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 SETD5 55209 broad.mit.edu 37 3 9482327 9482327 + Missense_Mutation SNP C C T TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr3:9482327C>T ENST00000402466.1 + 9 1229 c.461C>T c.(460-462)aCt>aTt p.T154I SETD5_ENST00000407969.1_Missense_Mutation_p.T271I|SETD5_ENST00000406341.1_Missense_Mutation_p.T252I|SETD5_ENST00000302463.6_Missense_Mutation_p.T154I|SETD5_ENST00000402198.1_Missense_Mutation_p.T252I Q9C0A6 SETD5_HUMAN SET domain containing 5 252 NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 Medulloblastoma(99;0.227) OV - Ovarian serous cystadenocarcinoma(96;0.112) ATTTTAGACACTATTAATAAG 0.393000 5 13 0 0 1 0 0 NRROS 375387 broad.mit.edu 37 3 196387348 196387348 + Silent SNP G G C TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr3:196387348G>C ENST00000328557.4 + 3 1037 c.834G>C c.(832-834)ctG>ctC p.L278L NM_198565.1 NP_940967.1 negative regulator of reactive oxygen species GGACCCTCCTGCTGCGCGACA 0.627000 34 92 0 0 1 0 0 GPC6 10082 broad.mit.edu 37 13 94482634 94482634 + Missense_Mutation SNP A A C TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr13:94482634A>C ENST00000377047.4 + 3 1162 c.547A>C c.(547-549)Agt>Cgt p.S183R GPC6-AS2_ENST00000445540.1_RNA NM_005708.3 NP_005699.1 Q9Y625 GPC6_HUMAN glypican 6 183 anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix heparan sulfate proteoglycan binding NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1) 38 all_neural(89;0.0684)|Medulloblastoma(90;0.163) all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217) GTATCACTTCAGTGAAGACTA 0.493000 6 45 0 0 1 0 0 LCE1C 353133 broad.mit.edu 37 1 152777911 152777911 + Missense_Mutation SNP T T A TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr1:152777911T>A ENST00000368768.1 - 2 94 c.44A>T c.(43-45)aAg>aTg p.K15M LCE1C_ENST00000607093.1_Missense_Mutation_p.K15M NM_178351.3 NP_848128.1 Q5T751 LCE1C_HUMAN late cornified envelope 1C 15 Pro-rich. keratinization NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1) 9 Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) gggggtgcacttgggagggGG 0.607000 9 20 0 0 1 0 0 BCKDK 10295 broad.mit.edu 37 16 31122082 31122082 + Splice_Site SNP G G T TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr16:31122082G>T ENST00000394951.1 + 9 1339 c.716_splice c.e9+1 p.R239_splice BCKDK_ENST00000287507.3_Splice_Site_p.R239_splice|BCKDK_ENST00000219794.6_Splice_Site_p.R239_splice|BCKDK_ENST00000394950.3_Splice_Site_p.R239_splice O14874 BCKD_HUMAN branched chain ketoacid dehydrogenase kinase 239 Histidine kinase. branched chain family amino acid catabolic process|peptidyl-histidine phosphorylation mitochondrial alpha-ketoglutarate dehydrogenase complex [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity|ATP binding|protein binding|protein serine/threonine kinase activity|two-component sensor activity breast(1)|stomach(1) 2 GACTTTGCCAGGTGAGGCAAG 0.577000 40 57 9.88483e-10 1.08262e-09 1 1 0 HMCN1 83872 broad.mit.edu 37 1 186052052 186052052 + Missense_Mutation SNP C C A TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr1:186052052C>A ENST00000271588.4 + 57 9072 c.8843C>A c.(8842-8844)aCa>aAa p.T2948K HMCN1_ENST00000367492.2_Missense_Mutation_p.T2948K NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 2948 Ig-like C2-type 27. response to stimulus|visual perception basement membrane calcium ion binding NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18) 308 GCTGAGAACACAGCTGGGAGT 0.353000 9 20 3.09899e-07 3.23985e-07 1 1 0 ARCN1 372 broad.mit.edu 37 11 118455289 118455289 + Missense_Mutation SNP A A G TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr11:118455289A>G ENST00000359415.4 + 6 1036 c.871A>G c.(871-873)Atg>Gtg p.M291V ARCN1_ENST00000392859.3_Missense_Mutation_p.M162V|ARCN1_ENST00000264028.4_Missense_Mutation_p.M250V|ARCN1_ENST00000534182.2_Intron P48444 COPD_HUMAN archain 1 250 MHD. COPI coating of Golgi vesicle|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER clathrin adaptor complex|COPI vesicle coat|cytosol endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1) 13 all_hematologic(175;0.0349) Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;3.28e-05) TGAAACCATCATGTCCTCTAG 0.413000 25 40 0 0 1 0 0 TTN 7273 broad.mit.edu 37 2 179534367 179534367 + Missense_Mutation SNP T T C TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr2:179534367T>C ENST00000589042.1 - 158 35646 c.35422A>G c.