant,p.S287I,ENST00000427738.8,c.860G>T,MODERATE,YES;CYLD,missense_variant,p.S287I,ENST00000566206.5,c.860G>T,MODERATE,;CYLD,missense_variant,p.S287I,ENST00000564326.5,c.860G>T,MODERATE,;CYLD,missense_variant,p.S287I,ENST00000311559.13,c.860G>T,MODERATE,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891.5,n.1255G>T,MODIFIER,;CYLD,missense_variant,p.S287I,ENST00000569418.5,c.860G>T,MODERATE, +SIGLEC1 6614 BI GRCh38 20 3693630 3693630 + missense_variant Missense_Mutation SNP C C T rs748962316 TCGA-YZ-A984-01A TCGA-YZ-A984-10A Somatic 13 13 c.3325G>A p.Val1109Met p.V1109M ENST00000344754.6 NM_023068.4 1109 Gtg/Atg 14/22 P1 T V/M protein_coding YES CCDS13060.1 3325/5130 CCACACAAGGC Gene3D:2.60.40.10;Pfam:PF13895;PROSITE_profiles:PS50835;PANTHER:PTHR47243;SMART:SM00409;Superfamily:SSF48726 ENSP00000341141 13/21 rs748962316 ENST00000344754 Transcript ENSG00000088827 HGNC:11127 MODERATE 2.903e-05 gnomAD_AMR missense_variant 1.0 probably_damaging(0.994) Unknown deleterious(0) Q9BZZ2.174 SIGLEC1 HGNC -1 1.0 UPI0000049BA6 Q9BZZ2-1 SNV SIGLEC1,missense_variant,p.V1109M,ENST00000344754,NM_023068.4&NM_001367089.1,c.3325G>A,MODERATE,YES,deleterious(0),probably_damaging(0.994),-1;SIGLEC1,upstream_gene_variant,,ENST00000419548,,,MODIFIER,,,,-1 3325/6720 muse;mutect2;varscan2 743fc661-9ba2-4fa8-966e-508fb4b965e0 4.023e-06 0.0 2.903e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 27 59c77c22-a720-4839-86c6-05f589e502d3 26 74b292a7-a2d4-4dad-974b-aed069b3007a SUCCESS SIGLEC1,missense_variant,p.V1109M,ENST00000707083.1,c.3325G>A,MODERATE,;SIGLEC1,missense_variant,p.V1109M,ENST00000344754.6,c.3325G>A,MODERATE,YES +PUM1 9698 BI GRCh38 1 30964877 30964877 + missense_variant Missense_Mutation SNP C C T rs1368398894 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 68 6 c.2120G>A p.Arg707His p.R707H ENST00000257075.9 NM_014676.3 707 cGt/cAt 14/22 A1 T R/H protein_coding CCDS338.1 2120/3561 AGTCACGGCGG PANTHER:PTHR12537:SF1;PANTHER:PTHR12537 ENSP00000257075 14/22 rs1368398894 ENST00000257075 Transcript 1.0 ENSG00000134644 HGNC:14957 MODERATE missense_variant probably_damaging(0.999) Unknown deleterious(0) Q14671.182 PUM1 HGNC -1 1.0 UPI000014FCE2 Q14671-1 SNV PUM1,missense_variant,p.R707H,ENST00000426105,NM_001020658.2,c.2120G>A,MODERATE,,deleterious(0),probably_damaging(0.966),-1;PUM1,missense_variant,p.R708H,ENST00000373747,,c.2123G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.R707H,ENST00000257075,NM_014676.3,c.2120G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.R465H,ENST00000424085,,c.1394G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.R743H,ENST00000373741,,c.2228G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.R681H,ENST00000440538,,c.2042G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.R648H,ENST00000373742,,c.1943G>A,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.R419H,ENST00000498419,,c.1256G>A,MODERATE,,deleterious(0),probably_damaging(0.993),-1;PUM1,intron_variant,,ENST00000525843,,c.2138+1105G>A,MODIFIER,,,,-1;PUM1,downstream_gene_variant,,ENST00000532678,,,MODIFIER,,,,-1;PUM1,downstream_gene_variant,,ENST00000490546,,,MODIFIER,,,,-1;PUM1,downstream_gene_variant,,ENST00000471894,,,MODIFIER,,,,-1;PUM1,downstream_gene_variant,,ENST00000498627,,,MODIFIER,,,,-1;PUM1,upstream_gene_variant,,ENST00000527498,,,MODIFIER,,,,-1 2214/5360 muse;mutect2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 78 f58bc53d-08f3-4030-908a-741a14b0c999 74 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS PUM1,missense_variant,p.R648H,ENST00000373742.6,c.1943G>A,MODERATE,;PUM1,missense_variant,p.R743H,ENST00000373741.8,c.2228G>A,MODERATE,;PUM1,synonymous_variant,p.P418=,ENST00000498419.5,c.1254G>A,LOW,;PUM1,missense_variant,p.R681H,ENST00000440538.6,c.2042G>A,MODERATE,;PUM1,intron_variant,,ENST00000525843.5,c.2138+1105G>A,MODIFIER,;PUM1,missense_variant,p.R707H,ENST00000257075.9,c.2120G>A,MODERATE,;PUM1,missense_variant,p.R465H,ENST00000424085.6,c.1394G>A,MODERATE,;PUM1,missense_variant,p.R707H,ENST00000426105.7,c.2120G>A,MODERATE,YES;PUM1,missense_variant,p.R708H,ENST00000373747.7,c.2123G>A,MODERATE, +MACF1 23499 BI GRCh38 1 39331278 39331278 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 29 6 c.4705G>C p.Gly1569Arg p.G1569R ENST00000372915.8 1569 Ggc/Cgc 36/96 A2 C G/R protein_coding 4705/22158 AAAAGGGCCTC Gene3D:3.90.1290.10;PANTHER:PTHR23169;PANTHER:PTHR23169:SF24;SMART:SM00250;Superfamily:SSF75399 ENSP00000362006 36/96 ENST00000372915 Transcript 1.0 ENSG00000127603 HGNC:13664 MODERATE missense_variant Unknown Q9UPN3.196 MACF1 HGNC 1 5.0 Q9UPN3-1 SNV MACF1,missense_variant,p.G1564R,ENST00000564288,,c.4690G>C,MODERATE,,deleterious(0.02),probably_damaging(1),1;MACF1,missense_variant,p.G1601R,ENST00000567887,,c.4801G>C,MODERATE,YES,deleterious(0.02),probably_damaging(1),1;MACF1,missense_variant,p.G1569R,ENST00000372915,,c.4705G>C,MODERATE,,,,1;MACF1,missense_variant,p.G1513R,ENST00000672812,,c.4537G>C,MODERATE,,tolerated(0.07),probably_damaging(0.997),1;MACF1,intron_variant,,ENST00000361689,NM_012090.5,c.4629+3925G>C,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000372925,,c.2029+3925G>C,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000530262,,c.5076+3925G>C,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000671089,,c.4476+3925G>C,MODIFIER,,,,1;MACF1,intron_variant,,ENST00000476350,,n.2029+3925G>C,MODIFIER,,,,1;MACF1,downstream_gene_variant,,ENST00000528611,,,MODIFIER,,,,1;MACF1,3_prime_UTR_variant,,ENST00000673926,,c.*164G>C,MODIFIER,,,,1;MACF1,non_coding_transcript_exon_variant,,ENST00000289893,,n.141G>C,MODIFIER,,,,1;MACF1,downstream_gene_variant,,ENST00000496804,,,MODIFIER,,,,1 4792/23431 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 48 f58bc53d-08f3-4030-908a-741a14b0c999 35 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS MACF1,non_coding_transcript_exon_variant,,ENST00000289893.8,n.141G>C,MODIFIER,;MACF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673926.1,c.*164G>C,MODIFIER,;MACF1,intron_variant,,ENST00000476350.1,n.2029+3925G>C,MODIFIER,;MACF1,intron_variant,,ENST00000372925.6,c.2029+3925G>C,MODIFIER,;MACF1,intron_variant,,ENST00000530262.5,c.5076+3925G>C,MODIFIER,;MACF1,intron_variant,,ENST00000671089.2,c.4476+3925G>C,MODIFIER,;MACF1,missense_variant,p.G1564R,ENST00000564288.6,c.4690G>C,MODERATE,YES;MACF1,missense_variant,p.G1513R,ENST00000672812.1,c.4537G>C,MODERATE,;MACF1,missense_variant,p.G1569R,ENST00000372915.8,c.4705G>C,MODERATE,;MACF1,missense_variant,p.G1601R,ENST00000567887.5,c.4801G>C,MODERATE,;MACF1,intron_variant,,ENST00000361689.7,c.4629+3925G>C,MODIFIER, +HHAT 55733 BI GRCh38 1 210349034 210349034 + missense_variant Missense_Mutation SNP A A G rs1183312420 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 50 16 c.59A>G p.Tyr20Cys p.Y20C ENST00000261458.8 NM_018194.6 20 tAt/tGt 2/12 P2 G Y/C protein_coding CCDS1495.1 59/1482 CTTCTATTCCT PANTHER:PTHR13285;PANTHER:PTHR13285:SF20;Transmembrane_helices:TMhelix ENSP00000261458 2/12 rs1183312420 ENST00000261458 Transcript 1.0 ENSG00000054392 HGNC:18270 MODERATE NM_018194.6 5.792e-05 gnomAD_AMR missense_variant probably_damaging(0.945) Unknown deleterious(0) Q5VTY9.143 HHAT HGNC 1 2.0 UPI000004A086 Q5VTY9-1 SNV HHAT,missense_variant,p.Y20C,ENST00000261458,NM_018194.6,c.59A>G,MODERATE,,deleterious(0),probably_damaging(0.945),1;HHAT,missense_variant,p.Y20C,ENST00000367010,NM_001170580.3,c.59A>G,MODERATE,,deleterious(0),probably_damaging(0.945),1;HHAT,missense_variant,p.Y20C,ENST00000413764,NM_001122834.3,c.59A>G,MODERATE,,deleterious(0),probably_damaging(0.945),1;HHAT,missense_variant,p.Y20C,ENST00000537898,NM_001170588.2,c.59A>G,MODERATE,,deleterious(0),possibly_damaging(0.754),1;HHAT,missense_variant,p.Y20C,ENST00000541565,NM_001170564.2,c.59A>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.754),1;HHAT,intron_variant,,ENST00000545154,NM_001170587.2,c.95-13818A>G,MODIFIER,YES,,,1 305/3639 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 1.591e-05 0.0 5.792e-05 0.0 5.437e-05 0.0 8.795e-06 0.0 0.0 0 60 f58bc53d-08f3-4030-908a-741a14b0c999 66 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS HHAT,missense_variant,p.Y20C,ENST00000367010.5,c.59A>G,MODERATE,;HHAT,missense_variant,p.Y20C,ENST00000537898.5,c.59A>G,MODERATE,;HHAT,intron_variant,,ENST00000545154.5,c.95-13818A>G,MODIFIER,;HHAT,missense_variant,p.Y20C,ENST00000261458.8,c.59A>G,MODERATE,YES;HHAT,missense_variant,p.Y20C,ENST00000541565.5,c.59A>G,MODERATE,;HHAT,missense_variant,p.Y20C,ENST00000413764.6,c.59A>G,MODERATE, +DYSF 8291 BI GRCh38 2 71528320 71528320 + synonymous_variant Silent SNP C C T rs757047049 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 12 5 c.1203C>T p.Asn401= p.N401= ENST00000258104.8 NM_003494.4 401 aaC/aaT 13/55 T N protein_coding CCDS1918.1 1203/6243 likely_benign GACAACGTGAA Gene3D:2.60.40.150;Pfam:PF00168;PROSITE_profiles:PS50004;PANTHER:PTHR12546;PANTHER:PTHR12546:SF44;SMART:SM00239;Superfamily:SSF49562;CDD:cd04018 ENSP00000258104 13/55 rs757047049;COSV99247642 ENST00000258104 Transcript 1.0 ENSG00000135636 HGNC:3097 LOW 2.894e-05 gnomAD_AMR synonymous_variant 1;1 Unknown 0;1 O75923.188 DYSF HGNC 1 1.0 UPI0000129A56 O75923-1 SNV DYSF,synonymous_variant,p.N401=,ENST00000258104,NM_003494.4&NM_001130976.2,c.1203C>T,LOW,,,,1;DYSF,synonymous_variant,p.N432=,ENST00000409582,NM_001130981.2,c.1296C>T,LOW,,,,1;DYSF,synonymous_variant,p.N433=,ENST00000410020,NM_001130987.2,c.1299C>T,LOW,YES,,,1;DYSF,synonymous_variant,p.N432=,ENST00000413539,NM_001130979.2,c.1296C>T,LOW,,,,1;DYSF,synonymous_variant,p.N401=,ENST00000429174,NM_001130978.2&NM_001130977.2,c.1203C>T,LOW,,,,1;DYSF,synonymous_variant,p.N432=,ENST00000409762,NM_001130980.2,c.1296C>T,LOW,,,,1;DYSF,synonymous_variant,p.N433=,ENST00000409651,NM_001130982.2,c.1299C>T,LOW,,,,1;DYSF,synonymous_variant,p.N402=,ENST00000409366,NM_001130983.2,c.1206C>T,LOW,,,,1;DYSF,synonymous_variant,p.N433=,ENST00000410041,NM_001130985.2,c.1299C>T,LOW,,,,1;DYSF,synonymous_variant,p.N402=,ENST00000409744,NM_001130984.2,c.1206C>T,LOW,,,,1;DYSF,synonymous_variant,p.N402=,ENST00000394120,NM_001130455.2&NM_001130986.2,c.1206C>T,LOW,,,,1 1480/6796 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 1.592e-05 0.0 2.894e-05 0.0 0.0 0.0 2.639e-05 0.0 0.0 0 24 f58bc53d-08f3-4030-908a-741a14b0c999 18 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS DYSF,synonymous_variant,p.N402=,ENST00000394120.6,c.1206C>T,LOW,;DYSF,synonymous_variant,p.N433=,ENST00000410041.1,c.1299C>T,LOW,;DYSF,synonymous_variant,p.N433=,ENST00000409651.5,c.1299C>T,LOW,;DYSF,synonymous_variant,p.N402=,ENST00000409744.5,c.1206C>T,LOW,;DYSF,synonymous_variant,p.N402=,ENST00000409366.5,c.1206C>T,LOW,;DYSF,synonymous_variant,p.N433=,ENST00000410020.8,c.1299C>T,LOW,YES;DYSF,synonymous_variant,p.N432=,ENST00000409762.5,c.1296C>T,LOW,;DYSF,synonymous_variant,p.N401=,ENST00000429174.6,c.1203C>T,LOW,;DYSF,synonymous_variant,p.N432=,ENST00000413539.6,c.1296C>T,LOW,;DYSF,synonymous_variant,p.N432=,ENST00000409582.7,c.1296C>T,LOW,;DYSF,synonymous_variant,p.N401=,ENST00000258104.8,c.1203C>T,LOW, +RAB11FIP5 26056 BI GRCh38 2 73088961 73088961 + synonymous_variant Silent SNP G G A rs774431399 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 46 9 c.786C>T p.Ser262= p.S262= ENST00000258098.6 NM_015470.3 262 agC/agT 2/5 P1 A S protein_coding CCDS1923.1 786/1962 CTCCCGCTGGC PANTHER:PTHR15746;PANTHER:PTHR15746:SF14;Low_complexity_(Seg):seg ENSP00000258098 2/5 rs774431399 ENST00000258098 Transcript ENSG00000135631 HGNC:24845 LOW 0.0001088 gnomAD_EAS synonymous_variant Unknown Q9BXF6.161 RAB11FIP5 HGNC -1 1.0 UPI000007079C SNV RAB11FIP5,synonymous_variant,p.S262=,ENST00000486777,NM_001371272.1,c.786C>T,LOW,YES,,,-1;RAB11FIP5,synonymous_variant,p.S262=,ENST00000258098,NM_015470.3,c.786C>T,LOW,,,,-1;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,,n.695C>T,MODIFIER,,,,-1;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000475951,,n.439C>T,MODIFIER,,,,-1;RAB11FIP5,upstream_gene_variant,,ENST00000479196,,,MODIFIER,,,,-1;RAB11FIP5,upstream_gene_variant,,ENST00000482554,,,MODIFIER,,,,-1 1027/4342 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 1.997e-05 0.0 0.0 0.0 0.0001088 0.0 0.0 0.0 9.816e-05 6.757580194971524e-06 0.0 0.0 6.620759813813493e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 53 f58bc53d-08f3-4030-908a-741a14b0c999 55 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000475951.1,n.439C>T,MODIFIER,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523.2,n.695C>T,MODIFIER,;RAB11FIP5,synonymous_variant,p.S262=,ENST00000486777.7,c.786C>T,LOW,YES;RAB11FIP5,synonymous_variant,p.S262=,ENST00000258098.6,c.786C>T,LOW, +MAP3K19 80122 BI GRCh38 2 134980903 134980903 + missense_variant Missense_Mutation SNP C C T rs779120521 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 36 6 c.3838G>A p.Gly1280Arg p.G1280R ENST00000375845.8 NM_001321177.2 1280 Gga/Aga 9/10 A2 T G/R protein_coding CCDS2176.2 3838/3987 TGCTCCGATGT Superfamily:SSF56112;SMART:SM00220;Gene3D:1.10.510.10;Pfam:PF00069;PANTHER:PTHR45832;PANTHER:PTHR45832:SF5;CDD:cd06631;PROSITE_profiles:PS50011 ENSP00000365005 9/10 rs779120521 ENST00000375845 Transcript ENSG00000176601 HGNC:26249 MODERATE 3.266e-05 gnomAD_SAS missense_variant probably_damaging(1) Unknown deleterious(0) Q56UN5.134 MAP3K19 HGNC -1 1.0 UPI00004F77F2 Q56UN5-1 SNV MAP3K19,missense_variant,p.G1280R,ENST00000392915,,c.3838G>A,MODERATE,YES,deleterious(0),probably_damaging(1),-1;MAP3K19,missense_variant,p.G1280R,ENST00000375845,NM_025052.4&NM_001321177.1,c.3838G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;MAP3K19,missense_variant,p.G1167R,ENST00000358371,NM_001018044.2,c.3499G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;MAP3K19,missense_variant,p.G670R,ENST00000437365,,c.2008G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;MAP3K19,missense_variant,p.G462R,ENST00000375844,NM_001018046.2,c.1384G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;MAP3K19,missense_variant,p.G414R,ENST00000392918,NM_001018047.2,c.1240G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;MAP3K19,missense_variant,p.G412R,ENST00000392917,NM_001282883.1,c.1234G>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;MAP3K19,downstream_gene_variant,,ENST00000637841,,,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,,n.4161G>A,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661220,,n.741G>A,MODIFIER,,,,-1;MAP3K19,downstream_gene_variant,,ENST00000669737,,,MODIFIER,,,,-1;MAP3K19,3_prime_UTR_variant,,ENST00000662522,,c.*3188G>A,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000669521,,n.750G>A,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000668969,,n.971G>A,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661533,,n.890G>A,MODIFIER,,,,-1;MAP3K19,non_coding_transcript_exon_variant,,ENST00000478805,,n.916G>A,MODIFIER,,,,-1 3869/4369 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 7.956e-06 0.0 0.0 0.0 0.0 0.0 8.797e-06 0.0 3.266e-05 0 35 f58bc53d-08f3-4030-908a-741a14b0c999 43 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025.2,n.4161G>A,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000478805.1,n.916G>A,MODIFIER,;MAP3K19,missense_variant,p.G670R,ENST00000437365.2,c.2008G>A,MODERATE,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000669521.1,n.750G>A,MODIFIER,;MAP3K19,missense_variant,p.G414R,ENST00000392918.7,c.1240G>A,MODERATE,;MAP3K19,missense_variant,p.G412R,ENST00000392917.8,c.1234G>A,MODERATE,;MAP3K19,missense_variant,p.G462R,ENST00000375844.7,c.1384G>A,MODERATE,;MAP3K19,missense_variant,p.G1280R,ENST00000375845.8,c.3838G>A,MODERATE,;MAP3K19,missense_variant,p.G1280R,ENST00000392915.7,c.3838G>A,MODERATE,YES;MAP3K19,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000662522.1,c.*3188G>A,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661533.1,n.890G>A,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000668969.1,n.971G>A,MODIFIER,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000661220.1,n.741G>A,MODIFIER,;MAP3K19,missense_variant,p.G1167R,ENST00000358371.9,c.3499G>A,MODERATE, +TTN 7273 BI GRCh38 2 178718746 178718746 + missense_variant Missense_Mutation SNP C C T rs397517507 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 45 12 c.23503G>A p.Val7835Ile p.V7835I ENST00000591111.5 7835 Gtt/Att 82/313 T V/I protein_coding 23503/103053 uncertain_significance TGTAACGAGGC COSM3837900;COSM3837901 Gene3D:2.60.40.10;Pfam:PF07679;PROSITE_profiles:PS50835;PANTHER:PTHR13817;PANTHER:PTHR13817:SF10;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096 ENSP00000465570 82/313 rs397517507;COSV60334381 ENST00000591111 Transcript 1.0 ENSG00000155657 HGNC:12403 MODERATE 0.0003316 gnomAD_OTH missense_variant 1;1 24033266 benign(0.012) Unknown 0;1 Q8WZ42.192 TTN HGNC -1 5.0 UPI00025287CD Q8WZ42-1 SNV TTN,missense_variant,p.V8152I,ENST00000589042,NM_001267550.2,c.24454G>A,MODERATE,YES,,benign(0.012),-1;TTN,missense_variant,p.V7835I,ENST00000591111,,c.23503G>A,MODERATE,,,benign(0.012),-1;TTN,missense_variant,p.V6908I,ENST00000342992,NM_133378.4&NM_001256850.1,c.20722G>A,MODERATE,,,benign(0.021),-1;TTN,intron_variant,,ENST00000342175,NM_133437.4,c.13858+19336G>A,MODIFIER,,,,-1;TTN,intron_variant,,ENST00000359218,NM_133432.3,c.13657+19336G>A,MODIFIER,,,,-1;TTN,intron_variant,,ENST00000460472,NM_003319.4,c.13282+19336G>A,MODIFIER,,,,-1;TTN-AS1,intron_variant,,ENST00000585451,,n.199-42194C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590773,,n.684-15758C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625480,,n.136-15758C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000653807,,n.416-15758C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000657023,,n.315-19188C>T,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000659121,,n.503-15758C>T,MODIFIER,YES,,,1;TTN-AS1,downstream_gene_variant,,ENST00000431752,,,MODIFIER,,,,1;TTN-AS1,downstream_gene_variant,,ENST00000589830,,,MODIFIER,,,,1;AC010680.1,upstream_gene_variant,,ENST00000590024,,,MODIFIER,YES,,,1;TTN-AS1,downstream_gene_variant,,ENST00000592600,,,MODIFIER,,,,1;TTN-AS1,downstream_gene_variant,,ENST00000592630,,,MODIFIER,,,,1;TTN-AS1,downstream_gene_variant,,ENST00000625536,,,MODIFIER,,,,1;TTN-AS1,downstream_gene_variant,,ENST00000626117,,,MODIFIER,,,,1;TTN-AS1,downstream_gene_variant,,ENST00000671355,,,MODIFIER,,,,1 23728/104301 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 5.632e-05 6.458e-05 5.797e-05 0.0 0.0002785 0.0 8.892e-06 0.0003316 9.807e-05 4.734659887617454e-05 7.298910350073129e-05 0.0 6.632180156884715e-05 0.0 0.0004043669905513 0.0 eas 0.0004043669905513 0.0 1.543729922559578e-05 0.0 0.0 0 83 f58bc53d-08f3-4030-908a-741a14b0c999 57 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS TTN-AS1,intron_variant,,ENST00000625480.2,n.136-15758C>T,MODIFIER,;TTN,missense_variant,p.V6908I,ENST00000342992.11,c.20722G>A,MODERATE,;TTN,missense_variant,p.V8152I,ENST00000425332.3,c.24454G>A,MODERATE,;TTN,missense_variant,p.V7835I,ENST00000591111.5,c.23503G>A,MODERATE,;TTN,missense_variant,p.V8152I,ENST00000589042.5,c.24454G>A,MODERATE,YES;TTN,missense_variant,p.V8014I,ENST00000715174.1,c.24040G>A,MODERATE,;TTN,intron_variant,,ENST00000342175.12,c.13858+19336G>A,MODIFIER,;TTN,intron_variant,,ENST00000460472.6,c.13282+19336G>A,MODIFIER,;TTN,missense_variant,p.V8060I,ENST00000436599.2,c.24178G>A,MODERATE,;TTN,intron_variant,,ENST00000359218.11,c.13657+19336G>A,MODIFIER,;TTN,missense_variant,p.V8152I,ENST00000446966.2,c.24454G>A,MODERATE,;TTN,missense_variant,p.V8152I,ENST00000426232.6,c.24454G>A,MODERATE,;TTN,missense_variant,p.V8152I,ENST00000412264.2,c.24454G>A,MODERATE,;TTN-AS1,intron_variant,,ENST00000657023.1,n.315-19188C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000585451.5,n.199-42194C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000653807.1,n.416-15758C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590773.6,n.684-15758C>T,MODIFIER,;TTN-AS1,intron_variant,,ENST00000659121.1,n.503-15758C>T,MODIFIER,YES +ZNF197 10168 BI GRCh38 3 44629167 44629167 + missense_variant Missense_Mutation SNP A A G rs1701835474 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 46 16 c.13A>G p.Asn5Asp p.N5D ENST00000344387.9 NM_001323293.2 5 Aat/Gat 2/6 P1 G N/D protein_coding YES CCDS2717.1 13/3090 GAGAAAATGTA ENSP00000345809 2/6 ENST00000344387 Transcript ENSG00000186448 HGNC:12988 MODERATE NM_006991.5 missense_variant 1.0 probably_damaging(0.952) Unknown tolerated_low_confidence(0.06) O14709.185 ZNF197 HGNC 1 1.0 UPI000013C317 O14709-1 SNV ZNF197,missense_variant,p.N5D,ENST00000344387,NM_001323293.2&NM_001323295.2&NM_006991.5&NM_001323296.2,c.13A>G,MODERATE,YES,tolerated_low_confidence(0.06),probably_damaging(0.952),1;ZNF197,missense_variant,p.N5D,ENST00000396058,NM_001351733.2&NM_001351732.2,c.13A>G,MODERATE,,tolerated_low_confidence(0.06),probably_damaging(0.952),1;ZNF197,missense_variant,p.N5D,ENST00000383745,NM_001351735.2&NM_001351734.2&NM_001024855.3&NM_001323294.2,c.13A>G,MODERATE,,deleterious_low_confidence(0.03),benign(0.339),1;ZNF197,missense_variant,p.N5D,ENST00000383744,,c.13A>G,MODERATE,,deleterious_low_confidence(0.03),benign(0.339),1;ZNF197,missense_variant,p.N5D,ENST00000412641,,c.13A>G,MODERATE,,tolerated_low_confidence(0.19),probably_damaging(0.952),1;ZNF197,missense_variant,p.N5D,ENST00000334075,,c.13A>G,MODERATE,,tolerated_low_confidence(0.13),benign(0.291),1;ZKSCAN7-AS1,intron_variant,,ENST00000457331,,n.220+32095T>C,MODIFIER,YES,,,-1;ZNF197-AS1,upstream_gene_variant,,ENST00000447691,,,MODIFIER,YES,,,-1 202/7530 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 6.7597698034660425e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002084199950331 0 102 f58bc53d-08f3-4030-908a-741a14b0c999 63 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS ZNF197,missense_variant,p.N5D,ENST00000396058.1,c.13A>G,MODERATE,;ZNF197,missense_variant,NMD_transcript_variant,p.N5D,ENST00000334075.6,c.13A>G,MODERATE,;ZNF197,missense_variant,p.N5D,ENST00000383745.6,c.13A>G,MODERATE,;ZNF197,missense_variant,p.N5D,ENST00000344387.9,c.13A>G,MODERATE,YES;ZNF197,missense_variant,p.N5D,ENST00000383744.8,c.13A>G,MODERATE,;ZNF197,missense_variant,p.N5D,ENST00000412641.1,c.13A>G,MODERATE,;ZKSCAN7-AS1,intron_variant,,ENST00000457331.2,n.232+32095T>C,MODIFIER,YES;ZKSCAN7-AS1,intron_variant,,ENST00000685649.2,n.224+32095T>C,MODIFIER, +MROH2B 133558 BI GRCh38 5 41039464 41039464 + frameshift_variant Frame_Shift_Del DEL A A - TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 6 4 c.2045del p.Phe682SerfsTer2 p.F682Sfs*2 ENST00000399564.5 NM_173489.5 682 tTc/tc 20/42 P2 - F/X protein_coding YES CCDS47202.1 2045/4758 TTCATGAAAAAC PANTHER:PTHR23120;PANTHER:PTHR23120:SF22;Superfamily:SSF48371 ENSP00000382476 20/42 COSV68181667 ENST00000399564 Transcript ENSG00000171495 HGNC:26857 HIGH NM_173489.5 frameshift_variant 1 1.0 Unknown 1 Q7Z745.131 MROH2B HGNC -1 1.0 UPI000020CA04 Q7Z745-1 deletion MROH2B,frameshift_variant,p.F682Sfs*2,ENST00000399564,NM_173489.5,c.2045del,HIGH,YES,,,-1;MROH2B,frameshift_variant,p.F237Sfs*2,ENST00000506092,,c.710del,HIGH,,,,-1;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,,n.1433del,MODIFIER,,,,-1;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,,n.1007del,MODIFIER,,,,-1 2535/5280 mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 10 f58bc53d-08f3-4030-908a-741a14b0c999 10 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS MROH2B,frameshift_variant,p.F237Sfs*2,ENST00000506092.6,c.710del,HIGH,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890.5,n.1007del,MODIFIER,;MROH2B,frameshift_variant,p.F682Sfs*2,ENST00000399564.5,c.2045del,HIGH,YES;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297.5,n.1433del,MODIFIER, +MCHR2 84539 BI GRCh38 6 99921201 99921201 + synonymous_variant Silent SNP C C T rs1177416702 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 70 15 c.762G>A p.Leu254= p.L254= ENST00000281806.7 NM_032503.3 254 ctG/ctA 6/6 P1 T L protein_coding YES CCDS5044.1 762/1023 AGCACCAGCAC Gene3D:1.20.1070.10;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24230;PANTHER:PTHR24230:SF7;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15339;Low_complexity_(Seg):seg ENSP00000281806 6/6 rs1177416702 ENST00000281806 Transcript ENSG00000152034 HGNC:20867 LOW NM_001040179.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q969V1.143 MCHR2 HGNC -1 2.0 UPI000003730F SNV MCHR2,synonymous_variant,p.L254=,ENST00000281806,NM_001040179.2,c.762G>A,LOW,YES,,,-1;MCHR2,synonymous_variant,p.L254=,ENST00000369212,NM_032503.2,c.762G>A,LOW,,,,-1 1077/3759 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 106 f58bc53d-08f3-4030-908a-741a14b0c999 85 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS MCHR2,synonymous_variant,p.L254=,ENST00000369212.2,c.762G>A,LOW,;MCHR2,synonymous_variant,p.L254=,ENST00000281806.7,c.762G>A,LOW,YES +AKAP9 10142 BI GRCh38 7 92029944 92029944 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 63 16 c.4198A>G p.Met1400Val p.M1400V ENST00000356239.8 NM_005751.5 1400 Atg/Gtg 15/50 A2 G M/V protein_coding YES 4198/11796 GAACAATGTAC PANTHER:PTHR44981;PANTHER:PTHR44981:SF1 ENSP00000351922 15/51 ENST00000359028 Transcript 1.0 ENSG00000127914 HGNC:379 MODERATE missense_variant 1.0 benign(0) Unknown tolerated(1) AKAP9 HGNC 1 A0A0A0MRF6.46 5.0 UPI0007DC7372 SNV AKAP9,missense_variant,p.M1400V,ENST00000356239,NM_005751.5&NM_147185.3,c.4198A>G,MODERATE,,tolerated(1),benign(0),1;AKAP9,missense_variant,p.M1400V,ENST00000359028,,c.4198A>G,MODERATE,YES,tolerated(1),benign(0),1;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,,n.4418A>G,MODIFIER,,,,1 4198/12219 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 98 f58bc53d-08f3-4030-908a-741a14b0c999 79 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS AKAP9,missense_variant,p.M1400V,ENST00000359028.7,c.4198A>G,MODERATE,;AKAP9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000674381.2,c.*3927A>G,MODIFIER,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453.1,n.4418A>G,MODIFIER,;AKAP9,missense_variant,NMD_transcript_variant,p.M1400V,ENST00000679448.1,c.4198A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680766.1,c.4198A>G,MODERATE,;AKAP9,non_coding_transcript_exon_variant,,ENST00000679474.1,n.4420A>G,MODIFIER,;AKAP9,non_coding_transcript_exon_variant,,ENST00000680074.1,n.4420A>G,MODIFIER,;AKAP9,missense_variant,p.M1400V,ENST00000681412.1,c.4198A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680952.1,c.4198A>G,MODERATE,;AKAP9,non_coding_transcript_exon_variant,,ENST00000679722.1,n.4420A>G,MODIFIER,;AKAP9,missense_variant,NMD_transcript_variant,p.M1400V,ENST00000679457.1,c.4198A>G,MODERATE,;AKAP9,non_coding_transcript_exon_variant,,ENST00000680047.1,n.4420A>G,MODIFIER,;AKAP9,missense_variant,p.M1400V,ENST00000356239.8,c.4198A>G,MODERATE,YES;AKAP9,missense_variant,p.M1400V,ENST00000681722.1,c.4198A>G,MODERATE,;AKAP9,missense_variant,p.M1382V,ENST00000679521.1,c.4144A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680181.1,c.4198A>G,MODERATE,;AKAP9,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000679554.1,c.*3983A>G,MODIFIER,;AKAP9,missense_variant,p.M1314V,ENST00000679821.1,c.3940A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680513.1,c.4198A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680534.1,c.4198A>G,MODERATE,;AKAP9,missense_variant,p.M1400V,ENST00000680072.1,c.4198A>G,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 59 17 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 83 f58bc53d-08f3-4030-908a-741a14b0c999 76 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +ITPR2 3709 BI GRCh38 12 26790185 26790185 + synonymous_variant Silent SNP G G A rs1418631524 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 58 18 c.135C>T p.Asp45= p.D45= ENST00000381340.8 NM_002223.4 45 gaC/gaT 2/57 P1 A D protein_coding YES CCDS41764.1 135/8106 GCAAGGTCCCC Pfam:PF08709;Gene3D:2.80.10.50 ENSP00000370744 2/57 rs1418631524 ENST00000381340 Transcript 1.0 ENSG00000123104 HGNC:6181 LOW NM_002223.4 synonymous_variant 1.0 Unknown Q14571.198 ITPR2 HGNC -1 1.0 UPI00001FB7D2 Q14571-1 SNV ITPR2,synonymous_variant,p.D45=,ENST00000381340,NM_002223.4,c.135C>T,LOW,YES,,,-1;ITPR2,synonymous_variant,p.D45=,ENST00000242737,,c.135C>T,LOW,,,,-1;ITPR2,intron_variant,,ENST00000545235,,c.92+42505C>T,MODIFIER,,,,-1 548/12564 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 6.766079877706943e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5436900866916403e-05 0.0 0.0 0 87 f58bc53d-08f3-4030-908a-741a14b0c999 76 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS ITPR2,synonymous_variant,p.D45=,ENST00000242737.5,c.135C>T,LOW,;ITPR2,intron_variant,NMD_transcript_variant,,ENST00000545235.1,c.92+42505C>T,MODIFIER,;ITPR2,synonymous_variant,p.D45=,ENST00000381340.8,c.135C>T,LOW,YES +WDR25 79446 BI GRCh38 14 100529915 100529915 + synonymous_variant Silent SNP C C T novel TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 59 14 c.1509C>T p.Arg503= p.R503= ENST00000335290.10 NM_001350947.2 503 cgC/cgT 7/7 P1 T R protein_coding YES CCDS32157.1 1509/1635 TTCCGCACAGC Gene3D:2.130.10.10;PROSITE_profiles:PS50294;PANTHER:PTHR42968;PANTHER:PTHR42968:SF4;Superfamily:SSF50978 ENSP00000334148 7/7 ENST00000335290 Transcript ENSG00000176473 HGNC:21064 LOW synonymous_variant 1.0 Unknown Q64LD2.139 WDR25 HGNC 1 A0A384NPW5.8 1.0 UPI0000D4CFD0 Q64LD2-1 SNV WDR25,synonymous_variant,p.R503=,ENST00000335290,NM_001350947.2&NM_024515.6,c.1509C>T,LOW,YES,,,1;WDR25,synonymous_variant,p.R503=,ENST00000402312,NM_001161476.2&NM_001350950.1,c.1509C>T,LOW,,,,1;WDR25,synonymous_variant,p.R503=,ENST00000554998,NM_001350948.1&NM_001350949.1,c.1509C>T,LOW,,,,1;WDR25,synonymous_variant,p.R246=,ENST00000542471,,c.738C>T,LOW,,,,1;WDR25,downstream_gene_variant,,ENST00000555201,,,MODIFIER,,,,1;WDR25,non_coding_transcript_exon_variant,,ENST00000557502,,n.697C>T,MODIFIER,,,,1;WDR25,non_coding_transcript_exon_variant,,ENST00000555865,,n.647C>T,MODIFIER,,,,1;WDR25,downstream_gene_variant,,ENST00000554492,,,MODIFIER,,,,1;WDR25,downstream_gene_variant,,ENST00000555775,,,MODIFIER,,,,1;WDR25,3_prime_UTR_variant,,ENST00000557710,,c.*491C>T,MODIFIER,,,,1 1735/2123 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 86 f58bc53d-08f3-4030-908a-741a14b0c999 73 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS WDR25,non_coding_transcript_exon_variant,,ENST00000557502.1,n.697C>T,MODIFIER,;WDR25,non_coding_transcript_exon_variant,,ENST00000555865.5,n.647C>T,MODIFIER,;WDR25,synonymous_variant,p.R246=,ENST00000542471.2,c.738C>T,LOW,;WDR25,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000557710.5,c.*491C>T,MODIFIER,;WDR25,synonymous_variant,p.R503=,ENST00000335290.10,c.1509C>T,LOW,;WDR25,synonymous_variant,p.R503=,ENST00000402312.8,c.1509C>T,LOW,YES;WDR25,synonymous_variant,p.R503=,ENST00000554998.5,c.1509C>T,LOW, +DTNA 1837 BI GRCh38 18 34879720 34879720 + splice_donor_variant Splice_Site SNP G G A TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 35 9 c.2081+1G>A p.X694_splice p.X694_splice ENST00000399113.7 NM_001390.5 694 A1 A protein_coding GACATGTGAGT COSM399776;COSM399777;COSM399778 ENSP00000382064 COSV52008415 ENST00000399113 Transcript NonExonic 1.0 ENSG00000134769 HGNC:3057 HIGH 19/20 splice_donor_variant 1 Unknown 1 Q9Y4J8.191 DTNA HGNC 1 5.0 UPI000013DD3C Q9Y4J8-1 SNV DTNA,splice_donor_variant,p.X403_splice,ENST00000269192,NM_001198942.1,c.1208+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X637_splice,ENST00000283365,NM_032975.3,c.1910+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X694_splice,ENST00000399113,,c.2081+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X641_splice,ENST00000399121,NM_001198939.2,c.1922+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X694_splice,ENST00000444659,NM_001390.4,c.2081+1G>A,HIGH,YES,,,1;DTNA,splice_donor_variant,p.X346_splice,ENST00000556414,NM_001198944.1,c.1037+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X120_splice,ENST00000590831,,c.359+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X342_splice,ENST00000591182,NM_032980.4,c.1025+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X634_splice,ENST00000595022,NM_001198940.2,c.1901+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X637_splice,ENST00000598142,,c.1910+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X634_splice,ENST00000598334,NM_001198938.2,c.1901+1G>A,HIGH,,,,1;DTNA,splice_donor_variant,p.X316_splice,ENST00000601125,NM_001198943.1,c.947+1G>A,HIGH,,,,1;DTNA,upstream_gene_variant,,ENST00000592449,,,MODIFIER,,,,1 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 41 f58bc53d-08f3-4030-908a-741a14b0c999 44 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS DTNA,splice_donor_variant,,ENST00000590831.2,n.421+1G>A,HIGH,;DTNA,splice_donor_variant,p.X354_splice,ENST00000681759.1,c.1061+1G>A,HIGH,;DTNA,splice_donor_variant,p.X346_splice,ENST00000556414.7,c.1037+1G>A,HIGH,;DTNA,splice_donor_variant,p.X342_splice,ENST00000591182.5,c.1025+1G>A,HIGH,;DTNA,splice_donor_variant,p.X373_splice,ENST00000682129.1,c.1118+1G>A,HIGH,;DTNA,splice_donor_variant,p.X403_splice,ENST00000269192.11,c.1208+1G>A,HIGH,;DTNA,splice_donor_variant,p.X316_splice,ENST00000601125.5,c.947+1G>A,HIGH,;DTNA,splice_donor_variant,p.X694_splice,ENST00000399113.7,c.2081+1G>A,HIGH,;DTNA,splice_donor_variant,p.X721_splice,ENST00000679796.1,c.2162+1G>A,HIGH,;DTNA,splice_donor_variant,p.X721_splice,ENST00000444659.6,c.2162+1G>A,HIGH,YES;DTNA,splice_donor_variant,p.X664_splice,ENST00000680822.1,c.1991+1G>A,HIGH,;DTNA,splice_donor_variant,p.X568_splice,ENST00000680767.2,c.1703+1G>A,HIGH,;DTNA,splice_donor_variant,p.X634_splice,ENST00000681241.1,c.1901+1G>A,HIGH,;DTNA,splice_donor_variant,p.X637_splice,ENST00000598142.5,c.1910+1G>A,HIGH,;DTNA,splice_donor_variant,p.X569_splice,ENST00000684377.1,c.1706+1G>A,HIGH,;DTNA,splice_donor_variant,p.X634_splice,ENST00000595022.5,c.1901+1G>A,HIGH,;DTNA,splice_donor_variant,p.X641_splice,ENST00000399121.9,c.1922+1G>A,HIGH,;DTNA,splice_donor_variant,p.X634_splice,ENST00000598334.5,c.1901+1G>A,HIGH,;DTNA,splice_donor_variant,p.X634_splice,ENST00000683705.1,c.1901+1G>A,HIGH,;DTNA,splice_donor_variant,p.X633_splice,ENST00000681470.1,c.1898+1G>A,HIGH,;DTNA,splice_donor_variant,NMD_transcript_variant,,ENST00000679372.1,c.*2002+1G>A,HIGH,;DTNA,splice_donor_variant,p.X637_splice,ENST00000684359.1,c.1910+1G>A,HIGH,;DTNA,splice_donor_variant,p.X637_splice,ENST00000683379.1,c.1910+1G>A,HIGH,;DTNA,splice_donor_variant,p.X664_splice,ENST00000684266.1,c.1991+1G>A,HIGH,;DTNA,splice_donor_variant,p.X634_splice,ENST00000283365.14,c.1901+1G>A,HIGH, +BPIFB1 92747 BI GRCh38 20 33303055 33303055 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 88 4 c.1121C>T p.Pro374Leu p.P374L ENST00000253354.2 NM_033197.3 374 cCt/cTt 11/16 P1 T P/L protein_coding YES CCDS13218.1 1121/1455 CCGCCCTTTGT CDD:cd00026;PANTHER:PTHR47395;PIRSF:PIRSF037186;Gene3D:3.15.20.10;Pfam:PF02886;Superfamily:SSF55394 ENSP00000253354 11/16 ENST00000253354 Transcript ENSG00000125999 HGNC:16108 MODERATE NM_033197.3 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q8TDL5.146 BPIFB1 HGNC 1 1.0 UPI000006EEF9 Q8TDL5-1 SNV BPIFB1,missense_variant,p.P374L,ENST00000253354,NM_033197.3,c.1121C>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;BPIFB1,non_coding_transcript_exon_variant,,ENST00000464032,,n.883C>T,MODIFIER,,,,1 1203/1641 muse;mutect2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 90 f58bc53d-08f3-4030-908a-741a14b0c999 92 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS BPIFB1,non_coding_transcript_exon_variant,,ENST00000464032.1,n.883C>T,MODIFIER,;BPIFB1,missense_variant,p.P374L,ENST00000253354.2,c.1121C>T,MODERATE,YES +GDAP1L1 78997 BI GRCh38 20 44279273 44279273 + synonymous_variant Silent SNP C C T TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 79 17 c.1077C>T p.Tyr359= p.Y359= ENST00000342560.10 NM_024034.6 359 taC/taT 6/6 P1 T Y protein_coding CCDS13328.1 1077/1104 GCCTACTGGTA Transmembrane_helices:TMhelix;PANTHER:PTHR44188;PANTHER:PTHR44188:SF2 ENSP00000341782 6/6 COSV100697664 ENST00000342560 Transcript ENSG00000124194 HGNC:4213 LOW NM_024034.6 synonymous_variant 1 Unknown 1 Q96MZ0.141 GDAP1L1 HGNC 1 1.0 UPI0000038D5C Q96MZ0-1 SNV GDAP1L1,synonymous_variant,p.Y378=,ENST00000537864,NM_001256737.1,c.1134C>T,LOW,YES,,,1;GDAP1L1,synonymous_variant,p.Y359=,ENST00000342560,NM_024034.6,c.1077C>T,LOW,,,,1;GDAP1L1,synonymous_variant,p.Y270=,ENST00000617075,NM_001256738.1,c.810C>T,LOW,,,,1;GDAP1L1,synonymous_variant,p.Y288=,ENST00000612599,NM_001256740.1,c.864C>T,LOW,,,,1;GDAP1L1,intron_variant,,ENST00000447658,,c.285+138C>T,MODIFIER,,,,1;GDAP1L1,downstream_gene_variant,,ENST00000438466,NM_001256739.2,,MODIFIER,,,,1 1104/2778 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 116 f58bc53d-08f3-4030-908a-741a14b0c999 96 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS GDAP1L1,intron_variant,,ENST00000447658.1,c.285+138C>T,MODIFIER,;GDAP1L1,synonymous_variant,p.Y359=,ENST00000342560.10,c.1077C>T,LOW,YES;GDAP1L1,synonymous_variant,p.Y378=,ENST00000537864.5,c.1134C>T,LOW,;GDAP1L1,synonymous_variant,p.Y288=,ENST00000612599.4,c.864C>T,LOW,;GDAP1L1,synonymous_variant,p.Y270=,ENST00000617075.4,c.810C>T,LOW, +CLCN5 1184 BI GRCh38 X 50080685 50080685 + missense_variant Missense_Mutation SNP C C T rs782605316 TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 65 4 c.485C>T p.Ala162Val p.A162V ENST00000307367.2 NM_001282163.2 162 gCg/gTg 5/12 P4 T A/V protein_coding CCDS14328.1 485/2241 GTTTGCGCCTT Gene3D:1.10.3080.10;Pfam:PF00654;PANTHER:PTHR45711;PANTHER:PTHR45711:SF7;Superfamily:SSF81340;Transmembrane_helices:TMhelix;CDD:cd03684;Low_complexity_(Seg):seg ENSP00000304257 5/12 rs782605316;CD1414752 ENST00000307367 Transcript 1.0 ENSG00000171365 HGNC:2023 MODERATE 2.442e-05 gnomAD_NFE missense_variant 0;1 probably_damaging(0.983) Unknown deleterious(0) P51795.189 CLCN5 HGNC 1 1.0 UPI0000127A9B P51795-1 SNV CLCN5,missense_variant,p.A232V,ENST00000376088,NM_001127899.4,c.695C>T,MODERATE,YES,deleterious(0),probably_damaging(0.991),1;CLCN5,missense_variant,p.A232V,ENST00000376091,NM_001127898.4,c.695C>T,MODERATE,,deleterious(0),probably_damaging(0.991),1;CLCN5,missense_variant,p.A162V,ENST00000307367,NM_001282163.1,c.485C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;CLCN5,missense_variant,p.A162V,ENST00000642885,,c.485C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;CLCN5,missense_variant,p.A162V,ENST00000376108,NM_000084.5,c.485C>T,MODERATE,,deleterious(0),probably_damaging(0.983),1;CLCN5,upstream_gene_variant,,ENST00000642383,,,MODIFIER,,,,1;CLCN5,missense_variant,p.A162V,ENST00000646398,,c.485C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;CLCN5,3_prime_UTR_variant,,ENST00000643129,,c.*792C>T,MODIFIER,,,,1 776/3177 muse;mutect2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 1.091e-05 0.0 0.0 0.0 0.0 0.0 2.442e-05 0.0 0.0 0 61 f58bc53d-08f3-4030-908a-741a14b0c999 69 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS CLCN5,missense_variant,NMD_transcript_variant,p.A162V,ENST00000646398.1,c.485C>T,MODERATE,;CLCN5,missense_variant,p.A162V,ENST00000307367.2,c.485C>T,MODERATE,;CLCN5,missense_variant,p.A162V,ENST00000642885.1,c.485C>T,MODERATE,;CLCN5,missense_variant,p.A162V,ENST00000376108.7,c.485C>T,MODERATE,;CLCN5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643129.1,c.*792C>T,MODIFIER,;CLCN5,missense_variant,p.A232V,ENST00000376088.7,c.695C>T,MODERATE,;CLCN5,missense_variant,p.A232V,ENST00000376091.8,c.695C>T,MODERATE,YES +RPS6KA6 27330 BI GRCh38 X 84119907 84119907 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8KM-01A TCGA-VD-A8KM-10C Somatic 35 27 c.767G>C p.Trp256Ser p.W256S ENST00000262752.5 NM_014496.5 256 tGg/tCg 9/22 P1 G W/S protein_coding YES CCDS14451.1 767/2238 ACCACCAATCA PDB-ENSP_mappings:6g76.A;PDB-ENSP_mappings:6g76.B;PDB-ENSP_mappings:6g77.A;PDB-ENSP_mappings:6g77.B;PDB-ENSP_mappings:6g78.A;PDB-ENSP_mappings:6g78.B;PROSITE_profiles:PS50011;CDD:cd05582;PANTHER:PTHR24351:SF98;PANTHER:PTHR24351;Pfam:PF00069;Gene3D:3.30.200.20;PIRSF:PIRSF000606;Gene3D:1.10.510.10;SMART:SM00220;Superfamily:SSF56112 ENSP00000262752 9/22 ENST00000262752 Transcript ENSG00000072133 HGNC:10435 MODERATE NM_014496.5 missense_variant 1.0 probably_damaging(0.997) Unknown deleterious(0) Q9UK32.179 RPS6KA6 HGNC -1 1.0 UPI0000035B52 Q9UK32-1 SNV RPS6KA6,missense_variant,p.W256S,ENST00000262752,NM_014496.5,c.767G>C,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1;RPS6KA6,missense_variant,p.W256S,ENST00000620340,NM_001330512.1,c.767G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1 1067/8465 muse;mutect2;varscan2 1a2ce30c-5891-4bf6-8c97-6d1f34d4fe48 0 80 f58bc53d-08f3-4030-908a-741a14b0c999 62 b80b362b-57eb-450d-94f2-4c0f8964ee9f SUCCESS RPS6KA6,missense_variant,p.W256S,ENST00000262752.5,c.767G>C,MODERATE,YES;RPS6KA6,missense_variant,p.W256S,ENST00000620340.4,c.767G>C,MODERATE, +GJA5 2702 BI GRCh38 1 147758969 147758979 + frameshift_variant Frame_Shift_Del DEL CAGAGAGGGCG CAGAGAGGGCG - novel TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 35 7 c.260_270del p.Val91ProfsTer128 p.V91Pfs*128 ENST00000579774.3 NM_181703.4 87 aCGCCCTCTCTG/a 2/2 P1 - TPSL/X protein_coding CCDS929.1 260-270/1077 GTACACCAGAGAGGGCGTGGAG Transmembrane_helices:TMhelix;PANTHER:PTHR11984:SF13;PANTHER:PTHR11984;Pfam:PF00029;Gene3D:1.20.1440.80;Prints:PR00206 ENSP00000463851 2/2 ENST00000579774 Transcript 1.0 ENSG00000265107 HGNC:4279 HIGH NM_181703.4 frameshift_variant Unknown P36382.184 GJA5 HGNC -1 X5D2H9.55 1.0 UPI000013D8D2 deletion GJA5,frameshift_variant,p.T87Sfs*132,ENST00000621517,NM_005266.6,c.260_270del,HIGH,YES,,,-1;GJA5,frameshift_variant,p.T87Sfs*132,ENST00000579774,NM_181703.4,c.260_270del,HIGH,,,,-1;GJA5,frameshift_variant,p.T87Sfs*132,ENST00000430508,,c.260_270del,HIGH,,,,-1;AC241644.3,downstream_gene_variant,,ENST00000612401,,,MODIFIER,,,,1;AC241644.3,downstream_gene_variant,,ENST00000622634,,,MODIFIER,YES,,,1 397-407/3177 mutect2;pindel;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 84 e9832c39-d743-4b2f-8918-9c22144c27c9 42 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS GJA5,frameshift_variant,p.V91Pfs*128,ENST00000430508.1,c.260_270del,HIGH,;GJA5,frameshift_variant,p.V91Pfs*128,ENST00000621517.1,c.260_270del,HIGH,;GJA5,frameshift_variant,p.V91Pfs*128,ENST00000579774.3,c.260_270del,HIGH,YES +FCGR2A 2212 BI GRCh38 1 161518089 161518089 + missense_variant Missense_Mutation SNP G G T TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 34 18 c.895G>T p.Asp299Tyr p.D299Y ENST00000271450.12 NM_001136219.3 299 Gat/Tat 7/7 A2 T D/Y protein_coding YES CCDS44264.1 895/954 CTGACGATGAT PANTHER:PTHR11481;PANTHER:PTHR11481:SF51 ENSP00000271450 7/7 COSV54839604 ENST00000271450 Transcript 1.0 ENSG00000143226 HGNC:3616 MODERATE NM_001136219.3 missense_variant 1 1.0 probably_damaging(0.995) Unknown deleterious_low_confidence(0.02) 1 P12318.215 FCGR2A HGNC 1 1.0 UPI000013D8DE P12318-1 SNV FCGR2A,missense_variant,p.D299Y,ENST00000271450,NM_001136219.3&NM_001375296.1,c.895G>T,MODERATE,YES,deleterious_low_confidence(0.02),probably_damaging(0.995),1;FCGR2A,missense_variant,p.D298Y,ENST00000367972,NM_021642.5&NM_001375297.1,c.892G>T,MODERATE,,deleterious_low_confidence(0.02),probably_damaging(0.998),1;FCGR2A,missense_variant,p.D51Y,ENST00000459885,,c.151G>T,MODERATE,,deleterious_low_confidence(0.01),probably_damaging(1),1;FCGR2A,non_coding_transcript_exon_variant,,ENST00000486608,,n.370G>T,MODIFIER,,,,1;FCGR2A,non_coding_transcript_exon_variant,,ENST00000461298,,n.304G>T,MODIFIER,,,,1;FCGR2A,non_coding_transcript_exon_variant,,ENST00000471026,,n.465G>T,MODIFIER,,,,1;FCGR2A,non_coding_transcript_exon_variant,,ENST00000491841,,n.115G>T,MODIFIER,,,,1;FCGR2A,3_prime_UTR_variant,,ENST00000467525,,c.*172G>T,MODIFIER,,,,1;FCGR2A,3_prime_UTR_variant,,ENST00000483665,,c.*597G>T,MODIFIER,,,,1;AL590385.2,non_coding_transcript_exon_variant,,ENST00000537821,,n.223G>T,MODIFIER,YES,,,1 906/2646 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 60 e9832c39-d743-4b2f-8918-9c22144c27c9 52 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS FCGR2A,non_coding_transcript_exon_variant,,ENST00000491841.1,n.115G>T,MODIFIER,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000486608.1,n.370G>T,MODIFIER,;FCGR2A,synonymous_variant,p.T50=,ENST00000459885.1,c.150G>T,LOW,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000461298.1,n.304G>T,MODIFIER,;ENSG00000273112,non_coding_transcript_exon_variant,,ENST00000537821.2,n.223G>T,MODIFIER,YES;FCGR2A,non_coding_transcript_exon_variant,,ENST00000471026.5,n.465G>T,MODIFIER,;FCGR2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000467525.5,c.*172G>T,MODIFIER,;FCGR2A,missense_variant,p.D160Y,ENST00000699279.1,c.478G>T,MODERATE,;FCGR2A,missense_variant,p.D299Y,ENST00000271450.12,c.895G>T,MODERATE,YES;FCGR2A,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000483665.6,c.*597G>T,MODIFIER,;FCGR2A,missense_variant,p.D213Y,ENST00000699278.1,c.637G>T,MODERATE,;FCGR2A,missense_variant,p.D258Y,ENST00000699277.1,c.772G>T,MODERATE,;FCGR2A,missense_variant,p.D298Y,ENST00000367972.8,c.892G>T,MODERATE, +SF3B1 23451 BI GRCh38 2 197402636 197402636 + missense_variant Missense_Mutation SNP T T G rs374250186 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 32 29 c.1997A>C p.Lys666Thr p.K666T ENST00000335508.11 NM_012433.4 666 aAg/aCg 14/25 P1 G K/T protein_coding YES CCDS33356.1 1997/3915 likely_pathogenic CAATCTTAATA COSM131556 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs374250186;COSV59205833;COSV59206062;COSV59207657 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 2.639e-05 gnomAD_NFE missense_variant 1;1;1;1 1.0 23634996 probably_damaging(0.992) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.K666T,ENST00000335508,NM_012433.4,c.1997A>C,MODERATE,YES,deleterious(0),probably_damaging(0.992),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*3064A>C,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2256A>C,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3881A>C,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 2026/6463 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 1.193e-05 0.0 0.0 0.0 0.0 0.0 2.639e-05 0.0 0.0 6.758129984518746e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.543160033179447e-05 0.0 0.0 0 58 e9832c39-d743-4b2f-8918-9c22144c27c9 62 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3881A>C,MODIFIER,;SF3B1,missense_variant,p.K666T,ENST00000335508.11,c.1997A>C,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*3064A>C,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2256A>C,MODIFIER, +LRRC66 339977 BI GRCh38 4 51995707 51995707 + missense_variant Missense_Mutation SNP C C G TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 107 46 c.1315G>C p.Glu439Gln p.E439Q ENST00000343457.3 439 Gag/Cag 4/4 P1 G E/Q protein_coding YES CCDS43229.1 1315/2643 GGTCTCTGGGT COSM1666749 PANTHER:PTHR24366;PANTHER:PTHR24366:SF118 ENSP00000341944 4/4 COSV58633372 ENST00000343457 Transcript ENSG00000188993 HGNC:34299 MODERATE missense_variant 1 1.0 benign(0.036) Unknown tolerated(0.59) 1 Q68CR7.121 LRRC66 HGNC -1 1.0 UPI0000425C5B SNV LRRC66,missense_variant,p.E439Q,ENST00000343457,NM_001024611.3,c.1315G>C,MODERATE,YES,tolerated(0.59),benign(0.036),-1 1322/3327 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 126 e9832c39-d743-4b2f-8918-9c22144c27c9 153 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS LRRC66,missense_variant,p.E439Q,ENST00000343457.3,c.1315G>C,MODERATE,;LRRC66,missense_variant,p.E439Q,ENST00000682860.1,c.1315G>C,MODERATE,YES +FAT4 79633 BI GRCh38 4 125452580 125452580 + missense_variant Missense_Mutation SNP C C T rs536513777 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 38 13 c.11570C>T p.Ala3857Val p.A3857V ENST00000394329.9 NM_001291303.3 3857 gCg/gTg 10/18 0.0002 0.0 0.0 0.001 0.0 0.0 P1 T A/V protein_coding YES 11570/14952 ATATGCGGGTA COSM1131262;COSM1131263 Gene3D:2.10.25.10;PROSITE_patterns:PS00022;PROSITE_patterns:PS01186;PROSITE_profiles:PS50026;PANTHER:PTHR24025;PANTHER:PTHR24025:SF19;SMART:SM00181;Superfamily:SSF57184 ENSP00000377862 10/18 rs536513777;COSV58680265 ENST00000394329 Transcript 1.0 ENSG00000196159 HGNC:23109 MODERATE NM_001291303.3 0.001 EAS missense_variant 0;1 1.0 benign(0.07) Unknown deleterious(0.03) 0;1 Q6V0I7.154 FAT4 HGNC 1 5.0 UPI000387DB11 Q6V0I7-1 SNV FAT4,missense_variant,p.A3857V,ENST00000394329,NM_001291303.3&NM_001291285.2&NM_024582.5,c.11570C>T,MODERATE,YES,deleterious(0.03),benign(0.07),1;FAT4,missense_variant,p.A2114V,ENST00000674496,,c.6341C>T,MODERATE,,tolerated(0.09),,1;FAT4,missense_variant,p.A2153V,ENST00000335110,,c.6458C>T,MODERATE,,tolerated(0.11),benign(0.086),1;FAT4,downstream_gene_variant,,ENST00000509444,,,MODIFIER,,,,1 12605/17151 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 7.964e-06 0.0 0.0 0.0 5.444e-05 0.0 8.81e-06 0.0 0.0 6.760590167687042e-06 0.0 0.0 0.0 0.0 0.0002018569939536 0.0 0.0 0.0 0.0 0.0 0 38 e9832c39-d743-4b2f-8918-9c22144c27c9 51 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS FAT4,missense_variant,p.A2153V,ENST00000335110.5,c.6458C>T,MODERATE,;FAT4,missense_variant,p.A3857V,ENST00000394329.9,c.11570C>T,MODERATE,YES;FAT4,missense_variant,p.A2114V,ENST00000674496.2,c.6341C>T,MODERATE, +SNX18 112574 BI GRCh38 5 54543372 54543372 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 39 10 c.1815A>G p.Ile605Met p.I605M ENST00000381410.5 NM_001145427.2 G protein_coding CCDS54851.1 ATAATATTTTT 99.0 ENSP00000317332 ENST00000326277 Transcript ENSG00000178996 HGNC:19245 MODIFIER downstream_gene_variant Unknown Q96RF0.163 SNX18 HGNC 1 2.0 UPI000194B737 Q96RF0-3 SNV SNX18,missense_variant,p.I605M,ENST00000381410,NM_001102575.2,c.1815A>G,MODERATE,,tolerated(0.11),benign(0.205),1;SNX18,downstream_gene_variant,,ENST00000326277,NM_001145427.2,,MODIFIER,,,,1 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 75 e9832c39-d743-4b2f-8918-9c22144c27c9 49 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS SNX18,missense_variant,p.I605M,ENST00000381410.5,c.1815A>G,MODERATE,YES +TFAP2B 7021 BI GRCh38 6 50837983 50837983 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 128 13 c.830C>T p.Ser277Leu p.S277L ENST00000393655.4 NM_003221.4 277 tCg/tTg 5/7 P1 T S/L protein_coding YES CCDS4934.2 830/1383 CAAATCGAAAA Pfam:PF03299;Prints:PR01748;PANTHER:PTHR10812;PANTHER:PTHR10812:SF14 ENSP00000377265 5/7 ENST00000393655 Transcript 1.0 ENSG00000008196 HGNC:11743 MODERATE NM_003221.4 missense_variant 1.0 probably_damaging(0.992) Unknown deleterious(0) Q92481.183 TFAP2B HGNC 1 1.0 UPI000020DE90 Q92481-1 SNV TFAP2B,missense_variant,p.S277L,ENST00000393655,NM_003221.4,c.830C>T,MODERATE,YES,deleterious(0),probably_damaging(0.992),1 851/5631 muse;mutect2 029cc59c-60df-4411-a044-3a2eeee7b110 0 88 e9832c39-d743-4b2f-8918-9c22144c27c9 141 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS TFAP2B,missense_variant,p.S277L,ENST00000393655.4,c.830C>T,MODERATE,YES +DLL1 28514 BI GRCh38 6 170285392 170285392 + stop_gained Nonsense_Mutation SNP G G T TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 17 30 c.894C>A p.Cys298Ter p.C298* ENST00000366756.4 NM_005618.4 298 tgC/tgA 7/11 P1 T C/* protein_coding YES CCDS5313.1 894/2172 TTCTTGCAGGG COSM1666750 PDB-ENSP_mappings:4xbm.A;PDB-ENSP_mappings:4xbm.B;CDD:cd00054;Pfam:PF00008;Gene3D:2.10.25.10;SMART:SM00179;SMART:SM00181;Superfamily:SSF57184;PROSITE_profiles:PS50026;PANTHER:PTHR24044;PANTHER:PTHR24044:SF380 ENSP00000355718 7/11 COSV64537345 ENST00000366756 Transcript 1.0 ENSG00000198719 HGNC:2908 HIGH NM_005618.4 stop_gained 1 1.0 Unknown 1 O00548.190 DLL1 HGNC -1 A0A384P5C6.9 1.0 UPI000004C656 O00548-1 SNV DLL1,stop_gained,p.C298*,ENST00000366756,NM_005618.4,c.894C>A,HIGH,YES,,,-1;DLL1,downstream_gene_variant,,ENST00000630500,,,MODIFIER,,,,-1 1833/3779 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 48 e9832c39-d743-4b2f-8918-9c22144c27c9 47 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS DLL1,stop_gained,p.C298*,ENST00000366756.4,c.894C>A,HIGH,YES +ZAN 7455 BI GRCh38 7 100747558 100747558 + missense_variant Missense_Mutation SNP C C T rs764974438 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 26 17 c.940C>T p.Arg314Trp p.R314W ENST00000613979.5 NM_003386.3 314 Cgg/Tgg 9/48 P1 T R/W protein_coding YES CCDS47664.2 940/8439 GTATCCGGAAA COSM1666753 Gene3D:2.60.120.200;Pfam:PF00629;PROSITE_profiles:PS50060;SMART:SM00137;Superfamily:SSF49899;CDD:cd06263 ENSP00000480750 9/48 rs764974438;COSV61808414 ENST00000613979 Transcript ENSG00000146839 HGNC:12857 MODERATE NM_003386.3 0.0002027 gnomAD_AMR missense_variant 0;1 1.0 possibly_damaging(0.755) Unknown deleterious(0) 0;1 Q9Y493.169 ZAN HGNC 1 1.0 UPI000441C79E Q9Y493-1 SNV ZAN,missense_variant,p.R314W,ENST00000613979,NM_003386.3,c.940C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.755),1;ZAN,missense_variant,p.R314W,ENST00000618565,,c.940C>T,MODERATE,,deleterious(0),possibly_damaging(0.755),1;ZAN,missense_variant,p.R314W,ENST00000620596,NM_173059.3,c.940C>T,MODERATE,,deleterious(0),benign(0.136),1;ZAN,missense_variant,p.R314W,ENST00000546292,,c.940C>T,MODERATE,,deleterious(0),benign(0.136),1;ZAN,missense_variant,p.R314W,ENST00000542585,,c.940C>T,MODERATE,,deleterious(0),benign(0.136),1;ZAN,missense_variant,p.R314W,ENST00000538115,,c.940C>T,MODERATE,,deleterious(0),possibly_damaging(0.858),1;ZAN,missense_variant,p.R314W,ENST00000546213,,c.940C>T,MODERATE,,deleterious(0),benign(0.136),1;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,,n.1105C>T,MODIFIER,,,,1 1136/8700 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 8.425e-05 0.0 0.0002027 0.0 0.0 0.0 9.733e-05 0.0001652 6.536e-05 1.353049992758315e-05 0.0 0.0 6.637460319325328e-05 0.0 0.0 0.0 0.0 1.5435000022989698e-05 0.0 0.0 0 63 e9832c39-d743-4b2f-8918-9c22144c27c9 43 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS ZAN,missense_variant,p.R314W,ENST00000618565.4,c.940C>T,MODERATE,;ZAN,missense_variant,p.R314W,ENST00000546292.2,c.940C>T,MODERATE,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868.4,n.1105C>T,MODIFIER,;ZAN,missense_variant,NMD_transcript_variant,p.R314W,ENST00000538115.5,c.940C>T,MODERATE,;ZAN,missense_variant,NMD_transcript_variant,p.R314W,ENST00000546213.5,c.940C>T,MODERATE,;ZAN,missense_variant,NMD_transcript_variant,p.R314W,ENST00000542585.5,c.940C>T,MODERATE,;ZAN,missense_variant,p.R314W,ENST00000620596.4,c.940C>T,MODERATE,;ZAN,missense_variant,p.R314W,ENST00000613979.5,c.940C>T,MODERATE,YES +UBR5 51366 BI GRCh38 8 102277085 102277085 + synonymous_variant Silent SNP A A G rs777572603 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 109 54 c.6396T>C p.Thr2132= p.T2132= ENST00000520539.6 NM_015902.6 2132 acT/acC 45/59 P5 G T protein_coding YES CCDS34933.1 6396/8400 CTCTCAGTTTC PANTHER:PTHR46276;MobiDB_lite:mobidb-lite ENSP00000429084 45/59 rs777572603 ENST00000520539 Transcript 1.0 ENSG00000104517 HGNC:16806 LOW NM_015902.6 8.794e-06 gnomAD_NFE synonymous_variant 1.0 Unknown O95071.209 UBR5 HGNC -1 1.0 UPI0000129BCB O95071-1 SNV UBR5,synonymous_variant,p.T2132=,ENST00000520539,NM_015902.6,c.6396T>C,LOW,YES,,,-1;UBR5,synonymous_variant,p.T2132=,ENST00000220959,NM_001282873.1,c.6396T>C,LOW,,,,-1;UBR5,synonymous_variant,p.T2126=,ENST00000521922,,c.6378T>C,LOW,,,,-1;UBR5,upstream_gene_variant,,ENST00000518205,,,MODIFIER,,,,-1;UBR5,upstream_gene_variant,,ENST00000521566,,,MODIFIER,,,,-1 6862/10895 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.794e-06 0.0 0.0 0 86 e9832c39-d743-4b2f-8918-9c22144c27c9 163 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS UBR5,synonymous_variant,p.T2126=,ENST00000521922.5,c.6378T>C,LOW,;UBR5,synonymous_variant,p.T2132=,ENST00000220959.8,c.6396T>C,LOW,;UBR5,synonymous_variant,p.T2132=,ENST00000520539.6,c.6396T>C,LOW,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 46 21 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 85 e9832c39-d743-4b2f-8918-9c22144c27c9 67 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +SSX5 6758 BI GRCh38 X 48195080 48195080 + intron_variant Intron SNP C C G novel TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 71 31 c.69+210G>C ENST00000347757.6 NM_175723.2 A2 G protein_coding CCDS14289.1 ACGGACTGAGA ENSP00000290558 ENST00000347757 Transcript ENSG00000165583 HGNC:11339 MODIFIER 2/7 intron_variant Unknown O60225.158 SSX5 HGNC -1 5.0 UPI000013DFFA O60225-1 SNV SSX5,missense_variant,p.S40T,ENST00000311798,NM_021015.4,c.119G>C,MODERATE,YES,tolerated_low_confidence(0.51),benign(0.003),-1;SSX5,intron_variant,,ENST00000347757,NM_175723.1,c.69+210G>C,MODIFIER,,,,-1;SSX5,upstream_gene_variant,,ENST00000403001,,,MODIFIER,,,,-1;AC245047.3,upstream_gene_variant,,ENST00000437312,,,MODIFIER,YES,,,1 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 68 e9832c39-d743-4b2f-8918-9c22144c27c9 102 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS SSX5,intron_variant,,ENST00000347757.6,c.69+210G>C,MODIFIER,YES;SSX5,missense_variant,p.S40T,ENST00000311798.5,c.119G>C,MODERATE, +NCBP2L 392517 BI GRCh38 X 107775275 107775275 + intron_variant Intron SNP G G T TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 37 55 c.-73+105G>T ENST00000639756.1 NM_001348372.2 49/200 P3 T R protein_coding YES CCDS14530.1 145/603 CTGCCGAAAGT PANTHER:PTHR12348:SF24;PANTHER:PTHR12348 ENSP00000361458 1/3 COSV59777565 ENST00000372383 Transcript ENSG00000157514 HGNC:3051 LOW synonymous_variant 1 1.0 Unknown 1 Q99576.184 TSC22D3 HGNC -1 2.0 UPI000006DE94 Q99576-3 SNV TSC22D3,synonymous_variant,p.R49=,ENST00000372383,NM_198057.3,c.145C>A,LOW,YES,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000315660,NM_001318468.1,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000372384,NM_001318470.1,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000506081,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000514897,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000510887,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000502650,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000480691,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000506724,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000502961,,c.145C>A,LOW,,,,-1;TSC22D3,synonymous_variant,p.R49=,ENST00000505965,,c.145C>A,LOW,,,,-1;TSC22D3,5_prime_UTR_variant,,ENST00000514426,,c.-60C>A,MODIFIER,,,,-1;NCBP2L,intron_variant,,ENST00000639756,,c.-73+105G>T,MODIFIER,YES,,,1;NCBP2L,upstream_gene_variant,,ENST00000509000,NM_001348372.2,,MODIFIER,,,,1 513/2266 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0 68 e9832c39-d743-4b2f-8918-9c22144c27c9 92 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS TSC22D3,synonymous_variant,p.R49=,ENST00000502961.1,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000505965.1,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000506724.1,c.145C>A,LOW,;NCBP2L,intron_variant,,ENST00000639756.1,c.-73+105G>T,MODIFIER,;TSC22D3,synonymous_variant,p.R49=,ENST00000502650.1,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000510887.5,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000480691.2,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000514897.5,c.145C>A,LOW,;TSC22D3,5_prime_UTR_variant,,ENST00000514426.1,c.-60C>A,MODIFIER,;TSC22D3,synonymous_variant,p.R49=,ENST00000506081.5,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000372384.6,c.145C>A,LOW,;TSC22D3,synonymous_variant,p.R49=,ENST00000372383.9,c.145C>A,LOW,YES;TSC22D3,synonymous_variant,p.R49=,ENST00000315660.8,c.145C>A,LOW, +GPR101 83550 BI GRCh38 X 137031333 137031333 + synonymous_variant Silent SNP G G A rs200302047 TCGA-V4-A9E5-01A TCGA-V4-A9E5-10A Somatic 8 14 c.342C>T p.Phe114= p.F114= ENST00000651716.2 NM_054021.2 114 ttC/ttT 2/2 P1 A F protein_coding YES CCDS14662.1 342/1527 AAGGCGAACAG Gene3D:1.20.1070.10;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24248;PANTHER:PTHR24248:SF2;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15215 ENSP00000498972 2/2 rs200302047 ENST00000651716 Transcript 1.0 ENSG00000165370 HGNC:14963 LOW NM_054021.2 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown Q96P66.139 GPR101 HGNC -1 UPI000003BCCD SNV GPR101,synonymous_variant,p.F114=,ENST00000651716,NM_054021.2,c.342C>T,LOW,YES,,,-1 628/8032 muse;mutect2;varscan2 029cc59c-60df-4411-a044-3a2eeee7b110 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 9.164469702227508e-06 3.266689964220859e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 24 e9832c39-d743-4b2f-8918-9c22144c27c9 22 11face56-c125-4a0c-be8a-e2c954a82d7b SUCCESS GPR101,synonymous_variant,p.F114=,ENST00000651716.2,c.342C>T,LOW,YES;ENSG00000291054,intron_variant,,ENST00000693626.2,n.394-29192G>A,MODIFIER,YES +PRAMEF17 391004 BI GRCh38 1 13389937 13389937 + missense_variant Missense_Mutation SNP C C T rs878949864 TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 0 12 c.280C>T p.Arg94Cys p.R94C ENST00000376098.4 NM_001099851.3 94 Cgc/Tgc 1/3 P1 T R/C protein_coding YES CCDS41264.1 280/1425 AGCTTCGCCCC PANTHER:PTHR14224:SF2;PANTHER:PTHR14224;PIRSF:PIRSF038286 ENSP00000365266 1/3 rs878949864 ENST00000376098 Transcript ENSG00000204479 HGNC:29485 MODERATE NM_001099851.3 0.0004112 gnomAD_AMR missense_variant 1.0 benign(0.015) Unknown tolerated(0.09) Q5VTA0.103 PRAMEF17 HGNC 1 1.0 UPI0000458AD3 SNV PRAMEF17,missense_variant,p.R94C,ENST00000376098,NM_001099851.3,c.280C>T,MODERATE,YES,tolerated(0.09),benign(0.015),1 306/1578 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0.0001062 0.0 0.0004112 0.0 0.0 0.0 0.0 0.0 0.0 8.113589865388349e-05 7.296779949683696e-05 0.0 0.0001326259953202 0.0 0.0004033879959024 0.0 eas 0.0004033879959024 0.0 6.173599831527099e-05 0.000494070991408 0.0 0 52 69e289e0-bb0e-41a8-acbc-a6215f000980 12 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS PRAMEF17,missense_variant,p.R94C,ENST00000376098.4,c.280C>T,MODERATE,YES +FAT1 2195 BI GRCh38 4 186617756 186617756 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 55 33 c.8830G>A p.Asp2944Asn p.D2944N ENST00000441802.7 NM_005245.4 2944 Gat/Aat 10/27 P4 T D/N protein_coding CCDS47177.1 8830/13767 AGCATCCGTGG Gene3D:2.60.40.60;Pfam:PF00028;PROSITE_profiles:PS50268;PANTHER:PTHR24025;PANTHER:PTHR24025:SF21;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000406229 10/27 ENST00000441802 Transcript 1.0 ENSG00000083857 HGNC:3595 MODERATE NM_005245.4 missense_variant possibly_damaging(0.741) Unknown deleterious(0) Q14517.189 FAT1 HGNC -1 5.0 UPI000051946B SNV FAT1,missense_variant,p.D2944N,ENST00000441802,NM_005245.4,c.8830G>A,MODERATE,,deleterious(0),possibly_damaging(0.741),-1;FAT1,missense_variant,p.D2946N,ENST00000614102,,c.8836G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.575),-1 9041/14776 muse;mutect2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 81 69e289e0-bb0e-41a8-acbc-a6215f000980 88 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS FAT1,missense_variant,p.D2944N,ENST00000441802.7,c.8830G>A,MODERATE,YES +CMYA5 202333 BI GRCh38 5 79736602 79736602 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 25 23 c.7837A>C p.Lys2613Gln p.K2613Q ENST00000446378.3 NM_153610.5 2613 Aag/Cag 2/13 P1 C K/Q protein_coding YES CCDS47238.1 7837/12210 AAGCAAAGGCA PANTHER:PTHR24099;PANTHER:PTHR24099:SF7 ENSP00000394770 2/13 ENST00000446378 Transcript ENSG00000164309 HGNC:14305 MODERATE NM_153610.5 missense_variant 1.0 probably_damaging(0.922) Unknown tolerated_low_confidence(0.09) Q8N3K9.142 CMYA5 HGNC 1 5.0 UPI00004F9478 SNV CMYA5,missense_variant,p.K2613Q,ENST00000446378,NM_153610.5,c.7837A>C,MODERATE,YES,tolerated_low_confidence(0.09),probably_damaging(0.922),1;CMYA5,upstream_gene_variant,,ENST00000506603,,,MODIFIER,,,,1 7909/12888 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 42 69e289e0-bb0e-41a8-acbc-a6215f000980 48 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS CMYA5,missense_variant,p.K2613Q,ENST00000446378.3,c.7837A>C,MODERATE,YES +COL9A1 1297 BI GRCh38 6 70255006 70255006 + missense_variant Missense_Mutation SNP C C T rs755767798 TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 0 19 c.1622G>A p.Gly541Asp p.G541D ENST00000357250.11 NM_001851.6 541 gGt/gAt 24/38 P1 T G/D protein_coding YES CCDS4971.1 1622/2766 CCACACCTGGC PANTHER:PTHR24023;PANTHER:PTHR24023:SF981 ENSP00000349790 24/38 rs755767798 ENST00000357250 Transcript 1.0 ENSG00000112280 HGNC:2217 MODERATE NM_001851.6 8.791e-06 gnomAD_NFE missense_variant 1.0 probably_damaging(0.992) Unknown deleterious(0.01) P20849.212 COL9A1 HGNC -1 1.0 UPI000020D14B P20849-1 SNV COL9A1,missense_variant,p.G541D,ENST00000357250,NM_001851.6,c.1622G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.992),-1;COL9A1,missense_variant,p.G298D,ENST00000320755,NM_001377290.1&NM_078485.4&NM_001377289.1,c.893G>A,MODERATE,,deleterious(0),probably_damaging(1),-1;COL9A1,non_coding_transcript_exon_variant,,ENST00000360859,,n.308G>A,MODIFIER,,,,-1;COL9A1,non_coding_transcript_exon_variant,,ENST00000489611,,n.714G>A,MODIFIER,,,,-1;COL9A1,upstream_gene_variant,,ENST00000447041,,,MODIFIER,,,,-1;COL9A1,3_prime_UTR_variant,,ENST00000644493,,c.*659G>A,MODIFIER,,,,-1;COL9A1,non_coding_transcript_exon_variant,,ENST00000493682,,n.595G>A,MODIFIER,,,,-1;COL9A1,upstream_gene_variant,,ENST00000489861,,,MODIFIER,,,,-1 1782/3697 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.791e-06 0.0 0.0 6.7584001044451725e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5428800907102413e-05 0.0 0.0 0 43 69e289e0-bb0e-41a8-acbc-a6215f000980 19 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS COL9A1,non_coding_transcript_exon_variant,,ENST00000489611.5,n.714G>A,MODIFIER,;COL9A1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644493.1,c.*659G>A,MODIFIER,;COL9A1,missense_variant,p.G298D,ENST00000683758.1,c.893G>A,MODERATE,;COL9A1,non_coding_transcript_exon_variant,,ENST00000684176.1,n.964G>A,MODIFIER,;COL9A1,non_coding_transcript_exon_variant,,ENST00000360859.12,n.308G>A,MODIFIER,;COL9A1,non_coding_transcript_exon_variant,,ENST00000493682.7,n.1616G>A,MODIFIER,;COL9A1,missense_variant,p.G541D,ENST00000357250.11,c.1622G>A,MODERATE,YES;COL9A1,missense_variant,p.G298D,ENST00000683980.2,c.893G>A,MODERATE,;COL9A1,non_coding_transcript_exon_variant,,ENST00000683602.1,n.2359G>A,MODIFIER,;COL9A1,missense_variant,p.G298D,ENST00000320755.12,c.893G>A,MODERATE, +KTN1 3895 BI GRCh38 14 55627988 55627988 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 22 18 c.1040A>G p.Asp347Gly p.D347G ENST00000395314.8 NM_001402686.1 347 gAt/gGt 6/44 P3 G D/G protein_coding YES CCDS41957.1 1040/4074 GGAAGATGCTG Coiled-coils_(Ncoils):Coil;PANTHER:PTHR18864 ENSP00000378725 6/44 ENST00000395314 Transcript 1.0 ENSG00000126777 HGNC:6467 MODERATE NM_001079521.2 missense_variant 1.0 possibly_damaging(0.775) Unknown deleterious(0.01) Q86UP2.169 KTN1 HGNC 1 A0A024R663.47 1.0 UPI0000190F88 Q86UP2-1 SNV KTN1,missense_variant,p.D347G,ENST00000395314,NM_001271014.2&NM_001079521.2,c.1040A>G,MODERATE,YES,deleterious(0.01),possibly_damaging(0.775),1;KTN1,missense_variant,p.D347G,ENST00000395311,NM_001079522.2,c.1040A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.753),1;KTN1,missense_variant,p.D347G,ENST00000413890,,c.1040A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.753),1;KTN1,missense_variant,p.D347G,ENST00000438792,NM_004986.4,c.1040A>G,MODERATE,,deleterious(0.01),probably_damaging(0.998),1;KTN1,missense_variant,p.D347G,ENST00000395308,,c.1040A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.753),1;KTN1,missense_variant,p.D347G,ENST00000395309,,c.1040A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.753),1;KTN1,5_prime_UTR_variant,,ENST00000554567,,c.-466A>G,MODIFIER,,,,1;KTN1,missense_variant,p.D347G,ENST00000459737,,c.1040A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.775),1 1218/4728 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 40 69e289e0-bb0e-41a8-acbc-a6215f000980 40 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS KTN1,missense_variant,p.D347G,ENST00000395309.7,c.1040A>G,MODERATE,;KTN1,missense_variant,p.D347G,ENST00000413890.6,c.1040A>G,MODERATE,;KTN1,missense_variant,p.D347G,ENST00000395311.5,c.1040A>G,MODERATE,;KTN1,missense_variant,p.D347G,ENST00000395308.5,c.1040A>G,MODERATE,;KTN1,missense_variant,NMD_transcript_variant,p.D347G,ENST00000459737.5,c.1040A>G,MODERATE,;KTN1,missense_variant,p.D347G,ENST00000438792.6,c.1040A>G,MODERATE,;KTN1,5_prime_UTR_variant,,ENST00000554567.1,c.-466A>G,MODIFIER,;KTN1,missense_variant,p.D347G,ENST00000395314.8,c.1040A>G,MODERATE,YES +EXOC5 10640 BI GRCh38 14 57209645 57209645 + synonymous_variant Silent SNP T T C novel TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 17 10 c.1860A>G p.Gln620= p.Q620= ENST00000621441.5 NM_006544.4 620 caA/caG 17/18 P4 C Q protein_coding CCDS45111.1 1860/2127 GAATATTGTTG Pfam:PF07393;PANTHER:PTHR12100;PANTHER:PTHR12100:SF4 ENSP00000484855 17/18 ENST00000621441 Transcript ENSG00000070367 HGNC:10696 LOW NM_006544.4 synonymous_variant Unknown O00471.153 EXOC5 HGNC -1 1.0 UPI0000047E53 SNV EXOC5,synonymous_variant,p.Q620=,ENST00000621441,NM_006544.4,c.1860A>G,LOW,,,,-1;EXOC5,synonymous_variant,p.Q623=,ENST00000413566,,c.1869A>G,LOW,YES,,,-1;EXOC5,synonymous_variant,p.Q555=,ENST00000340918,,c.1665A>G,LOW,,,,-1;EXOC5,3_prime_UTR_variant,,ENST00000555148,,c.