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 ENST00000369774.4 - 14 1640 c.1364C>T c.(1363-1365)aCc>aTc p.T455I SH3PXD2A_ENST00000355946.2_Missense_Mutation_p.T427I|SH3PXD2A_ENST00000538130.1_Missense_Mutation_p.T290I|SH3PXD2A_ENST00000540321.1_Missense_Mutation_p.T322I|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000315994.6_5'UTR Q5TCZ1 SPD2A_HUMAN SH3 and PX domains 2A 455 SH3 3. 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 0.144211 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 ENST00000307886.3 + 10 1096 c.1050T>C c.(1048-1050)aaT>aaC p.N350N CTSW_ENST00000528419.1_3'UTR NM_001335.3 NP_001326.2 P56202 CATW_HUMAN cathepsin W 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 0.139131 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 ENST00000371817.3 + 37 3346 c.2932C>T c.(2932-2934)Cct>Tct p.P978S NM_000093.3|NM_001278074.1 NP_000084.3|NP_001265003.1 P20908 CO5A1_HUMAN collagen, type V, alpha 1 978 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 0.029380 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 ENST00000498286.1 + 1 494 c.217_splice c.e1+1 p.G73_splice MTO1_ENST00000370305.1_Intron|MTO1_ENST00000370300.4_Splice_Site_p.G73_splice|MTO1_ENST00000415954.2_Splice_Site_p.G73_splice Q9Y2Z2 MTO1_HUMAN mitochondrial tRNA translation optimization 1 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 0.115264 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 ENST00000369005.1 + 9 7387 c.7047T>C c.(7045-7047)ccT>ccC p.P2349P TACC2_ENST00000369000.1_Silent_p.P53P|TACC2_ENST00000515603.1_Silent_p.P2304P|TACC2_ENST00000369004.3_Silent_p.P427P|TACC2_ENST00000453444.2_Silent_p.P2353P|TACC2_ENST00000360561.3_Silent_p.P427P|TACC2_ENST00000358010.1_Silent_p.P495P|TACC2_ENST00000260733.3_Silent_p.P427P|TACC2_ENST00000369001.1_Silent_p.P53P|TACC2_ENST00000513429.1_Silent_p.P495P|TACC2_ENST00000515273.1_Silent_p.P2353P|TACC2_ENST00000334433.3_Silent_p.P2349P|TACC2_ENST00000368999.1_Silent_p.P427P NM_206862.2 NP_996744.2 O95359 TACC2_HUMAN transforming, acidic coiled-coil containing protein 2 2349 SPAZ. microtubule organizing center|nucleus nuclear hormone receptor binding 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 0.009096 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 ENST00000360256.4 - 14 5117 c.4917C>T c.(4915-4917)ccC>ccT p.P1639P NM_000132.3 NP_000123.1 P00451 FA8_HUMAN coagulation factor VIII, procoagulant component 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(2) 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 0.091800 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 ENST00000322773.4 + 32 2209 c.2107G>A c.(2107-2109)Gtc>Atc p.V703I COL19A1_ENST00000393344.1_Missense_Mutation_p.V325I NM_001858.4 NP_001849.2 Q14993 COJA1_HUMAN collagen, type XIX, alpha 1 703 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 0.047766 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 ENST00000361511.4 + 17 2142 c.1648G>A c.(1648-1650)Gaa>Aaa p.E550K PPEF1_ENST00000544635.1_Missense_Mutation_p.E485K|PPEF1_ENST00000543630.1_3'UTR|PPEF1_ENST00000359763.6_Missense_Mutation_p.E497K|PPEF1_ENST00000349874.5_Missense_Mutation_p.E488K NM_006240.2|NM_152224.1 NP_006231.2|NP_689410.1 O14829 PPE1_HUMAN protein phosphatase, EF-hand calcium binding domain 1 550 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 0.093190 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 ENST00000352251.3 - 11 2658 c.1825A>G c.(1825-1827)Act>Gct p.T609A PROSER1_ENST00000350125.3_Missense_Mutation_p.T587A|PROSER1_ENST00000484434.2_Intron NM_025138.3 NP_079414.3 Q86XN7 CM023_HUMAN proline and serine rich 1 609 Ser-rich. GTGGGCTCAGTTTTGATCATA 0.532000 18 106 0 0 0.043863 0 0 MALAT1 0 broad.mit.edu 37 11 65268525 65268525 + RNA SNP A A 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.chr11:65268525A>C ENST00000534336.1 + 0 3293 NR_002819.2 TGAATTTGATAGCCAAATTGA 0.348000 25 51 0 0 0.091800 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 ENST00000225983.6 - 7 1001 c.678C>T c.