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 PTH2 113091 broad.mit.edu 37 19 49926533 49926533 + Missense_Mutation SNP G G C TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr19:49926533G>C ENST00000270631.1 - 1 165 c.64C>G c.(64-66)Ctg>Gtg p.L22V NM_178449.3 NP_848544.1 Q96A98 TIP39_HUMAN parathyroid hormone 2 22 neuropeptide signaling pathway extracellular region p.L22V(2) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836) GGCACCACcagcagcagcagc 0.692000 3 52 0 0 0.150653 0 0 SMARCA1 6594 broad.mit.edu 37 X 128649760 128649760 + Silent SNP C C G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chrX:128649760C>G ENST00000371122.4 - 5 663 c.534G>C c.(532-534)gtG>gtC p.V178V SMARCA1_ENST00000371123.1_Silent_p.V178V|SMARCA1_ENST00000371121.3_Silent_p.V178V|SMARCA1_ENST00000478420.1_5'UTR NM_003069.3 NP_003060.2 P28370 SMCA1_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 178 ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent NURF complex ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1) 45 GCCCCCCTTTCACATCTGGTG 0.343000 15 66 0 0 0.160694 0 0 ZNF92 168374 broad.mit.edu 37 7 64853813 64853813 + Splice_Site SNP A A G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr7:64853813A>G ENST00000328747.7 + 3 424 c.226_splice c.e3+1 p.P75_splice ZNF92_ENST00000357512.2_Intron|ZNF92_ENST00000431504.1_Intron|ZNF92_ENST00000450302.2_Splice_Site_p.P6_splice NM_152626.2 NP_689839.1 Q03936 ZNF92_HUMAN zinc finger protein 92 75 KRAB. nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1) 13 Lung NSC(55;0.159) ACAAAACCCCAGGTAGGTGAC 0.448000 3 73 0 0 0.115264 0 0 RP11-417J8.6 0 broad.mit.edu 37 1 142713773 142713773 + RNA SNP C C G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:142713773C>G ENST00000369381.2 - 0 832 TCTTTTTCCACATTGTCATTT 0.284000 4 27 0 0 0.150653 0 0 AHRR 57491 broad.mit.edu 37 5 353938 353938 + Silent SNP G G A rs150312721 by1000genomes TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr5:353938G>A ENST00000316418.5 + 3 212 c.168G>A c.(166-168)ccG>ccA p.P56P AHRR_ENST00000512529.1_Intron|AHRR_ENST00000515206.1_Silent_p.P52P|AHRR_ENST00000505113.1_Silent_p.P56P NM_020731.4 NP_065782.2 A9YTQ3 AHRR_HUMAN aryl-hydrocarbon receptor repressor 56 Helix-loop-helix motif. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|signal transducer activity breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1) 20 Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863) GCCTGCTGCCGTTCCCGCCTG 0.627000 4 117 0 0 0.150653 0 0 NAT10 55226 broad.mit.edu 37 11 34149080 34149080 + Missense_Mutation SNP T T C TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr11:34149080T>C ENST00000257829.3 + 12 1384 c.1178T>C c.(1177-1179)aTc>aCc p.I393T NAT10_ENST00000527971.1_Intron|NAT10_ENST00000531159.2_Missense_Mutation_p.I321T NM_024662.2 NP_078938.2 Q9H0A0 NAT10_HUMAN N-acetyltransferase 10 (GCN5-related) 393 nucleolus ATP binding|N-acetyltransferase activity|protein binding endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 23 Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231) GCTGCCGCCATCCCCCTCCCC 0.502000 4 177 0 0 0.014758 0 0 TUBB8P7 0 broad.mit.edu 37 16 90162620 90162620 + RNA SNP T T G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr16:90162620T>G ENST00000564451.1 + 0 1973 CTAGGTAAAGTGGGGAAGCAG 0.483000 5 179 0 0 0.029380 0 0 ZNF578 147660 broad.mit.edu 37 19 53014631 53014631 + Missense_Mutation SNP C C G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr19:53014631C>G ENST00000421239.2 + 6 1241 c.997C>G c.