*1694A>G,MODIFIER,,,,-1;EXOC5,non_coding_transcript_exon_variant,,ENST00000554011,,n.1579A>G,MODIFIER,,,,-1 2117/10486 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 24 69e289e0-bb0e-41a8-acbc-a6215f000980 27 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS EXOC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000555148.5,c.*1694A>G,MODIFIER,;EXOC5,synonymous_variant,p.Q555=,ENST00000340918.11,c.1665A>G,LOW,;EXOC5,non_coding_transcript_exon_variant,,ENST00000554011.5,n.1579A>G,MODIFIER,;EXOC5,synonymous_variant,p.Q620=,ENST00000621441.5,c.1860A>G,LOW,YES +ARHGDIA 396 BI GRCh38 17 81869230 81869230 + stop_gained Nonsense_Mutation SNP G G A rs587777553 TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 21 19 c.358C>T p.Arg120Ter p.R120* ENST00000269321.12 NM_004309.6 120 Cga/Tga 5/6 P1 A R/* protein_coding CCDS11788.1 358/615 pathogenic CTCTCGGTTAA COSM2805607 PDB-ENSP_mappings:1cc0.E;PDB-ENSP_mappings:1cc0.F;PDB-ENSP_mappings:1fso.A;PDB-ENSP_mappings:1fst.A;PDB-ENSP_mappings:1fst.B;PDB-ENSP_mappings:1ft0.A;PDB-ENSP_mappings:1ft0.B;PDB-ENSP_mappings:1ft3.A;PDB-ENSP_mappings:1ft3.B;PDB-ENSP_mappings:1hh4.D;PDB-ENSP_mappings:1hh4.E;PDB-ENSP_mappings:1kmt.A;PDB-ENSP_mappings:1kmt.B;PDB-ENSP_mappings:1qvy.A;PDB-ENSP_mappings:1qvy.B;PDB-ENSP_mappings:1qvy.C;PDB-ENSP_mappings:1qvy.D;PDB-ENSP_mappings:1rho.A;PDB-ENSP_mappings:1rho.B;PDB-ENSP_mappings:1rho.C;Gene3D:2.70.50.30;PDB-ENSP_mappings:2bxw.A;PDB-ENSP_mappings:2bxw.B;PDB-ENSP_mappings:2jhs.A;PDB-ENSP_mappings:2jht.A;PDB-ENSP_mappings:2jht.B;PDB-ENSP_mappings:2jht.C;PDB-ENSP_mappings:2jht.D;PDB-ENSP_mappings:2jhu.A;PDB-ENSP_mappings:2jhu.B;PDB-ENSP_mappings:2jhv.A;PDB-ENSP_mappings:2jhv.B;PDB-ENSP_mappings:2jhv.C;PDB-ENSP_mappings:2jhv.D;PDB-ENSP_mappings:2jhv.E;PDB-ENSP_mappings:2jhv.F;PDB-ENSP_mappings:2jhw.A;PDB-ENSP_mappings:2jhw.B;PDB-ENSP_mappings:2jhx.A;PDB-ENSP_mappings:2jhx.B;PDB-ENSP_mappings:2jhy.A;PDB-ENSP_mappings:2jhz.A;PDB-ENSP_mappings:2jhz.B;PDB-ENSP_mappings:2ji0.A;PDB-ENSP_mappings:2n80.B;Pfam:PF02115;PANTHER:PTHR10980;PANTHER:PTHR10980:SF9;Superfamily:SSF81296 ENSP00000269321 5/6 rs587777553;CM137001;COSV53907073 ENST00000269321 Transcript 1.0 ENSG00000141522 HGNC:678 HIGH NM_004309.6 stop_gained 1;1;1 Unknown 0;0;1 P52565.194 ARHGDIA HGNC -1 V9HWE8.54 1.0 UPI0000110BD8 P52565-1 SNV ARHGDIA,stop_gained,p.R120*,ENST00000269321,NM_004309.6&NM_001301243.2,c.358C>T,HIGH,,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000400721,NM_001185078.3,c.358C>T,HIGH,,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000541078,NM_001185077.3,c.358C>T,HIGH,,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000580685,,c.358C>T,HIGH,,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000584461,NM_001301240.2&NM_001301241.2,c.358C>T,HIGH,,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000583868,NM_001301242.2,c.358C>T,HIGH,YES,,,-1;ARHGDIA,stop_gained,p.R120*,ENST00000579121,,c.358C>T,HIGH,,,,-1;ARHGDIA,intron_variant,,ENST00000581876,,c.191-155C>T,MODIFIER,,,,-1;ARHGDIA,upstream_gene_variant,,ENST00000582520,,,MODIFIER,,,,-1;ARHGDIA,3_prime_UTR_variant,,ENST00000580033,,c.*2C>T,MODIFIER,,,,-1;ARHGDIA,3_prime_UTR_variant,,ENST00000578351,,c.*2C>T,MODIFIER,,,,-1;ARHGDIA,non_coding_transcript_exon_variant,,ENST00000582984,,n.560C>T,MODIFIER,,,,-1;ARHGDIA,non_coding_transcript_exon_variant,,ENST00000583111,,n.510C>T,MODIFIER,,,,-1;ARHGDIA,non_coding_transcript_exon_variant,,ENST00000583791,,n.222C>T,MODIFIER,,,,-1;ARHGDIA,downstream_gene_variant,,ENST00000582309,,,MODIFIER,,,,-1;ARHGDIA,downstream_gene_variant,,ENST00000583499,,,MODIFIER,,,,-1;ARHGDIA,downstream_gene_variant,,ENST00000584397,,,MODIFIER,,,,-1;AC145207.2,downstream_gene_variant,,ENST00000576021,,,MODIFIER,,,,1;AC145207.2,downstream_gene_variant,,ENST00000576554,,,MODIFIER,YES,,,1 425/1837 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 52 69e289e0-bb0e-41a8-acbc-a6215f000980 41 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS ARHGDIA,non_coding_transcript_exon_variant,,ENST00000583111.5,n.510C>T,MODIFIER,;ARHGDIA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000578351.1,c.*2C>T,MODIFIER,;ARHGDIA,non_coding_transcript_exon_variant,,ENST00000583791.1,n.222C>T,MODIFIER,;ARHGDIA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000580033.5,c.*2C>T,MODIFIER,;ARHGDIA,non_coding_transcript_exon_variant,,ENST00000582984.5,n.560C>T,MODIFIER,;ARHGDIA,stop_gained,p.R120*,ENST00000583868.5,c.358C>T,HIGH,;ARHGDIA,intron_variant,,ENST00000581876.5,c.191-155C>T,MODIFIER,;ARHGDIA,stop_gained,p.R120*,ENST00000579121.5,c.358C>T,HIGH,;ARHGDIA,stop_gained,p.R120*,ENST00000580685.5,c.358C>T,HIGH,;ARHGDIA,stop_gained,p.R120*,ENST00000541078.6,c.358C>T,HIGH,;ARHGDIA,stop_gained,p.R120*,ENST00000584461.5,c.358C>T,HIGH,;ARHGDIA,stop_gained,p.R120*,ENST00000400721.8,c.358C>T,HIGH,;ARHGDIA,stop_gained,p.R120*,ENST00000269321.12,c.358C>T,HIGH,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 27 24 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0 66 69e289e0-bb0e-41a8-acbc-a6215f000980 52 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +C3 718 BI GRCh38 19 6710837 6710837 + missense_variant Missense_Mutation SNP G G T rs1458826211 TCGA-V4-A9F5-01A TCGA-V4-A9F5-10A Somatic 10 15 c.1488C>A p.Asn496Lys p.N496K ENST00000245907.11 NM_000064.4 496 aaC/aaA 13/41 P1 T N/K protein_coding YES CCDS32883.1 1488/4992 CCCTTGTTCAT Gene3D:2.60.40.1930;PDB-ENSP_mappings:2a73.A;PDB-ENSP_mappings:2a74.A;PDB-ENSP_mappings:2a74.D;PDB-ENSP_mappings:2i07.A;PDB-ENSP_mappings:2ice.A;PDB-ENSP_mappings:2ice.D;PDB-ENSP_mappings:2icf.A;PDB-ENSP_mappings:2qki.A;PDB-ENSP_mappings:2qki.D;PDB-ENSP_mappings:2wii.A;PDB-ENSP_mappings:2win.A;PDB-ENSP_mappings:2win.C;PDB-ENSP_mappings:2win.E;PDB-ENSP_mappings:2win.G;PDB-ENSP_mappings:2xwb.A;PDB-ENSP_mappings:2xwb.C;PDB-ENSP_mappings:2xwj.A;PDB-ENSP_mappings:2xwj.C;PDB-ENSP_mappings:2xwj.E;PDB-ENSP_mappings:2xwj.G;PDB-ENSP_mappings:3g6j.A;PDB-ENSP_mappings:3g6j.C;PDB-ENSP_mappings:3l3o.A;PDB-ENSP_mappings:3l3o.D;PDB-ENSP_mappings:3l5n.A;PDB-ENSP_mappings:3nms.A;PDB-ENSP_mappings:3ohx.A;PDB-ENSP_mappings:3ohx.D;PDB-ENSP_mappings:3t4a.A;PDB-ENSP_mappings:3t4a.D;PDB-ENSP_mappings:5fo7.A;PDB-ENSP_mappings:5fo8.A;PDB-ENSP_mappings:5fo9.A;PDB-ENSP_mappings:5fo9.D;PDB-ENSP_mappings:5foa.A;PDB-ENSP_mappings:5foa.C;PDB-ENSP_mappings:5fob.A;PDB-ENSP_mappings:5o32.A;PDB-ENSP_mappings:5o32.E;PDB-ENSP_mappings:5o35.A;PDB-ENSP_mappings:6ehg.A;PDB-ENSP_mappings:6ru5.A;PDB-ENSP_mappings:6rur.A;PDB-ENSP_mappings:6rur.G;PDB-ENSP_mappings:6ruv.A;PDB-ENSP_mappings:6ruv.G;Pfam:PF07703;PANTHER:PTHR11412;PANTHER:PTHR11412:SF81;SMART:SM01359 ENSP00000245907 13/41 rs1458826211 ENST00000245907 Transcript 1.0 ENSG00000125730 HGNC:1318 MODERATE NM_000064.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.948) Unknown deleterious(0.01) P01024.244 C3 HGNC -1 V9HWA9.51 1.0 UPI000013EC9B SNV C3,missense_variant,p.N496K,ENST00000245907,NM_000064.4,c.1488C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.948),-1;C3,downstream_gene_variant,,ENST00000594270,,,MODIFIER,,,,-1;C3,downstream_gene_variant,,ENST00000597442,,,MODIFIER,,,,-1;C3,non_coding_transcript_exon_variant,,ENST00000600763,,n.121C>A,MODIFIER,,,,-1;C3,downstream_gene_variant,,ENST00000595577,,,MODIFIER,,,,-1 1549/5231 muse;mutect2;varscan2 bbf07e1f-8c17-4c2e-89ed-38332d82e455 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 26 69e289e0-bb0e-41a8-acbc-a6215f000980 25 22e928d7-5923-4773-b8e1-7c123d79e480 SUCCESS C3,non_coding_transcript_exon_variant,,ENST00000600763.1,n.121C>A,MODIFIER,;C3,missense_variant,p.N455K,ENST00000695652.1,c.1365C>A,MODERATE,;C3,missense_variant,NMD_transcript_variant,p.N131K,ENST00000695655.1,c.393C>A,MODERATE,;C3,non_coding_transcript_exon_variant,,ENST00000695692.1,n.852C>A,MODIFIER,;C3,missense_variant,p.N204K,ENST00000695654.1,c.612C>A,MODERATE,;C3,missense_variant,p.N496K,ENST00000245907.11,c.1488C>A,MODERATE,YES +ZBTB8A 653121 BI GRCh38 1 32593174 32593174 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 112 10 c.243C>G p.Asp81Glu p.D81E ENST00000373510.9 NM_001040441.3 81 gaC/gaG 3/5 P1 G D/E protein_coding YES CCDS30664.1 243/1326 TTGGACTTCGT PROSITE_profiles:PS50097;CDD:cd18329;PANTHER:PTHR24414:SF25;PANTHER:PTHR24414;Gene3D:3.30.710.10;Pfam:PF00651;SMART:SM00225;Superfamily:SSF54695 ENSP00000362609 3/5 ENST00000373510 Transcript ENSG00000160062 HGNC:24172 MODERATE NM_001040441.3 missense_variant 1.0 probably_damaging(0.998) Unknown deleterious(0) Q96BR9.170 ZBTB8A HGNC 1 1.0 UPI000006EA53 SNV ZBTB8A,missense_variant,p.D81E,ENST00000373510,NM_001040441.3,c.243C>G,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;ZBTB8A,missense_variant,p.D81E,ENST00000316459,NM_001291496.2,c.243C>G,MODERATE,,deleterious(0),probably_damaging(0.968),1;AL033529.1,3_prime_UTR_variant,,ENST00000480336,,c.*362C>G,MODIFIER,YES,,,1 472/7077 muse;mutect2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 133 0c6a7e7f-44e0-4011-8204-20ead8091990 122 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS ZBTB8A,missense_variant,p.D81E,ENST00000316459.4,c.243C>G,MODERATE,;ZBTB8A,missense_variant,p.D81E,ENST00000373510.9,c.243C>G,MODERATE,YES;ENSG00000254553,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000480336.1,c.*362C>G,MODIFIER,YES +NPR1 4881 BI GRCh38 1 153685844 153685844 + synonymous_variant Silent SNP C C T novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 49 28 c.1644C>T p.Gly548= p.G548= ENST00000368680.4 NM_000906.4 548 ggC/ggT 9/22 P1 T G protein_coding YES CCDS1051.1 1644/3186 GAGGGCCAGTT Gene3D:1.10.510.10;PROSITE_profiles:PS50011;PANTHER:PTHR11920;PANTHER:PTHR11920:SF300;CDD:cd14042 ENSP00000357669 9/22 ENST00000368680 Transcript ENSG00000169418 HGNC:7943 LOW NM_000906.4 synonymous_variant 1.0 Unknown P16066.208 NPR1 HGNC 1 A0A140VJE6.28 1.0 UPI0000125B3D SNV NPR1,synonymous_variant,p.G548=,ENST00000368680,NM_000906.4,c.1644C>T,LOW,YES,,,1;MIR8083,downstream_gene_variant,,ENST00000620823,,,MODIFIER,YES,,,-1;NPR1,downstream_gene_variant,,ENST00000413826,,,MODIFIER,,,,1;NPR1,upstream_gene_variant,,ENST00000368677,,,MODIFIER,,,,1 2065/4185 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 79 0c6a7e7f-44e0-4011-8204-20ead8091990 77 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS NPR1,synonymous_variant,p.G548=,ENST00000368680.4,c.1644C>T,LOW,YES +SLC40A1 30061 BI GRCh38 2 189563790 189563790 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 25 23 c.1196A>G p.Asp399Gly p.D399G ENST00000261024.7 NM_014585.6 399 gAc/gGc 7/8 P1 C D/G protein_coding YES CCDS2299.1 1196/1716 ACAAGTCCAGG Pfam:PF06963;PANTHER:PTHR11660;PANTHER:PTHR11660:SF47;Superfamily:SSF103473;CDD:cd17480 ENSP00000261024 7/8 ENST00000261024 Transcript 1.0 ENSG00000138449 HGNC:10909 MODERATE NM_014585.6 missense_variant 1.0 probably_damaging(0.942) Unknown deleterious(0) Q9NP59.171 SLC40A1 HGNC -1 1.0 UPI0000034CC2 SNV SLC40A1,missense_variant,p.D399G,ENST00000261024,NM_014585.6,c.1196A>G,MODERATE,YES,deleterious(0),probably_damaging(0.942),-1;SLC40A1,downstream_gene_variant,,ENST00000427241,,,MODIFIER,,,,-1 1522/3330 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 50 0c6a7e7f-44e0-4011-8204-20ead8091990 48 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS SLC40A1,missense_variant,p.D399G,ENST00000261024.7,c.1196A>G,MODERATE,YES +TGM4 7047 BI GRCh38 3 44911354 44911354 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 62 45 c.1861A>C p.Lys621Gln p.K621Q ENST00000296125.9 NM_003241.4 621 Aag/Cag 13/14 P1 C K/Q protein_coding YES CCDS2723.1 1861/2055 ACGTCAAGTTC PANTHER:PTHR11590:SF70;PANTHER:PTHR11590;PIRSF:PIRSF000459;Gene3D:2.60.40.10;Pfam:PF00927;Superfamily:SSF49309 ENSP00000296125 13/14 ENST00000296125 Transcript ENSG00000163810 HGNC:11780 MODERATE NM_003241.4 missense_variant 1.0 benign(0.105) Unknown deleterious(0.05) P49221.176 TGM4 HGNC 1 1.0 UPI0000136CCD SNV TGM4,missense_variant,p.K621Q,ENST00000296125,NM_003241.4,c.1861A>C,MODERATE,YES,deleterious(0.05),benign(0.105),1;ZDHHC3,downstream_gene_variant,,ENST00000339420,NM_001349377.2&NM_001349376.2&NM_001349378.2,,MODIFIER,,,,-1;ZDHHC3,downstream_gene_variant,,ENST00000424952,NM_001135179.2&NM_001349381.2&NM_001349380.2,,MODIFIER,,,,-1;TGM4,downstream_gene_variant,,ENST00000459830,,,MODIFIER,,,,1 1932/3391 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 94 0c6a7e7f-44e0-4011-8204-20ead8091990 107 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS TGM4,missense_variant,p.K621Q,ENST00000296125.9,c.1861A>C,MODERATE,YES;TGM4,missense_variant,p.K666Q,ENST00000705784.1,c.1996A>C,MODERATE, +PDIA5 10954 BI GRCh38 3 123102771 123102771 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 25 20 c.362A>G p.Glu121Gly p.E121G ENST00000316218.12 NM_006810.4 121 gAa/gGa 5/17 P1 G E/G protein_coding YES CCDS3020.1 362/1560 TACTGAATATA PDB-ENSP_mappings:4i6x.A;CDD:cd03067;PANTHER:PTHR45672:SF2;PANTHER:PTHR45672;Gene3D:3.40.30.10;Superfamily:SSF52833;Superfamily:SSF52833 ENSP00000323313 5/17 ENST00000316218 Transcript ENSG00000065485 HGNC:24811 MODERATE NM_006810.4 missense_variant 1.0 benign(0.309) Unknown deleterious(0.04) Q14554.173 PDIA5 HGNC 1 1.0 UPI000013148A Q14554-1 SNV PDIA5,missense_variant,p.E121G,ENST00000316218,NM_006810.4,c.362A>G,MODERATE,YES,deleterious(0.04),benign(0.309),1;PDIA5,missense_variant,p.E25G,ENST00000484644,,c.74A>G,MODERATE,,deleterious(0.03),benign(0.309),1;PDIA5,non_coding_transcript_exon_variant,,ENST00000495004,,n.381A>G,MODIFIER,,,,1;PDIA5,missense_variant,p.E121G,ENST00000489923,,c.362A>G,MODERATE,,deleterious(0.04),benign(0.224),1 502/1844 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 62 0c6a7e7f-44e0-4011-8204-20ead8091990 45 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS PDIA5,non_coding_transcript_exon_variant,,ENST00000495004.1,n.381A>G,MODIFIER,;PDIA5,missense_variant,p.E25G,ENST00000484644.5,c.74A>G,MODERATE,;PDIA5,missense_variant,NMD_transcript_variant,p.E121G,ENST00000489923.5,c.362A>G,MODERATE,;PDIA5,missense_variant,p.E121G,ENST00000316218.12,c.362A>G,MODERATE,YES +WDR41 55255 BI GRCh38 5 77492204 77492204 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 18 15 c.17T>G p.Ile6Ser p.I6S ENST00000296679.9 NM_018268.4 6 aTc/aGc 1/13 P1 C I/S protein_coding YES CCDS4038.1 17/1380 CCCCGATCAGC PDB-ENSP_mappings:6lt0.A;PDB-ENSP_mappings:6lt0.D ENSP00000296679 1/13 ENST00000296679 Transcript ENSG00000164253 HGNC:25601 MODERATE NM_018268.4 missense_variant 1.0 benign(0.134) Unknown deleterious(0) Q9HAD4.153 WDR41 HGNC -1 A0A0S2Z5E0.23 1.0 UPI00000744EF Q9HAD4-1 SNV WDR41,missense_variant,p.I6S,ENST00000296679,NM_018268.4,c.17T>G,MODERATE,YES,deleterious(0),benign(0.134),-1;WDR41,missense_variant,p.I6S,ENST00000507029,,c.17T>G,MODERATE,,deleterious_low_confidence(0),benign(0.266),-1;WDR41,missense_variant,p.I6S,ENST00000511036,,c.17T>G,MODERATE,,deleterious_low_confidence(0),benign(0.001),-1;WDR41,missense_variant,p.I6S,ENST00000514559,,c.17T>G,MODERATE,,deleterious(0),benign(0.134),-1;WDR41,missense_variant,p.I6S,ENST00000511791,,c.17T>G,MODERATE,,tolerated_low_confidence(0.2),benign(0),-1;WDR41,intron_variant,,ENST00000509971,,c.43-2632T>G,MODIFIER,,,,-1;WDR41,upstream_gene_variant,,ENST00000504895,,,MODIFIER,,,,-1;WDR41,upstream_gene_variant,,ENST00000507654,,,MODIFIER,,,,-1;WDR41,upstream_gene_variant,,ENST00000515253,,,MODIFIER,,,,-1;WDR41,non_coding_transcript_exon_variant,,ENST00000507452,,n.12T>G,MODIFIER,,,,-1;WDR41,non_coding_transcript_exon_variant,,ENST00000515321,,n.18T>G,MODIFIER,,,,-1;WDR41,intron_variant,,ENST00000509858,,n.178-2647T>G,MODIFIER,,,,-1;WDR41,intron_variant,,ENST00000512168,,n.256-9T>G,MODIFIER,,,,-1;WDR41,intron_variant,,ENST00000513917,,n.311-2632T>G,MODIFIER,,,,-1;WDR41,upstream_gene_variant,,ENST00000514451,,,MODIFIER,,,,-1;WDR41,missense_variant,p.I6S,ENST00000505129,,c.17T>G,MODERATE,,deleterious(0),benign(0.383),-1;WDR41,missense_variant,p.I6S,ENST00000509701,,c.17T>G,MODERATE,,deleterious(0),benign(0.203),-1;WDR41,missense_variant,p.I6S,ENST00000503035,,c.17T>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.453),-1;WDR41,missense_variant,p.I5S,ENST00000509892,,c.14T>G,MODERATE,,deleterious_low_confidence(0),benign(0.371),-1;WDR41,missense_variant,p.I6S,ENST00000506307,,c.17T>G,MODERATE,,deleterious(0),possibly_damaging(0.463),-1;WDR41,missense_variant,p.I6S,ENST00000513417,,c.17T>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.453),-1;WDR41,missense_variant,p.I6S,ENST00000506474,,c.17T>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.773),-1;WDR41,non_coding_transcript_exon_variant,,ENST00000507239,,n.19T>G,MODIFIER,,,,-1 113/3678 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 40 0c6a7e7f-44e0-4011-8204-20ead8091990 34 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS WDR41,intron_variant,,ENST00000512168.1,n.256-9T>G,MODIFIER,;WDR41,intron_variant,,ENST00000513917.5,n.311-2632T>G,MODIFIER,;WDR41,intron_variant,,ENST00000509858.5,n.178-2647T>G,MODIFIER,;WDR41,non_coding_transcript_exon_variant,,ENST00000507239.5,n.19T>G,MODIFIER,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000506474.5,c.17T>G,MODERATE,;WDR41,intron_variant,,ENST00000509971.5,c.43-2632T>G,MODIFIER,;WDR41,missense_variant,p.I6S,ENST00000511036.5,c.17T>G,MODERATE,;WDR41,missense_variant,p.I6S,ENST00000514559.5,c.17T>G,MODERATE,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000503035.5,c.17T>G,MODERATE,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000513417.5,c.17T>G,MODERATE,;WDR41,non_coding_transcript_exon_variant,,ENST00000515321.5,n.18T>G,MODIFIER,;WDR41,missense_variant,NMD_transcript_variant,p.D4E,ENST00000509892.5,c.12T>G,MODERATE,;WDR41,non_coding_transcript_exon_variant,,ENST00000507452.5,n.12T>G,MODIFIER,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000506307.5,c.17T>G,MODERATE,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000505129.5,c.17T>G,MODERATE,;WDR41,missense_variant,p.I6S,ENST00000511791.1,c.17T>G,MODERATE,;WDR41,missense_variant,NMD_transcript_variant,p.I6S,ENST00000509701.5,c.17T>G,MODERATE,;WDR41,missense_variant,p.I6S,ENST00000507029.5,c.17T>G,MODERATE,;WDR41,missense_variant,p.I6S,ENST00000296679.9,c.17T>G,MODERATE,YES +NREP 9315 BI GRCh38 5 111730962 111730962 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 30 35 c.166G>A p.Glu56Lys p.E56K ENST00000257435.12 NM_004772.4 56 Gaa/Aaa 4/4 P2 T E/K protein_coding CCDS4105.1 166/207 GAGTTCACTGC Pfam:PF11092;PANTHER:PTHR17102 ENSP00000257435 4/4 ENST00000257435 Transcript ENSG00000134986 HGNC:16834 MODERATE NM_004772.4 missense_variant benign(0.142) Unknown tolerated(0.14) Q16612.137 NREP HGNC -1 1.0 UPI0000047FA1 Q16612-1 SNV NREP,missense_variant,p.E56K,ENST00000379671,NM_001142478.2,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000447165,NM_001142483.1,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000446294,NM_001142481.1&NM_001142482.1,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000257435,NM_004772.4,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E100K,ENST00000395634,NM_001142474.2&NM_001142475.2,c.298G>A,MODERATE,YES,tolerated(0.13),possibly_damaging(0.583),-1;NREP,missense_variant,p.E56K,ENST00000419114,NM_001142480.1&NM_001142479.1,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000455559,NM_001142476.1&NM_001142477.1,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000450761,,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000509427,,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000453526,,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000513100,,c.166G>A,MODERATE,,tolerated(0.15),benign(0.142),-1;NREP,missense_variant,p.E56K,ENST00000508870,,c.166G>A,MODERATE,,tolerated(0.14),benign(0.142),-1;NREP,3_prime_UTR_variant,,ENST00000515855,,c.*131G>A,MODIFIER,,,,-1;NREP,3_prime_UTR_variant,,ENST00000509979,,c.*131G>A,MODIFIER,,,,-1;NREP,intron_variant,,ENST00000509025,,c.81+4468G>A,MODIFIER,,,,-1;NREP,downstream_gene_variant,,ENST00000507032,,,MODIFIER,,,,-1;NREP,downstream_gene_variant,,ENST00000508161,,,MODIFIER,,,,-1;NREP,non_coding_transcript_exon_variant,,ENST00000507742,,n.257G>A,MODIFIER,,,,-1;NREP,non_coding_transcript_exon_variant,,ENST00000504018,,n.645G>A,MODIFIER,,,,-1;NREP,intron_variant,,ENST00000514515,,c.81+4468G>A,MODIFIER,,,,-1;NREP,downstream_gene_variant,,ENST00000503429,,,MODIFIER,,,,-1;NREP,downstream_gene_variant,,ENST00000505864,,,MODIFIER,,,,-1;STARD4-AS1,non_coding_transcript_exon_variant,,ENST00000666013,,n.4148C>T,MODIFIER,,,,1;STARD4-AS1,intron_variant,,ENST00000500779,,n.1037-819C>T,MODIFIER,YES,,,1;STARD4-AS1,intron_variant,,ENST00000513221,,n.122+452C>T,MODIFIER,,,,1;STARD4-AS1,upstream_gene_variant,,ENST00000654777,,,MODIFIER,,,,1 283/1942 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 62 0c6a7e7f-44e0-4011-8204-20ead8091990 65 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS NREP,non_coding_transcript_exon_variant,,ENST00000504018.1,n.645G>A,MODIFIER,;NREP,missense_variant,p.E56K,ENST00000513100.5,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000508870.5,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000455559.6,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000453526.6,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000509427.5,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000419114.6,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000450761.6,c.166G>A,MODERATE,;NREP,3_prime_UTR_variant,,ENST00000509979.5,c.*131G>A,MODIFIER,;NREP,non_coding_transcript_exon_variant,,ENST00000507742.5,n.257G>A,MODIFIER,;NREP,3_prime_UTR_variant,,ENST00000515855.5,c.*131G>A,MODIFIER,;STARD4-AS1,intron_variant,,ENST00000513221.1,n.122+452C>T,MODIFIER,;NREP,missense_variant,p.E100K,ENST00000395634.7,c.298G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000446294.6,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000257435.12,c.166G>A,MODERATE,YES;NREP,missense_variant,p.E56K,ENST00000447165.6,c.166G>A,MODERATE,;NREP,missense_variant,p.E56K,ENST00000379671.7,c.166G>A,MODERATE,;NREP,intron_variant,,ENST00000509025.5,c.81+4468G>A,MODIFIER,;NREP,intron_variant,NMD_transcript_variant,,ENST00000514515.5,c.81+4468G>A,MODIFIER,;STARD4-AS1,intron_variant,,ENST00000500779.2,n.1037-819C>T,MODIFIER,YES;STARD4-AS1,non_coding_transcript_exon_variant,,ENST00000666013.1,n.4148C>T,MODIFIER, +CARMIL1 55604 BI GRCh38 6 25500185 25500185 + missense_variant Missense_Mutation SNP G G C TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 17 14 c.1345G>C p.Ala449Pro p.A449P ENST00000329474.7 NM_017640.6 449 Gct/Cct 17/37 P1 C A/P protein_coding YES CCDS54973.1 1345/4116 GCCTGGCTTGT Gene3D:3.80.10.10;PANTHER:PTHR24112;PANTHER:PTHR24112:SF39;Superfamily:SSF52047 ENSP00000331983 17/37 COSV100278809 ENST00000329474 Transcript ENSG00000079691 HGNC:21581 MODERATE NM_017640.6 missense_variant 1 1.0 possibly_damaging(0.83) Unknown deleterious(0) 1 Q5VZK9.147 CARMIL1 HGNC 1 1.0 UPI00004588AB Q5VZK9-1 SNV CARMIL1,missense_variant,p.A449P,ENST00000329474,NM_017640.6&NM_001173977.2,c.1345G>C,MODERATE,YES,deleterious(0),possibly_damaging(0.83),1;CARMIL1,missense_variant,p.A39P,ENST00000635618,,c.115G>C,MODERATE,,deleterious(0.01),possibly_damaging(0.697),1 1767/5485 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 36 0c6a7e7f-44e0-4011-8204-20ead8091990 31 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS CARMIL1,missense_variant,NMD_transcript_variant,p.A39P,ENST00000635618.1,c.115G>C,MODERATE,;CARMIL1,missense_variant,p.A449P,ENST00000700669.1,c.1345G>C,MODERATE,;CARMIL1,missense_variant,p.A449P,ENST00000329474.7,c.1345G>C,MODERATE,YES +ZNF680 340252 BI GRCh38 7 64544359 64544359 + missense_variant Missense_Mutation SNP C C T rs1472467735 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 119 6 c.104G>A p.Arg35Gln p.R35Q ENST00000309683.11 NM_178558.5 35 cGg/cAg 2/4 P1 T R/Q protein_coding YES CCDS34644.1 104/1593 AATTCCGTTGT Pfam:PF01352;PROSITE_profiles:PS50805;PANTHER:PTHR24384;PANTHER:PTHR24384:SF201;SMART:SM00349;Superfamily:SSF109640;CDD:cd07765 ENSP00000309330 2/4 rs1472467735;COSV59016994 ENST00000309683 Transcript ENSG00000173041 HGNC:26897 MODERATE NM_178558.5 3.266e-05 gnomAD_SAS missense_variant 0;1 1.0 benign(0.042) Unknown tolerated(1) 0;1 Q8NEM1.154 ZNF680 HGNC -1 1.0 UPI000019980A Q8NEM1-1 SNV ZNF680,missense_variant,p.R35Q,ENST00000309683,NM_178558.5,c.104G>A,MODERATE,YES,tolerated(1),benign(0.042),-1;ZNF680,missense_variant,p.R35Q,ENST00000447137,NM_001130022.1,c.104G>A,MODERATE,,tolerated_low_confidence(1),benign(0.024),-1;ZNF680,non_coding_transcript_exon_variant,,ENST00000473601,,n.553G>A,MODIFIER,,,,-1;ZNF680,intron_variant,,ENST00000476563,,n.99-557G>A,MODIFIER,,,,-1;ZNF680,upstream_gene_variant,,ENST00000470847,,,MODIFIER,,,,-1 221/2993 muse;mutect2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 3.977e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.266e-05 0 216 0c6a7e7f-44e0-4011-8204-20ead8091990 125 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS ZNF680,non_coding_transcript_exon_variant,,ENST00000473601.1,n.553G>A,MODIFIER,;ZNF680,missense_variant,p.R35Q,ENST00000447137.2,c.104G>A,MODERATE,;ZNF680,intron_variant,,ENST00000476563.1,n.99-557G>A,MODIFIER,;ZNF680,missense_variant,p.R35Q,ENST00000309683.11,c.104G>A,MODERATE,YES +KAT6A 7994 BI GRCh38 8 41932756 41932756 + missense_variant Missense_Mutation SNP T T C rs769858065 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 39 32 c.5464A>G p.Asn1822Asp p.N1822D ENST00000265713.8 NM_006766.5 1822 Aac/Gac 17/17 P4 C N/D protein_coding CCDS6124.1 5464/6015 GAGGTTCATGG ENSP00000265713 17/17 rs769858065 ENST00000265713 Transcript 1.0 ENSG00000083168 HGNC:13013 MODERATE NM_006766.5 8.79e-06 gnomAD_NFE missense_variant benign(0.411) Unknown deleterious_low_confidence(0) Q92794.205 KAT6A HGNC -1 1.0 UPI000013D666 SNV KAT6A,missense_variant,p.N1824D,ENST00000406337,,c.5470A>G,MODERATE,YES,deleterious_low_confidence(0),possibly_damaging(0.616),-1;KAT6A,missense_variant,p.N1822D,ENST00000265713,NM_006766.5,c.5464A>G,MODERATE,,deleterious_low_confidence(0),benign(0.411),-1;KAT6A,missense_variant,p.N1822D,ENST00000396930,,c.5464A>G,MODERATE,,deleterious_low_confidence(0),benign(0.411),-1;KAT6A,missense_variant,p.N1383D,ENST00000649817,,c.4147A>G,MODERATE,,deleterious_low_confidence(0.04),possibly_damaging(0.616),-1;KAT6A,downstream_gene_variant,,ENST00000648335,,,MODIFIER,,,,-1;KAT6A,downstream_gene_variant,,ENST00000418721,,,MODIFIER,,,,-1;KAT6A,downstream_gene_variant,,ENST00000649827,,,MODIFIER,,,,-1;KAT6A,downstream_gene_variant,,ENST00000650495,,,MODIFIER,,,,-1 5876/9153 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 3.976e-06 0.0 0.0 0.0 0.0 0.0 8.79e-06 0.0 0.0 0 68 0c6a7e7f-44e0-4011-8204-20ead8091990 71 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS KAT6A,missense_variant,p.E1382G,ENST00000649817.1,c.4145A>G,MODERATE,;KAT6A,missense_variant,p.N1822D,ENST00000396930.4,c.5464A>G,MODERATE,;KAT6A,missense_variant,p.N1824D,ENST00000406337.6,c.5470A>G,MODERATE,;KAT6A,missense_variant,p.N1822D,ENST00000265713.8,c.5464A>G,MODERATE,YES +ZNF658 26149 BI GRCh38 9 66919461 66919461 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 152 54 c.1895G>A p.Cys632Tyr p.C632Y ENST00000612867.4 NM_001317916.2 632 tGt/tAt 5/5 P1 A C/Y protein_coding YES CCDS75846.1 1895/3180 TGAATGTAATG Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24379;PANTHER:PTHR24379;PANTHER:PTHR24379;PANTHER:PTHR24379:SF92;PANTHER:PTHR24379:SF92;PANTHER:PTHR24379:SF92;SMART:SM00355;Superfamily:SSF57667 ENSP00000482540 5/5 ENST00000612867 Transcript ENSG00000274349 HGNC:25226 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q5TYW1.138 ZNF658 HGNC 1 2.0 UPI000046D388 Q5TYW1-1 SNV ZNF658,missense_variant,p.C632Y,ENST00000612867,NM_001317916.1,c.1895G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;ZNF658,missense_variant,p.C632Y,ENST00000621410,NM_033160.6,c.1895G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ZNF658,downstream_gene_variant,,ENST00000616544,,,MODIFIER,,,,1;ZNF658,downstream_gene_variant,,ENST00000619925,,,MODIFIER,,,,1;ZNF658,downstream_gene_variant,,ENST00000621015,,,MODIFIER,,,,1;ZNF658,intron_variant,,ENST00000622180,,c.1792+103G>A,MODIFIER,,,,1 2195/4160 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 349 0c6a7e7f-44e0-4011-8204-20ead8091990 206 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS ZNF658,missense_variant,p.C632Y,ENST00000612867.4,c.1895G>A,MODERATE,;ZNF658,missense_variant,p.C632Y,ENST00000621410.5,c.1895G>A,MODERATE,YES;ZNF658,intron_variant,NMD_transcript_variant,,ENST00000622180.4,c.1792+103G>A,MODIFIER, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 50 46 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 86 0c6a7e7f-44e0-4011-8204-20ead8091990 96 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +OGN 4969 BI GRCh38 9 92385691 92385691 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 74 5 c.826C>A p.Pro276Thr p.P276T ENST00000262551.8 NM_033014.4 276 Cca/Aca 7/7 P1 T P/T protein_coding CCDS6695.1 826/897 GATTGGATTGC Gene3D:3.80.10.10;PANTHER:PTHR46269;PANTHER:PTHR46269:SF1;Superfamily:SSF52058 ENSP00000262551 7/7 ENST00000262551 Transcript ENSG00000106809 HGNC:8126 MODERATE missense_variant probably_damaging(0.998) Unknown deleterious(0) P20774.192 OGN HGNC -1 A8K0R3.110 5.0 UPI00000540ED SNV OGN,missense_variant,p.P276T,ENST00000375561,NM_014057.5&NM_024416.4,c.826C>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;OGN,missense_variant,p.P276T,ENST00000262551,NM_033014.3,c.826C>A,MODERATE,,deleterious(0),probably_damaging(0.998),-1;CENPP,intron_variant,,ENST00000375587,NM_001286969.1&NM_001012267.3,c.564+5832G>T,MODIFIER,YES,,,1;OGN,downstream_gene_variant,,ENST00000447356,,,MODIFIER,,,,-1;OGN,downstream_gene_variant,,ENST00000468743,,,MODIFIER,,,,-1 1247/2971 muse;mutect2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 84 0c6a7e7f-44e0-4011-8204-20ead8091990 79 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS OGN,missense_variant,p.P276T,ENST00000262551.8,c.826C>A,MODERATE,;OGN,missense_variant,p.P276T,ENST00000375561.10,c.826C>A,MODERATE,YES;CENPP,intron_variant,,ENST00000375587.8,c.564+5832G>T,MODIFIER,YES +STIP1 10963 BI GRCh38 11 64204073 64204073 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 62 38 c.1579A>G p.Ile527Val p.I527V ENST00000305218.9 NM_006819.3 527 Ata/Gta 14/14 P1 G I/V protein_coding CCDS8058.1 1579/1632 CTGTAATAGCA PANTHER:PTHR22904:SF517;PANTHER:PTHR22904;Gene3D:1.10.260.100;Pfam:PF17830;SMART:SM00727 ENSP00000305958 14/14 ENST00000305218 Transcript ENSG00000168439 HGNC:11387 MODERATE NM_006819.3 missense_variant benign(0.13) Unknown tolerated(0.5) P31948.211 STIP1 HGNC 1 V9HW72.56 1.0 UPI000012D225 P31948-1 SNV STIP1,missense_variant,p.I574V,ENST00000358794,NM_001282652.1,c.1720A>G,MODERATE,YES,tolerated(0.78),possibly_damaging(0.54),1;STIP1,missense_variant,p.I527V,ENST00000305218,NM_006819.3,c.1579A>G,MODERATE,,tolerated(0.5),benign(0.13),1;STIP1,missense_variant,p.I503V,ENST00000538945,NM_001282653.2,c.1507A>G,MODERATE,,tolerated(0.6),benign(0.389),1;STIP1,3_prime_UTR_variant,,ENST00000540887,,c.*393A>G,MODIFIER,,,,1;FERMT3,upstream_gene_variant,,ENST00000279227,NM_178443.3&NM_001382362.1&NM_001382364.1,,MODIFIER,YES,,,1;FERMT3,upstream_gene_variant,,ENST00000345728,NM_001382448.1&NM_031471.6&NM_001382361.1&NM_001382363.1,,MODIFIER,,,,1;FERMT3,upstream_gene_variant,,ENST00000541252,,,MODIFIER,,,,1;FERMT3,upstream_gene_variant,,ENST00000544997,,,MODIFIER,,,,1;STIP1,downstream_gene_variant,,ENST00000537479,,,MODIFIER,,,,1;STIP1,3_prime_UTR_variant,,ENST00000536973,,c.*98A>G,MODIFIER,,,,1;STIP1,downstream_gene_variant,,ENST00000355603,,,MODIFIER,,,,1;STIP1,downstream_gene_variant,,ENST00000538497,,,MODIFIER,,,,1 1670/2140 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 6.758129984518746e-06 0.0 0.0 0.0 0.0 0.0 9.410880011273548e-05 0.0 0.0 0.0 0.0 0 106 0c6a7e7f-44e0-4011-8204-20ead8091990 100 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS STIP1,3_prime_UTR_variant,,ENST00000540887.1,c.*393A>G,MODIFIER,;STIP1,missense_variant,p.I503V,ENST00000538945.5,c.1507A>G,MODERATE,;STIP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000536973.5,c.*98A>G,MODIFIER,;STIP1,missense_variant,p.I527V,ENST00000305218.9,c.1579A>G,MODERATE,YES;STIP1,missense_variant,p.I574V,ENST00000358794.9,c.1720A>G,MODERATE, +KRT83 3889 BI GRCh38 12 52316927 52316927 + missense_variant Missense_Mutation SNP T T C rs942790024 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 56 34 c.847A>G p.Ile283Val p.I283V ENST00000293670.3 NM_002282.3 283 Atc/Gtc 5/9 P1 C I/V protein_coding YES CCDS8823.1 847/1482 CTTGATCTCGG Gene3D:1.20.5.500;Pfam:PF00038;PROSITE_profiles:PS51842;PANTHER:PTHR45616;PANTHER:PTHR45616:SF41;SMART:SM01391;Superfamily:SSF57184 ENSP00000293670 5/9 rs942790024 ENST00000293670 Transcript 1.0 ENSG00000170523 HGNC:6460 MODERATE NM_002282.3 missense_variant 1.0 benign(0.255) Unknown tolerated(0.6) P78385.164 KRT83 HGNC -1 1.0 UPI0000070AF2 SNV KRT83,missense_variant,p.I283V,ENST00000293670,NM_002282.3,c.847A>G,MODERATE,YES,tolerated(0.6),benign(0.255),-1 910/1875 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 101 0c6a7e7f-44e0-4011-8204-20ead8091990 90 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS KRT83,missense_variant,p.I283V,ENST00000293670.3,c.847A>G,MODERATE,YES +SNORD116-11 100033423 BI GRCh38 15 25075978 25075978 + non_coding_transcript_exon_variant RNA SNP T T G novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 23 21 n.50T>G ENST00000383882.1 1/1 G snoRNA YES CAAAATGAGTG 1/1 ENST00000383882 Transcript ENSG00000206609 HGNC:33077 MODIFIER non_coding_transcript_exon_variant Unknown SNORD116-11 HGNC 1 SNV SNORD116-11,non_coding_transcript_exon_variant,,ENST00000383882,,n.50T>G,MODIFIER,YES,,,1;SNORD116-10,downstream_gene_variant,,ENST00000363791,,,MODIFIER,YES,,,1;SNORD116-14,upstream_gene_variant,,ENST00000383894,,,MODIFIER,YES,,,1;SNORD116-9,downstream_gene_variant,,ENST00000384000,,,MODIFIER,YES,,,1;SNORD116-13,upstream_gene_variant,,ENST00000384408,,,MODIFIER,YES,,,1;SNORD116-12,upstream_gene_variant,,ENST00000384468,,,MODIFIER,YES,,,1;SNHG14,intron_variant,,ENST00000549804,,n.1109+112T>G,MODIFIER,YES,,,1;SNHG14,intron_variant,,ENST00000640631,,n.2890+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000653407,,n.1054+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000654223,,n.2367+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000655153,,n.594+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000656510,,n.2240+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000657237,,n.1120+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000660542,,n.96+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000660717,,n.2646+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000661253,,n.2541+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000662834,,n.3765+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000664256,,n.770+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000664545,,n.2713+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000665819,,n.425+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000666289,,n.1123+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000666606,,n.425+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000667393,,n.2605+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000667925,,n.1112+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000668750,,n.2049+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000668953,,n.425+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000669673,,n.2605+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000670394,,n.1123+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000670542,,n.902+112T>G,MODIFIER,,,,1;SNHG14,intron_variant,,ENST00000671374,,n.544+112T>G,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000553108,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000654902,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000656600,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000660956,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000661738,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000662370,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000667531,,,MODIFIER,,,,1;SNHG14,upstream_gene_variant,,ENST00000671491,,,MODIFIER,,,,1 50/92 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 miRNA_loop 142 0c6a7e7f-44e0-4011-8204-20ead8091990 44 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS SNORD116-11,non_coding_transcript_exon_variant,,ENST00000383882.1,n.50T>G,MODIFIER,YES;SNHG14,intron_variant,,ENST00000660542.1,n.96+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000665819.1,n.425+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000668953.1,n.425+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000666606.1,n.425+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000671374.1,n.544+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000653407.1,n.1054+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000667925.1,n.1112+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000670394.1,n.1123+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000657237.1,n.1120+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000666289.1,n.1123+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000655153.1,n.594+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000664256.1,n.770+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000670542.1,n.902+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000660717.1,n.2646+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000661253.1,n.2541+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000549804.7,n.1109+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000654223.1,n.2367+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000656510.1,n.2240+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000669673.1,n.2605+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000668750.1,n.2049+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000662834.1,n.3765+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000667393.1,n.2605+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000664545.1,n.2713+112T>G,MODIFIER,;SNHG14,intron_variant,,ENST00000640631.2,n.2890+112T>G,MODIFIER, +SHPK 23729 BI GRCh38 17 3610769 3610769 + synonymous_variant Silent SNP G G A novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 34 40 c.1228C>T p.Leu410= p.L410= ENST00000225519.5 NM_013276.4 410 Ctg/Ttg 7/7 P1 A L protein_coding YES CCDS11030.1 1228/1437 GTGCAGGTTCT Gene3D:3.30.420.40;PANTHER:PTHR10196;PANTHER:PTHR10196:SF67;Superfamily:SSF53067;CDD:cd07777 ENSP00000225519 7/7 ENST00000225519 Transcript 1.0 ENSG00000197417 HGNC:1492 LOW NM_013276.4 synonymous_variant 1.0 Unknown Q9UHJ6.147 SHPK HGNC -1 1.0 UPI0000070BB8 SNV SHPK,synonymous_variant,p.L410=,ENST00000225519,NM_013276.4,c.1228C>T,LOW,YES,,,-1;TRPV1,upstream_gene_variant,,ENST00000572705,NM_080704.4,,MODIFIER,,,,-1;AC027796.3,synonymous_variant,p.L410=,ENST00000572919,,c.1228C>T,LOW,YES,,,-1 1259/3788 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 106 0c6a7e7f-44e0-4011-8204-20ead8091990 75 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS SHPK,synonymous_variant,p.L410=,ENST00000225519.5,c.1228C>T,LOW,YES;ENSG00000262304,synonymous_variant,NMD_transcript_variant,p.L410=,ENST00000572919.1,c.1228C>T,LOW,YES +RECQL5 9400 BI GRCh38 17 75627466 75627466 + missense_variant Missense_Mutation SNP C C T rs766805103 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 60 19 c.2932G>A p.Glu978Lys p.E978K ENST00000317905.10 NM_004259.7 978 Gag/Aag 20/20 P1 T E/K protein_coding YES CCDS42380.1 2932/2976 GCTCTCGCACC COSM1263973 ENSP00000317636 20/20 rs766805103;COSV58639425 ENST00000317905 Transcript ENSG00000108469 HGNC:9950 MODERATE NM_004259.7 6.536e-05 gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.945) Unknown deleterious(0.01) 0;1 O94762.199 RECQL5 HGNC -1 A0A024R8M9.54 1.0 UPI0000133477 O94762-1 SNV RECQL5,missense_variant,p.E978K,ENST00000317905,NM_004259.7,c.2932G>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.945),-1;RECQL5,missense_variant,p.E951K,ENST00000423245,,c.2851G>A,MODERATE,,deleterious(0.01),probably_damaging(0.967),-1;RECQL5,intron_variant,,ENST00000581825,,c.479-242G>A,MODIFIER,,,,-1;RECQL5,downstream_gene_variant,,ENST00000578201,,,MODIFIER,,,,-1;MYO15B,downstream_gene_variant,,ENST00000578220,,,MODIFIER,,,,1;RECQL5,downstream_gene_variant,,ENST00000580707,,,MODIFIER,,,,-1;RECQL5,downstream_gene_variant,,ENST00000582548,,,MODIFIER,,,,-1;MYO15B,downstream_gene_variant,,ENST00000610510,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000633867,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000642007,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000645453,NM_001309242.1,,MODIFIER,YES,,,1;RECQL5,non_coding_transcript_exon_variant,,ENST00000443199,,n.2468G>A,MODIFIER,,,,-1;RECQL5,downstream_gene_variant,,ENST00000583673,,,MODIFIER,,,,-1;RECQL5,non_coding_transcript_exon_variant,,ENST00000578865,,n.555G>A,MODIFIER,,,,-1;MYO15B,downstream_gene_variant,,ENST00000577948,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000577986,,,MODIFIER,,,,1;RECQL5,downstream_gene_variant,,ENST00000579265,,,MODIFIER,,,,-1;MYO15B,downstream_gene_variant,,ENST00000580096,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000580262,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000580414,,,MODIFIER,,,,1;RECQL5,downstream_gene_variant,,ENST00000582464,,,MODIFIER,,,,-1;RECQL5,downstream_gene_variant,,ENST00000585205,,,MODIFIER,,,,-1;MYO15B,downstream_gene_variant,,ENST00000612587,,,MODIFIER,,,,1;MYO15B,downstream_gene_variant,,ENST00000621743,,,MODIFIER,,,,1 3057/3669 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 1.604e-05 0.0 0.0 0.0 0.0 0.0 1.767e-05 0.0 6.536e-05 6.759220013918821e-06 2.4311999368364923e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 96 0c6a7e7f-44e0-4011-8204-20ead8091990 79 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS RECQL5,intron_variant,,ENST00000581825.1,c.479-242G>A,MODIFIER,;RECQL5,missense_variant,p.E978K,ENST00000317905.10,c.2932G>A,MODERATE,YES;RECQL5,missense_variant,p.E951K,ENST00000423245.6,c.2851G>A,MODERATE,;RECQL5,non_coding_transcript_exon_variant,,ENST00000578865.5,n.555G>A,MODIFIER,;RECQL5,non_coding_transcript_exon_variant,,ENST00000443199.6,n.2468G>A,MODIFIER, +LAMA1 284217 BI GRCh38 18 6999965 6999965 + missense_variant Missense_Mutation SNP T T C rs1233781191 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 18 4 c.4415A>G p.His1472Arg p.H1472R ENST00000389658.4 NM_005559.4 1472 cAc/cGc 31/63 P1 C H/R protein_coding YES CCDS32787.1 4415/9228 AATCGTGGTCC Gene3D:2.10.25.10;Pfam:PF00053;PROSITE_profiles:PS50027;PANTHER:PTHR10574;PANTHER:PTHR10574:SF291;SMART:SM00180;SMART:SM00181;Superfamily:SSF57196;CDD:cd00055 ENSP00000374309 31/63 rs1233781191 ENST00000389658 Transcript 1.0 ENSG00000101680 HGNC:6481 MODERATE NM_005559.4 8.791e-06 gnomAD_NFE missense_variant 1.0 benign(0.124) Unknown tolerated(0.25) P25391.206 LAMA1 HGNC -1 1.0 UPI00001C1FF9 SNV LAMA1,missense_variant,p.H1472R,ENST00000389658,NM_005559.4,c.4415A>G,MODERATE,YES,tolerated(0.25),benign(0.124),-1;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,,n.5430A>G,MODIFIER,,,,-1 4492/9642 muse;mutect2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 3.977e-06 0.0 0.0 0.0 0.0 0.0 8.791e-06 0.0 0.0 0 22 0c6a7e7f-44e0-4011-8204-20ead8091990 22 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS LAMA1,non_coding_transcript_exon_variant,,ENST00000579014.5,n.5430A>G,MODIFIER,;LAMA1,missense_variant,p.H1472R,ENST00000389658.4,c.4415A>G,MODERATE,YES +MUC16 94025 BI GRCh38 19 8888760 8888760 + missense_variant Missense_Mutation SNP T T C rs1310600107 TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 142 61 c.40739A>G p.Glu13580Gly p.E13580G ENST00000397910.8 NM_024690.2 13580 gAg/gGg 56/84 P1 C E/G protein_coding YES CCDS54212.1 40739/43524 CCAGCTCAGTG Gene3D:3.30.70.960;Pfam:PF01390;PROSITE_profiles:PS50024;PANTHER:PTHR14672;SMART:SM00200;Superfamily:SSF82671 ENSP00000381008 56/84 rs1310600107 ENST00000397910 Transcript 1.0 ENSG00000181143 HGNC:15582 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 probably_damaging(0.946) Unknown tolerated_low_confidence(0.11) Q8WXI7.134 MUC16 HGNC -1 5.0 UPI000065CA24 SNV MUC16,missense_variant,p.E13580G,ENST00000397910,NM_024690.2,c.40739A>G,MODERATE,YES,tolerated_low_confidence(0.11),probably_damaging(0.946),-1;MUC16,missense_variant,p.E420G,ENST00000599436,,c.1259A>G,MODERATE,,deleterious(0.03),benign(0.15),-1;MUC16,missense_variant,p.E420G,ENST00000601404,,c.1259A>G,MODERATE,,deleterious(0.02),probably_damaging(0.987),-1;MUC16,missense_variant,p.E200G,ENST00000596768,,c.599A>G,MODERATE,,deleterious(0.02),benign(0.125),-1 40943/43816 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 180 0c6a7e7f-44e0-4011-8204-20ead8091990 203 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS MUC16,missense_variant,p.S420G,ENST00000599436.1,c.1258A>G,MODERATE,;MUC16,missense_variant,NMD_transcript_variant,p.S420G,ENST00000601404.5,c.1258A>G,MODERATE,;MUC16,stop_lost,NMD_transcript_variant,p.*199Wext*39,ENST00000596768.5,c.597A>G,HIGH,;MUC16,missense_variant,p.E13580G,ENST00000397910.8,c.40739A>G,MODERATE,;MUC16,missense_variant,p.E13642G,ENST00000711672.1,c.40925A>G,MODERATE,YES;MUC16,missense_variant,p.E13620G,ENST00000710609.1,c.40859A>G,MODERATE,;MUC16,missense_variant,p.E10522G,ENST00000710610.1,c.31565A>G,MODERATE, +PPP1R12C 54776 BI GRCh38 19 55091521 55091521 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 18 21 c.2300A>G p.Lys767Arg p.K767R ENST00000263433.8 NM_001271618.2 767 aAg/aGg 22/22 P1 C K/R protein_coding YES CCDS12916.1 2300/2349 CATCCTTGAGG Coiled-coils_(Ncoils):Coil;PANTHER:PTHR24179;PANTHER:PTHR24179:SF27;Pfam:PF15898;PIRSF:PIRSF038141 ENSP00000263433 22/22 ENST00000263433 Transcript ENSG00000125503 HGNC:14947 MODERATE NM_017607.4 missense_variant 1.0 probably_damaging(0.98) Unknown deleterious(0.01) Q9BZL4.148 PPP1R12C HGNC -1 1.0 UPI000006FEE1 Q9BZL4-1 SNV PPP1R12C,missense_variant,p.K767R,ENST00000263433,NM_001271618.2&NM_017607.4,c.2300A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.98),-1;PPP1R12C,missense_variant,p.K692R,ENST00000435544,,c.2075A>G,MODERATE,,deleterious(0.01),probably_damaging(0.98),-1;PPP1R12C,missense_variant,p.K722R,ENST00000592993,,c.2165A>G,MODERATE,,deleterious(0.01),probably_damaging(0.999),-1;PPP1R12C,missense_variant,p.K219R,ENST00000591938,,c.656A>G,MODERATE,,deleterious(0.01),benign(0.411),-1;EPS8L1,downstream_gene_variant,,ENST00000201647,NM_133180.3,,MODIFIER,YES,,,1;EPS8L1,downstream_gene_variant,,ENST00000245618,NM_017729.3,,MODIFIER,,,,1;EPS8L1,downstream_gene_variant,,ENST00000540810,,,MODIFIER,,,,1;EPS8L1,downstream_gene_variant,,ENST00000586329,,,MODIFIER,,,,1;EPS8L1,downstream_gene_variant,,ENST00000588359,,,MODIFIER,,,,1;EPS8L1,downstream_gene_variant,,ENST00000587901,,,MODIFIER,,,,1;PPP1R12C,non_coding_transcript_exon_variant,,ENST00000590268,,n.517A>G,MODIFIER,,,,-1;PPP1R12C,downstream_gene_variant,,ENST00000586197,,,MODIFIER,,,,-1;EPS8L1,downstream_gene_variant,,ENST00000587715,,,MODIFIER,,,,1;PPP1R12C,downstream_gene_variant,,ENST00000588277,,,MODIFIER,,,,-1;EPS8L1,downstream_gene_variant,,ENST00000589362,,,MODIFIER,,,,1;EPS8L1,downstream_gene_variant,,ENST00000592102,,,MODIFIER,,,,1;PPP1R12C,downstream_gene_variant,,ENST00000592754,,,MODIFIER,,,,-1 2394/2997 muse;mutect2;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 44 0c6a7e7f-44e0-4011-8204-20ead8091990 39 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS PPP1R12C,missense_variant,p.R722G,ENST00000592993.1,c.2164A>G,MODERATE,;PPP1R12C,missense_variant,p.K692R,ENST00000435544.6,c.2075A>G,MODERATE,;PPP1R12C,non_coding_transcript_exon_variant,,ENST00000590268.1,n.517A>G,MODIFIER,;PPP1R12C,missense_variant,p.K767R,ENST00000263433.8,c.2300A>G,MODERATE,YES;PPP1R12C,missense_variant,p.R219G,ENST00000591938.5,c.655A>G,MODERATE, +HMGXB4 10042 BI GRCh38 22 35265479 35265479 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-AA8M-01A TCGA-VD-AA8M-10A Somatic 16 29 c.1091C>A p.Pro364His p.P364H ENST00000216106.6 NM_001003681.3 364 cCc/cAc 5/11 P1 A P/H protein_coding YES CCDS33641.1 1091/1806 TCCTCCCAGCA PANTHER:PTHR46584;MobiDB_lite:mobidb-lite ENSP00000216106 5/11 ENST00000216106 Transcript ENSG00000100281 HGNC:5003 MODERATE NM_001003681.3 missense_variant 1.0 benign(0.241) Unknown deleterious_low_confidence(0.01) Q9UGU5.159 HMGXB4 HGNC 1 5.0 UPI00003765B4 SNV HMGXB4,missense_variant,p.P364H,ENST00000216106,NM_001003681.3&NM_001362972.2,c.1091C>A,MODERATE,YES,deleterious_low_confidence(0.01),benign(0.241),1;HMGXB4,missense_variant,p.P255H,ENST00000455359,,c.764C>A,MODERATE,,deleterious_low_confidence(0),benign(0.241),1;HMGXB4,missense_variant,p.P255H,ENST00000420166,,c.764C>A,MODERATE,,deleterious_low_confidence(0),benign(0.241),1;HMGXB4,3_prime_UTR_variant,,ENST00000418170,,c.*927C>A,MODIFIER,,,,1;HMGXB4,downstream_gene_variant,,ENST00000464480,,,MODIFIER,,,,1;HMGXB4,downstream_gene_variant,,ENST00000498325,,,MODIFIER,,,,1 1224/4095 muse;varscan2 9dc5cc23-c903-4fe2-8354-64f8316ff0d4 0 52 0c6a7e7f-44e0-4011-8204-20ead8091990 46 ef479058-cbc3-442d-9683-114453f55a05 SUCCESS HMGXB4,missense_variant,p.P255H,ENST00000455359.5,c.764C>A,MODERATE,;HMGXB4,missense_variant,p.P364H,ENST00000216106.6,c.1091C>A,MODERATE,YES;HMGXB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000418170.5,c.*927C>A,MODIFIER,;HMGXB4,missense_variant,p.P255H,ENST00000420166.5,c.764C>A,MODERATE, +ZNF281 23528 BI GRCh38 1 200408328 200408328 + missense_variant Missense_Mutation SNP T T C novel TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 32 26 c.1378A>G p.Lys460Glu p.K460E ENST00000294740.3 460 Aag/Gag 2/2 P4 C K/E protein_coding YES CCDS1402.1 1378/2688 CCTCTTCTGCA PANTHER:PTHR24404;PANTHER:PTHR24404:SF56 ENSP00000294740 2/2 ENST00000294740 Transcript ENSG00000162702 HGNC:13075 MODERATE missense_variant 1.0 possibly_damaging(0.679) Unknown tolerated(1) Q9Y2X9.180 ZNF281 HGNC -1 1.0 UPI000013C345 Q9Y2X9-1 SNV ZNF281,missense_variant,p.K460E,ENST00000294740,,c.1378A>G,MODERATE,YES,tolerated(1),possibly_damaging(0.679),-1;ZNF281,missense_variant,p.K460E,ENST00000367353,NM_012482.5&NM_001281293.2,c.1378A>G,MODERATE,,tolerated(1),possibly_damaging(0.679),-1;ZNF281,missense_variant,p.K424E,ENST00000367352,NM_001281294.2,c.1270A>G,MODERATE,,tolerated(0.91),possibly_damaging(0.679),-1;AC104461.1,intron_variant,,ENST00000637430,,n.484+44800T>C,MODIFIER,,,,1;AC104461.1,upstream_gene_variant,,ENST00000634596,,,MODIFIER,YES,,,1;AC104461.1,upstream_gene_variant,,ENST00000635220,,,MODIFIER,,,,1;AC104461.1,upstream_gene_variant,,ENST00000647823,,,MODIFIER,,,,1;AC104461.1,upstream_gene_variant,,ENST00000654000,,,MODIFIER,,,,1;AC104461.1,upstream_gene_variant,,ENST00000659976,,,MODIFIER,,,,1;AC104461.1,upstream_gene_variant,,ENST00000660351,,,MODIFIER,,,,1 1503/4891 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 6.758310064469697e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0 0 49 aa662510-7cd7-4b00-9f65-c72dab867c9e 58 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS ZNF281,missense_variant,p.K424E,ENST00000367352.3,c.1270A>G,MODERATE,;ZNF281,missense_variant,p.K460E,ENST00000367353.2,c.1378A>G,MODERATE,YES;ZNF281,missense_variant,p.K460E,ENST00000294740.3,c.1378A>G,MODERATE,;ENSG00000230623,intron_variant,,ENST00000637430.1,n.484+44800T>C,MODIFIER,YES +LMOD3 56203 BI GRCh38 3 69119216 69119216 + missense_variant Missense_Mutation SNP G G A rs765223466 TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 73 9 c.1139C>T p.Pro380Leu p.P380L ENST00000420581.7 NM_001304418.3 380 cCg/cTg 2/3 P1 A P/L protein_coding YES CCDS46862.1 1139/1683 uncertain_significance GACCCGGAAGC PANTHER:PTHR10901;PANTHER:PTHR10901:SF3;Gene3D:3.80.10.10;Superfamily:SSF52047 ENSP00000414670 2/3 rs765223466 ENST00000420581 Transcript 1.0 ENSG00000163380 HGNC:6649 MODERATE NM_198271.5 5.793e-05 gnomAD_AMR missense_variant 1 1.0 probably_damaging(0.914) Unknown deleterious(0) Q0VAK6.112 LMOD3 HGNC -1 1.0 UPI00001612AC Q0VAK6-1 SNV LMOD3,missense_variant,p.P380L,ENST00000420581,NM_001304418.3&NM_198271.5,c.1139C>T,MODERATE,YES,deleterious(0),probably_damaging(0.914),-1;LMOD3,missense_variant,p.P380L,ENST00000475434,,c.1139C>T,MODERATE,,deleterious(0),probably_damaging(0.914),-1;LMOD3,missense_variant,p.P380L,ENST00000489031,,c.1139C>T,MODERATE,,deleterious(0),probably_damaging(0.914),-1 1348/4922 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 1.607e-05 0.0 5.793e-05 0.0 0.0 0.0 1.774e-05 0.0 0.0 2.032880001934245e-05 4.8763798986328766e-05 0.0 0.0 0.0 0.0 0.0 afr 4.8763798986328766e-05 0.0 1.543970029160846e-05 0.0 0.0 0 90 aa662510-7cd7-4b00-9f65-c72dab867c9e 82 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS LMOD3,missense_variant,p.P380L,ENST00000475434.1,c.1139C>T,MODERATE,;LMOD3,missense_variant,p.P380L,ENST00000489031.5,c.1139C>T,MODERATE,;LMOD3,missense_variant,p.P380L,ENST00000420581.7,c.1139C>T,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 38 36 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 0 102 aa662510-7cd7-4b00-9f65-c72dab867c9e 74 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +IQSEC3 440073 BI GRCh38 12 157580 157580 + missense_variant Missense_Mutation SNP G G A rs1555094828 TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 66 36 c.2329G>A p.Asp777Asn p.D777N ENST00000538872.6 NM_001170738.2 777 Gac/Aac 7/14 P3 A D/N protein_coding YES CCDS53728.1 2329/3549 ACCCCGACACC COSM1733213;COSM1733214 PROSITE_profiles:PS50190;CDD:cd00171;PANTHER:PTHR10663:SF318;PANTHER:PTHR10663;Pfam:PF01369;Gene3D:1.10.1000.11;SMART:SM00222;Superfamily:SSF48425 ENSP00000437554 7/14 rs1555094828;COSV58288880 ENST00000538872 Transcript ENSG00000120645 HGNC:29193 MODERATE NM_001170738.2 8.802e-06 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q9UPP2.154 IQSEC3 HGNC 1 5.0 UPI0000DBEEF0 Q9UPP2-1 SNV IQSEC3,missense_variant,p.D777N,ENST00000538872,NM_001170738.2,c.2329G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;IQSEC3,missense_variant,p.D474N,ENST00000382841,NM_015232.1,c.1420G>A,MODERATE,,deleterious(0.02),probably_damaging(0.999),1 2445/7087 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 3.98e-06 0.0 0.0 0.0 0.0 0.0 8.802e-06 0.0 0.0 6.761139957234263e-06 2.4322600438608788e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 76 aa662510-7cd7-4b00-9f65-c72dab867c9e 102 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS IQSEC3,missense_variant,p.D474N,ENST00000382841.2,c.1420G>A,MODERATE,;IQSEC3,missense_variant,p.D777N,ENST00000538872.6,c.2329G>A,MODERATE,YES +PSG1 5669 BI GRCh38 19 42878248 42878248 + missense_variant Missense_Mutation SNP G G A rs200054291 TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 83 117 c.95C>T p.Thr32Ile p.T32I ENST00000436291.7 NM_001184825.2 32 aCc/aTc 2/6 A2 A T/I protein_coding CCDS54275.1 95/1260 CAGTGGTGGGC Cleavage_site_(Signalp):SignalP-noTM;PANTHER:PTHR44427:SF16;PANTHER:PTHR44427 ENSP00000413041 2/6 rs200054291;COSV99741912 ENST00000436291 Transcript ENSG00000231924 HGNC:9514 MODERATE NM_001184825.2 8.853e-06 gnomAD_NFE missense_variant 0;1 benign(0.049) Unknown deleterious(0.01) 0;1 P11464.190 PSG1 HGNC -1 1.0 UPI000013279D P11464-1 SNV PSG1,missense_variant,p.T32I,ENST00000244296,NM_006905.3,c.95C>T,MODERATE,,deleterious(0.01),benign(0.093),-1;PSG1,missense_variant,p.T32I,ENST00000436291,NM_001184825.2,c.95C>T,MODERATE,,deleterious(0.01),benign(0.049),-1;PSG1,missense_variant,p.T32I,ENST00000595356,NM_001184826.2,c.95C>T,MODERATE,,deleterious(0.01),benign(0.16),-1;PSG1,missense_variant,p.T32I,ENST00000312439,NM_001297773.2,c.95C>T,MODERATE,YES,deleterious(0.01),benign(0.106),-1;PSG1,missense_variant,p.T32I,ENST00000403380,NM_001330524.2,c.95C>T,MODERATE,,tolerated(0.07),benign(0.067),-1;PSG1,missense_variant,p.T32I,ENST00000595124,,c.95C>T,MODERATE,,tolerated(0.07),benign(0.001),-1;PSG1,5_prime_UTR_variant,,ENST00000595930,,c.-119C>T,MODIFIER,,,,-1;PSG1,upstream_gene_variant,,ENST00000597058,,,MODIFIER,,,,-1;PSG1,non_coding_transcript_exon_variant,,ENST00000601073,,n.336C>T,MODIFIER,,,,-1;PSG1,non_coding_transcript_exon_variant,,ENST00000601456,,n.194C>T,MODIFIER,,,,-1 227/2062 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 4.007e-06 0.0 0.0 0.0 0.0 0.0 8.853e-06 0.0 0.0 6.805590146541363e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5483199604204856e-05 0.0 0.0 0 182 aa662510-7cd7-4b00-9f65-c72dab867c9e 200 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS PSG1,non_coding_transcript_exon_variant,,ENST00000601073.1,n.336C>T,MODIFIER,;PSG1,non_coding_transcript_exon_variant,,ENST00000601456.5,n.194C>T,MODIFIER,;PSG1,5_prime_UTR_variant,,ENST00000595930.1,c.-119C>T,MODIFIER,;PSG1,missense_variant,p.T32I,ENST00000244296.6,c.95C>T,MODERATE,;PSG1,missense_variant,p.T32I,ENST00000312439.10,c.95C>T,MODERATE,;PSG1,missense_variant,p.T32I,ENST00000403380.7,c.95C>T,MODERATE,;PSG1,missense_variant,p.T32I,ENST00000595356.5,c.95C>T,MODERATE,;PSG1,missense_variant,p.T32I,ENST00000595124.5,c.95C>T,MODERATE,;PSG1,missense_variant,p.T32I,ENST00000436291.7,c.95C>T,MODERATE,YES +OSBPL2 9885 BI GRCh38 20 62293808 62293808 + missense_variant Missense_Mutation SNP C C G novel TCGA-WC-A87T-01A TCGA-WC-A87T-10A Somatic 40 27 c.1364C>G p.Pro455Arg p.P455R ENST00000313733.9 NM_144498.4 455 cCc/cGc 14/14 P4 G P/R protein_coding YES CCDS13495.1 1364/1443 TAACCCCTACA PDB-ENSP_mappings:5zm8.A;PDB-ENSP_mappings:5zm8.B;Superfamily:SSF144000;Pfam:PF01237;Gene3D:1.20.120.1290;PANTHER:PTHR10972;PANTHER:PTHR10972:SF153 ENSP00000316649 14/14 ENST00000313733 Transcript 1.0 ENSG00000130703 HGNC:15761 MODERATE NM_144498.4 missense_variant 1.0 probably_damaging(0.988) Unknown deleterious(0.01) Q9H1P3.154 OSBPL2 HGNC 1 1.0 UPI0000130E96 Q9H1P3-1 SNV OSBPL2,missense_variant,p.P455R,ENST00000313733,NM_144498.4,c.1364C>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P443R,ENST00000358053,NM_014835.4,c.1328C>G,MODERATE,,deleterious(0.01),probably_damaging(0.972),1;OSBPL2,missense_variant,p.P322A,ENST00000439951,,c.964C>G,MODERATE,,tolerated_low_confidence(0.12),benign(0.027),1;OSBPL2,missense_variant,p.P455R,ENST00000643412,,c.1364C>G,MODERATE,,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P455R,ENST00000643981,,c.1364C>G,MODERATE,,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P388R,ENST00000644775,,c.1163C>G,MODERATE,,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P423R,ENST00000644702,,c.1268C>G,MODERATE,,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P363R,ENST00000645442,NM_001363878.1,c.1088C>G,MODERATE,,deleterious(0.01),probably_damaging(0.988),1;OSBPL2,missense_variant,p.P322A,ENST00000645520,NM_001278649.2,c.964C>G,MODERATE,,tolerated_low_confidence(0.12),benign(0.027),1;OSBPL2,3_prime_UTR_variant,,ENST00000642714,,c.*3C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000645426,,c.*1490C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000643174,,c.*1156C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000644535,,c.*406C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000642516,,c.*1085C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000642932,,c.*1370C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000646968,,c.*786C>G,MODIFIER,,,,1;OSBPL2,3_prime_UTR_variant,,ENST00000646834,,c.*877C>G,MODIFIER,,,,1;OSBPL2,non_coding_transcript_exon_variant,,ENST00000471817,,n.256C>G,MODIFIER,,,,1 1569/3944 muse;mutect2;varscan2 3eb7aded-8887-4c27-a464-1b50ec090133 0 68 aa662510-7cd7-4b00-9f65-c72dab867c9e 67 01817ad1-6647-453d-99fc-66bb6be9229c SUCCESS OSBPL2,non_coding_transcript_exon_variant,,ENST00000471817.2,n.256C>G,MODIFIER,;OSBPL2,3_prime_UTR_variant,,ENST00000642714.1,c.*3C>G,MODIFIER,;OSBPL2,missense_variant,p.P455R,ENST00000643981.1,c.1364C>G,MODERATE,;OSBPL2,missense_variant,p.P423R,ENST00000644702.1,c.1268C>G,MODERATE,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645426.1,c.*1490C>G,MODIFIER,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646968.1,c.*786C>G,MODIFIER,;OSBPL2,missense_variant,p.P455R,ENST00000643412.1,c.1364C>G,MODERATE,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000646834.1,c.*877C>G,MODIFIER,;OSBPL2,missense_variant,p.P363R,ENST00000645442.1,c.1088C>G,MODERATE,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000643174.1,c.*1156C>G,MODIFIER,;OSBPL2,missense_variant,p.P388R,ENST00000644775.1,c.1163C>G,MODERATE,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642516.1,c.*1085C>G,MODIFIER,;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642932.1,c.*1370C>G,MODIFIER,;OSBPL2,missense_variant,p.P322A,ENST00000645520.1,c.964C>G,MODERATE,;OSBPL2,missense_variant,p.P443R,ENST00000358053.3,c.1328C>G,MODERATE,;OSBPL2,missense_variant,p.P455R,ENST00000313733.9,c.1364C>G,MODERATE,YES;OSBPL2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644535.1,c.*406C>G,MODIFIER,;OSBPL2,missense_variant,p.P322A,ENST00000439951.6,c.964C>G,MODERATE, +ITPKB 3707 BI GRCh38 1 226735597 226735597 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9F2-01A TCGA-V4-A9F2-10A Somatic 41 52 c.1862G>C p.Ser621Thr p.S621T ENST00000272117.8 621 aGt/aCt 2/8 P1 G S/T protein_coding CCDS1555.1 1862/2841 GGTCACTGGAG PANTHER:PTHR12400;PANTHER:PTHR12400:SF4;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000272117 1/7 ENST00000272117 Transcript ENSG00000143772 HGNC:6179 MODERATE missense_variant probably_damaging(0.994) Unknown deleterious(0) P27987.180 ITPKB HGNC -1 1.0 UPI000013D92B P27987-1 SNV ITPKB,missense_variant,p.S621T,ENST00000429204,NM_002221.3,c.1862G>C,MODERATE,YES,deleterious(0),probably_damaging(0.994),-1;ITPKB,missense_variant,p.S621T,ENST00000272117,,c.1862G>C,MODERATE,,deleterious(0),probably_damaging(0.994),-1;ITPKB,missense_variant,p.S621T,ENST00000366784,,c.1862G>C,MODERATE,,deleterious(0),probably_damaging(0.994),-1 1862/5822 muse;mutect2;varscan2 411ddf79-fe92-44ad-8d10-eeb703f11be7 0 126 aa397b20-4d84-4c48-a13c-32b31ccc19a4 93 8a6be1b8-f44a-4643-8de4-f902bc7c2a62 SUCCESS ITPKB,missense_variant,p.S621T,ENST00000366784.1,c.1862G>C,MODERATE,;ITPKB,missense_variant,p.S621T,ENST00000272117.8,c.1862G>C,MODERATE,;ITPKB,missense_variant,p.S621T,ENST00000429204.6,c.1862G>C,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9F2-01A TCGA-V4-A9F2-10A Somatic 27 22 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 411ddf79-fe92-44ad-8d10-eeb703f11be7 0 85 aa397b20-4d84-4c48-a13c-32b31ccc19a4 49 8a6be1b8-f44a-4643-8de4-f902bc7c2a62 SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +ARHGEF17 9828 BI GRCh38 11 73310019 73310019 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9F2-01A TCGA-V4-A9F2-10A Somatic 24 7 c.1381T>G p.Ser461Ala p.S461A ENST00000263674.4 NM_014786.4 461 Tcc/Gcc 1/21 P3 G S/A protein_coding YES CCDS8221.1 1381/6192 GGAAGTCCCTG MobiDB_lite:mobidb-lite;PANTHER:PTHR12877:SF15;PANTHER:PTHR12877 ENSP00000263674 1/21 ENST00000263674 Transcript ENSG00000110237 HGNC:21726 MODERATE NM_014786.4 missense_variant 1.0 probably_damaging(0.978) Unknown deleterious_low_confidence(0.01) Q96PE2.148 ARHGEF17 HGNC 1 1.0 UPI000004980B SNV ARHGEF17,missense_variant,p.S461A,ENST00000263674,NM_014786.4,c.1381T>G,MODERATE,YES,deleterious_low_confidence(0.01),probably_damaging(0.978),1;ARHGEF17,upstream_gene_variant,,ENST00000544519,,,MODIFIER,,,,1;AP002761.3,upstream_gene_variant,,ENST00000546324,,,MODIFIER,YES,,,-1 1744/8163 muse;mutect2;varscan2 411ddf79-fe92-44ad-8d10-eeb703f11be7 0 39 aa397b20-4d84-4c48-a13c-32b31ccc19a4 31 8a6be1b8-f44a-4643-8de4-f902bc7c2a62 SUCCESS ARHGEF17,missense_variant,p.S461A,ENST00000263674.4,c.1381T>G,MODERATE,YES +MRPS35 60488 BI GRCh38 12 27710939 27710939 + synonymous_variant Silent SNP C C T rs887984082 TCGA-V4-A9F2-01A TCGA-V4-A9F2-10A Somatic 6 6 c.96C>T p.Val32= p.V32= ENST00000081029.8 NM_021821.4 32 gtC/gtT 1/8 P1 T V protein_coding YES CCDS8714.1 96/972 CCGGTCCCGAC PDB-ENSP_mappings:3j9m.A1;PDB-ENSP_mappings:6nu3.A1;PDB-ENSP_mappings:6rw4.1;PDB-ENSP_mappings:6rw5.1 ENSP00000081029 1/8 rs887984082 ENST00000081029 Transcript ENSG00000061794 HGNC:16635 LOW NM_021821.