(676-678)tcC>tcT p.S226S HDAC5_ENST00000586802.1_Silent_p.S225S|HDAC5_ENST00000336057.5_Silent_p.S225S|HDAC5_ENST00000393622.2_Silent_p.S225S Q9UQL6 HDAC5_HUMAN histone deacetylase 5 225 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 histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-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 0.080935 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 ENST00000353383.1 + 3 482 c.13C>T c.(13-15)Cga>Tga p.R5* RAI1_ENST00000261641.6_Nonsense_Mutation_p.R5* NM_030665.3 NP_109590.3 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 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 0.043863 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 ENST00000274258.7 - 40 8090 c.4503A>G c.(4501-4503)ctA>ctG p.L1501L C5orf42_ENST00000425232.2_Intron|C5orf42_ENST00000508244.1_Intron E9PH94 E9PH94_HUMAN chromosome 5 open reading frame 42 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 0.029380 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 ENST00000324545.7 + 3 814 c.181G>T c.(181-183)Gaa>Taa p.E61* USP9X_ENST00000378308.2_Nonsense_Mutation_p.E61* NM_001039590.2|NM_001039591.2 NP_001034679.2|NP_001034680.2 Q93008 USP9X_HUMAN ubiquitin specific peptidase 9, X-linked 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 1.52009e-12 1.90011e-12 0.132662 1 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 ENST00000238738.4 + 3 678 c.359G>A c.(358-360)gGa>gAa p.G120E RP11-417F21.1_ENST00000506009.2_RNA|RHOQ_ENST00000465198.1_3'UTR NM_012249.3 NP_036381.2 P17081 RHOQ_HUMAN ras homolog family member Q 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 0.080935 0 0 AC024560.3 0 broad.mit.edu 37 3 197348674 197348674 + RNA SNP A A G rs144273946 by1000genomes 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.chr3:197348674A>G ENST00000418868.1 - 0 585 NR_003266.2 GGCTCTGTCCACCAAATGCAC 0.478000 3 61 0 0 0.115264 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 ENST00000369701.3 + 18 2610 c.2383C>T c.(2383-2385)Cgg>Tgg p.R795W SORCS3_ENST00000369699.4_Missense_Mutation_p.R81W NM_014978.1 NP_055793.1 Q9UPU3 SORC3_HUMAN sortilin-related VPS10 domain containing receptor 3 795 integral to membrane neuropeptide receptor activity 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 0.058154 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 ENST00000263579.4 + 3 763 c.434G>A c.(433-435)cGc>cAc p.R145H DCPS_ENST00000530860.1_3'UTR NM_014026.3 NP_054745.1 Q96C86 DCPS_HUMAN decapping enzyme, scavenger 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(1) 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 0.009096 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 ENST00000408999.3 + 13 1850 c.1773T>G c.(1771-1773)aaT>aaG p.N591K RGPD4_ENST00000354986.4_Missense_Mutation_p.N591K NM_182588.2 NP_872394.2 Q7Z3J3 RGPD4_HUMAN RANBP2-like and GRIP domain containing 4 591 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 0.104719 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 ENST00000261537.6 + 8 1387 c.1123A>T c.(1123-1125)Att>Ttt p.I375F MIB1_ENST00000578646.1_3'UTR NM_020774.2 NP_065825.1 Q86YT6 MIB1_HUMAN mindbomb E3 ubiquitin protein ligase 1 375 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 0.058154 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 ENST00000521072.2 - 2 809 c.229A>G c.(229-231)Agg>Ggg p.R77G PPIL6_ENST00000424445.2_Intron|PPIL6_ENST00000440797.2_Missense_Mutation_p.R77G NM_173672.4 NP_775943.1 Q8IXY8 PPIL6_HUMAN peptidylprolyl isomerase (cyclophilin)-like 6 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 0.115264 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 ENST00000372927.1 + 11 1438 c.1161G>A c.