(997-999)Cat>Gat p.H333D CTD-3099C6.5_ENST00000599143.1_RNA NM_001099694.1 NP_001093164.1 Q96N58 ZN578_HUMAN zinc finger protein 578 108 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01) CCTTACATGCCATCATAGGTG 0.428000 20 94 0 0 0.055883 0 0 NUP214 8021 broad.mit.edu 37 9 134072930 134072930 + Missense_Mutation SNP A A G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr9:134072930A>G ENST00000359428.5 + 29 4193 c.4049A>G c.(4048-4050)aAt>aGt p.N1350S NUP214_ENST00000483497.2_Missense_Mutation_p.N176S|NUP214_ENST00000465486.2_3'UTR|NUP214_ENST00000451030.1_Missense_Mutation_p.N1351S|NUP214_ENST00000411637.2_Missense_Mutation_p.N1340S P35658 NU214_HUMAN nucleoporin 214kDa 1350 11 X 5 AA approximate repeats.|Pro/Ser/Thr-rich. carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore|nucleoplasm protein binding NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 86 all_hematologic(7;0.0028) Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256) AAACCAACCAATAAGGCTTCA 0.512000 T """DEK, SET, ABL1""" """AML, T-ALL""" 13 103 0 0 0.175082 0 0 TRPM4 54795 broad.mit.edu 37 19 49700047 49700047 + Missense_Mutation SNP A A G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr19:49700047A>G ENST00000252826.5 + 17 2687 c.2561A>G c.(2560-2562)cAg>cGg p.Q854R TRPM4_ENST00000355712.5_Missense_Mutation_p.Q500R|TRPM4_ENST00000427978.2_Intron NM_017636.3 NP_060106.2 Q8TD43 TRPM4_HUMAN transient receptor potential cation channel, subfamily M, member 4 854 dendritic cell chemotaxis|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell proliferation|protein sumoylation|regulation of T cell cytokine production endoplasmic reticulum|Golgi apparatus|integral to membrane|plasma membrane ATP binding|calcium activated cation channel activity|calmodulin binding breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 49 all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15) all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751) TCACTGAGCCAGCGCCTGCGC 0.726000 5 10 0 0 0.038147 0 0 BAGE2 85319 broad.mit.edu 37 21 11058349 11058349 + RNA SNP T T G rs209032 TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr21:11058349T>G ENST00000470054.1 - 0 324 B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) GAGAGAAATCTCTTTATAAAA 0.338000 12 94 0 0 0.105934 0 0 CASC3 22794 broad.mit.edu 37 17 38318284 38318284 + Silent SNP G G A TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr17:38318284G>A ENST00000264645.7 + 5 712 c.486G>A c.(484-486)gtG>gtA p.V162V NM_007359.4 NP_031385.2 O15234 CASC3_HUMAN cancer susceptibility candidate 3 162 Necessary for RNA-binding, interaction with MAGOH and localization in nucleus speckles.|Sufficient to form the EJC. mRNA processing|mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|response to stress|RNA splicing exon-exon junction complex|nuclear speck|perinuclear region of cytoplasm identical protein binding|RNA binding|ubiquitin protein ligase binding p.V162V(1) endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2) 16 AGAACAAAGTGGGTAAAAAGG 0.468000 7 40 0 0 0.038147 0 0 RP11-423O2.5 0 broad.mit.edu 37 1 142803493 142803493 + RNA SNP T T C rs80149641 by1000genomes TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:142803493T>C ENST00000423385.1 - 0 1472 TGTACATTTATTATTGATTTA 0.323000 7 58 0 0 0.038147 0 0 NUTM2F 54754 broad.mit.edu 37 9 97082748 97082748 + Missense_Mutation SNP G G C TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr9:97082748G>C ENST00000253262.4 - 5 1130 c.1110C>G c.