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 SH3PXD2A 9644 broad.mit.edu 37 10 105365619 105365619 + Missense_Mutation SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr10:105365619G>A uc001kxj.1 - 12 1420 c.1280C>T c.(1279-1281)aCc>aTc p.T427I SH3PXD2A_uc010qqr.2_Intron|SH3PXD2A_uc010qqs.1_Missense_Mutation_p.T262I|SH3PXD2A_uc010qqt.1_Missense_Mutation_p.T304I|SH3PXD2A_uc009xxn.1_Missense_Mutation_p.T262I|SH3PXD2A_uc010qqu.1_Missense_Mutation_p.T370I NM_014631 NP_055446 Q5TCZ1 SPD2A_HUMAN Homo sapiens SH3 and PX domains 2A (SH3PXD2A), mRNA. 455 cell communication|superoxide metabolic process cell junction|cell projection|cytoplasm|podosome phosphatidylinositol binding|protein binding breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1) 38 Colorectal(252;0.0815)|Breast(234;0.131) Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119) TTCGGCAATGGTGTAGTACTC 0.537000 OREG0020500 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 32 38 0 0 1 0 0 CTSW 1521 broad.mit.edu 37 11 65651008 65651008 + Silent SNP T T C TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr11:65651008T>C uc001ogc.1 + 9 1092 c.1050T>C c.(1048-1050)aaT>aaC p.N350N NM_001335 NP_001326 P56202 CATW_HUMAN Homo sapiens cathepsin W (CTSW), mRNA. 350 immune response|proteolysis cysteine-type endopeptidase activity central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5) 9 READ - Rectum adenocarcinoma(159;0.168) GAGGGAGCAATACCTGTGGCA 0.622000 47 77 0 0 1 0 0 COL5A1 1289 broad.mit.edu 37 9 137690287 137690287 + Missense_Mutation SNP C C T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr9:137690287C>T uc004cfe.3 + 36 3314 c.2932C>T c.(2932-2934)Cct>Tct p.P978S NM_000093 NP_000084 P20908 CO5A1_HUMAN Homo sapiens collagen, type V, alpha 1 (COL5A1), mRNA. 978 Triple-helical region. axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells collagen type V heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4) 115 Myeloproliferative disorder(178;0.0341) all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131) CCCAGGACACCCTGGACAGAG 0.577000 6 65 0 0 1 0 0 MTO1 25821 broad.mit.edu 37 6 74171794 74171794 + Splice_Site SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr6:74171794G>A uc010kav.3 + 1 341 c.217_splice c.e1+1 p.G73_splice MTO1_uc003pgy.4_Splice_Site_p.G73_splice|MTO1_uc003pgz.4_Splice_Site_p.G73_splice|MTO1_uc003pha.4_Splice_Site|MTO1_uc003phb.4_Intron|MTO1_uc003phc.1_5'Flank NM_001123226 NP_001116698 Q9Y2Z2 MTO1_HUMAN Homo sapiens mitochondrial translation optimization 1 homolog (S. cerevisiae) (MTO1), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA. 73 tRNA processing mitochondrion flavin adenine dinucleotide binding breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1) 27 GGACACGATCGGTGAGGAGCG 0.657000 3 48 0 0 1 0 0 TACC2 10579 broad.mit.edu 37 10 123970987 123970987 + Silent SNP T T C TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr10:123970987T>C uc001lfv.3 + 8 7407 c.7047T>C c.(7045-7047)ccT>ccC p.P2349P TACC2_uc001lfw.3_Silent_p.P495P|TACC2_uc009xzx.3_Silent_p.P2304P|TACC2_uc010qtv.2_Silent_p.P2353P|TACC2_uc001lfx.3_Silent_p.P53P|TACC2_uc001lfy.3_Silent_p.P53P|TACC2_uc001lfz.3_Silent_p.P427P|TACC2_uc001lga.3_Silent_p.P427P|TACC2_uc009xzy.3_Silent_p.P427P|TACC2_uc001lgb.3_Silent_p.P384P|TACC2_uc010qtw.1_Silent_p.P444P NM_206862 NP_996744 O95359 TACC2_HUMAN Homo sapiens transforming, acidic coiled-coil containing protein 2 (TACC2), transcript variant 1, mRNA. 2349 SPAZ. microtubule organizing center|nucleus nuclear hormone receptor binding p.N2348S(1) NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 83 all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197) ATTTTAACCCTTTTTCTTCCA 0.468000 4 219 0 0 1 0 0 F8 2157 broad.mit.edu 37 X 154157148 154157148 + Silent SNP G G A rs147629393 TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chrX:154157148G>A uc004fmt.3 - 13 5088 c.4917C>T c.