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 RCVRN 5957 broad.mit.edu 37 17 9801501 9801501 + Missense_Mutation SNP A A G TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr17:9801501A>G uc002gme.1 - 2 701 c.514T>C c.(514-516)Ttc>Ctc p.F172L NM_002903 NP_002894 P35243 RECO_HUMAN Homo sapiens recoverin (RCVRN), mRNA. 172 EF-hand 4. visual perception calcium ion binding|calcium sensitive guanylate cyclase activator activity endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1) 12 CCCTCAATGAATTCTTTCTCT 0.413000 46 99 0 0 1 0 0 GLA 2717 broad.mit.edu 37 X 100658838 100658838 + Silent SNP A A C TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chrX:100658838A>C uc004ehl.1 - 1 440 c.330T>G c.(328-330)ccT>ccG p.P110P RPL36A-HNRNPH2_uc022cag.1_Intron|RPL36A-HNRNPH2_uc022cah.1_Intron|GLA_uc011mrj.1_Silent_p.P110P NM_000169 NP_000160 P06280 AGAL_HUMAN Homo sapiens galactosidase, alpha (GLA), mRNA. 110 glycoside catabolic process|glycosphingolipid catabolic process|glycosylceramide catabolic process|negative regulation of nitric oxide biosynthetic process|negative regulation of nitric-oxide synthase activity|oligosaccharide metabolic process Golgi apparatus|extracellular region|lysosome cation binding|protein homodimerization activity|raffinose alpha-galactosidase activity|receptor binding endometrium(1)|kidney(1)|large_intestine(4)|lung(8) 14 Agalsidase beta(DB00103) GAAAGCGCTGAGGGTCTGCCT 0.463000 8 94 0 0 1 0 0 MAPKBP1 23005 broad.mit.edu 37 15 42114280 42114280 + Silent SNP C C T TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr15:42114280C>T uc001zok.4 + 25 3307 c.3021C>T c.(3019-3021)tgC>tgT p.C1007C MAPKBP1_uc010bci.3_Silent_p.C1001C|MAPKBP1_uc010udb.2_Silent_p.C840C|MAPKBP1_uc001zoj.4_Silent_p.C1001C|MAPKBP1_uc010bcj.3_Silent_p.C508C|MAPKBP1_uc010bck.3_Silent_p.C218C|MAPKBP1_uc010bcl.3_Silent_p.C508C NM_001128608 NP_001122080 O60336 MABP1_HUMAN Homo sapiens mitogen-activated protein kinase binding protein 1 (MAPKBP1), transcript variant 2, mRNA. 1007 breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1) 56 all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262) OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225) GCAGCAGCTGCCTTTCCAGCC 0.647000 6 10 0 0 1 0 0 NSD1 64324 broad.mit.edu 37 5 176673763 176673763 + Missense_Mutation SNP A A G TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr5:176673763A>G uc003mfr.4 + 9 4601 c.4463A>G c.(4462-4464)aAt>aGt p.N1488S NSD1_uc003mft.4_Missense_Mutation_p.N1219S|NSD1_uc003mfs.1_Missense_Mutation_p.N1385S|NSD1_uc011dfx.2_Missense_Mutation_p.N1136S NM_022455 NP_071900 Q96L73 NSD1_HUMAN Homo sapiens nuclear receptor binding SET domain protein 1 (NSD1), transcript variant 2, mRNA. 1488 negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3) 96 all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002) all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198) Kidney(146;0.235) AAAGTGAAAAATGATGACTCG 0.428000 T NUP98 AML Sotos Syndrome Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome HNSCC(47;0.14) 16 27 0 0 1 0 0 CSF2RA 1438 broad.mit.edu 37 X 1428413 1428413 + Silent SNP C C T TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chrX:1428413C>T uc004cpp.2 + 10 1259 c.1065C>T c.(1063-1065)tcC>tcT p.S355S CRLF2_uc022brt.1_Intron|CSF2RA_uc010nct.2_3'UTR|CSF2RA_uc004cpq.2_3'UTR|CSF2RA_uc004cpn.2_3'UTR|CSF2RA_uc004cpo.2_3'UTR|CSF2RA_uc010ncu.2_Non-coding_Transcript|CSF2RA_uc011mhc.1_3'UTR|CSF2RA_uc010ncv.2_3'UTR|CSF2RA_uc004cpr.2_3'UTR NM_172246 NP_758449 P15509 CSF2R_HUMAN Homo sapiens colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) (CSF2RA), transcript variant 3, mRNA. 0 extracellular region|integral to plasma membrane cytokine receptor activity central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 45 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) Sargramostim(DB00020) TCTCCGCCTCCGCGACACGGG 0.498000 9 152 0 0 1 0 0 PADI6 353238 broad.mit.edu 37 1 17720532 17720532 + Missense_Mutation SNP C C T TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr1:17720532C>T uc001bak.1 + 10 1136 c.1136C>T c.