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 CEP104 9731 broad.mit.edu 37 1 3768869 3768869 + Missense_Mutation SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr1:3768869G>A ENST00000378230.3 - 2 427 c.103C>T c.(103-105)Cgg>Tgg p.R35W CEP104_ENST00000378223.3_Missense_Mutation_p.R35W NM_014704.3 NP_055519.1 O60308 CE104_HUMAN centrosomal protein 104kDa 35 centriole binding breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3) 39 CTAGGTGACCGCCACCCACTG 0.622000 3 21 0 0 1 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 4 32 0 0 1 0 0 RP11-1166P10.6 0 broad.mit.edu 37 16 32070612 32070612 + RNA SNP A A C TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr16:32070612A>C ENST00000566806.1 - 0 499 GGTCTCCTGCAAGGCTTCTGG 0.552000 3 59 0 0 1 0 0 NF1 4763 broad.mit.edu 37 17 29670155 29670155 + Splice_Site SNP T T A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:29670155T>A ENST00000358273.4 + 48 7572 c.e48+2 NF1_ENST00000356175.3_Splice_Site|NF1_ENST00000444181.2_Splice_Site|NF1_ENST00000417592.2_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.?(3) 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) TTTTAAAAGGTAAAAAAGCCT 0.318000 """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) 6 34 0 0 1 0 0 ENKD1 84080 broad.mit.edu 37 16 67700039 67700039 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr16:67700039C>T ENST00000243878.4 - 2 536 c.215G>A c.(214-216)cGc>cAc p.R72H ENKD1_ENST00000602644.1_Missense_Mutation_p.R72H NM_032140.1 NP_115516.1 enkurin domain containing 1 CCCGACGCCGCGCTGGCCGCG 0.662000 8 44 0 0 1 0 0 JAG2 3714 broad.mit.edu 37 14 105615619 105615619 + Silent SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr14:105615619G>A ENST00000331782.3 - 13 2044 c.1641C>T c.(1639-1641)aaC>aaT p.N547N JAG2_ENST00000347004.2_Silent_p.N509N NM_002226.4 NP_002217.3 Q9Y219 JAG2_HUMAN jagged 2 547 EGF-like 9. auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection integral to plasma membrane calcium ion binding|growth factor activity|Notch binding breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5) 22 all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155) OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272) Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208) AGCGAGCGCCGTTCCGGCAGG 0.662000 44 70 0 0 1 0 0 ITLN1 55600 broad.mit.edu 37 1 160850421 160850421 + Silent SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr1:160850421G>A ENST00000326245.3 - 6 757 c.642C>T c.(640-642)ggC>ggT p.G214G ITLN1_ENST00000487531.1_5'UTR NM_017625.2 NP_060095.2 Q8WWA0 ITLN1_HUMAN intelectin 1 (galactofuranose binding) 214 Fibrinogen C-terminal. positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction anchored to membrane|brush border membrane|extracellular region|membrane raft receptor binding|sugar binding breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1) 21 all_cancers(52;2.99e-17)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00737) TCTGGGCGTCGCCAAAATCAT 0.443000 7 261 0 0 1 0 0 ZNRD1-AS1 0 broad.mit.edu 37 6 29977359 29977359 + RNA SNP G G A rs3831361 by1000genomes TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:29977359G>A ENST00000376797.3 - 0 731 ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA ATTTGTTCATGCCTTCCCTTT 0.453000 8 43 0 0 1 0 0 TRBV7-6 0 broad.mit.edu 37 7 142139349 142139349 + RNA SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr7:142139349G>A ENST00000390374.3 - 0 320 GAGTGGAGACGGATCCCTCAG 0.567000 27 94 0 0 1 0 0 NPY1R 0 broad.mit.edu 37 4 164247119 164247119 + Silent SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr4:164247119G>A ENST00000296533.2 - 2 1119 c.588C>T c.