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 KRTAP4-6 81871 broad.mit.edu 37 17 39296466 39296466 + Missense_Mutation SNP G G A rs35985080 by1000genomes TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr17:39296466G>A ENST00000345847.4 - 1 273 c.274C>T c.(274-276)Ccc>Tcc p.P92S NM_030976.1 NP_112238.1 Q9BYQ5 KRA46_HUMAN keratin associated protein 4-6 88 29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP]. keratin filament endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1) 9 CAGCACTGGGGTCTGCAGCAG 0.657000 6 70 0 0 1 0 0 PTPN11 5781 broad.mit.edu 37 12 112888197 112888197 + Missense_Mutation SNP T T A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr12:112888197T>A ENST00000351677.2 + 3 411 c.213T>A c.(211-213)ttT>ttA p.F71L PTPN11_ENST00000392597.1_Missense_Mutation_p.F71L NM_002834.3 NP_002825.3 Q06124 PTN11_HUMAN protein tyrosine phosphatase, non-receptor type 11 71 SH2 1. F -> K (in acute myeloid leukemia; requires 2 nucleotide substitutions).|F -> L (in myelodysplastic syndrome). axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway cytosol non-membrane spanning protein tyrosine phosphatase activity|protein binding p.F71L(5)|p.F71K(1) NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3) 451 GGGAGAAATTTGCCACTTTGG 0.418000 Mis """JMML, AML, MDS""" Noonan Syndrome Noonan syndrome 50 97 0 0 1 0 0 DNAH8 1769 broad.mit.edu 37 6 38810444 38810444 + Missense_Mutation SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr6:38810444G>A ENST00000359357.3 + 33 4213 c.3959G>A c.(3958-3960)cGt>cAt p.R1320H DNAH8_ENST00000441566.1_Missense_Mutation_p.R1320H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R1537H dynein, axonemal, heavy chain 8 NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4) 260 GAAAGATGTCGTAAACTTCCA 0.323000 24 67 0 0 1 0 0 APEX2 27301 broad.mit.edu 37 X 55033116 55033116 + Missense_Mutation SNP C C T rs145122391 TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chrX:55033116C>T ENST00000374987.3 + 6 871 c.805C>T c.(805-807)Cat>Tat p.H269Y APEX2_ENST00000471758.1_3'UTR NM_014481.2 NP_055296.2 Q9UBZ4 APEX2_HUMAN APEX nuclease (apurinic/apyrimidinic endonuclease) 2 269 H -> Y (identified in a patient with mtDNA maintenance disorders). cell cycle|DNA recombination|DNA repair nucleus DNA binding|DNA-(apurinic or apyrimidinic site) lyase activity|endonuclease activity|exonuclease activity|zinc ion binding breast(1)|endometrium(8)|large_intestine(4)|lung(6)|prostate(1)|urinary_tract(1) 21 TGGCGCCCGCCATCTCAACTA 0.597000 Other BER factors 3 22 0 0 1 0 0 SDHAP1 0 broad.mit.edu 37 3 195712586 195712586 + RNA SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr3:195712586C>T ENST00000427841.1 - 0 250 NR_003264.2 AAATGCAGCTCGCAAAGCCGG 0.493000 4 55 0 0 1 0 0 RIBC1 158787 broad.mit.edu 37 X 53455598 53455598 + Silent SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chrX:53455598C>T ENST00000457095.1 + 5 771 c.567C>T c.(565-567)gaC>gaT p.D189D RIBC1_ENST00000375327.3_Intron|RIBC1_ENST00000490702.1_Intron|RIBC1_ENST00000414955.2_Intron NM_144968.2 NP_659405.1 Q8N443 RIBC1_HUMAN RIB43A domain with coiled-coils 1 0 lung(2) 2 GCCCTCCAGACTCAGAGACCT 0.552000 5 19 0 0 1 0 0 VPS9D1 9605 broad.mit.edu 37 16 89785502 89785502 + Silent SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr16:89785502G>A ENST00000389386.3 - 2 232 c.108C>T c.(106-108)taC>taT p.Y36Y VPS9D1_ENST00000561976.1_5'UTR NM_004913.2 NP_004904.2 VPS9 domain containing 1 GGTATTCCGTGTATGCCTCCT 0.552000 17 107 0 0 1 0 0 EXOC4 60412 broad.mit.edu 37 7 133749244 133749244 + Missense_Mutation SNP A A G TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr7:133749244A>G ENST00000253861.4 + 18 2917 c.2888A>G c.