Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand 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 Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut WFS1 7466 broad.mit.edu 37 4 6302918 6302918 + Missense_Mutation SNP G G C TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr4:6302918G>C ENST00000226760.1 + 8 1566 c.1396G>C c.(1396-1398)Ggc>Cgc p.G466R WFS1_ENST00000503569.1_Missense_Mutation_p.G466R NM_001145853.1|NM_006005.3 NP_001139325.1|NP_005996.2 O76024 WFS1_HUMAN Wolfram syndrome 1 (wolframin) 466 endoplasmic reticulum calcium ion homeostasis|endoplasmic reticulum unfolded protein response|ER overload response|ER-associated protein catabolic process|glucose homeostasis|kidney development|negative regulation of neuron apoptosis|negative regulation of sequence-specific DNA binding transcription factor activity|polyubiquitinated misfolded protein transport|positive regulation of calcium ion transport|positive regulation of growth|positive regulation of protein ubiquitination|positive regulation of proteolysis|protein stabilization|renal water homeostasis|sensory perception of sound|visual perception dendrite|integral to endoplasmic reticulum membrane activating transcription factor binding|ATPase binding|transporter activity|ubiquitin protein ligase binding central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1) 21 Colorectal(103;0.0512) GGTCACCGCCGGCCTGCTATC 0.642000 6 75 0 0 0.217242 0 0 AFM 173 broad.mit.edu 37 4 74357625 74357625 + Missense_Mutation SNP T T G TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr4:74357625T>G ENST00000226355.3 + 8 973 c.880T>G c.(880-882)Tct>Gct p.S294A NM_001133.2 NP_001124.1 P43652 AFAM_HUMAN afamin 294 Albumin 2. vitamin transport vitamin E binding breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 32 Breast(15;0.00102) Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) AAAACAAGATTCTATCTCCAG 0.358000 5 104 0 0 0.217242 0 0 SNHG14 0 broad.mit.edu 37 15 25448253 25448253 + RNA SNP G G A TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr15:25448253G>A ENST00000424208.1 + 0 2099 SNHG14_ENST00000424333.1_RNA NR_003305.1 TCATCCCGGCGTCCAGCCCCT 0.617000 7 51 0 0 0.248553 0 0 TMTC1 83857 broad.mit.edu 37 12 29689068 29689068 + Missense_Mutation SNP T T C rs71450781 by1000genomes TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr12:29689068T>C ENST00000381224.2 - 13 2194 c.1721A>G c.(1720-1722)tAc>tGc p.Y574C TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000551659.1_Intron|TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000319685.8_Intron Q8IUR5 TMTC1_HUMAN transmembrane and tetratricopeptide repeat containing 1 0 integral to membrane binding breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 75 Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032) AAATCATTAGTACAAAAATCT 0.308000 3 18 0 0 0.115264 0 0 SYNE2 23224 broad.mit.edu 37 14 64680925 64680925 + Missense_Mutation SNP A A G TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr14:64680925A>G ENST00000357395.3 + 107 19369 c.8225A>G c.(8224-8226)gAa>gGa p.E2742G SYNE2_ENST00000555002.1_Missense_Mutation_p.E2991G|SYNE2_ENST00000555022.1_Missense_Mutation_p.E235G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000458046.2_5'UTR|SYNE2_ENST00000554805.1_Missense_Mutation_p.E140G|SYNE2_ENST00000554584.1_Missense_Mutation_p.E6299G|SYNE2_ENST00000358025.3_Missense_Mutation_p.E6357G|SYNE2_ENST00000344113.4_Missense_Mutation_p.E6357G|SYNE2_ENST00000394768.2_Missense_Mutation_p.E2742G Q8WXH0 SYNE2_HUMAN spectrin repeat containing, nuclear envelope 2 6357 centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc actin binding|protein binding NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4) 224 all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681) TTGGAAGATGAAAAGGAGGCC 0.458000 7 103 0 0 0.248553 0 0 RP11-24M17.5 0 broad.mit.edu 37 15 76067987 76067987 + RNA SNP A A G rs34243492 by1000genomes TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr15:76067987A>G ENST00000395215.3 + 0 94 GAAGAAACTCAACAGAGTAAA 0.537000 3 31 0 0 0.115264 0 0 ZNF235 9310 broad.mit.edu 37 19 44807571 44807571 + Translation_Start_Site SNP C C A TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr19:44807571C>A ENST00000291182.4 - 0 89 ZNF235_ENST00000589799.1_De_novo_Start_InFrame|ZNF235_ENST00000589248.1_De_novo_Start_InFrame NM_004234.4 NP_004225.3 Q14590 ZN235_HUMAN zinc finger protein 235 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 29 Prostate(69;0.0352)|all_neural(266;0.116) TCCCCTCCTCCTTCTGGGAAA 0.438000 8 92 0.00307968 0.00324177 0.278610 1 0 FLOT1 10211 broad.mit.edu 37 6 30707994 30707994 + Missense_Mutation SNP C C T TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr6:30707994C>T ENST00000376389.3 - 8 884 c.664G>A c.