(586-588)taC>taT p.Y196Y NPY1R_ENST00000509586.1_Intron NM_000909.5 NP_000900.1 P25929 NPY1R_HUMAN neuropeptide Y receptor Y1 196 inhibition of adenylate cyclase activity by G-protein signaling pathway|outflow tract morphogenesis integral to plasma membrane protein binding breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4) 30 all_hematologic(180;0.166) Prostate(90;0.0959)|all_neural(102;0.223) CAAAGCACACGTATTTGTCTT 0.408000 35 35 0 0 1 0 0 OR1J2 26740 broad.mit.edu 37 9 125273992 125273992 + Silent SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr9:125273992C>A ENST00000335302.5 + 1 912 c.912C>A c.(910-912)ctC>ctA p.L304L NM_054107.1 NP_473448.1 Q8NGS2 OR1J2_HUMAN olfactory receptor, family 1, subfamily J, member 2 304 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1) 26 TTGGGAAACTCTTCAGTAGAG 0.383000 5 77 0.217242 0.22218 1 1 0 THEMIS 387357 broad.mit.edu 37 6 128135074 128135074 + Nonsense_Mutation SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:128135074G>A ENST00000368250.1 - 5 973 c.475C>T c.(475-477)Cga>Tga p.R159* THEMIS_ENST00000368248.2_Nonsense_Mutation_p.R238*|THEMIS_ENST00000537166.1_Nonsense_Mutation_p.R203*|THEMIS_ENST00000543064.1_Nonsense_Mutation_p.R238* Q8N1K5 THMS1_HUMAN thymocyte selection associated 238 CABIT 1. negative T cell selection|positive T cell selection|T cell receptor signaling pathway cytoplasm|nucleus breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3) 60 ATATCTTTTCGAACTAAAAAG 0.333000 37 53 0 0 1 0 0 ZNRD1-AS1 0 broad.mit.edu 37 6 29977358 29977358 + RNA SNP T T C rs146982767 by1000genomes TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:29977358T>C ENST00000376797.3 - 0 731 ZNRD1-AS1_ENST00000420251.1_RNA|ZNRD1-AS1_ENST00000425604.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA GATTTGTTCATGCCTTCCCTT 0.448000 7 43 0 0 1 0 0 SRSF9 8683 broad.mit.edu 37 12 120903592 120903592 + Splice_Site SNP T T A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr12:120903592T>A ENST00000229390.3 - 2 372 c.e2-2 NM_003769.2 NP_003760.1 Q13242 SRSF9_HUMAN serine/arginine-rich splicing factor 9 mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription nucleoplasm nucleotide binding|RNA binding cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1) 9 TCTGCATCTCTAAAAAAAACA 0.453000 3 33 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113112 209113112 + Missense_Mutation SNP C C T rs121913500 TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr2:209113112C>T ENST00000415913.1 - 4 776 c.395G>A c.(394-396)cGt>cAt p.R132H IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) ATAAGCATGACGACCTATGAT 0.393000 Mis gliobastoma 22 51 0 0 1 0 0 IRF2 3660 broad.mit.edu 37 4 185339801 185339801 + Silent SNP G G A rs148758064 byFrequency TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr4:185339801G>A ENST00000393593.3 - 4 456 c.249C>T c.(247-249)tgC>tgT p.C83C IRF2_ENST00000512020.1_5'UTR NM_002199.3 NP_002190.2 P14316 IRF2_HUMAN interferon regulatory factor 2 83 blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway focal adhesion|nucleoplasm DNA binding|protein binding|sequence-specific DNA binding transcription factor activity cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2) 22 all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592) all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419) AATTCATGGCGCATCTGAAAT 0.398000 4 45 0 0 1 0 0 PGLYRP2 114770 broad.mit.edu 37 19 15582755 15582755 + Missense_Mutation SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr19:15582755C>A ENST00000292609.4 - 3 1418 c.1289G>T c.