(2887-2889)aAg>aGg p.K963R EXOC4_ENST00000539845.1_Missense_Mutation_p.K862R|EXOC4_ENST00000545148.1_Missense_Mutation_p.K573R|EXOC4_ENST00000541309.1_Missense_Mutation_p.K251R NM_021807.3 NP_068579.3 Q96A65 EXOC4_HUMAN exocyst complex component 4 963 vesicle docking involved in exocytosis exocyst protein N-terminus binding NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2) 50 Esophageal squamous(399;0.129) GCTGCCATCAAGCAAGCCACC 0.572000 21 68 0 0 1 0 0 KLHL25 64410 broad.mit.edu 37 15 86311637 86311637 + Missense_Mutation SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr15:86311637C>T ENST00000337975.5 - 2 1679 c.1405G>A c.(1405-1407)Gag>Aag p.E469K KLHL25_ENST00000536947.1_Missense_Mutation_p.E469K|KLHL25_ENST00000559131.1_Intron NM_022480.3 NP_071925.2 Q9H0H3 ENC2_HUMAN kelch-like family member 25 469 cytoplasm breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 25 CACCTGTTCTCCGAGGGGTCA 0.602000 18 137 0 0 1 0 0 HMGN2P46 0 broad.mit.edu 37 15 45848224 45848224 + RNA SNP G G T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr15:45848224G>T ENST00000409454.1 + 0 1219 TGCAGATTTTGTTTAGCTTTT 0.318000 8 19 1.76689e-08 1.88736e-08 1 1 0 NPAP1 23742 broad.mit.edu 37 15 24921605 24921605 + Silent SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr15:24921605C>T ENST00000329468.2 + 1 1065 c.591C>T c.(589-591)gaC>gaT p.D197D NM_018958.2 NP_061831.2 nuclear pore associated protein 1 CCCAGGGAGACGTGGCCTCCT 0.592000 6 44 0 0 1 0 0 POU6F2 11281 broad.mit.edu 37 7 39500263 39500263 + Missense_Mutation SNP A A C TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr7:39500263A>C ENST00000518318.2 + 9 1562 c.1520A>C c.(1519-1521)cAg>cCg p.Q507P POU6F2_ENST00000559001.1_Missense_Mutation_p.Q452P|POU6F2_ENST00000403058.1_Missense_Mutation_p.Q507P P78424 PO6F2_HUMAN POU class 6 homeobox 2 507 POU-specific. central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity p.Q507L(1)|p.Q507R(1) NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 42 CAGGTGGGACAGGCTCTCAGT 0.602000 6 11 0 0 1 0 0 OR10C1 442194 broad.mit.edu 37 6 29407957 29407957 + Missense_Mutation SNP G G T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr6:29407957G>T ENST00000444197.2 + 1 875 c.165G>T c.(163-165)caG>caT p.Q55H OR11A1_ENST00000377149.1_Intron NM_013941.3 NP_039229.3 Q96KK4 O10C1_HUMAN olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene) 55 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|breast(2)|kidney(1)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 27 CTGCCCTCCAGTCCCCTATGT 0.567000 20 159 5.35267e-07 5.59056e-07 1 1 0 TET2 54790 broad.mit.edu 37 4 106155166 106155166 + Missense_Mutation SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr4:106155166C>T ENST00000540549.1 + 3 927 c.67C>T c.(67-69)Ccc>Tcc p.P23S TET2_ENST00000394764.1_Missense_Mutation_p.P23S|TET2_ENST00000305737.2_Missense_Mutation_p.P23S|TET2_ENST00000413648.2_Missense_Mutation_p.P23S|TET2_ENST00000380013.4_Missense_Mutation_p.P23S|TET2_ENST00000513237.1_Missense_Mutation_p.P44S|TET2_ENST00000545826.1_Missense_Mutation_p.P23S Q6N021 TET2_HUMAN tet methylcytosine dioxygenase 2 23 cell cycle|myeloid cell differentiation metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 1314 Myeloproliferative disorder(5;0.0393) OV - Ovarian serous cystadenocarcinoma(123;7.18e-08) ACCATCACCTCCCATTTGCCA 0.527000 """Mis N, F""" MDS 11 43 0 0 1 0 0 ABCA4 24 broad.mit.edu 37 1 94528252 94528252 + Silent SNP G G T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr1:94528252G>T ENST00000370225.3 - 13 1904 c.1818C>A c.