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 ACRC 93953 broad.mit.edu 37 X 70824051 70824051 + Missense_Mutation SNP G G C TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chrX:70824051G>C ENST00000373695.1 + 7 1461 c.924G>C c.(922-924)aaG>aaC p.K308N ACRC_ENST00000373696.3_Missense_Mutation_p.K308N Q96QF7 ACRC_HUMAN acidic repeat containing 308 Asp/Ser-rich. nucleus autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1) 54 Renal(35;0.156) CCGACGACAAGAGTGATGATT 0.498000 4 231 0 0 1 0 0 FBXW7 0 broad.mit.edu 37 4 153247321 153247321 + Nonsense_Mutation SNP A A C TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr4:153247321A>C ENST00000281708.4 - 10 2710 c.1481T>G c.(1480-1482)tTa>tGa p.L494* FBXW7_ENST00000296555.5_Nonsense_Mutation_p.L376*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.L318*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.L494*|FBXW7_ENST00000603548.1_Nonsense_Mutation_p.L494*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.L414* NM_033632.3 NP_361014.1 Q969H0 FBXW7_HUMAN F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase 494 interspecies interaction between organisms|lipid homeostasis|negative regulation of DNA endoreduplication|negative regulation of hepatocyte proliferation|negative regulation of Notch signaling pathway|negative regulation of triglyceride biosynthetic process|positive regulation of epidermal growth factor receptor activity|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|protein ubiquitination|regulation of lipid storage|regulation of protein localization|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|sister chromatid cohesion|vasculature development nucleolus|nucleoplasm|SCF ubiquitin ligase complex protein binding p.?(1) NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6) 462 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067) CAAAACATGTAAACACTGGCC 0.433000 """Mis, N, D, F""" """colorectal, endometrial, T-ALL""" 24 78 0 0 1 0 0 SDC1 6382 broad.mit.edu 37 2 20402576 20402576 + Missense_Mutation SNP T T C TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr2:20402576T>C ENST00000381150.1 - 6 1274 c.884A>G c.(883-885)aAc>aGc p.N295S SDC1_ENST00000403076.1_Intron|SDC1_ENST00000482879.1_Intron|SDC1_ENST00000254351.4_Missense_Mutation_p.N295S NM_001006946.1 NP_001006947.1 P18827 SDC1_HUMAN syndecan 1 295 lipid metabolic process|lipoprotein metabolic process|myoblast development|striated muscle cell development cytoplasm|extracellular region|focal adhesion|integral to plasma membrane cytoskeletal protein binding|protein C-terminus binding NS(1)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(4)|skin(2) 21 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) OV - Ovarian serous cystadenocarcinoma(76;0.221) GGCCCCGCCGTTGGCTTGTTT 0.607000 39 101 0 0 1 0 0 NCOA6 23054 broad.mit.edu 37 20 33345756 33345756 + Silent SNP T T C TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr20:33345756T>C ENST00000374796.2 - 8 3365 c.795A>G c.(793-795)caA>caG p.Q265Q NCOA6_ENST00000359003.2_Silent_p.Q265Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 265 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q265Q(1) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gttgttgttgttgctgctgct 0.537000 3 50 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 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 14 43 0 0 1 0 0 NLGN4X 57502 broad.mit.edu 37 X 6069243 6069243 + Nonsense_Mutation SNP G G A TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chrX:6069243G>A ENST00000381095.3 - 2 892 c.265C>T c.(265-267)Cag>Tag p.Q89* NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000381093.2_Nonsense_Mutation_p.Q89*|NLGN4X_ENST00000381092.1_Nonsense_Mutation_p.Q89*|NLGN4X_ENST00000275857.6_Nonsense_Mutation_p.Q89*|NLGN4X_ENST00000538097.1_Nonsense_Mutation_p.Q89* NM_181332.1 NP_851849.1 Q8N0W4 NLGNX_HUMAN neuroligin 4, X-linked 89 brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior cell surface|dendrite|integral to plasma membrane|synapse chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1) 81 TCTGGGGGCTGAAACCGCCTC 0.582000 4 52 0 0 1 0 0 SLC26A9 115019 broad.mit.edu 37 1 205888065 205888065 + Missense_Mutation SNP C C T TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr1:205888065C>T ENST00000367135.3 - 19 2272 c.2159G>A c.