(35422-35424)Aaa>Gaa p.K11808E TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000591111.1_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin 9930 Glu-rich.|Pro-rich. ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCACGAACTTTTTCTTCTGGG 0.343000 54 121 0 0 1 0 0 LRRC37A16P 0 broad.mit.edu 37 17 66126552 66126552 + RNA SNP G G A rs74196682 by1000genomes TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr17:66126552G>A ENST00000590019.1 - 0 298 CACAGGGCTGGGCAGAAAGGT 0.488000 3 35 0 0 1 0 0 UGT1A3 0 broad.mit.edu 37 2 234638599 234638599 + Missense_Mutation SNP T T C TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr2:234638599T>C ENST00000482026.1 + 1 846 c.827T>C c.(826-828)aTt>aCt p.I276T UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A8_ENST00000373450.4_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron NM_019093.2 NP_061966.1 breast(2)|endometrium(7)|kidney(18)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|urinary_tract(1) 46 Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128) Epithelial(121;2.4e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000476)|Lung(119;0.00243)|LUSC - Lung squamous cell carcinoma(224;0.00599) ATGGTCTTCATTGGGGGCATC 0.473000 7 142 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr7:140453136A>T ENST00000288602.6 - 15 1859 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN v-raf murine sarcoma viral oncogene homolog B 600 Protein kinase. V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3) 27380 Melanoma(164;0.00956) Sorafenib(DB00398) TCGAGATTTCACTGTAGCTAG 0.368000 V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN) 61 """Mis, T, O""" """AKAP9, KIAA1549""" """melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma""" Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome 25 45 0 0 1 0 0 SSX1 6756 broad.mit.edu 37 X 48118021 48118021 + Missense_Mutation SNP T T A TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chrX:48118021T>A ENST00000376919.3 + 4 371 c.235T>A c.(235-237)Ttc>Atc p.F79I NM_001278691.1|NM_005635.2 NP_001265620.1|NP_005626.1 Q16384 SSX1_HUMAN synovial sarcoma, X breakpoint 1 79 KRAB-related. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding|transcription corepressor activity SS18/SSX1(1169)|SS18L1/SSX1(2) endometrium(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1) 9 GGCCACAGACTTCCAGGGGAA 0.453000 T SS18 synovial sarcoma 62 94 0 0 1 0 0 ASTE1 28990 broad.mit.edu 37 3 130733047 130733047 + Frame_Shift_Del DEL T T - TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr3:130733047delT ENST00000264992.3 - 6 2335 c.1894delA c.(1894-1896)ggfs p.R632fs ASTE1_ENST00000514044.1_Frame_Shift_Del_p.R657fs|ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000507488.2_Intron|ATP2C1_ENST00000504381.1_Intron|ATP2C1_ENST00000422190.2_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000359644.3_Intron|ATP2C1_ENST00000328560.8_Intron NM_014065.2 NP_054784.2 Q2TB18 ASTE1_HUMAN asteroid homolog 1 (Drosophila) 632 DNA repair nuclease activity p.R632fs*33(2) endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1) 22 TTCTTCTGCCTTTTTTTTTTT 0.403 7 55 --- --- --- --- NELL2 4753 broad.mit.edu 37 12 45269298 45269298 + Frame_Shift_Del DEL A A - TCGA-EL-A4K0-01A-11D-A257-08 TCGA-EL-A4K0-11A-11D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx 220d117b-cc76-4c53-8f51-5eee3409a703 939a3085-5656-44fb-a757-67e40ab49b32 g.chr12:45269298delA ENST00000395487.2 - 1 139 c.44delT c.(43-45)cgfs p.L15fs NELL2_ENST00000333837.4_Intron|NELL2_ENST00000549027.1_Frame_Shift_Del_p.L15fs|NELL2_ENST00000437801.2_Intron|NELL2_ENST00000452445.2_Intron|NELL2_ENST00000429094.2_Intron|NELL2_ENST00000551601.1_Frame_Shift_Del_p.L15fs|NELL2_ENST00000548826.1_Intron NM_001145109.1 NP_001138581.1 Q99435 NELL2_HUMAN NEL-like 2 (chicken) 0 cell adhesion extracellular region calcium ion binding|protein binding|structural molecule activity NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 65 Lung SC(27;0.192) Lung NSC(34;0.144) GBM - Glioblastoma multiforme(48;0.092) ACCTGAGATCAGCAGCCAAGC 0.557 6 13 --- --- --- ---