(4915-4917)ccC>ccT p.P1639P NM_000132 NP_000123 P00451 FA8_HUMAN Homo sapiens coagulation factor VIII, procoagulant component (F8), transcript variant 1, mRNA. 1639 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding p.P1639P(3) NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2) 120 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) CTTCTATTTCGGGCTTATTTT 0.423000 25 77 0 0 1 0 0 COL19A1 1310 broad.mit.edu 37 6 70866046 70866046 + Missense_Mutation SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr6:70866046G>A uc003pfc.1 + 31 2224 c.2107G>A c.(2107-2109)Gtc>Atc p.V703I COL19A1_uc010kam.2_Missense_Mutation_p.V599I NM_001858 NP_001849 Q14993 COJA1_HUMAN Homo sapiens collagen, type XIX, alpha 1 (COL19A1), mRNA. 703 Triple-helical region 4 (COL4). cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development collagen extracellular matrix structural constituent|protein binding, bridging breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2) 109 CCAAGCCAGTGTCCCAGGGCT 0.463000 9 7 0 0 1 0 0 PPEF1 5475 broad.mit.edu 37 X 18842187 18842187 + Missense_Mutation SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chrX:18842187G>A uc004cyq.3 + 16 2129 c.1648G>A c.(1648-1650)Gaa>Aaa p.E550K PPEF1_uc004cyp.3_Missense_Mutation_p.E522K|PPEF1_uc004cyr.3_Missense_Mutation_p.E488K|PPEF1_uc004cys.3_Missense_Mutation_p.E550K|PPEF1_uc011mja.2_Missense_Mutation_p.E485K|PPEF1_uc011mjb.2_Missense_Mutation_p.E494K NM_006240 NP_006231 O14829 PPE1_HUMAN Homo sapiens protein phosphatase, EF-hand calcium binding domain 1 (PPEF1), transcript variant 1, mRNA. 550 detection of stimulus involved in sensory perception|protein dephosphorylation calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 43 Hepatocellular(33;0.183) TATCCGCATTGAAAAACCTGT 0.463000 13 27 0 0 1 0 0 PROSER1 80209 broad.mit.edu 37 13 39587564 39587564 + Missense_Mutation SNP T T C TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr13:39587564T>C uc001uwy.3 - 10 2698 c.1825A>G c.(1825-1827)Act>Gct p.T609A PROSER1_uc001uwz.3_Missense_Mutation_p.T587A NM_025138 NP_079414 Q86XN7 CM023_HUMAN Homo sapiens proline and serine rich 1 (PROSER1), transcript variant 1, mRNA. 609 Ser-rich. GTGGGCTCAGTTTTGATCATA 0.532000 18 106 0 0 1 0 0 HDAC5 10014 broad.mit.edu 37 17 42170141 42170141 + Silent SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr17:42170141G>A uc002iff.1 - 6 1010 c.678C>T c.(676-678)tcC>tcT p.S226S HDAC5_uc002ifd.1_Silent_p.S225S|HDAC5_uc002ife.1_Silent_p.S225S|HDAC5_uc010czp.1_Silent_p.S225S|HDAC5_uc002ifh.2_Silent_p.S225S NM_001015053 NP_001015053 Q9UQL6 HDAC5_HUMAN Homo sapiens histone deacetylase 5 (HDAC5), transcript variant 3, mRNA. 225 B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent cytoplasm|histone deacetylase complex NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|histone deacetylase activity (H3-K16 specific)|protein kinase C binding|repressing transcription factor binding central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1) 21 Breast(137;0.00637)|Prostate(33;0.0313) BRCA - Breast invasive adenocarcinoma(366;0.118) TCTGGGGAGGGGAACTCTGGT 0.642000 11 20 0 0 1 0 0 RAI1 10743 broad.mit.edu 37 17 17696275 17696275 + Nonsense_Mutation SNP C C T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr17:17696275C>T uc002grm.3 + 2 482 c.13C>T c.