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 PCDHGB3 0 broad.mit.edu 37 5 140750149 140750149 + Missense_Mutation SNP C C T TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr5:140750149C>T ENST00000576222.1 + 1 319 c.188C>T c.(187-189)aCt>aTt p.T63I PCDHGA3_ENST00000253812.6_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron NM_018924.2|NM_032097.1 NP_061747.1|NP_115268.1 endometrium(1)|kidney(1)|lung(3) 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GATTTACCTACTAGGAACCTG 0.547000 49 130 0 0 1 0 0 PRDM13 59336 broad.mit.edu 37 6 100061166 100061166 + Missense_Mutation SNP C C A TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr6:100061166C>A ENST00000369214.1 + 4 946 c.685C>A c.(685-687)Cag>Aag p.Q229K PRDM13_ENST00000369215.4_Missense_Mutation_p.Q219K NM_021620.3 NP_067633.2 Q9H4Q3 PRD13_HUMAN PR domain containing 13 219 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(9)|prostate(1) 17 all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186) BRCA - Breast invasive adenocarcinoma(108;0.0598) GCCACCAGTTCAGGCCTGCGG 0.711000 2 2 0.0784 0.0784 1 1 0 ASTN2 23245 broad.mit.edu 37 9 119976991 119976991 + Missense_Mutation SNP G G C TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr9:119976991G>C ENST00000313400.4 - 3 761 c.661C>G c.(661-663)Ctg>Gtg p.L221V ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.L221V|ASTN2_ENST00000373996.3_Missense_Mutation_p.L221V O75129 ASTN2_HUMAN astrotactin 2 221 integral to membrane breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1) 102 GTGAACACCAGCAGCAGCAGC 0.602000 3 35 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd 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 22 53 0 0 1 0 0 AC008103.5 0 broad.mit.edu 37 22 18844888 18844888 + RNA SNP A A G TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr22:18844888A>G ENST00000412938.1 + 0 3138 GCTCACGGAAATACAGCTTCA 0.587000 4 41 0 0 1 0 0 PKHD1 5314 broad.mit.edu 37 6 51900392 51900392 + Silent SNP G G A TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr6:51900392G>A ENST00000371117.3 - 28 3500 c.3225C>T c.(3223-3225)ccC>ccT p.P1075P PKHD1_ENST00000340994.4_Silent_p.P1075P NM_138694.3 NP_619639.3 P08F94 PKHD1_HUMAN polycystic kidney and hepatic disease 1 (autosomal recessive) 1075 IPT/TIG 5. cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body protein binding|receptor activity NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5) 304 Lung NSC(77;0.0605) CACTTACCCTGGGTGGAACTT 0.393000 4 138 0 0 1 0 0 TAS2R7 50837 broad.mit.edu 37 12 10954956 10954956 + Missense_Mutation SNP A A G TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr12:10954956A>G ENST00000240687.2 - 1 270 c.214T>C c.(214-216)Tat>Cat p.Y72H NM_023919.2 NP_076408.1 Q9NYW3 TA2R7_HUMAN taste receptor, type 2, member 7 72 sensory perception of taste integral to membrane taste receptor activity kidney(1)|large_intestine(1)|lung(3)|skin(2)|stomach(3) 10 ACATCTGGATATAGCACCAAT 0.373000 28 51 0 0 1 0 0 WASH3P 0 broad.mit.edu 37 15 102515299 102515299 + RNA SNP G G A TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr15:102515299G>A ENST00000557932.1 + 0 1145 p.G374S(10) central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1) 25 TGGGGGCATCGGCAAGGCCAA 0.652000 3 23 0 0 1 0 0 RP11-206L10.2 0 broad.mit.edu 37 1 700514 700514 + RNA DEL A A - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr1:700514delA ENST00000428504.1 - 0 1039 NR_033908.1 actccatctcaaaaaaaaaaa 0.453 2 4 --- --- --- --- AC074391.1 0 broad.mit.edu 37 2 65738862 65738863 + RNA DEL TG TG - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr2:65738862_65738863delTG ENST00000377977.3 + 0 862 TTTTTTTTTTTGTCCAGGAGGC 0.302 2 4 --- --- --- --- FAM157A 0 broad.mit.edu 37 3 197880131 197880133 + RNA DEL GCA GCA - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr3:197880131_197880133delGCA ENST00000437428.2 + 0 11_13 C9JC47 F157A_HUMAN NS(1)|skin(1) 2 ACAAGAACTGgcagcagcagcag 0.537 2 4 --- --- --- --- GTF2H2B 0 broad.mit.edu 37 5 69730714 69730715 + RNA INS - - T TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr5:69730714_69730715insT ENST00000513202.1 + 0 753 NR_033417.1 CTATGAAGGTGTTTTTTTTTCC 0.322 7 83 --- --- --- --- CACNA2D1 781 broad.mit.edu 37 7 81630992 81630992 + Frame_Shift_Del DEL T T - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr7:81630992delT ENST00000356253.5 - 19 1885 c.1630delA c.(1630-1632)ggfs p.R545fs CACNA2D1_ENST00000356860.3_Intron P54289 CA2D1_HUMAN calcium channel, voltage-dependent, alpha 2/delta subunit 1 545 Cache. voltage-gated calcium channel complex metal ion binding breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 81 Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115) TTGGGTCTCCTTTTTCTTAAA 0.358 2 4 --- --- --- --- LMX1B 4010 broad.mit.edu 37 9 129456049 129456051 + In_Frame_Del DEL CAG CAG - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr9:129456049_129456051delCAG ENST00000355497.5 + 6 851_853 c.844_846delCAG c.(844-846)del p.Q285del LMX1B_ENST00000526117.1_In_Frame_Del_p.Q285del|LMX1B_ENST00000373474.4_In_Frame_Del_p.Q285del|LMX1B_ENST00000425646.2_In_Frame_Del_p.Q262del|LMX1B_ENST00000561065.1_In_Frame_Del_p.Q262del NM_001174146.1 NP_001167617.1 O60663 LMX1B_HUMAN LIM homeobox transcription factor 1, beta 262 dorsal/ventral pattern formation|in utero embryonic development nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding endometrium(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1) 15 GCGGCGGCACCAGCAGCAGCAGG 0.754 Nail-Patella Syndrome 2 4 --- --- --- --- TYSND1 219743 broad.mit.edu 37 10 71905929 71905931 + In_Frame_Del DEL CAG CAG - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr10:71905929_71905931delCAG ENST00000287078.6 - 1 411_413 c.412_414delCTG c.(412-414)del p.L138del TYSND1_ENST00000335494.5_In_Frame_Del_p.L138del NM_173555.2 NP_775826.2 Q2T9J0 TYSD1_HUMAN trypsin domain containing 1 138 proteolysis peroxisome serine-type endopeptidase activity endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1) 9 CCGGGCAGCTCAGCAGCAGCAGC 0.739 2 4 --- --- --- --- DNM1P47 0 broad.mit.edu 37 15 102292874 102292876 + RNA DEL CTC CTC - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr15:102292874_102292876delCTC ENST00000561463.1 + 0 920_922 AGTTCATCTTCTCAGAGCTGCTG 0.581 4 4 --- --- --- --- CDK12 51755 broad.mit.edu 37 17 37686901 37686901 + Frame_Shift_Del DEL C C - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr17:37686901delC ENST00000447079.4 + 14 3838 c.3805delC c.(3805-3807)ccfs p.P1270fs CDK12_ENST00000430627.2_Frame_Shift_Del_p.P1261fs NM_015083.1|NM_016507.2 NP_055898.1|NP_057591.2 Q9NYV4 CDK12_HUMAN cyclin-dependent kinase 12 1270 Poly-Pro. mRNA processing|phosphorylation of RNA polymerase II C-terminal domain|protein autophosphorylation|regulation of MAP kinase activity|RNA splicing nuclear cyclin-dependent protein kinase holoenzyme complex|nuclear speck|nucleolus ATP binding|cyclin-dependent protein kinase activity|protein binding|RNA polymerase II carboxy-terminal domain kinase activity NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3) 70 GCCCCCTGAGCCCCCCGGACC 0.562 """Mis, N, F""" serous ovarian TCGA Ovarian(9;0.13) 9 401 --- --- --- --- CBR3-AS1 0 broad.mit.edu 37 21 37518894 37518894 + RNA DEL T T - TCGA-FE-A3PB-01A-11D-A21Z-08 TCGA-FE-A3PB-10A-01D-A21Z-08 Untested Somatic Phase_I WXS none Illumina GAIIx a7c8abdf-02bc-455f-9e43-f49227b349b2 60e3b235-1934-460a-b420-b02c1f4a3acd g.chr21:37518894delT ENST00000413862.1 - 0 79 CBR3-AS1_ENST00000427491.1_RNA|CBR3-AS1_ENST00000453159.1_RNA NR_038892.1 atttctgttcttttttttttt 0.448 2 4 --- --- --- ---