(664-666)Gcc>Acc p.A222T FLOT1_ENST00000470643.1_5'UTR|FLOT1_ENST00000456573.2_Missense_Mutation_p.A174T NM_005803.2 NP_005794.1 O75955 FLOT1_HUMAN flotillin 1 222 centriolar satellite|endosome|integral to membrane|melanosome|membrane fraction breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1) 13 ATGTCATAGGCGGCCTTCTTC 0.562000 4 51 0 0 0.150653 0 0 EIF1AX 1964 broad.mit.edu 37 X 20156731 20156731 + Missense_Mutation SNP C C T TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chrX:20156731C>T ENST00000379607.5 - 2 229 c.26G>A c.(25-27)gGt>gAt p.G9D EIF1AX_ENST00000379593.1_Intron NM_001412.3 NP_001403.1 P47813 IF1AX_HUMAN eukaryotic translation initiation factor 1A, X-linked 9 cytosol translation initiation factor activity endometrium(2)|lung(1)|ovary(1)|prostate(1) 5 TCTGTTTTTACCTCCTTTACC 0.313000 15 56 0 0 0.500413 0 0 TMTC1 83857 broad.mit.edu 37 12 29689066 29689066 + Nonstop_Mutation SNP A A G rs71450781 by1000genomes TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr12:29689066A>G ENST00000381224.2 - 13 2196 c.1723T>C c.(1723-1725)Taa>Caa p.*575Q TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000551659.1_Intron|TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000319685.8_Intron Q8IUR5 TMTC1_HUMAN transmembrane and tetratricopeptide repeat containing 1 0 integral to membrane binding breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 75 Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032) ttAAATCATTAGTACAAAAAT 0.308000 3 18 0 0 0.115264 0 0 CDH8 1006 broad.mit.edu 37 16 61687935 61687935 + Silent SNP G G A TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr16:61687935G>A ENST00000577390.1 - 12 2931 c.1977C>T c.(1975-1977)gaC>gaT p.D659D CDH8_ENST00000299345.6_Silent_p.D659D|CDH8_ENST00000577730.1_Silent_p.D659D NM_001796.4 NP_001787.2 P55286 CADH8_HUMAN cadherin 8, type 2 659 adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4) 112 Ovarian(137;0.0799)|Melanoma(118;0.16) UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249) TTTCTCGAACGTCTTCATCAT 0.393000 8 122 0 0 0.335167 0 0 KCNMA1 3778 broad.mit.edu 37 10 79011015 79011015 + Splice_Site SNP C C T TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr10:79011015C>T ENST00000286627.5 - 3 1493 c.e3-1 KCNMA1_ENST00000372443.1_Splice_Site|KCNMA1_ENST00000404857.1_Splice_Site|KCNMA1_ENST00000354353.5_Splice_Site|KCNMA1_ENST00000406533.3_Splice_Site|KCNMA1_ENST00000372440.1_Splice_Site|KCNMA1_ENST00000404771.3_Splice_Site|KCNMA1_ENST00000286628.8_Splice_Site NM_002247.3 NP_002238.2 Q12791 KCMA1_HUMAN potassium large conductance calcium-activated channel, subfamily M, alpha member 1 cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity p.?(2) breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2) 68 all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198) OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183) Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021) CTAAGACAACCTGTAAAAGAA 0.398000 OREG0020289 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 3 35 0 0 0.150653 0 0 AC016995.3 0 broad.mit.edu 37 2 38710017 38710019 + RNA DEL AAT AAT - rs2005502 by1000genomes TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr2:38710017_38710019delAAT ENST00000417039.1 - 0 696 TTCTTtaaaaaataaataaataa 0.246 2 4 --- --- --- --- C12orf71 728858 broad.mit.edu 37 12 27234923 27234923 + Frame_Shift_Del DEL C C - TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr12:27234923delC ENST00000429849.2 - 1 524 c.494delG c.(493-495)gcfs p.G165fs NM_001080406.1 NP_001073875.1 A8MTZ7 CL071_HUMAN chromosome 12 open reading frame 71 165 endometrium(2)|large_intestine(1)|lung(4)|skin(1) 8 CGGAGGGGAGCCGCTGGATAG 0.423 2 4 --- --- --- --- TRAV9-2 0 broad.mit.edu 37 14 22409532 22409540 + RNA DEL TCTCTCTCT TCTCTCTCT - rs57759840 TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr14:22409532_22409540delTCTCTCTCT ENST00000390441.2 + 0 102 tctctctctctctctctctTTTTTTTTTT 0.411 4 2 --- --- --- --- BACH1 571 broad.mit.edu 37 21 30699014 30699014 + Frame_Shift_Del DEL A A - TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr21:30699014delA ENST00000399921.1 + 3 1112 c.869delA c.(868-870)gafs p.E290fs BACH1_ENST00000286800.3_Frame_Shift_Del_p.E290fs NM_206866.1 NP_996749.1 O14867 BACH1_HUMAN BTB and CNC homology 1, basic leucine zipper transcription factor 1 290 nucleus protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2) 27 GAACCTGAAGAAACGAAGAAA 0.428 13 121 --- --- --- --- AC008103.5 0 broad.mit.edu 37 22 18842473 18842473 + RNA DEL G G - rs66618606 TCGA-EL-A3CO-01A-11D-A19J-08 TCGA-EL-A3CO-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx ba1f48c1-8d38-4a91-ba08-a8ecb63cac88 bc492b5b-036e-4452-ac96-4fa312ce29ef g.chr22:18842473delG ENST00000412938.1 + 0 2208 AGCTGCTGGTGGGGAGGTCTT 0.647 7 8 --- --- --- ---