(13-15)Cga>Tga p.R5* RAI1_uc002grn.1_Nonsense_Mutation_p.R5* NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN Homo sapiens retinoic acid induced 1 (RAI1), mRNA. 5 cytoplasm|nucleus zinc ion binding breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7) 48 READ - Rectum adenocarcinoma(1115;0.0276) GCAGTCTTTTCGAGAAAGGTG 0.562000 17 10 0 0 1 0 0 C5orf42 65250 broad.mit.edu 37 5 37157920 37157920 + Silent SNP T T C TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr5:37157920T>C uc011coz.1 - 24 5117 c.5088A>G c.(5086-5088)ctA>ctG p.L1696L C5orf42_uc011cpa.1_Intron|C5orf42_uc003jkp.1_Non-coding_Transcript|C5orf42_uc011coy.1_Silent_p.L1121L|C5orf42_uc003jks.2_Non-coding_Transcript NM_023073 NP_075561 E9PH94 E9PH94_HUMAN Homo sapiens chromosome 5 open reading frame 42 (C5orf42), mRNA. 2604 breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3) 79 all_lung(31;0.000616) COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202) GTAATTCCTGTAGAAGATCAT 0.358000 7 13 0 0 1 0 0 USP9X 8239 broad.mit.edu 37 X 40988337 40988337 + Nonsense_Mutation SNP G G T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chrX:40988337G>T uc004dfb.3 + 2 814 c.181G>T c.(181-183)Gaa>Taa p.E61* USP9X_uc004dfc.3_Nonsense_Mutation_p.E61* NM_001039590 NP_001034679 Q93008 USP9X_HUMAN Homo sapiens ubiquitin specific peptidase 9, X-linked (USP9X), transcript variant 3, mRNA. 61 BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process cytoplasm co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 87 ACCACAGCTTGAAGATGAGGA 0.458000 14 15 0 0 1 0 0 RHOQ 23433 broad.mit.edu 37 2 46803383 46803383 + Missense_Mutation SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr2:46803383G>A uc002rva.3 + 2 678 c.359G>A c.(358-360)gGa>gAa p.G120E BC048424_uc002rvb.3_Intron NM_012249 NP_036381 P17081 RHOQ_HUMAN Homo sapiens ras homolog gene family, member Q (RHOQ), mRNA. 120 cortical actin cytoskeleton organization|insulin receptor signaling pathway|negative regulation of establishment of protein localization in plasma membrane|positive regulation of filopodium assembly|positive regulation of glucose import|positive regulation of transcription from RNA polymerase II promoter|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction actin filament|cytosol|plasma membrane GBD domain binding|GTP binding|GTPase activity|profilin binding skin(2) 2 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) LUSC - Lung squamous cell carcinoma(58;0.114) TTATTAATAGGAACTCAGGTA 0.418000 12 18 0 0 1 0 0 SORCS3 22986 broad.mit.edu 37 10 106974207 106974207 + Missense_Mutation SNP C C T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr10:106974207C>T uc001kyi.1 + 17 2610 c.2383C>T c.(2383-2385)Cgg>Tgg p.R795W SORCS3_uc010qqz.1_Non-coding_Transcript NM_014978 NP_055793 Q9UPU3 SORC3_HUMAN Homo sapiens sortilin-related VPS10 domain containing receptor 3 (SORCS3), mRNA. 795 integral to membrane neuropeptide receptor activity p.R794R(1)|p.R795R(1) autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2) 131 Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191) Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628) TAGGTATCGGCGGATTGTGTC 0.483000 8 15 0 0 1 0 0 RGPD4 285190 broad.mit.edu 37 2 108477236 108477236 + Missense_Mutation SNP T T G TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr2:108477236T>G uc010ywk.2 + 12 1855 c.1773T>G c.