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS synonymous_variant 1.0 Unknown P82673.138 MRPS35 HGNC 1 1.0 UPI000003B0E7 P82673-1 SNV MRPS35,synonymous_variant,p.V32=,ENST00000081029,NM_021821.4,c.96C>T,LOW,YES,,,1;MRPS35,synonymous_variant,p.V32=,ENST00000538315,NM_001190864.1,c.96C>T,LOW,,,,1;MRPS35,synonymous_variant,p.V31=,ENST00000542791,,c.93C>T,LOW,,,,1;MRPS35,synonymous_variant,p.V18=,ENST00000542199,,c.54C>T,LOW,,,,1;MRPS35,synonymous_variant,p.V32=,ENST00000536569,,c.96C>T,LOW,,,,1;AC009509.1,upstream_gene_variant,,ENST00000536317,,,MODIFIER,YES,,,-1;AC009509.2,downstream_gene_variant,,ENST00000538640,,,MODIFIER,YES,,,1;AC009509.1,upstream_gene_variant,,ENST00000542660,,,MODIFIER,,,,-1;AC009509.1,upstream_gene_variant,,ENST00000656583,,,MODIFIER,,,,-1 108/1829 muse;mutect2;varscan2 411ddf79-fe92-44ad-8d10-eeb703f11be7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 21 aa397b20-4d84-4c48-a13c-32b31ccc19a4 12 8a6be1b8-f44a-4643-8de4-f902bc7c2a62 SUCCESS MRPS35,missense_variant,NMD_transcript_variant,p.S18F,ENST00000542199.1,c.53C>T,MODERATE,;MRPS35,synonymous_variant,p.V31=,ENST00000542791.1,c.93C>T,LOW,;MRPS35,synonymous_variant,p.V32=,ENST00000538315.5,c.96C>T,LOW,;MRPS35,synonymous_variant,p.V32=,ENST00000081029.8,c.96C>T,LOW,YES;MRPS35,synonymous_variant,NMD_transcript_variant,p.V32=,ENST00000536569.1,c.96C>T,LOW, +WDR47 22911 BI GRCh38 1 109011155 109011155 + synonymous_variant Silent SNP G G C novel TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 228 139 c.891C>G p.Ser297= p.S297= ENST00000369962.8 NM_001142551.2 297 tcC/tcG 5/15 P4 C S protein_coding CCDS44187.1 891/2760 ATTGGGGATGA PANTHER:PTHR19863:SF5;PANTHER:PTHR19863 ENSP00000358979 5/15 ENST00000369962 Transcript ENSG00000085433 HGNC:29141 LOW NM_001142551.2 synonymous_variant Unknown O94967.162 WDR47 HGNC -1 1.0 UPI0000139DD3 O94967-1 SNV WDR47,synonymous_variant,p.S297=,ENST00000369965,NM_014969.5,c.891C>G,LOW,,,,-1;WDR47,synonymous_variant,p.S297=,ENST00000369962,NM_001142551.2,c.891C>G,LOW,,,,-1;WDR47,synonymous_variant,p.S269=,ENST00000357672,,c.807C>G,LOW,,,,-1;WDR47,synonymous_variant,p.S304=,ENST00000400794,NM_001142550.1,c.912C>G,LOW,YES,,,-1;WDR47,synonymous_variant,p.S269=,ENST00000361054,,c.807C>G,LOW,,,,-1;WDR47,downstream_gene_variant,,ENST00000528747,,,MODIFIER,,,,-1;WDR47,downstream_gene_variant,,ENST00000529074,,,MODIFIER,,,,-1;WDR47,downstream_gene_variant,,ENST00000530772,,,MODIFIER,,,,-1;WDR47,downstream_gene_variant,,ENST00000531337,,,MODIFIER,,,,-1 1141/4226 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 0 264 bd180da4-6429-41fb-a926-caaf693a2db8 367 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS WDR47,synonymous_variant,p.S269=,ENST00000361054.7,c.807C>G,LOW,;WDR47,synonymous_variant,p.S297=,ENST00000369965.8,c.891C>G,LOW,;WDR47,synonymous_variant,p.S304=,ENST00000400794.7,c.912C>G,LOW,;WDR47,synonymous_variant,p.S297=,ENST00000369962.8,c.891C>G,LOW,YES +LRP1B 53353 BI GRCh38 2 140444393 140444393 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 85 58 c.10231C>T p.Pro3411Ser p.P3411S ENST00000389484.8 NM_018557.3 3411 Cca/Tca 65/91 P1 A P/S protein_coding YES CCDS2182.1 10231/13800 TACTGGGATAC PROSITE_patterns:PS01209;PANTHER:PTHR22722:SF6;PANTHER:PTHR22722;PROSITE_profiles:PS50068;Superfamily:SSF57424;SMART:SM00192;Gene3D:4.10.400.10;Pfam:PF00057;CDD:cd00112 ENSP00000374135 65/91 ENST00000389484 Transcript 1.0 ENSG00000168702 HGNC:6693 MODERATE NM_018557.3 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0.01) Q9NZR2.166 LRP1B HGNC -1 1.0 UPI00001B045B SNV LRP1B,missense_variant,p.P3411S,ENST00000389484,NM_018557.3,c.10231C>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),-1 10518/15850 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 0 106 bd180da4-6429-41fb-a926-caaf693a2db8 143 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS LRP1B,missense_variant,p.P3411S,ENST00000389484.8,c.10231C>T,MODERATE,YES +SYTL3 100500851 BI GRCh38 6 158760661 158760661 + missense_variant Missense_Mutation SNP G G A rs749669847 TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 19 47 c.1330G>A p.Val444Ile p.V444I ENST00000611299.5 444/610 P1 A V/I protein_coding YES CCDS56458.1 1330/1833 ACAGCGTTCCT PANTHER:PTHR45716:SF1;PANTHER:PTHR45716;Gene3D:2.60.40.150 ENSP00000483936 15/18 rs749669847;COSV51908623 ENST00000611299 Transcript ENSG00000164674 HGNC:15587 MODERATE 5.437e-05 gnomAD_EAS missense_variant 0;1 1.0 benign(0) Unknown tolerated(0.54) 0;1 Q4VX76.130 SYTL3 HGNC 1 5.0 UPI000015FE68 Q4VX76-1 SNV SYTL3,missense_variant,p.V444I,ENST00000611299,NM_001242394.1&NM_001318745.1,c.1330G>A,MODERATE,YES,tolerated(0.54),benign(0),1;SYTL3,missense_variant,p.V376I,ENST00000367081,NM_001242395.1&NM_001009991.3,c.1126G>A,MODERATE,,tolerated(0.23),benign(0.003),1;SYTL3,missense_variant,p.V444I,ENST00000360448,NM_001242384.1,c.1330G>A,MODERATE,,tolerated(0.54),benign(0),1;MIR3918,downstream_gene_variant,,ENST00000581555,,,MODIFIER,YES,,,-1 2121/2896 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 1.591e-05 0.0 0.0 0.0 5.437e-05 0.0 1.758e-05 0.0 3.266e-05 6.761229997209739e-06 0.0 0.0 6.626029789913446e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 86 bd180da4-6429-41fb-a926-caaf693a2db8 66 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS SYTL3,missense_variant,p.V444I,ENST00000611299.5,c.1330G>A,MODERATE,YES;SYTL3,missense_variant,p.V444I,ENST00000360448.8,c.1330G>A,MODERATE,;SYTL3,missense_variant,p.V376I,ENST00000367081.7,c.1126G>A,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 74 55 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 0 100 bd180da4-6429-41fb-a926-caaf693a2db8 129 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +SERPINB4 6318 BI GRCh38 18 63637998 63637998 + synonymous_variant Silent SNP C C T rs776882459 TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 57 27 c.894G>A p.Thr298= p.T298= ENST00000341074.10 NM_002974.4 298 acG/acA 8/8 P1 T T protein_coding YES CCDS11986.1 894/1173 CTCAACGTGTC COSM4166841 PANTHER:PTHR11461;PANTHER:PTHR11461:SF320;Pfam:PF00079;Gene3D:2.30.39.10;Gene3D:3.30.497.10;SMART:SM00093;Superfamily:SSF56574 ENSP00000343445 8/8 rs776882459;COSV61984620 ENST00000341074 Transcript ENSG00000206073 HGNC:10570 LOW NM_002974.4 0.0001632 gnomAD_OTH synonymous_variant 0;1 1.0 Unknown 0;1 P48594.176 SERPINB4 HGNC -1 1.0 UPI0000038A1A SNV SERPINB4,synonymous_variant,p.T298=,ENST00000341074,NM_002974.4,c.894G>A,LOW,YES,,,-1;SERPINB4,synonymous_variant,p.T279=,ENST00000413673,NM_175041.2,c.837G>A,LOW,,,,-1;SERPINB4,downstream_gene_variant,,ENST00000436264,,,MODIFIER,,,,-1;SERPINB4,downstream_gene_variant,,ENST00000498496,,,MODIFIER,,,,-1 968/1707 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 7.966e-06 0.0 2.903e-05 0.0 0.0 0.0 0.0 0.0001632 0.0 1.353229981759796e-05 2.4336799469892867e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.544070073578041e-05 0.0 0.0 0 69 bd180da4-6429-41fb-a926-caaf693a2db8 84 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS SERPINB4,missense_variant,p.R279H,ENST00000413673.5,c.836G>A,MODERATE,;SERPINB4,synonymous_variant,p.T298=,ENST00000341074.10,c.894G>A,LOW,YES +ZNF473 25888 BI GRCh38 19 50046375 50046375 + frameshift_variant Frame_Shift_Del DEL C C - novel TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 48 22 c.1934del p.Pro645LeufsTer22 p.P645Lfs*22 ENST00000270617.8 NM_015428.4 644 caC/ca 5/5 P1 - H/X protein_coding CCDS33077.1 1932/2616 GGAGCACCCTTT PDB-ENSP_mappings:2emc.A;Gene3D:3.30.160.60;PANTHER:PTHR24376;PANTHER:PTHR24376:SF93;Superfamily:SSF57667 ENSP00000270617 5/5 ENST00000270617 Transcript ENSG00000142528 HGNC:23239 2.0 HIGH NM_015428.4 frameshift_variant Unknown Q8WTR7.164 ZNF473 HGNC 1 A0A024QZI1.43 1.0 UPI000006ED91 deletion ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000595661,,c.1934del,HIGH,YES,,,1;ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000391821,,c.1934del,HIGH,,,,1;ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000270617,NM_015428.4&NM_001006656.4,c.1934del,HIGH,,,,1;ZNF473,frameshift_variant,p.P633Lfs*22,ENST00000445728,NM_001308424.3,c.1898del,HIGH,,,,1;ZNF473,intron_variant,,ENST00000601364,,c.226+4558del,MODIFIER,,,,1;ZNF473,downstream_gene_variant,,ENST00000598809,,,MODIFIER,,,,1;ZNF473,downstream_gene_variant,,ENST00000599155,,,MODIFIER,,,,1;ZNF473,downstream_gene_variant,,ENST00000594968,,,MODIFIER,,,,1;ZNF473,downstream_gene_variant,,ENST00000598802,,,MODIFIER,,,,1;AC010624.3,intron_variant,,ENST00000599410,,n.295+1584del,MODIFIER,,,,-1;AC010624.3,intron_variant,,ENST00000599914,,n.182-1588del,MODIFIER,,,,-1;AC010624.3,intron_variant,,ENST00000655988,,n.122-1588del,MODIFIER,YES,,,-1;AC010624.1,upstream_gene_variant,,ENST00000527209,,,MODIFIER,YES,,,1 2241/4642 mutect2;pindel;varscan2 8de236f1-c029-44df-a2a9-319145488baa 0 45 bd180da4-6429-41fb-a926-caaf693a2db8 70 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS ENSG00000269091,intron_variant,,ENST00000655988.1,n.122-1588del,MODIFIER,;ENSG00000269091,intron_variant,,ENST00000599410.1,n.295+1584del,MODIFIER,;ENSG00000269091,intron_variant,,ENST00000599914.5,n.182-1588del,MODIFIER,YES;ZNF473,intron_variant,,ENST00000601364.5,c.226+4556del,MODIFIER,;ZNF473,frameshift_variant,p.P633Lfs*22,ENST00000445728.7,c.1898del,HIGH,;ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000270617.8,c.1934del,HIGH,YES;ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000391821.6,c.1934del,HIGH,;ZNF473,frameshift_variant,p.P645Lfs*22,ENST00000595661.5,c.1934del,HIGH, +EWSR1 2130 BI GRCh38 22 29278061 29278061 + stop_gained Nonsense_Mutation SNP C C G novel TCGA-V4-A9EL-01A TCGA-V4-A9EL-10A Somatic 11 13 c.258C>G p.Tyr86Ter p.Y86* ENST00000397938.7 NM_005243.4 86 taC/taG 5/17 A1 G Y/* protein_coding CCDS13851.1 258/1971 GCATACAGCCA PANTHER:PTHR23238;PANTHER:PTHR23238:SF3 ENSP00000381031 5/17 ENST00000397938 Transcript 1.0 ENSG00000182944 HGNC:3508 HIGH NM_005243.4 stop_gained Unknown Q01844.225 EWSR1 HGNC 1 1.0 UPI000012A2B1 Q01844-1 SNV EWSR1,stop_gained,p.Y86*,ENST00000332050,,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y87*,ENST00000629659,,c.261C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y86*,ENST00000397938,NM_005243.4,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y86*,ENST00000331029,,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y86*,ENST00000406548,NM_001163285.2,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y92*,ENST00000414183,NM_013986.4,c.276C>G,HIGH,YES,,,1;EWSR1,stop_gained,p.Y86*,ENST00000332035,NM_001163286.2,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y86*,ENST00000333395,NM_001163287.2,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y87*,ENST00000437155,,c.261C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y86*,ENST00000455726,,c.258C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y92*,ENST00000447973,,c.276C>G,HIGH,,,,1;EWSR1,stop_gained,p.Y93*,ENST00000436425,,c.279C>G,HIGH,,,,1;EWSR1,intron_variant,,ENST00000415761,,c.103-70C>G,MODIFIER,,,,1;EWSR1,downstream_gene_variant,,ENST00000444626,,,MODIFIER,,,,1;EWSR1,non_coding_transcript_exon_variant,,ENST00000479135,,n.2433C>G,MODIFIER,,,,1;EWSR1,non_coding_transcript_exon_variant,,ENST00000483415,,n.282C>G,MODIFIER,,,,1;EWSR1,downstream_gene_variant,,ENST00000485037,,,MODIFIER,,,,1;EWSR1,downstream_gene_variant,,ENST00000493426,,,MODIFIER,,,,1 327/2400 muse;mutect2;varscan2 8de236f1-c029-44df-a2a9-319145488baa 0 41 bd180da4-6429-41fb-a926-caaf693a2db8 24 e8891c3a-5ac2-49d6-b1a3-9623b28a328e SUCCESS EWSR1,non_coding_transcript_exon_variant,,ENST00000479135.5,n.2433C>G,MODIFIER,;EWSR1,stop_gained,p.Y86*,ENST00000455726.5,c.258C>G,HIGH,;EWSR1,stop_gained,p.Y86*,ENST00000332035.10,c.258C>G,HIGH,;EWSR1,stop_gained,p.Y92*,ENST00000414183.6,c.276C>G,HIGH,;EWSR1,non_coding_transcript_exon_variant,,ENST00000483415.5,n.282C>G,MODIFIER,;EWSR1,stop_gained,p.Y86*,ENST00000331029.11,c.258C>G,HIGH,;EWSR1,intron_variant,,ENST00000415761.5,c.103-70C>G,MODIFIER,;EWSR1,stop_gained,p.Y87*,ENST00000437155.6,c.261C>G,HIGH,;EWSR1,stop_gained,p.Y86*,ENST00000406548.5,c.258C>G,HIGH,;EWSR1,stop_gained,p.Y86*,ENST00000333395.11,c.258C>G,HIGH,;EWSR1,stop_gained,p.Y86*,ENST00000397938.7,c.258C>G,HIGH,YES;EWSR1,stop_gained,p.Y93*,ENST00000436425.5,c.279C>G,HIGH,;EWSR1,stop_gained,p.Y92*,ENST00000447973.5,c.276C>G,HIGH,;EWSR1,stop_gained,p.Y87*,ENST00000629659.2,c.261C>G,HIGH,;EWSR1,stop_gained,p.Y86*,ENST00000332050.10,c.258C>G,HIGH, +EYA3 2140 BI GRCh38 1 28013260 28013260 + missense_variant Missense_Mutation SNP T T C rs1367960963 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 45 38 c.620A>G p.Gln207Arg p.Q207R ENST00000373871.8 NM_001282562.2 207 cAg/cGg 9/18 P4 C Q/R protein_coding YES CCDS316.1 620/1722 GGTACTGATTC PANTHER:PTHR10190;PANTHER:PTHR10190:SF5 ENSP00000362978 9/18 rs1367960963 ENST00000373871 Transcript ENSG00000158161 HGNC:3521 MODERATE NM_001990.4 missense_variant 1.0 probably_damaging(0.993) Unknown deleterious(0) Q99504.173 EYA3 HGNC -1 1.0 UPI000015FFE5 Q99504-1 SNV EYA3,missense_variant,p.Q207R,ENST00000373871,NM_001990.4,c.620A>G,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;EYA3,missense_variant,p.Q154R,ENST00000436342,NM_001282562.1,c.461A>G,MODERATE,,deleterious(0),probably_damaging(0.993),-1;EYA3,missense_variant,p.Q161R,ENST00000540618,NM_001282561.1,c.482A>G,MODERATE,,deleterious(0),probably_damaging(0.969),-1;EYA3,missense_variant,p.Q51R,ENST00000373864,,c.152A>G,MODERATE,,deleterious(0),probably_damaging(0.969),-1;EYA3,missense_variant,p.Q161R,ENST00000373863,NM_001282560.2,c.482A>G,MODERATE,,deleterious(0),probably_damaging(0.985),-1;EYA3,non_coding_transcript_exon_variant,,ENST00000471498,,n.762A>G,MODIFIER,,,,-1;EYA3,non_coding_transcript_exon_variant,,ENST00000468665,,n.257A>G,MODIFIER,,,,-1;EYA3,upstream_gene_variant,,ENST00000495923,,,MODIFIER,,,,-1 775/5999 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 79 08f49558-b35f-493e-a269-8c626446b5b7 84 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS EYA3,non_coding_transcript_exon_variant,,ENST00000468665.1,n.257A>G,MODIFIER,;EYA3,non_coding_transcript_exon_variant,,ENST00000471498.5,n.762A>G,MODIFIER,;EYA3,missense_variant,p.Q161R,ENST00000373863.3,c.482A>G,MODERATE,;EYA3,missense_variant,p.Q51R,ENST00000373864.5,c.152A>G,MODERATE,;EYA3,missense_variant,p.Q161R,ENST00000540618.5,c.482A>G,MODERATE,;EYA3,missense_variant,p.Q154R,ENST00000436342.6,c.461A>G,MODERATE,;EYA3,missense_variant,p.Q207R,ENST00000373871.8,c.620A>G,MODERATE,YES +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 29 20 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 60 08f49558-b35f-493e-a269-8c626446b5b7 49 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +CNTN3 5067 BI GRCh38 3 74486471 74486471 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 35 11 c.343A>C p.Lys115Gln p.K115Q ENST00000263665.7 NM_020872.3 115 Aaa/Caa 4/23 P1 G K/Q protein_coding YES CCDS33790.1 343/3087 AAGTTTGGCTT Gene3D:2.60.40.10;PROSITE_profiles:PS50835;PANTHER:PTHR44170;PANTHER:PTHR44170:SF18;SMART:SM00409;Superfamily:SSF48726 ENSP00000263665 3/22 ENST00000263665 Transcript ENSG00000113805 HGNC:2173 MODERATE missense_variant 1.0 benign(0.009) Unknown tolerated(0.1) Q9P232.156 CNTN3 HGNC -1 1.0 UPI00001A7974 SNV CNTN3,missense_variant,p.K115Q,ENST00000263665,NM_020872.2,c.343A>C,MODERATE,YES,tolerated(0.1),benign(0.009),-1 371/4948 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 44 08f49558-b35f-493e-a269-8c626446b5b7 46 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS CNTN3,missense_variant,p.K115Q,ENST00000263665.7,c.343A>C,MODERATE,YES +EVC 2121 BI GRCh38 4 5733410 5733410 + missense_variant Missense_Mutation SNP C C T rs201583621 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 249 45 c.677C>T p.Thr226Met p.T226M ENST00000264956.11 NM_153717.3 226 aCg/aTg 5/21 0.0002 0.0 0.0 0.0 0.0 0.001 P2 T T/M protein_coding YES CCDS3383.1 677/2979 likely_benign;uncertain_significance GGACACGGCAC COSM1056294 PANTHER:PTHR16795;PANTHER:PTHR16795:SF13 ENSP00000264956 0.0 0.0002326 5/21 rs201583621;COSV53833359 ENST00000264956 Transcript 1.0 ENSG00000072840 HGNC:3497 MODERATE NM_153717.3 0.001 SAS missense_variant 1;1 1.0 benign(0.024) Unknown deleterious(0.04) 0;1 P57679.146 EVC HGNC 1 1.0 UPI000012A2A5 SNV EVC,missense_variant,p.T226M,ENST00000264956,NM_153717.3&NM_001306090.2,c.677C>T,MODERATE,YES,deleterious(0.04),benign(0.024),1;EVC,missense_variant,p.T226M,ENST00000509451,NM_001306092.2,c.677C>T,MODERATE,,tolerated(0.05),benign(0.024),1 857/6427 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 5.568e-05 0.000123 0.0 9.921e-05 0.0 0.0 2.638e-05 0.0 0.0002613 8.111939678201452e-05 0.000145929006976 0.0 0.0 0.0 0.0 0.0 sas 0.0004178849922027 0.0 6.171320274006575e-05 0.0 0.0004178849922027 0 323 08f49558-b35f-493e-a269-8c626446b5b7 294 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS EVC,missense_variant,p.T226M,ENST00000509451.1,c.677C>T,MODERATE,;EVC,missense_variant,p.T226M,ENST00000264956.11,c.677C>T,MODERATE,YES +HCG21 102723346 BI GRCh38 6 30952118 30952118 + intron_variant Intron SNP C C G novel TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 69 24 n.224+949G>C ENST00000419481.1 342/517 A2 G T protein_coding 1026/1554 CTGACCACTGA PANTHER:PTHR22094;Low_complexity_(Seg):seg ENSP00000305948 3/4 ENST00000304311 Transcript 1.0 ENSG00000168631 HGNC:21666 LOW synonymous_variant Unknown Q3MIW9.107 MUCL3 HGNC 1 5.0 UPI0001642865 Q3MIW9-1 SNV MUCL3,synonymous_variant,p.T1285=,ENST00000636043,,c.3855C>G,LOW,YES,,,1;MUCL3,synonymous_variant,p.T1218=,ENST00000462446,NM_080870.4,c.3654C>G,LOW,,,,1;MUCL3,synonymous_variant,p.T342=,ENST00000304311,,c.1026C>G,LOW,,,,1;SFTA2,intron_variant,,ENST00000634371,,c.-9+244G>C,MODIFIER,,,,-1;HCG21,intron_variant,,ENST00000419481,,n.224+949G>C,MODIFIER,YES,,,-1 1026/2658 muse;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 60 08f49558-b35f-493e-a269-8c626446b5b7 95 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS HCG21,intron_variant,,ENST00000419481.1,n.224+949G>C,MODIFIER,YES;MUCL3,synonymous_variant,p.T1218=,ENST00000462446.6,c.3654C>G,LOW,YES;MUCL3,synonymous_variant,p.T1285=,ENST00000636043.1,c.3855C>G,LOW,;SFTA2,intron_variant,,ENST00000634371.1,c.-9+244G>C,MODIFIER, +MUCL3 135656 BI GRCh38 6 30952222 30952222 + missense_variant Missense_Mutation SNP C C G rs1347896822 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 107 34 c.3758C>G p.Ser1253Cys p.S1253C ENST00000462446.6 377 tCt/tGt 3/4 A2 G S/C protein_coding 1130/1554 CAAATCTCTCA PANTHER:PTHR22094 ENSP00000305948 3/4 rs1347896822;COSV100423891 ENST00000304311 Transcript 1.0 ENSG00000168631 HGNC:21666 MODERATE 8.797e-06 gnomAD_NFE missense_variant 0;1 probably_damaging(0.923) Unknown deleterious(0.01) 0;1 Q3MIW9.107 MUCL3 HGNC 1 5.0 UPI0001642865 Q3MIW9-1 SNV MUCL3,missense_variant,p.S1320C,ENST00000636043,,c.3959C>G,MODERATE,YES,deleterious(0),probably_damaging(0.989),1;MUCL3,missense_variant,p.S1253C,ENST00000462446,NM_080870.4,c.3758C>G,MODERATE,,deleterious(0),probably_damaging(0.949),1;MUCL3,missense_variant,p.S377C,ENST00000304311,,c.1130C>G,MODERATE,,deleterious(0.01),probably_damaging(0.923),1;SFTA2,intron_variant,,ENST00000634371,,c.-9+140G>C,MODIFIER,,,,-1;HCG21,intron_variant,,ENST00000419481,,n.224+845G>C,MODIFIER,YES,,,-1 1130/2658 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 3.979e-06 0.0 0.0 0.0 0.0 0.0 8.797e-06 0.0 0.0 0 70 08f49558-b35f-493e-a269-8c626446b5b7 141 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS HCG21,intron_variant,,ENST00000419481.1,n.224+845G>C,MODIFIER,YES;MUCL3,missense_variant,p.S1253C,ENST00000462446.6,c.3758C>G,MODERATE,YES;MUCL3,missense_variant,p.S1320C,ENST00000636043.1,c.3959C>G,MODERATE,;SFTA2,intron_variant,,ENST00000634371.1,c.-9+140G>C,MODIFIER, +MUCL3 135656 BI GRCh38 6 30952325 30952325 + missense_variant Missense_Mutation SNP C C G rs751853704 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 125 54 c.3861C>G p.Ile1287Met p.I1287M ENST00000462446.6 411 atC/atG 3/4 A2 G I/M protein_coding 1233/1554 TCTATCACATC PANTHER:PTHR22094 ENSP00000305948 3/4 rs751853704 ENST00000304311 Transcript 1.0 ENSG00000168631 HGNC:21666 MODERATE 0.0001633 gnomAD_OTH missense_variant benign(0.181) Unknown tolerated(0.1) Q3MIW9.107 MUCL3 HGNC 1 5.0 UPI0001642865 Q3MIW9-1 SNV MUCL3,missense_variant,p.I1354M,ENST00000636043,,c.4062C>G,MODERATE,YES,tolerated(0.08),benign(0.215),1;MUCL3,missense_variant,p.I1287M,ENST00000462446,NM_080870.4,c.3861C>G,MODERATE,,tolerated(0.17),possibly_damaging(0.899),1;MUCL3,missense_variant,p.I411M,ENST00000304311,,c.1233C>G,MODERATE,,tolerated(0.1),benign(0.181),1;SFTA2,intron_variant,,ENST00000634371,,c.-9+37G>C,MODIFIER,,,,-1;HCG21,intron_variant,,ENST00000419481,,n.224+742G>C,MODIFIER,YES,,,-1 1233/2658 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 4.379e-05 0.0 0.0 0.0 0.0 0.0 8.801e-05 0.0001633 0.0 4.055149838677608e-05 4.863339927396737e-05 0.0 0.0 0.0 0.0 0.0 nfe 6.171510176500306e-05 0.0 6.171510176500306e-05 0.0 0.0 0 76 08f49558-b35f-493e-a269-8c626446b5b7 179 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS HCG21,intron_variant,,ENST00000419481.1,n.224+742G>C,MODIFIER,YES;MUCL3,missense_variant,p.I1287M,ENST00000462446.6,c.3861C>G,MODERATE,YES;MUCL3,missense_variant,p.I1354M,ENST00000636043.1,c.4062C>G,MODERATE,;SFTA2,intron_variant,,ENST00000634371.1,c.-9+37G>C,MODIFIER, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 47 38 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 77 08f49558-b35f-493e-a269-8c626446b5b7 85 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +ZNF195 7748 BI GRCh38 11 3359432 3359432 + missense_variant Missense_Mutation SNP C C T rs376637698 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 55 43 c.1576G>A p.Glu526Lys p.E526K ENST00000399602.9 NM_001130520.3 526 Gaa/Aaa 6/6 P4 T E/K protein_coding CCDS44522.1 1576/1890 ACATTCGTCAC Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24384;PANTHER:PTHR24384:SF87;SMART:SM00355;Superfamily:SSF57667 ENSP00000382511 6/6 rs376637698 ENST00000399602 Transcript ENSG00000005801 HGNC:12986 MODERATE NM_001130520.3 3.269e-05 gnomAD_SAS missense_variant probably_damaging(0.959) Unknown tolerated(0.05) O14628.180 ZNF195 HGNC -1 1.0 UPI0000D6258D O14628-1 SNV ZNF195,missense_variant,p.E530K,ENST00000620374,,c.1588G>A,MODERATE,YES,tolerated(0.05),possibly_damaging(0.877),-1;ZNF195,missense_variant,p.E526K,ENST00000399602,NM_001130520.3,c.1576G>A,MODERATE,,tolerated(0.05),probably_damaging(0.959),-1;ZNF195,missense_variant,p.E458K,ENST00000343338,NM_001256825.1&NM_001242843.2,c.1372G>A,MODERATE,,deleterious(0.04),benign(0.105),-1;ZNF195,missense_variant,p.E454K,ENST00000354599,NM_007152.5,c.1360G>A,MODERATE,,deleterious(0.04),benign(0.105),-1;ZNF195,missense_variant,p.E458K,ENST00000429541,,c.1372G>A,MODERATE,,deleterious(0.04),benign(0.105),-1;ZNF195,missense_variant,p.E503K,ENST00000005082,NM_001130519.3,c.1507G>A,MODERATE,,deleterious(0.03),probably_damaging(0.932),-1;ZNF195,missense_variant,p.E507K,ENST00000526601,NM_001256824.2&NM_001242841.2,c.1519G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.762),-1;ZNF195,intron_variant,,ENST00000528796,,c.226+11543G>A,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000427810,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000438262,NM_001256823.2,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000528410,NM_001242842.2,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000529678,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000533036,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000534569,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000618467,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000330692,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000524857,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000528636,,,MODIFIER,,,,-1;ZNF195,non_coding_transcript_exon_variant,,ENST00000649622,,n.8614G>A,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000525313,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000526540,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000526598,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000528218,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000529228,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000529789,,,MODIFIER,,,,-1;ZNF195,downstream_gene_variant,,ENST00000530643,,,MODIFIER,,,,-1 1682/3187 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 4.009e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.269e-05 0 156 08f49558-b35f-493e-a269-8c626446b5b7 98 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS ZNF195,missense_variant,p.E507K,ENST00000526601.5,c.1519G>A,MODERATE,;ZNF195,missense_variant,p.E503K,ENST00000005082.13,c.1507G>A,MODERATE,;ZNF195,missense_variant,p.E458K,ENST00000429541.6,c.1372G>A,MODERATE,;ZNF195,non_coding_transcript_exon_variant,,ENST00000649622.1,n.8614G>A,MODIFIER,;ZNF195,missense_variant,p.E458K,ENST00000343338.11,c.1372G>A,MODERATE,;ZNF195,missense_variant,p.E530K,ENST00000620374.4,c.1588G>A,MODERATE,;ZNF195,missense_variant,p.E526K,ENST00000399602.9,c.1576G>A,MODERATE,YES;ZNF195,missense_variant,p.E454K,ENST00000354599.10,c.1360G>A,MODERATE,;ZNF195,intron_variant,,ENST00000528796.5,c.226+11543G>A,MODIFIER, +USP35 57558 BI GRCh38 11 78200220 78200220 + missense_variant Missense_Mutation SNP G G A rs1273026171 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 30 7 c.1024G>A p.Glu342Lys p.E342K ENST00000529308.6 NM_020798.4 342 Gaa/Aaa 5/11 P1 A E/K protein_coding YES CCDS41693.1 1024/3057 CCCACGAAGCC COSM932254;COSM932255 PANTHER:PTHR24006:SF660;PANTHER:PTHR24006;Superfamily:SSF48371 ENSP00000431876 5/11 rs1273026171;COSV71572701 ENST00000529308 Transcript ENSG00000118369 HGNC:20061 MODERATE NM_020798.4 1.767e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(0.994) Unknown deleterious(0) 0;1 Q9P2H5.149 USP35 HGNC 1 5.0 UPI0000456553 Q9P2H5-1 SNV USP35,missense_variant,p.E342K,ENST00000529308,NM_020798.4,c.1024G>A,MODERATE,YES,deleterious(0),probably_damaging(0.994),1;USP35,missense_variant,p.E73K,ENST00000526425,,c.217G>A,MODERATE,,deleterious(0.01),probably_damaging(0.994),1;USP35,missense_variant,p.E98K,ENST00000528910,,c.292G>A,MODERATE,,deleterious(0.01),probably_damaging(0.994),1;USP35,intron_variant,,ENST00000530267,,c.-99-5622G>A,MODIFIER,,,,1;USP35,intron_variant,,ENST00000530535,,n.336-9228G>A,MODIFIER,,,,1;USP35,3_prime_UTR_variant,,ENST00000530546,,c.*18G>A,MODIFIER,,,,1 1273/4725 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 8.018e-06 0.0 0.0 0.0 0.0 0.0 1.767e-05 0.0 0.0 6.776349891879363e-06 0.0 0.0 6.63305982016027e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 34 08f49558-b35f-493e-a269-8c626446b5b7 37 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS USP35,missense_variant,p.E73K,ENST00000526425.1,c.217G>A,MODERATE,;USP35,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000530546.5,c.*18G>A,MODIFIER,;USP35,missense_variant,p.E342K,ENST00000529308.6,c.1024G>A,MODERATE,YES;USP35,missense_variant,p.E98K,ENST00000528910.5,c.292G>A,MODERATE,;USP35,intron_variant,,ENST00000530535.5,n.336-9228G>A,MODIFIER,;USP35,intron_variant,,ENST00000530267.5,c.-99-5622G>A,MODIFIER, +FANCM 57697 BI GRCh38 14 45198808 45198808 + missense_variant Missense_Mutation SNP G G T novel TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 34 17 c.5881G>T p.Val1961Phe p.V1961F ENST00000267430.10 NM_020937.4 1961 Gtt/Ttt 22/23 P1 T V/F protein_coding YES CCDS32070.1 5881/6147 TTCATGTTCCA Gene3D:3.40.50.10130;PDB-ENSP_mappings:4bxo.A;PDB-ENSP_mappings:4m6w.A;PANTHER:PTHR14074;PANTHER:PTHR14074:SF33 ENSP00000267430 22/23 ENST00000267430 Transcript 1.0 ENSG00000187790 HGNC:23168 MODERATE NM_020937.4 missense_variant 1.0 benign(0.018) Unknown deleterious(0.01) Q8IYD8.162 FANCM HGNC 1 1.0 UPI000059F032 Q8IYD8-1 SNV FANCM,missense_variant,p.V1961F,ENST00000267430,NM_020937.4,c.5881G>T,MODERATE,YES,deleterious(0.01),benign(0.018),1;FANCM,missense_variant,p.V1935F,ENST00000542564,NM_001308133.2,c.5803G>T,MODERATE,,deleterious(0.01),benign(0.007),1;FANCM,missense_variant,p.V1477F,ENST00000556250,,c.4429G>T,MODERATE,,deleterious(0.02),benign(0.107),1;FANCM,missense_variant,p.V929F,ENST00000554809,,c.2785G>T,MODERATE,,deleterious(0.02),benign(0.227),1;FANCM,missense_variant,p.V87F,ENST00000555484,,c.259G>T,MODERATE,,deleterious(0.02),benign(0.059),1;MIS18BP1,downstream_gene_variant,,ENST00000310806,NM_018353.5,,MODIFIER,YES,,,-1;FANCM,3_prime_UTR_variant,,ENST00000557110,,c.*45G>T,MODIFIER,,,,1;FANCM,non_coding_transcript_exon_variant,,ENST00000553551,,n.374G>T,MODIFIER,,,,1 5983/7131 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 0 51 08f49558-b35f-493e-a269-8c626446b5b7 52 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS FANCM,non_coding_transcript_exon_variant,,ENST00000553551.2,n.2081G>T,MODIFIER,;FANCM,non_coding_transcript_exon_variant,,ENST00000696651.1,n.2321G>T,MODIFIER,;FANCM,non_coding_transcript_exon_variant,,ENST00000696645.1,n.1771G>T,MODIFIER,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000557110.2,c.*45G>T,MODIFIER,;FANCM,missense_variant,p.M553I,ENST00000555484.2,c.1659G>T,MODERATE,;FANCM,intron_variant,,ENST00000696665.1,c.1495-1062G>T,MODIFIER,;FANCM,non_coding_transcript_exon_variant,,ENST00000696686.1,n.2618G>T,MODIFIER,;FANCM,3_prime_UTR_variant,,ENST00000696659.1,c.*114G>T,MODIFIER,;FANCM,missense_variant,p.V1400F,ENST00000554809.6,c.4198G>T,MODERATE,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696663.1,c.*1720G>T,MODIFIER,;FANCM,missense_variant,p.M1571I,ENST00000696664.1,c.4713G>T,MODERATE,;FANCM,missense_variant,p.M1503I,ENST00000696683.1,c.4509G>T,MODERATE,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696685.1,c.*143G>T,MODIFIER,;FANCM,intron_variant,,ENST00000696684.1,c.4158-1062G>T,MODIFIER,;FANCM,missense_variant,p.V1909F,ENST00000696649.1,c.5725G>T,MODERATE,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696648.1,c.*3906G>T,MODIFIER,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696675.1,c.*1637G>T,MODIFIER,;FANCM,missense_variant,p.V1935F,ENST00000542564.6,c.5803G>T,MODERATE,;FANCM,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696647.1,c.*114G>T,MODIFIER,;FANCM,missense_variant,p.V1961F,ENST00000267430.10,c.5881G>T,MODERATE,YES;FANCM,missense_variant,p.V1892F,ENST00000556250.6,c.5674G>T,MODERATE, +NEDD4 4734 BI GRCh38 15 55916705 55916705 + missense_variant Missense_Mutation SNP T T C rs148700559 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 106 22 c.127A>G p.Thr43Ala p.T43A ENST00000508342.5 NM_001284338.2 43 Acg/Gcg 1/25 C T/A protein_coding YES CCDS61644.1 127/3960 AGACGTTGAAA PANTHER:PTHR11254;PANTHER:PTHR11254:SF282 ENSP00000424827 0.0 0.0001165 1/25 rs148700559 ENST00000508342 Transcript ENSG00000069869 HGNC:7727 MODERATE 0.0001307 gnomAD_SAS missense_variant 1.0 benign(0) Unknown tolerated_low_confidence(1) P46934.209 NEDD4 HGNC -1 1.0 UPI00001FE52D P46934-1 SNV NEDD4,missense_variant,p.T43A,ENST00000508342,NM_001284338.1,c.127A>G,MODERATE,YES,tolerated_low_confidence(1),benign(0),-1;NEDD4,missense_variant,p.T43A,ENST00000338963,NM_198400.3&NM_001329212.2,c.127A>G,MODERATE,,tolerated_low_confidence(1),benign(0),-1;NEDD4,missense_variant,p.T43A,ENST00000506154,NM_001284339.1,c.127A>G,MODERATE,,tolerated_low_confidence(1),benign(0),-1;NEDD4,intron_variant,,ENST00000435532,NM_006154.4,c.291+7941A>G,MODIFIER,,,,-1;NEDD4,upstream_gene_variant,,ENST00000508871,NM_001284340.1,,MODIFIER,,,,-1;NEDD4,intron_variant,,ENST00000514893,,n.264+7941A>G,MODIFIER,,,,-1;NEDD4,intron_variant,,ENST00000502612,,c.*86+7941A>G,MODIFIER,,,,-1;NEDD4,intron_variant,,ENST00000507063,,c.79+7941A>G,MODIFIER,,,,-1;NEDD4,intron_variant,,ENST00000648451,,c.*70+7941A>G,MODIFIER,,,,-1;NEDD4,upstream_gene_variant,,ENST00000503468,,,MODIFIER,,,,-1 427/7235 muse;mutect2;varscan2 4b9fd822-17aa-4a22-8e17-175a72931d5d 4.375e-05 6.152e-05 0.0 0.0 0.0 0.0 5.276e-05 0.0 0.0001307 6.083879998186603e-05 4.861690104007721e-05 0.0 0.0001326960045844 0.0 0.0 0.0 amr 0.0001326960045844 0.0 6.17397963651456e-05 0.0004950499860569 0.0 0 133 08f49558-b35f-493e-a269-8c626446b5b7 128 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS NEDD4,intron_variant,NMD_transcript_variant,,ENST00000507063.1,c.79+7941A>G,MODIFIER,;NEDD4,intron_variant,,ENST00000514893.5,n.264+7941A>G,MODIFIER,;NEDD4,intron_variant,NMD_transcript_variant,,ENST00000502612.5,c.*86+7941A>G,MODIFIER,;NEDD4,missense_variant,p.T43A,ENST00000506154.1,c.127A>G,MODERATE,;NEDD4,intron_variant,NMD_transcript_variant,,ENST00000648451.1,c.*70+7941A>G,MODIFIER,;NEDD4,missense_variant,p.T43A,ENST00000508342.5,c.127A>G,MODERATE,;NEDD4,intron_variant,,ENST00000435532.8,c.291+7941A>G,MODIFIER,YES;NEDD4,missense_variant,p.T43A,ENST00000338963.6,c.127A>G,MODERATE, +ALYREF 51529 BI GRCh38 17 81890759 81890759 + missense_variant Missense_Mutation SNP G G A rs866240403 TCGA-V4-A9F4-01A TCGA-V4-A9F4-10A Somatic 56 5 c.320C>T p.Ala107Val p.A107V ENST00000505490.3 NM_001002248.3 107/264 P1 A A/V protein_coding YES CCDS32768.2 320/795 CGCCGGCACCA Gene3D:3.30.70.330;PANTHER:PTHR19965;PANTHER:PTHR19965:SF52;Low_complexity_(Seg):seg ENSP00000421592 2/6 rs866240403 ENST00000505490 Transcript ENSG00000183684 HGNC:19071 MODERATE NM_005782.4 missense_variant 1.0 benign(0.029) Unknown tolerated(0.1) ALYREF HGNC -1 E9PB61.79 1.0 UPI00001AFE08 SNV ALYREF,missense_variant,p.A107V,ENST00000505490,NM_005782.4,c.320C>T,MODERATE,YES,tolerated(0.1),benign(0.029),-1;ANAPC11,upstream_gene_variant,,ENST00000344877,NM_001002248.3,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000357385,NM_001002244.2,,MODIFIER,YES,,,1;ANAPC11,upstream_gene_variant,,ENST00000392376,NM_001002249.2,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000571024,NM_001002247.2&NM_001002245.2,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000571570,NM_001289414.1,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000571874,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000572639,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000572851,NM_001289415.1,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000574924,NM_016476.11&NM_001002246.2,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000575195,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000577425,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000577747,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000578544,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000578550,NM_001289417.1,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000579133,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000579978,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000582222,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000583839,NM_001289416.1,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000584197,NM_001289420.1,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000584314,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000585259,,,MODIFIER,,,,1;ANAPC11,upstream_gene_variant,,ENST00000612413,,,MODIFIER,,,,1;ALYREF,non_coding_transcript_exon_variant,,ENST00000512673,,n.134C>T,MODIFIER,,,,-1;ALYREF,upstream_gene_variant,,ENST00000504015,,,MODIFIER,,,,-1;ALYREF,non_coding_transcript_exon_variant,,ENST00000511412,,n.247C>T,MODIFIER,,,,-1 326/1097 muse;mutect2 4b9fd822-17aa-4a22-8e17-175a72931d5d 6.763700184819754e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5435400200658478e-05 0.0 0.0 0 60 08f49558-b35f-493e-a269-8c626446b5b7 61 e1580f98-15d2-408b-a83e-0746c7dd70fc SUCCESS ALYREF,non_coding_transcript_exon_variant,,ENST00000511412.1,n.247C>T,MODIFIER,;ALYREF,non_coding_transcript_exon_variant,,ENST00000512673.1,n.134C>T,MODIFIER,;ALYREF,missense_variant,p.A107V,ENST00000505490.3,c.320C>T,MODERATE,YES +SPTA1 6708 BI GRCh38 1 158642941 158642941 + missense_variant Missense_Mutation SNP C C T rs544007770 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 32 41 c.4478G>A p.Arg1493Gln p.R1493Q ENST00000643759.2 NM_003126.4 1493 cGg/cAg 32/52 P1 T R/Q protein_coding YES CCDS41423.1 4478/7260 TTGTCCGCTCA COSM5211683 Gene3D:1.20.58.60;Pfam:PF00435;PANTHER:PTHR11915;PANTHER:PTHR11915:SF431;SMART:SM00150;Superfamily:SSF46966;Superfamily:SSF46966;CDD:cd00176 ENSP00000495214 32/52 rs544007770;COSV63755443;COSV63760682 ENST00000643759 Transcript 1.0 ENSG00000163554 HGNC:11272 MODERATE NM_003126.4 missense_variant 0;1;1 1.0 possibly_damaging(0.814) Unknown tolerated(0.05) 0;1;1 P02549.231 SPTA1 HGNC -1 UPI0000458906 P02549-1 SNV SPTA1,missense_variant,p.R1493Q,ENST00000643759,NM_003126.4,c.4478G>A,MODERATE,YES,tolerated(0.05),possibly_damaging(0.814),-1;SPTA1,upstream_gene_variant,,ENST00000465741,,,MODIFIER,,,,-1 4676/8018 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 86 01ccaec6-9392-406c-a2df-b33124c6e240 73 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS SPTA1,missense_variant,p.R1493Q,ENST00000643759.2,c.4478G>A,MODERATE,YES +PAPPA2 60676 BI GRCh38 1 176594580 176594580 + missense_variant Missense_Mutation SNP C C T rs368485332 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 51 21 c.976C>T p.Arg326Cys p.R326C ENST00000367662.5 NM_020318.3 326 Cgc/Tgc 3/23 P1 T R/C protein_coding YES CCDS41438.1 976/5376 GGATCCGCTCA COSM322465;COSM322466 Gene3D:2.60.120.200;Pfam:PF13385;PANTHER:PTHR46130;PANTHER:PTHR46130:SF1;SMART:SM00560;Superfamily:SSF49899 ENSP00000356634 3/23 rs368485332;COSV62776395 ENST00000367662 Transcript ENSG00000116183 HGNC:14615 MODERATE NM_020318.3 0.001304 gnomAD_AMR missense_variant 0;1 1.0 possibly_damaging(0.901) Unknown deleterious(0) 0;1 Q9BXP8.166 PAPPA2 HGNC 1 1.0 UPI000004A835 Q9BXP8-1 SNV PAPPA2,missense_variant,p.R326C,ENST00000367662,NM_020318.3,c.976C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.901),1;PAPPA2,missense_variant,p.R326C,ENST00000367661,NM_021936.3,c.976C>T,MODERATE,,deleterious(0),probably_damaging(0.954),1 2136/9683 muse;mutect2 cba920f4-c57f-47bc-958d-9b7872df01c8 0.0002327 0.0 0.001304 0.0 0.0 9.283e-05 7.961e-05 0.0001652 3.268e-05 5.4074498621048406e-05 0.0 0.0 0.0001324500044574 0.0 0.0 9.42507031140849e-05 amr 0.0001324500044574 0.0 7.716049731243402e-05 0.0 0.0 0 64 01ccaec6-9392-406c-a2df-b33124c6e240 72 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS PAPPA2,missense_variant,p.R326C,ENST00000367662.5,c.976C>T,MODERATE,YES;PAPPA2,missense_variant,p.R326C,ENST00000367661.7,c.976C>T,MODERATE, +CDKL4 344387 BI GRCh38 2 39229533 39229533 + 5_prime_UTR_variant 5'UTR SNP T T C rs1558583289 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 62 69 c.-1A>G ENST00000395035.4 NM_001346911.1 A2 C protein_coding YES CCDS86834.1 TCCATTATAGC 1.0 ENSP00000378476 rs1558583289 ENST00000395035 Transcript ENSG00000205111 HGNC:19287 MODIFIER upstream_gene_variant 1.0 Unknown Q5MAI5.127 CDKL4 HGNC -1 1.0 UPI000067C9FA Q5MAI5-1 SNV CDKL4,upstream_gene_variant,,ENST00000378803,NM_001009565.2,,MODIFIER,,,,-1;CDKL4,upstream_gene_variant,,ENST00000395035,NM_001346911.1,,MODIFIER,YES,,,-1;CDKL4,5_prime_UTR_variant,,ENST00000419111,,c.-1A>G,MODIFIER,,,,-1 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 76 01ccaec6-9392-406c-a2df-b33124c6e240 132 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS CDKL4,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000419111.2,c.-1A>G,MODIFIER,;CDKL4,5_prime_UTR_variant,,ENST00000378803.6,c.-1A>G,MODIFIER,;CDKL4,5_prime_UTR_variant,,ENST00000395035.4,c.-1A>G,MODIFIER,;CDKL4,5_prime_UTR_variant,,ENST00000451199.7,c.-1A>G,MODIFIER,YES;CDKL4,5_prime_UTR_variant,,ENST00000699627.1,c.-1A>G,MODIFIER,;CDKL4,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000699628.1,c.-1A>G,MODIFIER, +SCN9A 6335 BI GRCh38 2 166199564 166199564 + missense_variant Missense_Mutation SNP A A G novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 126 114 c.5075T>C p.Phe1692Ser p.F1692S ENST00000303354.11 1692 tTc/tCc 27/27 A2 G F/S protein_coding 5075/5967 TTTGGAACAGG PDB-ENSP_mappings:6j8g.A;PDB-ENSP_mappings:6j8h.A;PDB-ENSP_mappings:6j8i.A;PDB-ENSP_mappings:6j8j.A;PANTHER:PTHR10037;PANTHER:PTHR10037:SF221;Pfam:PF00520;Gene3D:1.10.287.70;Superfamily:SSF81324 ENSP00000304748 27/27 ENST00000303354 Transcript 1.0 ENSG00000169432 HGNC:10597 MODERATE missense_variant probably_damaging(0.993) Unknown deleterious(0) Q15858.189 SCN9A HGNC -1 5.0 UPI0001881757 Q15858-1 SNV SCN9A,missense_variant,p.F1681S,ENST00000409672,NM_002977.3,c.5042T>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;SCN9A,missense_variant,p.F1692S,ENST00000642356,NM_001365536.1,c.5075T>C,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SCN9A,missense_variant,p.F1692S,ENST00000303354,,c.5075T>C,MODERATE,,deleterious(0),probably_damaging(0.993),-1;SCN9A,missense_variant,p.F1681S,ENST00000645907,,c.5042T>C,MODERATE,,deleterious(0),probably_damaging(0.998),-1;SCN9A,missense_variant,p.F1640S,ENST00000644316,,c.4919T>C,MODERATE,,deleterious(0),probably_damaging(0.998),-1;SCN9A,missense_variant,p.F1692S,ENST00000409435,,c.5075T>C,MODERATE,,deleterious(0),probably_damaging(1),-1;SCN9A,non_coding_transcript_exon_variant,,ENST00000646694,,n.1452T>C,MODIFIER,,,,-1;SCN1A-AS1,intron_variant,,ENST00000447809,,n.432-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000630020,,n.129-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000651013,,n.565-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000651574,,n.1110-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000651782,,n.526-75A>G,MODIFIER,YES,,,1;SCN1A-AS1,intron_variant,,ENST00000657189,,n.569-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000660239,,n.507-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000660342,,n.285-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000668514,,n.526-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000668610,,n.483-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000670867,,n.334-75A>G,MODIFIER,,,,1;SCN1A-AS1,intron_variant,,ENST00000671220,,n.347-75A>G,MODIFIER,,,,1 5323/9698 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 191 01ccaec6-9392-406c-a2df-b33124c6e240 240 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS SCN9A,non_coding_transcript_exon_variant,,ENST00000646694.1,n.1452T>C,MODIFIER,;SCN9A,missense_variant,p.F1681S,ENST00000645907.1,c.5042T>C,MODERATE,;SCN9A,missense_variant,p.F1692S,ENST00000303354.11,c.5075T>C,MODERATE,;SCN9A,missense_variant,p.F1681S,ENST00000409672.5,c.5042T>C,MODERATE,;SCN9A,missense_variant,p.F1692S,ENST00000642356.2,c.5075T>C,MODERATE,YES;SCN1A-AS1,intron_variant,,ENST00000714451.1,n.127-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000630020.3,n.129-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000660342.1,n.285-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000668610.1,n.483-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000670867.1,n.334-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000660239.1,n.507-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000671220.1,n.347-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000668514.1,n.526-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000651782.1,n.526-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000651013.1,n.565-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000657189.1,n.569-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000447809.2,n.432-75A>G,MODIFIER,;SCN1A-AS1,intron_variant,,ENST00000651574.1,n.1110-75A>G,MODIFIER,YES +SPEG 10290 BI GRCh38 2 219488251 219488251 + missense_variant Missense_Mutation SNP C C G novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 43 22 c.7799C>G p.Ala2600Gly p.A2600G ENST00000312358.12 NM_005876.5 2600 gCa/gGa 32/41 P1 G A/G protein_coding YES CCDS42824.1 7799/9804 GGAGGCAGCCA Gene3D:2.60.40.10;Pfam:PF07679;PROSITE_profiles:PS50835;PANTHER:PTHR47633;PANTHER:PTHR47633:SF3;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;Superfamily:SSF49265;Low_complexity_(Seg):seg ENSP00000311684 32/41 ENST00000312358 Transcript 1.0 ENSG00000072195 HGNC:16901 MODERATE NM_005876.5 missense_variant possibly_damaging(0.696) Unknown tolerated(0.16) Q15772.182 SPEG HGNC 1 5.0 UPI000066D99E Q15772-5 SNV SPEG,missense_variant,p.A2600G,ENST00000312358,NM_005876.5,c.7799C>G,MODERATE,YES,tolerated(0.16),possibly_damaging(0.696),1;AC053503.6,upstream_gene_variant,,ENST00000412982,,,MODIFIER,YES,,,1;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,,n.7042C>G,MODIFIER,,,,1;ASIC4-AS1,intron_variant,,ENST00000429882,,n.183-5842G>C,MODIFIER,YES,,,-1 7934/10782 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 93 01ccaec6-9392-406c-a2df-b33124c6e240 65 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS ASIC4-AS1,intron_variant,,ENST00000429882.1,n.183-5842G>C,MODIFIER,YES;SPEG,non_coding_transcript_exon_variant,,ENST00000485813.5,n.7042C>G,MODIFIER,;SPEG,missense_variant,p.A2600G,ENST00000312358.12,c.7799C>G,MODERATE,YES +IGSF10 285313 BI GRCh38 3 151448099 151448099 + missense_variant Missense_Mutation SNP C C T novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 64 19 c.1882G>A p.Gly628Ser p.G628S ENST00000282466.4 NM_001385061.1 628 Ggc/Agc 6/8 P1 T G/S protein_coding YES CCDS3160.1 1882/7872 TGTGCCATTGT PROSITE_profiles:PS50835;CDD:cd00096;PANTHER:PTHR45842;PANTHER:PTHR45842:SF2;Gene3D:2.60.40.10;Pfam:PF13927;SMART:SM00406;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726 ENSP00000282466 4/6 ENST00000282466 Transcript ENSG00000152580 HGNC:26384 MODERATE missense_variant 1.0 probably_damaging(0.926) Unknown deleterious(0.02) Q6WRI0.140 IGSF10 HGNC -1 1.0 UPI00001D629A Q6WRI0-1 SNV IGSF10,missense_variant,p.G628S,ENST00000282466,NM_178822.4,c.1882G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.926),-1;IGSF10,upstream_gene_variant,,ENST00000489791,,,MODIFIER,,,,-1 1882/11067 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 112 01ccaec6-9392-406c-a2df-b33124c6e240 83 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS IGSF10,missense_variant,p.G628S,ENST00000282466.4,c.1882G>A,MODERATE,YES +PPM1L 151742 BI GRCh38 3 161068868 161068868 + missense_variant Missense_Mutation SNP G G A rs1214162439 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 70 4 c.794G>A p.Arg265Gln p.R265Q ENST00000498165.6 NM_139245.4 265 cGg/cAg 4/4 P1 A R/Q protein_coding YES CCDS33886.1 794/1083 GTCTCGGTCCC COSM3915240;COSM3915241 PROSITE_profiles:PS51746;CDD:cd00143;PANTHER:PTHR13832:SF686;PANTHER:PTHR13832;Gene3D:3.60.40.10;Pfam:PF00481;SMART:SM00331;SMART:SM00332;Superfamily:SSF81606 ENSP00000417659 4/4 rs1214162439;COSV55565633 ENST00000498165 Transcript ENSG00000163590 HGNC:16381 MODERATE NM_139245.4 missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 Q5SGD2.133 PPM1L HGNC 1 1.0 UPI000046F91B Q5SGD2-1 SNV PPM1L,missense_variant,p.R265Q,ENST00000498165,NM_139245.4,c.794G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;PPM1L,missense_variant,p.R86Q,ENST00000464260,NM_001317912.2,c.257G>A,MODERATE,,deleterious(0),probably_damaging(1),1;PPM1L,missense_variant,p.R138Q,ENST00000295839,NM_001317911.2,c.413G>A,MODERATE,,deleterious(0),probably_damaging(1),1;PPM1L,non_coding_transcript_exon_variant,,ENST00000480117,,n.814G>A,MODIFIER,,,,1 872/10906 muse;mutect2 cba920f4-c57f-47bc-958d-9b7872df01c8 1.353090010525193e-05 2.4349899831577204e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5433099179062992e-05 0.0 0.0 0 50 01ccaec6-9392-406c-a2df-b33124c6e240 75 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS PPM1L,non_coding_transcript_exon_variant,,ENST00000480117.1,n.814G>A,MODIFIER,;PPM1L,missense_variant,p.R138Q,ENST00000295839.9,c.413G>A,MODERATE,;PPM1L,missense_variant,p.R86Q,ENST00000464260.5,c.257G>A,MODERATE,;PPM1L,missense_variant,p.R265Q,ENST00000498165.6,c.794G>A,MODERATE,YES +ANK2 287 BI GRCh38 4 113353779 113353779 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 74 111 c.5161G>A p.Ala1721Thr p.A1721T ENST00000357077.9 NM_001148.6 1721 Gct/Act 38/46 A2 A A/T protein_coding CCDS3702.1 5161/11874 TACAAGCTAGT PDB-ENSP_mappings:4d8o.A;Coiled-coils_(Ncoils):Coil;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000349588 38/46 ENST00000357077 Transcript 1.0 ENSG00000145362 HGNC:493 MODERATE NM_001148.6 missense_variant benign(0.006) Unknown tolerated_low_confidence(0.31) Q01484.212 ANK2 HGNC 1 1.0 UPI0000441EF3 Q01484-4 SNV ANK2,missense_variant,p.A1748T,ENST00000672240,NM_001354237.1,c.5242G>A,MODERATE,,tolerated_low_confidence(0.27),benign(0.102),1;ANK2,missense_variant,p.A1736T,ENST00000671971,,c.5206G>A,MODERATE,,tolerated_low_confidence(0.28),benign(0.102),1;ANK2,missense_variant,p.A1703T,ENST00000673363,,c.5107G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000672209,,c.4999G>A,MODERATE,YES,tolerated_low_confidence(0.28),benign(0.102),1;ANK2,missense_variant,p.A1700T,ENST00000672830,,c.5098G>A,MODERATE,,tolerated_low_confidence(0.28),benign(0.102),1;ANK2,missense_variant,p.A1688T,ENST00000672502,,c.5062G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.001),1;ANK2,missense_variant,p.A1679T,ENST00000671809,,c.5035G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000672090,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1659T,ENST00000671906,,c.4975G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1655T,ENST00000672251,,c.4963G>A,MODERATE,,tolerated_low_confidence(0.32),benign(0.102),1;ANK2,missense_variant,p.A1646T,ENST00000673573,,c.4936G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1634T,ENST00000672934,,c.4900G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1626T,ENST00000673109,,c.4876G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000672068,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.28),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000673298,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.102),1;ANK2,missense_variant,p.A1721T,ENST00000357077,NM_001148.6,c.5161G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.006),1;ANK2,missense_variant,p.A1667T,ENST00000673555,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.29),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000672930,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.25),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000673334,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.25),benign(0.102),1;ANK2,missense_variant,p.A1660T,ENST00000671882,,c.4978G>A,MODERATE,,tolerated_low_confidence(0.26),benign(0.102),1;ANK2,missense_variant,p.A1667T,ENST00000503423,,c.4999G>A,MODERATE,,tolerated_low_confidence(0.28),benign(0.102),1;ANK2,missense_variant,p.A1688T,ENST00000264366,,c.5062G>A,MODERATE,,tolerated_low_confidence(0.31),benign(0.001),1;ANK2,intron_variant,,ENST00000394537,NM_001354225.1&NM_001354246.1&NM_001354265.1&NM_020977.4,c.4426+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000504415,,c.383+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000505342,,c.1813+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000506722,NM_001354252.1&NM_001127493.2,c.4399+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000509550,NM_001354281.1,c.1954+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000510275,,c.136+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000514960,,c.1430+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671704,NM_001354261.1&NM_001354267.1,c.4240+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671727,NM_001354236.1&NM_001354228.1,c.4327+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671756,NM_001354275.1,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671762,NM_001354235.1&NM_001354232.1,c.4462+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671793,,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671825,NM_001354254.1&NM_001354256.1&NM_001354255.1,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671854,NM_001354257.1,c.4165+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671893,NM_001354277.1,c.4042+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671951,NM_001354271.1,c.4141+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672045,NM_001354245.1,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672088,NM_001354249.1,c.4240+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672177,,c.4276+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672221,NM_001354264.1,c.4261+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672246,NM_001354272.1,c.4249+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672312,NM_001354262.1,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672315,,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672350,NM_001354253.1,c.4201+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672356,NM_001354260.1,c.4141+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672362,NM_001354239.1,c.4399+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672366,NM_001354258.1&NM_001354273.1,c.4327+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672402,NM_001354244.1&NM_001354243.1,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672411,NM_001354282.1,c.1990+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672684,,c.4165+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672696,,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672731,NM_001354276.1,c.4240+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672759,,c.4141+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672779,NM_001354241.1,c.4471+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672793,,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672854,NM_001354268.1,c.4228+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672880,,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672915,,c.1813+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672955,NM_001354266.1,c.4240+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672965,,c.4300+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672986,,c.3844+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000672990,NM_001354230.1,c.4300+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673044,,c.4363+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673048,NM_001354280.1,c.1975+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673231,NM_001354279.1,c.1990+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673240,NM_001354269.1&NM_001354231.1&NM_001354242.1&NM_001354240.1,c.4471+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673255,,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673353,NM_001354278.1,c.1954+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673430,,c.4264+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673453,NM_001354274.1,c.4192+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673536,,c.3934+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673546,NM_001354270.1,c.4201+3530G>A,MODIFIER,,,,1;ANK2,downstream_gene_variant,,ENST00000504454,,,MODIFIER,,,,1;ANK2,upstream_gene_variant,,ENST00000612754,,,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000508007,,n.535+3530G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000671863,,c.4242+5471G>A,MODIFIER,,,,1;ANK2,intron_variant,,ENST00000673538,,c.1932+5471G>A,MODIFIER,,,,1;ANK2,downstream_gene_variant,,ENST00000512298,,,MODIFIER,,,,1 5237/14215 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 199 01ccaec6-9392-406c-a2df-b33124c6e240 185 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS ANK2,intron_variant,,ENST00000508007.5,n.535+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000504415.5,c.383+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000510275.8,c.1108+3530G>A,MODIFIER,;ANK2,non_coding_transcript_exon_variant,,ENST00000683972.1,n.2006G>A,MODIFIER,;ANK2,intron_variant,,ENST00000682049.1,n.1271+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000514960.5,c.1430+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000684470.1,n.2570+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000683826.1,n.2806+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000684225.1,n.2152+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000681990.1,n.2063+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673048.1,c.1975+3530G>A,MODIFIER,;ANK2,intron_variant,NMD_transcript_variant,,ENST00000673538.1,c.1932+5471G>A,MODIFIER,;ANK2,intron_variant,,ENST00000509550.5,c.1954+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000505342.6,c.1813+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672915.1,c.1813+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673353.1,c.1954+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673231.1,c.1990+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672411.1,c.1990+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000683723.1,n.3439+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1660T,ENST00000671882.1,c.4978G>A,MODERATE,;ANK2,missense_variant,p.A1768T,ENST00000506344.6,c.5302G>A,MODERATE,;ANK2,intron_variant,,ENST00000705785.1,c.4507+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1703T,ENST00000673363.1,c.5107G>A,MODERATE,;ANK2,missense_variant,p.A1736T,ENST00000671971.1,c.5206G>A,MODERATE,;ANK2,missense_variant,p.A1748T,ENST00000672240.1,c.5242G>A,MODERATE,;ANK2,intron_variant,,ENST00000673240.1,c.4471+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1688T,ENST00000264366.10,c.5062G>A,MODERATE,;ANK2,intron_variant,,ENST00000672779.1,c.4471+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000394537.7,c.4426+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1721T,ENST00000357077.9,c.5161G>A,MODERATE,YES;ANK2,intron_variant,,ENST00000672854.1,c.4228+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672045.1,c.4264+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1655T,ENST00000672251.1,c.4963G>A,MODERATE,;ANK2,intron_variant,,ENST00000671727.1,c.4327+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671762.1,c.4462+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672366.1,c.4327+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1688T,ENST00000672502.1,c.5062G>A,MODERATE,;ANK2,intron_variant,,ENST00000672221.1,c.4261+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671704.1,c.4240+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671951.1,c.4141+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672986.1,c.3844+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673536.1,c.3934+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000506722.5,c.4399+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000673555.1,c.4999G>A,MODERATE,;ANK2,missense_variant,p.A1679T,ENST00000671809.1,c.5035G>A,MODERATE,;ANK2,intron_variant,,ENST00000672990.1,c.4300+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000672090.1,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000672880.1,c.4264+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000672068.1,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000671893.1,c.4042+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672759.1,c.4141+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000673334.1,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000673255.1,c.4264+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672793.1,c.4264+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1659T,ENST00000671906.1,c.4975G>A,MODERATE,;ANK2,intron_variant,,ENST00000671756.1,c.4264+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1626T,ENST00000673109.1,c.4876G>A,MODERATE,;ANK2,intron_variant,,ENST00000672177.1,c.4276+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672362.1,c.4399+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000672209.1,c.4999G>A,MODERATE,;ANK2,missense_variant,p.A1667T,ENST00000673298.1,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000673453.1,c.4192+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672246.1,c.4249+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000672930.1,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000672965.1,c.4300+3530G>A,MODIFIER,;ANK2,intron_variant,NMD_transcript_variant,,ENST00000671863.1,c.4242+5471G>A,MODIFIER,;ANK2,missense_variant,p.A1667T,ENST00000503423.6,c.4999G>A,MODERATE,;ANK2,intron_variant,,ENST00000673430.1,c.4264+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671854.1,c.4165+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1634T,ENST00000672934.1,c.4900G>A,MODERATE,;ANK2,intron_variant,,ENST00000672684.1,c.4165+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672731.1,c.4240+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1646T,ENST00000673573.1,c.4936G>A,MODERATE,;ANK2,intron_variant,,ENST00000672350.1,c.4201+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673546.1,c.4201+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671825.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672315.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672696.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672312.1,c.4264+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000673044.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672402.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000671793.1,c.4363+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672088.1,c.4240+3530G>A,MODIFIER,;ANK2,missense_variant,p.A1700T,ENST00000672830.1,c.5098G>A,MODERATE,;ANK2,intron_variant,,ENST00000672955.1,c.4240+3530G>A,MODIFIER,;ANK2,intron_variant,,ENST00000672356.1,c.4141+3530G>A,MODIFIER, +PGBD1 84547 BI GRCh38 6 28301119 28301119 + missense_variant Missense_Mutation SNP T T G novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 72 112 c.1265T>G p.Leu422Arg p.L422R ENST00000259883.3 NM_001184743.2 422 cTt/cGt 7/7 P1 G L/R protein_coding YES CCDS4648.1 1265/2430 AGAGCTTTTTG Pfam:PF13843;PANTHER:PTHR47055;PANTHER:PTHR47055:SF1;Low_complexity_(Seg):seg ENSP00000259883 7/7 ENST00000259883 Transcript ENSG00000137338 HGNC:19398 MODERATE missense_variant 1.0 possibly_damaging(0.876) Unknown deleterious(0) Q96JS3.134 PGBD1 HGNC 1 1.0 UPI000006ED63 SNV PGBD1,missense_variant,p.L422R,ENST00000259883,NM_001184743.1&NM_032507.3,c.1265T>G,MODERATE,YES,deleterious(0),possibly_damaging(0.876),1 1670/3100 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 104 01ccaec6-9392-406c-a2df-b33124c6e240 184 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS PGBD1,missense_variant,p.L422R,ENST00000259883.3,c.1265T>G,MODERATE,;PGBD1,missense_variant,p.L422R,ENST00000682144.1,c.1265T>G,MODERATE,YES +ARMT1 79624 BI GRCh38 6 151469013 151469013 + missense_variant Missense_Mutation SNP G G A rs1480883671 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 36 22 c.1229G>A p.Gly410Asp p.G410D ENST00000367294.4 NM_024573.3 410 gGt/gAt 5/5 P1 A G/D protein_coding YES CCDS5233.1 1229/1326 GGTTGGTCTGC Pfam:PF01937;PANTHER:PTHR12260;PANTHER:PTHR12260:SF6;Superfamily:SSF111321 ENSP00000356263 5/5 rs1480883671 ENST00000367294 Transcript ENSG00000146476 HGNC:17872 MODERATE NM_024573.3 3.267e-05 gnomAD_SAS missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q9H993.136 ARMT1 HGNC 1 1.0 UPI00000708C7 SNV ARMT1,missense_variant,p.G291D,ENST00000545879,NM_001286562.1,c.872G>A,MODERATE,,deleterious(0),probably_damaging(1),1;ARMT1,missense_variant,p.G410D,ENST00000367294,NM_024573.3,c.1229G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;ARMT1,downstream_gene_variant,,ENST00000483931,,,MODIFIER,,,,1;ARMT1,downstream_gene_variant,,ENST00000494826,,,MODIFIER,,,,1 1309/2397 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 3.999e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.267e-05 0 61 01ccaec6-9392-406c-a2df-b33124c6e240 58 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS ARMT1,missense_variant,p.G410D,ENST00000367294.4,c.1229G>A,MODERATE,YES;ARMT1,missense_variant,p.G291D,ENST00000545879.5,c.872G>A,MODERATE, +MUC17 140453 BI GRCh38 7 101036071 101036071 + missense_variant Missense_Mutation SNP G G A novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 129 12 c.4655G>A p.Ser1552Asn p.S1552N ENST00000306151.9 NM_001040105.2 1552 aGt/aAt 3/13 P1 A S/N protein_coding YES CCDS34711.1 4655/13482 AGCCAGTTCAT PANTHER:PTHR37999;MobiDB_lite:mobidb-lite ENSP00000302716 3/13 ENST00000306151 Transcript ENSG00000169876 HGNC:16800 MODERATE NM_001040105.2 missense_variant 1.0 benign(0.092) Unknown tolerated(0.05) Q685J3.132 MUC17 HGNC 1 1.0 UPI0000D5BB56 Q685J3-1 SNV MUC17,missense_variant,p.S1552N,ENST00000306151,NM_001040105.2,c.4655G>A,MODERATE,YES,tolerated(0.05),benign(0.092),1;MUC17,missense_variant,p.S1552N,ENST00000379439,,c.4655G>A,MODERATE,,deleterious(0.05),benign(0.092),1 4710/14352 muse;mutect2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 356 01ccaec6-9392-406c-a2df-b33124c6e240 141 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS MUC17,missense_variant,p.S1552N,ENST00000306151.9,c.4655G>A,MODERATE,YES;MUC17,missense_variant,NMD_transcript_variant,p.S1552N,ENST00000379439.3,c.4655G>A,MODERATE, +TP53INP1 94241 BI GRCh38 8 94939892 94939892 + synonymous_variant Silent SNP C C T novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 64 21 c.441G>A p.Gly147= p.G147= ENST00000342697.5 NM_033285.4 147 ggG/ggA 3/4 P1 T G protein_coding YES CCDS6265.1 441/723 TCAGTCCCACG PANTHER:PTHR31671;PANTHER:PTHR31671:SF0;Pfam:PF14839 ENSP00000344215 3/4 ENST00000342697 Transcript ENSG00000164938 HGNC:18022 LOW NM_033285.4 synonymous_variant 1.0 Unknown Q96A56.130 TP53INP1 HGNC -1 A0A024R9C8.35 1.0 UPI00000725F8 Q96A56-1 SNV TP53INP1,synonymous_variant,p.G147=,ENST00000448464,NM_001135733.2,c.441G>A,LOW,,,,-1;TP53INP1,synonymous_variant,p.G147=,ENST00000342697,NM_033285.4,c.441G>A,LOW,YES,,,-1;NDUFAF6,intron_variant,,ENST00000396113,,c.-935-5591C>T,MODIFIER,,,,1;NDUFAF6,intron_variant,,ENST00000519136,NM_001354534.1,c.-440-18103C>T,MODIFIER,,,,1;NDUFAF6,intron_variant,,ENST00000523378,,c.-387-18103C>T,MODIFIER,,,,1 816/5605 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 72 01ccaec6-9392-406c-a2df-b33124c6e240 85 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS TP53INP1,synonymous_variant,p.G147=,ENST00000342697.5,c.441G>A,LOW,YES;TP53INP1,synonymous_variant,p.G147=,ENST00000448464.6,c.441G>A,LOW,;NDUFAF6,intron_variant,,ENST00000519136.5,c.-440-18103C>T,MODIFIER,;NDUFAF6,intron_variant,,ENST00000697356.1,n.107-5591C>T,MODIFIER,;NDUFAF6,intron_variant,,ENST00000396113.5,c.-935-5591C>T,MODIFIER,;NDUFAF6,intron_variant,,ENST00000523378.5,c.-387-18103C>T,MODIFIER,;NDUFAF6,intron_variant,NMD_transcript_variant,,ENST00000697355.1,c.-387-18103C>T,MODIFIER,;NDUFAF6,intron_variant,,ENST00000697354.1,n.347-18103C>T,MODIFIER,;NDUFAF6,intron_variant,,ENST00000521840.2,n.396-18103C>T,MODIFIER, +NFX1 4799 BI GRCh38 9 33301355 33301355 + missense_variant Missense_Mutation SNP A A T novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 85 29 c.1126A>T p.Ser376Cys p.S376C ENST00000379540.8 NM_001318758.2 376 Agc/Tgc 3/24 P1 T S/C protein_coding YES CCDS6538.1 1126/3363 GTCAGAGCTGT PROSITE_patterns:PS01359;PROSITE_profiles:PS50016;PROSITE_profiles:PS50089;PANTHER:PTHR12360;PANTHER:PTHR12360:SF0;SMART:SM00184;Superfamily:SSF57850;CDD:cd16696 ENSP00000368856 3/24 ENST00000379540 Transcript ENSG00000086102 HGNC:7803 MODERATE NM_002504.6 missense_variant 1.0 benign(0.067) Unknown deleterious(0.01) Q12986.192 NFX1 HGNC 1 1.0 UPI0000072140 Q12986-1 SNV NFX1,missense_variant,p.S376C,ENST00000379540,NM_001318758.2&NM_002504.6,c.1126A>T,MODERATE,YES,deleterious(0.01),benign(0.067),1;NFX1,missense_variant,p.S376C,ENST00000318524,NM_147134.4,c.1126A>T,MODERATE,,deleterious(0),benign(0.244),1;NFX1,non_coding_transcript_exon_variant,,ENST00000379521,,n.1187A>T,MODIFIER,,,,1 1183/4599 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 121 01ccaec6-9392-406c-a2df-b33124c6e240 114 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS NFX1,missense_variant,p.S376C,ENST00000318524.6,c.1126A>T,MODERATE,;NFX1,missense_variant,p.S376C,ENST00000379540.8,c.1126A>T,MODERATE,YES;NFX1,non_coding_transcript_exon_variant,,ENST00000379521.8,n.1187A>T,MODIFIER, +ASB6 140459 BI GRCh38 9 129637917 129637917 + missense_variant Missense_Mutation SNP C C T rs371398374 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 12 17 c.1139G>A p.Arg380His p.R380H ENST00000277458.5 NM_017873.4 380 cGt/cAt 6/6 P1 T R/H protein_coding YES CCDS6924.1 1139/1266 CCACACGGCAC PROSITE_profiles:PS50225;CDD:cd03725;PANTHER:PTHR24132;PANTHER:PTHR24132:SF17;Pfam:PF07525;Gene3D:1.10.750.20;SMART:SM00969;SMART:SM00253;Superfamily:SSF158235 ENSP00000277458 0.0 0.0001163 6/6 rs371398374 ENST00000277458 Transcript ENSG00000148331 HGNC:17181 MODERATE NM_017873.4 0.000127 gnomAD_ASJ missense_variant 1.0 probably_damaging(0.928) Unknown deleterious_low_confidence(0) Q9NWX5.156 ASB6 HGNC -1 1.0 UPI000004A09F Q9NWX5-1 SNV ASB6,missense_variant,p.R380H,ENST00000277458,NM_017873.4,c.1139G>A,MODERATE,YES,deleterious_low_confidence(0),probably_damaging(0.928),-1;ASB6,missense_variant,p.R351H,ENST00000450050,NM_001202403.1,c.1052G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;ASB6,3_prime_UTR_variant,,ENST00000277459,NM_177999.3,c.*436G>A,MODIFIER,,,,-1;NTMT1,downstream_gene_variant,,ENST00000372480,NM_001286799.1,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000372481,NM_001286801.1&NM_001286800.1,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000372483,NM_014064.4,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000372486,NM_001286796.1,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000459968,,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000482347,,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000611055,NM_001286798.1,,MODIFIER,YES,,,1;NTMT1,downstream_gene_variant,,ENST00000613644,NM_001286797.1,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000617943,NM_001286802.1&NM_001286803.1,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000486391,,,MODIFIER,,,,1;NTMT1,downstream_gene_variant,,ENST00000481189,,,MODIFIER,,,,1;AL590369.1,upstream_gene_variant,,ENST00000455074,,,MODIFIER,YES,,,1 1291/4603 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 1.312e-05 0.0 0.0 0.000127 0.0 0.0 1.942e-05 0.0 0.0 0 62 01ccaec6-9392-406c-a2df-b33124c6e240 30 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS ASB6,3_prime_UTR_variant,,ENST00000277459.8,c.*436G>A,MODIFIER,;ASB6,missense_variant,p.R380H,ENST00000277458.5,c.1139G>A,MODERATE,YES;ASB6,missense_variant,p.R351H,ENST00000450050.6,c.1052G>A,MODERATE, +CYSLTR2 57105 BI GRCh38 13 48707203 48707203 + missense_variant Missense_Mutation SNP T T A TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 150 111 c.386T>A p.Leu129Gln p.L129Q ENST00000282018.4 NM_001308471.3 129 cTg/cAg 1/1 P1 A L/Q protein_coding YES CCDS9412.1 386/1041 TTTCCTGACCG COSM1666392 Gene3D:1.20.1070.10;PDB-ENSP_mappings:6rz6.A;PDB-ENSP_mappings:6rz7.A;PDB-ENSP_mappings:6rz8.A;PDB-ENSP_mappings:6rz9.A;Pfam:PF00001;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR24230;PANTHER:PTHR24230:SF10;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15157 ENSP00000282018 1/1 COSV56166671 ENST00000282018 Transcript 1.0 ENSG00000152207 HGNC:18274 MODERATE missense_variant 1 1.0 probably_damaging(0.997) Unknown deleterious(0) 1 Q9NS75.162 CYSLTR2 HGNC 1 Q5KU17.121 UPI000003BCCC SNV CYSLTR2,missense_variant,p.L129Q,ENST00000282018,NM_001308471.3,c.386T>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),1;CYSLTR2,missense_variant,p.L129Q,ENST00000614739,NM_001308465.3&NM_001308476.3&NM_001308468.3&NM_001308467.3&NM_020377.5&NM_001308469.3&NM_001308470.3,c.386T>A,MODERATE,,deleterious(0),probably_damaging(0.997),1;CYSLTR2,downstream_gene_variant,,ENST00000617562,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000621321,,,MODIFIER,,,,1;CYSLTR2,downstream_gene_variant,,ENST00000622559,,,MODIFIER,,,,1 649/4672 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 181 01ccaec6-9392-406c-a2df-b33124c6e240 261 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS CYSLTR2,missense_variant,p.L129Q,ENST00000282018.4,c.386T>A,MODERATE,;CYSLTR2,missense_variant,p.L129Q,ENST00000682523.1,c.386T>A,MODERATE,YES;CYSLTR2,missense_variant,p.L129Q,ENST00000614739.4,c.386T>A,MODERATE, +SPRY2 10253 BI GRCh38 13 80337656 80337656 + missense_variant Missense_Mutation SNP G G A rs372480996 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 49 48 c.50C>T p.Thr17Met p.T17M ENST00000377102.5 NM_001318538.1 17 aCg/aTg 2/2 P1 A T/M protein_coding YES CCDS9463.1 50/948 GGGGCGTCTGC PANTHER:PTHR12365;PANTHER:PTHR12365:SF8;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000366306 0.000227 0.0 2/2 rs372480996 ENST00000377102 Transcript 1.0 ENSG00000136158 HGNC:11270 MODERATE 0.0002464 gnomAD_AFR missense_variant 1.0 benign(0) Unknown tolerated(0.18) O43597.178 SPRY2 HGNC -1 1.0 UPI0000001301 SNV SPRY2,missense_variant,p.T17M,ENST00000377102,NM_001318538.1&NM_001318537.1,c.50C>T,MODERATE,YES,tolerated(0.18),benign(0),-1;SPRY2,missense_variant,p.T17M,ENST00000377104,NM_005842.4&NM_001318536.1,c.50C>T,MODERATE,,tolerated(0.18),benign(0),-1 1028/2708 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 1.595e-05 0.0002464 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 102 01ccaec6-9392-406c-a2df-b33124c6e240 97 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS SPRY2,missense_variant,p.T17M,ENST00000377104.4,c.50C>T,MODERATE,YES;SPRY2,missense_variant,p.T17M,ENST00000377102.5,c.50C>T,MODERATE, +ATOSA 56204 BI GRCh38 15 52611146 52611146 + stop_gained Nonsense_Mutation SNP G G A rs1371724805 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 70 15 c.514C>T p.Arg172Ter p.R172* ENST00000619572.5 NM_001385015.1 172 Cga/Tga 5/13 P4 A R/* protein_coding CCDS45263.1 514/3231 ATTTCGTGGAA PANTHER:PTHR13199:SF13;PANTHER:PTHR13199 ENSP00000261844 5/13 rs1371724805 ENST00000261844 Transcript ENSG00000047346 HGNC:25609 HIGH 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS stop_gained Unknown Q32MH5.101 FAM214A HGNC -1 1.0 UPI00001C1F8D Q32MH5-1 SNV FAM214A,stop_gained,p.R172*,ENST00000261844,NM_019600.3,c.514C>T,HIGH,,,,-1;FAM214A,stop_gained,p.R179*,ENST00000546305,NM_001286495.2,c.535C>T,HIGH,YES,,,-1;FAM214A,stop_gained,p.R172*,ENST00000619572,,c.514C>T,HIGH,,,,-1;FAM214A,stop_gained,p.R84*,ENST00000399202,,c.250C>T,HIGH,,,,-1;FAM214A,downstream_gene_variant,,ENST00000561490,,,MODIFIER,,,,-1;FAM214A,downstream_gene_variant,,ENST00000561543,,,MODIFIER,,,,-1;FAM214A,downstream_gene_variant,,ENST00000562135,,,MODIFIER,,,,-1;FAM214A,downstream_gene_variant,,ENST00000566768,,,MODIFIER,,,,-1;FAM214A,downstream_gene_variant,,ENST00000568863,,,MODIFIER,,,,-1;FAM214A,stop_gained,p.R172*,ENST00000534964,,c.514C>T,HIGH,,,,-1;FAM214A,upstream_gene_variant,,ENST00000566948,,,MODIFIER,,,,-1 667/4217 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 86 01ccaec6-9392-406c-a2df-b33124c6e240 85 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS ATOSA,stop_gained,p.R84*,ENST00000399202.8,c.250C>T,HIGH,;ATOSA,stop_gained,p.R179*,ENST00000546305.6,c.535C>T,HIGH,;ATOSA,stop_gained,p.R172*,ENST00000261844.11,c.514C>T,HIGH,;ATOSA,stop_gained,p.R172*,ENST00000619572.5,c.514C>T,HIGH,YES;ATOSA,stop_gained,NMD_transcript_variant,p.R172*,ENST00000534964.6,c.514C>T,HIGH, +MARF1 9665 BI GRCh38 16 15596756 15596756 + missense_variant Missense_Mutation SNP C C G novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 29 53 c.5166G>C p.Lys1722Asn p.K1722N ENST00000396368.8 NM_014647.4 1722 aaG/aaC 27/27 P5 G K/N protein_coding YES CCDS10562.2 5166/5229 GGTTGCTTTTT MobiDB_lite:mobidb-lite ENSP00000379654 27/27 ENST00000396368 Transcript ENSG00000166783 HGNC:29562 MODERATE NM_014647.4 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q9Y4F3.155 MARF1 HGNC -1 1.0 UPI00006881BC Q9Y4F3-1 SNV MARF1,missense_variant,p.K1722N,ENST00000396368,NM_014647.4,c.5166G>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;MARF1,missense_variant,p.K1557N,ENST00000540441,,c.4671G>C,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;MARF1,missense_variant,p.K1722N,ENST00000551742,NM_001184998.2,c.5166G>C,MODERATE,,deleterious(0.01),probably_damaging(0.999),-1;MARF1,missense_variant,p.K1719N,ENST00000548025,NM_001184999.2,c.5157G>C,MODERATE,,deleterious(0),possibly_damaging(0.552),-1;BMERB1,intron_variant,,ENST00000565857,,c.