(1288-1290)cGc>cTc p.R430L PGLYRP2_ENST00000340880.4_Missense_Mutation_p.R430L Q96PD5 PGRP2_HUMAN peptidoglycan recognition protein 2 430 defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process extracellular region|intracellular|membrane N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1) 28 CTGCATGGAGCGCATGTTGGC 0.672000 3 45 0.150653 0.157661 1 1 0 GTF2IRD1 9569 broad.mit.edu 37 7 74016720 74016720 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr7:74016720C>T ENST00000265755.3 + 27 3233 c.2840C>T c.(2839-2841)gCc>gTc p.A947V GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A932V|GTF2IRD1_ENST00000476977.1_3'UTR|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A964V NM_005685.3|NM_016328.2 NP_005676.3|NP_057412.1 Q9UHL9 GT2D1_HUMAN GTF2I repeat domain containing 1 947 nucleus DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 49 GTGGACTATGCCGGCCTGAAC 0.468000 3 80 0 0 1 0 0 ZNF782 158431 broad.mit.edu 37 9 99581580 99581580 + Missense_Mutation SNP G G C TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr9:99581580G>C ENST00000481138.1 - 6 1386 c.725C>G c.(724-726)tCt>tGt p.S242C ZNF782_ENST00000535338.1_Missense_Mutation_p.S110C NM_001001662.1 NP_001001662.1 Q6ZMW2 ZN782_HUMAN zinc finger protein 782 242 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3) 33 Acute lymphoblastic leukemia(62;0.0527) GAAATTGTAAGATTTTCCTTT 0.333000 7 85 0 0 1 0 0 NF1 4763 broad.mit.edu 37 17 29553697 29553697 + Nonsense_Mutation SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:29553697C>A ENST00000358273.4 + 18 2629 c.2246C>A c.(2245-2247)tCa>tAa p.S749* NF1_ENST00000356175.3_Nonsense_Mutation_p.S749* NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 749 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)|p.S749*(1) 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) AATATGATGTCAACAGGTAAA 0.403000 """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) 7 162 0.00198382 0.00212552 1 1 0 NOS1 4842 broad.mit.edu 37 12 117669890 117669890 + Silent SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr12:117669890G>A ENST00000317775.6 - 22 3967 c.3282C>T c.(3280-3282)acC>acT p.T1094T NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000338101.4_Silent_p.T1128T NM_000620.4|NM_001204218.1 NP_000611.1|NP_001191147.1 P29475 NOS1_HUMAN nitric oxide synthase 1 (neuronal) 1094 FAD-binding FR-type. multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 117 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) BRCA - Breast invasive adenocarcinoma(302;0.0561) L-Citrulline(DB00155) CCTGGAAGATGGTGCAGGGCG 0.592000 19 19 0 0 1 0 0 PHACTR3 116154 broad.mit.edu 37 20 58381107 58381107 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr20:58381107C>T ENST00000371015.1 + 8 1653 c.1186C>T c.(1186-1188)Cgg>Tgg p.R396W PHACTR3_ENST00000355648.4_Missense_Mutation_p.R355W|PHACTR3_ENST00000361300.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000395636.2_Missense_Mutation_p.R355W|PHACTR3_ENST00000395639.4_Missense_Mutation_p.R285W|PHACTR3_ENST00000359926.3_Missense_Mutation_p.R393W|PHACTR3_ENST00000541461.1_Missense_Mutation_p.R355W NM_080672.3 NP_542403.1 Q96KR7 PHAR3_HUMAN phosphatase and actin regulator 3 396 nuclear matrix actin binding|protein phosphatase inhibitor activity endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|liver(2)|lung(32)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 59 all_lung(29;0.00344) BRCA - Breast invasive adenocarcinoma(7;2.76e-09) AACACTGCCACGGAAATGCAA 0.547000 61 249 0 0 1 0 0 KRTAP13-1 140258 broad.mit.edu 37 21 31768834 31768834 + Missense_Mutation SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr21:31768834G>A ENST00000355459.2 + 1 443 c.430G>A c.