(1135-1137)aCa>aTa p.T379I NM_207421 NP_997304 Q6TGC4 PADI6_HUMAN Homo sapiens peptidyl arginine deiminase, type VI (PADI6), mRNA. 371 peptidyl-citrulline biosynthetic process from peptidyl-arginine cytoplasm|nucleus calcium ion binding|protein-arginine deiminase activity breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2) 29 Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189) L-Citrulline(DB00155) ATCCTCGACACACCTCAGGCC 0.542000 6 29 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr7:140453136A>T uc003vwc.4 - 14 1860 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333 NP_004324 P15056 BRAF_HUMAN Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA. 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(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(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 23 38 0 0 1 0 0 TSPYL1 7259 broad.mit.edu 37 6 116600261 116600261 + Nonsense_Mutation SNP G G A TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr6:116600261G>A uc003pwp.4 - 0 1020 c.733C>T c.(733-735)Cag>Tag p.Q245* DSE_uc011ebf.1_Intron|DSE_uc003pwq.1_5'Flank|DSE_uc003pwr.3_5'Flank|DSE_uc003pws.3_5'Flank NM_003309 NP_003300 Q9H0U9 TSYL1_HUMAN Homo sapiens TSPY-like 1 (TSPYL1), mRNA. 245 nucleosome assembly nucleolus breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1) 11 all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234) all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094) CTGTCGGCCTGAGCATTCACA 0.597000 20 36 0 0 1 0 0 APC 324 broad.mit.edu 37 5 112176431 112176431 + Missense_Mutation SNP G G T rs148275069 TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr5:112176431G>T uc003kpz.4 + 16 5333 c.5140G>T c.(5140-5142)Gat>Tat p.D1714Y APC_uc011cvt.2_Missense_Mutation_p.D1696Y|APC_uc003kpy.4_Missense_Mutation_p.D1714Y|APC_uc010jbz.3_Missense_Mutation_p.D1431Y|APC_uc010jca.3_Missense_Mutation_p.D1014Y NM_001127510 NP_001120982 P25054 APC_HUMAN Homo sapiens adenomatous polyposis coli (APC), transcript variant 2, mRNA. 1714 Ser-rich. canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|adherens junction|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity p.K1192fs*3(1)|p.?(1) NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20) 3261 all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133) OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191) ACCTGAATTGGATGACAATAA 0.403000 12 """D, Mis, N, F, S""" """colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS""" """colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS""" Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis TSP Lung(16;0.13) 10 28 0 0 1 0 0 OR10X1 128367 broad.mit.edu 37 1 158548923 158548923 + Missense_Mutation SNP G G T TCGA-DJ-A4UW-01A-11D-A257-08 TCGA-DJ-A4UW-10A-01D-A25A-08 Untested Somatic Phase_I WXS none Illumina GAIIx f9efac75-394f-40a0-91bf-70bd024facda a4ec77c8-d042-493a-9975-a87d25a8a93d g.chr1:158548923G>T uc010pin.2 - 0 767 c.767C>A c.(766-768)aCc>aAc p.T256N NM_001004477 NP_001004477 Q8NGY0 O10X1_HUMAN Homo sapiens olfactory receptor, family 10, subfamily X, member 1 (OR10X1), mRNA. 256 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.T256S(2) breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1) 37 all_hematologic(112;0.0378) GGAGGCACAGGTGGTGAAGGC 0.483000 7 132 0 0 1 0 0