(2158-2160)aGt>aAt p.S720N SLC26A9_ENST00000367134.2_Missense_Mutation_p.S720N|SLC26A9_ENST00000340781.4_Missense_Mutation_p.S720N NM_052934.3 NP_443166.1 Q7LBE3 S26A9_HUMAN solute carrier family 26 (anion exchanger), member 9 720 STAS. integral to membrane chloride channel activity|secondary active sulfate transmembrane transporter activity NS(1)|breast(3)|endometrium(11)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|skin(7)|urinary_tract(5) 52 Breast(84;0.201) BRCA - Breast invasive adenocarcinoma(75;0.0458) GCATTCTAGACTCCCATCCTC 0.493000 OREG0014164 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 7 269 0 0 1 0 0 KIF4B 285643 broad.mit.edu 37 5 154394835 154394835 + Silent SNP G G T TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr5:154394835G>T ENST00000435029.4 + 1 1576 c.1416G>T c.(1414-1416)ctG>ctT p.L472L NM_001099293.1 NP_001092763.1 Q2VIQ3 KIF4B_HUMAN kinesin family member 4B 472 axon guidance|blood coagulation|microtubule-based movement cytosol|microtubule|nuclear matrix ATP binding|DNA binding|microtubule motor activity breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1) 58 Renal(175;0.00488) Medulloblastoma(196;0.0523) KIRC - Kidney renal clear cell carcinoma(527;0.00112) TGCAGCAACTGATTACCCAGT 0.448000 16 58 9.16793e-09 1.03139e-08 1 1 0 FAM46D 169966 broad.mit.edu 37 X 79698776 79698776 + Silent SNP C C A TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chrX:79698776C>A ENST00000538312.1 + 5 1072 c.738C>A c.(736-738)ggC>ggA p.G246G FAM46D_ENST00000308293.5_Silent_p.G246G NM_001170574.1 NP_001164045.1 Q8NEK8 FA46D_HUMAN family with sequence similarity 46, member D 246 kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1) 23 TGGTTCATGGCTTCAAGCCAG 0.398000 14 32 1.5842e-08 1.67739e-08 1 1 0 GLRA3 8001 broad.mit.edu 37 4 175564959 175564959 + Missense_Mutation SNP T T A TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr4:175564959T>A ENST00000274093.3 - 10 1875 c.1373A>T c.(1372-1374)gAt>gTt p.D458V GLRA3_ENST00000340217.5_Missense_Mutation_p.D443V NM_006529.2 NP_006520.2 O75311 GLRA3_HUMAN glycine receptor, alpha 3 458 synaptic transmission cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1) 35 Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107) all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421) Glycine(DB00145) CTGATGAATATCCTCATGCCT 0.388000 5 85 0 0 1 0 0 MKNK2 2872 broad.mit.edu 37 19 2039729 2039729 + Silent SNP G G T TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr19:2039729G>T ENST00000250896.3 - 14 1525 c.1281C>A c.(1279-1281)gtC>gtA p.V427V MKNK2_ENST00000309340.7_Intron|MKNK2_ENST00000541165.1_Silent_p.V296V|MKNK2_ENST00000591601.1_Silent_p.V427V|MKNK2_ENST00000591142.1_Intron NM_199054.2 NP_951009.1 Q9HBH9 MKNK2_HUMAN MAP kinase interacting serine/threonine kinase 2 427 cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation ATP binding|metal ion binding|protein serine/threonine kinase activity breast(1)|kidney(3)|large_intestine(3)|lung(3) 10 Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) AGGTAGCTCGGACCAGGACGG 0.706000 9 21 0.000274275 0.000274275 1 1 0 ZAN 7455 broad.mit.edu 37 7 100350361 100350361 + RNA SNP T T C TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr7:100350361T>C ENST00000542585.1 + 0 2781 ZAN_ENST00000349350.6_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546213.1_RNA NM_003386.1 NP_003377.1 Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) binding of sperm to zona pellucida|cell-cell adhesion integral to membrane|plasma membrane NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) ACGGAAAAACTCACCATCCCC 0.502000 7 151 0 0 1 0 0 GBAP1 0 broad.mit.edu 37 1 155186821 155186821 + RNA SNP C C T TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr1:155186821C>T ENST00000486869.1 - 0 483 NR_002188.2 TCAGGGGTATCTAGAGACAAA 0.592000 3 6 0 0 1 0 0 MACF1 23499 broad.mit.edu 37 1 39799059 39799060 + Frame_Shift_Ins INS - - G TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr1:39799059_39799060insG ENST00000564288.1 + 37 7576_7577 c.6799_6800insG c.