(430-432)Gtt>Att p.V144I NM_181599.2 NP_853630.2 Q8IUC0 KR131_HUMAN keratin associated protein 13-1 144 intermediate filament endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 GGGCTATGGCGTTGGATTCTG 0.542000 15 16 0 0 1 0 0 ZDHHC11 79844 broad.mit.edu 37 5 814876 814876 + Splice_Site SNP C C G rs138424733 TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr5:814876C>G ENST00000283441.8 - 11 1564 c.1181_splice c.e11+1 p.G394_splice ZDHHC11_ENST00000424784.2_Splice_Site_p.G394_splice|ZDHHC11_ENST00000503758.2_5'UTR NM_024786.2 NP_079062.1 Q9H8X9 ZDH11_HUMAN zinc finger, DHHC-type containing 11 394 integral to membrane acyltransferase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1) 21 Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863) ACGAACTTACCCAAGTGTAGA 0.378000 25 31 0 0 1 0 0 KIF26A 26153 broad.mit.edu 37 14 104643666 104643666 + Nonsense_Mutation SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr14:104643666C>A ENST00000315264.7 + 11 4502 c.4124C>A c.(4123-4125)tCg>tAg p.S1375* KIF26A_ENST00000423312.2_Nonsense_Mutation_p.S1514* Q9ULI4 KI26A_HUMAN kinesin family member 26A 1514 blood coagulation|enteric nervous system development|microtubule-based movement|negative regulation of signal transduction|regulation of cell growth by extracellular stimulus cytosol|microtubule ATP binding|microtubule binding|microtubule motor activity autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2) 21 all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767) Epithelial(46;0.152) Epithelial(152;0.161) CTGGGGCCTTCGGTGAAGCTG 0.736000 2 4 1 1 1 1 0 IRF2BP1 26145 broad.mit.edu 37 19 46387378 46387378 + Missense_Mutation SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr19:46387378C>A ENST00000302165.3 - 1 1998 c.1655G>T c.(1654-1656)tGc>tTc p.C552F NM_015649.1 NP_056464.1 Q8IU81 I2BP1_HUMAN interferon regulatory factor 2 binding protein 1 552 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus cervix(1)|kidney(1)|lung(2) 4 all_neural(266;0.113)|Ovarian(192;0.127) OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231) GACCAGCGGGCACTTGTCTCC 0.642000 13 4 7.93312e-07 8.92476e-07 1 1 0 PWP2 5822 broad.mit.edu 37 21 45540355 45540355 + Missense_Mutation SNP G G A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr21:45540355G>A ENST00000291576.7 + 11 1442 c.1315G>A c.(1315-1317)Gtg>Atg p.V439M NM_005049.2 NP_005040.2 Q15269 PWP2_HUMAN PWP2 periodic tryptophan protein homolog (yeast) 439 cytoplasm|nucleolus signal transducer activity cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1) 21 STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2) GGACGGGACCGTGCGAGCCTT 0.597000 67 80 0 0 1 0 0 NPTX1 4884 broad.mit.edu 37 17 78444660 78444660 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:78444660C>T ENST00000306773.4 - 5 1409 c.1252G>A c.(1252-1254)Gga>Aga p.G418R NM_002522.3 NP_002513.2 Q15818 NPTX1_HUMAN neuronal pentraxin I 418 Pentaxin. central nervous system development|synaptic transmission|transport transport vesicle metal ion binding kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1) 11 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487) GTGGCCCCTCCGTAGATCTCG 0.662000 7 48 0 0 1 0 0 NT5C 30833 broad.mit.edu 37 17 73126675 73126675 + Missense_Mutation SNP C C A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:73126675C>A ENST00000245552.2 - 5 601 c.514G>T c.