*12+5641C>G,MODIFIER,,,,1;MARF1,3_prime_UTR_variant,,ENST00000552553,,c.*1876G>C,MODIFIER,,,,-1;MARF1,3_prime_UTR_variant,,ENST00000551878,,c.*420G>C,MODIFIER,,,,-1;MARF1,non_coding_transcript_exon_variant,,ENST00000552771,,n.1789G>C,MODIFIER,,,,-1;MARF1,downstream_gene_variant,,ENST00000549337,,,MODIFIER,,,,-1;MARF1,downstream_gene_variant,,ENST00000551579,,,MODIFIER,,,,-1 5361/7730 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 100 01ccaec6-9392-406c-a2df-b33124c6e240 82 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS MARF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000552553.5,c.*1876G>C,MODIFIER,;MARF1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000551878.1,c.*420G>C,MODIFIER,;MARF1,missense_variant,p.K1722N,ENST00000551742.5,c.5166G>C,MODERATE,;MARF1,missense_variant,p.K1719N,ENST00000548025.5,c.5157G>C,MODERATE,;MARF1,non_coding_transcript_exon_variant,,ENST00000552771.5,n.1789G>C,MODIFIER,;MARF1,missense_variant,p.K1722N,ENST00000396368.8,c.5166G>C,MODERATE,YES;MARF1,missense_variant,p.K1557N,ENST00000540441.6,c.4671G>C,MODERATE,;BMERB1,intron_variant,,ENST00000565857.1,c.*12+5641C>G,MODIFIER, +BAHCC1 57597 BI GRCh38 17 81444745 81444745 + missense_variant Missense_Mutation SNP T T A novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 21 18 c.2590T>A p.Phe864Ile p.F864I ENST00000584436.7 NM_001291324.3 864 Ttc/Atc 8/29 P4 A F/I protein_coding YES CCDS74173.1 2590/7920 CTGTCTTCCCC PANTHER:PTHR12505;PANTHER:PTHR12505:SF22 ENSP00000462154 8/29 ENST00000584436 Transcript ENSG00000266074 HGNC:29279 MODERATE missense_variant 1.0 possibly_damaging(0.839) Unknown deleterious(0.01) Q9P281.116 BAHCC1 HGNC 1 5.0 UPI0003EAE637 SNV BAHCC1,missense_variant,p.F864I,ENST00000584436,NM_001291324.3,c.2590T>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.839),1;BAHCC1,missense_variant,p.F864I,ENST00000675386,NM_001377448.1,c.2590T>A,MODERATE,,deleterious(0.01),possibly_damaging(0.759),1;BAHCC1,missense_variant,p.F864I,ENST00000307745,,c.2590T>A,MODERATE,,deleterious(0.01),possibly_damaging(0.759),1;BAHCC1,downstream_gene_variant,,ENST00000585224,,,MODIFIER,,,,1 2957/10801 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 42 01ccaec6-9392-406c-a2df-b33124c6e240 39 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS BAHCC1,missense_variant,p.F864I,ENST00000584436.7,c.2590T>A,MODERATE,;BAHCC1,missense_variant,p.F864I,ENST00000675386.2,c.2590T>A,MODERATE,YES +TBCD 6904 BI GRCh38 17 82870293 82870293 + missense_variant Missense_Mutation SNP T T C novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 31 25 c.1388T>C p.Val463Ala p.V463A ENST00000355528.9 NM_005993.5 463 gTc/gCc 14/39 P2 C V/A protein_coding CCDS45818.1 1388/3579 CAACGTCAGGG PANTHER:PTHR12658;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000347719 14/39 ENST00000355528 Transcript 1.0 ENSG00000141556 HGNC:11581 MODERATE NM_005993.5 missense_variant possibly_damaging(0.459) Unknown deleterious(0) Q9BTW9.162 TBCD HGNC 1 1.0 UPI000020053F Q9BTW9-1 SNV TBCD,missense_variant,p.V463A,ENST00000355528,NM_005993.5,c.1388T>C,MODERATE,,deleterious(0),possibly_damaging(0.459),1;TBCD,missense_variant,p.V463A,ENST00000539345,,c.1388T>C,MODERATE,YES,deleterious(0),probably_damaging(0.933),1;TBCD,5_prime_UTR_variant,,ENST00000576160,,c.-299T>C,MODIFIER,,,,1;TBCD,5_prime_UTR_variant,,ENST00000571712,,c.-356T>C,MODIFIER,,,,1;TBCD,5_prime_UTR_variant,,ENST00000576996,,c.-299T>C,MODIFIER,,,,1;TBCD,non_coding_transcript_exon_variant,,ENST00000574801,,n.207T>C,MODIFIER,,,,1 1517/7159 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 60 01ccaec6-9392-406c-a2df-b33124c6e240 57 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS TBCD,non_coding_transcript_exon_variant,,ENST00000682099.1,n.285T>C,MODIFIER,;TBCD,non_coding_transcript_exon_variant,,ENST00000683584.1,n.211T>C,MODIFIER,;TBCD,non_coding_transcript_exon_variant,,ENST00000574801.5,n.207T>C,MODIFIER,;TBCD,5_prime_UTR_variant,,ENST00000576996.5,c.-299T>C,MODIFIER,;TBCD,5_prime_UTR_variant,,ENST00000571712.5,c.-356T>C,MODIFIER,;TBCD,5_prime_UTR_variant,,ENST00000576160.6,c.-299T>C,MODIFIER,;TBCD,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000682654.1,c.-299T>C,MODIFIER,;TBCD,5_prime_UTR_variant,,ENST00000683821.1,c.-299T>C,MODIFIER,;TBCD,non_coding_transcript_exon_variant,,ENST00000682610.1,n.628T>C,MODIFIER,;TBCD,missense_variant,p.V439A,ENST00000684429.1,c.1316T>C,MODERATE,;TBCD,missense_variant,p.V400A,ENST00000684188.1,c.1199T>C,MODERATE,;TBCD,missense_variant,p.V491A,ENST00000684000.1,c.1472T>C,MODERATE,;TBCD,missense_variant,p.V463A,ENST00000539345.6,c.1388T>C,MODERATE,;TBCD,missense_variant,p.V463A,ENST00000684349.1,c.1388T>C,MODERATE,;TBCD,missense_variant,NMD_transcript_variant,p.V463A,ENST00000682213.1,c.1388T>C,MODERATE,;TBCD,non_coding_transcript_exon_variant,,ENST00000683009.1,n.1508T>C,MODIFIER,;TBCD,missense_variant,NMD_transcript_variant,p.V463A,ENST00000683041.1,c.1388T>C,MODERATE,;TBCD,missense_variant,p.V463A,ENST00000684760.1,c.1388T>C,MODERATE,;TBCD,non_coding_transcript_exon_variant,,ENST00000682921.1,n.1310T>C,MODIFIER,;TBCD,synonymous_variant,NMD_transcript_variant,p.R431=,ENST00000684776.1,c.1293T>C,LOW,;TBCD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000683444.1,c.*965T>C,MODIFIER,;TBCD,missense_variant,p.V463A,ENST00000355528.9,c.1388T>C,MODERATE,YES;TBCD,missense_variant,p.V463A,ENST00000684408.1,c.1388T>C,MODERATE,;TBCD,missense_variant,p.V463A,ENST00000683282.1,c.1388T>C,MODERATE,;TBCD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000683184.1,c.*1041T>C,MODIFIER,;TBCD,missense_variant,NMD_transcript_variant,p.V463A,ENST00000684361.1,c.1388T>C,MODERATE,;TBCD,non_coding_transcript_exon_variant,,ENST00000681983.1,n.1524T>C,MODIFIER,;TBCD,missense_variant,p.V463A,ENST00000684544.1,c.1388T>C,MODERATE,;TBCD,missense_variant,p.V463A,ENST00000684464.1,c.1388T>C,MODERATE,;TBCD,missense_variant,p.V446A,ENST00000682722.1,c.1337T>C,MODERATE,;TBCD,missense_variant,p.V493A,ENST00000682479.1,c.1478T>C,MODERATE, +MUC16 94025 BI GRCh38 19 8972656 8972656 + missense_variant Missense_Mutation SNP G G A rs1214516805 TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 13 5 c.8483C>T p.Ala2828Val p.A2828V ENST00000397910.8 NM_024690.2 2828 gCc/gTc 1/84 P1 A A/V protein_coding YES CCDS54212.1 8483/43524 ACATGGCTGTA ENSP00000381008 1/84 rs1214516805 ENST00000397910 Transcript 1.0 ENSG00000181143 HGNC:15582 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.866) Unknown deleterious_low_confidence(0) Q8WXI7.134 MUC16 HGNC -1 5.0 UPI000065CA24 SNV MUC16,missense_variant,p.A2828V,ENST00000397910,NM_024690.2,c.8483C>T,MODERATE,YES,deleterious_low_confidence(0),possibly_damaging(0.866),-1 8687/43816 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 38 01ccaec6-9392-406c-a2df-b33124c6e240 18 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS MUC16,missense_variant,p.A2828V,ENST00000397910.8,c.8483C>T,MODERATE,;MUC16,missense_variant,p.A2868V,ENST00000711672.1,c.8603C>T,MODERATE,YES;MUC16,missense_variant,p.A2868V,ENST00000710609.1,c.8603C>T,MODERATE,;MUC16,intron_variant,,ENST00000710610.1,c.302-2777C>T,MODIFIER, +PPP2R1A 5518 BI GRCh38 19 52221002 52221002 + missense_variant Missense_Mutation SNP A A C novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 25 19 c.1387A>C p.Thr463Pro p.T463P ENST00000322088.11 NM_014225.6 463 Acc/Ccc 12/15 P1 C T/P protein_coding YES CCDS12849.1 1387/1770 CAGCCACCAGC PDB-ENSP_mappings:1b3u.A;PDB-ENSP_mappings:1b3u.B;PDB-ENSP_mappings:2ie3.A;PDB-ENSP_mappings:2ie4.A;PDB-ENSP_mappings:2npp.A;PDB-ENSP_mappings:2npp.D;PDB-ENSP_mappings:2nyl.A;PDB-ENSP_mappings:2nyl.D;PDB-ENSP_mappings:2nym.A;PDB-ENSP_mappings:2nym.D;PDB-ENSP_mappings:2pkg.A;PDB-ENSP_mappings:2pkg.B;PDB-ENSP_mappings:3c5w.A;PDB-ENSP_mappings:3dw8.A;PDB-ENSP_mappings:3dw8.D;PDB-ENSP_mappings:3k7v.A;PDB-ENSP_mappings:3k7w.A;PDB-ENSP_mappings:4i5l.A;PDB-ENSP_mappings:4i5l.D;PDB-ENSP_mappings:4i5n.A;PDB-ENSP_mappings:4i5n.D;PDB-ENSP_mappings:4lac.A;PDB-ENSP_mappings:5w0w.A;PDB-ENSP_mappings:5w0w.D;PDB-ENSP_mappings:5w0w.G;PDB-ENSP_mappings:5w0w.J;PDB-ENSP_mappings:6iur.A;PDB-ENSP_mappings:6iur.B;PDB-ENSP_mappings:6iur.E;PDB-ENSP_mappings:6iur.F;PDB-ENSP_mappings:6nts.A;PANTHER:PTHR10648;PANTHER:PTHR10648:SF2;Pfam:PF13646;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000324804 12/15 ENST00000322088 Transcript 1.0 ENSG00000105568 HGNC:9302 MODERATE NM_014225.6 missense_variant 1.0 benign(0.027) Unknown deleterious(0) P30153.210 PPP2R1A HGNC 1 A8K7B7.111 1.0 UPI000006EB9C SNV PPP2R1A,missense_variant,p.T463P,ENST00000322088,NM_014225.6,c.1387A>C,MODERATE,YES,deleterious(0),benign(0.027),1;PPP2R1A,missense_variant,p.T284P,ENST00000462990,NM_001363656.2,c.850A>C,MODERATE,,deleterious(0),benign(0.027),1;PPP2R1A,missense_variant,p.T8P,ENST00000391791,,c.22A>C,MODERATE,,deleterious(0),probably_damaging(0.982),1;PPP2R1A,downstream_gene_variant,,ENST00000454220,,,MODIFIER,,,,1;MIR6801,upstream_gene_variant,,ENST00000614975,,,MODIFIER,YES,,,1;PPP2R1A,downstream_gene_variant,,ENST00000473820,,,MODIFIER,,,,1;AC010320.2,downstream_gene_variant,,ENST00000593857,,,MODIFIER,,,,-1 1432/5352 muse;mutect2;varscan2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 81 01ccaec6-9392-406c-a2df-b33124c6e240 44 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS PPP2R1A,missense_variant,p.H7P,ENST00000391791.4,c.20A>C,MODERATE,;PPP2R1A,intron_variant,NMD_transcript_variant,,ENST00000703401.1,c.312-1109A>C,MODIFIER,;PPP2R1A,missense_variant,p.T284P,ENST00000462990.5,c.850A>C,MODERATE,;PPP2R1A,missense_variant,p.T284P,ENST00000703423.1,c.850A>C,MODERATE,;PPP2R1A,missense_variant,p.T477P,ENST00000703398.1,c.1429A>C,MODERATE,;PPP2R1A,missense_variant,p.T284P,ENST00000703397.1,c.850A>C,MODERATE,;PPP2R1A,missense_variant,p.T463P,ENST00000322088.11,c.1387A>C,MODERATE,YES;PPP2R1A,missense_variant,p.T503P,ENST00000454220.7,c.1507A>C,MODERATE,;PPP2R1A,missense_variant,p.T455P,ENST00000703422.1,c.1363A>C,MODERATE,;PPP2R1A,missense_variant,p.T284P,ENST00000703395.1,c.850A>C,MODERATE, +MIR450A1 554214 BI GRCh38 X 134540356 134540356 + mature_miRNA_variant mature_miRNA_variant SNP C C A novel TCGA-YZ-A982-01A TCGA-YZ-A982-10A Somatic 55 4 n.76G>T ENST00000362262.1 1/1 A miRNA YES CAAAACTATAC 1/1 ENST00000362262 Transcript ENSG00000199132 HGNC:28008 MODIFIER non_coding_transcript_exon_variant Unknown MIR450A1 HGNC -1 SNV MIR450A1,non_coding_transcript_exon_variant,,ENST00000362262,,n.76G>T,MODIFIER,YES,,,-1;MIR450A2,downstream_gene_variant,,ENST00000385022,,,MODIFIER,YES,,,-1;MIR542,downstream_gene_variant,,ENST00000385050,,,MODIFIER,YES,,,-1;MIR450B,upstream_gene_variant,,ENST00000401182,,,MODIFIER,YES,,,-1;MIR503HG,downstream_gene_variant,,ENST00000414769,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000440570,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000441492,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000445415,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000457876,,,MODIFIER,YES,,,-1;MIR503HG,downstream_gene_variant,,ENST00000655068,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000659680,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000666697,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000670930,,,MODIFIER,,,,-1;MIR503HG,downstream_gene_variant,,ENST00000673627,,,MODIFIER,,,,-1 76/91 muse;mutect2 cba920f4-c57f-47bc-958d-9b7872df01c8 0 miRNA_stem 96 01ccaec6-9392-406c-a2df-b33124c6e240 59 a426df42-beb7-48c7-b7b9-174e95772cf9 SUCCESS MIR450A1,mature_miRNA_variant,,ENST00000362262.1,n.76G>T,MODIFIER,YES +VAV3 10451 BI GRCh38 1 107574154 107574154 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 41 27 c.2395T>A p.Phe799Ile p.F799I ENST00000370056.9 NM_006113.5 799 Ttc/Atc 26/27 P1 T F/I protein_coding CCDS785.1 2395/2544 ACAGAAGTCAT CDD:cd11978;Gene3D:2.30.30.40;Pfam:PF07653;SMART:SM00326;Superfamily:SSF50044;Superfamily:SSF55550;PROSITE_profiles:PS50002;PANTHER:PTHR45818:SF1;PANTHER:PTHR45818;Prints:PR00452 ENSP00000359073 26/27 ENST00000370056 Transcript ENSG00000134215 HGNC:12659 MODERATE NM_006113.5 missense_variant probably_damaging(0.996) Unknown deleterious(0) Q9UKW4.195 VAV3 HGNC -1 1.0 UPI0000138212 Q9UKW4-1 SNV VAV3,missense_variant,p.F799I,ENST00000370056,NM_006113.5,c.2395T>A,MODERATE,,deleterious(0),probably_damaging(0.996),-1;VAV3,missense_variant,p.F827I,ENST00000527011,,c.2479T>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;VAV3,missense_variant,p.F239I,ENST00000415432,NM_001079874.2,c.715T>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;VAV3,non_coding_transcript_exon_variant,,ENST00000343258,,n.2241T>A,MODIFIER,,,,-1;VAV3,non_coding_transcript_exon_variant,,ENST00000525460,,n.893T>A,MODIFIER,,,,-1;VAV3,3_prime_UTR_variant,,ENST00000529413,,c.*510T>A,MODIFIER,,,,-1 2706/5025 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 69 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 68 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS VAV3,non_coding_transcript_exon_variant,,ENST00000343258.8,n.2241T>A,MODIFIER,;VAV3,missense_variant,p.F239I,ENST00000415432.6,c.715T>A,MODERATE,;VAV3,non_coding_transcript_exon_variant,,ENST00000525460.5,n.893T>A,MODIFIER,;VAV3,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000529413.5,c.*510T>A,MODIFIER,;VAV3,missense_variant,p.F827I,ENST00000527011.5,c.2479T>A,MODERATE,;VAV3,missense_variant,p.F799I,ENST00000370056.9,c.2395T>A,MODERATE,YES +CR1L 1379 BI GRCh38 1 207677402 207677402 + synonymous_variant Silent SNP C C T novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 51 42 c.111C>T p.Val37= p.V37= ENST00000508064.7 NM_175710.2 37 gtC/gtT 2/12 P1 T V protein_coding YES CCDS44310.1 111/1710 AATGTCCCGGA Gene3D:2.10.70.10;Pfam:PF00084;PROSITE_profiles:PS50923;PANTHER:PTHR19325;PANTHER:PTHR19325:SF505;SMART:SM00032;Superfamily:SSF57535 ENSP00000421736 2/12 ENST00000508064 Transcript ENSG00000197721 HGNC:2335 LOW NM_175710.2 synonymous_variant 1.0 Unknown Q2VPA4.118 CR1L HGNC 1 1.0 UPI0000DD792A Q2VPA4-1 SNV CR1L,synonymous_variant,p.V37=,ENST00000508064,NM_175710.2,c.111C>T,LOW,YES,,,1;CR1L,non_coding_transcript_exon_variant,,ENST00000530905,,n.141C>T,MODIFIER,,,,1;CR1L,non_coding_transcript_exon_variant,,ENST00000430248,,n.115C>T,MODIFIER,,,,1;CR1L,non_coding_transcript_exon_variant,,ENST00000531844,,n.232C>T,MODIFIER,,,,1;CR1L,upstream_gene_variant,,ENST00000294997,,,MODIFIER,,,,1 212/1829 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 70 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 93 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS CR1L,non_coding_transcript_exon_variant,,ENST00000530905.1,n.141C>T,MODIFIER,;CR1L,non_coding_transcript_exon_variant,,ENST00000430248.5,n.115C>T,MODIFIER,;CR1L,synonymous_variant,p.V37=,ENST00000508064.7,c.111C>T,LOW,YES;CR1L,non_coding_transcript_exon_variant,,ENST00000531844.5,n.232C>T,MODIFIER, +TTN 7273 BI GRCh38 2 178581924 178581924 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 26 18 c.61522T>G p.Tyr20508Asp p.Y20508D ENST00000591111.5 20508 Tat/Gat 265/313 C Y/D protein_coding 61522/103053 AGCATAAGCGG Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR13817;PANTHER:PTHR13817:SF10;Superfamily:SSF49265 ENSP00000465570 265/313 ENST00000591111 Transcript 1.0 ENSG00000155657 HGNC:12403 MODERATE missense_variant possibly_damaging(0.656) Unknown Q8WZ42.192 TTN HGNC -1 5.0 UPI00025287CD Q8WZ42-1 SNV TTN,missense_variant,p.Y22149D,ENST00000589042,NM_001267550.2,c.66445T>G,MODERATE,YES,,possibly_damaging(0.656),-1;TTN,missense_variant,p.Y20508D,ENST00000591111,,c.61522T>G,MODERATE,,,possibly_damaging(0.656),-1;TTN,missense_variant,p.Y19581D,ENST00000342992,NM_133378.4&NM_001256850.1,c.58741T>G,MODERATE,,,possibly_damaging(0.454),-1;TTN,missense_variant,p.Y13084D,ENST00000460472,NM_003319.4,c.39250T>G,MODERATE,,,benign(0.011),-1;TTN,missense_variant,p.Y13276D,ENST00000342175,NM_133437.4,c.39826T>G,MODERATE,,,,-1;TTN,missense_variant,p.Y13209D,ENST00000359218,NM_133432.3,c.39625T>G,MODERATE,,,possibly_damaging(0.454),-1;TTN-AS1,intron_variant,,ENST00000419746,,n.2044-648A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000438095,,n.345-648A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000456053,,n.563+10475A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000585451,,n.198+58288A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586452,,n.225-9215A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586707,,n.346-1789A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586831,,n.215-648A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590773,,n.598-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590807,,n.75-1600A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590932,,n.616-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000591332,,n.443-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592600,,n.346-2649A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592630,,n.434-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592689,,n.463-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592750,,n.346-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625480,,n.50-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625536,,n.22-9215A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626117,,n.75-9215A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626138,,n.50-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626954,,n.75-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628296,,n.50-9215A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628826,,n.49+53111A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000630096,,n.552-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000653807,,n.220-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000657023,,n.119-15672A>C,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000659121,,n.417-15672A>C,MODIFIER,YES,,,1;TTN-AS1,upstream_gene_variant,,ENST00000589907,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000590743,,,MODIFIER,,,,1;AC010680.2,downstream_gene_variant,,ENST00000603521,,,MODIFIER,YES,,,1;AC010680.3,downstream_gene_variant,,ENST00000604215,,,MODIFIER,YES,,,1;TTN-AS1,upstream_gene_variant,,ENST00000626517,,,MODIFIER,,,,1;TTN-AS1,upstream_gene_variant,,ENST00000629117,,,MODIFIER,,,,1 61747/104301 muse;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 52 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 44 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS TTN-AS1,intron_variant,,ENST00000590932.5,n.616-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000438095.1,n.345-648A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625536.2,n.22-9215A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628826.2,n.49+53111A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626138.2,n.50-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625480.2,n.50-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628296.2,n.50-9215A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626954.2,n.75-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592689.5,n.463-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626117.2,n.75-9215A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590807.5,n.75-1600A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586452.5,n.225-9215A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586831.5,n.215-648A>C,MODIFIER,;TTN,missense_variant,p.Y19581D,ENST00000342992.11,c.58741T>G,MODERATE,;TTN,missense_variant,p.Y22121D,ENST00000425332.3,c.66361T>G,MODERATE,;TTN,missense_variant,p.Y20508D,ENST00000591111.5,c.61522T>G,MODERATE,;TTN,missense_variant,p.Y22149D,ENST00000589042.5,c.66445T>G,MODERATE,YES;TTN,missense_variant,p.Y22011D,ENST00000715174.1,c.66031T>G,MODERATE,;TTN,missense_variant,p.Y13276D,ENST00000342175.12,c.39826T>G,MODERATE,;TTN,missense_variant,p.Y13084D,ENST00000460472.6,c.39250T>G,MODERATE,;TTN,missense_variant,p.Y22057D,ENST00000436599.2,c.66169T>G,MODERATE,;TTN,missense_variant,p.Y13209D,ENST00000359218.11,c.39625T>G,MODERATE,;TTN,missense_variant,p.Y22097D,ENST00000446966.2,c.66289T>G,MODERATE,;TTN,missense_variant,p.Y21963D,ENST00000426232.6,c.65887T>G,MODERATE,;TTN,missense_variant,p.Y22149D,ENST00000412264.2,c.66445T>G,MODERATE,;TTN-AS1,intron_variant,,ENST00000657023.1,n.119-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000585451.5,n.198+58288A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000653807.1,n.220-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000591332.5,n.443-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592630.5,n.434-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592600.6,n.346-2649A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592750.5,n.346-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586707.6,n.346-1789A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590773.6,n.598-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000456053.5,n.563+10475A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000659121.1,n.417-15672A>C,MODIFIER,YES;TTN-AS1,intron_variant,,ENST00000702938.1,n.431-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000630096.2,n.552-15672A>C,MODIFIER,;TTN-AS1,intron_variant,,ENST00000419746.5,n.2044-648A>C,MODIFIER, +PCDH10 57575 BI GRCh38 4 133163050 133163050 + synonymous_variant Silent SNP T T C rs937490253 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 44 30 c.2871T>C p.Ser957= p.S957= ENST00000264360.7 NM_032961.3 957 tcT/tcC 4/5 P2 C S protein_coding YES CCDS34063.1 2871/3123 CCTTCTTTTGT COSM732573 PANTHER:PTHR24028;PANTHER:PTHR24028:SF0 ENSP00000264360 4/5 rs937490253;COSV52090649 ENST00000264360 Transcript ENSG00000138650 HGNC:13404 LOW NM_032961.3 1.76e-05 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q9P2E7.153 PCDH10 HGNC 1 X5D999.45 1.0 UPI0000161C61 Q9P2E7-1 SNV PCDH10,synonymous_variant,p.S957=,ENST00000264360,NM_032961.3,c.2871T>C,LOW,YES,,,1;PCDH10,non_coding_transcript_exon_variant,,ENST00000511112,,n.205T>C,MODIFIER,,,,1 3718/8510 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 7.958e-06 0.0 0.0 0.0 0.0 0.0 1.76e-05 0.0 0.0 1.3516600120055957e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.085850039497018e-05 0.0 3.085850039497018e-05 0.0 0.0 0 55 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 75 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS PCDH10,non_coding_transcript_exon_variant,,ENST00000511112.2,n.205T>C,MODIFIER,;PCDH10,synonymous_variant,p.S957=,ENST00000264360.7,c.2871T>C,LOW,YES +LIFR 3977 BI GRCh38 5 38496548 38496548 + synonymous_variant Silent SNP T T C rs183990367 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 45 39 c.1719A>G p.Val573= p.V573= ENST00000263409.8 NM_002310.6 573 gtA/gtG 13/20 0.0002 0.0 0.0 0.0 0.001 0.0 P1 C V protein_coding CCDS3927.1 1719/3294 CACGATACATT COSM449624;COSM449625 Gene3D:2.60.40.10;PROSITE_profiles:PS50853;PANTHER:PTHR23036;PANTHER:PTHR23036:SF105;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000263409 13/20 rs183990367;COSV54699447 ENST00000263409 Transcript 1.0 ENSG00000113594 HGNC:6597 LOW 0.001 EUR synonymous_variant 0;1 Unknown 0;1 P42702.188 LIFR HGNC -1 1.0 UPI000004CAC2 P42702-1 SNV LIFR,synonymous_variant,p.V573=,ENST00000453190,NM_001127671.2&NM_001364298.1&NM_001364297.1,c.1719A>G,LOW,YES,,,-1;LIFR,synonymous_variant,p.V573=,ENST00000263409,NM_002310.6,c.1719A>G,LOW,,,,-1;LIFR,non_coding_transcript_exon_variant,,ENST00000503088,,n.1882A>G,MODIFIER,,,,-1;LIFR,intron_variant,,ENST00000506003,,c.111-14A>G,MODIFIER,,,,-1 1882/10089 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 1.193e-05 0.0 2.891e-05 0.0 0.0 4.62e-05 8.797e-06 0.0 0.0 1.3513699741452e-05 0.0 0.0 6.62339007249102e-05 0.0 0.0 9.414419764652848e-05 0.0 0.0 0.0 0.0 0 75 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 84 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS LIFR,non_coding_transcript_exon_variant,,ENST00000503088.1,n.1882A>G,MODIFIER,;LIFR,intron_variant,NMD_transcript_variant,,ENST00000506003.5,c.111-14A>G,MODIFIER,;LIFR,synonymous_variant,p.V573=,ENST00000263409.8,c.1719A>G,LOW,;LIFR,synonymous_variant,p.V573=,ENST00000453190.7,c.1719A>G,LOW,YES +F12 2161 BI GRCh38 5 177404397 177404397 + missense_variant Missense_Mutation SNP T T A novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 21 12 c.817A>T p.Ile273Phe p.I273F ENST00000253496.4 NM_000505.4 273 Atc/Ttc 9/14 P1 A I/F protein_coding YES CCDS34302.1 817/1848 GCGGATGTCGT CDD:cd00108;Pfam:PF00051;Gene3D:2.40.20.10;PIRSF:PIRSF001146;SMART:SM00130;Superfamily:SSF57440;PROSITE_profiles:PS50070;PANTHER:PTHR24264;PANTHER:PTHR24264:SF46;PROSITE_patterns:PS00021;Prints:PR00018 ENSP00000253496 9/14 ENST00000253496 Transcript 1.0 ENSG00000131187 HGNC:3530 MODERATE NM_000505.4 missense_variant 1.0 benign(0.141) Unknown deleterious(0.04) P00748.232 F12 HGNC -1 1.0 UPI000048055F SNV F12,missense_variant,p.I273F,ENST00000253496,NM_000505.4,c.817A>T,MODERATE,YES,deleterious(0.04),benign(0.141),-1;GRK6,intron_variant,,ENST00000502598,,c.-45+871T>A,MODIFIER,,,,1;PFN3,upstream_gene_variant,,ENST00000358571,NM_001029886.3,,MODIFIER,YES,,,-1;GRK6,upstream_gene_variant,,ENST00000506296,,,MODIFIER,,,,1;F12,upstream_gene_variant,,ENST00000514943,,,MODIFIER,,,,-1;F12,non_coding_transcript_exon_variant,,ENST00000510358,,n.76A>T,MODIFIER,,,,-1;F12,non_coding_transcript_exon_variant,,ENST00000502854,,n.76A>T,MODIFIER,,,,-1;F12,non_coding_transcript_exon_variant,,ENST00000503736,,n.189A>T,MODIFIER,,,,-1;F12,upstream_gene_variant,,ENST00000504406,,,MODIFIER,,,,-1 854/2036 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 28 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 33 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS F12,non_coding_transcript_exon_variant,,ENST00000503736.1,n.189A>T,MODIFIER,;GRK6,intron_variant,,ENST00000502598.5,c.-45+871T>A,MODIFIER,;F12,non_coding_transcript_exon_variant,,ENST00000510358.5,n.76A>T,MODIFIER,;F12,non_coding_transcript_exon_variant,,ENST00000502854.5,n.76A>T,MODIFIER,;F12,missense_variant,p.I273F,ENST00000253496.4,c.817A>T,MODERATE,YES;F12,missense_variant,p.I273F,ENST00000696201.1,c.817A>T,MODERATE,;F12,non_coding_transcript_exon_variant,,ENST00000696195.1,n.3620A>T,MODIFIER,;F12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696194.1,c.*407A>T,MODIFIER,;F12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696193.1,c.*1187A>T,MODIFIER,;F12,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696192.1,c.*483A>T,MODIFIER,;F12,non_coding_transcript_exon_variant,,ENST00000696200.1,n.920A>T,MODIFIER, +EFHC1 114327 BI GRCh38 6 52454208 52454208 + synonymous_variant Silent SNP C C T rs752122624 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 113 18 c.837C>T p.His279= p.H279= ENST00000371068.11 NM_018100.4 279 caC/caT 5/11 P1 T H protein_coding CCDS4942.1 837/1923 GTCCACGAACG PROSITE_profiles:PS51336;PANTHER:PTHR12086;PANTHER:PTHR12086:SF9;Gene3D:2.30.29.170;Pfam:PF06565;SMART:SM00676 ENSP00000360107 5/11 rs752122624 ENST00000371068 Transcript 1.0 ENSG00000096093 HGNC:16406 LOW NM_018100.4 0.0001307 gnomAD_SAS synonymous_variant Unknown Q5JVL4.150 EFHC1 HGNC 1 B2CKC5.102 1.0 UPI0000141099 Q5JVL4-1 SNV EFHC1,synonymous_variant,p.H279=,ENST00000371068,NM_018100.4,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H260=,ENST00000538167,,c.780C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000637353,,c.837C>T,LOW,YES,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000636107,,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H171=,ENST00000635984,,c.513C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H168=,ENST00000636343,,c.504C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000635996,,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H260=,ENST00000636489,,c.780C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H269=,ENST00000636702,,c.807C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000637089,,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H260=,ENST00000636954,NM_001172420.2,c.780C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000637263,,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H171=,ENST00000635760,,c.513C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H183=,ENST00000636379,,c.549C>T,LOW,,,,1;EFHC1,downstream_gene_variant,,ENST00000638075,,,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000637849,,n.901C>T,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000637892,,n.1041C>T,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000636311,,n.731C>T,MODIFIER,,,,1;EFHC1,downstream_gene_variant,,ENST00000636253,,,MODIFIER,,,,1;EFHC1,synonymous_variant,p.H279=,ENST00000480623,,c.837C>T,LOW,,,,1;EFHC1,synonymous_variant,p.H1=,ENST00000637874,,c.3C>T,LOW,,,,1;EFHC1,3_prime_UTR_variant,,ENST00000635812,,c.*138C>T,MODIFIER,,,,1;EFHC1,3_prime_UTR_variant,,ENST00000635866,,c.*706C>T,MODIFIER,,,,1;EFHC1,3_prime_UTR_variant,,ENST00000637602,,c.*538C>T,MODIFIER,,,,1;EFHC1,3_prime_UTR_variant,,ENST00000636398,,c.*138C>T,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000637340,,n.2762C>T,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000635911,,n.2355C>T,MODIFIER,,,,1;EFHC1,non_coding_transcript_exon_variant,,ENST00000636616,,n.453C>T,MODIFIER,,,,1;EFHC1,downstream_gene_variant,,ENST00000637200,,,MODIFIER,,,,1 906/6849 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 1.989e-05 0.0 0.0 0.0 5.437e-05 0.0 0.0 0.0 0.0001307 0 78 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 131 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS EFHC1,synonymous_variant,splice_region_variant,NMD_transcript_variant,p.H1=,ENST00000637874.1,c.3C>T,LOW,;EFHC1,non_coding_transcript_exon_variant,,ENST00000636616.1,n.453C>T,MODIFIER,;EFHC1,missense_variant,p.T168M,ENST00000636343.1,c.503C>T,MODERATE,;EFHC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636398.1,c.*138C>T,MODIFIER,;EFHC1,synonymous_variant,p.H260=,ENST00000538167.2,c.780C>T,LOW,;EFHC1,synonymous_variant,p.H260=,ENST00000636954.1,c.780C>T,LOW,;EFHC1,synonymous_variant,p.H183=,ENST00000636379.1,c.549C>T,LOW,;EFHC1,non_coding_transcript_exon_variant,,ENST00000636311.1,n.731C>T,MODIFIER,;EFHC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000637602.1,c.*538C>T,MODIFIER,;EFHC1,synonymous_variant,p.H279=,ENST00000635996.1,c.837C>T,LOW,;EFHC1,synonymous_variant,p.H269=,ENST00000636702.1,c.807C>T,LOW,;EFHC1,synonymous_variant,p.H279=,ENST00000636107.1,c.837C>T,LOW,;EFHC1,synonymous_variant,p.H279=,ENST00000371068.11,c.837C>T,LOW,YES;EFHC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000635812.1,c.*138C>T,MODIFIER,;EFHC1,synonymous_variant,p.H279=,ENST00000637263.1,c.837C>T,LOW,;EFHC1,synonymous_variant,NMD_transcript_variant,p.H279=,ENST00000480623.6,c.837C>T,LOW,;EFHC1,synonymous_variant,p.H279=,ENST00000637353.1,c.837C>T,LOW,;EFHC1,synonymous_variant,p.H279=,ENST00000637089.1,c.837C>T,LOW,;EFHC1,non_coding_transcript_exon_variant,,ENST00000635911.1,n.2355C>T,MODIFIER,;EFHC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000635866.1,c.*706C>T,MODIFIER,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637892.1,n.1041C>T,MODIFIER,;EFHC1,synonymous_variant,p.H260=,ENST00000636489.1,c.780C>T,LOW,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637340.1,n.2762C>T,MODIFIER,;EFHC1,synonymous_variant,p.H171=,ENST00000635760.1,c.513C>T,LOW,;EFHC1,synonymous_variant,p.H171=,ENST00000635984.1,c.513C>T,LOW,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637849.1,n.901C>T,MODIFIER, +QKI 9444 BI GRCh38 6 163478898 163478898 + splice_donor_variant Splice_Site SNP T T A novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 103 16 c.402+2T>A p.X134_splice p.X134_splice ENST00000361752.8 NM_006775.3 134 P4 A protein_coding YES CCDS5285.1 AAAGGTAAGTC ENSP00000355094 ENST00000361752 Transcript NonExonic 1.0 ENSG00000112531 HGNC:21100 HIGH 3/7 NM_006775.3 splice_donor_variant 1.0 Unknown Q96PU8.163 QKI HGNC 1 1.0 UPI0000029EBD Q96PU8-1 SNV QKI,splice_donor_variant,p.X134_splice,ENST00000275262,NM_206854.3,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000361195,NM_001301085.2,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000361752,NM_006775.3,c.402+2T>A,HIGH,YES,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000392127,NM_206855.3,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000424802,,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000453779,NM_206853.3,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X79_splice,ENST00000537041,,c.237+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X79_splice,ENST00000544436,,c.237+2T>A,HIGH,,,,1;QKI,splice_donor_variant,p.X79_splice,ENST00000544823,,c.237+2T>A,HIGH,,,,1;QKI,intron_variant,,ENST00000537883,,c.91+23477T>A,MODIFIER,,,,1;QKI,downstream_gene_variant,,ENST00000537124,,,MODIFIER,,,,1;QKI,splice_donor_variant,p.X134_splice,ENST00000361758,,c.402+2T>A,HIGH,,,,1;QKI,splice_donor_variant,,ENST00000545346,,c.*282+2T>A,HIGH,,,,1;QKI,splice_donor_variant,,ENST00000545607,,c.*112+2T>A,HIGH,,,,1 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 60 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 119 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS QKI,intron_variant,,ENST00000537883.5,c.91+23477T>A,MODIFIER,;QKI,splice_donor_variant,p.X79_splice,ENST00000544823.5,c.237+2T>A,HIGH,;QKI,splice_donor_variant,NMD_transcript_variant,,ENST00000545346.1,c.*282+2T>A,HIGH,;QKI,splice_donor_variant,p.X79_splice,ENST00000537041.5,c.237+2T>A,HIGH,;QKI,splice_donor_variant,p.X79_splice,ENST00000544436.5,c.237+2T>A,HIGH,;QKI,splice_donor_variant,NMD_transcript_variant,p.X35_splice,ENST00000545607.5,c.*112+2T>A,HIGH,;QKI,splice_donor_variant,p.X134_splice,ENST00000424802.7,c.402+2T>A,HIGH,;QKI,splice_donor_variant,p.X134_splice,ENST00000361195.6,c.402+2T>A,HIGH,;QKI,splice_donor_variant,p.X134_splice,ENST00000361752.8,c.402+2T>A,HIGH,YES;QKI,splice_donor_variant,p.X134_splice,ENST00000275262.11,c.402+2T>A,HIGH,;QKI,splice_donor_variant,p.X134_splice,ENST00000392127.6,c.402+2T>A,HIGH,;QKI,splice_donor_variant,p.X134_splice,ENST00000453779.6,c.402+2T>A,HIGH,;QKI,splice_donor_variant,NMD_transcript_variant,p.X134_splice,ENST00000361758.8,c.402+2T>A,HIGH, +KCNU1 157855 BI GRCh38 8 36834814 36834814 + missense_variant Missense_Mutation SNP T T C rs1363114837 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 19 6 c.1241T>C p.Ile414Thr p.I414T ENST00000399881.8 NM_001031836.3 414 aTa/aCa 12/27 P1 C I/T protein_coding YES CCDS55220.1 1241/3450 GATTATAGCCA PDB-ENSP_mappings:4hpf.A;PDB-ENSP_mappings:4hpf.B;PANTHER:PTHR10027:SF23;PANTHER:PTHR10027;Gene3D:3.40.50.720;Prints:PR01449 ENSP00000382770 12/27 rs1363114837 ENST00000399881 Transcript ENSG00000215262 HGNC:18867 MODERATE NM_001031836.3 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.518) Unknown deleterious(0) A8MYU2.117 KCNU1 HGNC 1 2.0 UPI0000F079EF SNV KCNU1,missense_variant,p.I414T,ENST00000399881,NM_001031836.3,c.1241T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.518),1;KCNU1,missense_variant,p.I414T,ENST00000522372,,c.1241T>C,MODERATE,,deleterious(0),benign(0.119),1 1278/3692 muse;mutect2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 19 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 25 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS KCNU1,missense_variant,NMD_transcript_variant,p.I414T,ENST00000522372.5,c.1241T>C,MODERATE,;KCNU1,missense_variant,p.I414T,ENST00000399881.8,c.1241T>C,MODERATE,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 50 88 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 100 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 138 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +CPEB3 22849 BI GRCh38 10 92081501 92081501 + missense_variant,splice_region_variant Missense_Mutation SNP A A G novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 21 17 c.1688T>C p.Val563Ala p.V563A ENST00000265997.5 NM_014912.5 563 gTt/gCt 9/10 P4 G V/A protein_coding YES CCDS31246.1 1688/2097 GTTCAACTGCA PROSITE_profiles:PS50102;CDD:cd12726;PANTHER:PTHR12566;PANTHER:PTHR12566:SF7;Gene3D:3.30.70.330;SMART:SM00360;Superfamily:SSF54928 ENSP00000265997 9/10 ENST00000265997 Transcript 1.0 ENSG00000107864 HGNC:21746 MODERATE NM_014912.5 missense_variant 1.0 benign(0.007) Unknown tolerated(0.11) Q8NE35.147 CPEB3 HGNC -1 1.0 UPI000013F7DE Q8NE35-1 SNV CPEB3,missense_variant,p.V563A,ENST00000265997,NM_014912.5,c.1688T>C,MODERATE,YES,tolerated(0.11),benign(0.007),-1;CPEB3,missense_variant,p.V549A,ENST00000412050,NM_001178137.2,c.1646T>C,MODERATE,,tolerated(0.12),benign(0.132),-1;CPEB3,missense_variant,p.V563A,ENST00000614585,,c.1688T>C,MODERATE,,tolerated(0.11),benign(0.007),-1 1852/7781 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 41 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 38 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS CPEB3,missense_variant,splice_region_variant,p.V563A,ENST00000614585.4,c.1688T>C,MODERATE,;CPEB3,missense_variant,splice_region_variant,p.V549A,ENST00000412050.8,c.1646T>C,MODERATE,;CPEB3,missense_variant,splice_region_variant,p.V563A,ENST00000265997.5,c.1688T>C,MODERATE,YES +TECTA 7007 BI GRCh38 11 121109378 121109378 + missense_variant Missense_Mutation SNP G G T TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 37 4 c.366G>T p.Leu122Phe p.L122F ENST00000264037.2 122 ttG/ttT 3/23 P1 T L/F protein_coding CCDS8434.1 366/6468 ATCTTGAAAAG PROSITE_profiles:PS51220;PANTHER:PTHR46160;PANTHER:PTHR46160:SF3;SMART:SM00539 ENSP00000264037 3/23 COSV50757519 ENST00000264037 Transcript 1.0 ENSG00000109927 HGNC:11720 MODERATE missense_variant 1 probably_damaging(0.996) Unknown deleterious(0) 1 O75443.172 TECTA HGNC 1 1.0 UPI000045659D SNV TECTA,missense_variant,p.L122F,ENST00000392793,NM_005422.4,c.366G>T,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;TECTA,missense_variant,p.L122F,ENST00000642222,NM_001378761.1,c.366G>T,MODERATE,,deleterious(0),probably_damaging(1),1;TECTA,missense_variant,p.L122F,ENST00000264037,,c.366G>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;TBCEL-TECTA,missense_variant,p.L425F,ENST00000645041,,c.1275G>T,MODERATE,YES,deleterious_low_confidence(0),unknown(0),1;TBCEL-TECTA,non_coding_transcript_exon_variant,,ENST00000644541,,n.1507G>T,MODIFIER,,,,1 366/6468 muse;mutect2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 37 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 41 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS TECTA,missense_variant,p.L122F,ENST00000264037.2,c.366G>T,MODERATE,;TECTA,missense_variant,p.L122F,ENST00000642222.1,c.366G>T,MODERATE,;TECTA,missense_variant,p.L122F,ENST00000392793.6,c.366G>T,MODERATE,YES;TBCEL-TECTA,missense_variant,p.L425F,ENST00000645041.1,c.1275G>T,MODERATE,YES;TBCEL-TECTA,non_coding_transcript_exon_variant,,ENST00000644541.1,n.1507G>T,MODIFIER, +MYF6 4618 BI GRCh38 12 80707821 80707821 + synonymous_variant Silent SNP T T C rs1035874570 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 67 4 c.102T>C p.Tyr34= p.Y34= ENST00000228641.4 NM_002469.3 34 taT/taC 1/3 P1 C Y protein_coding YES CCDS9019.1 102/729 TTGTATCCAGG PANTHER:PTHR11534:SF4;PANTHER:PTHR11534;Pfam:PF01586;SMART:SM00520 ENSP00000228641 1/3 rs1035874570 ENST00000228641 Transcript 1.0 ENSG00000111046 HGNC:7566 LOW NM_002469.3 4.395e-05 gnomAD_NFE synonymous_variant 1.0 Unknown P23409.181 MYF6 HGNC 1 1.0 UPI0000001050 SNV MYF6,synonymous_variant,p.Y34=,ENST00000228641,NM_002469.3,c.102T>C,LOW,YES,,,1 188/1329 muse;mutect2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 1.988e-05 0.0 0.0 0.0 0.0 0.0 4.395e-05 0.0 0.0 0 70 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 71 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS MYF6,synonymous_variant,p.Y34=,ENST00000228641.4,c.102T>C,LOW,YES +RAB20 55647 BI GRCh38 13 110523940 110523940 + synonymous_variant Silent SNP T T G novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 34 25 c.430A>C p.Arg144= p.R144= ENST00000267328.5 NM_017817.3 144 Agg/Cgg 2/2 P1 G R protein_coding YES CCDS9512.1 430/705 TGCCCTTGGGG MobiDB_lite:mobidb-lite;PROSITE_profiles:PS51419;CDD:cd04126;PANTHER:PTHR24073:SF941;PANTHER:PTHR24073;Pfam:PF00071;Gene3D:3.40.50.300;SMART:SM00173;SMART:SM00174;SMART:SM00175;Superfamily:SSF52540 ENSP00000267328 2/2 ENST00000267328 Transcript ENSG00000139832 HGNC:18260 LOW NM_017817.3 synonymous_variant 1.0 Unknown Q9NX57.168 RAB20 HGNC -1 1.0 UPI0000001299 SNV RAB20,synonymous_variant,p.R144=,ENST00000267328,NM_017817.3,c.430A>C,LOW,YES,,,-1 633/1507 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 69 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 59 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS RAB20,synonymous_variant,p.R144=,ENST00000267328.5,c.430A>C,LOW,YES +TPPP2 122664 BI GRCh38 14 21030714 21030714 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 12 11 c.133G>A p.Val45Ile p.V45I ENST00000321760.11 NM_173846.5 45 Gtc/Atc 2/4 P1 A V/I protein_coding YES CCDS9566.1 133/513 AGACAGTCACC PANTHER:PTHR12932:SF21;PANTHER:PTHR12932;Pfam:PF05517;Gene3D:1.10.238.10;Superfamily:SSF47473 ENSP00000317595 2/4 ENST00000321760 Transcript ENSG00000179636 HGNC:19293 MODERATE NM_173846.5 missense_variant 1.0 benign(0.031) Unknown tolerated(0.08) P59282.118 TPPP2 HGNC 1 1.0 UPI0000161004 SNV TPPP2,missense_variant,p.V45I,ENST00000321760,NM_173846.5,c.133G>A,MODERATE,YES,tolerated(0.08),benign(0.031),1;TPPP2,missense_variant,p.V45I,ENST00000530140,,c.133G>A,MODERATE,,tolerated(0.08),benign(0.031),1;TPPP2,missense_variant,p.V45I,ENST00000460647,,c.133G>A,MODERATE,,tolerated(0.18),benign(0.031),1;TPPP2,missense_variant,p.V45I,ENST00000472458,,c.133G>A,MODERATE,,tolerated(0.1),benign(0.031),1;TPPP2,missense_variant,p.V40I,ENST00000481535,,c.118G>A,MODERATE,,tolerated(0.1),benign(0.11),1;NDRG2,intron_variant,,ENST00000403829,NM_001282211.1,c.25-7393C>T,MODIFIER,,,,-1;NDRG2,intron_variant,,ENST00000555026,,c.-6-7393C>T,MODIFIER,,,,-1;NDRG2,upstream_gene_variant,,ENST00000298687,NM_001354570.1&NM_001354565.1&NM_201535.2&NM_001354559.2&NM_001354567.2,,MODIFIER,,,,-1;NDRG2,upstream_gene_variant,,ENST00000350792,NM_001354569.1&NM_016250.3&NM_001354561.2,,MODIFIER,,,,-1;NDRG2,upstream_gene_variant,,ENST00000360463,NM_201536.2,,MODIFIER,,,,-1;RNASE13,downstream_gene_variant,,ENST00000382951,NM_001012264.4,,MODIFIER,YES,,,-1;NDRG2,upstream_gene_variant,,ENST00000397847,NM_001282215.2,,MODIFIER,,,,-1;NDRG2,upstream_gene_variant,,ENST00000397858,NM_201537.1&NM_001354562.2,,MODIFIER,,,,-1;NDRG2,upstream_gene_variant,,ENST00000554419,,,MODIFIER,,,,-1;TPPP2,upstream_gene_variant,,ENST00000555751,,,MODIFIER,,,,1;NDRG2,upstream_gene_variant,,ENST00000556974,,,MODIFIER,,,,-1;TPPP2,missense_variant,p.V37I,ENST00000495665,,c.109G>A,MODERATE,,tolerated(0.12),benign(0.083),1;TPPP2,non_coding_transcript_exon_variant,,ENST00000534434,,n.321G>A,MODIFIER,,,,1;TPPP2,non_coding_transcript_exon_variant,,ENST00000533755,,n.438G>A,MODIFIER,,,,1;TPPP2,non_coding_transcript_exon_variant,,ENST00000529496,,n.112G>A,MODIFIER,,,,1;TPPP2,non_coding_transcript_exon_variant,,ENST00000525425,,n.325G>A,MODIFIER,,,,1;TPPP2,non_coding_transcript_exon_variant,,ENST00000532060,,n.270G>A,MODIFIER,,,,1;NDRG2,upstream_gene_variant,,ENST00000557669,,,MODIFIER,,,,-1;AL161668.2,upstream_gene_variant,,ENST00000531638,,,MODIFIER,YES,,,1;AL161668.4,downstream_gene_variant,,ENST00000532213,,,MODIFIER,,,,1;AL161668.4,downstream_gene_variant,,ENST00000533984,,,MODIFIER,YES,,,1 290/1408 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 31 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 23 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS TPPP2,synonymous_variant,NMD_transcript_variant,p.Q36=,ENST00000495665.2,c.108G>A,LOW,;TPPP2,non_coding_transcript_exon_variant,,ENST00000529496.1,n.112G>A,MODIFIER,;TPPP2,missense_variant,p.V40I,ENST00000481535.5,c.118G>A,MODERATE,;TPPP2,missense_variant,p.V45I,ENST00000530140.6,c.133G>A,MODERATE,;TPPP2,missense_variant,p.V45I,ENST00000472458.5,c.133G>A,MODERATE,;TPPP2,missense_variant,p.V45I,ENST00000460647.6,c.133G>A,MODERATE,;TPPP2,non_coding_transcript_exon_variant,,ENST00000532060.1,n.270G>A,MODIFIER,;TPPP2,non_coding_transcript_exon_variant,,ENST00000525425.2,n.325G>A,MODIFIER,;TPPP2,missense_variant,p.V45I,ENST00000321760.11,c.133G>A,MODERATE,YES;TPPP2,non_coding_transcript_exon_variant,,ENST00000534434.2,n.321G>A,MODIFIER,;TPPP2,non_coding_transcript_exon_variant,,ENST00000533755.5,n.438G>A,MODIFIER,;NDRG2,intron_variant,,ENST00000555026.5,c.-6-7393C>T,MODIFIER,;NDRG2,intron_variant,,ENST00000403829.7,c.25-7393C>T,MODIFIER, +C14orf39 317761 BI GRCh38 14 60466955 60466955 + missense_variant Missense_Mutation SNP C C T rs1171467636 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 48 4 c.857G>A p.Arg286Lys p.R286K ENST00000321731.8 NM_174978.3 286 aGa/aAa 10/18 P1 T R/K protein_coding YES CCDS9746.1 857/1764 TTGGTCTTACT COSM5594280 Pfam:PF15676;PANTHER:PTHR35449 ENSP00000324920 10/18 rs1171467636;COSV58781469 ENST00000321731 Transcript ENSG00000179008 HGNC:19849 MODERATE NM_174978.3 missense_variant 0;1 1.0 benign(0.009) Unknown tolerated(0.17) 0;1 Q8N1H7.113 C14orf39 HGNC -1 1.0 UPI0000140C15 SNV C14orf39,missense_variant,p.R286K,ENST00000321731,NM_174978.3,c.857G>A,MODERATE,YES,tolerated(0.17),benign(0.009),-1;C14orf39,downstream_gene_variant,,ENST00000555476,,,MODIFIER,,,,-1;C14orf39,3_prime_UTR_variant,,ENST00000557138,,c.*171G>A,MODIFIER,,,,-1 984/2780 muse;mutect2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 6.778650003980147e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5481300579267554e-05 0.0 0.0 0 28 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 52 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS C14orf39,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000557138.5,c.*171G>A,MODIFIER,;C14orf39,missense_variant,p.R286K,ENST00000321731.8,c.857G>A,MODERATE,YES +CWC25 54883 BI GRCh38 17 38814908 38814908 + synonymous_variant Silent SNP A A T novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 21 6 c.381T>A p.Leu127= p.L127= ENST00000614790.5 NM_017748.5 127 ctT/ctA 3/10 P1 T L protein_coding YES CCDS45663.1 381/1278 TCAAGAAGGGA PDB-ENSP_mappings:5yzg.X;Pfam:PF12542;PANTHER:PTHR16196 ENSP00000478070 3/10 ENST00000614790 Transcript ENSG00000273559 HGNC:25989 LOW NM_017748.5 synonymous_variant 1.0 Unknown Q9NXE8.128 CWC25 HGNC -1 1.0 UPI000007081D Q9NXE8-1 SNV CWC25,synonymous_variant,p.L127=,ENST00000614790,NM_017748.5,c.381T>A,LOW,YES,,,-1;CWC25,non_coding_transcript_exon_variant,,ENST00000619818,,n.449T>A,MODIFIER,,,,-1;CWC25,3_prime_UTR_variant,,ENST00000619299,,c.*291T>A,MODIFIER,,,,-1;CWC25,3_prime_UTR_variant,,ENST00000618122,,c.*291T>A,MODIFIER,,,,-1;CWC25,3_prime_UTR_variant,,ENST00000622665,,c.*291T>A,MODIFIER,,,,-1;CWC25,upstream_gene_variant,,ENST00000619462,,,MODIFIER,,,,-1 519/3067 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 24 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 27 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS CWC25,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000622665.1,c.*291T>A,MODIFIER,;CWC25,non_coding_transcript_exon_variant,,ENST00000619818.4,n.449T>A,MODIFIER,;CWC25,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000618122.4,c.*291T>A,MODIFIER,;CWC25,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000619299.4,c.*291T>A,MODIFIER,;CWC25,synonymous_variant,p.L127=,ENST00000614790.5,c.381T>A,LOW,YES +COG1 9382 BI GRCh38 17 73197068 73197068 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 27 15 c.729C>G p.Asn243Lys p.N243K ENST00000299886.9 NM_018714.3 243 aaC/aaG 3/14 P2 G N/K protein_coding YES CCDS11692.1 729/2943 CTCAACCAGCC PANTHER:PTHR31658 ENSP00000299886 3/14 ENST00000299886 Transcript 1.0 ENSG00000166685 HGNC:6545 MODERATE NM_018714.3 missense_variant 1.0 benign(0.075) Unknown deleterious(0.03) Q8WTW3.156 COG1 HGNC 1 1.0 UPI0000127E34 SNV COG1,missense_variant,p.N243K,ENST00000438720,,c.729C>G,MODERATE,,deleterious(0.03),benign(0.012),1;COG1,missense_variant,p.N243K,ENST00000618996,,c.729C>G,MODERATE,,deleterious(0.03),benign(0.144),1;COG1,missense_variant,p.N243K,ENST00000299886,NM_018714.3,c.729C>G,MODERATE,YES,deleterious(0.03),benign(0.075),1;COG1,3_prime_UTR_variant,,ENST00000582587,,c.*353C>G,MODIFIER,,,,1;AC097641.1,downstream_gene_variant,,ENST00000580671,,,MODIFIER,YES,,,1 744/3014 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 38 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 42 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS COG1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000582587.2,c.*353C>G,MODIFIER,;COG1,missense_variant,p.P243A,ENST00000438720.7,c.727C>G,MODERATE,;COG1,missense_variant,p.N243K,ENST00000299886.9,c.729C>G,MODERATE,YES +ACOX1 51 BI GRCh38 17 75946790 75946790 + synonymous_variant Silent SNP G G A rs768307965 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 37 5 c.1941C>T p.His647= p.H647= ENST00000301608.9 NM_007292.6 647 caC/caT 14/14 A1 A H protein_coding CCDS11735.1 1941/1983 GATTCGTGGAC Pfam:PF01756;PIRSF:PIRSF000168;PANTHER:PTHR10909;PANTHER:PTHR10909:SF250;Superfamily:SSF47203 ENSP00000301608 14/14 rs768307965 ENST00000301608 Transcript 1.0 ENSG00000161533 HGNC:119 LOW 1.759e-05 gnomAD_NFE synonymous_variant Unknown Q15067.201 ACOX1 HGNC -1 1.0 UPI000013E731 Q15067-1 SNV ACOX1,synonymous_variant,p.H647=,ENST00000293217,NM_004035.7&NM_001185039.2,c.1941C>T,LOW,YES,,,-1;ACOX1,synonymous_variant,p.H647=,ENST00000301608,NM_007292.6,c.1941C>T,LOW,,,,-1;ACOX1,synonymous_variant,p.H119=,ENST00000587927,,c.357C>T,LOW,,,,-1;ACOX1,intron_variant,,ENST00000588968,,c.389+1461C>T,MODIFIER,,,,-1;ACOX1,upstream_gene_variant,,ENST00000591963,,,MODIFIER,,,,-1;ACOX1,3_prime_UTR_variant,,ENST00000572047,,c.*1899C>T,MODIFIER,,,,-1;ACOX1,3_prime_UTR_variant,,ENST00000573078,,c.*1430C>T,MODIFIER,,,,-1;AC087289.4,downstream_gene_variant,,ENST00000587348,,,MODIFIER,YES,,,1 2002/2215 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 7.957e-06 0.0 0.0 0.0 0.0 0.0 1.759e-05 0.0 0.0 1.3522299923351966e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086130163865164e-05 0.0 3.086130163865164e-05 0.0 0.0 0 32 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 42 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS ACOX1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000573078.5,c.*1430C>T,MODIFIER,;ACOX1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000572047.5,c.*1899C>T,MODIFIER,;ACOX1,missense_variant,p.T119M,ENST00000587927.5,c.356C>T,MODERATE,;ACOX1,intron_variant,,ENST00000588968.5,c.389+1461C>T,MODIFIER,;ACOX1,synonymous_variant,p.H647=,ENST00000293217.10,c.1941C>T,LOW,YES;ACOX1,synonymous_variant,p.H647=,ENST00000301608.9,c.1941C>T,LOW, +EIF1AX 1964 BI GRCh38 X 20138614 20138614 + missense_variant Missense_Mutation SNP C C G TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 9 59 c.25G>C p.Gly9Arg p.G9R ENST00000379607.10 NM_001412.4 9 Ggt/Cgt 2/7 P1 G G/R protein_coding YES CCDS14196.1 25/435 TTTACCTCCTT COSM3372214 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309272 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1 1.0 probably_damaging(0.991) Unknown tolerated(0.09) 1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G9R,ENST00000379607,NM_001412.4,c.25G>C,MODERATE,YES,tolerated(0.09),probably_damaging(0.991),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2773G>C,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 223/4414 muse;mutect2;varscan2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 0 146 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 68 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2773G>C,MODIFIER,;EIF1AX,missense_variant,p.G9R,ENST00000379607.10,c.25G>C,MODERATE,YES +CLDN2 9075 BI GRCh38 X 106928530 106928530 + missense_variant Missense_Mutation SNP G G C rs1194923745 TCGA-VD-A8KE-01A TCGA-VD-A8KE-10A Somatic 58 4 c.302G>C p.Gly101Ala p.G101A ENST00000336803.2 NM_020384.4 101 gGc/gCc 2/2 P1 C G/A protein_coding YES CCDS14524.1 302/693 GGTGGGCATGA Gene3D:1.20.140.150;Pfam:PF00822;Prints:PR01077;PANTHER:PTHR12002;PANTHER:PTHR12002:SF110;Transmembrane_helices:TMhelix ENSP00000336571 2/2 rs1194923745;COSV100390096 ENST00000336803 Transcript ENSG00000165376 HGNC:2041 MODERATE 1.226e-05 gnomAD_NFE missense_variant 0;1 1.0 probably_damaging(1) Unknown deleterious(0) 0;1 P57739.161 CLDN2 HGNC 1 2.0 UPI0000001BF3 SNV CLDN2,missense_variant,p.G101A,ENST00000336803,NM_020384.4,c.302G>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;CLDN2,missense_variant,p.G101A,ENST00000540876,NM_001171095.1,c.302G>C,MODERATE,,deleterious(0),probably_damaging(1),1;CLDN2,missense_variant,p.G101A,ENST00000541806,NM_001171092.1,c.302G>C,MODERATE,,deleterious(0),probably_damaging(1),1;MORC4,intron_variant,,ENST00000604604,,c.111+64700C>G,MODIFIER,,,,-1 628/2959 muse;mutect2 c9bfc2a7-0914-4080-a0a3-1c6a4e58e1ab 5.461e-06 0.0 0.0 0.0 0.0 0.0 1.226e-05 0.0 0.0 0 105 c9ec4a81-0fd1-4bda-a078-f6fbbf544863 62 8bb3002a-9b6f-4bfe-9eaa-aef1c6b95678 SUCCESS CLDN2,missense_variant,p.G101A,ENST00000336803.2,c.302G>C,MODERATE,YES;CLDN2,missense_variant,p.G101A,ENST00000540876.1,c.302G>C,MODERATE,;CLDN2,missense_variant,p.G101A,ENST00000541806.6,c.302G>C,MODERATE,;MORC4,intron_variant,,ENST00000604604.1,c.111+64700C>G,MODIFIER, +CHST2 9435 BI GRCh38 3 143121603 143121603 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 2 8 c.787C>T p.Leu263Phe p.L263F ENST00000309575.5 NM_004267.5 263 Ctc/Ttc 2/2 P1 T L/F protein_coding YES CCDS3129.1 787/1593 CACCACTCTGC PANTHER:PTHR10704;PANTHER:PTHR10704:SF3;PIRSF:PIRSF005883;Pfam:PF00685;Superfamily:SSF52540 ENSP00000307911 2/2 ENST00000309575 Transcript ENSG00000175040 HGNC:1970 MODERATE NM_004267.5 missense_variant 1.0 probably_damaging(0.993) Unknown tolerated(0.06) Q9Y4C5.146 CHST2 HGNC 1 V9HVX9.40 1.0 UPI0000073CBC Q9Y4C5-1 SNV CHST2,missense_variant,p.L263F,ENST00000309575,NM_004267.5,c.787C>T,MODERATE,YES,tolerated(0.06),probably_damaging(0.993),1;AC018450.1,upstream_gene_variant,,ENST00000483262,,,MODIFIER,,,,1 1731/4142 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0 13 c88378c6-5cb2-4bac-905a-b9c178611f14 10 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS CHST2,missense_variant,p.L263F,ENST00000309575.5,c.787C>T,MODERATE,YES +H2AZ1 3015 BI GRCh38 4 99949313 99949313 + missense_variant Missense_Mutation SNP G G A rs1167095035 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 29 14 c.155C>T p.Ala52Val p.A52V ENST00000296417.6 NM_002106.4 52 gCt/gTt 3/5 P3 A A/V protein_coding YES CCDS3654.1 155/387 ACACAGCGGCA Gene3D:1.10.20.10;PDB-ENSP_mappings:1f66.C;PDB-ENSP_mappings:1f66.G;PDB-ENSP_mappings:3wa9.C;PDB-ENSP_mappings:3wa9.G;PDB-ENSP_mappings:4cay.A;PDB-ENSP_mappings:4nft.A;PDB-ENSP_mappings:4nft.B;PDB-ENSP_mappings:4nft.C;PDB-ENSP_mappings:4nft.D;PDB-ENSP_mappings:5b31.G;PDB-ENSP_mappings:5b32.G;PDB-ENSP_mappings:5b33.C;PDB-ENSP_mappings:5b33.G;PDB-ENSP_mappings:5chl.B;PDB-ENSP_mappings:5fug.A;PDB-ENSP_mappings:5fug.D;PDB-ENSP_mappings:5fug.G;PDB-ENSP_mappings:5fug.J;PDB-ENSP_mappings:5z30.C;PDB-ENSP_mappings:5z30.G;PDB-ENSP_mappings:6jou.C;PDB-ENSP_mappings:6jou.G;Pfam:PF00125;Prints:PR00620;PANTHER:PTHR23430;PANTHER:PTHR23430:SF47;SMART:SM00414;Superfamily:SSF47113;CDD:cd00074 ENSP00000296417 3/5 rs1167095035 ENST00000296417 Transcript ENSG00000164032 HGNC:4741 MODERATE NM_002106.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 1.0 possibly_damaging(0.793) Unknown deleterious(0.03) P0C0S5.148 H2AZ1 HGNC -1 1.0 UPI0000000FEF SNV H2AZ1,missense_variant,p.A52V,ENST00000651623,,c.155C>T,MODERATE,,deleterious(0.02),benign(0.383),-1;H2AZ1,missense_variant,p.A52V,ENST00000296417,NM_002106.4,c.155C>T,MODERATE,YES,deleterious(0.03),possibly_damaging(0.793),-1;DNAJB14,upstream_gene_variant,,ENST00000442697,NM_001278310.2&NM_001031723.4,,MODIFIER,YES,,,-1;DNAJB14,upstream_gene_variant,,ENST00000610281,NM_001278311.2,,MODIFIER,,,,-1;H2AZ1,non_coding_transcript_exon_variant,,ENST00000529158,,n.204C>T,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000471738,,,MODIFIER,,,,-1;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511203,,n.987C>T,MODIFIER,,,,-1;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511348,,n.616C>T,MODIFIER,,,,-1;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511319,,n.680C>T,MODIFIER,,,,-1;H2AZ1,non_coding_transcript_exon_variant,,ENST00000527366,,n.232C>T,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000334223,,,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000398991,,,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000426476,,,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000469942,,,MODIFIER,,,,-1;DNAJB14,upstream_gene_variant,,ENST00000474664,,,MODIFIER,,,,-1;H2AZ1-DT,upstream_gene_variant,,ENST00000501976,,,MODIFIER,,,,1;H2AZ1-DT,upstream_gene_variant,,ENST00000507494,,,MODIFIER,YES,,,1;H2AZ1-DT,upstream_gene_variant,,ENST00000514624,,,MODIFIER,,,,1;H2AZ1-DT,upstream_gene_variant,,ENST00000666876,,,MODIFIER,,,,1 260/866 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 53 c88378c6-5cb2-4bac-905a-b9c178611f14 43 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS H2AZ1,non_coding_transcript_exon_variant,,ENST00000527366.1,n.232C>T,MODIFIER,;H2AZ1,non_coding_transcript_exon_variant,,ENST00000529158.5,n.204C>T,MODIFIER,;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511319.5,n.680C>T,MODIFIER,;H2AZ1,missense_variant,p.A52V,ENST00000296417.6,c.155C>T,MODERATE,YES;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511203.1,n.987C>T,MODIFIER,;H2AZ1,missense_variant,p.A52V,ENST00000651623.1,c.155C>T,MODERATE,;H2AZ1,non_coding_transcript_exon_variant,,ENST00000511348.1,n.616C>T,MODIFIER, +NR3C1 2908 BI GRCh38 5 143400614 143400614 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 77 55 c.226C>T p.Pro76Ser p.P76S ENST00000343796.6 NM_001018075.1 76 Cca/Tca 2/9 P4 A P/S protein_coding CCDS4278.1 226/2334 ATCTGGCTGCT Pfam:PF02155;PANTHER:PTHR24084:SF4;PANTHER:PTHR24084;Prints:PR00528 ENSP00000343205 2/9 ENST00000343796 Transcript 1.0 ENSG00000113580 HGNC:7978 MODERATE missense_variant benign(0.26) Unknown deleterious_low_confidence(0.01) P04150.265 NR3C1 HGNC -1 F1D8N4.72 5.0 UPI000012B301 P04150-1 SNV NR3C1,missense_variant,p.P76S,ENST00000343796,NM_001018075.1&NM_001018074.1&NM_001018077.1,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000394464,NM_001364180.2&NM_001364181.2&NM_000176.3&NM_001204258.2&NM_001204259.2&NM_001204260.2&NM_001204261.2&NM_001204262.2&NM_001204263.2&NM_001204264.2&NM_001364182.1,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000424646,NM_001204265.2,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.287),-1;NR3C1,missense_variant,p.P76S,ENST00000415690,NM_001020825.2,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.648),-1;NR3C1,missense_variant,p.P76S,ENST00000231509,NM_001024094.2&NM_001364185.1,c.226C>T,MODERATE,YES,deleterious_low_confidence(0.01),possibly_damaging(0.524),-1;NR3C1,missense_variant,p.P76S,ENST00000504572,NM_001364183.2,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.524),-1;NR3C1,missense_variant,p.P76S,ENST00000394466,NM_001364184.2,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.524),-1;NR3C1,missense_variant,p.P76S,ENST00000652686,,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.182),-1;NR3C1,missense_variant,p.P76S,ENST00000503201,NM_001018076.2,c.226C>T,MODERATE,,deleterious_low_confidence(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000514699,,c.226C>T,MODERATE,,deleterious(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000502500,,c.226C>T,MODERATE,,deleterious(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000510170,,c.226C>T,MODERATE,,deleterious(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000508760,,c.226C>T,MODERATE,,deleterious(0.01),benign(0.26),-1;NR3C1,missense_variant,p.P76S,ENST00000502892,,c.226C>T,MODERATE,,deleterious(0.01),benign(0.26),-1 1220/7286 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0 160 c88378c6-5cb2-4bac-905a-b9c178611f14 132 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS NR3C1,missense_variant,p.P76S,ENST00000502500.1,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000508760.5,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000514699.1,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000502892.5,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000510170.5,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000503201.1,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000652686.1,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000231509.7,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000394466.6,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000504572.5,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000424646.6,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000415690.6,c.226C>T,MODERATE,;NR3C1,missense_variant,p.P76S,ENST00000394464.7,c.226C>T,MODERATE,YES;NR3C1,missense_variant,p.P76S,ENST00000343796.6,c.226C>T,MODERATE, +SYNE1 23345 BI GRCh38 6 152442203 152442203 + stop_gained Nonsense_Mutation SNP G G A novel TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 50 21 c.3880C>T p.Gln1294Ter p.Q1294* ENST00000367255.10 NM_182961.4 1294 Cag/Tag 31/146 P3 A Q/* protein_coding YES CCDS5236.2 3880/26394 CTGCTGCTGCA PANTHER:PTHR14514;PANTHER:PTHR14514:SF3;Low_complexity_(Seg):seg ENSP00000356224 31/146 ENST00000367255 Transcript 1.0 ENSG00000131018 HGNC:17089 HIGH NM_182961.4 stop_gained 1.0 Unknown Q8NF91.188 SYNE1 HGNC -1 1.0 UPI000204AF58 Q8NF91-1 SNV SYNE1,stop_gained,p.Q1294*,ENST00000367255,NM_182961.4,c.3880C>T,HIGH,YES,,,-1;SYNE1,stop_gained,p.Q1301*,ENST00000423061,NM_033071.3,c.3901C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1343*,ENST00000341594,,c.4027C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1284*,ENST00000367248,,c.3850C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1275*,ENST00000672122,,c.3823C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1294*,ENST00000367253,,c.3880C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1294*,ENST00000413186,,c.3880C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q1292*,ENST00000673281,,c.3874C>T,HIGH,,,,-1;SYNE1,stop_gained,p.Q393*,ENST00000671915,,c.1177C>T,HIGH,,,,-1;SYNE1,3_prime_UTR_variant,,ENST00000673163,,c.*3850C>T,MODIFIER,,,,-1;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,,n.4098C>T,MODIFIER,,,,-1 4445/27708 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0 77 c88378c6-5cb2-4bac-905a-b9c178611f14 71 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS SYNE1,stop_gained,p.Q1294*,ENST00000413186.6,c.3880C>T,HIGH,;SYNE1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000673163.1,c.*3850C>T,MODIFIER,;SYNE1,stop_gained,p.Q393*,ENST00000671915.1,c.1177C>T,HIGH,;SYNE1,stop_gained,p.Q1275*,ENST00000672122.1,c.3823C>T,HIGH,;SYNE1,stop_gained,p.Q1284*,ENST00000367248.7,c.3850C>T,HIGH,;SYNE1,stop_gained,p.Q1292*,ENST00000673281.1,c.3874C>T,HIGH,;SYNE1,stop_gained,p.Q1294*,ENST00000367253.8,c.3880C>T,HIGH,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872.6,n.4098C>T,MODIFIER,;SYNE1,stop_gained,p.Q1301*,ENST00000423061.6,c.3901C>T,HIGH,;SYNE1,stop_gained,p.Q1294*,ENST00000367255.10,c.3880C>T,HIGH,YES +LINC00174 285908 BI GRCh38 7 66377583 66377583 + non_coding_transcript_exon_variant RNA SNP A A T rs1261401321 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 17 6 n.3163T>A ENST00000421767.1 7/7 T lncRNA YES ATTTCAGGACG 7/7 rs1261401321 ENST00000421767 Transcript ENSG00000179406 HGNC:27788 MODIFIER 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS non_coding_transcript_exon_variant 1.0 Unknown LINC00174 HGNC -1 5.0 SNV TPST1,intron_variant,,ENST00000490159,,n.99+20712A>T,MODIFIER,,,,1;LINC00174,non_coding_transcript_exon_variant,,ENST00000421767,,n.3163T>A,MODIFIER,YES,,,-1;LINC00174,downstream_gene_variant,,ENST00000416572,,,MODIFIER,,,,-1;LINC00174,downstream_gene_variant,,ENST00000438894,,,MODIFIER,,,,-1 3163/4702 muse;mutect2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 30 c88378c6-5cb2-4bac-905a-b9c178611f14 23 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS LINC00174,non_coding_transcript_exon_variant,,ENST00000421767.1,n.3163T>A,MODIFIER,;TPST1,intron_variant,,ENST00000490159.1,n.99+20712A>T,MODIFIER, +FBXL13 222235 BI GRCh38 7 103028743 103028743 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 46 4 c.74G>A p.Trp25Ter p.W25* ENST00000313221.8 NM_001287150.2 25 tGg/tAg 4/20 P1 T W/* protein_coding YES CCDS5726.1 74/2208 CTCTCCAAGTG ENSP00000321927 4/20 ENST00000313221 Transcript ENSG00000161040 HGNC:21658 HIGH stop_gained 1.0 Unknown Q8NEE6.148 FBXL13 HGNC -1 2.0 UPI000020F830 Q8NEE6-1 SNV FBXL13,stop_gained,p.W25*,ENST00000313221,NM_145032.3,c.74G>A,HIGH,YES,,,-1;FBXL13,stop_gained,p.W115*,ENST00000379308,,c.344G>A,HIGH,,,,-1;FBXL13,stop_gained,p.W25*,ENST00000436908,,c.74G>A,HIGH,,,,-1;FBXL13,stop_gained,p.W25*,ENST00000379305,NM_001287150.2,c.74G>A,HIGH,,,,-1;FBXL13,stop_gained,p.W25*,ENST00000455112,NM_001111038.2,c.74G>A,HIGH,,,,-1;FBXL13,stop_gained,p.W25*,ENST00000456695,,c.74G>A,HIGH,,,,-1;FBXL13,stop_gained,p.W115*,ENST00000440067,,c.344G>A,HIGH,,,,-1;FBXL13,intron_variant,,ENST00000471074,,n.485+608G>A,MODIFIER,,,,-1;FBXL13,stop_gained,p.W115*,ENST00000448002,,c.344G>A,HIGH,,,,-1;AC073127.1,upstream_gene_variant,,ENST00000447336,,,MODIFIER,YES,,,1 501/2744 muse;mutect2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0 76 c88378c6-5cb2-4bac-905a-b9c178611f14 50 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS FBXL13,intron_variant,NMD_transcript_variant,,ENST00000471074.1,c.*276+608G>A,MODIFIER,;FBXL13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000455112.7,c.*73G>A,MODIFIER,;FBXL13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000456695.6,c.*73G>A,MODIFIER,;FBXL13,non_coding_transcript_exon_variant,,ENST00000436908.5,n.334G>A,MODIFIER,;FBXL13,stop_gained,p.W25*,ENST00000313221.8,c.74G>A,HIGH,;FBXL13,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000379305.7,c.*73G>A,MODIFIER,;FBXL13,stop_gained,NMD_transcript_variant,p.W115*,ENST00000448002.6,c.344G>A,HIGH,;FBXL13,stop_gained,p.W115*,ENST00000440067.4,c.344G>A,HIGH,YES +PRKD1 5587 BI GRCh38 14 29638838 29638838 + stop_gained Nonsense_Mutation SNP G G A rs765821685 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 36 24 c.763C>T p.Arg255Ter p.R255* ENST00000331968.11 NM_002742.3 255 Cga/Tga 5/18 P3 A R/* protein_coding CCDS9637.1 763/2739 TGGTCGTCCAA PIRSF:PIRSF000552;PANTHER:PTHR22968;PANTHER:PTHR22968:SF9 ENSP00000333568 5/18 rs765821685 ENST00000331968 Transcript 1.0 ENSG00000184304 HGNC:9407 HIGH NM_002742.3 8.808e-06 gnomAD_NFE stop_gained Unknown Q15139.201 PRKD1 HGNC -1 1.0 UPI0000456761 SNV PRKD1,stop_gained,p.R255*,ENST00000331968,NM_002742.3,c.763C>T,HIGH,,,,-1;PRKD1,stop_gained,p.R255*,ENST00000616995,,c.763C>T,HIGH,,,,-1;PRKD1,stop_gained,p.R263*,ENST00000415220,NM_001330069.2&NM_001348390.1,c.787C>T,HIGH,YES,,,-1;PRKD1,upstream_gene_variant,,ENST00000546371,,,MODIFIER,,,,-1;PRKD1,non_coding_transcript_exon_variant,,ENST00000551644,,n.286C>T,MODIFIER,,,,-1;PRKD1,3_prime_UTR_variant,,ENST00000651571,,c.*428C>T,MODIFIER,,,,-1;PRKD1,3_prime_UTR_variant,,ENST00000651616,,c.