(1108-1110)aaC>aaG p.N370K NUTM2F_ENST00000341207.4_Intron|NUTM2F_ENST00000335456.7_Intron NM_017561.1 NP_060031.1 NUT family member 2F GCAGGTGGGCGTTGGTCTCCG 0.692000 3 88 0 0 0.115264 0 0 HGFAC 3083 broad.mit.edu 37 4 3443797 3443797 + Silent SNP C C G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr4:3443797C>G ENST00000382774.3 + 1 184 c.69C>G c.(67-69)ctC>ctG p.L23L HGFAC_ENST00000511533.1_Silent_p.L23L NM_001528.2 NP_001519.1 Q04756 HGFA_HUMAN HGF activator 23 proteolysis extracellular space protein binding|serine-type endopeptidase activity central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2) 22 UCEC - Uterine corpus endometrioid carcinoma (64;0.163) TCCTCCTCCTCCTGCTGCTGC 0.716000 3 38 0 0 0.150653 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e 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 15 61 0 0 0.146539 0 0 FRG1B 0 broad.mit.edu 37 20 29625877 29625877 + Missense_Mutation SNP G G A rs7266938 by1000genomes TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr20:29625877G>A ENST00000278882.3 + 5 501 c.121G>A c.(121-123)Gcc>Acc p.A41T FRG1B_ENST00000439954.2_Missense_Mutation_p.A46T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A41T p.A41T(2) endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 GTACAGAATCGCCCTGAAATC 0.358000 3 50 0 0 0.150653 0 0 RP11-417J8.6 0 broad.mit.edu 37 1 142713774 142713774 + RNA SNP A A G TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:142713774A>G ENST00000369381.2 - 0 831 CTTTTTCCACATTGTCATTTT 0.284000 4 27 0 0 0.014758 0 0 DNAJC11 55735 broad.mit.edu 37 1 6727803 6727804 + Frame_Shift_Del DEL TC TC - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:6727803_6727804delTC ENST00000377577.5 - 4 466_467 c.343_344delGA c.(343-345)afs p.E116fs DNAJC11_ENST00000349363.6_Frame_Shift_Del_p.E78fs|DNAJC11_ENST00000377573.5_Frame_Shift_Del_p.E26fs|DNAJC11_ENST00000542246.1_Frame_Shift_Del_p.E78fs|DNAJC11_ENST00000294401.7_Frame_Shift_Del_p.E116fs NM_018198.3 NP_060668.2 Q9NVH1 DJC11_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 11 116 protein folding heat shock protein binding|unfolded protein binding NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1) 32 Ovarian(185;0.0265)|all_lung(157;0.154) all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156) Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649) TCTCCTCTCTTCTCTCTCTCTC 0.505 7 80 --- --- --- --- AADACL3 126767 broad.mit.edu 37 1 12785494 12785494 + Frame_Shift_Del DEL G G - rs7513079 by1000genomes TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:12785494delG ENST00000332530.3 + 3 600 c.374delG c.(373-375)ttfs p.C125fs AADACL3_ENST00000359318.5_Frame_Shift_Del_p.C195fs NM_001103169.1 NP_001096639.1 Q5VUY0 ADCL3_HUMAN arylacetamide deacetylase-like 3 195 hydrolase activity breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1) 15 Ovarian(185;0.249) Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649) ATCTGCTACTGTTTTTTTCAA 0.458 8 171 --- --- --- --- MAST2 23139 broad.mit.edu 37 1 46494559 46494559 + Frame_Shift_Del DEL T T - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:46494559delT ENST00000361297.2 + 18 2455 c.2172delT c.(2170-2172)ccfs p.P724fs MAST2_ENST00000372009.2_Frame_Shift_Del_p.P654fs|MAST2_ENST00000372008.1_Frame_Shift_Del_p.P609fs NM_015112.2 NP_055927.2 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 2 724 Protein kinase. regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity breast(1)|lung(3)|ovary(5)|stomach(2) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) GCTGCGTCCCTTTTTTTGGAG 0.552 7 328 --- --- --- --- NOTCH2 4853 broad.mit.edu 37 1 120612003 120612004 + Frame_Shift_Del DEL GG GG - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr1:120612003_120612004delGG ENST00000256646.2 - 1 236_237 c.17_18delCC c.