(1771-1773)aaT>aaG p.N591K RGPD4_uc002tdu.3_5'UTR|RGPD4_uc010ywl.2_Non-coding_Transcript NM_182588 NP_872394 Q7Z3J3 RGPD4_HUMAN Homo sapiens RANBP2-like and GRIP domain containing 4 (RGPD4), mRNA. 591 intracellular transport binding breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3) 43 GTGGTCTTAATTCTTTTTATG 0.323000 38 65 0 0 1 0 0 MIB1 57534 broad.mit.edu 37 18 19378075 19378075 + Missense_Mutation SNP A A T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr18:19378075A>T uc002ktq.3 + 7 1123 c.1123A>T c.(1123-1125)Att>Ttt p.I375F MIB1_uc002ktp.3_Missense_Mutation_p.I14F NM_020774 NP_065825 Q86YT6 MIB1_HUMAN Homo sapiens mindbomb homolog 1 (Drosophila) (MIB1), mRNA. 375 Notch signaling pathway centrosome|nuclear membrane|plasma membrane ubiquitin-protein ligase activity|zinc ion binding breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5) 27 STAD - Stomach adenocarcinoma(5;0.212) AGTACAACAGATTTATTCAGA 0.378000 10 33 0 0 1 0 0 PPIL6 285755 broad.mit.edu 37 6 109757309 109757309 + Missense_Mutation SNP T T C TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr6:109757309T>C uc010kdp.3 - 1 810 c.229A>G c.(229-231)Agg>Ggg p.R77G PPIL6_uc003ptg.4_Missense_Mutation_p.R77G|PPIL6_uc021zdq.1_Non-coding_Transcript|Mir_584_uc021zdr.1_5'Flank NM_001111298 NP_001104768 Q8IXY8 PPIL6_HUMAN Homo sapiens peptidylprolyl isomerase (cyclophilin)-like 6 (PPIL6), transcript variant 2, mRNA. 77 protein folding peptidyl-prolyl cis-trans isomerase activity large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1) 6 all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548) Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259) TCCTTTACCCTTTTTTTCTCC 0.338000 3 97 0 0 1 0 0 CENPI 2491 broad.mit.edu 37 X 100383791 100383791 + Silent SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chrX:100383791G>A uc004egx.3 + 10 1431 c.1161G>A c.(1159-1161)agG>agA p.R387R CENPI_uc011mrg.2_Silent_p.R387R|CENPI_uc004egy.3_Silent_p.R387R NM_006733 NP_006724 Q92674 CENPI_HUMAN Homo sapiens centromere protein I (CENPI), mRNA. 387 CenH3-containing nucleosome assembly at centromere|mitotic prometaphase cytosol|kinetochore|nucleoplasm protein binding breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2) 30 TCTTGCTGAGGTTTTATTACT 0.413000 25 43 0 0 1 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 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 11 11 0 0 1 0 0 JAKMIP3 282973 broad.mit.edu 37 10 133930583 133930583 + Silent SNP C C T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr10:133930583C>T uc001lkx.4 + 1 138 c.138C>T c.(136-138)gtC>gtT p.V46V NM_001105521 NP_001098991 Homo sapiens Janus kinase and microtubule interacting protein 3 (JAKMIP3), mRNA. breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2) 31 all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175) OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224) TCTTTCAGGTCAGCAAAGTGG 0.572000 9 32 0 0 1 0 0 DCPS 28960 broad.mit.edu 37 11 126201357 126201357 + Missense_Mutation SNP G G A TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr11:126201357G>A uc001qdp.3 + 2 763 c.434G>A c.(433-435)cGc>cAc p.R145H NM_014026 NP_054745 Q96C86 DCPS_HUMAN Homo sapiens decapping enzyme, scavenger (DCPS), mRNA. 145 deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay cytosol|nucleus exoribonuclease activity|protein binding p.R145H(2) endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1) 17 all_hematologic(175;0.145) Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604) BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08) AAGTACCTGCGCCAGGACCTC 0.557000 4 96 0 0 1 0 0 HLA-DMB 3109 broad.mit.edu 37 6 32906598 32906598 + Missense_Mutation SNP C C T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr6:32906598C>T uc003ocl.2 - 1 463 c.200G>A c.