*167C>T,MODIFIER,,,,-1;PRKD1,non_coding_transcript_exon_variant,,ENST00000468370,,n.334C>T,MODIFIER,,,,-1 1098/3833 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 3.981e-06 0.0 0.0 0.0 0.0 0.0 8.808e-06 0.0 0.0 1.3598199984699022e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0918599804863334e-05 0.0 3.0918599804863334e-05 0.0 0.0 0 100 c88378c6-5cb2-4bac-905a-b9c178611f14 60 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS PRKD1,non_coding_transcript_exon_variant,,ENST00000468370.5,n.334C>T,MODIFIER,;PRKD1,non_coding_transcript_exon_variant,,ENST00000551644.5,n.286C>T,MODIFIER,;PRKD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000651616.1,c.*167C>T,MODIFIER,;PRKD1,stop_gained,p.R263*,ENST00000415220.6,c.787C>T,HIGH,;PRKD1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000651571.1,c.*428C>T,MODIFIER,;PRKD1,non_coding_transcript_exon_variant,,ENST00000616995.5,n.534C>T,MODIFIER,;PRKD1,stop_gained,p.R255*,ENST00000331968.11,c.763C>T,HIGH,YES +EXD1 161829 BI GRCh38 15 41209531 41209531 + synonymous_variant Silent SNP T T C rs370262959 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 40 15 c.330A>G p.Val110= p.V110= ENST00000314992.9 NM_152596.4 110 gtA/gtG 5/10 A2 C V protein_coding CCDS10072.1 330/1545 CGACATACATT CDD:cd06148;PANTHER:PTHR46628;Pfam:PF01612;Gene3D:3.30.420.10;SMART:SM00474;Superfamily:SSF53098 ENSP00000321029 0.0 0.0001163 5/10 rs370262959 ENST00000314992 Transcript ENSG00000178997 HGNC:28507 LOW 0.0003261 gnomAD_OTH synonymous_variant Unknown Q8NHP7.136 EXD1 HGNC -1 1.0 UPI00001BBFD3 Q8NHP7-1 SNV EXD1,synonymous_variant,p.V110=,ENST00000314992,NM_152596.4,c.330A>G,LOW,,,,-1;EXD1,synonymous_variant,p.V168=,ENST00000458580,NM_001286441.2,c.504A>G,LOW,YES,,,-1 521/2942 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 7.957e-05 0.0 0.0 0.0 0.0 0.0 0.0001584 0.0003261 0.0 2.027549999183975e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.628629903891124e-05 0.0 4.628629903891124e-05 0.0 0.0 0 50 c88378c6-5cb2-4bac-905a-b9c178611f14 55 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS EXD1,synonymous_variant,p.V168=,ENST00000458580.7,c.504A>G,LOW,YES;EXD1,synonymous_variant,p.V110=,ENST00000314992.9,c.330A>G,LOW, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 25 10 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 0 79 c88378c6-5cb2-4bac-905a-b9c178611f14 35 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +HIRA 7290 BI GRCh38 22 19355831 19355831 + synonymous_variant Silent SNP C C T rs782074548 TCGA-V4-A9EV-01A TCGA-V4-A9EV-10A Somatic 20 9 c.2490G>A p.Thr830= p.T830= ENST00000263208.5 NM_003325.4 830 acG/acA 21/25 P1 T T protein_coding YES CCDS13759.1 2490/3054 likely_benign TGCTGCGTCAG PDB-ENSP_mappings:5yje.A;PDB-ENSP_mappings:5yje.B;PDB-ENSP_mappings:5yje.C;Pfam:PF07569;PANTHER:PTHR13831;PANTHER:PTHR13831:SF0 ENSP00000263208 21/25 rs782074548 ENST00000263208 Transcript 1.0 ENSG00000100084 HGNC:4916 LOW NM_003325.4 6.155e-05 gnomAD_AFR synonymous_variant 1 1.0 Unknown P54198.193 HIRA HGNC -1 1.0 UPI0000074373 P54198-1 SNV HIRA,synonymous_variant,p.T830=,ENST00000263208,NM_003325.4,c.2490G>A,LOW,YES,,,-1;HIRA,synonymous_variant,p.T623=,ENST00000340170,,c.1869G>A,LOW,,,,-1;C22orf39,intron_variant,,ENST00000509549,,c.*2331+399G>A,MODIFIER,,,,-1 2747/4053 muse;mutect2;varscan2 da6f0ed2-a6d5-4d87-823e-122ebd59aaba 7.96e-06 6.155e-05 0.0 0.0 0.0 0.0 8.8e-06 0.0 0.0 4.056189936818555e-05 7.296069816220552e-05 0.0 6.629539711866528e-05 0.0 0.0 0.0 afr 7.296069816220552e-05 0.0 3.086039941990748e-05 0.0 0.0 0 49 c88378c6-5cb2-4bac-905a-b9c178611f14 29 a6eada12-7e58-4fb5-b3e5-fdcd838868ed SUCCESS C22orf39,intron_variant,NMD_transcript_variant,,ENST00000509549.5,c.*2331+399G>A,MODIFIER,;HIRA,synonymous_variant,p.T623=,ENST00000340170.8,c.1869G>A,LOW,;HIRA,synonymous_variant,p.T830=,ENST00000263208.5,c.2490G>A,LOW,YES +CTDSP1 58190 BI GRCh38 2 218403404 218403404 + missense_variant Missense_Mutation SNP A A G novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 24 15 c.644A>G p.His215Arg p.H215R ENST00000273062.7 NM_001400273.1 215 cAt/cGt 6/7 P1 G H/R protein_coding CCDS2416.1 644/786 CTTCCATCCAG PDB-ENSP_mappings:1t9z.A;PDB-ENSP_mappings:1ta0.A;PDB-ENSP_mappings:2ghq.A;PDB-ENSP_mappings:2ghq.B;PDB-ENSP_mappings:2ght.A;PDB-ENSP_mappings:2ght.B;Gene3D:3.40.50.1000;PDB-ENSP_mappings:3l0b.A;PDB-ENSP_mappings:3l0b.B;PDB-ENSP_mappings:3l0c.A;PDB-ENSP_mappings:3l0c.B;PDB-ENSP_mappings:3l0y.A;PDB-ENSP_mappings:3l0y.B;PDB-ENSP_mappings:3pgl.A;PDB-ENSP_mappings:3pgl.B;PDB-ENSP_mappings:4ygy.A;PDB-ENSP_mappings:4ygy.B;PDB-ENSP_mappings:4yh1.A;PDB-ENSP_mappings:4yh1.B;PDB-ENSP_mappings:6du3.A;PDB-ENSP_mappings:6du3.B;Pfam:PF03031;PROSITE_profiles:PS50969;PANTHER:PTHR12210;PANTHER:PTHR12210:SF139;SFLD:SFLDG01124;SFLD:SFLDS00003;SMART:SM00577;Superfamily:SSF56784;TIGRFAM:TIGR02251;CDD:cd07521 ENSP00000273062 6/7 ENST00000273062 Transcript ENSG00000144579 HGNC:21614 MODERATE NM_021198.3 missense_variant possibly_damaging(0.82) Unknown deleterious(0.04) Q9GZU7.166 CTDSP1 HGNC 1 1.0 UPI000013007C Q9GZU7-1 SNV CTDSP1,missense_variant,p.H215R,ENST00000273062,NM_021198.3&NM_182642.3,c.644A>G,MODERATE,,deleterious(0.04),possibly_damaging(0.82),1;CTDSP1,missense_variant,p.H214R,ENST00000443891,NM_001206878.2,c.641A>G,MODERATE,,deleterious(0),possibly_damaging(0.82),1;CTDSP1,missense_variant,p.H216R,ENST00000428361,,c.647A>G,MODERATE,YES,deleterious(0),probably_damaging(0.995),1;CTDSP1,missense_variant,p.H208R,ENST00000452977,,c.623A>G,MODERATE,,deleterious(0),probably_damaging(0.998),1;CTDSP1,downstream_gene_variant,,ENST00000431127,,,MODIFIER,,,,1;MIR26B,downstream_gene_variant,,ENST00000362251,,,MODIFIER,YES,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000488627,,n.628A>G,MODIFIER,,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000464255,,n.622A>G,MODIFIER,,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000498160,,n.866A>G,MODIFIER,,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000491064,,n.651A>G,MODIFIER,,,,1;CTDSP1,downstream_gene_variant,,ENST00000473420,,,MODIFIER,,,,1;CTDSP1,downstream_gene_variant,,ENST00000492545,,,MODIFIER,,,,1;CTDSP1,downstream_gene_variant,,ENST00000496785,,,MODIFIER,,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000497677,,n.661A>G,MODIFIER,,,,1;CTDSP1,non_coding_transcript_exon_variant,,ENST00000482272,,n.971A>G,MODIFIER,,,,1;CTDSP1,downstream_gene_variant,,ENST00000494067,,,MODIFIER,,,,1;AC021016.2,upstream_gene_variant,,ENST00000608367,,,MODIFIER,YES,,,-1 867/2525 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 33 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 39 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS CTDSP1,missense_variant,p.H74R,ENST00000464255.2,c.221A>G,MODERATE,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000482272.5,n.971A>G,MODIFIER,;CTDSP1,missense_variant,p.H74R,ENST00000488627.6,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000710839.1,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000428361.6,c.221A>G,MODERATE,;CTDSP1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000710838.1,c.*316A>G,MODIFIER,;CTDSP1,missense_variant,p.H222R,ENST00000452977.6,c.665A>G,MODERATE,;CTDSP1,non_coding_transcript_exon_variant,,ENST00000497677.5,n.661A>G,MODIFIER,;CTDSP1,missense_variant,p.H214R,ENST00000710837.1,c.641A>G,MODERATE,;CTDSP1,missense_variant,p.H215R,ENST00000273062.7,c.644A>G,MODERATE,YES;CTDSP1,missense_variant,p.H74R,ENST00000498160.6,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000473420.6,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000443891.6,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000491064.6,c.221A>G,MODERATE,;CTDSP1,missense_variant,p.H74R,ENST00000710828.1,c.221A>G,MODERATE, +INKA1 389119 BI GRCh38 3 49804788 49804788 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 4 52 c.659C>A p.Pro220His p.P220H ENST00000333323.6 NM_203370.2 220 cCc/cAc 2/2 P1 A P/H protein_coding YES 659/858 TCGGCCCCCTC PANTHER:PTHR28615;PANTHER:PTHR28615:SF1;Gene3D:3.30.200.20 ENSP00000329735 2/2 ENST00000333323 Transcript ENSG00000185614 HGNC:32480 MODERATE NM_203370.2 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0.01) INKA1 HGNC 1 A0A499FIG1.5 1.0 UPI000007127C SNV INKA1,missense_variant,p.P220H,ENST00000333323,NM_203370.2&NM_001366281.1,c.659C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.999),1;UBA7,downstream_gene_variant,,ENST00000333486,NM_003335.3,,MODIFIER,YES,,,-1;CDHR4,upstream_gene_variant,,ENST00000343366,,,MODIFIER,,,,-1;CDHR4,upstream_gene_variant,,ENST00000412678,NM_001007540.4,,MODIFIER,YES,,,-1;CDHR4,upstream_gene_variant,,ENST00000487256,,,MODIFIER,,,,-1;MIR5193,downstream_gene_variant,,ENST00000584510,,,MODIFIER,YES,,,-1;UBA7,downstream_gene_variant,,ENST00000473992,,,MODIFIER,,,,-1;UBA7,downstream_gene_variant,,ENST00000478875,,,MODIFIER,,,,-1;UBA7,downstream_gene_variant,,ENST00000483751,,,MODIFIER,,,,-1;UBA7,downstream_gene_variant,,ENST00000488536,,,MODIFIER,,,,-1;UBA7,downstream_gene_variant,,ENST00000497908,,,MODIFIER,,,,-1 791/1033 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 94 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 56 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS INKA1,missense_variant,p.P220H,ENST00000333323.6,c.659C>A,MODERATE,YES +TWF2 11344 BI GRCh38 3 52229143 52229143 + missense_variant Missense_Mutation SNP G G C novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 3 32 c.941C>G p.Pro314Arg p.P314R ENST00000305533.10 NM_007284.4 314 cCc/cGc 9/9 P1 C P/R protein_coding YES CCDS2849.1 941/1050 GCTTGGGGTGC PANTHER:PTHR13759;PANTHER:PTHR13759:SF9;Gene3D:3.40.20.10;Superfamily:SSF55753 ENSP00000303908 9/9 ENST00000305533 Transcript ENSG00000247596 HGNC:9621 MODERATE NM_007284.4 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) Q6IBS0.147 TWF2 HGNC -1 1.0 UPI0000035B57 SNV TWF2,missense_variant,p.P314R,ENST00000305533,NM_007284.4,c.941C>G,MODERATE,YES,deleterious(0),probably_damaging(1),-1;TWF2,missense_variant,p.P216R,ENST00000679296,,c.647C>G,MODERATE,,deleterious(0),probably_damaging(1),-1;TWF2,missense_variant,p.P216R,ENST00000678838,,c.647C>G,MODERATE,,deleterious(0),probably_damaging(1),-1;TWF2,3_prime_UTR_variant,,ENST00000678330,,c.*443C>G,MODIFIER,,,,-1;TWF2,3_prime_UTR_variant,,ENST00000499914,,c.*54C>G,MODIFIER,,,,-1;AC097637.1,intron_variant,,ENST00000494383,,c.463+518C>G,MODIFIER,YES,,,-1;TLR9,upstream_gene_variant,,ENST00000360658,NM_017442.3,,MODIFIER,YES,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000678882,,n.993C>G,MODIFIER,,,,-1;TWF2,3_prime_UTR_variant,,ENST00000676988,,c.*252C>G,MODIFIER,,,,-1;TWF2,3_prime_UTR_variant,,ENST00000676989,,c.*780C>G,MODIFIER,,,,-1;TWF2,3_prime_UTR_variant,,ENST00000678549,,c.*780C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000472755,,n.2469C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000678700,,n.2010C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000677127,,n.2002C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000678681,,n.1981C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000676800,,n.1870C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000676552,,n.1631C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000678352,,n.1000C>G,MODIFIER,,,,-1;TWF2,non_coding_transcript_exon_variant,,ENST00000679180,,n.989C>G,MODIFIER,,,,-1;AC097637.1,intron_variant,,ENST00000478201,,c.113+518C>G,MODIFIER,,,,-1;TWF2,downstream_gene_variant,,ENST00000677058,,,MODIFIER,,,,-1 1083/1614 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 86 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 35 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS TWF2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676988.1,c.*252C>G,MODIFIER,;TWF2,3_prime_UTR_variant,,ENST00000678330.1,c.*443C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000472755.2,n.2469C>G,MODIFIER,;TWF2,3_prime_UTR_variant,,ENST00000499914.2,c.*54C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000676800.1,n.1870C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000677127.1,n.2002C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000678681.1,n.1981C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000676552.1,n.1631C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000678700.1,n.2010C>G,MODIFIER,;TWF2,non_coding_transcript_exon_variant,,ENST00000678882.1,n.993C>G,MODIFIER,;TWF2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000678549.1,c.*780C>G,MODIFIER,;TWF2,missense_variant,p.P216R,ENST00000679296.1,c.647C>G,MODERATE,;TWF2,non_coding_transcript_exon_variant,,ENST00000679180.1,n.989C>G,MODIFIER,;TWF2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000676989.1,c.*780C>G,MODIFIER,;TWF2,missense_variant,p.P314R,ENST00000305533.10,c.941C>G,MODERATE,YES;TWF2,non_coding_transcript_exon_variant,,ENST00000678352.1,n.1000C>G,MODIFIER,;TWF2,missense_variant,p.P216R,ENST00000678838.1,c.647C>G,MODERATE,;ENSG00000173366,intron_variant,NMD_transcript_variant,,ENST00000478201.1,c.113+518C>G,MODIFIER,;ENSG00000173366,intron_variant,,ENST00000494383.1,c.463+518C>G,MODIFIER,YES +FAM13B 51306 BI GRCh38 5 137952697 137952697 + missense_variant Missense_Mutation SNP C C A rs1440211074 TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 4 49 c.1795G>T p.Asp599Tyr p.D599Y ENST00000033079.7 NM_001385866.1 599 Gat/Tat 16/23 P2 A D/Y protein_coding YES CCDS4195.1 1795/2748 AATATCACTGT PANTHER:PTHR15904;PANTHER:PTHR15904:SF16 ENSP00000033079 16/23 rs1440211074;COSV50372349 ENST00000033079 Transcript ENSG00000031003 HGNC:1335 MODERATE 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 probably_damaging(0.999) Unknown deleterious(0) 0;1 Q9NYF5.148 FAM13B HGNC -1 A0A2X0SG06.10 1.0 UPI000004A03C Q9NYF5-1 SNV FAM13B,missense_variant,p.D599Y,ENST00000033079,NM_016603.3,c.1795G>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;FAM13B,missense_variant,p.D599Y,ENST00000420893,NM_001101800.2,c.1795G>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;FAM13B,missense_variant,p.D503Y,ENST00000425075,NM_001101801.2,c.1507G>T,MODERATE,,deleterious(0),probably_damaging(1),-1;FAM13B,downstream_gene_variant,,ENST00000505281,,,MODIFIER,,,,-1 2247/5465 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 146 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 54 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS FAM13B,missense_variant,p.D599Y,ENST00000420893.6,c.1795G>T,MODERATE,;FAM13B,missense_variant,p.D503Y,ENST00000425075.6,c.1507G>T,MODERATE,;FAM13B,missense_variant,p.D599Y,ENST00000033079.7,c.1795G>T,MODERATE,;FAM13B,missense_variant,p.D621Y,ENST00000689681.1,c.1861G>T,MODERATE,YES +SYBU 55638 BI GRCh38 8 109577969 109577969 + synonymous_variant Silent SNP G G T novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 64 104 c.783C>A p.Pro261= p.P261= ENST00000276646.14 NM_001099754.2 261 ccC/ccA 6/7 P4 T P protein_coding CCDS47912.1 783/1992 TTTGGGGGTCT PANTHER:PTHR16208;PANTHER:PTHR16208:SF4;Pfam:PF15290 ENSP00000276646 6/7 ENST00000276646 Transcript ENSG00000147642 HGNC:26011 LOW NM_001099754.2 synonymous_variant Unknown Q9NX95.140 SYBU HGNC -1 1.0 UPI00000407AB Q9NX95-1 SNV SYBU,synonymous_variant,p.P258=,ENST00000399066,NM_001099756.1,c.774C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P260=,ENST00000533895,NM_017786.6,c.780C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000422135,NM_001099744.1,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000433638,NM_001099750.1,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000276646,NM_001099754.2,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000440310,NM_001099752.1,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P266=,ENST00000424158,,c.798C>A,LOW,YES,,,-1;SYBU,synonymous_variant,p.P260=,ENST00000528647,NM_001099751.1,c.780C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000408908,NM_001099748.1,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P260=,ENST00000446070,NM_001099743.2&NM_001099747.2&NM_001099753.2,c.780C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P142=,ENST00000408889,NM_001099746.1,c.426C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P193=,ENST00000532779,,c.579C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P55=,ENST00000529175,,c.165C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P142=,ENST00000533065,NM_001099755.2,c.426C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P142=,ENST00000528331,NM_001099749.2,c.426C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P261=,ENST00000533171,NM_001099745.2,c.783C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P131=,ENST00000529690,NM_001330596.2,c.393C>A,LOW,,,,-1;SYBU,synonymous_variant,p.P98=,ENST00000533394,NM_001363032.2,c.294C>A,LOW,,,,-1;SYBU,downstream_gene_variant,,ENST00000528045,,,MODIFIER,,,,-1;SYBU,downstream_gene_variant,,ENST00000528569,,,MODIFIER,,,,-1;SYBU,downstream_gene_variant,,ENST00000529190,,,MODIFIER,,,,-1;SYBU,downstream_gene_variant,,ENST00000532189,,,MODIFIER,,,,-1;SYBU,non_coding_transcript_exon_variant,,ENST00000527707,,n.433C>A,MODIFIER,,,,-1;SYBU,downstream_gene_variant,,ENST00000527664,,,MODIFIER,,,,-1;SYBU,3_prime_UTR_variant,,ENST00000532594,,c.*292C>A,MODIFIER,,,,-1;SYBU,downstream_gene_variant,,ENST00000528735,,,MODIFIER,,,,-1 946/3083 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 110 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 168 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS SYBU,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000532594.1,c.*292C>A,MODIFIER,;SYBU,synonymous_variant,p.P98=,ENST00000533394.5,c.294C>A,LOW,;SYBU,non_coding_transcript_exon_variant,,ENST00000527707.5,n.433C>A,MODIFIER,;SYBU,synonymous_variant,p.P261=,ENST00000533171.5,c.783C>A,LOW,;SYBU,synonymous_variant,p.P131=,ENST00000529690.5,c.393C>A,LOW,;SYBU,synonymous_variant,p.P142=,ENST00000533065.5,c.426C>A,LOW,;SYBU,synonymous_variant,p.P142=,ENST00000408889.7,c.426C>A,LOW,;SYBU,synonymous_variant,p.P261=,ENST00000440310.5,c.783C>A,LOW,;SYBU,synonymous_variant,p.P261=,ENST00000433638.1,c.783C>A,LOW,;SYBU,synonymous_variant,p.P261=,ENST00000408908.6,c.783C>A,LOW,;SYBU,synonymous_variant,p.P261=,ENST00000422135.5,c.783C>A,LOW,;SYBU,synonymous_variant,p.P260=,ENST00000528647.5,c.780C>A,LOW,;SYBU,synonymous_variant,p.P55=,ENST00000529175.5,c.165C>A,LOW,;SYBU,synonymous_variant,p.P142=,ENST00000528331.5,c.426C>A,LOW,;SYBU,synonymous_variant,p.P260=,ENST00000446070.6,c.780C>A,LOW,;SYBU,synonymous_variant,p.P258=,ENST00000399066.7,c.774C>A,LOW,;SYBU,synonymous_variant,p.P266=,ENST00000424158.6,c.798C>A,LOW,;SYBU,synonymous_variant,p.P193=,ENST00000532779.5,c.579C>A,LOW,;SYBU,synonymous_variant,p.P261=,ENST00000276646.14,c.783C>A,LOW,YES;SYBU,synonymous_variant,p.P260=,ENST00000533895.5,c.780C>A,LOW, +LY6S-AS1 0 BI GRCh38 8 143043187 143043187 + non_coding_transcript_exon_variant RNA SNP G G A rs1223664491 TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 17 23 n.252G>A ENST00000669519.1 2/6 A lncRNA YES CAGGGGCTGCT 3/6 rs1223664491 ENST00000395172 Transcript ENSG00000177335 HGNC:26731 MODIFIER 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS non_coding_transcript_exon_variant 1.0 Unknown C8orf31 HGNC 1 2.0 SNV C8orf31,non_coding_transcript_exon_variant,,ENST00000523099,,n.539G>A,MODIFIER,,,,1;C8orf31,upstream_gene_variant,,ENST00000520786,,,MODIFIER,,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000395172,,n.463G>A,MODIFIER,YES,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000517653,,n.371G>A,MODIFIER,,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000669519,,n.252G>A,MODIFIER,,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000524181,,n.449G>A,MODIFIER,,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000665431,,n.298G>A,MODIFIER,,,,1;C8orf31,non_coding_transcript_exon_variant,,ENST00000622366,,n.111G>A,MODIFIER,,,,1;C8orf31,intron_variant,,ENST00000519775,,n.275+3618G>A,MODIFIER,,,,1;C8orf31,downstream_gene_variant,,ENST00000523766,,,MODIFIER,,,,1 463/1875 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 21 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 40 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS LY6S,synonymous_variant,p.S113=,ENST00000715552.1,c.339C>T,LOW,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000622366.3,n.111G>A,MODIFIER,;LY6S,3_prime_UTR_variant,,ENST00000715543.1,c.*148C>T,MODIFIER,;LY6S,synonymous_variant,p.S113=,ENST00000715551.1,c.339C>T,LOW,;LY6S,synonymous_variant,p.S113=,ENST00000706920.2,c.339C>T,LOW,YES;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000669519.1,n.252G>A,MODIFIER,YES;LY6S-AS1,intron_variant,,ENST00000519775.2,n.275+3618G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000665431.1,n.298G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000520786.4,n.535G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000395172.5,n.463G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000702083.1,n.319G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000524181.5,n.449G>A,MODIFIER,;LY6S-AS1,intron_variant,,ENST00000702010.1,n.310-1462G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000689572.2,n.333G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000685395.1,n.553G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000523099.7,n.568G>A,MODIFIER,;LY6S-AS1,non_coding_transcript_exon_variant,,ENST00000517653.5,n.371G>A,MODIFIER, +CEMIP2 23670 BI GRCh38 9 71709387 71709387 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 36 30 c.2857A>G p.Ile953Val p.I953V ENST00000377044.9 NM_013390.3 953 Att/Gtt 17/24 P1 C I/V protein_coding YES CCDS6638.1 2857/4152 ATCAATGTCAT PANTHER:PTHR15535;PANTHER:PTHR15535:SF26;Superfamily:SSF51126 ENSP00000366243 17/24 ENST00000377044 Transcript ENSG00000135048 HGNC:11869 MODERATE NM_013390.3 missense_variant 1.0 benign(0) Unknown tolerated(1) Q9UHN6.137 CEMIP2 HGNC -1 A0A024R229.38 1.0 UPI0000071E8D Q9UHN6-1 SNV CEMIP2,missense_variant,p.I953V,ENST00000377044,NM_013390.3,c.2857A>G,MODERATE,YES,tolerated(1),benign(0),-1;CEMIP2,missense_variant,p.I890V,ENST00000377066,NM_001135820.2&NM_001349784.2,c.2668A>G,MODERATE,,tolerated(1),benign(0),-1;CEMIP2,missense_variant,p.I54V,ENST00000377043,,c.160A>G,MODERATE,,tolerated(1),benign(0),-1;CEMIP2,upstream_gene_variant,,ENST00000377055,,,MODIFIER,,,,-1;CEMIP2,upstream_gene_variant,,ENST00000396272,,,MODIFIER,,,,-1;CEMIP2,3_prime_UTR_variant,,ENST00000542935,,c.*1080A>G,MODIFIER,,,,-1;CEMIP2,non_coding_transcript_exon_variant,,ENST00000537329,,n.449A>G,MODIFIER,,,,-1;CEMIP2,upstream_gene_variant,,ENST00000474495,,,MODIFIER,,,,-1 3026/6152 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 68 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 66 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS CEMIP2,non_coding_transcript_exon_variant,,ENST00000537329.1,n.449A>G,MODIFIER,;CEMIP2,missense_variant,p.I54V,ENST00000377043.2,c.160A>G,MODERATE,;CEMIP2,missense_variant,p.I890V,ENST00000377066.9,c.2668A>G,MODERATE,;CEMIP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000542935.5,c.*1080A>G,MODIFIER,;CEMIP2,missense_variant,p.I953V,ENST00000377044.9,c.2857A>G,MODERATE,YES +ALG1 56052 BI GRCh38 16 5071850 5071850 + start_lost Translation_Start_Site SNP A A G rs1332958042 TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 10 7 c.1A>G p.Met1? p.M1? ENST00000262374.10 NM_019109.5 1 Atg/Gtg 1/13 G M/V protein_coding YES CCDS10528.1 1/1395 CCAAGATGGCG Cleavage_site_(Signalp):SignalP-TM;PANTHER:PTHR13036;PANTHER:PTHR13036:SF1 ENSP00000262374 1/13 rs1332958042 ENST00000262374 Transcript 1.0 ENSG00000033011 HGNC:18294 HIGH NM_019109.5 3.325e-05 gnomAD_SAS start_lost 1.0 benign(0.006) Unknown tolerated_low_confidence(0.09) Q9BT22.171 ALG1 HGNC 1 1.0 UPI000003B09B Q9BT22-1 SNV ALG1,start_lost,p.M1?,ENST00000262374,NM_019109.5,c.1A>G,HIGH,YES,tolerated_low_confidence(0.09),benign(0.006),1;ALG1,start_lost,p.M1?,ENST00000586840,,c.1A>G,HIGH,,deleterious_low_confidence(0),benign(0.013),1;ALG1,intron_variant,,ENST00000588623,,c.-125-1101A>G,MODIFIER,,,,1;ALG1,upstream_gene_variant,,ENST00000544428,NM_001330504.1,,MODIFIER,,,,1;ALG1,upstream_gene_variant,,ENST00000591783,,,MODIFIER,,,,1;ALG1,intron_variant,,ENST00000650085,,n.1013-1101A>G,MODIFIER,,,,1;ALG1,start_lost,p.M1?,ENST00000591822,,c.1A>G,HIGH,,tolerated_low_confidence(0.08),benign(0.013),1;ALG1,non_coding_transcript_exon_variant,,ENST00000592793,,n.8A>G,MODIFIER,,,,1 8/3900 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 4.283e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.325e-05 0 9 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 17 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS ALG1,start_lost,splice_region_variant,NMD_transcript_variant,p.M1?,ENST00000684008.1,c.1A>G,HIGH,;ALG1,start_lost,splice_region_variant,NMD_transcript_variant,p.M1?,ENST00000591822.5,c.1A>G,HIGH,;ALG1,non_coding_transcript_exon_variant,,ENST00000682703.1,n.8A>G,MODIFIER,;ALG1,non_coding_transcript_exon_variant,,ENST00000682349.1,n.8A>G,MODIFIER,;ALG1,start_lost,p.M1?,ENST00000262374.10,c.1A>G,HIGH,YES;ALG1,non_coding_transcript_exon_variant,,ENST00000592793.6,n.8A>G,MODIFIER,;ALG1,start_lost,NMD_transcript_variant,p.M1?,ENST00000683710.1,c.1A>G,HIGH,;ALG1,start_lost,p.M1?,ENST00000586840.1,c.1A>G,HIGH,;ALG1,start_lost,p.M1?,ENST00000684335.1,c.1A>G,HIGH,;ALG1,non_coding_transcript_exon_variant,,ENST00000683685.1,n.45A>G,MODIFIER,;ALG1,start_lost,NMD_transcript_variant,p.M1?,ENST00000682206.1,c.1A>G,HIGH,;ALG1,start_lost,p.M1?,ENST00000684190.1,c.1A>G,HIGH,;ALG1,non_coding_transcript_exon_variant,,ENST00000682314.1,n.45A>G,MODIFIER,;ALG1,start_lost,NMD_transcript_variant,p.M1?,ENST00000682797.1,c.1A>G,HIGH,;ALG1,non_coding_transcript_exon_variant,,ENST00000683772.1,n.45A>G,MODIFIER,;ALG1,intron_variant,,ENST00000588623.5,c.-125-1101A>G,MODIFIER,;ALG1,intron_variant,,ENST00000683433.1,c.-55-5595A>G,MODIFIER,;ALG1,intron_variant,,ENST00000682327.1,c.-99-3538A>G,MODIFIER,;ALG1,intron_variant,NMD_transcript_variant,,ENST00000650085.1,c.-297-1101A>G,MODIFIER,;ALG1,intron_variant,,ENST00000682985.1,c.-99-3538A>G,MODIFIER,;ALG1,intron_variant,,ENST00000682020.1,c.-55-5595A>G,MODIFIER, +OSGIN1 29948 BI GRCh38 16 83965637 83965637 + non_coding_transcript_exon_variant RNA SNP A A G rs1015014267 TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 15 19 n.1696A>G ENST00000343939.6 7/7 G retained_intron CCCCTATGAGG 7/7 rs1015014267 ENST00000343939 Transcript ENSG00000140961 HGNC:30093 MODIFIER 8.867e-06 gnomAD_NFE non_coding_transcript_exon_variant Unknown OSGIN1 HGNC 1 2.0 SNV OSGIN1,missense_variant,p.Y355C,ENST00000361711,,c.1064A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.921),1;OSGIN1,missense_variant,p.Y355C,ENST00000393306,NM_182981.3,c.1064A>G,MODERATE,,deleterious(0.01),probably_damaging(0.921),1;NECAB2,upstream_gene_variant,,ENST00000305202,NM_019065.2&NM_001329748.1,,MODIFIER,YES,,,1;OSGIN1,downstream_gene_variant,,ENST00000565123,,,MODIFIER,,,,1;OSGIN1,downstream_gene_variant,,ENST00000567707,,,MODIFIER,,,,1;OSGIN1,non_coding_transcript_exon_variant,,ENST00000343939,,n.1696A>G,MODIFIER,,,,1 1696/2391 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 3.996e-06 0.0 0.0 0.0 0.0 0.0 8.867e-06 0.0 0.0 0 33 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 35 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS OSGIN1,missense_variant,p.Y355C,ENST00000393306.6,c.1064A>G,MODERATE,YES;OSGIN1,missense_variant,p.Y355C,ENST00000361711.7,c.1064A>G,MODERATE,;OSGIN1,non_coding_transcript_exon_variant,,ENST00000343939.6,n.1696A>G,MODIFIER, +SLC13A5 284111 BI GRCh38 17 6690777 6690777 + splice_donor_variant Splice_Site SNP A A T novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 61 42 c.1437+2T>A p.X479_splice p.X479_splice ENST00000433363.7 NM_177550.5 479 P1 T protein_coding YES CCDS11079.1 TACTTACCATG ENSP00000406220 ENST00000433363 Transcript NonExonic 1.0 ENSG00000141485 HGNC:23089 HIGH 10/11 NM_177550.5 splice_donor_variant 1.0 Unknown Q86YT5.131 SLC13A5 HGNC -1 1.0 UPI000000D834 Q86YT5-1 SNV SLC13A5,splice_donor_variant,p.X462_splice,ENST00000293800,NM_001284509.2,c.1386+2T>A,HIGH,,,,-1;SLC13A5,splice_donor_variant,p.X436_splice,ENST00000381074,NM_001284510.2,c.1308+2T>A,HIGH,,,,-1;SLC13A5,splice_donor_variant,p.X479_splice,ENST00000433363,NM_177550.5,c.1437+2T>A,HIGH,YES,,,-1;SLC13A5,splice_donor_variant,p.X36_splice,ENST00000570687,,c.106+2T>A,HIGH,,,,-1;SLC13A5,splice_donor_variant,p.X479_splice,ENST00000573648,NM_001143838.3,c.1437+2T>A,HIGH,,,,-1;SLC13A5,splice_donor_variant,,ENST00000572727,,n.546+2T>A,HIGH,,,,-1;ALOX15P1,intron_variant,,ENST00000634558,,n.662+750A>T,MODIFIER,,,,1;ALOX15P1,intron_variant,,ENST00000634823,,n.265-2088A>T,MODIFIER,,,,1;C17orf100,intron_variant,,ENST00000635042,,c.*325-2088A>T,MODIFIER,,,,1;SLC13A5,upstream_gene_variant,,ENST00000574580,,,MODIFIER,,,,-1;SLC13A5,downstream_gene_variant,,ENST00000574824,,,MODIFIER,,,,-1 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 95 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 103 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS SLC13A5,splice_donor_variant,,ENST00000572727.1,n.546+2T>A,HIGH,;SLC13A5,splice_donor_variant,p.X36_splice,ENST00000570687.1,c.106+2T>A,HIGH,;SLC13A5,splice_donor_variant,p.X479_splice,ENST00000573648.5,c.1437+2T>A,HIGH,;SLC13A5,splice_donor_variant,p.X436_splice,ENST00000381074.8,c.1308+2T>A,HIGH,;SLC13A5,splice_donor_variant,p.X462_splice,ENST00000293800.10,c.1386+2T>A,HIGH,;SLC13A5,splice_donor_variant,p.X479_splice,ENST00000433363.7,c.1437+2T>A,HIGH,YES;ENSG00000290366,intron_variant,,ENST00000634823.1,n.265-2088A>T,MODIFIER,;ENSG00000290366,intron_variant,,ENST00000634558.1,n.662+750A>T,MODIFIER,YES;C17orf100,intron_variant,NMD_transcript_variant,,ENST00000635042.1,c.*325-2088A>T,MODIFIER, +DNAH17 8632 BI GRCh38 17 78567036 78567036 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 24 4 c.1415C>T p.Ala472Val p.A472V ENST00000389840.7 NM_173628.4 472 gCc/gTc 10/81 P1 A A/V protein_coding YES CCDS11757.2 1415/13389 AGTCGGCAAAA Pfam:PF08385;PANTHER:PTHR10676;PANTHER:PTHR10676:SF284 ENSP00000374490 10/81 ENST00000389840 Transcript 1.0 ENSG00000187775 HGNC:2946 MODERATE NM_173628.4 missense_variant 1.0 benign(0.065) Unknown tolerated(0.16) Q9UFH2.131 DNAH17 HGNC -1 5.0 UPI0001B25601 Q9UFH2-1 SNV DNAH17,missense_variant,p.A472V,ENST00000389840,NM_173628.4,c.1415C>T,MODERATE,YES,tolerated(0.16),benign(0.065),-1;DNAH17,non_coding_transcript_exon_variant,,ENST00000589793,,n.627C>T,MODIFIER,,,,-1 1542/13725 muse;mutect2 b224e42d-8b6d-4578-963c-bf528b954900 0 24 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 28 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS DNAH17,non_coding_transcript_exon_variant,,ENST00000589793.1,n.627C>T,MODIFIER,;DNAH17,missense_variant,p.A472V,ENST00000389840.7,c.1415C>T,MODERATE,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 45 35 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 64 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 80 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ZNF446 55663 BI GRCh38 19 58479642 58479642 + splice_acceptor_variant Splice_Site SNP G G C TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 6 7 c.628-1G>C p.X210_splice p.X210_splice ENST00000594369.6 NM_017908.4 210 P4 C protein_coding YES CCDS12982.1 CCGCAGGAGGA ENSP00000472802 COSV59991238 ENST00000594369 Transcript ENSG00000083838 HGNC:21036 HIGH 4/6 NM_017908.4 splice_acceptor_variant 1 1.0 Unknown 1 Q9NWS9.160 ZNF446 HGNC 1 1.0 UPI0000071779 Q9NWS9-1 SNV ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000594369,NM_017908.4,c.628-1G>C,HIGH,YES,,,1;ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000596341,NM_001304453.1,c.628-1G>C,HIGH,,,,1;ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000610298,,c.628-1G>C,HIGH,,,,1;ZNF446,intron_variant,,ENST00000335841,,c.628-288G>C,MODIFIER,,,,1;ZNF446,intron_variant,,ENST00000622313,,c.628-287G>C,MODIFIER,,,,1;ZNF324,downstream_gene_variant,,ENST00000196482,NM_014347.3,,MODIFIER,,,,1;ZNF324,downstream_gene_variant,,ENST00000536459,,,MODIFIER,YES,,,1;ZNF446,downstream_gene_variant,,ENST00000600013,,,MODIFIER,,,,1;RNU6-1337P,downstream_gene_variant,,ENST00000516525,,,MODIFIER,YES,,,-1;ZNF446,splice_acceptor_variant,,ENST00000391694,,n.723-1G>C,HIGH,,,,1;SLC27A5,3_prime_UTR_variant,,ENST00000595851,,c.*1424C>G,MODIFIER,,,,-1;ZNF446,downstream_gene_variant,,ENST00000594468,,,MODIFIER,,,,1;AC012313.7,upstream_gene_variant,,ENST00000598051,,,MODIFIER,YES,,,-1 muse;mutect2 b224e42d-8b6d-4578-963c-bf528b954900 0 10 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 13 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS SLC27A5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000595851.5,c.*1424C>G,MODIFIER,;ZNF446,splice_acceptor_variant,,ENST00000391694.4,n.723-1G>C,HIGH,;ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000610298.1,c.628-1G>C,HIGH,;ZNF446,intron_variant,,ENST00000335841.8,c.628-288G>C,MODIFIER,;ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000594369.6,c.628-1G>C,HIGH,YES;ZNF446,splice_acceptor_variant,p.X210_splice,ENST00000596341.5,c.628-1G>C,HIGH, +CDH4 1002 BI GRCh38 20 61894996 61895009 + frameshift_variant Frame_Shift_Del DEL CATCACGGTGACAG CATCACGGTGACAG - novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 77 31 c.1137_1150del p.Ile380CysfsTer3 p.I380Cfs*3 ENST00000614565.5 NM_001794.5 379 atCATCACGGTGACAGat/atat 8/16 P1 - IITVTD/IX protein_coding YES CCDS13488.1 1137-1150/2751 AGCCATCATCACGGTGACAGATGTG Gene3D:2.60.40.60;Pfam:PF00028;Prints:PR00205;PROSITE_patterns:PS00232;PROSITE_profiles:PS50268;PANTHER:PTHR24027;PANTHER:PTHR24027:SF81;SMART:SM00112;Superfamily:SSF49313;CDD:cd11304 ENSP00000484928 8/16 ENST00000614565 Transcript ENSG00000179242 HGNC:1763 HIGH NM_001794.5 frameshift_variant 1.0 Unknown P55283.168 CDH4 HGNC 1 1.0 UPI000015FE86 P55283-1 deletion CDH4,frameshift_variant,p.I380Cfs*3,ENST00000614565,NM_001794.5,c.1137_1150del,HIGH,YES,,,1;CDH4,frameshift_variant,p.I286Cfs*3,ENST00000611855,,c.855_868del,HIGH,,,,1;CDH4,frameshift_variant,p.I306Cfs*3,ENST00000543233,NM_001252339.3&NM_001252338.2,c.915_928del,HIGH,,,,1 1390-1403/6678 mutect2;pindel;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 127 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 108 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS CDH4,frameshift_variant,p.I306Cfs*3,ENST00000543233.2,c.915_928del,HIGH,;CDH4,frameshift_variant,p.I286Cfs*3,ENST00000611855.4,c.855_868del,HIGH,;CDH4,frameshift_variant,p.I380Cfs*3,ENST00000614565.5,c.1137_1150del,HIGH,YES +TMEM35A 59353 BI GRCh38 X 101094768 101094768 + stop_gained Nonsense_Mutation SNP C C T novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 55 51 c.316C>T p.Gln106Ter p.Q106* ENST00000372930.5 NM_021637.3 106 Cag/Tag 2/2 P1 T Q/* protein_coding YES CCDS14478.1 316/504 TCCACCAGCTG Low_complexity_(Seg):seg;Transmembrane_helices:TMhelix;PANTHER:PTHR13163;PANTHER:PTHR13163:SF0;Pfam:PF13564 ENSP00000362021 2/2 ENST00000372930 Transcript ENSG00000126950 HGNC:25864 HIGH NM_021637.3 stop_gained 1.0 Unknown Q53FP2.100 TMEM35A HGNC 1 1.0 UPI0000035FFB SNV TMEM35A,stop_gained,p.Q106*,ENST00000372930,NM_021637.3,c.316C>T,HIGH,YES,,,1;CENPI,upstream_gene_variant,,ENST00000403304,,,MODIFIER,,,,1;CENPI,upstream_gene_variant,,ENST00000435570,,,MODIFIER,,,,1;TMEM35A,non_coding_transcript_exon_variant,,ENST00000478351,,n.572C>T,MODIFIER,,,,1;TRMT2B-AS1,upstream_gene_variant,,ENST00000443801,,,MODIFIER,YES,,,-1 440/2039 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 82 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 106 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS TMEM35A,non_coding_transcript_exon_variant,,ENST00000478351.1,n.572C>T,MODIFIER,;TMEM35A,stop_gained,p.Q106*,ENST00000372930.5,c.316C>T,HIGH,YES +RAB33A 9363 BI GRCh38 X 130184367 130184367 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-AA8P-01A TCGA-VD-AA8P-10A Somatic 34 24 c.341T>C p.Val114Ala p.V114A ENST00000257017.5 NM_004794.3 114 gTc/gCc 2/2 P1 C V/A protein_coding YES CCDS14621.1 341/714 CGTGGTCTTCG PROSITE_profiles:PS51419;CDD:cd04115;PANTHER:PTHR24073:SF326;PANTHER:PTHR24073;TIGRFAM:TIGR00231;Gene3D:3.40.50.300;Pfam:PF00071;SMART:SM00176;SMART:SM00174;SMART:SM00175;SMART:SM00173;Superfamily:SSF52540 ENSP00000257017 2/2 ENST00000257017 Transcript ENSG00000134594 HGNC:9773 MODERATE NM_004794.3 missense_variant 1.0 probably_damaging(0.991) Unknown deleterious(0) Q14088.179 RAB33A HGNC 1 1.0 UPI000000126B SNV RAB33A,missense_variant,p.V114A,ENST00000257017,NM_004794.3,c.341T>C,MODERATE,YES,deleterious(0),probably_damaging(0.991),1 442/945 muse;mutect2;varscan2 b224e42d-8b6d-4578-963c-bf528b954900 0 46 d69cbbca-bbd4-4030-a2ef-b1f35b2988a2 58 973cfc2c-6fbf-4f8c-9af9-fffffab022ab SUCCESS RAB33A,missense_variant,p.V114A,ENST00000257017.5,c.341T>C,MODERATE,YES +SZT2 23334 BI GRCh38 1 43447122 43447122 + synonymous_variant Silent SNP C C T novel TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 14 13 c.9069C>T p.Ala3023= p.A3023= ENST00000562955.2 NM_015284.4 3023 gcC/gcT 65/71 P4 T A protein_coding YES 9240/10299 CTGGCCCACCA PANTHER:PTHR14918 ENSP00000489255 66/72 ENST00000634258 Transcript 1.0 ENSG00000198198 HGNC:29040 LOW NM_001365999.1 synonymous_variant Unknown Q5T011.129 SZT2 HGNC 1 5.0 UPI0001E24F45 Q5T011-1 SNV SZT2,synonymous_variant,p.A3080=,ENST00000634258,NM_001365999.1,c.9240C>T,LOW,YES,,,1;SZT2,synonymous_variant,p.A3023=,ENST00000562955,NM_015284.4,c.9069C>T,LOW,,,,1;HYI,downstream_gene_variant,,ENST00000372430,NM_001190880.2,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000372432,NM_031207.6,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000372433,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000372434,NM_001330526.2,,MODIFIER,YES,,,-1;HYI,downstream_gene_variant,,ENST00000470662,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000486909,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000487366,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000583037,NM_001243526.1,,MODIFIER,,,,-1;MIR6735,upstream_gene_variant,,ENST00000615179,,,MODIFIER,YES,,,1;SZT2,non_coding_transcript_exon_variant,,ENST00000649403,,n.3990C>T,MODIFIER,,,,1;SZT2,non_coding_transcript_exon_variant,,ENST00000648058,,n.5694C>T,MODIFIER,,,,1;SZT2,non_coding_transcript_exon_variant,,ENST00000460536,,n.1057C>T,MODIFIER,,,,1;SZT2,non_coding_transcript_exon_variant,,ENST00000638263,,n.1214C>T,MODIFIER,,,,1;SZT2,non_coding_transcript_exon_variant,,ENST00000640484,,n.672C>T,MODIFIER,,,,1;HYI,downstream_gene_variant,,ENST00000372427,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000483618,,,MODIFIER,,,,-1;HYI,downstream_gene_variant,,ENST00000496142,,,MODIFIER,,,,-1;SZT2-AS1,downstream_gene_variant,,ENST00000396885,,,MODIFIER,YES,,,-1 9310/14136 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 15 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 27 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS SZT2,non_coding_transcript_exon_variant,,ENST00000640484.1,n.672C>T,MODIFIER,;SZT2,non_coding_transcript_exon_variant,,ENST00000460536.1,n.1057C>T,MODIFIER,;SZT2,non_coding_transcript_exon_variant,,ENST00000638263.1,n.1214C>T,MODIFIER,;SZT2,non_coding_transcript_exon_variant,,ENST00000649403.1,n.3990C>T,MODIFIER,;SZT2,non_coding_transcript_exon_variant,,ENST00000648058.1,n.5694C>T,MODIFIER,;SZT2,synonymous_variant,p.A3080=,ENST00000634258.3,c.9240C>T,LOW,YES;SZT2,synonymous_variant,p.A3023=,ENST00000562955.2,c.9069C>T,LOW, +GLI2 2736 BI GRCh38 2 120990556 120990556 + stop_gained Nonsense_Mutation SNP C C T rs1237907959 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 106 74 c.4591C>T p.Arg1531Ter p.R1531* ENST00000361492.9 NM_001374353.1 1531 Cga/Tga 14/14 A2 T R/* protein_coding 4591/4710 CCCCCCGAAAC PANTHER:PTHR45718;PANTHER:PTHR45718:SF6 ENSP00000354586 14/14 COSV58046108 ENST00000361492 Transcript 1.0 ENSG00000074047 HGNC:4318 HIGH NM_001374353.1 stop_gained 1 Unknown 1 P10070.210 GLI2 HGNC 1 1.0 UPI000387D74C P10070-5 SNV GLI2,stop_gained,p.R1531*,ENST00000361492,NM_001374353.1&NM_001374354.1,c.4591C>T,HIGH,,,,1;GLI2,stop_gained,p.R1548*,ENST00000452319,NM_001371271.1&NM_005270.5,c.4642C>T,HIGH,YES,,,1;GLI2,3_prime_UTR_variant,,ENST00000445186,,c.*3741C>T,MODIFIER,,,,1;GLI2,3_prime_UTR_variant,,ENST00000341310,,c.*3690C>T,MODIFIER,,,,1;GLI2,intron_variant,,ENST00000438299,,c.*2544-34C>T,MODIFIER,,,,1;GLI2,intron_variant,,ENST00000452692,,c.*2493-34C>T,MODIFIER,,,,1;GLI2,downstream_gene_variant,,ENST00000437950,,,MODIFIER,,,,1 5039/7136 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 173 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 180 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS GLI2,stop_gained,p.R1548*,ENST00000452319.6,c.4642C>T,HIGH,;GLI2,intron_variant,NMD_transcript_variant,,ENST00000452692.5,c.*2493-34C>T,MODIFIER,;GLI2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000341310.10,c.*3690C>T,MODIFIER,;GLI2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000445186.5,c.*3741C>T,MODIFIER,;GLI2,intron_variant,NMD_transcript_variant,,ENST00000438299.5,c.*2544-34C>T,MODIFIER,;GLI2,stop_gained,p.R1531*,ENST00000361492.9,c.4591C>T,HIGH,YES +RAI14 26064 BI GRCh38 5 34823781 34823781 + missense_variant Missense_Mutation SNP G G A novel TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 23 19 c.1939G>A p.Glu647Lys p.E647K ENST00000265109.8 NM_015577.3 647 Gag/Aag 15/18 P1 A E/K protein_coding CCDS34142.1 1939/2943 TGAGCGAGCTG Coiled-coils_(Ncoils):Coil;PANTHER:PTHR24129;CDD:cd09607 ENSP00000265109 15/18 ENST00000265109 Transcript ENSG00000039560 HGNC:14873 MODERATE NM_015577.3 missense_variant possibly_damaging(0.546) Unknown deleterious(0) Q9P0K7.158 RAI14 HGNC 1 1.0 UPI000013F319 Q9P0K7-1 SNV RAI14,missense_variant,p.E647K,ENST00000428746,NM_001145520.1,c.1939G>A,MODERATE,,deleterious(0),possibly_damaging(0.546),1;RAI14,missense_variant,p.E647K,ENST00000265109,NM_015577.3,c.1939G>A,MODERATE,,deleterious(0),possibly_damaging(0.546),1;RAI14,missense_variant,p.E650K,ENST00000515799,NM_001145525.1,c.1948G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.87),1;RAI14,missense_variant,p.E647K,ENST00000503673,NM_001145521.1,c.1939G>A,MODERATE,,deleterious(0),possibly_damaging(0.546),1;RAI14,missense_variant,p.E639K,ENST00000506376,NM_001145523.1,c.1915G>A,MODERATE,,deleterious(0),possibly_damaging(0.749),1;RAI14,missense_variant,p.E618K,ENST00000512629,NM_001145522.2,c.1852G>A,MODERATE,,deleterious(0),possibly_damaging(0.678),1;RAI14,upstream_gene_variant,,ENST00000507883,,,MODIFIER,,,,1;RAI14,downstream_gene_variant,,ENST00000508777,,,MODIFIER,,,,1;RAI14,upstream_gene_variant,,ENST00000513772,,,MODIFIER,,,,1 2135/4986 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 40 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 42 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS RAI14,missense_variant,p.E639K,ENST00000506376.1,c.1915G>A,MODERATE,;RAI14,missense_variant,p.E650K,ENST00000515799.5,c.1948G>A,MODERATE,;RAI14,missense_variant,p.E647K,ENST00000503673.5,c.1939G>A,MODERATE,;RAI14,missense_variant,p.E647K,ENST00000428746.6,c.1939G>A,MODERATE,;RAI14,missense_variant,p.E618K,ENST00000512629.5,c.1852G>A,MODERATE,;RAI14,missense_variant,p.E647K,ENST00000265109.8,c.1939G>A,MODERATE,YES +BICC1 80114 BI GRCh38 10 58789688 58789688 + missense_variant Missense_Mutation SNP A A G rs755739904 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 91 77 c.802A>G p.Thr268Ala p.T268A ENST00000373886.8 NM_001080512.3 268 Act/Gct 8/21 P1 G T/A protein_coding YES CCDS31206.1 802/2925 AAGGAACTGCC PANTHER:PTHR10627;PANTHER:PTHR10627:SF46;Superfamily:SSF54791 ENSP00000362993 8/21 rs755739904 ENST00000373886 Transcript 1.0 ENSG00000122870 HGNC:19351 MODERATE NM_001080512.3 5.437e-05 gnomAD_EAS missense_variant 1.0 benign(0.003) Unknown tolerated(0.06) Q9H694.126 BICC1 HGNC 1 1.0 UPI000059D156 Q9H694-1 SNV BICC1,missense_variant,p.T268A,ENST00000373886,NM_001080512.3,c.802A>G,MODERATE,YES,tolerated(0.06),benign(0.003),1;BICC1,upstream_gene_variant,,ENST00000263103,,,MODIFIER,,,,1 1074/5741 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 3.982e-06 0.0 0.0 0.0 5.437e-05 0.0 0.0 0.0 0.0 0 138 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 168 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS BICC1,missense_variant,p.T268A,ENST00000373886.8,c.802A>G,MODERATE,YES +MUC5AC 4586 BI GRCh38 11 1168936 1168936 + missense_variant Missense_Mutation SNP G G A rs1357774544 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 15 15 c.1780G>A p.Ala594Thr p.A594T ENST00000621226.2 NM_001304359.2 594 Gcg/Acg 15/49 P1 A A/T protein_coding YES CCDS76369.1 1780/16965 CCGCTGCGGCC PROSITE_profiles:PS51233;PANTHER:PTHR11339;PANTHER:PTHR11339:SF371;Low_complexity_(Seg):seg ENSP00000485659 15/49 rs1357774544;COSV100650586 ENST00000621226 Transcript ENSG00000215182 HGNC:7515 MODERATE NM_001304359.2 0.0001124 gnomAD_EAS missense_variant 0;1 1.0 unknown(0) Unknown deleterious(0.01) 0;1 P98088.180 MUC5AC HGNC 1 5.0 UPI0004F23658 SNV MUC5AC,missense_variant,p.A594T,ENST00000621226,NM_001304359.2,c.1780G>A,MODERATE,YES,deleterious(0.01),unknown(0),1 1827/17448 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 8.362e-06 0.0 0.0 0.0 0.0001124 0.0 0.0 0.0 0.0 0 21 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 30 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS MUC5AC,missense_variant,p.A594T,ENST00000621226.2,c.1780G>A,MODERATE,YES +GNB3 2784 BI GRCh38 12 6843869 6843869 + missense_variant Missense_Mutation SNP A A G rs1041974039 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 36 26 c.590A>G p.Asn197Ser p.N197S ENST00000229264.8 NM_002075.4 197 aAt/aGt 8/10 P1 G N/S protein_coding YES CCDS8564.1 590/1023 CTTCAATCTCT CDD:cd00200;Gene3D:2.130.10.10;PIRSF:PIRSF002394;Pfam:PF00400;SMART:SM00320;Superfamily:SSF50978;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR19850:SF31;PANTHER:PTHR19850 ENSP00000229264 8/10 rs1041974039 ENST00000229264 Transcript 1.0 ENSG00000111664 HGNC:4400 MODERATE NM_002075.4 0.000123 gnomAD_AFR missense_variant benign(0.007) Unknown tolerated(0.1) P16520.207 GNB3 HGNC 1 F1T0G5.73 5.0 UPI0000030A36 P16520-1 SNV GNB3,missense_variant,p.N197S,ENST00000229264,NM_002075.4,c.590A>G,MODERATE,YES,tolerated(0.1),benign(0.007),1;GNB3,missense_variant,p.N196S,ENST00000435982,NM_001297571.2,c.587A>G,MODERATE,,tolerated(0.1),benign(0.007),1;GNB3,missense_variant,p.N197S,ENST00000541978,,c.590A>G,MODERATE,,tolerated(0.15),benign(0.007),1;GNB3,missense_variant,p.N196S,ENST00000541257,,c.587A>G,MODERATE,,tolerated(0.11),benign(0.007),1;GNB3,intron_variant,,ENST00000537035,,c.498-31A>G,MODIFIER,,,,1;CDCA3,downstream_gene_variant,,ENST00000229265,NM_001297602.3,,MODIFIER,,,,-1;P3H3,downstream_gene_variant,,ENST00000290510,NM_014262.5,,MODIFIER,YES,,,1;CDCA3,downstream_gene_variant,,ENST00000422785,NM_001297603.3,,MODIFIER,,,,-1;CDCA3,downstream_gene_variant,,ENST00000535406,,,MODIFIER,YES,,,-1;CDCA3,downstream_gene_variant,,ENST00000538862,NM_031299.7,,MODIFIER,,,,-1;CDCA3,downstream_gene_variant,,ENST00000540683,NM_001331019.2&NM_001297604.3,,MODIFIER,,,,-1;GNB3,downstream_gene_variant,,ENST00000675241,,,MODIFIER,,,,1;CDCA3,downstream_gene_variant,,ENST00000544610,,,MODIFIER,,,,-1;CDCA3,downstream_gene_variant,,ENST00000603043,,,MODIFIER,,,,-1;CDCA3,downstream_gene_variant,,ENST00000604599,,,MODIFIER,,,,-1;GNB3,non_coding_transcript_exon_variant,,ENST00000540458,,n.1941A>G,MODIFIER,,,,1;P3H3,downstream_gene_variant,,ENST00000536140,,,MODIFIER,,,,1;CDCA3,downstream_gene_variant,,ENST00000536241,,,MODIFIER,,,,-1;GNB3,downstream_gene_variant,,ENST00000539127,,,MODIFIER,,,,1;GNB3,upstream_gene_variant,,ENST00000542751,,,MODIFIER,,,,1;GNB3,downstream_gene_variant,,ENST00000542868,,,MODIFIER,,,,1;P3H3,downstream_gene_variant,,ENST00000612048,,,MODIFIER,,,,1 729/1657 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 1.193e-05 0.000123 0.0 0.0 0.0 0.0 0.0 0.0 3.266e-05 1.3533400306187104e-05 4.873770012636669e-05 0.0 0.0 0.0 0.0 0.0 afr 4.873770012636669e-05 0.0 0.0 0.0 0.0 0 58 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 62 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS GNB3,intron_variant,,ENST00000537035.1,c.498-31A>G,MODIFIER,;GNB3,missense_variant,p.N196S,ENST00000435982.6,c.587A>G,MODERATE,;GNB3,missense_variant,p.N197S,ENST00000229264.8,c.590A>G,MODERATE,YES;GNB3,missense_variant,p.N197S,ENST00000541978.5,c.590A>G,MODERATE,;GNB3,missense_variant,p.N196S,ENST00000541257.5,c.587A>G,MODERATE,;GNB3,non_coding_transcript_exon_variant,,ENST00000540458.5,n.1941A>G,MODIFIER, +MYH2 4620 BI GRCh38 17 10523563 10523563 + missense_variant Missense_Mutation SNP C C T rs777282924 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 59 48 c.5405G>A p.Arg1802His p.R1802H ENST00000245503.10 NM_017534.6 1802 cGt/cAt 37/40 P1 T R/H protein_coding CCDS11156.1 5405/5826 CCAGACGGAGC COSM1380803 Coiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR45615;PANTHER:PTHR45615:SF39;Superfamily:SSF57997 ENSP00000245503 37/40 rs777282924;COSV55447559;COSV55449799 ENST00000245503 Transcript 1.0 ENSG00000125414 HGNC:7572 MODERATE NM_017534.6 9.239e-05 gnomAD_FIN missense_variant 0;1;1 benign(0.365) Unknown deleterious(0.01) 0;1;1 Q9UKX2.190 MYH2 HGNC -1 1.0 UPI000012FB6C Q9UKX2-1 SNV MYH2,missense_variant,p.R1802H,ENST00000397183,NM_001100112.1,c.5405G>A,MODERATE,YES,deleterious(0.01),benign(0.365),-1;MYH2,missense_variant,p.R1802H,ENST00000245503,NM_017534.6,c.5405G>A,MODERATE,,deleterious(0.01),benign(0.365),-1;MYH2,intron_variant,,ENST00000532183,,c.1975-2131G>A,MODIFIER,,,,-1;MYH2,intron_variant,,ENST00000622564,,c.1975-2131G>A,MODIFIER,,,,-1;AC005323.2,intron_variant,,ENST00000399342,,n.207-9761C>T,MODIFIER,YES,,,1;AC005323.2,intron_variant,,ENST00000581304,,n.144-9761C>T,MODIFIER,,,,1;MYHAS,intron_variant,,ENST00000587182,,n.156-43974C>T,MODIFIER,YES,,,1 5491/6044 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 2.784e-05 0.0 2.891e-05 0.0 0.0 9.239e-05 3.517e-05 0.0 0.0 2.7037300242227506e-05 4.863580033998005e-05 0.0 6.622519867960364e-05 0.0 0.0 0.0 afr 4.863580033998005e-05 0.0 1.542919926578179e-05 0.0 0.0 0 88 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 107 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS MYH2,intron_variant,,ENST00000622564.4,c.1975-2131G>A,MODIFIER,;MYH2,missense_variant,p.R1802H,ENST00000397183.6,c.5405G>A,MODERATE,;MYH2,intron_variant,,ENST00000532183.6,c.1975-2131G>A,MODIFIER,;MYH2,missense_variant,p.R1802H,ENST00000245503.10,c.5405G>A,MODERATE,YES;MYHAS,intron_variant,,ENST00000581304.2,n.144-9761C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000587182.3,n.156-43974C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000399342.6,n.207-9761C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000715727.1,n.170-74510C>T,MODIFIER,;MYHAS,intron_variant,,ENST00000584139.2,n.531-84791C>T,MODIFIER,YES;MYHAS,intron_variant,,ENST00000715356.1,n.307-84791C>T,MODIFIER, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 29 28 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 76 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 58 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +RYR1 6261 BI GRCh38 19 38492574 38492574 + missense_variant Missense_Mutation SNP G G A rs139775280 TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 21 15 c.6212G>A p.Arg2071Gln p.R2071Q ENST00000359596.8 NM_000540.3 2071 cGg/cAg 38/106 0.0002 0.0 0.0 0.001 0.0 0.0 A2 A R/Q protein_coding YES CCDS33011.1 6212/15117 uncertain_significance AGTGCGGCTGG PANTHER:PTHR13715;PANTHER:PTHR13715:SF15;Low_complexity_(Seg):seg ENSP00000352608 0.000227 0.0 38/106 rs139775280;COSV62099638 ENST00000359596 Transcript 1.0 ENSG00000196218 HGNC:10483 MODERATE NM_000540.3 0.001197 gnomAD_EAS missense_variant 1;1 1.0 benign(0.27) Unknown tolerated(0.19) 0;1 P21817.226 RYR1 HGNC 1 5.0 UPI0000D7E62F P21817-1 SNV RYR1,missense_variant,p.R2071Q,ENST00000359596,NM_000540.3,c.6212G>A,MODERATE,YES,tolerated(0.19),benign(0.27),1;RYR1,missense_variant,p.R2071Q,ENST00000355481,NM_001042723.2,c.6212G>A,MODERATE,,tolerated(0.19),benign(0.003),1;RYR1,upstream_gene_variant,,ENST00000594335,,,MODIFIER,,,,1 6351/15400 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0.0001035 6.161e-05 0.0 0.0 0.001197 0.0 2.641e-05 0.0 0.0 1.3521899745683186e-05 0.0 0.0 0.0 0.0 0.0004037139879073 0.0 eas 0.0004037139879073 0.0 0.0 0.0 0.0 0 25 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 36 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS RYR1,missense_variant,NMD_transcript_variant,p.R2071Q,ENST00000599547.7,c.6212G>A,MODERATE,;RYR1,missense_variant,p.R2071Q,ENST00000355481.8,c.6212G>A,MODERATE,;RYR1,missense_variant,p.R2031Q,ENST00000713953.1,c.6092G>A,MODERATE,;RYR1,missense_variant,p.R2071Q,ENST00000689936.2,c.6212G>A,MODERATE,;RYR1,missense_variant,p.R2071Q,ENST00000359596.8,c.6212G>A,MODERATE,YES;RYR1,missense_variant,NMD_transcript_variant,p.R2071Q,ENST00000688602.2,c.6212G>A,MODERATE,;RYR1,missense_variant,p.R2071Q,ENST00000713952.1,c.6212G>A,MODERATE,;RYR1,missense_variant,NMD_transcript_variant,p.R2071Q,ENST00000594335.6,c.6212G>A,MODERATE,;RYR1,missense_variant,NMD_transcript_variant,p.R2071Q,ENST00000593322.2,c.6212G>A,MODERATE, +GTSE1 51512 BI GRCh38 22 46308648 46308648 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 43 35 c.467A>C p.Lys156Thr p.K156T ENST00000454366.2 NM_016426.7 156 aAa/aCa 4/12 P1 C K/T protein_coding YES CCDS14074.2 467/2220 GAAGAAAAGCC Pfam:PF15259;PANTHER:PTHR21584;PANTHER:PTHR21584:SF10;MobiDB_lite:mobidb-lite ENSP00000415430 4/12 ENST00000454366 Transcript ENSG00000075218 HGNC:13698 MODERATE NM_016426.7 missense_variant 1.0 probably_damaging(0.996) Unknown deleterious(0) Q9NYZ3.157 GTSE1 HGNC 1 1.0 UPI000021D19B SNV GTSE1,missense_variant,p.K156T,ENST00000454366,NM_016426.7,c.467A>C,MODERATE,YES,deleterious(0),probably_damaging(0.996),1 550/2983 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 90 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 78 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS GTSE1,missense_variant,p.K156T,ENST00000454366.2,c.467A>C,MODERATE,YES +EIF1AX 1964 BI GRCh38 X 20138622 20138622 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-VD-AA8R-01A TCGA-VD-AA8R-10A Somatic 4 37 c.17G>A p.Gly6Asp p.G6D ENST00000379607.10 NM_001412.4 6 gGt/gAt 2/7 P1 T G/D protein_coding YES CCDS14196.1 17/435 CTTTACCTGAT COSM3736694 PDB-ENSP_mappings:1d7q.A;PDB-ENSP_mappings:3zjy.C;PDB-ENSP_mappings:4kzy.n;PDB-ENSP_mappings:4kzz.n;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR21668;PANTHER:PTHR21668:SF4;Gene3D:2.40.50.140;Superfamily:SSF50249 ENSP00000368927 2/7 COSV63309376 ENST00000379607 Transcript 1.0 ENSG00000173674 HGNC:3250 MODERATE NM_001412.4 missense_variant 1 1.0 possibly_damaging(0.894) Unknown deleterious(0.01) 1 P47813.189 EIF1AX HGNC -1 1.0 UPI00000041DF SNV EIF1AX,missense_variant,p.G6D,ENST00000379607,NM_001412.4,c.17G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.894),-1;EIF1AX,intron_variant,,ENST00000379593,,c.17-2781G>A,MODIFIER,,,,-1;AL732366.1,upstream_gene_variant,,ENST00000364722,,,MODIFIER,YES,,,-1;AL732366.2,upstream_gene_variant,,ENST00000365012,,,MODIFIER,YES,,,-1;EIF1AX-AS1,upstream_gene_variant,,ENST00000424026,,,MODIFIER,YES,,,1 215/4414 muse;mutect2;varscan2 995fcbf5-90aa-4d4a-b57b-46a7129209e0 0 124 0691390a-eabe-47ab-bd6c-6b1fdcaabf5d 41 ea671b0c-8d81-4d8e-ae04-96841a8270c2 SUCCESS EIF1AX,intron_variant,,ENST00000379593.1,c.17-2781G>A,MODIFIER,;EIF1AX,missense_variant,splice_region_variant,p.G6D,ENST00000379607.10,c.17G>A,MODERATE,YES +M1AP 130951 BI GRCh38 2 74615062 74615062 + missense_variant Missense_Mutation SNP C C G TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 39 41 c.328G>C p.Ala110Pro p.A110P ENST00000290536.9 NM_138804.5 110 Gct/Cct 3/11 A2 G A/P protein_coding YES CCDS33229.1 328/1593 AGAAGCACCTT COSM1666824 PANTHER:PTHR28642 ENSP00000290536 3/11 COSV51842671;COSV51847831 ENST00000290536 Transcript ENSG00000159374 HGNC:25183 MODERATE missense_variant 1;1 1.0 benign(0.059) Unknown tolerated(0.2) 1;1 Q8TC57.115 M1AP HGNC -1 1.0 UPI0000072570 Q8TC57-1 SNV M1AP,missense_variant,p.A110P,ENST00000290536,NM_001321739.2&NM_138804.4,c.328G>C,MODERATE,YES,tolerated(0.2),benign(0.059),-1;M1AP,missense_variant,p.A110P,ENST00000536235,NM_001281296.1&NM_001281295.2,c.328G>C,MODERATE,,tolerated(0.2),benign(0.059),-1;M1AP,missense_variant,p.A110P,ENST00000409585,,c.328G>C,MODERATE,,tolerated(0.2),benign(0.059),-1;M1AP,missense_variant,p.A110P,ENST00000421985,,c.328G>C,MODERATE,,tolerated(0.24),benign(0.059),-1;M1AP,non_coding_transcript_exon_variant,,ENST00000478437,,n.416G>C,MODIFIER,,,,-1;M1AP,missense_variant,p.A110P,ENST00000422394,,c.328G>C,MODERATE,,tolerated(0.2),possibly_damaging(0.466),-1;M1AP,intron_variant,,ENST00000438226,,c.240+24974G>C,MODIFIER,,,,-1;TOR1BP1,downstream_gene_variant,,ENST00000428904,,,MODIFIER,YES,,,-1 445/2543 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 71 4532f82e-59f3-4df3-a0ff-a737c47d014d 80 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS M1AP,non_coding_transcript_exon_variant,,ENST00000478437.1,n.416G>C,MODIFIER,;M1AP,non_coding_transcript_exon_variant,,ENST00000422394.5,n.425G>C,MODIFIER,;M1AP,intron_variant,NMD_transcript_variant,,ENST00000438226.5,c.240+24974G>C,MODIFIER,;M1AP,missense_variant,p.A110P,ENST00000409585.5,c.328G>C,MODERATE,;M1AP,missense_variant,p.A110P,ENST00000536235.5,c.328G>C,MODERATE,;M1AP,missense_variant,p.A110P,ENST00000421985.2,c.328G>C,MODERATE,YES;M1AP,missense_variant,p.A110P,ENST00000290536.9,c.328G>C,MODERATE, +SF3B1 23451 BI GRCh38 2 197402759 197402759 + missense_variant Missense_Mutation SNP C C T rs1057519961 TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 29 15 c.1874G>A p.Arg625His p.R625H ENST00000335508.11 NM_012433.4 625 cGt/cAt 14/25 P1 T R/H protein_coding YES CCDS33356.1 1874/3915 likely_pathogenic TGTTACGGACA COSM255276 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs1057519961;COSV59205431;COSV59206122;COSV59206364 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625H,ENST00000335508,NM_012433.4,c.1874G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2941G>A,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2133G>A,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3758G>A,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1903/6463 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 46 4532f82e-59f3-4df3-a0ff-a737c47d014d 44 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3758G>A,MODIFIER,;SF3B1,missense_variant,p.R625H,ENST00000335508.11,c.1874G>A,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2941G>A,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2133G>A,MODIFIER, +CAP2 10486 BI GRCh38 6 17541090 17541090 + missense_variant Missense_Mutation SNP C C A rs888404839 TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 62 30 c.944C>A p.Ser315Tyr p.S315Y ENST00000229922.7 NM_006366.3 315 tCt/tAt 9/13 P1 A S/Y protein_coding YES CCDS4539.1 944/1434 TAAATCTTATC COSM1666826 Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR10652:SF2;PANTHER:PTHR10652 ENSP00000229922 9/13 rs888404839;COSV57729706 ENST00000229922 Transcript 1.0 ENSG00000112186 HGNC:20039 MODERATE NM_006366.3 missense_variant 0;1 1.0 benign(0.243) Unknown deleterious(0.02) 0;1 P40123.169 CAP2 HGNC 1 1.0 UPI0000126EC6 P40123-1 SNV CAP2,missense_variant,p.S315Y,ENST00000229922,NM_006366.3,c.944C>A,MODERATE,YES,deleterious(0.02),benign(0.243),1;CAP2,missense_variant,p.S232Y,ENST00000616440,,c.695C>A,MODERATE,,deleterious(0.02),possibly_damaging(0.549),1;CAP2,missense_variant,p.S232Y,ENST00000611958,,c.695C>A,MODERATE,,deleterious(0.02),possibly_damaging(0.492),1;CAP2,missense_variant,p.S289Y,ENST00000378990,NM_001363534.1,c.866C>A,MODERATE,,deleterious(0.02),benign(0.212),1;CAP2,missense_variant,p.S203Y,ENST00000489374,NM_001363533.1,c.608C>A,MODERATE,,deleterious(0.02),benign(0.44),1;CAP2,missense_variant,p.S251Y,ENST00000465994,,c.752C>A,MODERATE,,deleterious(0.02),benign(0.197),1;CAP2,intron_variant,,ENST00000493172,,c.223-1747C>A,MODIFIER,,,,1;CAP2,3_prime_UTR_variant,,ENST00000479291,,c.*385C>A,MODIFIER,,,,1;CAP2,downstream_gene_variant,,ENST00000476263,,,MODIFIER,,,,1 1097/2925 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 78 4532f82e-59f3-4df3-a0ff-a737c47d014d 92 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS CAP2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000479291.5,c.*385C>A,MODIFIER,;CAP2,missense_variant,p.S251Y,ENST00000465994.5,c.752C>A,MODERATE,;CAP2,intron_variant,,ENST00000493172.5,c.223-1747C>A,MODIFIER,;CAP2,missense_variant,p.S289Y,ENST00000378990.6,c.866C>A,MODERATE,;CAP2,missense_variant,p.S203Y,ENST00000489374.5,c.608C>A,MODERATE,;CAP2,missense_variant,p.S315Y,ENST00000229922.7,c.944C>A,MODERATE,YES +FOXD4L6 653404 BI GRCh38 9 41127662 41127662 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 12 6 c.722C>T p.Ala241Val p.A241V ENST00000622588.2 NM_001085476.4 241 gCc/gTc 1/1 P1 A A/V protein_coding YES CCDS43826.1 722/1254 GCGGGGCAGGG Low_complexity_(Seg):seg;PANTHER:PTHR11829:SF350;PANTHER:PTHR11829 ENSP00000484875 1/1 ENST00000622588 Transcript ENSG00000273514 HGNC:31986 MODERATE missense_variant possibly_damaging(0.76) Unknown tolerated_low_confidence(0.08) Q3SYB3.130 FOXD4L6 HGNC -1 UPI0000519166 SNV FOXD4L6,missense_variant,p.A241V,ENST00000622588,NM_001085476.2,c.722C>T,MODERATE,YES,tolerated_low_confidence(0.08),possibly_damaging(0.76),-1;CBWD6,downstream_gene_variant,,ENST00000377391,NM_001085457.1,,MODIFIER,YES,,,-1;CBWD6,downstream_gene_variant,,ENST00000456520,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000613716,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000457288,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000610358,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000613125,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000617722,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000622791,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000382436,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000486387,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000494538,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000611553,,,MODIFIER,,,,-1;CBWD6,downstream_gene_variant,,ENST00000617917,,,MODIFIER,,,,-1;FRG1HP,intron_variant,,ENST00000617940,,n.412-67439G>A,MODIFIER,,,,1 802/2034 mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 64 4532f82e-59f3-4df3-a0ff-a737c47d014d 18 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS FOXD4L6,missense_variant,p.A241V,ENST00000622588.2,c.722C>T,MODERATE,YES;FRG1HP,intron_variant,,ENST00000617940.2,n.412-67439G>A,MODIFIER,YES +TRPM6 140803 BI GRCh38 9 74775925 74775925 + missense_variant Missense_Mutation SNP G G C TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 72 26 c.3361C>G p.His1121Asp p.H1121D ENST00000360774.6 NM_017662.5 1121 Cat/Gat 24/39 P4 C H/D protein_coding YES CCDS6647.1 3361/6069 TCGATGACAGC COSM1666827;COSM1666828 PANTHER:PTHR13800:SF15;PANTHER:PTHR13800 ENSP00000354006 24/39 COSV62502764 ENST00000360774 Transcript 1.0 ENSG00000119121 HGNC:17995 MODERATE NM_017662.5 missense_variant 1 1.0 benign(0.065) Unknown deleterious(0.03) 1 Q9BX84.156 TRPM6 HGNC -1 1.0 UPI000006E041 Q9BX84-1 SNV TRPM6,missense_variant,p.H1116D,ENST00000361255,NM_001177311.1,c.3346C>G,MODERATE,,deleterious(0.03),benign(0.098),-1;TRPM6,missense_variant,p.H1121D,ENST00000360774,NM_017662.5,c.3361C>G,MODERATE,YES,deleterious(0.03),benign(0.065),-1;TRPM6,missense_variant,p.H1116D,ENST00000449912,NM_001177310.1,c.3346C>G,MODERATE,,deleterious(0.03),benign(0.137),-1 3426/8252 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 46 4532f82e-59f3-4df3-a0ff-a737c47d014d 98 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS TRPM6,missense_variant,p.H1121D,ENST00000360774.6,c.3361C>G,MODERATE,YES;TRPM6,missense_variant,p.H1116D,ENST00000449912.6,c.3346C>G,MODERATE,;TRPM6,missense_variant,p.H1116D,ENST00000361255.7,c.3346C>G,MODERATE,;TRPM6,missense_variant,NMD_transcript_variant,p.H1121D,ENST00000715553.1,c.3361C>G,MODERATE, +GNAQ 2776 BI GRCh38 9 77797577 77797577 + missense_variant Missense_Mutation SNP C C T rs397514698 TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 44 60 c.548G>A p.Arg183Gln p.R183Q ENST00000286548.9 NM_002072.5 183 cGa/cAa 4/7 P1 T R/Q protein_coding YES CCDS6658.1 548/1080 pathogenic GGACTCGAACT COSM4785077;COSM52975 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;Gene3D:1.10.400.10;SMART:SM00275;Superfamily:SSF47895;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 4/7 rs397514698;CM1412391;COSV54106047;COSV54107425 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 23656586;25188413 probably_damaging(0.958) Unknown deleterious(0.03) 0;0;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.R183Q,ENST00000286548,NM_002072.5,c.548G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.958),-1;GNAQ,missense_variant,p.R154Q,ENST00000411677,,c.461G>A,MODERATE,,tolerated(0.06),probably_damaging(0.924),-1 1124/6882 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 50 4532f82e-59f3-4df3-a0ff-a737c47d014d 104 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS GNAQ,missense_variant,p.R154Q,ENST00000411677.1,c.461G>A,MODERATE,;GNAQ,missense_variant,p.R183Q,ENST00000286548.9,c.548G>A,MODERATE,YES +OR2D3 120775 BI GRCh38 11 6921812 6921812 + missense_variant Missense_Mutation SNP G G A rs1454070399 TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 47 48 c.811G>A p.Gly271Arg p.G271R ENST00000317834.5 NM_001004684.1 271 Gga/Aga 1/1 P1 A G/R protein_coding YES CCDS31417.1 811/993 GGTCAGGAATA COSM1666829 Gene3D:1.20.1070.10;Pfam:PF13853;PROSITE_profiles:PS50262;PANTHER:PTHR26453;PANTHER:PTHR26453:SF136;Superfamily:SSF81321;Transmembrane_helices:TMhelix;CDD:cd15428 ENSP00000320560 1/1 rs1454070399;COSV53491594 ENST00000317834 Transcript ENSG00000178358 HGNC:15146 MODERATE 6.297e-05 gnomAD_AFR missense_variant 0;1 possibly_damaging(0.877) Unknown deleterious(0) 0;1 Q8NGH3.141 OR2D3 HGNC 1 UPI0000041C7D SNV OR2D3,missense_variant,p.G271R,ENST00000317834,NM_001004684.1,c.811G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.877),1;ZNF215,upstream_gene_variant,,ENST00000278319,NM_001354856.2&NM_001354858.2&NM_001354853.2&NM_001354857.2&NM_001354859.2&NM_013250.4&NM_001354855.2&NM_001354860.2,,MODIFIER,YES,,,1;ZNF215,upstream_gene_variant,,ENST00000414517,,,MODIFIER,,,,1;ZNF215,upstream_gene_variant,,ENST00000610573,,,MODIFIER,,,,1;ZNF215,upstream_gene_variant,,ENST00000527171,,,MODIFIER,,,,1;ZNF215,upstream_gene_variant,,ENST00000529755,,,MODIFIER,,,,1;ZNF215,upstream_gene_variant,,ENST00000636097,,,MODIFIER,,,,1;ZNF215,upstream_gene_variant,,ENST00000636606,,,MODIFIER,,,,1;AC087280.2,intron_variant,,ENST00000637205,,n.605+2686C>T,MODIFIER,YES,,,-1 839/1070 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 4.484e-06 6.297e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 6.761510121577885e-06 2.4330900487257168e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 76 4532f82e-59f3-4df3-a0ff-a737c47d014d 95 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS OR2D3,missense_variant,p.G271R,ENST00000317834.5,c.811G>A,MODERATE,YES;ENSG00000283415,intron_variant,,ENST00000637205.2,n.605+2686C>T,MODIFIER,YES +CBX5 23468 BI GRCh38 12 54257515 54257515 + missense_variant,splice_region_variant Missense_Mutation SNP C C T TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 43 26 c.136G>A p.Glu46Lys p.E46K ENST00000209875.9 NM_012117.3 46 Gag/Aag 2/5 P1 T E/K protein_coding YES CCDS8875.1 136/576 TTACTCAGAAA COSM1666830 Gene3D:2.40.50.40;PDB-ENSP_mappings:3fdt.A;Pfam:PF00385;Prints:PR00504;PROSITE_patterns:PS00598;PROSITE_profiles:PS50013;PANTHER:PTHR22812;PANTHER:PTHR22812:SF85;SMART:SM00298;Superfamily:SSF54160;CDD:cd18651 ENSP00000209875 2/5 COSV52935568 ENST00000209875 Transcript ENSG00000094916 HGNC:1555 MODERATE NM_012117.3 missense_variant 1 1.0 benign(0.326) Unknown deleterious(0.01) 1 P45973.202 CBX5 HGNC -1 V9HWG0.59 1.0 UPI00001271FC SNV CBX5,missense_variant,p.E46K,ENST00000209875,NM_012117.3,c.136G>A,MODERATE,YES,deleterious(0.01),benign(0.326),-1;CBX5,missense_variant,p.E46K,ENST00000439541,NM_001127321.1,c.136G>A,MODERATE,,deleterious(0.01),benign(0.326),-1;CBX5,missense_variant,p.E46K,ENST00000550411,NM_001127322.1,c.136G>A,MODERATE,,deleterious(0.01),benign(0.326),-1;CBX5,missense_variant,p.E46K,ENST00000552562,,c.136G>A,MODERATE,,deleterious(0),benign(0.326),-1;RN7SL390P,upstream_gene_variant,,ENST00000470634,,,MODIFIER,YES,,,-1;CBX5,upstream_gene_variant,,ENST00000547872,,,MODIFIER,,,,-1 293/11546 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 84 4532f82e-59f3-4df3-a0ff-a737c47d014d 69 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS CBX5,missense_variant,splice_region_variant,p.E46K,ENST00000552562.1,c.136G>A,MODERATE,;CBX5,missense_variant,splice_region_variant,p.E46K,ENST00000550411.5,c.136G>A,MODERATE,;CBX5,missense_variant,splice_region_variant,p.E46K,ENST00000439541.6,c.136G>A,MODERATE,;CBX5,missense_variant,splice_region_variant,p.E46K,ENST00000209875.9,c.136G>A,MODERATE,YES +TTLL13 440307 BI GRCh38 15 90256247 90256247 + missense_variant Missense_Mutation SNP C C T rs754001735 TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 0 29 c.655C>T p.Arg219Trp p.R219W ENST00000641754.2 219 Cgg/Tgg 5/14 P4 T R/W protein_coding YES 655/2448 ATCCCCGGGAG COSM1666831;COSM1666832 Gene3D:3.30.1490.20;Gene3D:3.30.470.20;Pfam:PF03133;PROSITE_profiles:PS51221;PANTHER:PTHR12241;PANTHER:PTHR12241:SF91;Superfamily:SSF56059 ENSP00000491066 6/15 rs754001735;COSV60036038 ENST00000438251 Transcript ENSG00000213471 HGNC:32484 MODERATE 0.0002718 gnomAD_EAS missense_variant 0;1 probably_damaging(0.925) Unknown deleterious(0) 0;1 A6NNM8.106 TTLL13P HGNC 1 5.0 UPI0001663064 A6NNM8-1 SNV TTLL13P,missense_variant,p.R219W,ENST00000438251,,c.655C>T,MODERATE,YES,deleterious(0),probably_damaging(0.925),1;TTLL13P,missense_variant,p.R219W,ENST00000641754,,c.655C>T,MODERATE,,deleterious(0),probably_damaging(0.963),1;AC091167.7,intron_variant,,ENST00000641334,,n.458+2880C>T,MODIFIER,,,,1;TTLL13P,missense_variant,p.R219W,ENST00000617037,,c.655C>T,MODERATE,,deleterious(0),probably_damaging(0.973),1;TTLL13P,non_coding_transcript_exon_variant,,ENST00000339615,,n.945C>T,MODIFIER,,,,1;AC091167.2,intron_variant,,ENST00000561573,,c.418-891C>T,MODIFIER,YES,,,1;TTLL13P,intron_variant,,ENST00000621485,,c.411-1390C>T,MODIFIER,,,,1;AC091167.7,intron_variant,,ENST00000641199,,c.