(16-18)cfs p.P6fs NM_024408.3 NP_077719.2 Q04721 NOTC2_HUMAN notch 2 6 anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity p.P6fs*27(2) breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 158 all_neural(166;0.153) all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809) Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133) ACAGCAGAGCGGGGCGCAGGGC 0.762 """N, F, Mis""" """marginal zone lymphoma, DLBCL""" Alagille Syndrome 15 53 --- --- --- --- XPC 7508 broad.mit.edu 37 3 14219966 14219968 + Splice_Site DEL CCT CCT - rs72561774 TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr3:14219966_14219968delCCT ENST00000285021.7 - 1 315_317 c.103_splice c.e1+1 p.ED34_splice XPC_ENST00000449060.2_Splice_Site_p.ED34_splice|LSM3_ENST00000306024.3_5'UTR NM_001145769.1|NM_004628.4 NP_001139241.1|NP_004619.3 Q01831 XPC_HUMAN xeroderma pigmentosum, complementation group C 34 Glu-rich (acidic).|Poly-Glu. nucleotide-excision repair, DNA damage recognition|nucleotide-excision repair, DNA damage removal cytoplasm|nucleoplasm|XPC complex bubble DNA binding|damaged DNA binding|loop DNA binding|protein binding|single-stranded DNA binding p.E34delE(1) NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 TCGCTCTCACCCTCCTCCTCCTC 0.734 """Mis, N, F, S""" """skin basal cell, skin squamous cell, melanoma""" Nucleotide excision repair (NER) Xeroderma Pigmentosum 10 119 --- --- --- --- RP11-3P17.4 0 broad.mit.edu 37 3 161146872 161146873 + RNA DEL AT AT - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr3:161146872_161146873delAT ENST00000473595.1 + 0 1231 NR_102265.1 TGGTGAAAAGATATATATATAT 0.342 3 6 --- --- --- --- TRIM26 7726 broad.mit.edu 37 6 30157254 30157254 + Frame_Shift_Del DEL T T - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr6:30157254delT ENST00000454678.2 - 8 1281 c.845delA c.(844-846)agfs p.K282fs TRIM26_ENST00000437089.1_Frame_Shift_Del_p.K282fs|TRIM26_ENST00000453195.1_Frame_Shift_Del_p.K282fs NM_003449.4 NP_003440.1 Q12899 TRI26_HUMAN tripartite motif containing 26 282 DNA binding|zinc ion binding p.K282fs*16(1) lung(1)|ovary(2) 3 TTCTCCGGTCTTTTTTTTAAC 0.483 10 128 --- --- --- --- TMEM229A 730130 broad.mit.edu 37 7 123672457 123672459 + In_Frame_Del DEL GCT GCT - rs72310362 TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr7:123672457_123672459delGCT ENST00000455783.1 - 1 1064_1066 c.599_601delAGC c.(598-603)cgg>c p.QR200del RP5-921G16.1_ENST00000484322.1_RNA NM_001136002.1 NP_001129474.1 B2RXF0 T229A_HUMAN transmembrane protein 229A 200 host cell nucleus|integral to membrane sequence-specific DNA binding transcription factor activity endometrium(3)|kidney(3) 6 GCGCCCCTCCgctgctgctgctg 0.754 6 7 --- --- --- --- PTGDR2 11251 broad.mit.edu 37 11 60620167 60620169 + In_Frame_Del DEL GCG GCG - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr11:60620167_60620169delGCG ENST00000332539.4 - 2 1138_1140 c.1027_1029delCGC c.(1027-1029)del p.R343del NM_004778.2 NP_004769.2 Q9Y5Y4 GPR44_HUMAN prostaglandin D2 receptor 2 343 immune response integral to plasma membrane N-formyl peptide receptor activity TGGAGGAGGTGCGGCGGCGGCGG 0.749 3 6 --- --- --- --- GCN1L1 10985 broad.mit.edu 37 12 120595737 120595739 + In_Frame_Del DEL CTC CTC - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr12:120595737_120595739delCTC ENST00000300648.6 - 26 3013_3015 c.3001_3003delGAG c.