(1816-1818)ggC>ggA p.G606G ABCA4_ENST00000535735.1_Silent_p.G606G NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 606 phototransduction, visible light|visual perception integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of substances NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171) AGGCAAACCCGCCCCAGATGT 0.562000 10 30 0.000442599 0.000442599 1 1 0 UBR5 51366 broad.mit.edu 37 8 103266680 103266680 + Silent SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr8:103266680G>A ENST00000520539.1 - 59 8856 c.8250C>T c.(8248-8250)ccC>ccT p.P2750P UBR5_ENST00000518205.1_Silent_p.P478P|UBR5_ENST00000220959.4_Silent_p.P2749P|UBR5_ENST00000521922.1_Silent_p.P2743P NM_015902.5 NP_056986.2 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 5 2750 HECT.|Pro-rich. cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2) 124 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) TTGTGATTGAGGGCATAGGCT 0.408000 10 68 0 0 1 0 0 ANKK1 255239 broad.mit.edu 37 11 113267965 113267965 + Silent SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr11:113267965C>T ENST00000303941.3 + 6 952 c.858C>T c.(856-858)gaC>gaT p.D286D NM_178510.1 NP_848605.1 Q8NFD2 ANKK1_HUMAN ankyrin repeat and kinase domain containing 1 286 Protein kinase. ATP binding|protein serine/threonine kinase activity NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1) 29 all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194) BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238) TCGAGACAGACATACTGCTGT 0.582000 10 37 0 0 1 0 0 HERC2P2 0 broad.mit.edu 37 15 23283162 23283162 + RNA SNP T T C rs409694 TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr15:23283162T>C ENST00000560464.1 - 0 5097 TCCTGTAGGGTGTGTGATGAG 0.547000 5 12 0 0 1 0 0 AP001347.6 0 broad.mit.edu 37 21 15399864 15399864 + RNA SNP T T C rs2298673 by1000genomes TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr21:15399864T>C ENST00000428809.1 + 0 123 TGTGACCTGCTGGCATTGAAT 0.587000 4 49 0 0 1 0 0 NAA15 80155 broad.mit.edu 37 4 140262069 140262069 + Nonsense_Mutation SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr4:140262069G>A ENST00000296543.5 + 4 571 c.248G>A c.(247-249)tGg>tAg p.W83* NAA15_ENST00000480277.2_3'UTR|NAA15_ENST00000398947.1_Nonsense_Mutation_p.W83* NM_057175.3 NP_476516.1 Q9BXJ9 NAA15_HUMAN N(alpha)-acetyltransferase 15, NatA auxiliary subunit 83 angiogenesis|cell differentiation|N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|transcription factor complex protein binding NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 29 TCTTTAGGTTGGCACGTTTAT 0.363000 26 51 0 0 1 0 0 DUSP22 56940 broad.mit.edu 37 6 348272 348272 + Nonsense_Mutation SNP C C T TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr6:348272C>T ENST00000604971.1 + 3 1237 c.124C>T c.(124-126)Cag>Tag p.Q42* DUSP22_ENST00000344450.5_Nonsense_Mutation_p.Q145*|DUSP22_ENST00000605315.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000603453.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000419235.2_Nonsense_Mutation_p.Q145*|DUSP22_ENST00000605035.1_Nonsense_Mutation_p.Q42*|DUSP22_ENST00000605863.1_Nonsense_Mutation_p.Q42* Q9NRW4 DUS22_HUMAN dual specificity phosphatase 22 145 apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway cytoplasm|nucleus protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2) 26 all_hematologic(77;0.228) Breast(5;0.0249)|all_hematologic(90;0.0489) OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669) TGAGGTCCATCAGGTAAGCAG 0.577000 14 132 0 0 1 0 0 FMNL3 91010 broad.mit.edu 37 12 50043069 50043069 + Silent SNP A A G TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr12:50043069A>G ENST00000335154.5 - 20 2591 c.2358T>C c.