(199-201)gGg>gAg p.G67E HLA-DMB_uc003ock.2_5'Flank|HLA-DMB_uc010jud.2_5'Flank|HLA-DMB_uc010jue.2_5'Flank|HLA-DMB_uc010juf.2_5'Flank|HLA-DMB_uc003ocj.2_Missense_Mutation_p.G67E|HLA-DMB_uc011dql.2_Missense_Mutation_p.G67E NM_002118 NP_002109 P28068 DMB_HUMAN Homo sapiens major histocompatibility complex, class II, DM beta (HLA-DMB), mRNA. 67 Beta-1. T cell costimulation|T cell receptor signaling pathway|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway MHC class II protein complex|integral to membrane|late endosome membrane|lysosomal membrane breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1) 13 ATTCAGCACCCCAAATTCGCA 0.517000 23 25 0 0 1 0 0 SNX18 112574 broad.mit.edu 37 5 53814143 53814143 + Frame_Shift_Del DEL C C - TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr5:53814143delC uc003jpj.4 + 0 551 c.361delC c.(361-363)ccgfs p.P121fs SNX18_uc011cqg.2_Frame_Shift_Del_p.P121fs|SNX18_uc003jpi.4_Frame_Shift_Del_p.P121fs NM_052870 NP_443102 Q96RF0 SNX18_HUMAN Homo sapiens sorting nexin 18 (SNX18), transcript variant 2, mRNA. 121 cell communication|endocytosis|positive regulation of GTPase activity|protein transport endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane phosphatidylinositol binding|protein binding endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2) 18 Lung NSC(810;3.46e-05)|Breast(144;0.102) CACCTTCCAGCCGCCCGGCGC 0.746 2 4 --- --- --- --- MMS19 64210 broad.mit.edu 37 10 99220481 99220481 + Frame_Shift_Del DEL G G - TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr10:99220481delG uc001kns.4 - 24 2665 c.2440delC c.(2440-2442)catfs p.H814fs MMS19_uc001knq.3_Frame_Shift_Del_p.H77fs|MMS19_uc009xvs.3_Frame_Shift_Del_p.H399fs|MMS19_uc009xvt.3_Frame_Shift_Del_p.H558fs|MMS19_uc001knr.3_Frame_Shift_Del_p.H655fs|MMS19_uc010qox.2_Frame_Shift_Del_p.H792fs|MMS19_uc001knt.3_Frame_Shift_Del_p.H814fs|MMS19_uc001knu.1_Non-coding_Transcript NM_022362 NP_071757 Q96T76 MMS19_HUMAN Homo sapiens MMS19 nucleotide excision repair homolog (S. cerevisiae) (MMS19), mRNA. 814 chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay) MMXD complex|cytoplasm|holo TFIIH complex estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1) 16 Colorectal(252;0.0846) Epithelial(162;3.33e-10)|all cancers(201;2.74e-08) CTGAGAGGATGGTATCTGAGC 0.488 Direct reversal of damage 2 4 --- --- --- --- CTSA 5476 broad.mit.edu 37 20 44520006 44520007 + Frame_Shift_Ins INS - - T TCGA-FE-A22Z-01A-11D-A17V-08 TCGA-FE-A22Z-10A-01D-A17V-08 Untested Somatic Phase_I WXS none Illumina GAIIx ec59b115-b96a-42ff-9649-a9a518456c2b c79d1a81-e40f-439c-ace4-aaaef0237060 g.chr20:44520006_44520007insT uc002xqh.3 + 0 416_417 c.42_43insT c.(40-45)cgcgggfs p.R14fs NEURL2_uc002xqg.1_5'Flank|CTSA_uc002xqj.4_5'UTR|CTSA_uc010zxi.2_Frame_Shift_Ins_p.R14fs|CTSA_uc002xqi.3_Non-coding_Transcript NM_000308 NP_001121167 P10619 PPGB_HUMAN Homo sapiens cathepsin A (CTSA), transcript variant 1, mRNA. 0 intracellular protein transport|proteolysis endoplasmic reticulum|lysosome|nucleus enzyme activator activity|protein binding|serine-type carboxypeptidase activity breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1) 21 Myeloproliferative disorder(115;0.0122) AGCAAGGACGCGGGGGAGCAGA 0.698 2 4 --- --- --- ---