(3001-3003)del p.E1001del NM_006836.1 NP_006827.1 Q92616 GCN1L_HUMAN GCN1 general control of amino-acid synthesis 1-like 1 (yeast) 1001 regulation of translation ribosome protein binding|translation factor activity, nucleic acid binding NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 94 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GGGCCATCCACTCCTCCTCCTCC 0.631 8 146 --- --- --- --- RP11-519G16.3 0 broad.mit.edu 37 15 45754119 45754121 + RNA DEL CAC CAC - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr15:45754119_45754121delCAC ENST00000560077.1 + 0 41 RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA ccaccaccatcaccaccaccacc 0.571 4 8 --- --- --- --- RP11-44F14.1 0 broad.mit.edu 37 16 53404542 53404543 + RNA INS - - A TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr16:53404542_53404543insA ENST00000565421.1 - 0 410 TCTCCTTTCTCAAACTTAACCT 0.327 7 22 --- --- --- --- CHD3 1107 broad.mit.edu 37 17 7788146 7788148 + In_Frame_Del DEL GAG GAG - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr17:7788146_7788148delGAG ENST00000380358.4 + 1 23_25 c.22_24delGAG c.(22-24)del p.E14del LSMD1_ENST00000570555.1_Intron|LSMD1_ENST00000576861.1_Intron NM_001005271.2 NP_001005271.2 Q12873 CHD3_HUMAN chromodomain helicase DNA binding protein 3 429 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2) 65 Prostate(122;0.202) TCTGAGggacgaggaggaggagg 0.700 3 6 --- --- --- --- FRG1B 0 broad.mit.edu 37 20 29632612 29632614 + Splice_Site DEL AAG AAG - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr20:29632612_29632614delAAG ENST00000278882.3 + 8 807_809 c.425_splice c.e8-1 p.K144_splice FRG1B_ENST00000358464.4_Splice_Site_p.K144_splice endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 TCTTTGCAGAAAGAAATTTCAGA 0.276 7 251 --- --- --- --- TPTE 7179 broad.mit.edu 37 21 10944697 10944697 + Frame_Shift_Del DEL A A - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr21:10944697delA ENST00000298232.7 - 10 850 c.483delT c.(481-483)ttfs p.F161fs TPTE_ENST00000342420.5_Frame_Shift_Del_p.F141fs|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000361285.4_Frame_Shift_Del_p.F179fs NM_199259.2 NP_954868.1 P56180 TPTE_HUMAN transmembrane phosphatase with tensin homology 179 signal transduction integral to membrane ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1) 130 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ACTTAATGTCAAAAAAAATGT 0.299 8 190 --- --- --- --- PTTG1IP 754 broad.mit.edu 37 21 46276194 46276196 + In_Frame_Del DEL GCA GCA - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chr21:46276194_46276196delGCA ENST00000330938.3 - 4 581_583 c.361_363delTGC c.(361-363)del p.C121del PTTG1IP_ENST00000494690.1_5'UTR|PTTG1IP_ENST00000397886.3_In_Frame_Del_p.C100del|PTTG1IP_ENST00000397887.3_Intron|PTTG1IP_ENST00000445724.2_Intron NM_004339.3 NP_004330.1 P53801 PTTG_HUMAN pituitary tumor-transforming 1 interacting protein 121 Poly-Cys. protein import into nucleus cytoplasm|integral to membrane|nucleus ovary(1)|prostate(1) 2 Colorectal(79;0.0659) TCTTCCTCCTGCAGCAGCAGCAG 0.616 7 129 --- --- --- --- APOOL 139322 broad.mit.edu 37 X 84322155 84322155 + Frame_Shift_Del DEL T T - TCGA-FY-A3I4-01A-11D-A21A-08 TCGA-FY-A3I4-10A-01D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx e087d096-3086-4705-a308-75f12f9487eb a40b24b5-781b-44cf-9d3c-499ddd16136e g.chrX:84322155delT ENST00000373173.2 + 6 504 c.417delT c.(415-417)acfs p.T139fs NM_198450.5 NP_940852.3 Q6UXV4 APOOL_HUMAN apolipoprotein O-like 139 extracellular region central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1) 8 AGAAAATTACTTATCCTCTGG 0.333 2 4 --- --- --- ---