(2356-2358)taT>taC p.Y786Y FMNL3_ENST00000550488.1_Silent_p.Y786Y|FMNL3_ENST00000352151.5_Silent_p.Y735Y|FMNL3_ENST00000293590.5_Silent_p.Y786Y NM_175736.4 NP_783863.4 Q8IVF7 FMNL3_HUMAN formin-like 3 786 FH2. actin cytoskeleton organization actin binding|Rho GTPase binding breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1) 39 GCTTGAAGCCATACACAGCTC 0.572000 14 94 0 0 1 0 0 EMC10 284361 broad.mit.edu 37 19 50981247 50981247 + Nonsense_Mutation SNP C C G TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr19:50981247C>G ENST00000376918.3 + 2 222 c.176C>G c.(175-177)tCa>tGa p.S59* EMC10_ENST00000334976.6_Nonsense_Mutation_p.S59*|EMC10_ENST00000598585.1_Nonsense_Mutation_p.S59* NM_175063.4 NP_778233.4 ER membrane protein complex subunit 10 CTGGAGCACTCATTTGAGATC 0.607000 3 34 0 0 1 0 0 NF1 4763 broad.mit.edu 37 17 29576001 29576001 + Splice_Site SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr17:29576001G>A ENST00000358273.4 + 30 4357 c.e30-1 NF1_ENST00000356175.3_Splice_Site NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.0?(8)|p.?(4) NF1/ACCN1(2) autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9) 599 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) TTTTTTTGTAGGTTAGAACCA 0.368000 """D, Mis, N, F, S, O""" """neurofibroma, glioma""" """neurofibroma, glioma""" Neurofibromatosis, type 1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) 48 36 0 0 1 0 0 ABCA11P 0 broad.mit.edu 37 4 419639 419639 + RNA SNP T T C rs7681990 by1000genomes TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr4:419639T>C ENST00000451020.2 - 0 1399 NR_002451.2 CTTTACAGAGTTCTAAGAACA 0.438000 4 41 0 0 1 0 0 AC226119.5 0 broad.mit.edu 37 4 3948570 3948570 + RNA SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr4:3948570G>A ENST00000281228.8 - 0 815 FAM86EP_ENST00000313946.8_RNA GGAGCCCGCTGGTGCTCCCGG 0.622000 4 53 0 0 1 0 0 RP11-119F19.2 0 broad.mit.edu 37 10 81444193 81444193 + RNA SNP T T C TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr10:81444193T>C ENST00000600376.1 - 0 54 RP11-119F19.2_ENST00000596088.1_RNA ACGACAAGCTTCAGGGCCTGG 0.627000 2 12 0 0 1 0 0 FUCA1 2517 broad.mit.edu 37 1 24194728 24194728 + Missense_Mutation SNP G G C TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr1:24194728G>C ENST00000374479.3 - 1 56 c.49C>G c.(49-51)Ctg>Gtg p.L17V NM_000147.4 NP_000138.2 P04066 FUCO_HUMAN fucosidase, alpha-L- 1, tissue 17 fucose metabolic process|glycosaminoglycan catabolic process lysosome alpha-L-fucosidase activity|cation binding breast(1)|endometrium(1)|large_intestine(3)|lung(3) 8 Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144) AGCAGCAGCAGCAACAGCGCG 0.746000 2 2 0 0 1 0 0 APOC1P1 0 broad.mit.edu 37 19 45430280 45430280 + RNA SNP C C G rs5112 by1000genomes TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr19:45430280C>G ENST00000574565.1 + 0 71 NR_028412.1 TTCTGTCGATCGTCTTGGAAG 0.607000 3 13 0 0 1 0 0 LINC00610 0 broad.mit.edu 37 11 36293264 36293264 + RNA SNP G G A TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr11:36293264G>A ENST00000355500.1 - 0 307 CAGGTACCAAGATTTTCTCAT 0.498000 9 36 0 0 1 0 0 PSME4 23198 broad.mit.edu 37 2 54148047 54148049 + In_Frame_Del DEL AGG AGG - TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr2:54148047_54148049delAGG ENST00000404125.1 - 18 2294_2296 c.2239_2241delCCT c.(2239-2241)del p.P747del PSME4_ENST00000421748.2_Intron NM_014614.2 NP_055429.2 Q14997 PSME4_HUMAN proteasome (prosome, macropain) activator subunit 4 747 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|multicellular organismal development|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|spermatogenesis|viral reproduction nuclear speck|proteasome complex binding breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2) 60 Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181) AGTATTCAGAAGGAGGCTTGTCA 0.374 22 75 --- --- --- --- ANKRD20A8P 0 broad.mit.edu 37 2 95513688 95513689 + RNA INS - - TA TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr2:95513688_95513689insTA ENST00000432432.2 - 0 850 NR_040113.1 CTCACCTAATGTATAAGATGGA 0.327 8 192 --- --- --- --- C4orf17 84103 broad.mit.edu 37 4 100443784 100443785 + Frame_Shift_Ins INS - - G rs36110345 byFrequency TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr4:100443784_100443785insG ENST00000514652.1 + 3 609_610 c.255_256insG c.