*125-891C>T,MODIFIER,YES,,,1 945/2738 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 2.386e-05 0.0 0.0 0.0 0.0002718 0.0 0.0 0.0001629 0.0 1.352320032310672e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.0867999157635495e-05 0.0 3.0867999157635495e-05 0.0 0.0 0 66 4532f82e-59f3-4df3-a0ff-a737c47d014d 29 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS TTLL13,intron_variant,NMD_transcript_variant,,ENST00000621485.4,c.411-1390C>T,MODIFIER,;TTLL13,missense_variant,p.R219W,ENST00000641754.2,c.655C>T,MODERATE,YES;ENSG00000261147,intron_variant,NMD_transcript_variant,,ENST00000561573.1,c.418-891C>T,MODIFIER,YES;TTLL13,missense_variant,p.R219W,ENST00000438251.3,c.655C>T,MODERATE,;TTLL13,missense_variant,NMD_transcript_variant,p.R219W,ENST00000617037.4,c.655C>T,MODERATE,;TTLL13,non_coding_transcript_exon_variant,,ENST00000339615.9,n.945C>T,MODIFIER,;ENSG00000284626,intron_variant,,ENST00000641334.1,n.458+2880C>T,MODIFIER,;ENSG00000284626,intron_variant,NMD_transcript_variant,,ENST00000641199.1,c.*125-891C>T,MODIFIER,YES +ZNF560 147741 BI GRCh38 19 9467714 9467714 + missense_variant Missense_Mutation SNP T T A TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 15 15 c.1233A>T p.Lys411Asn p.K411N ENST00000301480.5 NM_001351678.2 411 aaA/aaT 10/10 P1 A K/N protein_coding YES CCDS12214.1 1233/2373 AAGGCTTTACC COSM1666834 Gene3D:3.30.160.60;Pfam:PF13912;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF44;SMART:SM00355;Superfamily:SSF57667;Superfamily:SSF57667 ENSP00000301480 10/10 COSV56865256 ENST00000301480 Transcript ENSG00000198028 HGNC:26484 MODERATE NM_152476.3 missense_variant 1 1.0 probably_damaging(0.999) Unknown tolerated(0.12) 1 Q96MR9.145 ZNF560 HGNC -1 1.0 UPI000013E720 SNV ZNF560,missense_variant,p.K411N,ENST00000301480,NM_001351678.2&NM_152476.3,c.1233A>T,MODERATE,YES,tolerated(0.12),probably_damaging(0.999),-1;ZNF560,downstream_gene_variant,,ENST00000585974,,,MODIFIER,,,,-1 1456/2815 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 26 4532f82e-59f3-4df3-a0ff-a737c47d014d 30 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS ZNF560,missense_variant,p.K411N,ENST00000301480.5,c.1233A>T,MODERATE,YES +DEPDC5 9681 BI GRCh38 22 31819213 31819213 + missense_variant,NMD_transcript_variant Missense_Mutation SNP A A G TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 36 37 c.1858A>G p.Thr620Ala p.T620A ENST00000400246.7 620 Act/Gct 22/41 G T/A nonsense_mediated_decay 1858/4032 TGCACACTTTT COSM1666835;COSM1666836 ENSP00000383105 22/41 COSV56690850 ENST00000400246 Transcript 1.0 ENSG00000100150 HGNC:18423 MODERATE missense_variant 1 benign(0.145) Unknown tolerated(0.11) 1 DEPDC5 HGNC 1 A0A5F9UWT1.3 1.0 UPI001149352F SNV DEPDC5,missense_variant,p.T620A,ENST00000651528,NM_001242896.3,c.1858A>G,MODERATE,YES,tolerated(0.11),probably_damaging(0.989),1;DEPDC5,missense_variant,p.T620A,ENST00000642696,NM_001369903.1,c.1858A>G,MODERATE,,tolerated(0.12),probably_damaging(0.985),1;DEPDC5,missense_variant,p.T620A,ENST00000645711,NM_001136029.3,c.1858A>G,MODERATE,,tolerated(0.12),possibly_damaging(0.907),1;DEPDC5,missense_variant,p.T620A,ENST00000382112,NM_001364318.1,c.1858A>G,MODERATE,,tolerated(0.11),probably_damaging(0.989),1;DEPDC5,missense_variant,p.T620A,ENST00000644331,NM_001363852.2,c.1858A>G,MODERATE,,tolerated(0.12),probably_damaging(0.994),1;DEPDC5,missense_variant,p.T620A,ENST00000400249,NM_001364320.1,c.1858A>G,MODERATE,,tolerated(0.12),probably_damaging(0.994),1;DEPDC5,missense_variant,p.T592A,ENST00000433147,NM_001369902.1&NM_001369901.1,c.1774A>G,MODERATE,,tolerated(0.1),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000400248,NM_014662.5,c.1858A>G,MODERATE,,tolerated(0.12),probably_damaging(0.985),1;DEPDC5,missense_variant,p.T620A,ENST00000646969,NM_001364319.1,c.1858A>G,MODERATE,,tolerated(0.14),probably_damaging(0.987),1;DEPDC5,missense_variant,p.T620A,ENST00000646465,,c.1858A>G,MODERATE,,tolerated(0.11),probably_damaging(0.987),1;DEPDC5,missense_variant,p.T620A,ENST00000382111,,c.1858A>G,MODERATE,,tolerated(0.22),probably_damaging(0.996),1;DEPDC5,missense_variant,p.T620A,ENST00000645560,NM_001363854.2,c.1858A>G,MODERATE,,tolerated(0.14),probably_damaging(0.987),1;DEPDC5,missense_variant,p.T620A,ENST00000535622,NM_001242897.2,c.1858A>G,MODERATE,,tolerated(0.19),probably_damaging(0.952),1;DEPDC5,missense_variant,p.T628A,ENST00000645407,,c.1882A>G,MODERATE,,tolerated(0.11),probably_damaging(0.99),1;DEPDC5,missense_variant,p.T592A,ENST00000647343,,c.1774A>G,MODERATE,,tolerated(0.1),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000642974,,c.1858A>G,MODERATE,,tolerated(0.3),probably_damaging(0.987),1;DEPDC5,missense_variant,p.T620A,ENST00000645564,,c.1858A>G,MODERATE,,tolerated(0.25),probably_damaging(0.992),1;DEPDC5,missense_variant,p.T620A,ENST00000645693,,c.1858A>G,MODERATE,,tolerated(0.28),probably_damaging(0.995),1;Z82190.2,missense_variant,p.T592A,ENST00000646701,,c.1774A>G,MODERATE,YES,tolerated(0.28),probably_damaging(0.995),1;DEPDC5,downstream_gene_variant,,ENST00000400242,NM_001007188.3,,MODIFIER,,,,1;DEPDC5,downstream_gene_variant,,ENST00000646755,,,MODIFIER,,,,1;DEPDC5,downstream_gene_variant,,ENST00000647438,,,MODIFIER,,,,1;DEPDC5,missense_variant,p.T620A,ENST00000400246,,c.1858A>G,MODERATE,,tolerated(0.11),benign(0.145),1;DEPDC5,missense_variant,p.T620A,ENST00000646515,,c.1858A>G,MODERATE,,tolerated(0.23),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000645494,,c.1858A>G,MODERATE,,tolerated(0.28),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000646998,,c.1858A>G,MODERATE,,tolerated(0.21),probably_damaging(0.984),1;DEPDC5,missense_variant,p.T620A,ENST00000642771,,c.1858A>G,MODERATE,,tolerated(0.28),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000643751,,c.1858A>G,MODERATE,,tolerated(0.26),probably_damaging(0.995),1;DEPDC5,missense_variant,p.T620A,ENST00000643395,,c.1858A>G,MODERATE,,tolerated(0.34),probably_damaging(0.987),1;DEPDC5,missense_variant,p.T50A,ENST00000448753,,c.148A>G,MODERATE,,tolerated(0.23),probably_damaging(0.97),1;DEPDC5,3_prime_UTR_variant,,ENST00000642684,,c.*1551A>G,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000644162,,c.*486A>G,MODIFIER,,,,1;DEPDC5,3_prime_UTR_variant,,ENST00000645755,,c.*852A>G,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000642551,,n.1594A>G,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000645893,,n.715A>G,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000643166,,n.1945A>G,MODIFIER,,,,1;DEPDC5,non_coding_transcript_exon_variant,,ENST00000647289,,n.1489A>G,MODIFIER,,,,1;DEPDC5,downstream_gene_variant,,ENST00000645967,,,MODIFIER,,,,1;AL022331.1,upstream_gene_variant,,ENST00000429025,,,MODIFIER,YES,,,-1 1957/5725 muse;mutect2;varscan2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 43 4532f82e-59f3-4df3-a0ff-a737c47d014d 74 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS DEPDC5,missense_variant,NMD_transcript_variant,p.T50A,ENST00000448753.6,c.148A>G,MODERATE,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000647289.1,n.1489A>G,MODIFIER,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000645893.1,n.715A>G,MODIFIER,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000642551.1,n.1594A>G,MODIFIER,;DEPDC5,missense_variant,p.T628A,ENST00000645407.1,c.1882A>G,MODERATE,;ENSG00000285404,missense_variant,p.T592A,ENST00000646701.1,c.1774A>G,MODERATE,YES;DEPDC5,missense_variant,p.T620A,ENST00000382111.6,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000400249.7,c.1858A>G,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000643395.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000645564.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000646465.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000645494.1,c.1858A>G,MODERATE,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000643166.1,n.1945A>G,MODIFIER,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000646998.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000651528.2,c.1858A>G,MODERATE,YES;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000642684.1,c.*1551A>G,MODIFIER,;DEPDC5,missense_variant,p.T592A,ENST00000647343.1,c.1774A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000642696.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000646969.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000643751.2,c.1858A>G,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000646515.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000642771.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000400248.7,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000382112.8,c.1858A>G,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000644162.1,c.*486A>G,MODIFIER,;DEPDC5,missense_variant,NMD_transcript_variant,p.T620A,ENST00000400246.7,c.1858A>G,MODERATE,;DEPDC5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000645755.1,c.*852A>G,MODIFIER,;DEPDC5,missense_variant,p.T592A,ENST00000433147.2,c.1774A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000645560.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000644331.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000645711.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000645693.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000642974.1,c.1858A>G,MODERATE,;DEPDC5,missense_variant,p.T620A,ENST00000535622.6,c.1858A>G,MODERATE, +BCOR 54880 BI GRCh38 X 40073194 40073194 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9ES-01A TCGA-V4-A9ES-10A Somatic 25 30 c.2152G>C p.Asp718His p.D718H ENST00000378444.9 NM_001123385.2 718 Gat/Cat 4/15 P4 G D/H protein_coding YES CCDS48093.1 2152/5268 GGCATCTTGGT PANTHER:PTHR24117;PANTHER:PTHR24117:SF8 ENSP00000367705 4/15 ENST00000378444 Transcript 1.0 ENSG00000183337 HGNC:20893 MODERATE NM_001123385.2 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q6W2J9.159 BCOR HGNC -1 1.0 UPI00002318CF Q6W2J9-1 SNV BCOR,missense_variant,p.D718H,ENST00000378444,NM_001123385.2,c.2152G>C,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;BCOR,missense_variant,p.D718H,ENST00000342274,NM_001123383.1,c.2152G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;BCOR,missense_variant,p.D718H,ENST00000378455,NM_001123384.2,c.2152G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;BCOR,missense_variant,p.D718H,ENST00000397354,NM_017745.6,c.2152G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;BCOR,missense_variant,p.D718H,ENST00000673391,,c.2152G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;BCOR,missense_variant,p.D189H,ENST00000427012,,c.565G>C,MODERATE,,deleterious(0),possibly_damaging(0.794),-1;BCOR,missense_variant,p.D718H,ENST00000406200,,c.2152G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;BCOR,missense_variant,p.D125H,ENST00000615339,,c.373G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;BCOR,downstream_gene_variant,,ENST00000412952,,,MODIFIER,,,,-1;BCOR,downstream_gene_variant,,ENST00000672922,,,MODIFIER,,,,-1;BCOR,non_coding_transcript_exon_variant,,ENST00000490976,,n.2192G>C,MODIFIER,,,,-1 2936/6910 muse;mutect2 c510a423-6ab1-431e-9248-d2ac91fdedba 0 60 4532f82e-59f3-4df3-a0ff-a737c47d014d 55 c6ec27fc-4047-4d18-ace9-84485d794767 SUCCESS BCOR,non_coding_transcript_exon_variant,,ENST00000490976.5,n.2192G>C,MODIFIER,;BCOR,missense_variant,p.D718H,ENST00000406200.4,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000427012.3,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000673391.1,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000442018.6,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000672922.2,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000680831.1,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000378444.9,c.2152G>C,MODERATE,YES;BCOR,missense_variant,p.D718H,ENST00000615339.2,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000679513.1,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000342274.8,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000378455.8,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000397354.7,c.2152G>C,MODERATE,;BCOR,missense_variant,p.D718H,ENST00000413905.6,c.2152G>C,MODERATE, +IFNLR1 163702 BI GRCh38 1 24157781 24157781 + synonymous_variant Silent SNP C C T rs543005854 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 37 50 c.912G>A p.Pro304= p.P304= ENST00000327535.6 NM_170743.4 304 ccG/ccA 7/7 0.0002 0.0 0.0 0.0 0.0 0.001 P1 T P protein_coding YES CCDS248.1 912/1563 GGCGTCGGCCT PDB-ENSP_mappings:5l04.B;PANTHER:PTHR20859;PANTHER:PTHR20859:SF55;MobiDB_lite:mobidb-lite ENSP00000327824 7/7 rs543005854 ENST00000327535 Transcript ENSG00000185436 HGNC:18584 LOW NM_170743.4 0.001 SAS synonymous_variant 1.0 Unknown Q8IU57.152 IFNLR1 HGNC -1 1.0 UPI000004D3FC Q8IU57-1 SNV IFNLR1,synonymous_variant,p.P304=,ENST00000327535,NM_170743.4,c.912G>A,LOW,YES,,,-1;IFNLR1,synonymous_variant,p.P275=,ENST00000374421,NM_173064.3,c.825G>A,LOW,,,,-1;IFNLR1,3_prime_UTR_variant,,ENST00000327575,NM_173065.3,c.*46G>A,MODIFIER,,,,-1;IFNLR1,downstream_gene_variant,,ENST00000374418,,,MODIFIER,,,,-1;IFNLR1,downstream_gene_variant,,ENST00000374419,,,MODIFIER,,,,-1 953/4566 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 5.57e-05 0.000123 0.0001157 0.0 0.0 4.619e-05 3.519e-05 0.000163 6.533e-05 7.435750012518838e-05 2.4326200218638405e-05 0.0 0.0001324850018136 0.0 0.0 0.0001881820062408 sas 0.0004168399900663 0.0 6.171889981487766e-05 0.0 0.0004168399900663 0 138 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 87 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS IFNLR1,synonymous_variant,p.P275=,ENST00000374421.7,c.825G>A,LOW,;IFNLR1,3_prime_UTR_variant,,ENST00000327575.6,c.*46G>A,MODIFIER,;IFNLR1,synonymous_variant,p.P304=,ENST00000327535.6,c.912G>A,LOW,YES +IL12RB2 3595 BI GRCh38 1 67379991 67379991 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 42 18 c.1723C>A p.Pro575Thr p.P575T ENST00000262345.5 575 Ccc/Acc 13/16 P2 A P/T protein_coding CCDS638.1 1723/2589 AAATTCCCTAC Superfamily:SSF49265;SMART:SM00060;Gene3D:2.60.40.10;PANTHER:PTHR23036:SF79;PANTHER:PTHR23036;CDD:cd00063;PROSITE_profiles:PS50853 ENSP00000262345 13/16 ENST00000262345 Transcript ENSG00000081985 HGNC:5972 MODERATE missense_variant possibly_damaging(0.824) Unknown deleterious(0.01) Q99665.189 IL12RB2 HGNC 1 1.0 UPI0000046B13 Q99665-1 SNV IL12RB2,missense_variant,p.P575T,ENST00000674203,NM_001374259.2,c.1723C>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.824),1;IL12RB2,missense_variant,p.P575T,ENST00000262345,NM_001559.2,c.1723C>A,MODERATE,,deleterious(0.01),possibly_damaging(0.824),1;IL12RB2,missense_variant,p.P489T,ENST00000544434,NM_001258215.1,c.1465C>A,MODERATE,,tolerated(0.07),possibly_damaging(0.895),1;IL12RB2,missense_variant,p.P575T,ENST00000648487,,c.1723C>A,MODERATE,,deleterious(0.01),possibly_damaging(0.824),1;IL12RB2,missense_variant,p.P489T,ENST00000541374,,c.1465C>A,MODERATE,,deleterious(0.02),probably_damaging(0.948),1;IL12RB2,missense_variant,p.P575T,ENST00000371000,NM_001258214.1&NM_001319233.1&NM_001258216.1,c.1723C>A,MODERATE,,deleterious(0.01),benign(0.39),1;IL12RB2,non_coding_transcript_exon_variant,,ENST00000465396,,n.64C>A,MODIFIER,,,,1 2363/4040 muse;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 55 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 60 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS IL12RB2,non_coding_transcript_exon_variant,,ENST00000465396.1,n.64C>A,MODIFIER,;IL12RB2,non_coding_transcript_exon_variant,,ENST00000696763.1,n.815C>A,MODIFIER,;IL12RB2,non_coding_transcript_exon_variant,,ENST00000696762.1,n.1749C>A,MODIFIER,;IL12RB2,missense_variant,p.P575T,ENST00000648487.1,c.1723C>A,MODERATE,;IL12RB2,missense_variant,NMD_transcript_variant,p.P575T,ENST00000696759.1,c.1723C>A,MODERATE,;IL12RB2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000696758.1,c.*911C>A,MODIFIER,;IL12RB2,missense_variant,p.P575T,ENST00000696757.1,c.1723C>A,MODERATE,;IL12RB2,missense_variant,p.P575T,ENST00000674203.2,c.1723C>A,MODERATE,YES;IL12RB2,missense_variant,p.P575T,ENST00000371000.5,c.1723C>A,MODERATE,;IL12RB2,missense_variant,p.P489T,ENST00000541374.6,c.1465C>A,MODERATE,;IL12RB2,missense_variant,p.P575T,ENST00000696754.1,c.1723C>A,MODERATE,;IL12RB2,missense_variant,p.P575T,ENST00000696755.1,c.1723C>A,MODERATE,;IL12RB2,missense_variant,p.P489T,ENST00000544434.5,c.1465C>A,MODERATE,;IL12RB2,missense_variant,p.P575T,ENST00000262345.5,c.1723C>A,MODERATE, +CTTNBP2NL 55917 BI GRCh38 1 112457109 112457109 + synonymous_variant Silent SNP T T C novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 51 38 c.1617T>C p.Thr539= p.T539= ENST00000271277.11 NM_018704.3 539 acT/acC 6/6 P1 C T protein_coding YES CCDS845.1 1617/1920 AACACTGCCAA PANTHER:PTHR23166;PANTHER:PTHR23166:SF9 ENSP00000271277 6/6 ENST00000271277 Transcript ENSG00000143079 HGNC:25330 LOW NM_018704.3 synonymous_variant 1.0 Unknown Q9P2B4.140 CTTNBP2NL HGNC 1 1.0 UPI000006ED23 SNV CTTNBP2NL,synonymous_variant,p.T539=,ENST00000271277,NM_018704.3,c.1617T>C,LOW,YES,,,1;CTTNBP2NL,downstream_gene_variant,,ENST00000441739,,,MODIFIER,,,,1;MIR4256,downstream_gene_variant,,ENST00000636356,,,MODIFIER,YES,,,-1;CTTNBP2NL,non_coding_transcript_exon_variant,,ENST00000607039,,n.292T>C,MODIFIER,,,,1 1809/5864 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 82 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 89 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS CTTNBP2NL,non_coding_transcript_exon_variant,,ENST00000607039.1,n.292T>C,MODIFIER,;CTTNBP2NL,synonymous_variant,p.T539=,ENST00000271277.11,c.1617T>C,LOW,YES +ADAMTS4 9507 BI GRCh38 1 161194214 161194214 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 31 15 c.1269T>G p.Cys423Trp p.C423W ENST00000367996.6 NM_005099.6 423 tgT/tgG 5/9 P1 C C/W protein_coding YES CCDS1223.1 1269/2514 AAGAGACAGTG PDB-ENSP_mappings:2rjp.A;PDB-ENSP_mappings:2rjp.B;PDB-ENSP_mappings:2rjp.C;PDB-ENSP_mappings:2rjp.D;Gene3D:3.40.390.10;PDB-ENSP_mappings:3b2z.A;PDB-ENSP_mappings:3b2z.B;PDB-ENSP_mappings:3b2z.C;PDB-ENSP_mappings:3b2z.D;PDB-ENSP_mappings:3b2z.E;PDB-ENSP_mappings:3b2z.F;PDB-ENSP_mappings:3b2z.G;PDB-ENSP_mappings:3b2z.H;PDB-ENSP_mappings:4wk7.A;PDB-ENSP_mappings:4wke.A;PDB-ENSP_mappings:4wki.A;Pfam:PF01421;PROSITE_profiles:PS50215;PANTHER:PTHR13723;PANTHER:PTHR13723:SF38;Superfamily:SSF55486;CDD:cd04273 ENSP00000356975 5/9 ENST00000367996 Transcript ENSG00000158859 HGNC:220 MODERATE NM_005099.6 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) O75173.199 ADAMTS4 HGNC -1 1.0 UPI000014194C O75173-1 SNV ADAMTS4,missense_variant,p.C423W,ENST00000367996,NM_005099.6&NM_001320336.2,c.1269T>G,MODERATE,YES,deleterious(0),probably_damaging(1),-1;ADAMTS4,downstream_gene_variant,,ENST00000367995,,,MODIFIER,,,,-1;NDUFS2,upstream_gene_variant,,ENST00000676600,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677231,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677550,NM_001377300.1,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677579,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677846,,,MODIFIER,YES,,,1;NDUFS2,upstream_gene_variant,,ENST00000678507,NM_001377298.1,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678911,,,MODIFIER,,,,1;ADAMTS4,non_coding_transcript_exon_variant,,ENST00000478394,,n.295T>G,MODIFIER,,,,-1;NDUFS2,upstream_gene_variant,,ENST00000479948,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000496133,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000676535,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000676653,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677081,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677138,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677178,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677350,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677383,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677457,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677547,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677613,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677807,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677809,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000677925,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678052,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678492,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678605,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678613,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678793,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000678966,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000679064,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000679215,,,MODIFIER,,,,1;NDUFS2,upstream_gene_variant,,ENST00000679282,,,MODIFIER,,,,1 1696/9777 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 51 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 46 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS ADAMTS4,non_coding_transcript_exon_variant,,ENST00000478394.1,n.295T>G,MODIFIER,;ADAMTS4,missense_variant,p.C423W,ENST00000367996.6,c.1269T>G,MODERATE,YES +FBLN7 129804 BI GRCh38 2 112185308 112185308 + missense_variant Missense_Mutation SNP G G A rs937294316 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 39 3 c.916G>A p.Gly306Ser p.G306S ENST00000331203.7 NM_153214.3 306 Ggc/Agc 7/8 P1 A G/S protein_coding YES CCDS2095.1 916/1320 GCAGCGGCAAT Gene3D:2.10.25.10;Pfam:PF07645;SMART:SM00179;SMART:SM00181;PANTHER:PTHR24034:SF94;PANTHER:PTHR24034 ENSP00000331411 7/8 rs937294316;COSV55615841 ENST00000331203 Transcript ENSG00000144152 HGNC:26740 MODERATE NM_153214.3 8.795e-06 gnomAD_NFE missense_variant 0;1 1.0 benign(0.017) Unknown tolerated(0.15) 0;1 Q53RD9.138 FBLN7 HGNC 1 1.0 UPI000004E556 Q53RD9-1 SNV FBLN7,missense_variant,p.G306S,ENST00000331203,NM_153214.3,c.916G>A,MODERATE,YES,tolerated(0.15),benign(0.017),1;FBLN7,missense_variant,p.G306S,ENST00000409903,,c.916G>A,MODERATE,,tolerated(0.08),benign(0.405),1;FBLN7,missense_variant,p.G128S,ENST00000272559,,c.382G>A,MODERATE,,tolerated(0.15),benign(0.109),1;FBLN7,missense_variant,p.G260S,ENST00000409450,NM_001128165.1,c.778G>A,MODERATE,,tolerated(0.14),benign(0.027),1;FBLN7,missense_variant,p.G172S,ENST00000409667,,c.514G>A,MODERATE,,tolerated(0.24),benign(0.045),1;FBLN7,missense_variant,p.G200S,ENST00000441565,,c.598G>A,MODERATE,,tolerated(0.17),benign(0.025),1;AC092645.1,upstream_gene_variant,,ENST00000624058,,,MODIFIER,YES,,,1 1187/2303 muse;mutect2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 3.979e-06 0.0 0.0 0.0 0.0 0.0 8.795e-06 0.0 0.0 2.704090002225712e-05 2.4323799152625725e-05 0.0 0.0 0.0 0.0 0.0 nfe 4.629340037354268e-05 0.0 4.629340037354268e-05 0.0 0.0 0 56 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 42 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS FBLN7,missense_variant,p.G128S,ENST00000272559.4,c.382G>A,MODERATE,;FBLN7,missense_variant,p.G200S,ENST00000441565.5,c.598G>A,MODERATE,;FBLN7,missense_variant,p.G172S,ENST00000409667.7,c.514G>A,MODERATE,;FBLN7,missense_variant,p.G260S,ENST00000409450.7,c.778G>A,MODERATE,;FBLN7,missense_variant,p.G306S,ENST00000409903.5,c.916G>A,MODERATE,;FBLN7,missense_variant,p.G306S,ENST00000331203.7,c.916G>A,MODERATE,YES +DNER 92737 BI GRCh38 2 229367000 229367000 + missense_variant Missense_Mutation SNP C C T rs370587377 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 12 7 c.1975G>A p.Val659Met p.V659M ENST00000341772.5 NM_139072.4 659 Gtg/Atg 12/13 P1 T V/M protein_coding YES CCDS33390.1 1975/2214 CCCCACGATCA PANTHER:PTHR24044;PANTHER:PTHR24044:SF420;Transmembrane_helices:TMhelix ENSP00000345229 0.0 0.0001163 12/13 rs370587377 ENST00000341772 Transcript ENSG00000187957 HGNC:24456 MODERATE NM_139072.4 0.0001163 EA missense_variant 1.0 probably_damaging(0.997) Unknown deleterious(0) Q8NFT8.150 DNER HGNC -1 1.0 UPI0000048EB8 SNV DNER,missense_variant,p.V659M,ENST00000341772,NM_139072.4,c.1975G>A,MODERATE,YES,deleterious(0),probably_damaging(0.997),-1 2107/3257 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 7.963e-06 0.0 0.0 0.0 0.0 0.0 8.805e-06 0.0 3.268e-05 0 29 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 19 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS DNER,missense_variant,p.V659M,ENST00000341772.5,c.1975G>A,MODERATE,YES +PRDM8 56978 BI GRCh38 4 80202310 80202310 + missense_variant Missense_Mutation SNP T T A novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 9 8 c.848T>A p.Leu283His p.L283H ENST00000339711.8 NM_020226.4 283 cTc/cAc 10/10 P1 A L/H protein_coding YES CCDS43243.1 848/2070 GAGCCTCAGCA Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR16516:SF7;PANTHER:PTHR16516 ENSP00000339764 10/10 ENST00000339711 Transcript 1.0 ENSG00000152784 HGNC:13993 MODERATE missense_variant 1.0 possibly_damaging(0.552) Unknown deleterious_low_confidence(0.02) Q9NQV8.160 PRDM8 HGNC 1 A0A024RDC4.47 1.0 UPI0000422A1D Q9NQV8-1 SNV PRDM8,missense_variant,p.L283H,ENST00000339711,NM_020226.3,c.848T>A,MODERATE,YES,deleterious_low_confidence(0.02),possibly_damaging(0.552),1;PRDM8,missense_variant,p.L283H,ENST00000504452,,c.848T>A,MODERATE,,deleterious_low_confidence(0.02),possibly_damaging(0.552),1;PRDM8,missense_variant,p.L283H,ENST00000415738,NM_001099403.2,c.848T>A,MODERATE,,deleterious_low_confidence(0.02),possibly_damaging(0.552),1;PRDM8,missense_variant,p.L283H,ENST00000515013,,c.848T>A,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.552),1;AC021127.1,upstream_gene_variant,,ENST00000653209,,,MODIFIER,YES,,,-1 2079/4095 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 16 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 17 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS PRDM8,missense_variant,p.L283H,ENST00000415738.3,c.848T>A,MODERATE,YES;PRDM8,missense_variant,p.L283H,ENST00000515013.5,c.848T>A,MODERATE,;PRDM8,missense_variant,p.L283H,ENST00000339711.8,c.848T>A,MODERATE,;PRDM8,missense_variant,p.L283H,ENST00000504452.5,c.848T>A,MODERATE, +GRID2 2895 BI GRCh38 4 93772342 93772342 + synonymous_variant Silent SNP C C T rs775585013 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 39 20 c.2868C>T p.Asn956= p.N956= ENST00000282020.9 NM_001510.4 956 aaC/aaT 16/16 P1 T N protein_coding YES CCDS3637.1 2868/3024 GGCAACGTGCC PANTHER:PTHR18966;PANTHER:PTHR18966:SF109 ENSP00000282020 16/16 rs775585013 ENST00000282020 Transcript 1.0 ENSG00000152208 HGNC:4576 LOW NM_001510.4 0.0001633 gnomAD_OTH synonymous_variant 1.0 Unknown O43424.180 GRID2 HGNC 1 1.0 UPI00001AEA78 O43424-1 SNV GRID2,synonymous_variant,p.N956=,ENST00000282020,NM_001510.4,c.2868C>T,LOW,YES,,,1;GRID2,synonymous_variant,p.N875=,ENST00000611049,,c.2625C>T,LOW,,,,1;GRID2,synonymous_variant,p.N861=,ENST00000510992,NM_001286838.1,c.2583C>T,LOW,,,,1;GRID2,intron_variant,,ENST00000637838,,c.221+2892C>T,MODIFIER,,,,1 3559/5783 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 2.392e-05 6.153e-05 2.895e-05 0.0 5.438e-05 4.622e-05 0.0 0.0001633 3.266e-05 1.3520299944502767e-05 4.864999937126413e-05 0.0 0.0 0.0 0.0 0.0 afr 4.864999937126413e-05 0.0 0.0 0.0 0.0 0 47 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 59 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS GRID2,intron_variant,,ENST00000637838.1,c.221+2892C>T,MODIFIER,;GRID2,synonymous_variant,p.N875=,ENST00000611049.4,c.2625C>T,LOW,;GRID2,synonymous_variant,p.N861=,ENST00000510992.5,c.2583C>T,LOW,;GRID2,synonymous_variant,p.N956=,ENST00000282020.9,c.2868C>T,LOW,YES +SLC22A5 6584 BI GRCh38 5 132378465 132378465 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 109 64 c.481G>T p.Gly161Trp p.G161W ENST00000245407.8 NM_003060.4 161 Ggg/Tgg 2/10 P1 T G/W protein_coding CCDS4154.1 481/1674 TTTCAGGGCAG Transmembrane_helices:TMhelix;PROSITE_profiles:PS50850;CDD:cd17376;PANTHER:PTHR24064;PANTHER:PTHR24064:SF283;PROSITE_patterns:PS00216;Pfam:PF00083;Gene3D:1.20.1250.20;TIGRFAM:TIGR00898;Superfamily:SSF103473 ENSP00000245407 2/10 ENST00000245407 Transcript 1.0 ENSG00000197375 HGNC:10969 MODERATE NM_003060.4 missense_variant probably_damaging(1) Unknown deleterious(0) O76082.188 SLC22A5 HGNC 1 1.0 UPI0000130BB6 O76082-1 SNV SLC22A5,missense_variant,p.G161W,ENST00000245407,NM_003060.4,c.481G>T,MODERATE,,deleterious(0),probably_damaging(1),1;SLC22A5,missense_variant,p.G185W,ENST00000435065,NM_001308122.1,c.553G>T,MODERATE,YES,deleterious(0),probably_damaging(1),1;SLC22A5,missense_variant,p.G84W,ENST00000415928,,c.250G>T,MODERATE,,deleterious(0),probably_damaging(1),1;SLC22A5,non_coding_transcript_exon_variant,,ENST00000461013,,n.2238G>T,MODIFIER,,,,1;SLC22A5,intron_variant,,ENST00000437841,,c.394-6863G>T,MODIFIER,,,,1 744/3277 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 156 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 174 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS SLC22A5,missense_variant,NMD_transcript_variant,p.Q11H,ENST00000692355.1,c.33G>T,MODERATE,;SLC22A5,non_coding_transcript_exon_variant,,ENST00000461013.5,n.2238G>T,MODIFIER,;SLC22A5,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000692825.1,c.*132G>T,MODIFIER,;SLC22A5,intron_variant,NMD_transcript_variant,,ENST00000437841.6,c.394-6863G>T,MODIFIER,;SLC22A5,missense_variant,NMD_transcript_variant,p.G161W,ENST00000690900.1,c.481G>T,MODERATE,;SLC22A5,missense_variant,NMD_transcript_variant,p.G161W,ENST00000448810.6,c.481G>T,MODERATE,;SLC22A5,missense_variant,p.G161W,ENST00000415928.6,c.481G>T,MODERATE,;SLC22A5,missense_variant,p.G161W,ENST00000693308.1,c.481G>T,MODERATE,;SLC22A5,non_coding_transcript_exon_variant,,ENST00000693763.1,n.615G>T,MODIFIER,;SLC22A5,missense_variant,NMD_transcript_variant,p.G161W,ENST00000686757.1,c.481G>T,MODERATE,;SLC22A5,missense_variant,p.G161W,ENST00000689271.1,c.481G>T,MODERATE,;SLC22A5,missense_variant,p.G161W,ENST00000692413.1,c.481G>T,MODERATE,;SLC22A5,non_coding_transcript_exon_variant,,ENST00000687740.1,n.615G>T,MODIFIER,;SLC22A5,missense_variant,p.G185W,ENST00000435065.7,c.553G>T,MODERATE,;SLC22A5,missense_variant,p.G161W,ENST00000245407.8,c.481G>T,MODERATE,YES +KDM3B 51780 BI GRCh38 5 138415133 138415133 + synonymous_variant,splice_region_variant Silent SNP G G A novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 38 10 c.3201G>A p.Glu1067= p.E1067= ENST00000314358.10 NM_016604.4 1067 gaG/gaA 12/24 P1 A E protein_coding YES CCDS34242.1 3201/5286 TCAGAGACAGA PANTHER:PTHR12549;PANTHER:PTHR12549:SF8 ENSP00000326563 12/24 ENST00000314358 Transcript 1.0 ENSG00000120733 HGNC:1337 LOW NM_016604.4 splice_region_variant 1.0 Unknown Q7LBC6.136 KDM3B HGNC 1 1.0 UPI000020C6A8 Q7LBC6-1 SNV KDM3B,splice_region_variant,p.E1067=,ENST00000314358,NM_016604.4,c.3201G>A,LOW,YES,,,1;KDM3B,splice_region_variant,p.E65=,ENST00000542866,,c.195G>A,LOW,,,,1;KDM3B,upstream_gene_variant,,ENST00000508386,,,MODIFIER,,,,1;KDM3B,splice_region_variant,,ENST00000510866,,c.*2086G>A,LOW,,,,1;KDM3B,splice_region_variant,,ENST00000507996,,c.*554G>A,LOW,,,,1 3312/6724 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 22 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 48 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS KDM3B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000507996.5,c.*554G>A,MODIFIER,;KDM3B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000510866.5,c.*2086G>A,MODIFIER,;KDM3B,synonymous_variant,splice_region_variant,p.E1067=,ENST00000314358.10,c.3201G>A,LOW,YES +PTK7 5754 BI GRCh38 6 43143460 43143460 + synonymous_variant Silent SNP C C G novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 56 29 c.2091C>G p.Pro697= p.P697= ENST00000230419.9 NM_002821.5 697 ccC/ccG 14/20 P1 G P protein_coding CCDS4884.1 2091/3213 CCTCCCCCCTA PANTHER:PTHR24416;PANTHER:PTHR24416:SF521;Low_complexity_(Seg):seg ENSP00000230419 14/20 ENST00000230419 Transcript ENSG00000112655 HGNC:9618 LOW NM_002821.5 synonymous_variant Unknown Q13308.196 PTK7 HGNC 1 1.0 UPI0000001BDB Q13308-1 SNV PTK7,synonymous_variant,p.P697=,ENST00000230419,NM_002821.5,c.2091C>G,LOW,,,,1;PTK7,synonymous_variant,p.P657=,ENST00000345201,NM_152880.4,c.1971C>G,LOW,,,,1;PTK7,synonymous_variant,p.P641=,ENST00000352931,NM_152882.4,c.1923C>G,LOW,,,,1;PTK7,synonymous_variant,p.P567=,ENST00000349241,NM_152881.4,c.1701C>G,LOW,,,,1;PTK7,synonymous_variant,p.P705=,ENST00000481273,NM_001270398.1,c.2115C>G,LOW,YES,,,1;PTK7,intron_variant,,ENST00000489707,,c.312-1760C>G,MODIFIER,,,,1;PTK7,upstream_gene_variant,,ENST00000473339,,,MODIFIER,,,,1;PTK7,downstream_gene_variant,,ENST00000481946,,,MODIFIER,,,,1;PTK7,synonymous_variant,p.P697=,ENST00000230418,,c.2091C>G,LOW,,,,1;PTK7,3_prime_UTR_variant,,ENST00000470019,,c.*1426C>G,MODIFIER,,,,1;PTK7,3_prime_UTR_variant,,ENST00000497957,,c.*88C>G,MODIFIER,,,,1;PTK7,3_prime_UTR_variant,,ENST00000494146,,c.*120C>G,MODIFIER,,,,1;PTK7,3_prime_UTR_variant,,ENST00000461100,,c.*92C>G,MODIFIER,,,,1;PTK7,non_coding_transcript_exon_variant,,ENST00000487673,,n.3328C>G,MODIFIER,,,,1;PTK7,non_coding_transcript_exon_variant,,ENST00000493339,,n.1113C>G,MODIFIER,,,,1;PTK7,upstream_gene_variant,,ENST00000461389,,,MODIFIER,,,,1;PTK7,downstream_gene_variant,,ENST00000470471,,,MODIFIER,,,,1 2266/4222 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 90 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 85 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS PTK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000497957.1,c.*88C>G,MODIFIER,;PTK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000461100.5,c.*92C>G,MODIFIER,;PTK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000494146.5,c.*120C>G,MODIFIER,;PTK7,non_coding_transcript_exon_variant,,ENST00000493339.1,n.1113C>G,MODIFIER,;PTK7,intron_variant,,ENST00000489707.5,c.312-1760C>G,MODIFIER,;PTK7,synonymous_variant,p.P705=,ENST00000481273.5,c.2115C>G,LOW,;PTK7,non_coding_transcript_exon_variant,,ENST00000487673.5,n.3328C>G,MODIFIER,;PTK7,synonymous_variant,p.P657=,ENST00000345201.6,c.1971C>G,LOW,;PTK7,synonymous_variant,NMD_transcript_variant,p.P697=,ENST00000230418.8,c.2091C>G,LOW,;PTK7,synonymous_variant,p.P567=,ENST00000349241.6,c.1701C>G,LOW,;PTK7,synonymous_variant,p.P641=,ENST00000352931.6,c.1923C>G,LOW,;PTK7,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000470019.5,c.*1426C>G,MODIFIER,;PTK7,synonymous_variant,p.P697=,ENST00000230419.9,c.2091C>G,LOW,YES +CPVL 54504 BI GRCh38 7 29064228 29064228 + stop_gained Nonsense_Mutation SNP C C A novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 27 12 c.970G>T p.Glu324Ter p.E324* ENST00000265394.10 NM_001371262.1 324 Gag/Tag 11/13 P1 A E/* protein_coding CCDS5419.1 970/1431 ATCCTCAGGTT Gene3D:3.40.50.1820;Pfam:PF00450;PANTHER:PTHR11802;PANTHER:PTHR11802:SF98;Superfamily:SSF53474 ENSP00000265394 11/13 ENST00000265394 Transcript ENSG00000106066 HGNC:14399 HIGH NM_031311.5 stop_gained Unknown Q9H3G5.160 CPVL HGNC -1 A0A024RA40.36 1.0 UPI0000048F1B SNV CPVL,stop_gained,p.E324*,ENST00000409850,NM_001371268.1&NM_001371258.1&NM_001371256.1&NM_001371266.1&NM_001371265.1&NM_001371261.1&NM_001371264.1&NM_001371260.1&NM_001371255.1&NM_001371257.1&NM_001371263.1&NM_001371267.1&NM_001348052.1,c.970G>T,HIGH,YES,,,-1;CPVL,stop_gained,p.E324*,ENST00000265394,NM_001371262.1&NM_001348054.1&NM_019029.3&NM_031311.5,c.970G>T,HIGH,,,,-1;CPVL,stop_gained,p.E324*,ENST00000396276,,c.970G>T,HIGH,,,,-1;CPVL,stop_gained,p.E28*,ENST00000432534,,c.82G>T,HIGH,,,,-1;CPVL,intron_variant,,ENST00000455893,,c.132+7545G>T,MODIFIER,,,,-1;CPVL,downstream_gene_variant,,ENST00000448959,,,MODIFIER,,,,-1 1089/2087 muse;mutect2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 41 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 39 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS CPVL,stop_gained,p.E324*,ENST00000409850.5,c.970G>T,HIGH,;CPVL,intron_variant,,ENST00000455893.6,c.132+7545G>T,MODIFIER,;CPVL,stop_lost,p.*27Lext*14,ENST00000432534.5,c.80G>T,HIGH,;CPVL,stop_gained,p.E324*,ENST00000396276.7,c.970G>T,HIGH,;CPVL,stop_gained,p.E324*,ENST00000265394.10,c.970G>T,HIGH,YES +RPS25 6230 BI GRCh38 11 119017471 119017471 + synonymous_variant Silent SNP G G C novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 43 16 c.174C>G p.Leu58= p.L58= ENST00000527673.2 NM_001028.3 58 ctC/ctG 3/5 P1 C L protein_coding YES CCDS8406.1 174/378 TTACAGAGTTT Gene3D:1.10.10.10;PDB-ENSP_mappings:4ug0.SZ;PDB-ENSP_mappings:4v6x.AZ;PDB-ENSP_mappings:5a2q.Z;PDB-ENSP_mappings:5aj0.BZ;PDB-ENSP_mappings:5flx.Z;PDB-ENSP_mappings:5lks.SZ;PDB-ENSP_mappings:5oa3.Z;PDB-ENSP_mappings:5t2c.AR;PDB-ENSP_mappings:5vyc.Z1;PDB-ENSP_mappings:5vyc.Z2;PDB-ENSP_mappings:5vyc.Z3;PDB-ENSP_mappings:5vyc.Z4;PDB-ENSP_mappings:5vyc.Z5;PDB-ENSP_mappings:5vyc.Z6;PDB-ENSP_mappings:6ek0.SZ;PDB-ENSP_mappings:6fec.W;PDB-ENSP_mappings:6g18.Z;PDB-ENSP_mappings:6g4s.Z;PDB-ENSP_mappings:6g4w.Z;PDB-ENSP_mappings:6g51.Z;PDB-ENSP_mappings:6g53.Z;PDB-ENSP_mappings:6g5h.Z;PDB-ENSP_mappings:6g5i.Z;PDB-ENSP_mappings:6ip5.3O;PDB-ENSP_mappings:6ip6.3O;PDB-ENSP_mappings:6ip8.3O;PDB-ENSP_mappings:6ole.SZ;PDB-ENSP_mappings:6olf.SZ;PDB-ENSP_mappings:6olg.BZ;PDB-ENSP_mappings:6oli.SZ;PDB-ENSP_mappings:6olz.BZ;PDB-ENSP_mappings:6om0.SZ;PDB-ENSP_mappings:6om7.SZ;PDB-ENSP_mappings:6qzp.SZ;PDB-ENSP_mappings:6y0g.SZ;PDB-ENSP_mappings:6y2l.SZ;PDB-ENSP_mappings:6y57.SZ;Pfam:PF03297;PANTHER:PTHR12850;PANTHER:PTHR12850:SF19 ENSP00000435096 3/5 ENST00000527673 Transcript ENSG00000118181 HGNC:10413 LOW NM_001028.3 synonymous_variant 1.0 Unknown P62851.161 RPS25 HGNC -1 1.0 UPI000000411C SNV RPS25,synonymous_variant,p.L58=,ENST00000527673,NM_001028.3,c.174C>G,LOW,YES,,,-1;CENATAC,downstream_gene_variant,,ENST00000334418,NM_198489.3,,MODIFIER,YES,,,1;TRAPPC4,upstream_gene_variant,,ENST00000359005,NM_001318488.2,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000434101,NM_001318489.2,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000525303,NM_001318494.2,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000528230,NM_001318490.2,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000533058,,,MODIFIER,YES,,,1;TRAPPC4,upstream_gene_variant,,ENST00000533632,NM_001318492.2&NM_016146.6&NM_001318486.2,,MODIFIER,,,,1;AP003392.15,upstream_gene_variant,,ENST00000577421,,,MODIFIER,YES,,,1;TRAPPC4,upstream_gene_variant,,ENST00000526141,,,MODIFIER,,,,1;RPS25,downstream_gene_variant,,ENST00000528547,,,MODIFIER,,,,-1;CENATAC,downstream_gene_variant,,ENST00000580556,,,MODIFIER,,,,1;RPS25,3_prime_UTR_variant,,ENST00000532567,,c.*87C>G,MODIFIER,,,,-1;RPS25,non_coding_transcript_exon_variant,,ENST00000527853,,n.1221C>G,MODIFIER,,,,-1;RPS25,non_coding_transcript_exon_variant,,ENST00000524864,,n.968C>G,MODIFIER,,,,-1;RPS25,intron_variant,,ENST00000527791,,c.100-38C>G,MODIFIER,,,,-1;TRAPPC4,upstream_gene_variant,,ENST00000447216,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000524797,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000525079,,,MODIFIER,,,,1;CENATAC,downstream_gene_variant,,ENST00000526463,,,MODIFIER,,,,1;CENATAC,downstream_gene_variant,,ENST00000527356,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000527680,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000531290,,,MODIFIER,,,,1;CENATAC,downstream_gene_variant,,ENST00000532132,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000533012,,,MODIFIER,,,,1;TRAPPC4,upstream_gene_variant,,ENST00000533149,,,MODIFIER,,,,1;CENATAC,downstream_gene_variant,,ENST00000533787,,,MODIFIER,,,,1;CENATAC,downstream_gene_variant,,ENST00000583842,,,MODIFIER,,,,1 233/483 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 65 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 59 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS RPS25,non_coding_transcript_exon_variant,,ENST00000524864.1,n.968C>G,MODIFIER,;RPS25,non_coding_transcript_exon_variant,,ENST00000527853.1,n.1221C>G,MODIFIER,;RPS25,synonymous_variant,p.L58=,ENST00000527673.2,c.174C>G,LOW,YES;RPS25,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000532567.5,c.*87C>G,MODIFIER,;RPS25,intron_variant,NMD_transcript_variant,,ENST00000527791.5,c.100-38C>G,MODIFIER, +CGNL1 84952 BI GRCh38 15 57545624 57545624 + missense_variant Missense_Mutation SNP G G A rs757609826 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 12 8 c.3533G>A p.Arg1178Gln p.R1178Q ENST00000281282.6 NM_001252335.2 1178 cGg/cAg 17/19 P1 A R/Q protein_coding YES CCDS10161.1 3533/3909 CCGGCGGCTGG Coiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR46349;PANTHER:PTHR46349:SF2 ENSP00000281282 17/19 rs757609826 ENST00000281282 Transcript ENSG00000128849 HGNC:25931 MODERATE NM_032866.5 0.0002298 gnomAD_SAS missense_variant 1.0 probably_damaging(0.945) Unknown deleterious(0) Q0VF96.98 CGNL1 HGNC 1 1.0 UPI000019B4EF Q0VF96-1 SNV CGNL1,missense_variant,p.R1178Q,ENST00000281282,NM_001252335.2&NM_032866.5,c.3533G>A,MODERATE,YES,deleterious(0),probably_damaging(0.945),1 3611/7214 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 3.601e-05 6.21e-05 0.0 0.0 0.0 0.0 8.84e-06 0.0 0.0002298 2.027379923674744e-05 2.4304899852722883e-05 0.0 0.0 0.0 0.0 0.0 0.0 1.5429699487867765e-05 0.0 0.0002084199950331 0 23 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 20 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS CGNL1,missense_variant,p.R1178Q,ENST00000281282.6,c.3533G>A,MODERATE,YES +THSD4 79875 BI GRCh38 15 71771142 71771142 + missense_variant Missense_Mutation SNP T T G novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 75 55 c.2848T>G p.Cys950Gly p.C950G ENST00000355327.7 NM_001394532.1 950 Tgt/Ggt 17/18 P1 G C/G protein_coding YES CCDS10238.2 2848/3057 ACCTCTGTGAC Gene3D:2.20.100.10;Pfam:PF19030;PROSITE_profiles:PS50092;PANTHER:PTHR13723;PANTHER:PTHR13723:SF16;SMART:SM00209;Superfamily:SSF82895 ENSP00000347484 17/18 ENST00000355327 Transcript ENSG00000187720 HGNC:25835 MODERATE missense_variant 1.0 possibly_damaging(0.688) Unknown deleterious(0) Q6ZMP0.135 THSD4 HGNC 1 5.0 UPI00001A797D Q6ZMP0-1 SNV THSD4,missense_variant,p.C950G,ENST00000355327,NM_024817.2,c.2848T>G,MODERATE,YES,deleterious(0),possibly_damaging(0.688),1;THSD4,missense_variant,p.C590G,ENST00000357769,NM_001286429.2,c.1768T>G,MODERATE,,deleterious(0.01),possibly_damaging(0.688),1;THSD4,intron_variant,,ENST00000261862,,c.270-9400T>G,MODIFIER,,,,1;THSD4,downstream_gene_variant,,ENST00000567838,,,MODIFIER,,,,1 2982/9200 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 93 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 130 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS THSD4,missense_variant,p.C590G,ENST00000357769.4,c.1768T>G,MODERATE,;THSD4,missense_variant,p.C950G,ENST00000261862.8,c.2848T>G,MODERATE,YES;THSD4,missense_variant,p.C950G,ENST00000355327.7,c.2848T>G,MODERATE, +PRKCB 5579 BI GRCh38 16 24185548 24185548 + missense_variant Missense_Mutation SNP C C T TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 36 28 c.1703C>T p.Ala568Val p.A568V ENST00000643927.1 NM_002738.7 568 gCt/gTt 15/17 A1 T A/V protein_coding CCDS10618.1 1703/2016 GGAAGCTGTGG Gene3D:1.10.510.10;PDB-ENSP_mappings:2i0e.A;PDB-ENSP_mappings:2i0e.B;Pfam:PF00069;PIRSF:PIRSF000550;PROSITE_profiles:PS50011;PANTHER:PTHR24356;PANTHER:PTHR24356:SF158;SMART:SM00220;Superfamily:SSF56112;CDD:cd05616 ENSP00000318315 15/17 COSV100332745 ENST00000321728 Transcript 1.0 ENSG00000166501 HGNC:9395 MODERATE missense_variant 1 probably_damaging(0.981) Unknown deleterious(0) 1 P05771.242 PRKCB HGNC 1 1.0 UPI000012DF67 P05771-1 SNV PRKCB,missense_variant,p.A568V,ENST00000643927,NM_002738.7,c.1703C>T,MODERATE,YES,deleterious(0),probably_damaging(0.967),1;PRKCB,missense_variant,p.A568V,ENST00000321728,NM_212535.3,c.1703C>T,MODERATE,,deleterious(0),probably_damaging(0.981),1;PRKCB,missense_variant,p.A7V,ENST00000466124,,c.20C>T,MODERATE,,deleterious(0.01),possibly_damaging(0.867),1;PRKCB,downstream_gene_variant,,ENST00000472066,,,MODIFIER,,,,1;PRKCB,non_coding_transcript_exon_variant,,ENST00000487674,,n.674C>T,MODIFIER,,,,1 1896/2707 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 56 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 65 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS PRKCB,synonymous_variant,p.S6=,ENST00000466124.1,c.18C>T,LOW,;PRKCB,non_coding_transcript_exon_variant,,ENST00000487674.1,n.674C>T,MODIFIER,;PRKCB,missense_variant,p.A568V,ENST00000643927.1,c.1703C>T,MODERATE,YES;PRKCB,missense_variant,p.A568V,ENST00000321728.12,c.1703C>T,MODERATE, +CEP192 55125 BI GRCh38 18 13096256 13096256 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 48 25 c.6506G>T p.Trp2169Leu p.W2169L ENST00000506447.5 NM_032142.4 2169 tGg/tTg 36/45 P1 T W/L protein_coding YES CCDS32792.2 6506/7614 GTGCTGGCCAG PANTHER:PTHR16029 ENSP00000427550 36/45 ENST00000506447 Transcript ENSG00000101639 HGNC:25515 MODERATE NM_032142.4 missense_variant 1.0 probably_damaging(0.999) Unknown deleterious(0) Q8TEP8.136 CEP192 HGNC 1 5.0 UPI0001B09235 Q8TEP8-3 SNV CEP192,missense_variant,p.W2169L,ENST00000506447,NM_032142.4,c.6506G>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;CEP192,missense_variant,p.W1694L,ENST00000325971,,c.5081G>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;CEP192,missense_variant,p.W1708L,ENST00000511820,,c.5123G>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;CEP192,3_prime_UTR_variant,,ENST00000430049,,c.*498G>T,MODIFIER,,,,1;CEP192,non_coding_transcript_exon_variant,,ENST00000540847,,n.1111G>T,MODIFIER,,,,1;CEP192,downstream_gene_variant,,ENST00000507254,,,MODIFIER,,,,1;CEP192,missense_variant,p.W1769L,ENST00000510237,,c.5306G>T,MODERATE,,deleterious(0),probably_damaging(1),1;CEP192,missense_variant,p.W717L,ENST00000589993,,c.2150G>T,MODERATE,,deleterious(0.05),probably_damaging(0.998),1;CEP192,3_prime_UTR_variant,,ENST00000513432,,c.*6022G>T,MODIFIER,,,,1;CEP192,downstream_gene_variant,,ENST00000508150,,,MODIFIER,,,,1 6586/7960 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 55 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 73 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS CEP192,non_coding_transcript_exon_variant,,ENST00000540847.6,n.1111G>T,MODIFIER,;CEP192,missense_variant,NMD_transcript_variant,p.G717C,ENST00000589993.5,c.2149G>T,MODERATE,;CEP192,missense_variant,NMD_transcript_variant,p.W1769L,ENST00000510237.5,c.5306G>T,MODERATE,;CEP192,missense_variant,p.G1708C,ENST00000511820.6,c.5122G>T,MODERATE,;CEP192,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000513432.5,c.*6022G>T,MODIFIER,;CEP192,missense_variant,p.W1694L,ENST00000325971.12,c.5081G>T,MODERATE,;CEP192,missense_variant,p.W2169L,ENST00000506447.5,c.6506G>T,MODERATE,YES +TIMM50 6829 BI GRCh38 19 39480713 39480728 + frameshift_variant Frame_Shift_Del DEL TGCGGCAATCCGCCCG TGCGGCAATCCGCCCG - novel TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 13 8 c.169_184del p.Cys57MetfsTer122 p.C57Mfs*122 ENST00000544017.5 NM_001111020.3 P2 - protein_coding CGCGCCTGCGGCAATCCGCCCGATGCC 110.0 ENSP00000475531 ENST00000607714 Transcript 1.0 ENSG00000105197 HGNC:23656 MODIFIER NM_001001563.5 upstream_gene_variant Unknown Q3ZCQ8.150 TIMM50 HGNC 1 1.0 UPI0000202335 Q3ZCQ8-1 deletion TIMM50,frameshift_variant,p.C57Mfs*122,ENST00000544017,,c.169_184del,HIGH,YES,,,1;SUPT5H,downstream_gene_variant,,ENST00000359191,,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000402194,NM_001130825.1&NM_001319991.2,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000432763,NM_001111020.3&NM_001130824.2&NM_001319990.2,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000594583,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000597666,,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000598725,NM_003169.3,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000599117,,,MODIFIER,YES,,,1;TIMM50,upstream_gene_variant,,ENST00000599794,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000601403,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000602028,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000607714,NM_001001563.5&NM_001329559.2,,MODIFIER,,,,1;TIMM50,5_prime_UTR_variant,,ENST00000601358,,c.-141_-126del,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000595286,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000595961,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000596239,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000597782,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000598125,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000599733,,,MODIFIER,,,,1;SUPT5H,downstream_gene_variant,,ENST00000600818,,,MODIFIER,,,,1;TIMM50,upstream_gene_variant,,ENST00000602265,,,MODIFIER,,,,1 mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 36 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 21 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS TIMM50,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000601358.5,c.-141_-126del,MODIFIER,;TIMM50,frameshift_variant,p.C57Mfs*122,ENST00000544017.5,c.169_184del,HIGH, +PLCB4 5332 BI GRCh38 20 9409106 9409106 + missense_variant Missense_Mutation SNP G G T rs1568763104 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 49 31 c.1834G>T p.Asp612Tyr p.D612Y ENST00000278655.9 NM_182797.3 630 Gat/Tat 21/36 P4 T D/Y protein_coding CCDS13105.1 1888/3528 pathogenic GAGTCGATTCC COSM1666823 Gene3D:3.20.20.190;Pfam:PF00387;PIRSF:PIRSF000956;Prints:PR00390;PROSITE_profiles:PS50008;PANTHER:PTHR10336;PANTHER:PTHR10336:SF106;SMART:SM00149;Superfamily:SSF51695;CDD:cd08591 ENSP00000278655 21/36 rs1568763104;COSV53793606;COSV53801055 ENST00000278655 Transcript 1.0 ENSG00000101333 HGNC:9059 MODERATE missense_variant 1;1;1 probably_damaging(0.999) Unknown deleterious(0) 0;1;1 Q15147.204 PLCB4 HGNC 1 1.0 UPI0000131A94 Q15147-1 SNV PLCB4,missense_variant,p.D630Y,ENST00000378501,NM_001377134.2&NM_000933.4&NM_001377135.1,c.1888G>T,MODERATE,,deleterious(0),probably_damaging(0.995),1;PLCB4,missense_variant,p.D630Y,ENST00000378493,,c.1888G>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;PLCB4,missense_variant,p.D642Y,ENST00000378473,NM_001377142.1&NM_001377143.1,c.1924G>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;PLCB4,missense_variant,p.D630Y,ENST00000278655,NM_182797.3&NM_001377136.1,c.1888G>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;PLCB4,missense_variant,p.D642Y,ENST00000414679,NM_001172646.2,c.1924G>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,,n.1903G>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,,n.1665G>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,,n.1615G>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,,n.1579G>T,MODIFIER,,,,1 1966/5430 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 68 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 80 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS PLCB4,non_coding_transcript_exon_variant,,ENST00000688465.1,n.728G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000688049.1,n.1399G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000689976.1,n.979G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000687147.1,n.1456G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151.5,n.1579G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123.1,n.1615G>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199.5,n.1665G>T,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000689392.1,c.*1839G>T,MODIFIER,;PLCB4,missense_variant,NMD_transcript_variant,p.D630Y,ENST00000492632.5,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D612Y,ENST00000278655.9,c.1834G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000693005.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000688656.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000685310.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D535Y,ENST00000693090.1,c.1603G>T,MODERATE,;PLCB4,missense_variant,p.D612Y,ENST00000686253.1,c.1834G>T,MODERATE,;PLCB4,missense_variant,p.D535Y,ENST00000692395.1,c.1603G>T,MODERATE,;PLCB4,missense_variant,p.D634Y,ENST00000686893.1,c.1900G>T,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000685446.1,n.2086G>T,MODIFIER,;PLCB4,missense_variant,p.D479Y,ENST00000685482.1,c.1435G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000692085.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D562Y,ENST00000689010.1,c.1684G>T,MODERATE,;PLCB4,missense_variant,p.D642Y,ENST00000691112.1,c.1924G>T,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000686532.1,n.2122G>T,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686163.1,c.*380G>T,MODIFIER,;PLCB4,missense_variant,p.D642Y,ENST00000690960.1,c.1924G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000693160.1,c.1888G>T,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000693492.1,c.*1167G>T,MODIFIER,;PLCB4,missense_variant,p.D642Y,ENST00000685568.1,c.1924G>T,MODERATE,;PLCB4,missense_variant,p.D535Y,ENST00000686117.1,c.1603G>T,MODERATE,;PLCB4,missense_variant,p.D642Y,ENST00000685823.1,c.1924G>T,MODERATE,;PLCB4,missense_variant,p.D612Y,ENST00000687446.1,c.1834G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000686976.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000691007.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000686313.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000684997.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D642Y,ENST00000378473.9,c.1924G>T,MODERATE,YES;PLCB4,missense_variant,p.D529Y,ENST00000690729.1,c.1585G>T,MODERATE,;PLCB4,missense_variant,p.D642Y,ENST00000685298.1,c.1924G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000689910.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000685859.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630Y,ENST00000686584.1,c.1888G>T,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000687299.1,c.*894G>T,MODIFIER,;PLCB4,missense_variant,p.D577Y,ENST00000693502.1,c.1729G>T,MODERATE,;PLCB4,missense_variant,p.D535Y,ENST00000693544.1,c.1603G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000693752.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000688325.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000414679.7,c.1888G>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630Y,ENST00000685148.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000688837.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000686871.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630Y,ENST00000687765.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000685110.1,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000378493.6,c.1888G>T,MODERATE,;PLCB4,missense_variant,p.D630Y,ENST00000378501.3,c.1888G>T,MODERATE, +PLCB4 5332 BI GRCh38 20 9409107 9409107 + missense_variant Missense_Mutation SNP A A T rs1555839474 TCGA-VD-A8KD-01A TCGA-VD-A8KD-10A Somatic 49 32 c.1835A>T p.Asp612Val p.D612V ENST00000278655.9 NM_182797.3 630 gAt/gTt 21/36 P4 T D/V protein_coding CCDS13105.1 1889/3528 likely_pathogenic AGTCGATTCCA Gene3D:3.20.20.190;Pfam:PF00387;PIRSF:PIRSF000956;Prints:PR00390;PROSITE_profiles:PS50008;PANTHER:PTHR10336;PANTHER:PTHR10336:SF106;SMART:SM00149;Superfamily:SSF51695;CDD:cd08591 ENSP00000278655 21/36 rs1555839474 ENST00000278655 Transcript 1.0 ENSG00000101333 HGNC:9059 MODERATE missense_variant 1 probably_damaging(0.996) Unknown deleterious(0) Q15147.204 PLCB4 HGNC 1 1.0 UPI0000131A94 Q15147-1 SNV PLCB4,missense_variant,p.D630V,ENST00000378501,NM_001377134.2&NM_000933.4&NM_001377135.1,c.1889A>T,MODERATE,,deleterious(0),probably_damaging(0.918),1;PLCB4,missense_variant,p.D630V,ENST00000378493,,c.1889A>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;PLCB4,missense_variant,p.D642V,ENST00000378473,NM_001377142.1&NM_001377143.1,c.1925A>T,MODERATE,YES,deleterious(0),probably_damaging(0.992),1;PLCB4,missense_variant,p.D630V,ENST00000278655,NM_182797.3&NM_001377136.1,c.1889A>T,MODERATE,,deleterious(0),probably_damaging(0.996),1;PLCB4,missense_variant,p.D642V,ENST00000414679,NM_001172646.2,c.1925A>T,MODERATE,,deleterious(0),probably_damaging(0.951),1;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,,n.1904A>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,,n.1666A>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,,n.1616A>T,MODIFIER,,,,1;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,,n.1580A>T,MODIFIER,,,,1 1967/5430 muse;mutect2;varscan2 73b3e4dd-c53d-4fe3-8607-ee462c9cbbd1 0 67 37edc04b-46ae-4e1e-94d7-1b9c1f192b21 81 0fcd5b2f-ca15-495c-a3d4-6225c3a1aafa SUCCESS PLCB4,non_coding_transcript_exon_variant,,ENST00000688465.1,n.729A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000688049.1,n.1400A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000689976.1,n.980A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000687147.1,n.1457A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151.5,n.1580A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123.1,n.1616A>T,MODIFIER,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199.5,n.1666A>T,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000689392.1,c.*1840A>T,MODIFIER,;PLCB4,missense_variant,NMD_transcript_variant,p.D630V,ENST00000492632.5,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D612V,ENST00000278655.9,c.1835A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000693005.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000688656.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000685310.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D535V,ENST00000693090.1,c.1604A>T,MODERATE,;PLCB4,missense_variant,p.D612V,ENST00000686253.1,c.1835A>T,MODERATE,;PLCB4,missense_variant,p.D535V,ENST00000692395.1,c.1604A>T,MODERATE,;PLCB4,missense_variant,p.D634V,ENST00000686893.1,c.1901A>T,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000685446.1,n.2087A>T,MODIFIER,;PLCB4,missense_variant,p.D479V,ENST00000685482.1,c.1436A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000692085.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D562V,ENST00000689010.1,c.1685A>T,MODERATE,;PLCB4,missense_variant,p.D642V,ENST00000691112.1,c.1925A>T,MODERATE,;PLCB4,non_coding_transcript_exon_variant,,ENST00000686532.1,n.2123A>T,MODIFIER,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686163.1,c.*381A>T,MODIFIER,;PLCB4,missense_variant,p.D642V,ENST00000690960.1,c.1925A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000693160.1,c.1889A>T,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000693492.1,c.*1168A>T,MODIFIER,;PLCB4,missense_variant,p.D642V,ENST00000685568.1,c.1925A>T,MODERATE,;PLCB4,missense_variant,p.D535V,ENST00000686117.1,c.1604A>T,MODERATE,;PLCB4,missense_variant,p.D642V,ENST00000685823.1,c.1925A>T,MODERATE,;PLCB4,missense_variant,p.D612V,ENST00000687446.1,c.1835A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000686976.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000691007.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000686313.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000684997.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D642V,ENST00000378473.9,c.1925A>T,MODERATE,YES;PLCB4,missense_variant,p.D529V,ENST00000690729.1,c.1586A>T,MODERATE,;PLCB4,missense_variant,p.D642V,ENST00000685298.1,c.1925A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000689910.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000685859.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630V,ENST00000686584.1,c.1889A>T,MODERATE,;PLCB4,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000687299.1,c.*895A>T,MODIFIER,;PLCB4,missense_variant,p.D577V,ENST00000693502.1,c.1730A>T,MODERATE,;PLCB4,missense_variant,p.D535V,ENST00000693544.1,c.1604A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000693752.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000688325.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000414679.7,c.1889A>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630V,ENST00000685148.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000688837.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000686871.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,NMD_transcript_variant,p.D630V,ENST00000687765.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000685110.1,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000378493.6,c.1889A>T,MODERATE,;PLCB4,missense_variant,p.D630V,ENST00000378501.3,c.1889A>T,MODERATE, +RYR2 6262 BI GRCh38 1 237784264 237784264 + synonymous_variant Silent SNP G G A rs1300867476 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 46 32 c.12552G>A p.Glu4184= p.E4184= ENST00000366574.7 NM_001035.3 4184 gaG/gaA 90/105 P1 A E protein_coding YES CCDS55691.1 12552/14904 AAAGAGAAGAT COSM4847146;COSM4847147 PANTHER:PTHR12864;PANTHER:PTHR12864:SF45 ENSP00000355533 90/105 rs1300867476;COSV63678964 ENST00000366574 Transcript 1.0 ENSG00000198626 HGNC:10484 LOW NM_001035.3 8.869e-06 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 Q92736.216 RYR2 HGNC 1 1.0 UPI0000DD0308 Q92736-1 SNV RYR2,synonymous_variant,p.E4184=,ENST00000366574,NM_001035.3,c.12552G>A,LOW,YES,,,1;RYR2,synonymous_variant,p.E4168=,ENST00000360064,,c.12504G>A,LOW,,,,1;RYR2,synonymous_variant,p.E1577=,ENST00000659194,,c.4731G>A,LOW,,,,1;RYR2,synonymous_variant,p.E869=,ENST00000660292,,c.2607G>A,LOW,,,,1;RYR2,3_prime_UTR_variant,,ENST00000609119,,c.*3644G>A,MODIFIER,,,,1 12890/16583 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 4.016e-06 0.0 0.0 0.0 0.0 0.0 8.869e-06 0.0 0.0 2.028339986281935e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 4.629340037354268e-05 0.0 4.629340037354268e-05 0.0 0.0 0 94 ecbea0e3-c24c-4a2b-845f-67ea5322caac 78 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS RYR2,synonymous_variant,p.E3529=,ENST00000714022.1,c.10587G>A,LOW,;RYR2,synonymous_variant,p.E4192=,ENST00000661330.2,c.12576G>A,LOW,;RYR2,synonymous_variant,p.E4172=,ENST00000714019.1,c.12516G>A,LOW,;RYR2,synonymous_variant,p.E4180=,ENST00000659194.3,c.12540G>A,LOW,;RYR2,synonymous_variant,p.E4184=,ENST00000366574.7,c.12552G>A,LOW,YES;RYR2,synonymous_variant,p.E4191=,ENST00000660292.2,c.12573G>A,LOW,;RYR2,synonymous_variant,p.E4147=,ENST00000714018.1,c.12441G>A,LOW,;RYR2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000609119.2,c.