(6799-6801)ggafs p.G2267fs MACF1_ENST00000372915.3_Frame_Shift_Ins_p.G2272fs|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Frame_Shift_Ins_p.G707fs|MACF1_ENST00000567887.1_Frame_Shift_Ins_p.G2304fs Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 2272 cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing Golgi apparatus|microtubule|ruffle membrane actin filament binding|ATPase activity|calcium ion binding|microtubule binding breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10) 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) AGATAGTGGCAGGGAAATTTTT 0.391 19 73 --- --- --- --- SEC22B 9554 broad.mit.edu 37 1 145109312 145109313 + RNA INS - - A rs148903206 TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr1:145109312_145109313insA ENST00000453618.1 + 0 512 O75396 SC22B_HUMAN SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene) ER to Golgi vesicle-mediated transport|protein transport endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane|melanosome protein binding aaaccaaaaacaaaAAAAAAAG 0.416 3 3 --- --- --- --- NELFA 7469 broad.mit.edu 37 4 1986563 1986563 + Frame_Shift_Del DEL G G - TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr4:1986563delG ENST00000382882.3 - 8 2158 c.1041delC c.(1039-1041)tcfs p.S347fs NELFA_ENST00000411638.1_Frame_Shift_Del_p.S336fs|NELFA_ENST00000542778.1_Frame_Shift_Del_p.S201fs NM_005663.4 NP_005654.3 negative elongation factor complex member A TGGGGATGTAGGAGGAGGCGG 0.642 2 4 --- --- --- --- RP11-297P16.3 0 broad.mit.edu 37 4 104493406 104493406 + RNA DEL A A - TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr4:104493406delA ENST00000502936.1 + 0 189 RP11-297P16.3_ENST00000512401.1_RNA ATTCTACCATAAAGACAGTTT 0.438 2 4 --- --- --- --- CCDC129 223075 broad.mit.edu 37 7 31592800 31592800 + Splice_Site DEL G G - TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr7:31592800delG ENST00000319386.3 + 2 1155 c.163_splice c.e2+1 p.L54_splice CCDC129_ENST00000407970.3_Splice_Site_p.L54_splice|CCDC129_ENST00000482748.1_Intron|CCDC129_ENST00000451887.2_Splice_Site_p.L80_splice Q6ZRS4 CC129_HUMAN coiled-coil domain containing 129 54 p.L54L(2) cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31) 44 TCCCCATGCTGGGTGAGAAGG 0.552 2 4 --- --- --- --- FOXE1 2304 broad.mit.edu 37 9 100616701 100616706 + In_Frame_Del DEL GCCGCC GCCGCC - rs11279082 TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr9:100616701_100616706delGCCGCC ENST00000375123.3 + 1 1166_1171 c.505_510delGCCGCC c.(505-510)del p.AA177del NM_004473.3 NP_004464.2 O00358 FOXE1_HUMAN forkhead box E1 (thyroid transcription factor 2) 177 Ala-rich.|Poly-Ala. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1) 5 Acute lymphoblastic leukemia(62;0.158) Ggctgccgcagccgccgccgccgccg 0.767 7 15 --- --- --- --- KRTAP5-5 439915 broad.mit.edu 37 11 1651199 1651200 + In_Frame_Ins INS - - GGCTGTGGCTCC rs71025763 TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr11:1651199_1651200insGGCTGTGGCTCC ENST00000399676.2 + 1 167_168 c.129_130insGGCTGTGGCTCC c.(127-132)gggctg>ggGGCTGTGGCTCCgctg p.43_44GL>GAVAPL NM_001001480.2 NP_001001480.2 Q701N2 KRA55_HUMAN keratin associated protein 5-5 43 G -> GGCGS (in Ref. 1; BAD20201 and 2; CAF31639). keratin filament endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1) 33 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082) ccggctgtggaggctgtggggg 0.713 15 69 --- --- --- --- EP400 57634 broad.mit.edu 37 12 132547093 132547094 + In_Frame_Ins INS - - CAG rs113304321 by1000genomes TCGA-E8-A434-01A-11D-A23M-08 TCGA-E8-A434-10A-01D-A23K-08 Untested Somatic Phase_I WXS none Illumina GAIIx f3e7e827-91b5-4aa7-ae53-c2e5a8026386 8e990c86-db84-4b6e-9b12-40a7dcf45912 g.chr12:132547093_132547094insCAG ENST00000333577.4 + 48 8398_8399 c.8289_8290insCAG c.(8287-8292)caagca>caCAGagca p.2763_2763Q>HR EP400_ENST00000332482.4_In_Frame_Ins_p.2690_2690Q>HR|EP400_ENST00000330386.6_In_Frame_Ins_p.2646_2646Q>HR|EP400_ENST00000389562.2_In_Frame_Ins_p.2726_2726Q>HR|EP400_ENST00000389561.2_In_Frame_Ins_p.2727_2727Q>HR Q96L91 EP400_HUMAN E1A binding protein p400 2763 Interaction with ZNF42 (By similarity).|Poly-Gln. histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity p.Q2726Q(9) NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 161 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) agcagcaacaacagcagcagca 0.564 20 39 --- --- --- ---