(1159-1161)agG>agA p.R387R CENPI_ENST00000372926.1_Silent_p.R387R|CENPI_ENST00000423383.1_Silent_p.R387R|CENPI_ENST00000218507.5_Silent_p.R387R NM_006733.2 NP_006724.2 Q92674 CENPI_HUMAN centromere protein I 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 0.091800 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 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 11 11 0 0 0.080935 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 ENST00000298622.4 + 2 276 c.138C>T c.(136-138)gtC>gtT p.V46V NM_001105521.2 NP_001098991.1 Janus kinase and microtubule interacting protein 3 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 0.069234 0 0 KRTAP4-8 728224 broad.mit.edu 37 17 39254054 39254054 + Missense_Mutation SNP A A T rs76270529 by1000genomes 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.chr17:39254054A>T ENST00000333822.4 - 1 339 c.283T>A c.(283-285)Tgc>Agc p.C95S NM_031960.2 NP_114166.1 Q9BYQ9 KRA48_HUMAN keratin associated protein 4-8 95 25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR]. keratin filament p.C95S(4) endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1) 11 ctggagatgcagcagcTAGGG 0.677000 4 40 0 0 0.009096 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 ENST00000416244.2 - 2 394 c.200G>A c.(199-201)gGg>gAg p.G67E HLA-DMB_ENST00000418107.2_Missense_Mutation_p.G67E|XXbac-BPG181M17.5_ENST00000429234.1_Missense_Mutation_p.G99E P28068 DMB_HUMAN major histocompatibility complex, class II, DM beta 67 Beta-1. antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex 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 0.069288 0 0 KCNK12 56660 broad.mit.edu 37 2 47797390 47797392 + In_Frame_Del DEL GCA GCA - 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.chr2:47797390_47797392delGCA ENST00000327876.3 - 1 686_688 c.79_81delTGC c.(79-81)del p.C27del KCNK12_ENST00000493527.1_5'UTR NM_022055.1 NP_071338.1 Q9HB15 KCNKC_HUMAN potassium channel, subfamily K, member 12 27 Poly-Cys. integral to membrane potassium channel activity|voltage-gated ion channel activity p.0?(2)|p.?(1) NS(1)|endometrium(1)|lung(3)|ovary(1) 6 all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) GCGAAcggcggcagcagcagcag 0.759 2 4 --- --- --- --- 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 ENST00000343017.6 + 1 555 c.361delC c.(361-363)cgfs p.P122fs SNX18_ENST00000326277.3_Frame_Shift_Del_p.P122fs|SNX18_ENST00000381410.4_Frame_Shift_Del_p.P122fs NM_001145427.1 NP_001138899.1 Q96RF0 SNX18_HUMAN sorting nexin 18 122 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 ENST00000438925.2 - 25 2775 c.2440delC c.(2440-2442)atfs p.H814fs MMS19_ENST00000370782.2_Frame_Shift_Del_p.H814fs|MMS19_ENST00000355839.6_Frame_Shift_Del_p.H771fs|MMS19_ENST00000327277.7_3'UTR|MMS19_ENST00000327238.10_Frame_Shift_Del_p.H716fs NM_022362.4 NP_071757.4 Q96T76 MMS19_HUMAN MMS19 nucleotide excision repair homolog (S. cerevisiae) 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) cytoplasm|holo TFIIH complex|MMXD 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 ENST00000372484.3 + 1 324_325 c.42_43insT c.(40-45)cgggggfs p.RG14fs CTSA_ENST00000354880.5_Frame_Shift_Ins_p.RG14fs|CTSA_ENST00000191018.5_5'UTR NM_000308.2|NM_001127695.1 NP_000299.2|NP_001121167.1 P10619 PPGB_HUMAN cathepsin A 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 --- --- --- --- FAM120C 54954 broad.mit.edu 37 X 54209302 54209303 + In_Frame_Ins INS - - GGCGGC 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:54209302_54209303insGGCGGC ENST00000375180.2 - 1 385_386 c.329_330insGCCGCC c.(328-330)ccc>cGCCGCCcc p.109_110insRR FAM120C_ENST00000328235.4_In_Frame_Ins_p.109_110insRR|FAM120C_ENST00000477084.1_In_Frame_Ins_p.109_110insRR NM_017848.4 NP_060318.3 Q9NX05 F120C_HUMAN family with sequence similarity 120C 109 breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 28 GCAGCTGAGGGGGCGGCGGCGG 0.748 4 8 --- --- --- ---