*3644G>A,MODIFIER,;RYR2,synonymous_variant,p.E4190=,ENST00000714021.1,c.12570G>A,LOW, +NRXN1 9378 BI GRCh38 2 51028092 51028092 + missense_variant Missense_Mutation SNP C C T rs202205785 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 16 12 c.182G>A p.Arg61His p.R61H ENST00000406316.6 NM_001330083.2 61 cGc/cAc 2/22 T R/H protein_coding CCDS54360.1 182/4434 CGCTGCGAGTC Gene3D:2.60.120.200;Pfam:PF02210;PROSITE_profiles:PS50025;PANTHER:PTHR15036;PANTHER:PTHR15036:SF51;SMART:SM00282;Superfamily:SSF49899;CDD:cd00110 ENSP00000384311 2/22 rs202205785 ENST00000406316 Transcript 1.0 ENSG00000179915 HGNC:8008 MODERATE 1.065e-05 gnomAD_NFE missense_variant benign(0.272) Unknown tolerated(0.1) Q9ULB1.198 NRXN1 HGNC -1 5.0 UPI0000130A9D Q9ULB1-1 SNV NRXN1,missense_variant,p.R61H,ENST00000406316,NM_001330083.1&NM_001330095.1&NM_004801.5,c.182G>A,MODERATE,,tolerated(0.1),benign(0.272),-1;NRXN1,missense_variant,p.R61H,ENST00000401669,NM_001330078.2&NM_001330093.1&NM_001330094.1&NM_001330085.1&NM_001330086.1,c.182G>A,MODERATE,,tolerated(0.1),benign(0.009),-1;NRXN1,missense_variant,p.R61H,ENST00000625672,NM_001330082.1,c.182G>A,MODERATE,,tolerated(0.1),benign(0.007),-1;NRXN1,missense_variant,p.R61H,ENST00000404971,NM_001135659.2,c.182G>A,MODERATE,YES,tolerated(0.1),benign(0.005),-1;NRXN1,missense_variant,p.R61H,ENST00000675235,,c.182G>A,MODERATE,,tolerated(0.11),benign(0.022),-1;NRXN1,missense_variant,p.R61H,ENST00000405472,NM_001330096.1&NM_001330087.1&NM_001330084.1&NM_001330088.1,c.182G>A,MODERATE,,tolerated(0.09),possibly_damaging(0.708),-1;NRXN1,missense_variant,p.R61H,ENST00000405581,NM_001330081.2,c.182G>A,MODERATE,,tolerated(0.13),benign(0.055),-1;NRXN1,missense_variant,p.R61H,ENST00000630543,NM_001330077.1,c.182G>A,MODERATE,,tolerated(0.09),benign(0),-1;NRXN1,missense_variant,p.R61H,ENST00000637511,,c.182G>A,MODERATE,,tolerated(0.1),benign(0.078),-1;NRXN1,missense_variant,p.R61H,ENST00000628515,,c.182G>A,MODERATE,,tolerated(0.06),probably_damaging(0.93),-1;NRXN1,missense_variant,p.R61H,ENST00000626899,NM_001330079.2,c.182G>A,MODERATE,,tolerated(0.14),possibly_damaging(0.784),-1;NRXN1,upstream_gene_variant,,ENST00000496792,NM_001330089.1,,MODIFIER,,,,-1;NRXN1,upstream_gene_variant,,ENST00000627198,,,MODIFIER,,,,-1;NRXN1,upstream_gene_variant,,ENST00000636066,NM_001330090.1,,MODIFIER,,,,-1;NRXN1,downstream_gene_variant,,ENST00000635126,,,MODIFIER,,,,-1;NRXN1,downstream_gene_variant,,ENST00000635310,,,MODIFIER,,,,-1;NRXN1,downstream_gene_variant,,ENST00000636599,,,MODIFIER,,,,-1;NRXN1,downstream_gene_variant,,ENST00000637006,,,MODIFIER,,,,-1;NRXN1,upstream_gene_variant,,ENST00000637679,,,MODIFIER,,,,-1;NRXN1,downstream_gene_variant,,ENST00000638060,,,MODIFIER,,,,-1;AC007402.1,upstream_gene_variant,,ENST00000440698,,,MODIFIER,YES,,,1 1684/9375 muse;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 4.779e-06 0.0 0.0 0.0 0.0 0.0 1.065e-05 0.0 0.0 0 15 ecbea0e3-c24c-4a2b-845f-67ea5322caac 28 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS NRXN1,missense_variant,p.R61H,ENST00000626899.1,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000637511.1,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000675235.1,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000405581.3,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000628515.2,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000630543.2,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000405472.7,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000404971.5,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000625672.2,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000406316.6,c.182G>A,MODERATE,;NRXN1,missense_variant,p.R61H,ENST00000401669.7,c.182G>A,MODERATE,YES +MYO7B 4648 BI GRCh38 2 127566691 127566691 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 12 3 c.334C>T p.Pro112Ser p.P112S ENST00000409816.8 NM_001393586.1 112 Ccg/Tcg 5/48 P1 T P/S protein_coding CCDS46405.1 334/6351 TGCTGCCGCTC PROSITE_profiles:PS51456;CDD:cd01381;PANTHER:PTHR13140;PANTHER:PTHR13140:SF505;Gene3D:3.40.850.10;Pfam:PF00063;SMART:SM00242;Superfamily:SSF52540;Prints:PR00193 ENSP00000386461 4/46 ENST00000409816 Transcript ENSG00000169994 HGNC:7607 MODERATE missense_variant probably_damaging(1) Unknown tolerated(0.07) Q6PIF6.145 MYO7B HGNC 1 1.0 UPI00006C04F0 Q6PIF6-1 SNV MYO7B,missense_variant,p.P112S,ENST00000428314,NM_001080527.1,c.334C>T,MODERATE,YES,tolerated(0.07),probably_damaging(1),1;MYO7B,missense_variant,p.P112S,ENST00000409816,,c.334C>T,MODERATE,,tolerated(0.07),probably_damaging(1),1 366/6694 muse;mutect2 b533e555-90cf-4657-80c6-15b67da8ad26 0 13 ecbea0e3-c24c-4a2b-845f-67ea5322caac 15 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS MYO7B,missense_variant,p.P112S,ENST00000428314.5,c.334C>T,MODERATE,;MYO7B,missense_variant,p.P112S,ENST00000409816.8,c.334C>T,MODERATE,YES +THSD7B 80731 BI GRCh38 2 137450895 137450895 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 36 6 c.3010A>C p.Ser1004Arg p.S1004R ENST00000409968.6 NM_001316349.2 1004 Agc/Cgc 15/28 A2 C S/R protein_coding YES 3010/4827 AGTTAAGCGAT PROSITE_profiles:PS50092;PANTHER:PTHR11311:SF7;PANTHER:PTHR11311;Pfam:PF00090;Gene3D:2.20.100.10;SMART:SM00209;Superfamily:SSF82895 ENSP00000272643 14/27 ENST00000272643 Transcript ENSG00000144229 HGNC:29348 MODERATE missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) THSD7B HGNC 1 A0A5K1VW52.2 5.0 UPI0004E4C87A SNV THSD7B,missense_variant,p.S1004R,ENST00000409968,NM_001316349.2,c.3010A>C,MODERATE,,deleterious(0),probably_damaging(1),1;THSD7B,missense_variant,p.S1004R,ENST00000272643,,c.3010A>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;THSD7B,missense_variant,p.S973R,ENST00000413152,,c.2917A>C,MODERATE,,deleterious(0),probably_damaging(1),1 3010/5939 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 59 ecbea0e3-c24c-4a2b-845f-67ea5322caac 42 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS THSD7B,missense_variant,p.S1004R,ENST00000409968.6,c.3010A>C,MODERATE,YES +TTN 7273 BI GRCh38 2 178572930 178572930 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 39 3 c.68279C>T p.Ala22760Val p.A22760V ENST00000591111.5 22760 gCc/gTc 276/313 A A/V protein_coding 68279/103053 TCATGGCATAG Gene3D:2.60.40.10;Pfam:PF00041;PROSITE_profiles:PS50853;PANTHER:PTHR13817;PANTHER:PTHR13817:SF10;SMART:SM00060;Superfamily:SSF49265;CDD:cd00063 ENSP00000465570 276/313 ENST00000591111 Transcript 1.0 ENSG00000155657 HGNC:12403 MODERATE missense_variant probably_damaging(0.997) Unknown Q8WZ42.192 TTN HGNC -1 5.0 UPI00025287CD Q8WZ42-1 SNV TTN,missense_variant,p.A24401V,ENST00000589042,NM_001267550.2,c.73202C>T,MODERATE,YES,,probably_damaging(0.997),-1;TTN,missense_variant,p.A22760V,ENST00000591111,,c.68279C>T,MODERATE,,,probably_damaging(0.997),-1;TTN,missense_variant,p.A21833V,ENST00000342992,NM_133378.4&NM_001256850.1,c.65498C>T,MODERATE,,,probably_damaging(0.994),-1;TTN,missense_variant,p.A15336V,ENST00000460472,NM_003319.4,c.46007C>T,MODERATE,,,probably_damaging(0.998),-1;TTN,missense_variant,p.A15528V,ENST00000342175,NM_133437.4,c.46583C>T,MODERATE,,,,-1;TTN,missense_variant,p.A15461V,ENST00000359218,NM_133432.3,c.46382C>T,MODERATE,,,probably_damaging(0.998),-1;TTN-AS1,intron_variant,,ENST00000419746,,n.2044-9642G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000438095,,n.344+1481G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000456053,,n.563+1481G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000585451,,n.198+49294G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586452,,n.224+1481G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586707,,n.346-10783G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000586831,,n.215-9642G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590773,,n.598-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590807,,n.75-10594G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000590932,,n.616-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000591332,,n.443-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592600,,n.346-11643G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592630,,n.434-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592689,,n.463-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000592750,,n.346-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625480,,n.50-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000625536,,n.22-18209G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626117,,n.75-18209G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626138,,n.50-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000626954,,n.75-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000627564,,n.527+1481G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628296,,n.50-18209G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000628826,,n.49+44117G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000630096,,n.552-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000653807,,n.220-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000657023,,n.119-24666G>A,MODIFIER,,,,1;TTN-AS1,intron_variant,,ENST00000659121,,n.417-24666G>A,MODIFIER,YES,,,1;AC010680.3,upstream_gene_variant,,ENST00000604215,,,MODIFIER,YES,,,1 68504/104301 muse;mutect2 b533e555-90cf-4657-80c6-15b67da8ad26 0 28 ecbea0e3-c24c-4a2b-845f-67ea5322caac 42 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS TTN-AS1,intron_variant,,ENST00000590932.5,n.616-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000438095.1,n.344+1481G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000627564.2,n.527+1481G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625536.2,n.22-18209G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628826.2,n.49+44117G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626138.2,n.50-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000625480.2,n.50-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000628296.2,n.50-18209G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626954.2,n.75-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592689.5,n.463-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000626117.2,n.75-18209G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590807.5,n.75-10594G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586452.5,n.224+1481G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586831.5,n.215-9642G>A,MODIFIER,;TTN,missense_variant,p.A21833V,ENST00000342992.11,c.65498C>T,MODERATE,;TTN,missense_variant,p.A24373V,ENST00000425332.3,c.73118C>T,MODERATE,;TTN,missense_variant,p.A22760V,ENST00000591111.5,c.68279C>T,MODERATE,;TTN,missense_variant,p.A24401V,ENST00000589042.5,c.73202C>T,MODERATE,YES;TTN,missense_variant,p.A24263V,ENST00000715174.1,c.72788C>T,MODERATE,;TTN,missense_variant,p.A15528V,ENST00000342175.12,c.46583C>T,MODERATE,;TTN,missense_variant,p.A15336V,ENST00000460472.6,c.46007C>T,MODERATE,;TTN,missense_variant,p.A24309V,ENST00000436599.2,c.72926C>T,MODERATE,;TTN,missense_variant,p.A15461V,ENST00000359218.11,c.46382C>T,MODERATE,;TTN,missense_variant,p.A24349V,ENST00000446966.2,c.73046C>T,MODERATE,;TTN,missense_variant,p.A24215V,ENST00000426232.6,c.72644C>T,MODERATE,;TTN,missense_variant,p.A24401V,ENST00000412264.2,c.73202C>T,MODERATE,;TTN-AS1,intron_variant,,ENST00000657023.1,n.119-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000585451.5,n.198+49294G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000653807.1,n.220-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000591332.5,n.443-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592630.5,n.434-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592600.6,n.346-11643G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000592750.5,n.346-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000586707.6,n.346-10783G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000590773.6,n.598-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000456053.5,n.563+1481G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000659121.1,n.417-24666G>A,MODIFIER,YES;TTN-AS1,intron_variant,,ENST00000702938.1,n.431-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000630096.2,n.552-24666G>A,MODIFIER,;TTN-AS1,intron_variant,,ENST00000419746.5,n.2044-9642G>A,MODIFIER, +BAP1 8314 BI GRCh38 3 52402634 52402643 + frameshift_variant Frame_Shift_Del DEL ATGAACTCAT ATGAACTCAT - novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 8 19 c.2015_2024del p.Cys676SerfsTer13 p.C676Sfs*13 ENST00000460680.6 NM_004656.4 672 gATGAGTTCATc/gc 16/17 P1 - DEFI/X protein_coding YES CCDS2853.1 2015-2024/2190 GTGCAGATGAACTCATCGTAG PANTHER:PTHR10589:SF28;PANTHER:PTHR10589;Gene3D:1.20.58.860;Pfam:PF18031 ENSP00000417132 16/17 ENST00000460680 Transcript 1.0 ENSG00000163930 HGNC:950 HIGH NM_004656.4 frameshift_variant 1.0 Unknown Q92560.166 BAP1 HGNC -1 A0A024R305.46 1.0 UPI0000071B3D deletion BAP1,frameshift_variant,p.D672Afs*17,ENST00000460680,NM_004656.4,c.2015_2024del,HIGH,YES,,,-1;BAP1,frameshift_variant,p.D654Afs*17,ENST00000296288,,c.1961_1970del,HIGH,,,,-1;BAP1,frameshift_variant,p.D72Afs*17,ENST00000469613,,c.214_223del,HIGH,,,,-1;BAP1,frameshift_variant,p.D196Afs*17,ENST00000478368,,c.587_596del,HIGH,,,,-1;DNAH1,downstream_gene_variant,,ENST00000420323,NM_015512.5,,MODIFIER,YES,,,1;BAP1,downstream_gene_variant,,ENST00000470173,,,MODIFIER,,,,-1;BAP1,upstream_gene_variant,,ENST00000615113,,,MODIFIER,,,,-1;BAP1,non_coding_transcript_exon_variant,,ENST00000466093,,n.688_697del,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000471532,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000483984,,,MODIFIER,,,,-1;DNAH1,downstream_gene_variant,,ENST00000486752,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000488988,,,MODIFIER,,,,1;DNAH1,downstream_gene_variant,,ENST00000490713,,,MODIFIER,,,,1;BAP1,downstream_gene_variant,,ENST00000490804,,,MODIFIER,,,,-1;BAP1,downstream_gene_variant,,ENST00000490917,,,MODIFIER,,,,-1 2145-2154/3600 mutect2;pindel;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 96 ecbea0e3-c24c-4a2b-845f-67ea5322caac 27 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS BAP1,non_coding_transcript_exon_variant,,ENST00000466093.1,n.688_697del,MODIFIER,;BAP1,frameshift_variant,p.C200Sfs*13,ENST00000478368.1,c.587_596del,HIGH,;BAP1,frameshift_variant,p.C658Sfs*13,ENST00000296288.9,c.1961_1970del,HIGH,;BAP1,frameshift_variant,p.S75Yfs*38,ENST00000469613.5,c.214_223del,HIGH,;BAP1,frameshift_variant,p.C676Sfs*13,ENST00000460680.6,c.2015_2024del,HIGH,YES +POLK 51426 BI GRCh38 5 75596750 75596750 + missense_variant Missense_Mutation SNP A A C novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 18 7 c.2057A>C p.Tyr686Ser p.Y686S ENST00000241436.9 NM_001395893.1 686 tAt/tCt 13/15 P1 C Y/S protein_coding YES CCDS4030.1 2057/2613 AGATTATGAAG PIRSF:PIRSF036603 ENSP00000241436 13/15 ENST00000241436 Transcript ENSG00000122008 HGNC:9183 MODERATE missense_variant 1.0 benign(0) Unknown tolerated(0.4) Q9UBT6.169 POLK HGNC 1 A0A024RAP4.49 1.0 UPI0000073EF6 Q9UBT6-1 SNV POLK,missense_variant,p.Y686S,ENST00000241436,NM_001345922.1&NM_016218.3&NM_001345921.1,c.2057A>C,MODERATE,YES,tolerated(0.4),benign(0),1;POLK,missense_variant,p.Y488S,ENST00000508526,,c.1463A>C,MODERATE,,tolerated_low_confidence(0.17),benign(0),1;POLK,intron_variant,,ENST00000504026,,c.1357-997A>C,MODIFIER,,,,1;POLK,non_coding_transcript_exon_variant,,ENST00000506928,,n.2180A>C,MODIFIER,,,,1;POLK,3_prime_UTR_variant,,ENST00000514141,,c.*676A>C,MODIFIER,,,,1;POLK,3_prime_UTR_variant,,ENST00000505975,,c.*1898A>C,MODIFIER,,,,1;POLK,3_prime_UTR_variant,,ENST00000510815,,c.*580A>C,MODIFIER,,,,1;POLK,3_prime_UTR_variant,,ENST00000503479,,c.*580A>C,MODIFIER,,,,1;POLK,3_prime_UTR_variant,,ENST00000509126,,c.*415A>C,MODIFIER,,,,1;POLK,intron_variant,,ENST00000511527,,c.*1198-997A>C,MODIFIER,,,,1;POLK,upstream_gene_variant,,ENST00000502567,,,MODIFIER,,,,1;POLK,upstream_gene_variant,,ENST00000505069,,,MODIFIER,,,,1;AC010245.1,downstream_gene_variant,,ENST00000511329,,,MODIFIER,YES,,,-1 2229/5911 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 38 ecbea0e3-c24c-4a2b-845f-67ea5322caac 25 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS POLK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000509126.2,c.*415A>C,MODIFIER,;POLK,intron_variant,,ENST00000504026.5,c.1357-997A>C,MODIFIER,;POLK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000505975.5,c.*1898A>C,MODIFIER,;POLK,intron_variant,NMD_transcript_variant,,ENST00000511527.5,c.*1198-997A>C,MODIFIER,;POLK,missense_variant,p.Y488S,ENST00000508526.5,c.1463A>C,MODERATE,;POLK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000514141.5,c.*676A>C,MODIFIER,;POLK,non_coding_transcript_exon_variant,,ENST00000506928.5,n.2180A>C,MODIFIER,;POLK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000510815.6,c.*580A>C,MODIFIER,;POLK,missense_variant,p.Y686S,ENST00000241436.9,c.2057A>C,MODERATE,YES;POLK,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000503479.6,c.*580A>C,MODIFIER, +PCDHA9 9752 BI GRCh38 5 140848533 140848533 + missense_variant Missense_Mutation SNP C C T rs782015840 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 4 53 c.38C>T p.Pro13Leu p.P13L ENST00000532602.2 NM_031857.2 13 cCt/cTt 1/4 P1 T P/L protein_coding YES CCDS54920.1 38/2853 TCAGCCTCTAC PROSITE_profiles:PS50268;PANTHER:PTHR24028;PANTHER:PTHR24028:SF255;Cleavage_site_(Signalp):SignalP-noTM ENSP00000436042 1/4 rs782015840 ENST00000532602 Transcript ENSG00000204961 HGNC:8675 MODERATE NM_031857.2 0.0004353 gnomAD_EAS missense_variant 1.0 benign(0) Unknown tolerated_low_confidence(0.49) Q9Y5H5.175 PCDHA9 HGNC 1 1.0 UPI00001273D1 Q9Y5H5-1 SNV PCDHA9,missense_variant,p.P13L,ENST00000378122,NM_014005.4,c.38C>T,MODERATE,,tolerated_low_confidence(0.5),benign(0),1;PCDHA9,missense_variant,p.P13L,ENST00000532602,NM_031857.2,c.38C>T,MODERATE,YES,tolerated_low_confidence(0.49),benign(0),1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.3,c.1602+60641C>T,MODIFIER,,,,1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.4,c.2394+59849C>T,MODIFIER,YES,,,1;PCDHA4,intron_variant,,ENST00000512229,,c.2385+38961C>T,MODIFIER,,,,1;PCDHA3,intron_variant,,ENST00000522353,NM_018906.3,c.2394+44942C>T,MODIFIER,YES,,,1;PCDHA7,intron_variant,,ENST00000525929,NM_018910.3,c.2355+11795C>T,MODIFIER,YES,,,1;PCDHA2,intron_variant,,ENST00000526136,NM_018905.3,c.2388+51181C>T,MODIFIER,YES,,,1;PCDHA6,intron_variant,,ENST00000527624,NM_031849.3,c.1602+18840C>T,MODIFIER,,,,1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.4,c.2394+18048C>T,MODIFIER,YES,,,1;PCDHA5,intron_variant,,ENST00000529619,,c.2352+24406C>T,MODIFIER,,,,1;PCDHA5,intron_variant,,ENST00000529859,NM_018908.3,c.2352+24406C>T,MODIFIER,YES,,,1;PCDHA4,intron_variant,,ENST00000530339,NM_018907.4,c.2385+38961C>T,MODIFIER,YES,,,1;PCDHA8,intron_variant,,ENST00000531613,NM_018911.3,c.2394+4818C>T,MODIFIER,YES,,,1;PCDHA8,downstream_gene_variant,,ENST00000378123,NM_031856.1,,MODIFIER,,,,1;AC005609.2,downstream_gene_variant,,ENST00000623320,,,MODIFIER,YES,,,-1 152/5377 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 3.632e-05 0.0 2.929e-05 0.0 0.0004353 0.0 0.0 0.0 0.0 6.850630143162562e-06 0.0 0.0 0.0 0.0 0.0002027580048888 0.0 0.0 0.0 0.0 0.0 0 72 ecbea0e3-c24c-4a2b-845f-67ea5322caac 57 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS PCDHA9,missense_variant,p.P13L,ENST00000532602.2,c.38C>T,MODERATE,YES;PCDHA9,missense_variant,p.P13L,ENST00000378122.4,c.38C>T,MODERATE,;PCDHA8,intron_variant,,ENST00000531613.2,c.2394+4818C>T,MODIFIER,YES;PCDHA7,intron_variant,,ENST00000525929.2,c.2355+11795C>T,MODIFIER,YES;PCDHA6,intron_variant,,ENST00000527624.1,c.1602+18840C>T,MODIFIER,;PCDHA6,intron_variant,,ENST00000529310.6,c.2394+18048C>T,MODIFIER,YES;PCDHA5,intron_variant,,ENST00000529619.5,c.2352+24406C>T,MODIFIER,;PCDHA5,intron_variant,,ENST00000529859.2,c.2352+24406C>T,MODIFIER,YES;PCDHA4,intron_variant,,ENST00000512229.6,c.2385+38961C>T,MODIFIER,;PCDHA4,intron_variant,,ENST00000530339.2,c.2385+38961C>T,MODIFIER,YES;PCDHA3,intron_variant,,ENST00000522353.3,c.2394+44942C>T,MODIFIER,YES;PCDHA2,intron_variant,,ENST00000526136.2,c.2388+51181C>T,MODIFIER,YES;PCDHA1,intron_variant,,ENST00000394633.7,c.1602+60641C>T,MODIFIER,;PCDHA1,intron_variant,,ENST00000504120.4,c.2394+59849C>T,MODIFIER,YES +SPDL1 54908 BI GRCh38 5 169588522 169588522 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 20 17 c.106G>A p.Glu36Lys p.E36K ENST00000265295.9 NM_001329643.2 36 Gaa/Aaa 2/12 P1 A E/K protein_coding YES CCDS4370.1 106/1818 AAAATGAATTA Coiled-coils_(Ncoils):Coil;HAMAP:MF_03041;PANTHER:PTHR32123:SF9;PANTHER:PTHR32123 ENSP00000265295 2/12 ENST00000265295 Transcript ENSG00000040275 HGNC:26010 MODERATE NM_017785.5 missense_variant 1.0 possibly_damaging(0.894) Unknown deleterious(0.03) Q96EA4.139 SPDL1 HGNC 1 1.0 UPI000013D5F0 Q96EA4-1 SNV SPDL1,missense_variant,p.E36K,ENST00000265295,NM_001329643.2&NM_001329639.2&NM_017785.5&NM_001329640.2&NM_001329641.2,c.106G>A,MODERATE,YES,deleterious(0.03),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000513941,,c.106G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000506574,,c.106G>A,MODERATE,,deleterious_low_confidence(0.03),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000513795,,c.106G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000508247,,c.106G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000515224,,c.106G>A,MODERATE,,deleterious_low_confidence(0.03),possibly_damaging(0.894),1;SPDL1,missense_variant,p.E36K,ENST00000629457,,c.106G>A,MODERATE,,deleterious_low_confidence(0.05),benign(0.058),1;SPDL1,upstream_gene_variant,,ENST00000505977,NM_001329642.2,,MODIFIER,,,,1;SPDL1,non_coding_transcript_exon_variant,,ENST00000510751,,n.263G>A,MODIFIER,,,,1;SPDL1,downstream_gene_variant,,ENST00000503209,,,MODIFIER,,,,1;SPDL1,missense_variant,p.E36K,ENST00000512028,,c.106G>A,MODERATE,,deleterious_low_confidence(0.05),benign(0.058),1;SPDL1,missense_variant,p.E36K,ENST00000509785,,c.106G>A,MODERATE,,deleterious_low_confidence(0.05),benign(0.058),1;SPDL1,non_coding_transcript_exon_variant,,ENST00000508837,,n.243G>A,MODIFIER,,,,1;SPDL1,intron_variant,,ENST00000507232,,c.74+32G>A,MODIFIER,,,,1;SPDL1,upstream_gene_variant,,ENST00000503871,,,MODIFIER,,,,1 246/2529 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 32 ecbea0e3-c24c-4a2b-845f-67ea5322caac 37 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS SPDL1,non_coding_transcript_exon_variant,,ENST00000508837.1,n.243G>A,MODIFIER,;SPDL1,missense_variant,p.E36K,ENST00000513795.1,c.106G>A,MODERATE,;SPDL1,missense_variant,NMD_transcript_variant,p.E36K,ENST00000509785.5,c.106G>A,MODERATE,;SPDL1,missense_variant,NMD_transcript_variant,p.E36K,ENST00000512028.5,c.106G>A,MODERATE,;SPDL1,missense_variant,p.E36K,ENST00000513941.5,c.106G>A,MODERATE,;SPDL1,missense_variant,p.E36K,ENST00000265295.9,c.106G>A,MODERATE,YES;SPDL1,missense_variant,p.E36K,ENST00000508247.5,c.106G>A,MODERATE,;SPDL1,missense_variant,p.E36K,ENST00000629457.2,c.106G>A,MODERATE,;SPDL1,non_coding_transcript_exon_variant,,ENST00000510751.5,n.263G>A,MODIFIER,;SPDL1,intron_variant,NMD_transcript_variant,,ENST00000507232.5,c.74+32G>A,MODIFIER,;SPDL1,missense_variant,p.E36K,ENST00000515224.5,c.106G>A,MODERATE,;SPDL1,missense_variant,p.E36K,ENST00000506574.5,c.106G>A,MODERATE, +DYNC2H1 79659 BI GRCh38 11 103304682 103304682 + missense_variant Missense_Mutation SNP T T A novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 37 36 c.11344T>A p.Leu3782Ile p.L3782I ENST00000375735.7 NM_001377.3 3782 Tta/Ata 77/89 P4 A L/I protein_coding CCDS53701.1 11344/12924 AGAACTTACAT PDB-ENSP_mappings:4rh7.A;PANTHER:PTHR45703:SF8;PANTHER:PTHR45703;Pfam:PF03028;Gene3D:3.40.50.300 ENSP00000364887 77/89 ENST00000375735 Transcript 1.0 ENSG00000187240 HGNC:2962 MODERATE NM_001377.3 missense_variant probably_damaging(0.951) Unknown tolerated(0.06) Q8NCM8.147 DYNC2H1 HGNC 1 1.0 UPI0000418CA2 Q8NCM8-1 SNV DYNC2H1,missense_variant,p.L3782I,ENST00000375735,NM_001377.3,c.11344T>A,MODERATE,,tolerated(0.06),probably_damaging(0.951),1;DYNC2H1,missense_variant,p.L3789I,ENST00000650373,NM_001080463.2,c.11365T>A,MODERATE,YES,tolerated(0.06),probably_damaging(0.919),1;DYNC2H1,intron_variant,,ENST00000334267,,c.2206-131261T>A,MODIFIER,,,,1;DYNC2H1,missense_variant,p.L175I,ENST00000528670,,c.523T>A,MODERATE,,deleterious(0.04),possibly_damaging(0.767),1 11493/13683 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 59 ecbea0e3-c24c-4a2b-845f-67ea5322caac 74 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS DYNC2H1,missense_variant,NMD_transcript_variant,p.L175I,ENST00000528670.5,c.523T>A,MODERATE,;DYNC2H1,intron_variant,,ENST00000334267.11,c.2206-131261T>A,MODIFIER,;DYNC2H1,missense_variant,p.L3789I,ENST00000650373.2,c.11365T>A,MODERATE,;DYNC2H1,missense_variant,p.L3782I,ENST00000375735.7,c.11344T>A,MODERATE,YES +NACA 4666 BI GRCh38 12 56719423 56719423 + intron_variant Intron SNP T T G novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 15 14 c.71-4736A>C ENST00000356769.7 NM_001113202.2 P1 G protein_coding CCDS31837.1 AGCTGTAGGAA ENSP00000349212 ENST00000356769 Transcript 1.0 ENSG00000196531 HGNC:7629 MODIFIER 2/7 intron_variant Unknown Q13765.180 NACA HGNC -1 A0A024RB41.36 1.0 UPI0000073EC7 Q13765-1 SNV NACA,missense_variant,p.T703P,ENST00000454682,NM_001365896.1,c.2107A>C,MODERATE,YES,tolerated(1),benign(0),-1;NACA,intron_variant,,ENST00000356769,NM_001113202.2&NM_001320193.2,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000393891,NM_005594.6,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000546392,,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000546862,,c.-183-4720A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000548563,,c.-183-4720A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000549259,NM_001320194.2,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000549855,,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000550920,,c.130+114A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000550952,NM_001113203.3,c.1864+114A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000552055,,c.71-4748A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000552540,NM_001113201.3,c.71-4736A>C,MODIFIER,,,,-1;AC117378.1,intron_variant,,ENST00000647707,,c.513-4736A>C,MODIFIER,YES,,,-1;NACA,intron_variant,,ENST00000678047,,c.71-3313A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678066,,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678376,,c.-167-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000678416,,c.-167-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000679092,,c.71-4748A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551775,,n.115-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551793,,n.112-4736A>C,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000550343,,,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000547914,,c.71-4736A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000548084,,c.71-4720A>C,MODIFIER,,,,-1;NACA,intron_variant,,ENST00000551520,,n.106-4736A>C,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000548386,,,MODIFIER,,,,-1;NACA,upstream_gene_variant,,ENST00000676873,,,MODIFIER,,,,-1 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 23 ecbea0e3-c24c-4a2b-845f-67ea5322caac 29 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS ENSG00000285625,intron_variant,,ENST00000647707.1,c.513-4736A>C,MODIFIER,YES;NACA,intron_variant,NMD_transcript_variant,,ENST00000548084.1,c.71-4720A>C,MODIFIER,;NACA,intron_variant,,ENST00000551520.1,n.106-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000551793.5,n.112-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000549855.5,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000552055.5,c.71-4748A>C,MODIFIER,;NACA,intron_variant,,ENST00000551775.5,n.115-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000549259.5,c.71-4736A>C,MODIFIER,;NACA,intron_variant,NMD_transcript_variant,,ENST00000547914.5,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000546392.6,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000548563.5,c.-183-4720A>C,MODIFIER,;NACA,intron_variant,,ENST00000393891.8,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000552540.5,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000356769.7,c.71-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000678376.1,c.-167-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000550920.6,c.130+114A>C,MODIFIER,;NACA,missense_variant,p.T703P,ENST00000454682.6,c.2107A>C,MODERATE,YES;NACA,intron_variant,,ENST00000550952.6,c.1864+114A>C,MODIFIER,;NACA,intron_variant,,ENST00000546862.6,c.-183-4720A>C,MODIFIER,;NACA,intron_variant,,ENST00000678416.1,c.-167-4736A>C,MODIFIER,;NACA,intron_variant,,ENST00000679092.1,c.71-4748A>C,MODIFIER,;NACA,intron_variant,,ENST00000678047.1,c.71-3313A>C,MODIFIER,;NACA,intron_variant,,ENST00000678066.1,c.71-4736A>C,MODIFIER, +UTP14C 9724 BI GRCh38 13 52031010 52031010 + missense_variant Missense_Mutation SNP G G T novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 60 50 c.2206G>T p.Val736Leu p.V736L ENST00000521776.2 NM_021645.6 736 Gtg/Ttg 2/2 P1 T V/L protein_coding YES CCDS31978.1 2206/2301 AGGATGTGGGC PANTHER:PTHR14150;PANTHER:PTHR14150:SF16;MobiDB_lite:mobidb-lite ENSP00000428619 2/2 ENST00000521776 Transcript ENSG00000253797 HGNC:20321 MODERATE NM_021645.6 missense_variant 1.0 benign(0.077) Unknown tolerated(0.24) Q5TAP6.124 UTP14C HGNC 1 A0A024RDV0.46 1.0 UPI000006DB4B SNV UTP14C,missense_variant,p.V736L,ENST00000521776,NM_021645.6,c.2206G>T,MODERATE,YES,tolerated(0.24),benign(0.077),1;ALG11,3_prime_UTR_variant,,ENST00000521508,NM_001004127.3,c.*2420G>T,MODIFIER,YES,,,1;ALG11,3_prime_UTR_variant,,ENST00000649340,,c.*2625G>T,MODIFIER,,,,1;ALG11,downstream_gene_variant,,ENST00000523764,,,MODIFIER,,,,1;ALG11,downstream_gene_variant,,ENST00000519151,,,MODIFIER,,,,1;NEK5,downstream_gene_variant,,ENST00000652502,,,MODIFIER,,,,-1;NEK5,downstream_gene_variant,,ENST00000529080,,,MODIFIER,,,,-1;ALG11,downstream_gene_variant,,ENST00000650049,,,MODIFIER,,,,1 2939/5529 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 95 ecbea0e3-c24c-4a2b-845f-67ea5322caac 110 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS UTP14C,missense_variant,p.V736L,ENST00000521776.2,c.2206G>T,MODERATE,YES;ALG11,non_coding_transcript_exon_variant,,ENST00000680058.1,n.3802G>T,MODIFIER,;ALG11,non_coding_transcript_exon_variant,,ENST00000649651.2,n.8203G>T,MODIFIER,;ALG11,intron_variant,,ENST00000679495.1,n.44+18548G>T,MODIFIER,;ALG11,non_coding_transcript_exon_variant,,ENST00000681226.1,n.3087G>T,MODIFIER,;ALG11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000679359.1,c.*3651G>T,MODIFIER,;ALG11,non_coding_transcript_exon_variant,,ENST00000680950.1,n.4026G>T,MODIFIER,;ALG11,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681047.1,c.*3624G>T,MODIFIER,;ALG11,3_prime_UTR_variant,,ENST00000649340.2,c.*2420G>T,MODIFIER,;ALG11,3_prime_UTR_variant,,ENST00000679544.1,c.*2625G>T,MODIFIER,;ALG11,non_coding_transcript_exon_variant,,ENST00000680793.1,n.4891G>T,MODIFIER,;ALG11,3_prime_UTR_variant,,ENST00000681053.1,c.*2420G>T,MODIFIER,;ALG11,3_prime_UTR_variant,,ENST00000521508.2,c.*2420G>T,MODIFIER,YES;ALG11,intron_variant,,ENST00000649708.2,c.275+11867G>T,MODIFIER, +PCCA 5095 BI GRCh38 13 100368568 100368568 + synonymous_variant Silent SNP G G A rs2152811913 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 46 39 c.1740G>A p.Val580= p.V580= ENST00000376285.6 NM_000282.4 580 gtG/gtA 19/24 P1 A V protein_coding YES CCDS9496.2 1740/2187 TCAGTGTTCTC PANTHER:PTHR18866;PANTHER:PTHR18866:SF104;Gene3D:3.30.700.30;Pfam:PF18140 ENSP00000365462 19/24 ENST00000376285 Transcript 1.0 ENSG00000175198 HGNC:8653 LOW NM_000282.4 synonymous_variant 1.0 Unknown P05165.228 PCCA HGNC 1 1.0 UPI0000070089 P05165-1 SNV PCCA,synonymous_variant,p.V580=,ENST00000376285,NM_000282.4&NM_001352605.2&NM_001352606.2,c.1740G>A,LOW,YES,,,1;PCCA,synonymous_variant,p.V554=,ENST00000376286,NM_001127692.2&NM_001352607.2&NM_001352608.2,c.1662G>A,LOW,,,,1;PCCA,synonymous_variant,p.V580=,ENST00000376279,NM_001178004.1&NM_001352610.2&NM_001352611.2&NM_001352612.2&NM_001352609.2,c.1740G>A,LOW,,,,1;PCCA,synonymous_variant,p.V467=,ENST00000637657,,c.1401G>A,LOW,,,,1;PCCA,synonymous_variant,p.V33=,ENST00000458283,,c.99G>A,LOW,,,,1;PCCA,synonymous_variant,p.V114=,ENST00000424527,,c.342G>A,LOW,,,,1;PCCA,synonymous_variant,p.V24=,ENST00000413170,,c.72G>A,LOW,,,,1;PCCA,intron_variant,,ENST00000636366,,c.945-57065G>A,MODIFIER,,,,1;PCCA,3_prime_UTR_variant,,ENST00000647303,,c.*1224G>A,MODIFIER,,,,1;PCCA,3_prime_UTR_variant,,ENST00000636475,,c.*275G>A,MODIFIER,,,,1;AL353697.1,upstream_gene_variant,,ENST00000654085,,,MODIFIER,YES,,,-1 1768/2484 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 42 ecbea0e3-c24c-4a2b-845f-67ea5322caac 85 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS PCCA,missense_variant,p.V24I,ENST00000413170.1,c.70G>A,MODERATE,;PCCA,missense_variant,p.V33I,ENST00000458283.5,c.97G>A,MODERATE,;PCCA,synonymous_variant,p.V114=,ENST00000424527.5,c.342G>A,LOW,;PCCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000636475.1,c.*275G>A,MODIFIER,;PCCA,missense_variant,p.C467Y,ENST00000637657.1,c.1400G>A,MODERATE,;PCCA,intron_variant,,ENST00000636366.1,c.945-57065G>A,MODIFIER,;PCCA,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000647303.1,c.*1224G>A,MODIFIER,;PCCA,synonymous_variant,p.V580=,ENST00000376285.6,c.1740G>A,LOW,YES;PCCA,synonymous_variant,p.V554=,ENST00000376286.8,c.1662G>A,LOW,;PCCA,synonymous_variant,p.V580=,ENST00000376279.7,c.1740G>A,LOW, +OR4K1 79544 BI GRCh38 14 19936222 19936222 + missense_variant Missense_Mutation SNP G G A TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 48 48 c.556G>A p.Glu186Lys p.E186K ENST00000285600.4 186 Gag/Aag 1/1 P1 A E/K protein_coding CCDS32025.1 556/936 TGATAGAGCTG COSM3494494 Gene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00245;PROSITE_profiles:PS50262;PANTHER:PTHR26451;PANTHER:PTHR26451:SF182;Superfamily:SSF81321;CDD:cd15226 ENSP00000285600 1/1 COSV53461795 ENST00000285600 Transcript ENSG00000155249 HGNC:14726 MODERATE missense_variant 1 benign(0) Unknown tolerated(1) 1 Q8NGD4.138 OR4K1 HGNC 1 UPI0000041B4A SNV OR4K1,missense_variant,p.E186K,ENST00000641429,,c.556G>A,MODERATE,YES,tolerated(1),benign(0),1;OR4K1,missense_variant,p.E186K,ENST00000641172,,c.556G>A,MODERATE,,tolerated(1),benign(0),1;OR4K1,missense_variant,p.E186K,ENST00000285600,NM_001004063.2,c.556G>A,MODERATE,,tolerated(1),benign(0),1 615/1076 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 128 ecbea0e3-c24c-4a2b-845f-67ea5322caac 96 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS OR4K1,missense_variant,p.E186K,ENST00000285600.4,c.556G>A,MODERATE,;OR4K1,missense_variant,p.E186K,ENST00000641429.1,c.556G>A,MODERATE,;OR4K1,missense_variant,p.E186K,ENST00000641172.1,c.556G>A,MODERATE,YES +NIN 51199 BI GRCh38 14 50776960 50776960 + missense_variant Missense_Mutation SNP C C T rs1185253688 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 71 48 c.655G>A p.Val219Met p.V219M ENST00000382041.7 NM_182946.2 219 Gtg/Atg 7/30 A2 T V/M protein_coding CCDS32079.1 655/6273 ATCCACATTCT PROSITE_profiles:PS50222;PANTHER:PTHR18905;PANTHER:PTHR18905:SF11;Superfamily:SSF47473 ENSP00000371472 7/30 rs1185253688;COSV55388207 ENST00000382041 Transcript 1.0 ENSG00000100503 HGNC:14906 MODERATE 5.463e-05 gnomAD_EAS missense_variant 0;1 probably_damaging(0.919) Unknown deleterious(0.01) 0;1 Q8N4C6.165 NIN HGNC -1 1.0 UPI0000DBEF14 Q8N4C6-1 SNV NIN,missense_variant,p.V219M,ENST00000530997,NM_020921.4,c.655G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.79),-1;NIN,missense_variant,p.V219M,ENST00000476352,,c.655G>A,MODERATE,,deleterious(0.01),benign(0.187),-1;NIN,missense_variant,p.V219M,ENST00000453196,NM_182944.2,c.655G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.812),-1;NIN,missense_variant,p.V219M,ENST00000382041,NM_182946.1,c.655G>A,MODERATE,,deleterious(0.01),probably_damaging(0.919),-1;NIN,missense_variant,p.V219M,ENST00000324330,NM_016350.4,c.655G>A,MODERATE,,deleterious(0.01),benign(0.22),-1;NIN,missense_variant,p.V219M,ENST00000382043,,c.655G>A,MODERATE,,deleterious(0.01),benign(0.22),-1;NIN,missense_variant,p.V181M,ENST00000453401,,c.541G>A,MODERATE,,deleterious(0.02),probably_damaging(0.919),-1;NIN,missense_variant,p.V219M,ENST00000674030,,c.655G>A,MODERATE,,deleterious(0.01),benign(0.112),-1;NIN,missense_variant,p.V219M,ENST00000673657,,c.655G>A,MODERATE,,deleterious(0.01),probably_damaging(0.919),-1;NIN,upstream_gene_variant,,ENST00000474937,,,MODIFIER,,,,-1 846/6496 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 8.053e-06 0.0 0.0 0.0 5.463e-05 0.0 0.0 0.0 3.332e-05 6.75648016112973e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0002081599959637 0 91 ecbea0e3-c24c-4a2b-845f-67ea5322caac 119 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS NIN,missense_variant,p.V181M,ENST00000453401.6,c.541G>A,MODERATE,;NIN,non_coding_transcript_exon_variant,,ENST00000706710.1,n.1238G>A,MODIFIER,;NIN,missense_variant,p.V219M,ENST00000485005.2,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000453196.6,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000382041.7,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000324330.13,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000382043.8,c.655G>A,MODERATE,;NIN,missense_variant,NMD_transcript_variant,p.V219M,ENST00000674030.1,c.655G>A,MODERATE,;NIN,5_prime_UTR_variant,NMD_transcript_variant,,ENST00000706705.1,c.-12G>A,MODIFIER,;NIN,missense_variant,p.V219M,ENST00000706706.1,c.655G>A,MODERATE,;NIN,missense_variant,NMD_transcript_variant,p.V219M,ENST00000673657.1,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000476352.5,c.655G>A,MODERATE,;NIN,missense_variant,p.V219M,ENST00000530997.7,c.655G>A,MODERATE,YES +BTBD7 55727 BI GRCh38 14 93294290 93294290 + missense_variant Missense_Mutation SNP T T G novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 52 38 c.730A>C p.Met244Leu p.M244L ENST00000334746.10 NM_001002860.4 244 Atg/Ctg 3/11 P1 G M/L protein_coding YES CCDS32146.1 730/3399 ACACATGTAAT Gene3D:3.30.710.10;PANTHER:PTHR16064;PANTHER:PTHR16064:SF5;SMART:SM00225 ENSP00000335615 3/11 ENST00000334746 Transcript ENSG00000011114 HGNC:18269 MODERATE NM_001002860.4 missense_variant 1.0 possibly_damaging(0.833) Unknown tolerated(0.32) Q9P203.138 BTBD7 HGNC -1 1.0 UPI00001FDA78 Q9P203-1 SNV BTBD7,missense_variant,p.M244L,ENST00000334746,NM_001002860.4,c.730A>C,MODERATE,YES,tolerated(0.32),possibly_damaging(0.833),-1;BTBD7,missense_variant,p.M244L,ENST00000298896,NM_018167.5,c.730A>C,MODERATE,,tolerated(0.09),possibly_damaging(0.557),-1;BTBD7,missense_variant,p.M244L,ENST00000555525,,c.730A>C,MODERATE,,tolerated(0.25),possibly_damaging(0.743),-1;BTBD7,intron_variant,,ENST00000554565,NM_001289133.2,c.110-30297A>C,MODIFIER,,,,-1;BTBD7,upstream_gene_variant,,ENST00000553975,,,MODIFIER,,,,-1;BTBD7,downstream_gene_variant,,ENST00000554968,,,MODIFIER,,,,-1;BTBD7,non_coding_transcript_exon_variant,,ENST00000554644,,n.328A>C,MODIFIER,,,,-1;BTBD7,upstream_gene_variant,,ENST00000355125,,,MODIFIER,,,,-1 1053/8445 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 76 ecbea0e3-c24c-4a2b-845f-67ea5322caac 90 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS BTBD7,missense_variant,p.M244L,ENST00000555525.1,c.730A>C,MODERATE,;BTBD7,missense_variant,p.M244L,ENST00000298896.7,c.730A>C,MODERATE,;BTBD7,non_coding_transcript_exon_variant,,ENST00000554644.1,n.328A>C,MODIFIER,;BTBD7,intron_variant,,ENST00000554565.5,c.110-30297A>C,MODIFIER,;BTBD7,missense_variant,p.M244L,ENST00000334746.10,c.730A>C,MODERATE,YES +DYNC1H1 1778 BI GRCh38 14 102032287 102032287 + missense_variant Missense_Mutation SNP A A G novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 237 87 c.9899A>G p.Lys3300Arg p.K3300R ENST00000360184.10 NM_001376.5 3300 aAg/aGg 52/78 P1 G K/R protein_coding YES CCDS9966.1 9899/13941 GATCAAGAAGC Gene3D:1.20.920.20;Gene3D:1.20.920.20;PDB-ENSP_mappings:5nug.A;PDB-ENSP_mappings:5nug.B;Pfam:PF12777;PANTHER:PTHR45703;PANTHER:PTHR45703:SF14 ENSP00000348965 52/78 ENST00000360184 Transcript 1.0 ENSG00000197102 HGNC:2961 MODERATE NM_001376.5 missense_variant 1.0 benign(0.084) Unknown tolerated(0.12) Q14204.206 DYNC1H1 HGNC 1 1.0 UPI00001B515A SNV DYNC1H1,missense_variant,p.K3300R,ENST00000360184,NM_001376.5,c.9899A>G,MODERATE,YES,tolerated(0.12),benign(0.084),1;DYNC1H1,missense_variant,p.K645R,ENST00000645149,,c.1934A>G,MODERATE,,tolerated(0.17),possibly_damaging(0.555),1;DYNC1H1,missense_variant,p.K1345R,ENST00000643508,,c.4034A>G,MODERATE,,tolerated(0.12),benign(0.014),1;DYNC1H1,missense_variant,p.K172R,ENST00000644881,,c.515A>G,MODERATE,,tolerated(0.07),benign(0.011),1;DYNC1H1,upstream_gene_variant,,ENST00000553423,,,MODIFIER,,,,1;DYNC1H1,upstream_gene_variant,,ENST00000647204,,,MODIFIER,,,,1;AL118558.1,downstream_gene_variant,,ENST00000553701,,,MODIFIER,,,,-1;DYNC1H1,downstream_gene_variant,,ENST00000555204,,,MODIFIER,,,,1;DYNC1H1,upstream_gene_variant,,ENST00000556791,,,MODIFIER,,,,1;AL118558.1,downstream_gene_variant,,ENST00000557242,,,MODIFIER,,,,-1;AL118558.1,downstream_gene_variant,,ENST00000557551,,,MODIFIER,YES,,,-1;DYNC1H1,missense_variant,p.K735R,ENST00000645039,,c.2204A>G,MODERATE,,tolerated(0.11),benign(0.015),1;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000647366,,n.3453A>G,MODIFIER,,,,1;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000647307,,n.9A>G,MODIFIER,,,,1;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000645697,,n.562A>G,MODIFIER,,,,1;DYNC1H1,downstream_gene_variant,,ENST00000554854,,,MODIFIER,,,,1;DYNC1H1,downstream_gene_variant,,ENST00000642882,,,MODIFIER,,,,1;DYNC1H1,upstream_gene_variant,,ENST00000643437,,,MODIFIER,,,,1;DYNC1H1,upstream_gene_variant,,ENST00000643722,,,MODIFIER,,,,1;DYNC1H1,upstream_gene_variant,,ENST00000643829,,,MODIFIER,,,,1;DYNC1H1,downstream_gene_variant,,ENST00000647119,,,MODIFIER,,,,1 10018/19940 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 314 ecbea0e3-c24c-4a2b-845f-67ea5322caac 325 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS DYNC1H1,non_coding_transcript_exon_variant,,ENST00000647307.1,n.9A>G,MODIFIER,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000645697.1,n.562A>G,MODIFIER,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000647366.1,n.3453A>G,MODIFIER,;DYNC1H1,missense_variant,p.K3300R,ENST00000360184.10,c.9899A>G,MODERATE,YES;DYNC1H1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000680423.1,c.*1630A>G,MODIFIER,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000680200.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000643508.2,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000681010.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000680313.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000645039.2,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000645149.2,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000681123.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000680874.1,c.9899A>G,MODERATE,;DYNC1H1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000681536.1,c.*3098A>G,MODIFIER,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000680715.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000644881.2,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000679629.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000680137.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000681574.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,p.K3300R,ENST00000679720.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000679486.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000681066.1,c.9899A>G,MODERATE,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000681822.1,c.9899A>G,MODERATE,;DYNC1H1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000679910.1,c.*981A>G,MODIFIER,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000681283.1,c.9899A>G,MODERATE,;DYNC1H1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000684561.1,c.*1358A>G,MODIFIER,;DYNC1H1,missense_variant,NMD_transcript_variant,p.K3300R,ENST00000680120.1,c.9899A>G,MODERATE, +PDXDC1 23042 BI GRCh38 16 15008840 15008840 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 180 31 c.641A>T p.His214Leu p.H214L ENST00000396410.9 NM_015027.4 214 cAt/cTt 7/23 P4 T H/L protein_coding CCDS32393.1 641/2367 CCAGCATCAGA PANTHER:PTHR42735;PANTHER:PTHR42735:SF10;Pfam:PF00282;Gene3D:3.40.640.10;Superfamily:SSF53383 ENSP00000379691 7/23 ENST00000396410 Transcript ENSG00000179889 HGNC:28995 MODERATE NM_015027.4 missense_variant probably_damaging(0.984) Unknown deleterious(0.04) Q6P996.145 PDXDC1 HGNC 1 1.0 UPI000004A864 Q6P996-1 SNV PDXDC1,missense_variant,p.H214L,ENST00000396410,NM_001324019.2&NM_015027.4,c.641A>T,MODERATE,,deleterious(0.04),probably_damaging(0.984),1;PDXDC1,missense_variant,p.H123L,ENST00000450288,NM_001285448.1,c.368A>T,MODERATE,,deleterious(0.03),probably_damaging(0.968),1;PDXDC1,missense_variant,p.H187L,ENST00000569715,NM_001285444.2,c.560A>T,MODERATE,,deleterious(0.05),benign(0.029),1;PDXDC1,missense_variant,p.H232L,ENST00000563679,NM_001285447.1,c.695A>T,MODERATE,YES,deleterious(0.03),benign(0.162),1;PDXDC1,missense_variant,p.H186L,ENST00000627450,NM_001285445.2,c.557A>T,MODERATE,,deleterious(0.05),probably_damaging(0.984),1;PDXDC1,missense_variant,p.H214L,ENST00000535621,NM_001324020.1&NM_001324021.1&NM_001285449.1,c.641A>T,MODERATE,,deleterious(0.04),probably_damaging(0.97),1;PDXDC1,missense_variant,p.H214L,ENST00000325823,,c.641A>T,MODERATE,,deleterious(0.04),benign(0.013),1;PDXDC1,intron_variant,,ENST00000455313,NM_001285450.2,c.580-841A>T,MODIFIER,,,,1;PDXDC1,intron_variant,,ENST00000567306,,c.535-841A>T,MODIFIER,,,,1;PDXDC1,downstream_gene_variant,,ENST00000563522,,,MODIFIER,,,,1;PDXDC1,downstream_gene_variant,,ENST00000563667,,,MODIFIER,,,,1;MIR1972-1,downstream_gene_variant,,ENST00000459337,,,MODIFIER,YES,,,-1;PDXDC1,3_prime_UTR_variant,,ENST00000565362,,c.*426A>T,MODIFIER,,,,1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,,n.736A>T,MODIFIER,,,,1;PDXDC1,intron_variant,,ENST00000562119,,c.174+7052A>T,MODIFIER,,,,1;PDXDC1,upstream_gene_variant,,ENST00000561930,,,MODIFIER,,,,1 815/4598 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 181 ecbea0e3-c24c-4a2b-845f-67ea5322caac 211 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS PDXDC1,missense_variant,p.H123L,ENST00000450288.3,c.368A>T,MODERATE,;PDXDC1,intron_variant,,ENST00000567306.5,c.535-841A>T,MODIFIER,;PDXDC1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000565362.5,c.*426A>T,MODIFIER,;PDXDC1,missense_variant,p.H186L,ENST00000627450.2,c.557A>T,MODERATE,;PDXDC1,missense_variant,p.H187L,ENST00000569715.5,c.560A>T,MODERATE,;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001.5,n.736A>T,MODIFIER,;PDXDC1,intron_variant,NMD_transcript_variant,,ENST00000562119.5,c.174+7052A>T,MODIFIER,;PDXDC1,intron_variant,,ENST00000455313.6,c.580-841A>T,MODIFIER,;PDXDC1,missense_variant,p.H214L,ENST00000396410.9,c.641A>T,MODERATE,YES;PDXDC1,missense_variant,p.H214L,ENST00000535621.6,c.641A>T,MODERATE,;PDXDC1,missense_variant,p.H232L,ENST00000563679.5,c.695A>T,MODERATE, +PER1 5187 BI GRCh38 17 8141187 8141187 + missense_variant Missense_Mutation SNP C C T rs535590026 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 14 67 c.3754G>A p.Glu1252Lys p.E1252K ENST00000317276.9 NM_002616.3 1252 Gag/Aag 23/23 0.0002 0.0008 0.0 0.0 0.0 0.0 P1 T E/K protein_coding YES CCDS11131.1 3754/3873 CTCCTCGCAGC PANTHER:PTHR11269;PANTHER:PTHR11269:SF8;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000314420 23/23 rs535590026 ENST00000317276 Transcript 1.0 ENSG00000179094 HGNC:8845 MODERATE NM_002616.3 0.0008 AFR missense_variant 1.0 benign(0.012) Unknown tolerated_low_confidence(0.76) O15534.191 PER1 HGNC -1 1.0 UPI000013FFF5 O15534-1 SNV PER1,missense_variant,p.E1252K,ENST00000317276,NM_002616.3,c.3754G>A,MODERATE,YES,tolerated_low_confidence(0.76),benign(0.012),-1;PER1,missense_variant,p.E1229K,ENST00000581082,,c.3685G>A,MODERATE,,tolerated_low_confidence(0.81),benign(0.003),-1;PER1,downstream_gene_variant,,ENST00000354903,,,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000583559,,,MODIFIER,,,,-1;MIR6883,downstream_gene_variant,,ENST00000614952,,,MODIFIER,YES,,,-1;PER1,downstream_gene_variant,,ENST00000578089,,,MODIFIER,,,,-1;PER1,3_prime_UTR_variant,,ENST00000582719,,c.*668G>A,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000578950,,,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000579098,,,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000581395,,,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000583677,,,MODIFIER,,,,-1;PER1,downstream_gene_variant,,ENST00000585284,,,MODIFIER,,,,-1 3961/4676 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 1.991e-05 0.0001846 0.0 0.0 0.0 0.0 1.763e-05 0.0 0.0 2.027489972533658e-05 4.863099820795469e-05 0.0 0.0 0.0 0.0 0.0 afr 4.863099820795469e-05 0.0 1.5430699932039715e-05 0.0 0.0 0 197 ecbea0e3-c24c-4a2b-845f-67ea5322caac 81 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS PER1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000582719.5,c.*668G>A,MODIFIER,;PER1,missense_variant,p.E1229K,ENST00000581082.5,c.3685G>A,MODERATE,;PER1,missense_variant,p.E1252K,ENST00000317276.9,c.3754G>A,MODERATE,YES +MC2R 4158 BI GRCh38 18 13885230 13885230 + missense_variant Missense_Mutation SNP T T A rs1300489219 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 44 45 c.289A>T p.Ser97Cys p.S97C ENST00000327606.4 NM_001291911.1 97 Agt/Tgt 2/2 P1 A S/C protein_coding YES CCDS11869.1 289/894 AAAACTGCCAC Gene3D:1.20.1070.10;Pfam:PF00001;Prints:PR00520;PROSITE_profiles:PS50262;PANTHER:PTHR22750;PANTHER:PTHR22750:SF3;SMART:SM01381;Superfamily:SSF81321;CDD:cd15350 ENSP00000333821 2/2 rs1300489219 ENST00000327606 Transcript 1.0 ENSG00000185231 HGNC:6930 MODERATE NM_000529.2 5.782e-05 gnomAD_AMR missense_variant 1.0 possibly_damaging(0.506) Unknown deleterious(0.02) Q01718.182 MC2R HGNC -1 1.0 UPI00000503E5 SNV MC2R,missense_variant,p.S97C,ENST00000327606,NM_001291911.1&NM_000529.2,c.289A>T,MODERATE,YES,deleterious(0.02),possibly_damaging(0.506),-1;MC2R,missense_variant,p.S97C,ENST00000399821,,c.289A>T,MODERATE,,tolerated(0.06),possibly_damaging(0.506),-1 466/3652 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 7.953e-06 0.0 5.782e-05 0.0 0.0 0.0 0.0 0.0 0.0 0 95 ecbea0e3-c24c-4a2b-845f-67ea5322caac 89 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS MC2R,missense_variant,p.S97C,ENST00000399821.2,c.289A>T,MODERATE,;MC2R,missense_variant,p.S97C,ENST00000327606.4,c.289A>T,MODERATE,YES +SBNO2 22904 BI GRCh38 19 1119014 1119014 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 6 4 c.1524G>A p.Leu508= p.L508= ENST00000361757.8 NM_014963.3 508 ctG/ctA 14/32 P4 T L protein_coding YES CCDS45894.1 1524/4101 ACCAGCAGGGC PANTHER:PTHR12706;PANTHER:PTHR12706:SF5 ENSP00000354733 14/32 ENST00000361757 Transcript ENSG00000064932 HGNC:29158 LOW NM_014963.3 synonymous_variant 1.0 Unknown Q9Y2G9.127 SBNO2 HGNC -1 1.0 UPI0000140680 Q9Y2G9-1 SNV SBNO2,synonymous_variant,p.L508=,ENST00000361757,NM_014963.3,c.1524G>A,LOW,YES,,,-1;SBNO2,synonymous_variant,p.L508=,ENST00000587024,,c.1524G>A,LOW,,,,-1;SBNO2,synonymous_variant,p.L451=,ENST00000438103,NM_001100122.2,c.1353G>A,LOW,,,,-1;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222,,n.1377G>A,MODIFIER,,,,-1;SBNO2,non_coding_transcript_exon_variant,,ENST00000590446,,n.480G>A,MODIFIER,,,,-1 1747/4906 mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 16 ecbea0e3-c24c-4a2b-845f-67ea5322caac 10 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS SBNO2,non_coding_transcript_exon_variant,,ENST00000590446.2,n.480G>A,MODIFIER,;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222.5,n.1377G>A,MODIFIER,;SBNO2,synonymous_variant,p.L508=,ENST00000587024.5,c.1524G>A,LOW,;SBNO2,synonymous_variant,p.L508=,ENST00000361757.8,c.1524G>A,LOW,YES;SBNO2,synonymous_variant,p.L451=,ENST00000438103.6,c.1353G>A,LOW, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 31 19 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 79 ecbea0e3-c24c-4a2b-845f-67ea5322caac 50 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +ZNF20 7568 BI GRCh38 19 12133374 12133374 + missense_variant Missense_Mutation SNP C C T TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 35 20 c.812G>A p.Arg271His p.R271H ENST00000334213.10 NM_001203250.2 271 cGt/cAt 4/4 P1 T R/H protein_coding YES CCDS45986.1 812/1599 GTCTACGAATT Gene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF837;SMART:SM00355;Superfamily:SSF57667 ENSP00000335437 4/4 COSV61998666 ENST00000334213 Transcript ENSG00000132010 HGNC:12992 MODERATE NM_021143.4 missense_variant 1 1.0 benign(0.006) Unknown tolerated(0.12) 1 P17024.188 ZNF20 HGNC -1 1.0 UPI000013C404 SNV ZNF20,missense_variant,p.R271H,ENST00000334213,NM_001203250.2&NM_021143.4,c.812G>A,MODERATE,YES,tolerated(0.12),benign(0.006),-1;ZNF20,intron_variant,,ENST00000600335,,c.191+2126G>A,MODIFIER,,,,-1;ZNF20,downstream_gene_variant,,ENST00000418866,,,MODIFIER,,,,-1;ZNF20,intron_variant,,ENST00000480770,,n.221+2126G>A,MODIFIER,,,,-1;ZNF788P,intron_variant,,ENST00000601686,,n.165-2401C>T,MODIFIER,,,,1;ZNF20,downstream_gene_variant,,ENST00000480477,,,MODIFIER,,,,-1;ZNF20,downstream_gene_variant,,ENST00000485451,,,MODIFIER,,,,-1;ZNF625-ZNF20,3_prime_UTR_variant,,ENST00000430024,,c.*843G>A,MODIFIER,YES,,,-1;ZNF20,downstream_gene_variant,,ENST00000454949,,,MODIFIER,,,,-1;ZNF20,downstream_gene_variant,,ENST00000478942,,,MODIFIER,,,,-1 980/3004 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 6.759859843441518e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.542830068501644e-05 0.0 0.0 0 64 ecbea0e3-c24c-4a2b-845f-67ea5322caac 55 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS ZNF625-ZNF20,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000430024.5,c.*843G>A,MODIFIER,YES;ZNF20,missense_variant,p.R271H,ENST00000334213.10,c.812G>A,MODERATE,YES;ZNF20,intron_variant,,ENST00000480770.5,n.221+2126G>A,MODIFIER,;ZNF20,intron_variant,,ENST00000600335.5,c.191+2126G>A,MODIFIER,;ENSG00000290812,intron_variant,,ENST00000601686.1,n.165-2401C>T,MODIFIER,YES +ANKRD27 84079 BI GRCh38 19 32646464 32646464 + missense_variant Missense_Mutation SNP C C T novel TCGA-V4-A9EI-01A TCGA-V4-A9EI-10A Somatic 70 23 c.365G>A p.Ser122Asn p.S122N ENST00000306065.9 NM_032139.3 122 aGt/aAt 4/29 P1 T S/N protein_coding YES CCDS32986.1 365/3153 CTGAACTCTCT PANTHER:PTHR24170 ENSP00000304292 4/29 ENST00000306065 Transcript ENSG00000105186 HGNC:25310 MODERATE NM_032139.3 missense_variant 1.0 benign(0.003) Unknown tolerated(0.32) Q96NW4.146 ANKRD27 HGNC -1 1.0 UPI000004FDE9 SNV ANKRD27,missense_variant,p.S122N,ENST00000306065,NM_032139.3,c.365G>A,MODERATE,YES,tolerated(0.32),benign(0.003),-1;ANKRD27,missense_variant,p.S122N,ENST00000587352,,c.365G>A,MODERATE,,tolerated(0.3),benign(0.007),-1;ANKRD27,missense_variant,p.S122N,ENST00000586693,,c.365G>A,MODERATE,,tolerated(0.22),benign(0.007),-1;ANKRD27,5_prime_UTR_variant,,ENST00000586463,,c.-272G>A,MODIFIER,,,,-1;ANKRD27,downstream_gene_variant,,ENST00000590519,,,MODIFIER,,,,-1;ANKRD27,upstream_gene_variant,,ENST00000591100,,,MODIFIER,,,,-1;ANKRD27,intron_variant,,ENST00000588700,,c.214-1985G>A,MODIFIER,,,,-1;ANKRD27,upstream_gene_variant,,ENST00000593232,,,MODIFIER,,,,-1 505/4432 muse;mutect2;varscan2 b533e555-90cf-4657-80c6-15b67da8ad26 0 110 ecbea0e3-c24c-4a2b-845f-67ea5322caac 93 447add4c-55df-4fd0-9b03-d4756cbc810e SUCCESS ANKRD27,missense_variant,p.S122N,ENST00000586693.7,c.365G>A,MODERATE,;ANKRD27,intron_variant,NMD_transcript_variant,,ENST00000588700.5,c.214-1985G>A,MODIFIER,;ANKRD27,5_prime_UTR_variant,,ENST00000586463.5,c.-272G>A,MODIFIER,;ANKRD27,missense_variant,p.S122N,ENST00000587352.5,c.365G>A,MODERATE,;ANKRD27,missense_variant,p.S122N,ENST00000306065.9,c.365G>A,MODERATE,YES +PAX7 5081 BI GRCh38 1 18703264 18703264 + missense_variant Missense_Mutation SNP A A C novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 28 15 c.1123A>C p.Met375Leu p.M375L ENST00000420770.7 NM_001135254.2 375 Atg/Ctg 7/9 P1 C M/L protein_coding CCDS44074.1 1123/1518 ACCACATGAAC Pfam:PF12360;PANTHER:PTHR45636:SF26;PANTHER:PTHR45636 ENSP00000403389 7/9 ENST00000420770 Transcript 1.0 ENSG00000009709 HGNC:8621 MODERATE NM_001135254.2 missense_variant benign(0.031) Unknown tolerated(0.05) P23759.200 PAX7 HGNC 1 1.0 UPI0000E1E6AE P23759-3 SNV PAX7,missense_variant,p.M375L,ENST00000420770,NM_001135254.2,c.1123A>C,MODERATE,,tolerated(0.05),benign(0.031),1;PAX7,missense_variant,p.M375L,ENST00000375375,NM_002584.3,c.1123A>C,MODERATE,YES,deleterious_low_confidence(0.01),benign(0.196),1;PAX7,missense_variant,p.M373L,ENST00000400661,NM_013945.3,c.1117A>C,MODERATE,,deleterious_low_confidence(0.01),benign(0.067),1 1881/6213 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 82 5d0915dd-ef93-4790-aa83-25c2b1a2364d 44 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS PAX7,missense_variant,p.M373L,ENST00000400661.3,c.1117A>C,MODERATE,;PAX7,missense_variant,p.M375L,ENST00000375375.7,c.1123A>C,MODERATE,;PAX7,missense_variant,NMD_transcript_variant,p.M375L,ENST00000713641.1,c.1123A>C,MODERATE,;PAX7,missense_variant,p.M375L,ENST00000420770.7,c.1123A>C,MODERATE,YES;PAX7,missense_variant,p.M375L,ENST00000713640.1,c.1123A>C,MODERATE, +TMEM54 113452 BI GRCh38 1 32898212 32898212 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 37 3 c.124G>A p.Val42Met p.V42M ENST00000373463.8 NM_001329724.2 42 Gtg/Atg 2/6 P1 T V/M protein_coding YES CCDS371.1 124/669 CAGCACTGTGC Transmembrane_helices:TMhelix;PANTHER:PTHR31258;PANTHER:PTHR31258:SF2;Pfam:PF12304 ENSP00000362562 2/6 ENST00000373463 Transcript ENSG00000121900 HGNC:24143 MODERATE NM_033504.4 missense_variant 1.0 benign(0.27) Unknown tolerated(0.07) Q969K7.128 TMEM54 HGNC -1 1.0 UPI0000073706 Q969K7-1 SNV TMEM54,missense_variant,p.V42M,ENST00000373463,NM_001329724.2&NM_033504.4&NM_001329722.2,c.124G>A,MODERATE,YES,tolerated(0.07),benign(0.27),-1;TMEM54,missense_variant,p.V42M,ENST00000329151,NM_001329725.2&NM_001329723.2,c.124G>A,MODERATE,,tolerated(0.08),benign(0.177),-1;HPCA,downstream_gene_variant,,ENST00000373467,NM_002143.3,,MODIFIER,YES,,,1;TMEM54,non_coding_transcript_exon_variant,,ENST00000475208,,n.324G>A,MODIFIER,,,,-1;TMEM54,non_coding_transcript_exon_variant,,ENST00000474144,,n.238G>A,MODIFIER,,,,-1;HPCA,non_coding_transcript_exon_variant,,ENST00000470896,,n.274C>T,MODIFIER,,,,1;HPCA,downstream_gene_variant,,ENST00000459874,,,MODIFIER,,,,1;TMEM54,upstream_gene_variant,,ENST00000463914,,,MODIFIER,,,,-1;HPCA,downstream_gene_variant,,ENST00000470166,,,MODIFIER,,,,1;HPCA,downstream_gene_variant,,ENST00000480118,,,MODIFIER,,,,1;TMEM54,upstream_gene_variant,,ENST00000482771,,,MODIFIER,,,,-1 275/1030 muse;mutect2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 62 5d0915dd-ef93-4790-aa83-25c2b1a2364d 40 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS TMEM54,non_coding_transcript_exon_variant,,ENST00000475208.5,n.324G>A,MODIFIER,;TMEM54,non_coding_transcript_exon_variant,,ENST00000474144.5,n.238G>A,MODIFIER,;TMEM54,missense_variant,p.V42M,ENST00000373463.8,c.124G>A,MODERATE,YES;TMEM54,missense_variant,p.V42M,ENST00000329151.5,c.124G>A,MODERATE,;HPCA,non_coding_transcript_exon_variant,,ENST00000470896.1,n.274C>T,MODIFIER, +SOX14 8403 BI GRCh38 3 137765429 137765429 + synonymous_variant Silent SNP C C G rs1172708903 TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 5 10 c.645C>G p.Pro215= p.P215= ENST00000306087.3 NM_004189.4 215 ccC/ccG 1/1 P1 G P protein_coding YES CCDS3094.1 645/723 CCCCCCGTCGC PANTHER:PTHR10270:SF297;PANTHER:PTHR10270 ENSP00000305343 1/1 rs1172708903;COSV60163019 ENST00000306087 Transcript ENSG00000168875 HGNC:11193 LOW NM_004189.4 8.881e-06 gnomAD_NFE synonymous_variant 0;1 1.0 Unknown 0;1 O95416.164 SOX14 HGNC 1 UPI0000000B2D SNV SOX14,synonymous_variant,p.P215=,ENST00000306087,NM_004189.4,c.645C>G,LOW,YES,,,1 1115/2020 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 4.001e-06 0.0 0.0 0.0 0.0 0.0 8.881e-06 0.0 0.0 0 39 5d0915dd-ef93-4790-aa83-25c2b1a2364d 15 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS SOX14,synonymous_variant,p.P215=,ENST00000306087.3,c.645C>G,LOW,YES +DROSHA 29102 BI GRCh38 5 31526385 31526385 + frameshift_variant Frame_Shift_Del DEL T T - novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 29 22 c.548del p.Asn183IlefsTer43 p.N183Ifs*43 ENST00000344624.8 NM_001382508.1 183 aAt/at 5/36 P4 - N/X protein_coding CCDS47195.1 548/4125 AAACTATTAAAA MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000339845 2/33 ENST00000344624 Transcript 1.0 ENSG00000113360 HGNC:17904 HIGH frameshift_variant Unknown Q9NRR4.182 DROSHA HGNC -1 5.0 UPI0000134351 Q9NRR4-1 deletion DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000511367,NM_013235.5&NM_001382508.1,c.548del,HIGH,YES,,,-1;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000344624,,c.548del,HIGH,,,,-1;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000442743,,c.548del,HIGH,,,,-1;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000513349,NM_001100412.2,c.548del,HIGH,,,,-1;DROSHA,frameshift_variant,p.N13Ifs*43,ENST00000512076,,c.36del,HIGH,,,,-1;DROSHA,frameshift_variant,p.N183Ifs*?,ENST00000507438,,c.548del,HIGH,,,,-1;DROSHA,upstream_gene_variant,,ENST00000512302,,,MODIFIER,,,,-1;DROSHA,downstream_gene_variant,,ENST00000504361,,,MODIFIER,,,,-1 595/5102 mutect2;pindel;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 53 5d0915dd-ef93-4790-aa83-25c2b1a2364d 51 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS DROSHA,frameshift_variant,p.N183Ifs,ENST00000507438.5,c.548del,HIGH,;DROSHA,frameshift_variant,p.*12Yfs,ENST00000512076.1,c.36del,HIGH,;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000513349.5,c.548del,HIGH,;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000511367.6,c.548del,HIGH,;DROSHA,frameshift_variant,p.N183Ifs*43,ENST00000344624.8,c.548del,HIGH,YES +TRIM4 89122 BI GRCh38 7 99892240 99892240 + missense_variant Missense_Mutation SNP C C T novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 43 18 c.1426G>A p.Val476Ile p.V476I ENST00000355947.6 NM_033017.4 476 Gtc/Atc 7/7 A2 T V/I protein_coding YES CCDS5679.1 1426/1503 TGAGACAGAAG CDD:cd15809;Gene3D:2.60.120.920;Pfam:PF00622;SMART:SM00449;Superfamily:SSF49899;PROSITE_profiles:PS50188;PANTHER:PTHR24103;PANTHER:PTHR24103:SF559;Prints:PR01407 ENSP00000348216 7/7 ENST00000355947 Transcript ENSG00000146833 HGNC:16275 MODERATE missense_variant 1.0 benign(0.005) Unknown tolerated(0.3) Q9C037.159 TRIM4 HGNC -1 1.0 UPI000013DA79 Q9C037-1 SNV TRIM4,missense_variant,p.V476I,ENST00000355947,NM_033017.4,c.1426G>A,MODERATE,YES,tolerated(0.3),benign(0.005),-1;TRIM4,missense_variant,p.V450I,ENST00000349062,NM_033091.3,c.1348G>A,MODERATE,,tolerated(0.29),benign(0.003),-1;TRIM4,intron_variant,,ENST00000447480,,c.545+10978G>A,MODIFIER,,,,-1 1556/3383 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 91 5d0915dd-ef93-4790-aa83-25c2b1a2364d 61 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS TRIM4,missense_variant,p.V476I,ENST00000355947.6,c.1426G>A,MODERATE,;TRIM4,missense_variant,p.V450I,ENST00000349062.7,c.1348G>A,MODERATE,YES;TRIM4,intron_variant,,ENST00000447480.5,c.545+10978G>A,MODIFIER, +MYOF 26509 BI GRCh38 10 93351691 93351691 + missense_variant Missense_Mutation SNP T T A novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 43 28 c.3637A>T p.Met1213Leu p.M1213L ENST00000359263.9 NM_013451.4 1213 Atg/Ttg 33/54 P4 A M/L protein_coding YES CCDS41551.1 3637/6186 TTCCATGATAA Gene3D:2.60.40.150;Pfam:PF00168;PROSITE_profiles:PS50004;PANTHER:PTHR12546;PANTHER:PTHR12546:SF55;SMART:SM00239;Superfamily:SSF49562;CDD:cd04017 ENSP00000352208 33/54 ENST00000359263 Transcript ENSG00000138119 HGNC:3656 MODERATE NM_013451.4 missense_variant 1.0 benign(0) Unknown tolerated(0.45) Q9NZM1.183 MYOF HGNC -1 1.0 UPI000012FBA1 Q9NZM1-1 SNV MYOF,missense_variant,p.M1213L,ENST00000359263,NM_013451.4,c.3637A>T,MODERATE,YES,tolerated(0.45),benign(0),-1;MYOF,missense_variant,p.M1200L,ENST00000358334,NM_133337.3,c.3598A>T,MODERATE,,tolerated(0.42),benign(0),-1;MYOF,missense_variant,p.M588L,ENST00000463743,,c.1762A>T,MODERATE,,tolerated(0.45),benign(0),-1 3777/6860 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 93 5d0915dd-ef93-4790-aa83-25c2b1a2364d 71 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS MYOF,missense_variant,p.M1200L,ENST00000358334.9,c.3598A>T,MODERATE,;MYOF,synonymous_variant,NMD_transcript_variant,p.S587=,ENST00000463743.5,c.1761A>T,LOW,;MYOF,missense_variant,p.M1213L,ENST00000359263.9,c.3637A>T,MODERATE,YES +ANKK1 255239 BI GRCh38 11 113399341 113399341 + stop_gained Nonsense_Mutation SNP G G T TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 5 4 c.1372G>T p.Glu458Ter p.E458* ENST00000303941.4 NM_178510.2 458 Gaa/Taa 8/8 P1 T E/* protein_coding YES CCDS44734.1 1372/2298 CCCAGGAACGT Gene3D:1.25.40.20;Pfam:PF12796;Superfamily:SSF48403;PROSITE_profiles:PS50088;PROSITE_profiles:PS50297;PANTHER:PTHR24198;PANTHER:PTHR24198:SF175 ENSP00000306678 8/8 COSV58273709 ENST00000303941 Transcript ENSG00000170209 HGNC:21027 HIGH NM_178510.2 stop_gained 1 1.0 Unknown 1 Q8NFD2.140 ANKK1 HGNC 1 1.0 UPI000000DCCF SNV ANKK1,stop_gained,p.E458*,ENST00000303941,NM_178510.2,c.1372G>T,HIGH,YES,,,1;ANKK1,downstream_gene_variant,,ENST00000542948,,,MODIFIER,,,,1 1478/2553 muse;mutect2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 10 5d0915dd-ef93-4790-aa83-25c2b1a2364d 9 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS ANKK1,stop_gained,p.E458*,ENST00000303941.4,c.1372G>T,HIGH,YES +OR10G4 390264 BI GRCh38 11 124016167 124016167 + missense_variant Missense_Mutation SNP T T C novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 46 52 c.593T>C p.Ile198Thr p.I198T ENST00000641722.1 NM_001004462.2 198 aTc/aCc 2/2 P1 C I/T protein_coding CCDS31702.1 593/936 GGTCATCTTTG Gene3D:1.20.1070.10;Pfam:PF13853;PROSITE_profiles:PS50262;PANTHER:PTHR26453;PANTHER:PTHR26453:SF6;Superfamily:SSF81321;CDD:cd15916 ENSP00000325076 1/1 ENST00000320891 Transcript ENSG00000254737 HGNC:14809 MODERATE missense_variant probably_damaging(0.911) Unknown tolerated(1) Q8NGN3.143 OR10G4 HGNC 1 A0A126GWS5.24 UPI0000041BAD SNV OR10G4,missense_variant,p.I198T,ENST00000641521,,c.593T>C,MODERATE,YES,tolerated(1),probably_damaging(0.911),1;OR10G4,missense_variant,p.I198T,ENST00000641722,,c.593T>C,MODERATE,,tolerated(1),probably_damaging(0.911),1;OR10G4,missense_variant,p.I198T,ENST00000320891,NM_001004462.1,c.593T>C,MODERATE,,tolerated(1),probably_damaging(0.911),1 593/936 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 132 5d0915dd-ef93-4790-aa83-25c2b1a2364d 98 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS OR10G4,missense_variant,p.I198T,ENST00000641521.1,c.593T>C,MODERATE,;OR10G4,missense_variant,p.I198T,ENST00000641722.1,c.593T>C,MODERATE,YES +GRIN2B 2904 BI GRCh38 12 13564156 13564156 + missense_variant Missense_Mutation SNP G G A TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 24 14 c.3082C>T p.Pro1028Ser p.P1028S ENST00000609686.4 NM_000834.5 1028 Ccc/Tcc 14/14 P1 A P/S protein_coding YES CCDS8662.1 3082/4455 GGAGGGGAGGC Pfam:PF10565 ENSP00000477455 14/14 COSV101663147 ENST00000609686 Transcript 1.0 ENSG00000273079 HGNC:4586 MODERATE NM_000834.5 missense_variant 1 1.0 benign(0.068) Unknown deleterious(0.04) 1 Q13224.203 GRIN2B HGNC -1 1.0 UPI000013026C SNV GRIN2B,missense_variant,p.P1028S,ENST00000609686,NM_000834.5,c.3082C>T,MODERATE,YES,deleterious(0.04),benign(0.068),-1;GRIN2B,intron_variant,,ENST00000637214,,c.69+44447C>T,MODIFIER,,,,-1;GRIN2B,downstream_gene_variant,,ENST00000628166,,,MODIFIER,,,,-1;GRIN2B,upstream_gene_variant,,ENST00000636207,,,MODIFIER,,,,-1 3790/30609 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 39 5d0915dd-ef93-4790-aa83-25c2b1a2364d 38 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS GRIN2B,missense_variant,p.P1028S,ENST00000609686.4,c.3082C>T,MODERATE,YES;GRIN2B,missense_variant,p.P1028S,ENST00000630791.3,c.3082C>T,MODERATE,;GRIN2B,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000714048.1,c.*887C>T,MODIFIER,;GRIN2B,intron_variant,,ENST00000637214.1,c.69+44447C>T,MODIFIER, +IGHE 3497 BI GRCh38 14 105601657 105601657 + synonymous_variant Silent SNP G G A rs1555457222 TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 13 14 c.72C>T p.Ser24= p.S24= ENST00000390541.2 24 tcC/tcT 1/4 A2 A S IG_C_gene 72/1287 GTCACGGAGGT COSN5026549 ENSP00000374983 1/4 rs1555457222 cds_start_NF ENST00000390541 Transcript ENSG00000211891 HGNC:5522 LOW 5.565e-05 gnomAD_EAS synonymous_variant Unknown P01854.175 IGHE HGNC -1 UPI000004BB48 SNV IGHE,synonymous_variant,p.S24=,ENST00000641420,,c.72C>T,LOW,YES,,,-1;IGHE,synonymous_variant,p.S24=,ENST00000390541,,c.72C>T,LOW,,,,-1 72/1412 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 8.114e-06 0.0 0.0 0.0 5.565e-05 0.0 0.0 0.0 3.27e-05 0 27 5d0915dd-ef93-4790-aa83-25c2b1a2364d 27 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS IGHE,synonymous_variant,p.S24=,ENST00000390541.2,c.72C>T,LOW,;IGHE,synonymous_variant,p.S24=,ENST00000641420.1,c.72C>T,LOW,YES +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 24 21 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 70 5d0915dd-ef93-4790-aa83-25c2b1a2364d 45 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +UPK1A 11045 BI GRCh38 19 35673469 35673469 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 29 17 c.392A>T p.Gln131Leu p.Q131L ENST00000222275.3 NM_007000.4 131 cAg/cTg 5/8 P1 T Q/L protein_coding CCDS12470.1 392/777 CAAGCAGATGC CDD:cd03156;PANTHER:PTHR19282;PANTHER:PTHR19282:SF25;Pfam:PF00335;PIRSF:PIRSF002419;Superfamily:SSF48652 ENSP00000222275 4/7 ENST00000222275 Transcript ENSG00000105668 HGNC:12577 MODERATE missense_variant possibly_damaging(0.708) Unknown deleterious(0) O00322.151 UPK1A HGNC 1 1.0 UPI0000137CD9 O00322-1 SNV UPK1A,missense_variant,p.Q131L,ENST00000616789,NM_001281443.1,c.392A>T,MODERATE,YES,deleterious(0),possibly_damaging(0.794),1;UPK1A,missense_variant,p.Q131L,ENST00000617999,NM_007000.3,c.392A>T,MODERATE,,deleterious(0),possibly_damaging(0.708),1;UPK1A,missense_variant,p.Q131L,ENST00000222275,,c.392A>T,MODERATE,,deleterious(0),possibly_damaging(0.708),1;UPK1A,missense_variant,p.Q131L,ENST00000379013,,c.392A>T,MODERATE,,deleterious(0),possibly_damaging(0.794),1;UPK1A-AS1,upstream_gene_variant,,ENST00000443196,,,MODIFIER,YES,,,-1 392/1223 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 49 5d0915dd-ef93-4790-aa83-25c2b1a2364d 46 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS UPK1A,missense_variant,p.Q131L,ENST00000379013.6,c.392A>T,MODERATE,;UPK1A,missense_variant,p.Q131L,ENST00000222275.3,c.392A>T,MODERATE,YES +SGSM1 129049 BI GRCh38 22 24850335 24850335 + missense_variant Missense_Mutation SNP A A T novel TCGA-VD-A8K8-01A TCGA-VD-A8K8-10A Somatic 8 7 c.358A>T p.Asn120Tyr p.N120Y ENST00000400359.4 NM_001039948.4 120 Aac/Tac 5/26 A1 T N/Y protein_coding YES CCDS46674.1 358/3447 TGCCCAACTTG Gene3D:1.20.58.900;Pfam:PF02759;PROSITE_profiles:PS50826;Superfamily:SSF140741 ENSP00000383212 5/26 ENST00000400359 Transcript ENSG00000167037 HGNC:29410 MODERATE missense_variant 1.0 possibly_damaging(0.452) Unknown tolerated(0.14) Q2NKQ1.116 SGSM1 HGNC 1 5.0 UPI00006EB130 Q2NKQ1-1 SNV SGSM1,missense_variant,p.N120Y,ENST00000400358,NM_001098497.3&NM_001098498.3,c.358A>T,MODERATE,,tolerated(0.39),benign(0.202),1;SGSM1,missense_variant,p.N120Y,ENST00000610372,NM_133454.3,c.358A>T,MODERATE,,tolerated(0.23),benign(0.003),1;SGSM1,missense_variant,p.N120Y,ENST00000400359,NM_001039948.4,c.358A>T,MODERATE,YES,tolerated(0.14),possibly_damaging(0.452),1;SGSM1,non_coding_transcript_exon_variant,,ENST00000473458,,n.1732A>T,MODIFIER,,,,1;SGSM1,non_coding_transcript_exon_variant,,ENST00000480523,,n.451A>T,MODIFIER,,,,1 365/4317 muse;mutect2;varscan2 9b1ecfb2-9dfb-4e71-b51a-d2a0c5a7940e 0 20 5d0915dd-ef93-4790-aa83-25c2b1a2364d 15 fcbbc384-9665-4cd4-9a55-e9f331075725 SUCCESS SGSM1,non_coding_transcript_exon_variant,,ENST00000480523.1,n.451A>T,MODIFIER,;SGSM1,non_coding_transcript_exon_variant,,ENST00000473458.5,n.1732A>T,MODIFIER,;SGSM1,missense_variant,p.N120Y,ENST00000400359.4,c.358A>T,MODERATE,;SGSM1,missense_variant,p.N120Y,ENST00000400358.9,c.358A>T,MODERATE,YES;SGSM1,missense_variant,p.N120Y,ENST00000610372.4,c.358A>T,MODERATE, +LCE4A 199834 BI GRCh38 1 152709372 152709372 + synonymous_variant Silent SNP C C T novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 13 24 c.297C>T p.Cys99= p.C99= ENST00000368777.2 NM_001387222.1 99 tgC/tgT 2/2 P1 T C protein_coding YES CCDS1022.1 297/300 TGTTGCTGACC Pfam:PF14672;PANTHER:PTHR23263;PANTHER:PTHR23263:SF25;Low_complexity_(Seg):seg ENSP00000357766 2/2 ENST00000368777 Transcript ENSG00000187170 HGNC:16613 LOW synonymous_variant 1.0 Unknown Q5TA78.96 LCE4A HGNC 1 2.0 UPI0000192763 SNV LCE4A,synonymous_variant,p.C99=,ENST00000368777,NM_178356.3,c.297C>T,LOW,YES,,,1 553/672 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 35 57acb1a3-70b7-4ccb-b233-7ae363b0020a 37 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS LCE4A,synonymous_variant,p.C99=,ENST00000368777.2,c.297C>T,LOW,YES +SF3B1 23451 BI GRCh38 2 197402760 197402760 + missense_variant Missense_Mutation SNP G G A rs775623976 TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 18 19 c.1873C>T p.Arg625Cys p.R625C ENST00000335508.11 NM_012433.4 625 Cgt/Tgt 14/25 P1 A R/C protein_coding YES CCDS33356.1 1873/3915 likely_pathogenic GTTACGGACAT COSM110696 Gene3D:1.25.10.10;PDB-ENSP_mappings:5ife.C;PDB-ENSP_mappings:5o9z.v;PDB-ENSP_mappings:5z56.1;PDB-ENSP_mappings:5z57.1;PDB-ENSP_mappings:5z58.1;PDB-ENSP_mappings:5zya.C;PDB-ENSP_mappings:6ah0.1;PDB-ENSP_mappings:6en4.C;PDB-ENSP_mappings:6ff4.u;PDB-ENSP_mappings:6ff7.u;PDB-ENSP_mappings:6qx9.B1;PANTHER:PTHR12097;Superfamily:SSF48371 ENSP00000335321 14/25 rs775623976;COSV59205859;COSV59212489;COSV59228873 ENST00000335508 Transcript 1.0 ENSG00000115524 HGNC:10768 MODERATE NM_012433.4 8.812e-06 gnomAD_NFE missense_variant 1;1;1;1 1.0 26619011 probably_damaging(0.993) Unknown deleterious(0) 0;1;1;1 O75533.197 SF3B1 HGNC -1 1.0 UPI000013D493 O75533-1 SNV SF3B1,missense_variant,p.R625C,ENST00000335508,NM_012433.4,c.1873C>T,MODERATE,YES,deleterious(0),probably_damaging(0.993),-1;SF3B1,upstream_gene_variant,,ENST00000424674,,,MODIFIER,,,,-1;AC010746.1,upstream_gene_variant,,ENST00000365564,,,MODIFIER,YES,,,1;SF3B1,upstream_gene_variant,,ENST00000462613,,,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652026,,c.*2940C>T,MODIFIER,,,,-1;SF3B1,3_prime_UTR_variant,,ENST00000652738,,c.*2132C>T,MODIFIER,,,,-1;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,,n.3757C>T,MODIFIER,,,,-1;SF3B1,upstream_gene_variant,,ENST00000496458,,,MODIFIER,,,,-1 1902/6463 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 3.982e-06 0.0 0.0 0.0 0.0 0.0 8.812e-06 0.0 0.0 0 52 57acb1a3-70b7-4ccb-b233-7ae363b0020a 37 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS SF3B1,non_coding_transcript_exon_variant,,ENST00000470268.2,n.3757C>T,MODIFIER,;SF3B1,missense_variant,p.R625C,ENST00000335508.11,c.1873C>T,MODERATE,YES;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652026.1,c.