(253-258)tcgcacfs p.H86fs C4orf17_ENST00000503257.1_3'UTR|C4orf17_ENST00000326581.4_Frame_Shift_Ins_p.H86fs Q53FE4 CD017_HUMAN chromosome 4 open reading frame 17 86 central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3) 18 OV - Ovarian serous cystadenocarcinoma(123;2.08e-08) GTTACCCCTCCAGCACTGCAGT 0.500 7 93 --- --- --- --- CTC-338M12.9 0 broad.mit.edu 37 5 180708697 180708698 + RNA INS - - A rs1815381 TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr5:180708697_180708698insA ENST00000412295.2 + 0 238 ggggcggtaggcgggggctgga 0.718 3 3 --- --- --- --- RP11-440G9.1 0 broad.mit.edu 37 6 142860298 142860299 + RNA INS - - T rs143051118 by1000genomes TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr6:142860298_142860299insT ENST00000447311.1 - 0 364 NR_027312.1 ttaggccagtatttttttttta 0.470 4 3 --- --- --- --- ST8SIA6 338596 broad.mit.edu 37 10 17495614 17495614 + Frame_Shift_Del DEL G G - TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr10:17495614delG ENST00000377602.4 - 2 218 c.144delC c.(142-144)ccfs p.P48fs NM_001004470.1 NP_001004470.1 P61647 SIA8F_HUMAN ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 48 post-translational protein modification|protein N-linked glycosylation via asparagine integral to Golgi membrane alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1) 37 TCAGCGCTGCGGGGGTGCCGT 0.697 2 4 --- --- --- --- RP11-597A11.1 0 broad.mit.edu 37 14 20138373 20138374 + RNA INS - - AAG rs150133272 TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr14:20138373_20138374insAAG ENST00000548261.1 + 0 391 GAAACAaaagaaagaaagaaag 0.396 4 4 --- --- --- --- RP11-44F14.1 0 broad.mit.edu 37 16 53403273 53403273 + RNA DEL A A - TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr16:53403273delA ENST00000565421.1 - 0 1344 actccatctcaaaaaaaaaag 0.438 3 5 --- --- --- --- PLA2G15 23659 broad.mit.edu 37 16 68293167 68293171 + Frame_Shift_Del DEL CGTGC CGTGC - rs142263893 TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chr16:68293167_68293171delCGTGC ENST00000219345.5 + 6 929_933 c.846_850delCGTGC c.(844-852)ttagfs p.FVQ282fs PLA2G15_ENST00000566188.1_3'UTR|PLA2G15_ENST00000444212.2_Frame_Shift_Del_p.FVQ82fs|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000413021.2_Frame_Shift_Del_p.FVQ188fs NM_012320.3 NP_036452.1 Q8NCC3 PAG15_HUMAN phospholipase A2, group XV 282 fatty acid catabolic process extracellular region|lysosome lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1) 12 AGAAGGTGTTCGTGCAGACACCCAC 0.580 16 67 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76814303 76814306 + Frame_Shift_Del DEL ATAA ATAA - TCGA-HT-7857-01A-11D-2395-08 TCGA-HT-7857-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 58282498-c68f-4b15-89bb-68f49431393c 370dc8dd-90cf-4a60-be75-ccc17f9310fb g.chrX:76814303_76814306delATAA ENST00000373344.5 - 29 6552_6555 c.6338_6341delTTAT c.(6337-6342)tcfs p.FI2113fs ATRX_ENST00000395603.3_Frame_Shift_Del_p.FI2075fs|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 2113 Helicase C-terminal. DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.F2113fs*9(1)|p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) AGTAGAAATGATAAATAATCGTCC 0.289 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 18 68 --- --- --- ---