*2940C>T,MODIFIER,;SF3B1,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000652738.1,c.*2132C>T,MODIFIER, +ARID1B 57492 BI GRCh38 6 156901491 156901491 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 0 9 c.2102C>A p.Pro701Gln p.P701Q ENST00000636930.2 631 cCg/cAg 4/20 A P/Q protein_coding CCDS5251.2 1853/6711 TCTGCCGTCCC PANTHER:PTHR12656;PANTHER:PTHR12656:SF11;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg ENSP00000055163 3/19 cds_start_NF ENST00000350026 Transcript 1.0 ENSG00000049618 HGNC:18040 MODERATE missense_variant benign(0) Unknown tolerated_low_confidence(0.1) Q8NFD5.176 ARID1B HGNC 1 1.0 UPI000058E2EA Q8NFD5-1 SNV ARID1B,missense_variant,p.P714Q,ENST00000346085,NM_001371656.1&NM_001374820.1,c.2141C>A,MODERATE,,tolerated_low_confidence(0.08),benign(0.054),1;ARID1B,missense_variant,p.P701Q,ENST00000636930,NM_001374828.1,c.2102C>A,MODERATE,YES,tolerated_low_confidence(0.21),benign(0.033),1;ARID1B,missense_variant,p.P631Q,ENST00000647938,,c.1892C>A,MODERATE,,tolerated_low_confidence(0.09),benign(0.003),1;ARID1B,missense_variant,p.P128Q,ENST00000636748,,c.383C>A,MODERATE,,tolerated_low_confidence(0.28),possibly_damaging(0.649),1;ARID1B,missense_variant,p.P618Q,ENST00000350026,NM_017519.3,c.1853C>A,MODERATE,,tolerated_low_confidence(0.1),benign(0),1;ARID1B,missense_variant,p.P117Q,ENST00000414678,,c.350C>A,MODERATE,,tolerated_low_confidence(0.21),benign(0.01),1;ARID1B,missense_variant,p.P615Q,ENST00000674298,,c.1844C>A,MODERATE,,tolerated_low_confidence(0.12),benign(0.135),1;ARID1B,missense_variant,p.P39Q,ENST00000319584,,c.116C>A,MODERATE,,tolerated_low_confidence(0.17),benign(0.003),1;ARID1B,missense_variant,p.P107Q,ENST00000638000,,c.320C>A,MODERATE,,tolerated_low_confidence(0.17),benign(0.037),1;ARID1B,missense_variant,p.P43Q,ENST00000637532,,c.128C>A,MODERATE,,tolerated_low_confidence(0.13),benign(0.003),1;ARID1B,non_coding_transcript_exon_variant,,ENST00000674190,,n.809C>A,MODIFIER,,,,1;ARID1B,non_coding_transcript_exon_variant,,ENST00000636205,,n.165C>A,MODIFIER,,,,1 1853/7962 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 24 57acb1a3-70b7-4ccb-b233-7ae363b0020a 9 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS ARID1B,missense_variant,p.P39Q,ENST00000319584.11,c.116C>A,MODERATE,;ARID1B,missense_variant,p.P43Q,ENST00000637532.1,c.128C>A,MODERATE,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636205.1,n.165C>A,MODIFIER,;ARID1B,missense_variant,p.R107S,ENST00000638000.1,c.319C>A,MODERATE,;ARID1B,missense_variant,p.P128Q,ENST00000636748.1,c.383C>A,MODERATE,;ARID1B,non_coding_transcript_exon_variant,,ENST00000674190.1,n.809C>A,MODIFIER,;ARID1B,synonymous_variant,p.A614=,ENST00000674298.1,c.1842C>A,LOW,;ARID1B,missense_variant,p.P701Q,ENST00000414678.8,c.2102C>A,MODERATE,;ARID1B,missense_variant,p.P701Q,ENST00000350026.11,c.2102C>A,MODERATE,;ARID1B,missense_variant,p.P701Q,ENST00000637015.2,c.2102C>A,MODERATE,;ARID1B,missense_variant,p.P701Q,ENST00000636930.2,c.2102C>A,MODERATE,YES;ARID1B,missense_variant,p.P714Q,ENST00000346085.10,c.2141C>A,MODERATE, +LRRN3 54674 BI GRCh38 7 111123630 111123630 + synonymous_variant Silent SNP A A G novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 29 24 c.858A>G p.Leu286= p.L286= ENST00000308478.10 NM_001099658.2 286 ttA/ttG 3/3 P1 G L protein_coding CCDS5754.1 858/2127 CACTTAAAAGA Gene3D:3.80.10.10;PANTHER:PTHR24366;PANTHER:PTHR24366:SF73;Superfamily:SSF52058 ENSP00000312001 3/3 ENST00000308478 Transcript ENSG00000173114 HGNC:17200 LOW NM_001099658.2 synonymous_variant Unknown Q9H3W5.156 LRRN3 HGNC 1 A4D0T1.121 1.0 UPI0000037517 SNV LRRN3,synonymous_variant,p.L286=,ENST00000451085,NM_001099660.1,c.858A>G,LOW,YES,,,1;LRRN3,synonymous_variant,p.L286=,ENST00000422987,NM_018334.5,c.858A>G,LOW,,,,1;LRRN3,synonymous_variant,p.L286=,ENST00000308478,NM_001099658.2,c.858A>G,LOW,,,,1;IMMP2L,intron_variant,,ENST00000331762,NM_001350963.2&NM_001244606.2&NM_001350961.2&NM_001350959.2,c.240-160065T>C,MODIFIER,,,,-1;IMMP2L,intron_variant,,ENST00000405709,NM_001350960.2&NM_032549.4,c.240-160065T>C,MODIFIER,YES,,,-1;IMMP2L,intron_variant,,ENST00000447215,NM_001350962.2,c.240-160065T>C,MODIFIER,,,,-1;IMMP2L,intron_variant,,ENST00000450877,,c.186-160065T>C,MODIFIER,,,,-1;IMMP2L,intron_variant,,ENST00000452895,,c.240-160065T>C,MODIFIER,,,,-1;LRRN3,downstream_gene_variant,,ENST00000421101,,,MODIFIER,,,,1;IMMP2L,intron_variant,,ENST00000489381,,n.181-160065T>C,MODIFIER,,,,-1 1676/3500 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 61 57acb1a3-70b7-4ccb-b233-7ae363b0020a 53 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS LRRN3,synonymous_variant,p.L286=,ENST00000308478.10,c.858A>G,LOW,YES;LRRN3,synonymous_variant,p.L286=,ENST00000422987.3,c.858A>G,LOW,;LRRN3,synonymous_variant,p.L286=,ENST00000451085.5,c.858A>G,LOW,;IMMP2L,intron_variant,,ENST00000447215.5,c.240-160065T>C,MODIFIER,;IMMP2L,intron_variant,,ENST00000450877.5,c.186-160065T>C,MODIFIER,;IMMP2L,intron_variant,,ENST00000452895.5,c.240-160065T>C,MODIFIER,;IMMP2L,intron_variant,,ENST00000489381.1,n.181-160065T>C,MODIFIER,;IMMP2L,intron_variant,,ENST00000331762.7,c.240-160065T>C,MODIFIER,;IMMP2L,intron_variant,,ENST00000405709.7,c.240-160065T>C,MODIFIER,YES +FUT10 84750 BI GRCh38 8 33372576 33372589 + stop_lost,3_prime_UTR_variant Nonstop_Mutation DEL ATCAGTCCTTGAAT ATCAGTCCTTGAAT - novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 25 17 c.1428_*1del ENST00000327671.10 NM_032664.3 476 5/5 P2 - protein_coding YES CCDS6088.1 1428-?/1440 TTTGAAATCAGTCCTTGAATACTAG ENSP00000332757 5/5 ENST00000327671 Transcript ENSG00000172728 HGNC:19234 HIGH NM_032664.3 stop_lost 1.0 Unknown Q6P4F1.128 FUT10 HGNC -1 1.0 UPI00001C0364 Q6P4F1-1 deletion FUT10,stop_lost,,ENST00000327671,NM_032664.3,c.1428_*1del,HIGH,YES,,,-1;FUT10,stop_lost,,ENST00000518672,,c.1344_*1del,HIGH,,,,-1;FUT10,stop_lost,,ENST00000524021,,c.1344_*1del,HIGH,,,,-1;FUT10,non_coding_transcript_exon_variant,,ENST00000517891,,n.279_292del,MODIFIER,,,,-1;FUT10,intron_variant,,ENST00000517942,,n.449+55_449+68del,MODIFIER,,,,-1;FUT10,intron_variant,,ENST00000519440,,n.200+55_200+68del,MODIFIER,,,,-1 1784-1797/3549 mutect2;pindel;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 64 57acb1a3-70b7-4ccb-b233-7ae363b0020a 42 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS FUT10,non_coding_transcript_exon_variant,,ENST00000517891.1,n.279_292del,MODIFIER,;FUT10,stop_lost,3_prime_UTR_variant,,ENST00000524021.1,c.1344_*1del,HIGH,;FUT10,intron_variant,,ENST00000517942.1,n.449+55_449+68del,MODIFIER,;FUT10,intron_variant,,ENST00000519440.5,n.200+55_200+68del,MODIFIER,;FUT10,stop_lost,3_prime_UTR_variant,,ENST00000518672.5,c.1344_*1del,HIGH,;FUT10,stop_lost,3_prime_UTR_variant,,ENST00000327671.10,c.1428_*1del,HIGH,YES +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T G rs121913492 TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 46 35 c.626A>C p.Gln209Pro p.Q209P ENST00000286548.9 NM_002072.5 209 cAa/cCa 5/7 P1 G Q/P protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28758 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.998) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209P,ENST00000286548,NM_002072.5,c.626A>C,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 85 57acb1a3-70b7-4ccb-b233-7ae363b0020a 81 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS GNAQ,missense_variant,p.Q209P,ENST00000286548.9,c.626A>C,MODERATE,YES +PPP2R1B 5519 BI GRCh38 11 111765340 111765340 + synonymous_variant Silent SNP T T C novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 59 58 c.159A>G p.Ala53= p.A53= ENST00000527614.6 NM_002716.5 53 gcA/gcG 2/15 P2 C A protein_coding CCDS8349.1 159/1806 CCAAGTGCTAG PROSITE_profiles:PS50077;PANTHER:PTHR10648:SF9;PANTHER:PTHR10648;Gene3D:1.25.10.10;Superfamily:SSF48371 ENSP00000437193 2/15 ENST00000527614 Transcript 1.0 ENSG00000137713 HGNC:9303 LOW NM_002716.5 synonymous_variant Unknown P30154.190 PPP2R1B HGNC -1 1.0 UPI0000169868 P30154-1 SNV PPP2R1B,synonymous_variant,p.A53=,ENST00000527614,NM_002716.5,c.159A>G,LOW,,,,-1;PPP2R1B,synonymous_variant,p.A53=,ENST00000311129,NM_181699.3,c.159A>G,LOW,YES,,,-1;PPP2R1B,synonymous_variant,p.A53=,ENST00000341980,NM_001177562.2,c.159A>G,LOW,,,,-1;PPP2R1B,synonymous_variant,p.A53=,ENST00000393055,NM_001177563.2,c.159A>G,LOW,,,,-1;PPP2R1B,synonymous_variant,p.A38=,ENST00000531373,,c.114A>G,LOW,,,,-1;PPP2R1B,intron_variant,,ENST00000426998,NM_181700.2,c.114+908A>G,MODIFIER,,,,-1;PPP2R1B,synonymous_variant,p.A53=,ENST00000534521,,c.159A>G,LOW,,,,-1;PPP2R1B,synonymous_variant,p.A53=,ENST00000534500,,c.159A>G,LOW,,,,-1;AP001781.1,downstream_gene_variant,,ENST00000529841,,,MODIFIER,YES,,,-1;AP001781.1,downstream_gene_variant,,ENST00000534218,,,MODIFIER,,,,-1 187/5553 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 147 57acb1a3-70b7-4ccb-b233-7ae363b0020a 117 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS PPP2R1B,synonymous_variant,p.A38=,ENST00000531373.1,c.114A>G,LOW,;PPP2R1B,synonymous_variant,NMD_transcript_variant,p.A53=,ENST00000534500.5,c.159A>G,LOW,;PPP2R1B,synonymous_variant,p.A53=,ENST00000393055.6,c.159A>G,LOW,;PPP2R1B,synonymous_variant,p.A53=,ENST00000341980.10,c.159A>G,LOW,;PPP2R1B,synonymous_variant,NMD_transcript_variant,p.A53=,ENST00000534521.5,c.159A>G,LOW,;PPP2R1B,synonymous_variant,p.A53=,ENST00000527614.6,c.159A>G,LOW,YES;PPP2R1B,intron_variant,,ENST00000426998.6,c.114+908A>G,MODIFIER,;PPP2R1B,synonymous_variant,p.A53=,ENST00000311129.9,c.159A>G,LOW, +CYP1A1 1543 BI GRCh38 15 74722854 74722854 + missense_variant Missense_Mutation SNP G G T TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 14 17 c.244C>A p.Pro82Thr p.P82T ENST00000379727.8 NM_000499.5 82 Ccc/Acc 2/7 P1 T P/T protein_coding CCDS10268.1 244/1539 CACGGGTGTGG COSM4776912 Gene3D:1.10.630.10;PDB-ENSP_mappings:4i8v.A;PDB-ENSP_mappings:4i8v.B;PDB-ENSP_mappings:4i8v.C;PDB-ENSP_mappings:4i8v.D;PDB-ENSP_mappings:6dwm.A;PDB-ENSP_mappings:6dwm.B;PDB-ENSP_mappings:6dwm.C;PDB-ENSP_mappings:6dwm.D;PDB-ENSP_mappings:6dwn.A;PDB-ENSP_mappings:6dwn.B;PDB-ENSP_mappings:6dwn.C;PDB-ENSP_mappings:6dwn.D;PDB-ENSP_mappings:6o5y.A;PDB-ENSP_mappings:6o5y.B;PDB-ENSP_mappings:6o5y.C;PDB-ENSP_mappings:6o5y.D;Pfam:PF00067;Prints:PR00463;PANTHER:PTHR24299;PANTHER:PTHR24299:SF8;Superfamily:SSF48264 ENSP00000369050 2/7 COSV65697158 ENST00000379727 Transcript ENSG00000140465 HGNC:2595 MODERATE NM_001319217.2 missense_variant 1 probably_damaging(1) Unknown tolerated(0.05) 1 P04798.219 CYP1A1 HGNC -1 A0N0X8.130 1.0 UPI0000128195 P04798-1 SNV CYP1A1,missense_variant,p.P82T,ENST00000395048,,c.244C>A,MODERATE,YES,tolerated(0.05),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000379727,NM_000499.5&NM_001319217.2,c.244C>A,MODERATE,,tolerated(0.05),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000617691,NM_001319216.2,c.244C>A,MODERATE,,deleterious(0.05),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000612821,,c.244C>A,MODERATE,,tolerated(0.06),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000567032,,c.244C>A,MODERATE,,tolerated(0.05),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000395049,,c.244C>A,MODERATE,,deleterious(0.05),probably_damaging(1),-1;CYP1A1,intron_variant,,ENST00000564596,,c.-220-320C>A,MODIFIER,,,,-1;CYP1A1,intron_variant,,ENST00000566503,,c.-220-320C>A,MODIFIER,,,,-1;CYP1A1,missense_variant,p.P82T,ENST00000569630,,c.244C>A,MODERATE,,deleterious(0.03),probably_damaging(1),-1;CYP1A1,missense_variant,p.P82T,ENST00000562201,,c.244C>A,MODERATE,,deleterious(0.03),probably_damaging(1),-1 361/2603 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 49 57acb1a3-70b7-4ccb-b233-7ae363b0020a 31 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS CYP1A1,intron_variant,,ENST00000566503.1,c.-220-320C>A,MODIFIER,;CYP1A1,missense_variant,NMD_transcript_variant,p.P82T,ENST00000562201.5,c.244C>A,MODERATE,;CYP1A1,missense_variant,NMD_transcript_variant,p.P82T,ENST00000569630.5,c.244C>A,MODERATE,;CYP1A1,intron_variant,,ENST00000564596.5,c.-220-320C>A,MODIFIER,;CYP1A1,missense_variant,p.P82T,ENST00000395049.8,c.244C>A,MODERATE,;CYP1A1,missense_variant,p.P82T,ENST00000567032.5,c.244C>A,MODERATE,;CYP1A1,missense_variant,p.P82T,ENST00000379727.8,c.244C>A,MODERATE,YES;CYP1A1,missense_variant,p.P82T,ENST00000617691.4,c.244C>A,MODERATE,;CYP1A1,missense_variant,p.P82T,ENST00000395048.6,c.244C>A,MODERATE, +WDR90 197335 BI GRCh38 16 658649 658649 + missense_variant Missense_Mutation SNP C C G novel TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 15 10 c.2891C>G p.Pro964Arg p.P964R ENST00000293879.9 NM_145294.5 964 cCc/cGc 23/41 P4 G P/R protein_coding CCDS42092.1 2891/5247 AGGCCCCCAGG Gene3D:2.130.10.10;PANTHER:PTHR13720;PANTHER:PTHR13720:SF24;SMART:SM00320;Superfamily:SSF50998 ENSP00000293879 23/41 ENST00000293879 Transcript ENSG00000161996 HGNC:26960 MODERATE NM_145294.5 missense_variant possibly_damaging(0.463) Unknown tolerated(0.35) Q96KV7.151 WDR90 HGNC 1 5.0 UPI0000D67C48 Q96KV7-1 SNV WDR90,missense_variant,p.P964R,ENST00000549091,,c.2891C>G,MODERATE,YES,tolerated(0.34),possibly_damaging(0.461),1;WDR90,missense_variant,p.P964R,ENST00000293879,NM_145294.5,c.2891C>G,MODERATE,,tolerated(0.35),possibly_damaging(0.463),1;WDR90,upstream_gene_variant,,ENST00000550739,,,MODIFIER,,,,1;WDR90,intron_variant,,ENST00000548844,,n.55+35C>G,MODIFIER,,,,1;WDR90,upstream_gene_variant,,ENST00000547543,,,MODIFIER,,,,1;WDR90,upstream_gene_variant,,ENST00000548603,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000552648,,,MODIFIER,,,,1;WDR90,missense_variant,p.P269R,ENST00000552728,,c.806C>G,MODERATE,,tolerated(0.35),probably_damaging(0.997),1;WDR90,non_coding_transcript_exon_variant,,ENST00000552943,,n.4973C>G,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,,n.869C>G,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000546516,,n.1584C>G,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000552683,,n.322C>G,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000420061,,,MODIFIER,,,,1;WDR90,upstream_gene_variant,,ENST00000546923,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000548859,,,MODIFIER,,,,1;WDR90,upstream_gene_variant,,ENST00000549024,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000549648,,,MODIFIER,,,,1;WDR90,upstream_gene_variant,,ENST00000550902,,,MODIFIER,,,,1;AL022341.2,upstream_gene_variant,,ENST00000573609,,,MODIFIER,YES,,,-1 2943/5540 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 0 32 57acb1a3-70b7-4ccb-b233-7ae363b0020a 25 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS WDR90,intron_variant,,ENST00000548844.1,n.55+35C>G,MODIFIER,;WDR90,non_coding_transcript_exon_variant,,ENST00000552683.5,n.322C>G,MODIFIER,;WDR90,missense_variant,NMD_transcript_variant,p.P269R,ENST00000552728.5,c.806C>G,MODERATE,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407.5,n.869C>G,MODIFIER,;WDR90,non_coding_transcript_exon_variant,,ENST00000546516.5,n.1584C>G,MODIFIER,;WDR90,missense_variant,p.P964R,ENST00000293879.9,c.2891C>G,MODERATE,YES;WDR90,missense_variant,p.P964R,ENST00000549091.5,c.2891C>G,MODERATE,;WDR90,non_coding_transcript_exon_variant,,ENST00000552943.5,n.4973C>G,MODIFIER, +WTIP 126374 BI GRCh38 19 34500144 34500144 + synonymous_variant Silent SNP C C T rs370782319 TCGA-VD-A8K9-01A TCGA-VD-A8K9-10A Somatic 16 5 c.1168C>T p.Leu390= p.L390= ENST00000590071.7 NM_001080436.2 390 Ctg/Ttg 8/8 P1 T L protein_coding YES CCDS59375.1 1168/1293 TGCAGCTGAGC COSM4076862;COSM4076863 PROSITE_profiles:PS50023;CDD:cd09438;PANTHER:PTHR24219;PANTHER:PTHR24219:SF6;Gene3D:2.10.110.10;Pfam:PF00412;SMART:SM00132 ENSP00000466953 0.0 0.0001178 8/8 rs370782319 ENST00000590071 Transcript ENSG00000142279 HGNC:20964 LOW NM_001080436.2 0.0001178 EA synonymous_variant 1.0 Unknown A6NIX2.103 WTIP HGNC 1 1.0 UPI00006C19C5 SNV WTIP,synonymous_variant,p.L390=,ENST00000590071,NM_001080436.2,c.1168C>T,LOW,YES,,,1;WTIP,downstream_gene_variant,,ENST00000585928,,,MODIFIER,,,,1 1385/13545 muse;mutect2;varscan2 fa9089fa-9af9-4932-8ab7-0e7f2fd6b121 8.424e-06 0.0 0.0 0.0 5.598e-05 0.0 8.989e-06 0.0 0.0 1.352320032310672e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086130163865164e-05 0.0 3.086130163865164e-05 0.0 0.0 0 33 57acb1a3-70b7-4ccb-b233-7ae363b0020a 21 86015b99-6311-4a91-8fd4-c4f61ee183af SUCCESS WTIP,synonymous_variant,p.L390=,ENST00000590071.7,c.1168C>T,LOW,YES +KIAA2013 90231 BI GRCh38 1 11923314 11923314 + synonymous_variant Silent SNP C C A novel TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 26 4 c.1209G>T p.Gly403= p.G403= ENST00000376572.8 NM_138346.3 403 ggG/ggT 2/3 P1 A G protein_coding CCDS141.1 1209/1905 GCGTGCCCGCT Pfam:PF10222;PANTHER:PTHR31386 ENSP00000365756 2/3 ENST00000376572 Transcript ENSG00000116685 HGNC:28513 LOW NM_138346.3 synonymous_variant Unknown Q8IYS2.121 KIAA2013 HGNC -1 1.0 UPI00000741FB Q8IYS2-1 SNV KIAA2013,synonymous_variant,p.G403=,ENST00000376572,NM_138346.3,c.1209G>T,LOW,,,,-1;KIAA2013,synonymous_variant,p.G403=,ENST00000376576,,c.1209G>T,LOW,YES,,,-1;KIAA2013,synonymous_variant,p.G403=,ENST00000616327,,c.1209G>T,LOW,,,,-1 1399/2819 muse;mutect2 78039723-94a9-4903-8bb4-c00852e8e889 0 34 34bf81ce-1186-4987-9efc-620b8f6937bd 30 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS KIAA2013,synonymous_variant,p.G403=,ENST00000376576.3,c.1209G>T,LOW,;KIAA2013,synonymous_variant,p.G403=,ENST00000376572.8,c.1209G>T,LOW,YES +SPRR2A 6700 BI GRCh38 1 153056521 153056525 + frameshift_variant,stop_lost Frame_Shift_Del DEL TTGCT TTGCT - novel TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 46 33 c.211_215del p.Lys72ThrfsTer12 p.K72Tfs*12 ENST00000392653.3 NM_005988.3 71 AGCAAg/g 2/2 P1 - SK/X protein_coding YES CCDS1034.1 211-215/219 TGTTACTTGCTCTTCG Prints:PR01217;PANTHER:PTHR23263;PANTHER:PTHR23263:SF120 ENSP00000376423 2/2 ENST00000392653 Transcript ENSG00000241794 HGNC:11261 HIGH NM_005988.3 frameshift_variant 1.0 Unknown P35326.144 SPRR2A HGNC -1 1.0 UPI0000135D6D deletion SPRR2A,frameshift_variant,p.S71Vfs*13,ENST00000392653,NM_005988.3,c.211_215del,HIGH,YES,,,-1 272-276/677 mutect2;pindel;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 106 34bf81ce-1186-4987-9efc-620b8f6937bd 80 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS SPRR2A,frameshift_variant,stop_lost,p.K72Tfs*12,ENST00000392653.3,c.211_215del,HIGH,YES +LRRC15 131578 BI GRCh38 3 194360695 194360695 + missense_variant Missense_Mutation SNP G G T novel TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 1 18 c.349C>A p.Pro117Thr p.P117T ENST00000347624.4 NM_130830.5 117 Ccc/Acc 2/2 P2 T P/T protein_coding CCDS3306.1 349/1746 GATGGGCAGAA Gene3D:3.80.10.10;PROSITE_profiles:PS51450;PANTHER:PTHR24373;PANTHER:PTHR24373:SF262;SMART:SM00364;SMART:SM00369;Superfamily:SSF52058 ENSP00000306276 2/2 ENST00000347624 Transcript ENSG00000172061 HGNC:20818 MODERATE NM_130830.5 missense_variant probably_damaging(0.996) Unknown deleterious(0.01) Q8TF66.158 LRRC15 HGNC -1 1.0 UPI00005764CF Q8TF66-1 SNV LRRC15,missense_variant,p.P117T,ENST00000347624,NM_130830.5,c.349C>A,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;LRRC15,missense_variant,p.P123T,ENST00000428839,NM_001135057.3,c.367C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.984),-1 435/5881 muse;mutect2;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 47 34bf81ce-1186-4987-9efc-620b8f6937bd 20 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS LRRC15,missense_variant,p.P123T,ENST00000428839.1,c.367C>A,MODERATE,;LRRC15,missense_variant,p.P117T,ENST00000347624.4,c.349C>A,MODERATE,YES +ZFC3H1 196441 BI GRCh38 12 71663351 71663351 + stop_gained Nonsense_Mutation SNP G G T novel TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 60 45 c.260C>A p.Ser87Ter p.S87* ENST00000378743.9 NM_144982.5 87 tCa/tAa 1/35 P1 T S/* protein_coding YES CCDS41813.1 260/5970 AGCGTGAGAAA MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000368017 1/35 ENST00000378743 Transcript ENSG00000133858 HGNC:28328 HIGH NM_144982.5 stop_gained 1.0 Unknown O60293.160 ZFC3H1 HGNC -1 1.0 UPI00003668E9 O60293-1 SNV ZFC3H1,stop_gained,p.S87*,ENST00000378743,NM_144982.5,c.260C>A,HIGH,YES,,,-1;ZFC3H1,stop_gained,p.S87*,ENST00000548100,,c.260C>A,HIGH,,,,-1;ZFC3H1,stop_gained,p.S87*,ENST00000552037,,c.260C>A,HIGH,,,,-1;THAP2,upstream_gene_variant,,ENST00000308086,NM_031435.4,,MODIFIER,YES,,,1;THAP2,upstream_gene_variant,,ENST00000547843,,,MODIFIER,,,,1;THAP2,upstream_gene_variant,,ENST00000551238,,,MODIFIER,,,,1;THAP2,upstream_gene_variant,,ENST00000551488,,,MODIFIER,,,,1;ZFC3H1,non_coding_transcript_exon_variant,,ENST00000549407,,n.10C>A,MODIFIER,,,,-1;ZFC3H1,intron_variant,,ENST00000550712,,n.206-2924C>A,MODIFIER,,,,-1;ZFC3H1,stop_gained,p.S87*,ENST00000552994,,c.260C>A,HIGH,,,,-1 498/7037 muse;mutect2;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 99 34bf81ce-1186-4987-9efc-620b8f6937bd 105 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS ZFC3H1,non_coding_transcript_exon_variant,,ENST00000549407.1,n.10C>A,MODIFIER,;ZFC3H1,stop_gained,p.S87*,ENST00000548100.1,c.260C>A,HIGH,;ZFC3H1,stop_gained,p.S87*,ENST00000552037.1,c.260C>A,HIGH,;ZFC3H1,intron_variant,,ENST00000550712.1,n.206-2924C>A,MODIFIER,;ZFC3H1,stop_gained,NMD_transcript_variant,p.S87*,ENST00000552994.5,c.260C>A,HIGH,;ZFC3H1,stop_gained,p.S87*,ENST00000378743.9,c.260C>A,HIGH,YES +PCDH9 5101 BI GRCh38 13 67225951 67225951 + synonymous_variant Silent SNP G G A TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 53 52 c.2490C>T p.Ile830= p.I830= ENST00000377865.7 NM_203487.3 830 atC/atT 2/5 A1 A I protein_coding YES CCDS9444.1 2490/3714 ACGAAGATCAC Pfam:PF08374;PANTHER:PTHR24028;PANTHER:PTHR24028:SF248;Transmembrane_helices:TMhelix;Low_complexity_(Seg):seg ENSP00000367096 2/5 COSV60530621 ENST00000377865 Transcript ENSG00000184226 HGNC:8661 LOW NM_203487.3 synonymous_variant 1 1.0 Unknown 1 Q9HC56.155 PCDH9 HGNC -1 X5D7N0.40 1.0 UPI00001FCE90 Q9HC56-1 SNV PCDH9,synonymous_variant,p.I830=,ENST00000377861,NM_001318374.2,c.2490C>T,LOW,,,,-1;PCDH9,synonymous_variant,p.I830=,ENST00000544246,NM_001318373.2&NM_020403.5,c.2490C>T,LOW,,,,-1;PCDH9,synonymous_variant,p.I830=,ENST00000377865,NM_203487.3,c.2490C>T,LOW,YES,,,-1;PCDH9,synonymous_variant,p.I830=,ENST00000456367,NM_001318372.2,c.2490C>T,LOW,,,,-1 3182/6227 muse;mutect2;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 90 34bf81ce-1186-4987-9efc-620b8f6937bd 105 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS PCDH9,synonymous_variant,p.I830=,ENST00000377861.4,c.2490C>T,LOW,;PCDH9,synonymous_variant,p.I830=,ENST00000456367.5,c.2490C>T,LOW,;PCDH9,synonymous_variant,p.I830=,ENST00000544246.5,c.2490C>T,LOW,;PCDH9,synonymous_variant,p.I830=,ENST00000377865.7,c.2490C>T,LOW,YES +SAMD15 161394 BI GRCh38 14 77391179 77391179 + missense_variant Missense_Mutation SNP C C A novel TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 23 25 c.1960C>A p.Gln654Lys p.Q654K ENST00000216471.5 NM_001010860.2 654 Cag/Aag 3/3 P1 A Q/K protein_coding YES CCDS32126.1 1960/2025 GATTACAGGAT PANTHER:PTHR46829 ENSP00000216471 3/3 ENST00000216471 Transcript ENSG00000100583 HGNC:18631 MODERATE missense_variant benign(0.196) Unknown deleterious(0.01) Q9P1V8.117 SAMD15 HGNC 1 2.0 UPI0000072F0E Q9P1V8-1 SNV SAMD15,missense_variant,p.Q654K,ENST00000216471,NM_001010860.2,c.1960C>A,MODERATE,YES,deleterious(0.01),benign(0.196),1;SAMD15,missense_variant,p.Q68K,ENST00000533095,,c.202C>A,MODERATE,,tolerated(0.1),benign(0.196),1;NOXRED1,downstream_gene_variant,,ENST00000380835,NM_001113475.2,,MODIFIER,YES,,,-1;NOXRED1,downstream_gene_variant,,ENST00000555901,,,MODIFIER,,,,-1 2246/2564 muse;mutect2;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 46 34bf81ce-1186-4987-9efc-620b8f6937bd 49 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS SAMD15,missense_variant,p.Q654K,ENST00000216471.5,c.1960C>A,MODERATE,YES;SAMD15,missense_variant,p.Q68K,ENST00000533095.2,c.202C>A,MODERATE, +GNA11 2767 BI GRCh38 19 3118944 3118944 + missense_variant Missense_Mutation SNP A A T rs1057519742 TCGA-VD-A8KF-01A TCGA-VD-A8KF-10A Somatic 22 18 c.626A>T p.Gln209Leu p.Q209L ENST00000078429.9 NM_002067.5 209 cAg/cTg 5/7 P1 T Q/L protein_coding YES CCDS12103.1 626/1080 likely_pathogenic;pathogenic GGGCCAGCGGT COSM52969 PDB-ENSP_mappings:6oij.A;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF325;Gene3D:3.40.50.300;Pfam:PF00503;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000078429 5/7 rs1057519742;COSV50017277;COSV50017623;COSV50017882 ENST00000078429 Transcript 1.0 ENSG00000088256 HGNC:4379 MODERATE NM_002067.5 missense_variant 1;1;1;1 1.0 25157968;26619011;2549426;1328859;21083380;22733540;22808163;21444680;24141786 probably_damaging(0.973) Unknown deleterious(0) 0;1;1;1 P29992.194 GNA11 HGNC 1 1.0 UPI000004D209 SNV GNA11,missense_variant,p.Q209L,ENST00000078429,NM_002067.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.973),1;GNA11,missense_variant,p.Q58L,ENST00000587636,,c.173A>T,MODERATE,,deleterious(0),possibly_damaging(0.514),1;GNA11,downstream_gene_variant,,ENST00000588401,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000586180,,n.145A>T,MODIFIER,,,,1;GNA11,downstream_gene_variant,,ENST00000586763,,,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000590534,,n.1795A>T,MODIFIER,,,,1;GNA11,non_coding_transcript_exon_variant,,ENST00000591301,,n.132A>T,MODIFIER,,,,1;AC005262.2,non_coding_transcript_exon_variant,,ENST00000587701,,n.173T>A,MODIFIER,YES,,,-1;KF456478.1,downstream_gene_variant,,ENST00000585980,,,MODIFIER,YES,,,-1 916/4190 muse;mutect2;varscan2 78039723-94a9-4903-8bb4-c00852e8e889 0 65 34bf81ce-1186-4987-9efc-620b8f6937bd 40 96df73cb-a7a9-41dc-b100-8baee9634a08 SUCCESS GNA11,non_coding_transcript_exon_variant,,ENST00000591301.1,n.132A>T,MODIFIER,;GNA11,non_coding_transcript_exon_variant,,ENST00000586180.1,n.145A>T,MODIFIER,;ENSG00000267139,non_coding_transcript_exon_variant,,ENST00000587701.1,n.173T>A,MODIFIER,YES;GNA11,non_coding_transcript_exon_variant,,ENST00000590534.1,n.1795A>T,MODIFIER,;GNA11,missense_variant,p.S58C,ENST00000587636.1,c.172A>T,MODERATE,;GNA11,missense_variant,p.Q209L,ENST00000078429.9,c.626A>T,MODERATE,YES +E2F2 1870 BI GRCh38 1 23530644 23530644 + synonymous_variant Silent SNP C C T novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 26 3 c.150G>A p.Pro50= p.P50= ENST00000361729.3 NM_004091.4 50 ccG/ccA 1/7 P1 T P protein_coding YES CCDS236.1 150/1314 GTCTGCGGGTA Low_complexity_(Seg):seg;PANTHER:PTHR12081;PANTHER:PTHR12081:SF50 ENSP00000355249 1/7 ENST00000361729 Transcript ENSG00000007968 HGNC:3114 LOW NM_004091.4 synonymous_variant 1.0 Unknown Q14209.185 E2F2 HGNC -1 1.0 UPI0000129AC1 SNV E2F2,synonymous_variant,p.P50=,ENST00000361729,NM_004091.4,c.150G>A,LOW,YES,,,-1 590/5196 muse;mutect2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 14 5faf2c57-9042-4056-a8cc-37d37bf528b4 30 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS E2F2,synonymous_variant,p.P50=,ENST00000361729.3,c.150G>A,LOW,YES +MAPKAPK2 9261 BI GRCh38 1 206730727 206730727 + missense_variant Missense_Mutation SNP G G A novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 51 76 c.731G>A p.Cys244Tyr p.C244Y ENST00000367103.4 NM_032960.4 244 tGt/tAt 6/10 P1 A C/Y protein_coding YES CCDS31001.1 731/1203 GTCCTGTGACA Gene3D:1.10.510.10;PDB-ENSP_mappings:1kwp.A;PDB-ENSP_mappings:1kwp.B;PDB-ENSP_mappings:1nxk.A;PDB-ENSP_mappings:1nxk.B;PDB-ENSP_mappings:1nxk.C;PDB-ENSP_mappings:1nxk.D;PDB-ENSP_mappings:1ny3.A;PDB-ENSP_mappings:2jbo.A;PDB-ENSP_mappings:2jbp.A;PDB-ENSP_mappings:2jbp.B;PDB-ENSP_mappings:2jbp.C;PDB-ENSP_mappings:2jbp.D;PDB-ENSP_mappings:2jbp.E;PDB-ENSP_mappings:2jbp.F;PDB-ENSP_mappings:2jbp.G;PDB-ENSP_mappings:2jbp.H;PDB-ENSP_mappings:2jbp.I;PDB-ENSP_mappings:2jbp.J;PDB-ENSP_mappings:2jbp.K;PDB-ENSP_mappings:2jbp.L;PDB-ENSP_mappings:2onl.C;PDB-ENSP_mappings:2onl.D;PDB-ENSP_mappings:2oza.A;PDB-ENSP_mappings:2p3g.X;PDB-ENSP_mappings:2pzy.A;PDB-ENSP_mappings:2pzy.B;PDB-ENSP_mappings:2pzy.C;PDB-ENSP_mappings:2pzy.D;PDB-ENSP_mappings:3a2c.A;PDB-ENSP_mappings:3a2c.B;PDB-ENSP_mappings:3a2c.C;PDB-ENSP_mappings:3a2c.D;PDB-ENSP_mappings:3a2c.E;PDB-ENSP_mappings:3a2c.F;PDB-ENSP_mappings:3a2c.G;PDB-ENSP_mappings:3a2c.H;PDB-ENSP_mappings:3a2c.I;PDB-ENSP_mappings:3a2c.J;PDB-ENSP_mappings:3a2c.K;PDB-ENSP_mappings:3a2c.L;PDB-ENSP_mappings:3fpm.A;PDB-ENSP_mappings:3fyj.X;PDB-ENSP_mappings:3fyk.X;PDB-ENSP_mappings:3gok.A;PDB-ENSP_mappings:3gok.B;PDB-ENSP_mappings:3gok.C;PDB-ENSP_mappings:3gok.D;PDB-ENSP_mappings:3gok.E;PDB-ENSP_mappings:3gok.F;PDB-ENSP_mappings:3gok.G;PDB-ENSP_mappings:3gok.H;PDB-ENSP_mappings:3gok.I;PDB-ENSP_mappings:3gok.J;PDB-ENSP_mappings:3gok.K;PDB-ENSP_mappings:3gok.L;PDB-ENSP_mappings:3ka0.A;PDB-ENSP_mappings:3kc3.A;PDB-ENSP_mappings:3kc3.B;PDB-ENSP_mappings:3kc3.C;PDB-ENSP_mappings:3kc3.D;PDB-ENSP_mappings:3kc3.E;PDB-ENSP_mappings:3kc3.F;PDB-ENSP_mappings:3kc3.G;PDB-ENSP_mappings:3kc3.H;PDB-ENSP_mappings:3kc3.I;PDB-ENSP_mappings:3kc3.J;PDB-ENSP_mappings:3kc3.K;PDB-ENSP_mappings:3kc3.L;PDB-ENSP_mappings:3kga.A;PDB-ENSP_mappings:3m2w.A;PDB-ENSP_mappings:3m42.A;PDB-ENSP_mappings:3r2b.A;PDB-ENSP_mappings:3r2b.B;PDB-ENSP_mappings:3r2b.C;PDB-ENSP_mappings:3r2b.D;PDB-ENSP_mappings:3r2b.E;PDB-ENSP_mappings:3r2b.F;PDB-ENSP_mappings:3r2b.G;PDB-ENSP_mappings:3r2b.H;PDB-ENSP_mappings:3r2b.I;PDB-ENSP_mappings:3r2b.J;PDB-ENSP_mappings:3r2b.K;PDB-ENSP_mappings:3r2b.L;PDB-ENSP_mappings:3r2y.A;PDB-ENSP_mappings:3r30.A;PDB-ENSP_mappings:3wi6.A;PDB-ENSP_mappings:3wi6.B;PDB-ENSP_mappings:3wi6.C;PDB-ENSP_mappings:3wi6.D;PDB-ENSP_mappings:3wi6.E;PDB-ENSP_mappings:3wi6.F;PDB-ENSP_mappings:4tyh.A;Pfam:PF00069;PROSITE_profiles:PS50011;PANTHER:PTHR24349;PANTHER:PTHR24349:SF63;SMART:SM00220;Superfamily:SSF56112;CDD:cd14170 ENSP00000356070 6/10 ENST00000367103 Transcript ENSG00000162889 HGNC:6887 MODERATE NM_032960.4 missense_variant 1.0 probably_damaging(1) Unknown deleterious(0) P49137.205 MAPKAPK2 HGNC 1 1.0 UPI0000112289 P49137-1 SNV MAPKAPK2,missense_variant,p.C244Y,ENST00000367103,NM_032960.4,c.731G>A,MODERATE,YES,deleterious(0),probably_damaging(1),1;MAPKAPK2,missense_variant,p.C244Y,ENST00000294981,NM_004759.5,c.731G>A,MODERATE,,deleterious(0),probably_damaging(1),1;MAPKAPK2,upstream_gene_variant,,ENST00000479009,,,MODIFIER,,,,1;MAPKAPK2,downstream_gene_variant,,ENST00000493447,,,MODIFIER,,,,1 1056/3091 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 77 5faf2c57-9042-4056-a8cc-37d37bf528b4 127 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS MAPKAPK2,missense_variant,p.C244Y,ENST00000294981.8,c.731G>A,MODERATE,;MAPKAPK2,missense_variant,p.C244Y,ENST00000367103.4,c.731G>A,MODERATE,YES +HHAT 55733 BI GRCh38 1 210362859 210362859 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 68 26 c.99A>T p.Glu33Asp p.E33D ENST00000261458.8 NM_018194.6 33 gaA/gaT 3/12 P2 T E/D protein_coding CCDS1495.1 99/1482 CACGAAGAGGA PANTHER:PTHR13285;PANTHER:PTHR13285:SF20;Low_complexity_(Seg):seg ENSP00000261458 3/12 ENST00000261458 Transcript 1.0 ENSG00000054392 HGNC:18270 MODERATE NM_018194.6 missense_variant possibly_damaging(0.683) Unknown deleterious(0.01) Q5VTY9.143 HHAT HGNC 1 2.0 UPI000004A086 Q5VTY9-1 SNV HHAT,missense_variant,p.E33D,ENST00000261458,NM_018194.6,c.99A>T,MODERATE,,deleterious(0.01),possibly_damaging(0.683),1;HHAT,missense_variant,p.E33D,ENST00000367010,NM_001170580.3,c.99A>T,MODERATE,,deleterious(0.01),possibly_damaging(0.683),1;HHAT,missense_variant,p.E33D,ENST00000413764,NM_001122834.3,c.99A>T,MODERATE,,deleterious(0.01),possibly_damaging(0.683),1;HHAT,missense_variant,p.E34D,ENST00000545154,NM_001170587.2,c.102A>T,MODERATE,YES,deleterious(0.01),probably_damaging(0.971),1;HHAT,missense_variant,p.E33D,ENST00000537898,NM_001170588.2,c.99A>T,MODERATE,,deleterious(0),probably_damaging(0.956),1;HHAT,missense_variant,p.E33D,ENST00000541565,NM_001170564.2,c.99A>T,MODERATE,,deleterious_low_confidence(0),probably_damaging(0.956),1;HHAT,5_prime_UTR_variant,,ENST00000426968,,c.-91A>T,MODIFIER,,,,1;AL034351.4,downstream_gene_variant,,ENST00000670026,,,MODIFIER,YES,,,-1 345/3639 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 51 5faf2c57-9042-4056-a8cc-37d37bf528b4 94 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS HHAT,5_prime_UTR_variant,,ENST00000426968.2,c.-91A>T,MODIFIER,;HHAT,missense_variant,p.E33D,ENST00000367010.5,c.99A>T,MODERATE,;HHAT,missense_variant,p.E33D,ENST00000537898.5,c.99A>T,MODERATE,;HHAT,missense_variant,p.E34D,ENST00000545154.5,c.102A>T,MODERATE,;HHAT,missense_variant,p.E33D,ENST00000261458.8,c.99A>T,MODERATE,YES;HHAT,missense_variant,p.E33D,ENST00000541565.5,c.99A>T,MODERATE,;HHAT,missense_variant,p.E33D,ENST00000413764.6,c.99A>T,MODERATE, +EIF1B 10289 BI GRCh38 3 40310921 40310921 + missense_variant Missense_Mutation SNP C C G TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 45 23 c.60C>G p.Asp20Glu p.D20E ENST00000232905.4 NM_005875.3 20 gaC/gaG 2/4 P1 G D/E protein_coding YES CCDS2690.1 60/342 GGTGACGACTT Gene3D:3.30.780.10;PIRSF:PIRSF004499;PANTHER:PTHR10388;PANTHER:PTHR10388:SF51;Superfamily:SSF55159;TIGRFAM:TIGR01160 ENSP00000232905 2/4 COSV51763150 ENST00000232905 Transcript ENSG00000114784 HGNC:30792 MODERATE NM_005875.3 missense_variant 1 1.0 benign(0.02) Unknown tolerated(0.11) 1 O60739.159 EIF1B HGNC 1 Q6FG85.121 1.0 UPI0000003EA1 SNV EIF1B,missense_variant,p.D20E,ENST00000232905,NM_005875.3,c.60C>G,MODERATE,YES,tolerated(0.11),benign(0.02),1;EIF1B,non_coding_transcript_exon_variant,,ENST00000462088,,n.280C>G,MODIFIER,,,,1;EIF1B,non_coding_transcript_exon_variant,,ENST00000488260,,n.176C>G,MODIFIER,,,,1;EIF1B,non_coding_transcript_exon_variant,,ENST00000487151,,n.294C>G,MODIFIER,,,,1;EIF1B-AS1,upstream_gene_variant,,ENST00000626073,,,MODIFIER,,,,-1;ENTPD3-AS1,downstream_gene_variant,,ENST00000439293,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000625390,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000628298,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000629217,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000629723,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000631175,,,MODIFIER,YES,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000655651,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000657144,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000661550,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000663881,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000663919,,,MODIFIER,,,,-1;EIF1B-AS1,upstream_gene_variant,,ENST00000668232,,,MODIFIER,,,,-1 295/987 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 73 5faf2c57-9042-4056-a8cc-37d37bf528b4 68 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS EIF1B,non_coding_transcript_exon_variant,,ENST00000487151.1,n.294C>G,MODIFIER,;EIF1B,non_coding_transcript_exon_variant,,ENST00000488260.1,n.176C>G,MODIFIER,;EIF1B,non_coding_transcript_exon_variant,,ENST00000462088.1,n.280C>G,MODIFIER,;EIF1B,missense_variant,p.D20E,ENST00000232905.4,c.60C>G,MODERATE,YES;EIF1B-AS1,intron_variant,,ENST00000715680.1,n.307-9525G>C,MODIFIER, +SETD2 29072 BI GRCh38 3 47062338 47062338 + stop_gained Nonsense_Mutation SNP G G A rs976581260 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 113 87 c.6118C>T p.Arg2040Ter p.R2040* ENST00000409792.4 NM_001349370.2 2040 Cga/Tga 14/21 P1 A R/* protein_coding YES CCDS2749.2 6118/7695 TCCTCGTTCAG COSM4135357;COSM4135358 PANTHER:PTHR46711;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite ENSP00000386759 14/21 rs976581260;COSV57434358 ENST00000409792 Transcript 1.0 ENSG00000181555 HGNC:18420 HIGH NM_014159.7 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS stop_gained 0;1 1.0 Unknown 0;1 Q9BYW2.172 SETD2 HGNC -1 5.0 UPI00017E10FB Q9BYW2-1 SNV SETD2,stop_gained,p.R2040*,ENST00000409792,NM_001349370.2&NM_014159.7,c.6118C>T,HIGH,YES,,,-1;SETD2,downstream_gene_variant,,ENST00000638947,,,MODIFIER,,,,-1;SETD2,non_coding_transcript_exon_variant,,ENST00000492397,,n.568C>T,MODIFIER,,,,-1;SETD2,3_prime_UTR_variant,,ENST00000330022,,c.*1841C>T,MODIFIER,,,,-1;SETD2,3_prime_UTR_variant,,ENST00000431180,,c.*1443C>T,MODIFIER,,,,-1;SETD2,3_prime_UTR_variant,,ENST00000445387,,c.*68C>T,MODIFIER,,,,-1 6307/8541 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 197 5faf2c57-9042-4056-a8cc-37d37bf528b4 201 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS SETD2,non_coding_transcript_exon_variant,,ENST00000492397.1,n.568C>T,MODIFIER,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000445387.5,c.*68C>T,MODIFIER,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000685505.1,c.*324C>T,MODIFIER,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000692883.1,c.*324C>T,MODIFIER,;SETD2,non_coding_transcript_exon_variant,,ENST00000686792.1,n.340C>T,MODIFIER,;SETD2,intron_variant,NMD_transcript_variant,,ENST00000688290.1,c.*69+4732C>T,MODIFIER,;SETD2,non_coding_transcript_exon_variant,,ENST00000685237.1,n.2927C>T,MODIFIER,;SETD2,non_coding_transcript_exon_variant,,ENST00000692362.1,n.1923C>T,MODIFIER,;SETD2,stop_gained,NMD_transcript_variant,p.R1428*,ENST00000690461.1,c.4282C>T,HIGH,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000693321.1,c.*226C>T,MODIFIER,;SETD2,missense_variant,p.T638M,ENST00000691902.1,c.1913C>T,MODERATE,;SETD2,missense_variant,p.T824M,ENST00000690157.1,c.2471C>T,MODERATE,;SETD2,stop_gained,p.R1962*,ENST00000685005.1,c.5884C>T,HIGH,;SETD2,non_coding_transcript_exon_variant,,ENST00000693738.1,n.1559C>T,MODIFIER,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000686773.1,c.*224C>T,MODIFIER,;SETD2,stop_gained,p.R2040*,ENST00000409792.4,c.6118C>T,HIGH,YES;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000330022.11,c.*1841C>T,MODIFIER,;SETD2,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000431180.5,c.*1443C>T,MODIFIER,;SETD2,non_coding_transcript_exon_variant,,ENST00000687657.1,n.337C>T,MODIFIER,;SETD2,stop_gained,p.R392*,ENST00000691544.1,c.1174C>T,HIGH,;SETD2,stop_gained,p.R1996*,ENST00000638947.2,c.5986C>T,HIGH,;SETD2,missense_variant,p.T945M,ENST00000686876.1,c.2834C>T,MODERATE, +COL25A1 84570 BI GRCh38 4 108901126 108901126 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 32 18 c.827G>C p.Gly276Ala p.G276A ENST00000399132.6 NM_198721.4 276 gGa/gCa 14/38 G G/A protein_coding CCDS43258.1 827/1965 TAGGTCCTGGT PANTHER:PTHR24020;PANTHER:PTHR24020;PANTHER:PTHR24020:SF4;PANTHER:PTHR24020:SF4;Low_complexity_(Seg):seg ENSP00000382083 14/38 ENST00000399132 Transcript 1.0 ENSG00000188517 HGNC:18603 MODERATE NM_198721.4 missense_variant probably_damaging(0.981) Unknown deleterious(0) Q9BXS0.144 COL25A1 HGNC -1 5.0 UPI0000225CD2 Q9BXS0-1 SNV COL25A1,missense_variant,p.G276A,ENST00000642955,,c.827G>C,MODERATE,YES,deleterious(0.03),probably_damaging(1),-1;COL25A1,missense_variant,p.G276A,ENST00000399132,NM_198721.4,c.827G>C,MODERATE,,deleterious(0),probably_damaging(0.981),-1;COL25A1,missense_variant,p.G114A,ENST00000622134,,c.341G>C,MODERATE,,deleterious(0.03),probably_damaging(0.995),-1;COL25A1,missense_variant,p.G41A,ENST00000610288,,c.122G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;COL25A1,missense_variant,p.G276A,ENST00000399126,NM_032518.3,c.827G>C,MODERATE,,deleterious(0.01),probably_damaging(0.996),-1;COL25A1,missense_variant,p.G272A,ENST00000399127,NM_001256074.2,c.815G>C,MODERATE,,deleterious(0.03),probably_damaging(0.999),-1;COL25A1,missense_variant,p.G204A,ENST00000494183,,c.611G>C,MODERATE,,deleterious(0),possibly_damaging(0.883),-1 1373/7713 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 75 5faf2c57-9042-4056-a8cc-37d37bf528b4 50 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS COL25A1,missense_variant,p.G272A,ENST00000399127.5,c.815G>C,MODERATE,;COL25A1,missense_variant,p.G276A,ENST00000399126.1,c.827G>C,MODERATE,;COL25A1,missense_variant,NMD_transcript_variant,p.G204A,ENST00000494183.5,c.611G>C,MODERATE,;COL25A1,missense_variant,p.G276A,ENST00000399132.6,c.827G>C,MODERATE,YES;COL25A1,missense_variant,p.G276A,ENST00000642955.1,c.827G>C,MODERATE, +MARCHF6 10299 BI GRCh38 5 10426409 10426409 + missense_variant Missense_Mutation SNP G G A rs1207274476 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 126 67 c.2393G>A p.Arg798Gln p.R798Q ENST00000274140.10 NM_005885.4 798 cGg/cAg 24/26 P1 A R/Q protein_coding YES CCDS34135.1 2393/2733 CATCCGGAACA PANTHER:PTHR13145;PANTHER:PTHR13145:SF0 ENSP00000274140 24/26 rs1207274476;COSV99929529 ENST00000274140 Transcript 1.0 ENSG00000145495 HGNC:30550 MODERATE NM_005885.4 missense_variant 0;1 1.0 benign(0.44) Unknown deleterious(0.04) 0;1 O60337.153 MARCHF6 HGNC 1 1.0 UPI00001B94D6 O60337-4 SNV MARCHF6,missense_variant,p.R798Q,ENST00000274140,NM_005885.4,c.2393G>A,MODERATE,YES,deleterious(0.04),benign(0.44),1;MARCHF6,missense_variant,p.R750Q,ENST00000449913,NM_001270660.2,c.2249G>A,MODERATE,,deleterious(0.04),benign(0.426),1;MARCHF6,missense_variant,p.R693Q,ENST00000503788,NM_001270661.2,c.2078G>A,MODERATE,,deleterious(0.05),possibly_damaging(0.803),1;MARCHF6,missense_variant,p.R496Q,ENST00000510792,,c.1487G>A,MODERATE,,deleterious(0.04),probably_damaging(0.981),1;MARCHF6,downstream_gene_variant,,ENST00000505253,,,MODIFIER,,,,1;MARCHF6,non_coding_transcript_exon_variant,,ENST00000511802,,n.3793G>A,MODIFIER,,,,1;MARCHF6,downstream_gene_variant,,ENST00000512449,,,MODIFIER,,,,1 2597/9641 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 183 5faf2c57-9042-4056-a8cc-37d37bf528b4 193 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS MARCHF6,missense_variant,p.R496Q,ENST00000510792.1,c.1487G>A,MODERATE,;MARCHF6,missense_variant,p.R693Q,ENST00000503788.5,c.2078G>A,MODERATE,;MARCHF6,non_coding_transcript_exon_variant,,ENST00000511802.5,n.3793G>A,MODIFIER,;MARCHF6,missense_variant,p.R750Q,ENST00000449913.6,c.2249G>A,MODERATE,;MARCHF6,missense_variant,p.R798Q,ENST00000274140.10,c.2393G>A,MODERATE,YES +RSPH4A 345895 BI GRCh38 6 116622852 116622852 + synonymous_variant Silent SNP A A G rs1562389892 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 176 66 c.771A>G p.Gln257= p.Q257= ENST00000229554.10 NM_001010892.3 257 caA/caG 2/6 P1 G Q protein_coding YES CCDS34521.1 771/2151 AGCCAAGATGT Pfam:PF04712;PANTHER:PTHR13159;PANTHER:PTHR13159:SF4 ENSP00000229554 2/6 rs1562389892 ENST00000229554 Transcript 1.0 ENSG00000111834 HGNC:21558 LOW NM_001010892.3 8.815e-06 gnomAD_NFE synonymous_variant 1.0 Unknown Q5TD94.122 RSPH4A HGNC 1 1.0 UPI00001D80C4 Q5TD94-1 SNV RSPH4A,synonymous_variant,p.Q257=,ENST00000229554,NM_001010892.3,c.771A>G,LOW,YES,,,1;RSPH4A,synonymous_variant,p.Q257=,ENST00000368581,NM_001161664.1,c.771A>G,LOW,,,,1;RSPH4A,synonymous_variant,p.Q257=,ENST00000368580,,c.771A>G,LOW,,,,1 916/2840 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 3.983e-06 0.0 0.0 0.0 0.0 0.0 8.815e-06 0.0 0.0 0 195 5faf2c57-9042-4056-a8cc-37d37bf528b4 242 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS RSPH4A,synonymous_variant,p.Q257=,ENST00000368580.4,c.771A>G,LOW,;RSPH4A,synonymous_variant,p.Q257=,ENST00000229554.10,c.771A>G,LOW,YES;RSPH4A,synonymous_variant,p.Q257=,ENST00000368581.8,c.771A>G,LOW, +NBN 4683 BI GRCh38 8 89970529 89970529 + missense_variant Missense_Mutation SNP A A G rs1586087079 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 105 23 c.731T>C p.Phe244Ser p.F244S ENST00000265433.8 NM_002485.5 244 tTt/tCt 7/16 P1 G F/S protein_coding YES CCDS6249.1 731/2265 CTCCAAAGACA Gene3D:3.40.50.10980;Pfam:PF16508;PIRSF:PIRSF011869;PANTHER:PTHR12162 ENSP00000265433 7/16 ENST00000265433 Transcript 1.0 ENSG00000104320 HGNC:7652 MODERATE NM_002485.5 missense_variant 1.0 benign(0.362) Unknown deleterious(0) O60934.180 NBN HGNC -1 1.0 UPI0000073BF4 SNV NBN,missense_variant,p.F244S,ENST00000265433,NM_002485.5,c.731T>C,MODERATE,YES,deleterious(0),benign(0.362),-1;NBN,missense_variant,p.F162S,ENST00000409330,NM_001024688.2,c.485T>C,MODERATE,,deleterious(0),benign(0.362),-1;NBN,missense_variant,p.F162S,ENST00000517772,,c.485T>C,MODERATE,,deleterious(0),benign(0.362),-1;NBN,missense_variant,p.F156S,ENST00000519426,,c.467T>C,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.478),-1;NBN,3_prime_UTR_variant,,ENST00000396252,,c.*604T>C,MODIFIER,,,,-1 837/4622 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 86 5faf2c57-9042-4056-a8cc-37d37bf528b4 128 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS NBN,missense_variant,p.F162S,ENST00000517772.5,c.485T>C,MODERATE,;NBN,missense_variant,p.F156S,ENST00000519426.5,c.467T>C,MODERATE,;NBN,non_coding_transcript_exon_variant,,ENST00000697318.1,n.843T>C,MODIFIER,;NBN,non_coding_transcript_exon_variant,,ENST00000697317.1,n.841T>C,MODIFIER,;NBN,non_coding_transcript_exon_variant,,ENST00000697316.1,n.852T>C,MODIFIER,;NBN,missense_variant,NMD_transcript_variant,p.F244S,ENST00000697315.1,c.731T>C,MODERATE,;NBN,non_coding_transcript_exon_variant,,ENST00000697314.1,n.2522T>C,MODIFIER,;NBN,non_coding_transcript_exon_variant,,ENST00000697313.1,n.2522T>C,MODIFIER,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697312.1,c.*129T>C,MODIFIER,;NBN,missense_variant,NMD_transcript_variant,p.F244S,ENST00000697311.1,c.731T>C,MODERATE,;NBN,missense_variant,p.F244S,ENST00000697310.1,c.731T>C,MODERATE,;NBN,missense_variant,p.F244S,ENST00000697309.1,c.731T>C,MODERATE,;NBN,missense_variant,p.F162S,ENST00000409330.5,c.485T>C,MODERATE,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000396252.6,c.*604T>C,MODIFIER,;NBN,missense_variant,p.F162S,ENST00000523444.2,c.485T>C,MODERATE,;NBN,missense_variant,p.F244S,ENST00000265433.8,c.731T>C,MODERATE,YES;NBN,missense_variant,p.F244S,ENST00000697307.1,c.731T>C,MODERATE,;NBN,intron_variant,NMD_transcript_variant,,ENST00000697306.1,c.480+10205T>C,MODIFIER,;NBN,missense_variant,p.F244S,ENST00000697308.1,c.731T>C,MODERATE,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697294.1,c.*342T>C,MODIFIER,;NBN,missense_variant,p.F162S,ENST00000697299.1,c.485T>C,MODERATE,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697295.1,c.*40T>C,MODIFIER,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697301.1,c.*252T>C,MODIFIER,;NBN,non_coding_transcript_exon_variant,,ENST00000697297.1,n.2516T>C,MODIFIER,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697296.1,c.*399T>C,MODIFIER,;NBN,non_coding_transcript_exon_variant,,ENST00000494804.2,n.2033T>C,MODIFIER,;NBN,intron_variant,,ENST00000697304.1,c.585-6022T>C,MODIFIER,;NBN,missense_variant,p.F162S,ENST00000517337.2,c.485T>C,MODERATE,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697300.1,c.*335T>C,MODIFIER,;NBN,missense_variant,p.F162S,ENST00000697298.1,c.485T>C,MODERATE,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697302.1,c.*252T>C,MODIFIER,;NBN,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000697303.1,c.*335T>C,MODIFIER,;NBN,missense_variant,p.F244S,ENST00000697293.1,c.731T>C,MODERATE,;NBN,missense_variant,p.F244S,ENST00000697292.1,c.731T>C,MODERATE, +GNAQ 2776 BI GRCh38 9 77794572 77794572 + missense_variant Missense_Mutation SNP T T A rs121913492 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 46 55 c.626A>T p.Gln209Leu p.Q209L ENST00000286548.9 NM_002072.5 209 cAa/cTa 5/7 P1 A Q/L protein_coding YES CCDS6658.1 626/1080 pathogenic;likely_pathogenic ACCTTTGGCCC COSM28757 PDB-ENSP_mappings:6vu5.B;PROSITE_profiles:PS51882;CDD:cd00066;PANTHER:PTHR10218;PANTHER:PTHR10218:SF316;Pfam:PF00503;Gene3D:3.40.50.300;SMART:SM00275;Superfamily:SSF52540;Prints:PR00318 ENSP00000286548 5/7 rs121913492;COSV54105903;COSV54105914;COSV54108414 ENST00000286548 Transcript 1.0 ENSG00000156052 HGNC:4390 MODERATE NM_002072.5 missense_variant 1;1;1;1 1.0 25157968;2549426;1328859;18719078;19078957;21083380;22253748;22653968;22733540;22808163 probably_damaging(0.999) Unknown deleterious(0) 0;1;1;1 P50148.194 GNAQ HGNC -1 A0A024R240.43 1.0 UPI000006D0FB SNV GNAQ,missense_variant,p.Q209L,ENST00000286548,NM_002072.5,c.626A>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;GNAQ,downstream_gene_variant,,ENST00000411677,,,MODIFIER,,,,-1 1202/6882 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 99 5faf2c57-9042-4056-a8cc-37d37bf528b4 101 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS GNAQ,missense_variant,p.Q209L,ENST00000286548.9,c.626A>T,MODERATE,YES +VWF 7450 BI GRCh38 12 6019073 6019073 + missense_variant Missense_Mutation SNP G G C TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 32 24 c.4345C>G p.Gln1449Glu p.Q1449E ENST00000261405.10 NM_000552.5 1449 Caa/Gaa 28/52 P1 C Q/E protein_coding YES CCDS8539.1 4345/8442 CCTTTGCTGCT PDB-ENSP_mappings:1auq.A;PDB-ENSP_mappings:1fns.A;PDB-ENSP_mappings:1ijb.A;PDB-ENSP_mappings:1ijk.A;PDB-ENSP_mappings:1m10.A;PDB-ENSP_mappings:1oak.A;PDB-ENSP_mappings:1sq0.A;PDB-ENSP_mappings:1u0n.A;PDB-ENSP_mappings:1uex.C;Gene3D:3.40.50.410;PDB-ENSP_mappings:3hxo.A;PDB-ENSP_mappings:3hxq.A;PDB-ENSP_mappings:4c29.A;PDB-ENSP_mappings:4c29.B;PDB-ENSP_mappings:4c2a.A;PDB-ENSP_mappings:4c2b.A;PDB-ENSP_mappings:4c2b.C;PDB-ENSP_mappings:4c2b.E;PDB-ENSP_mappings:4c2b.G;PDB-ENSP_mappings:5bv8.A;Pfam:PF00092;PIRSF:PIRSF002495;PROSITE_profiles:PS50234;PANTHER:PTHR11339;PANTHER:PTHR11339:SF361;SMART:SM00327;Superfamily:SSF53300 ENSP00000261405 28/52 COSV54611598 ENST00000261405 Transcript 1.0 ENSG00000110799 HGNC:12726 MODERATE NM_000552.5 missense_variant 1 1.0 benign(0.049) Unknown tolerated(0.07) 1 P04275.252 VWF HGNC -1 1.0 UPI00001AE7EE P04275-1 SNV VWF,missense_variant,p.Q1449E,ENST00000261405,NM_000552.5,c.4345C>G,MODERATE,YES,tolerated(0.07),benign(0.049),-1;VWF,intron_variant,,ENST00000538635,,n.421-25139C>G,MODIFIER,,,,-1;VWF,downstream_gene_variant,,ENST00000539641,,,MODIFIER,,,,-1 4595/8830 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 57 5faf2c57-9042-4056-a8cc-37d37bf528b4 56 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS VWF,intron_variant,,ENST00000538635.5,n.421-25139C>G,MODIFIER,;VWF,missense_variant,p.Q1449E,ENST00000261405.10,c.4345C>G,MODERATE,YES +ARHGAP17 55114 BI GRCh38 16 24935608 24935608 + missense_variant Missense_Mutation SNP C C G novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 29 23 c.1756G>C p.Ala586Pro p.A586P ENST00000289968.11 NM_001006634.3 586 Gct/Cct 18/20 P2 G A/P protein_coding YES CCDS32409.1 1756/2646 CACAGCTGCAG PANTHER:PTHR14130;PANTHER:PTHR14130:SF3;MobiDB_lite:mobidb-lite ENSP00000289968 18/20 ENST00000289968 Transcript ENSG00000140750 HGNC:18239 MODERATE NM_001006634.3 missense_variant 1.0 benign(0.003) Unknown tolerated(0.41) Q68EM7.146 ARHGAP17 HGNC -1 1.0 UPI00000433FD Q68EM7-1 SNV ARHGAP17,missense_variant,p.A586P,ENST00000289968,NM_001006634.3,c.1756G>C,MODERATE,YES,tolerated(0.41),benign(0.003),-1;ARHGAP17,missense_variant,p.A508P,ENST00000303665,NM_018054.6,c.1522G>C,MODERATE,,tolerated(0.17),probably_damaging(0.981),-1;ARHGAP17,upstream_gene_variant,,ENST00000571406,,,MODIFIER,,,,-1;ARHGAP17,upstream_gene_variant,,ENST00000571843,,,MODIFIER,,,,-1;ARHGAP17,upstream_gene_variant,,ENST00000573765,,,MODIFIER,,,,-1;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000572314,,n.3838G>C,MODIFIER,,,,-1;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000570320,,n.1220G>C,MODIFIER,,,,-1;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000575283,,n.590G>C,MODIFIER,,,,-1 1864/3495 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 49 5faf2c57-9042-4056-a8cc-37d37bf528b4 52 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS ARHGAP17,non_coding_transcript_exon_variant,,ENST00000572314.5,n.3838G>C,MODIFIER,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000575283.5,n.590G>C,MODIFIER,;ARHGAP17,missense_variant,p.A508P,ENST00000303665.9,c.1522G>C,MODERATE,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000570320.5,n.1220G>C,MODIFIER,;ARHGAP17,missense_variant,p.A586P,ENST00000289968.11,c.1756G>C,MODERATE,YES +ACD 50855 BI GRCh38 16 67658966 67658966 + missense_variant Missense_Mutation SNP G G C novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 56 45 c.607C>G p.Pro203Ala p.P203A ENST00000620761.6 NM_016948.3 289/544 A2 C P/A protein_coding YES CCDS42181.1 865/1635 GACAGGGGGTG PANTHER:PTHR14487 ENSP00000483117 7/12 ENST00000620338 Transcript 1.0 ENSG00000102977 HGNC:25070 MODERATE missense_variant 1.0 benign(0.005) Unknown tolerated(0.08) ACD HGNC -1 A0A590TQL1.3 1.0 UPI0000246BB2 SNV ACD,missense_variant,p.P289A,ENST00000620338,,c.865C>G,MODERATE,YES,tolerated(0.08),benign(0.005),-1;ACD,missense_variant,p.P200A,ENST00000219251,NM_022914.3,c.598C>G,MODERATE,,deleterious(0.02),benign(0.011),-1;ACD,missense_variant,p.P203A,ENST00000620761,NM_001082486.2,c.607C>G,MODERATE,,deleterious(0.03),benign(0.005),-1;ACD,missense_variant,p.P200A,ENST00000602320,,c.598C>G,MODERATE,,tolerated(0.08),benign(0.018),-1;ACD,missense_variant,p.P51A,ENST00000602382,,c.151C>G,MODERATE,,deleterious_low_confidence(0.03),benign(0.003),-1;PARD6A,upstream_gene_variant,,ENST00000219255,NM_016948.3,,MODIFIER,YES,,,1;ENKD1,downstream_gene_variant,,ENST00000243878,NM_032140.3,,MODIFIER,YES,,,-1;CARMIL2,downstream_gene_variant,,ENST00000334583,NM_001013838.3,,MODIFIER,YES,,,1;PARD6A,upstream_gene_variant,,ENST00000458121,NM_001037281.2,,MODIFIER,,,,1;CARMIL2,downstream_gene_variant,,ENST00000545661,NM_001317026.3,,MODIFIER,,,,1;ENKD1,downstream_gene_variant,,ENST00000602409,,,MODIFIER,,,,-1;PARD6A,upstream_gene_variant,,ENST00000602551,,,MODIFIER,,,,1;ENKD1,downstream_gene_variant,,ENST00000602644,,,MODIFIER,,,,-1;ENKD1,downstream_gene_variant,,ENST00000602415,,,MODIFIER,,,,-1;ACD,3_prime_UTR_variant,,ENST00000602850,,c.*387C>G,MODIFIER,,,,-1;ACD,non_coding_transcript_exon_variant,,ENST00000602622,,n.1225C>G,MODIFIER,,,,-1;ACD,non_coding_transcript_exon_variant,,ENST00000602860,,n.1045C>G,MODIFIER,,,,-1;ACD,non_coding_transcript_exon_variant,,ENST00000602945,,n.677C>G,MODIFIER,,,,-1;CARMIL2,downstream_gene_variant,,ENST00000602368,,,MODIFIER,,,,1;ACD,downstream_gene_variant,,ENST00000602423,,,MODIFIER,,,,-1;ACD,downstream_gene_variant,,ENST00000602519,,,MODIFIER,,,,-1;ENKD1,downstream_gene_variant,,ENST00000602642,,,MODIFIER,,,,-1;ACD,upstream_gene_variant,,ENST00000602656,,,MODIFIER,,,,-1;CARMIL2,downstream_gene_variant,,ENST00000602705,,,MODIFIER,,,,1;PARD6A,upstream_gene_variant,,ENST00000602727,,,MODIFIER,,,,1;ACD,downstream_gene_variant,,ENST00000602780,,,MODIFIER,,,,-1;ACD,downstream_gene_variant,,ENST00000602821,,,MODIFIER,,,,-1;CARMIL2,downstream_gene_variant,,ENST00000602924,,,MODIFIER,,,,1;ENKD1,downstream_gene_variant,,ENST00000602942,,,MODIFIER,,,,-1 1202/2065 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 94 5faf2c57-9042-4056-a8cc-37d37bf528b4 101 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS ACD,non_coding_transcript_exon_variant,,ENST00000602945.6,n.749C>G,MODIFIER,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695650.1,c.*369C>G,MODIFIER,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695713.1,c.*86C>G,MODIFIER,;ACD,intron_variant,NMD_transcript_variant,,ENST00000695736.1,c.158-150C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000602519.2,n.1097C>G,MODIFIER,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695661.1,c.*86C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695702.1,n.722C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695701.1,n.990C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695649.1,n.1600C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695660.1,n.1120C>G,MODIFIER,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000602850.6,c.*387C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695700.1,n.972C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695735.1,n.114C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695710.1,n.860C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695699.1,n.895C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695698.1,n.857C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695709.1,n.259C>G,MODIFIER,;ACD,missense_variant,p.P203A,ENST00000695697.1,c.607C>G,MODERATE,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695712.1,c.*357C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000602860.6,n.1527C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695696.1,n.988C>G,MODIFIER,;ACD,missense_variant,p.P197A,ENST00000695648.1,c.589C>G,MODERATE,;ACD,non_coding_transcript_exon_variant,,ENST00000602780.2,n.1231C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695695.1,n.673C>G,MODIFIER,;ACD,missense_variant,p.P203A,ENST00000695659.1,c.607C>G,MODERATE,;ACD,missense_variant,NMD_transcript_variant,p.P203A,ENST00000695711.1,c.607C>G,MODERATE,;ACD,missense_variant,p.P200A,ENST00000602320.1,c.598C>G,MODERATE,;ACD,non_coding_transcript_exon_variant,,ENST00000695641.1,n.1524C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000602622.5,n.1225C>G,MODIFIER,;ACD,missense_variant,p.P203A,ENST00000695658.1,c.607C>G,MODERATE,;ACD,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000695662.1,c.*86C>G,MODIFIER,;ACD,non_coding_transcript_exon_variant,,ENST00000695657.1,n.1012C>G,MODIFIER,;ACD,missense_variant,p.P203A,ENST00000602382.6,c.607C>G,MODERATE,;ACD,non_coding_transcript_exon_variant,,ENST00000695656.1,n.1054C>G,MODIFIER,;ACD,missense_variant,p.P203A,ENST00000695733.1,c.607C>G,MODERATE,;ACD,synonymous_variant,NMD_transcript_variant,p.P38=,ENST00000695731.1,c.114C>G,LOW,;ACD,missense_variant,p.P203A,ENST00000695734.1,c.607C>G,MODERATE,;ACD,missense_variant,p.P188A,ENST00000695694.1,c.562C>G,MODERATE,;ACD,missense_variant,p.P203A,ENST00000620761.6,c.607C>G,MODERATE,YES;ACD,missense_variant,p.P200A,ENST00000219251.13,c.598C>G,MODERATE,;ACD,missense_variant,p.P203A,ENST00000695732.1,c.607C>G,MODERATE, +SRSF2 6427 BI GRCh38 17 76736864 76736887 + inframe_deletion In_Frame_Del DEL GTGTGAGTCCGGGGGGCGGCCGTA GTGTGAGTCCGGGGGGCGGCCGTA - novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 40 12 c.274_297del p.His100_Pro107del p.H100_P107del ENST00000359995.10 NM_001195427.2 92 TACGGCCGCCCCCCGGACTCACAC/- 1/3 P1 - YGRPPDSH/- protein_coding CCDS11749.1 274-297/666 GCTGTGGTGTGAGTCCGGGGGGCGGCCGTAGCGCG PDB-ENSP_mappings:2kn4.A;PDB-ENSP_mappings:2lea.A;PDB-ENSP_mappings:2leb.A;PDB-ENSP_mappings:2lec.A;Gene3D:3.30.70.330;PROSITE_profiles:PS50102;PANTHER:PTHR23147;PANTHER:PTHR23147:SF119;Superfamily:SSF54928;MobiDB_lite:mobidb-lite ENSP00000353089 1/3 ENST00000359995 Transcript 1.0 ENSG00000161547 HGNC:10783 MODERATE NM_001195427.2 inframe_deletion Unknown Q01130.232 SRSF2 HGNC -1 A0A024R8U5.53 1.0 UPI0000000C2A Q01130-1 deletion SRSF2,inframe_deletion,p.Y92_H99del,ENST00000392485,NM_003016.4,c.274_297del,MODERATE,YES,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000359995,NM_001195427.2,c.274_297del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000508921,,c.274_297del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000358156,,c.274_297del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000583836,,c.274_297del,MODERATE,,,,-1;MFSD11,5_prime_UTR_variant,,ENST00000588460,NM_001353018.1,c.-1488_-1465del,MODIFIER,YES,,,1;MFSD11,5_prime_UTR_variant,,ENST00000586622,,c.-298_-275del,MODIFIER,,,,1;MFSD11,5_prime_UTR_variant,,ENST00000621483,NM_001242534.2&NM_001353017.1,c.-298_-275del,MODIFIER,,,,1;MFSD11,5_prime_UTR_variant,,ENST00000591864,,c.-298_-275del,MODIFIER,,,,1;AC005837.2,intron_variant,,ENST00000587459,,c.239-1417_239-1394del,MODIFIER,YES,,,1;MFSD11,upstream_gene_variant,,ENST00000336509,NM_001353019.1&NM_001242535.2&NM_024311.4&NM_001242532.4,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000341249,NM_001378349.1&NM_001378351.1&NM_001080510.5&NM_001378352.1,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000355954,NM_001242536.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586200,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000586689,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586738,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000586752,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000587661,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588302,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588563,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588783,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588822,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000588964,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589977,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590393,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000590514,NM_001242533.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000590964,NM_001206987.2&NM_001206986.2&NM_001206985.2&NM_001302704.1&NM_001378354.1,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000591571,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000592849,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000593181,NM_001242537.2,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000615984,NM_001206983.2&NM_001302703.1&NM_001206984.2&NM_001302705.1&NM_001378348.1&NM_001378353.1&NM_001378350.1,,MODIFIER,YES,,,1;MIR636,upstream_gene_variant,,ENST00000384825,,,MODIFIER,YES,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000585202,,c.274_297del,MODERATE,,,,-1;SRSF2,inframe_deletion,p.Y92_H99del,ENST00000452355,,c.274_297del,MODERATE,,,,-1;SRSF2,upstream_gene_variant,,ENST00000582449,,,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000586778,,,MODIFIER,,,,-1;MFSD11,upstream_gene_variant,,ENST00000588031,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588670,,,MODIFIER,,,,1;MFSD11,upstream_gene_variant,,ENST00000588768,,,MODIFIER,,,,1;METTL23,downstream_gene_variant,,ENST00000589581,,,MODIFIER,,,,1;SRSF2,upstream_gene_variant,,ENST00000589919,,,MODIFIER,,,,-1;SRSF2,upstream_gene_variant,,ENST00000592676,,,MODIFIER,,,,-1 445-468/1888 mutect2;pindel 711eb720-4cb7-48de-9350-5c729bf9f0da 0 48 5faf2c57-9042-4056-a8cc-37d37bf528b4 52 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS MFSD11,5_prime_UTR_variant,,ENST00000591864.1,c.-299_-276del,MODIFIER,;MFSD11,5_prime_UTR_variant,,ENST00000621483.4,c.-299_-276del,MODIFIER,;SRSF2,inframe_deletion,p.H100_P107del,ENST00000583836.1,c.274_297del,MODERATE,;MFSD11,5_prime_UTR_variant,,ENST00000586622.5,c.-299_-276del,MODIFIER,;SRSF2,inframe_deletion,p.H100_P107del,ENST00000508921.7,c.274_297del,MODERATE,;SRSF2,inframe_deletion,NMD_transcript_variant,p.H100_P107del,ENST00000452355.7,c.274_297del,MODERATE,;SRSF2,inframe_deletion,NMD_transcript_variant,p.H100_P107del,ENST00000585202.5,c.274_297del,MODERATE,;SRSF2,inframe_deletion,p.H100_P107del,ENST00000359995.10,c.274_297del,MODERATE,YES;SRSF2,inframe_deletion,p.H100_P107del,ENST00000392485.2,c.274_297del,MODERATE,;SRSF2,inframe_deletion,p.H100_P107del,ENST00000358156.7,c.274_297del,MODERATE,;ENSG00000267168,intron_variant,,ENST00000587459.1,c.239-1418_239-1395del,MODIFIER,YES +MAP1S 55201 BI GRCh38 19 17725141 17725142 + frameshift_variant Frame_Shift_Del DEL AG AG - rs752646082 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 86 17 c.396_397del p.Gly134LeufsTer40 p.G134Lfs*40 ENST00000324096.9 NM_018174.6 132 acAGgg/acgg 4/7 P4 - TG/TX protein_coding YES CCDS32954.1 396-397/3180 ACAGACAGGGGGC PANTHER:PTHR13843;PANTHER:PTHR13843:SF11;Low_complexity_(Seg):seg ENSP00000325313 4/7 rs752646082 ENST00000324096 Transcript ENSG00000130479 HGNC:15715 HIGH NM_018174.6 4.406e-05 gnomAD_NFE frameshift_variant 1.0 Unknown Q66K74.138 MAP1S HGNC 1 1.0 UPI00002036F9 Q66K74-1 deletion MAP1S,frameshift_variant,p.G108Lfs*40,ENST00000544059,NM_001308363.1,c.318_319del,HIGH,,,,1;MAP1S,frameshift_variant,p.G134Lfs*40,ENST00000324096,NM_018174.6,c.396_397del,HIGH,YES,,,1;MAP1S,frameshift_variant,p.G100Lfs*40,ENST00000600186,,c.294_295del,HIGH,,,,1;MAP1S,frameshift_variant,p.G134Lfs*40,ENST00000594625,,c.396_397del,HIGH,,,,1;MAP1S,intron_variant,,ENST00000597735,,c.351+45_351+46del,MODIFIER,,,,1;MAP1S,upstream_gene_variant,,ENST00000597000,,,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000601544,,n.434_435del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000599494,,n.315_316del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000594340,,n.383_384del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000595338,,n.421_422del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000598916,,n.347_348del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000597067,,n.464_465del,MODIFIER,,,,1;MAP1S,intron_variant,,ENST00000597681,,n.125-2148_125-2147del,MODIFIER,,,,1;MAP1S,upstream_gene_variant,,ENST00000598756,,,MODIFIER,,,,1;MAP1S,3_prime_UTR_variant,,ENST00000594212,,c.*97_*98del,MODIFIER,,,,1;MAP1S,3_prime_UTR_variant,,ENST00000594365,,c.*235_*236del,MODIFIER,,,,1;MAP1S,non_coding_transcript_exon_variant,,ENST00000598769,,n.490_491del,MODIFIER,,,,1;MAP1S,downstream_gene_variant,,ENST00000593593,,,MODIFIER,,,,1;MAP1S,downstream_gene_variant,,ENST00000596637,,,MODIFIER,,,,1;MAP1S,downstream_gene_variant,,ENST00000600608,,,MODIFIER,,,,1;AC008761.1,downstream_gene_variant,,ENST00000595363,,,MODIFIER,YES,,,-1 419-420/3288 mutect2;pindel;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 1.991e-05 0.0 0.0 0.0 0.0 0.0 4.406e-05 0.0 0.0 1.3524499991035556e-05 0.0 0.0 0.0 0.0 0.0 0.0 nfe 3.086320066358894e-05 0.0 3.086320066358894e-05 0.0 0.0 0 95 5faf2c57-9042-4056-a8cc-37d37bf528b4 103 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS MAP1S,non_coding_transcript_exon_variant,,ENST00000598916.1,n.347_348del,MODIFIER,;MAP1S,non_coding_transcript_exon_variant,,ENST00000598769.5,n.490_491del,MODIFIER,;MAP1S,non_coding_transcript_exon_variant,,ENST00000595338.5,n.421_422del,MODIFIER,;MAP1S,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000594365.5,c.*235_*236del,MODIFIER,;MAP1S,frameshift_variant,p.G108Lfs*40,ENST00000544059.2,c.318_319del,HIGH,;MAP1S,non_coding_transcript_exon_variant,,ENST00000599494.5,n.315_316del,MODIFIER,;MAP1S,non_coding_transcript_exon_variant,,ENST00000597067.5,n.464_465del,MODIFIER,;MAP1S,non_coding_transcript_exon_variant,,ENST00000594340.5,n.383_384del,MODIFIER,;MAP1S,intron_variant,,ENST00000597681.1,n.125-2148_125-2147del,MODIFIER,;MAP1S,non_coding_transcript_exon_variant,,ENST00000601544.5,n.434_435del,MODIFIER,;MAP1S,frameshift_variant,p.G100Lfs*40,ENST00000600186.5,c.294_295del,HIGH,;MAP1S,frameshift_variant,p.G134Lfs*40,ENST00000324096.9,c.396_397del,HIGH,YES;MAP1S,3_prime_UTR_variant,NMD_transcript_variant,,ENST00000594212.5,c.*97_*98del,MODIFIER,;MAP1S,intron_variant,,ENST00000597735.5,c.351+45_351+46del,MODIFIER,;MAP1S,frameshift_variant,p.G134Lfs*40,ENST00000594625.5,c.396_397del,HIGH, +RHPN2 85415 BI GRCh38 19 33026574 33026574 + missense_variant Missense_Mutation SNP A A T novel TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 117 85 c.244T>A p.Ser82Thr p.S82T ENST00000254260.8 NM_033103.5 82 Tca/Aca 3/15 P1 T S/T protein_coding YES CCDS12427.1 244/2061 GTCTGAGTTGA Coiled-coils_(Ncoils):Coil;PROSITE_profiles:PS51860;CDD:cd11634;PANTHER:PTHR23031;PANTHER:PTHR23031:SF5;Pfam:PF02185;Gene3D:1.10.287.160;SMART:SM00742;Superfamily:SSF46585 ENSP00000254260 3/15 ENST00000254260 Transcript ENSG00000131941 HGNC:19974 MODERATE NM_033103.5 missense_variant 1.0 possibly_damaging(0.467) Unknown deleterious(0) Q8IUC4.152 RHPN2 HGNC -1 1.0 UPI00000747A3 Q8IUC4-1 SNV RHPN2,missense_variant,p.S82T,ENST00000254260,NM_033103.5,c.244T>A,MODERATE,YES,deleterious(0),possibly_damaging(0.467),-1;RHPN2,missense_variant,p.S82T,ENST00000588388,,c.244T>A,MODERATE,,deleterious(0),probably_damaging(0.979),-1;RHPN2,non_coding_transcript_exon_variant,,ENST00000544458,,n.698T>A,MODIFIER,,,,-1 280/3501 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0 171 5faf2c57-9042-4056-a8cc-37d37bf528b4 202 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS RHPN2,missense_variant,NMD_transcript_variant,p.S82T,ENST00000588388.5,c.244T>A,MODERATE,;RHPN2,non_coding_transcript_exon_variant,,ENST00000544458.6,n.698T>A,MODIFIER,;RHPN2,missense_variant,p.S82T,ENST00000254260.8,c.244T>A,MODERATE,YES +MYBPC2 4606 BI GRCh38 19 50435823 50435823 + missense_variant Missense_Mutation SNP G G C rs765476587 TCGA-V4-A9EM-01A TCGA-V4-A9EM-10A Somatic 6 9 c.157G>C p.Val53Leu p.V53L ENST00000357701.6 NM_004533.4 53 Gtt/Ctt 3/28 P1 C V/L protein_coding YES CCDS46152.1 157/3426 CCGGCGTTTTC Gene3D:2.60.40.10;PDB-ENSP_mappings:2edn.A;Pfam:PF07679;PANTHER:PTHR13817;PANTHER:PTHR13817:SF17;MobiDB_lite:mobidb-lite ENSP00000350332 3/28 rs765476587;COSV63094943 ENST00000357701 Transcript ENSG00000086967 HGNC:7550 MODERATE NM_004533.4 0.0 gnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS missense_variant 0;1 1.0 benign(0) Unknown tolerated(1) 0;1 Q14324.178 MYBPC2 HGNC 1 A0A140VJQ0.20 1.0 UPI000013C628 SNV MYBPC2,missense_variant,p.V53L,ENST00000357701,NM_004533.4,c.157G>C,MODERATE,YES,tolerated(1),benign(0),1;SPIB,downstream_gene_variant,,ENST00000439922,NM_001244000.2&NM_001243998.1,,MODIFIER,,,,1;SPIB,downstream_gene_variant,,ENST00000595883,NM_003121.5,,MODIFIER,YES,,,1 219/3604 muse;mutect2;varscan2 711eb720-4cb7-48de-9350-5c729bf9f0da 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0 21 5faf2c57-9042-4056-a8cc-37d37bf528b4 15 88f8ce09-2e9b-41a1-9d1b-f1a1914e6003 SUCCESS MYBPC2,missense_variant,p.V53L,ENST00000357701.6,c.157G>C,MODERATE,YES