(514-516)Gtc>Ttc p.V172F NT5C_ENST00000578337.1_3'UTR|NT5C_ENST00000582170.1_Missense_Mutation_p.G170V|NT5C_ENST00000582160.1_Missense_Mutation_p.V86F NM_014595.2 NP_055410.1 Q8TCD5 NT5C_HUMAN 5', 3'-nucleotidase, cytosolic 172 purine base metabolic process|purine nucleotide catabolic process|pyrimidine base metabolic process|pyrimidine deoxyribonucleotide catabolic process|pyrimidine nucleoside catabolic process cytosol|nucleus 5'-nucleotidase activity|metal ion binding|pyrimidine nucleotide binding all_lung(278;0.14)|Lung NSC(278;0.168) LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235) GGGGGCAGGACCAGGTGCCGA 0.607000 OREG0024728 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 25 42 9.93527e-08 1.14638e-07 1 1 0 TXK 7294 broad.mit.edu 37 4 48114404 48114404 + Silent SNP A A G TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr4:48114404A>G ENST00000264316.4 - 4 385 c.300T>C c.(298-300)aaT>aaC p.N100N TXK_ENST00000510457.1_5'UTR NM_003328.2 NP_003319.2 P42681 TXK_HUMAN TXK tyrosine kinase 100 SH3. cytoplasm ATP binding|non-membrane spanning protein tyrosine kinase activity breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2) 25 TTAAGGCTAAATTACAGGGTT 0.468000 26 136 0 0 1 0 0 DNAH8 1769 broad.mit.edu 37 6 38690599 38690599 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:38690599C>T ENST00000449981.2 + 2 123 c.14C>T c.(13-15)gCt>gTt p.A5V 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 GAGAAGGATGCTGAAGATGGC 0.532000 9 13 0 0 1 0 0 FKBP8 23770 broad.mit.edu 37 19 18650228 18650228 + Silent SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr19:18650228C>T ENST00000597960.2 - 4 624 c.504G>A c.(502-504)acG>acA p.T168T FKBP8_ENST00000453489.2_Silent_p.T197T|FKBP8_ENST00000222308.3_Silent_p.T168T|FKBP8_ENST00000544835.2_Intron|FKBP8_ENST00000596558.1_Silent_p.T168T Q14318 FKBP8_HUMAN FK506 binding protein 8, 38kDa 168 PPIase FKBP-type. apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding integral to endoplasmic reticulum membrane|mitochondrial membrane FK506 binding|peptidyl-prolyl cis-trans isomerase activity|protein binding breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1) 15 TGACCATGGCCGTCTCCCCCA 0.637000 49 48 0 0 1 0 0 FRMPD4 9758 broad.mit.edu 37 X 12701668 12701668 + Missense_Mutation SNP C C T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chrX:12701668C>T ENST00000380682.1 + 6 1041 c.535C>T c.(535-537)Cgc>Tgc p.R179C NM_014728.3 NP_055543.2 Q14CM0 FRPD4_HUMAN FERM and PDZ domain containing 4 179 positive regulation of synapse structural plasticity cytoskeleton|dendritic spine phosphatidylinositol-4,5-bisphosphate binding|protein binding breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3) 22 TGTCAAAGTACGCTTCTCTGA 0.423000 24 3 0 0 1 0 0 PLEKHG4B 153478 broad.mit.edu 37 5 143249 143249 + Missense_Mutation SNP G G A rs115149634 byFrequency TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr5:143249G>A ENST00000283426.6 + 2 547 c.497G>A c.(496-498)cGg>cAg p.R166Q NM_052909.3 NP_443141.3 Q96PX9 PKH4B_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 4B 166 regulation of Rho protein signal transduction intracellular Rho guanyl-nucleotide exchange factor activity endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3) 11 all cancers(22;0.0253)|Lung(60;0.113) Kidney(1;0.119) GTGCCTGCCCGGCAGCCACAC 0.647000 18 52 0 0 1 0 0 SMC4 10051 broad.mit.edu 37 3 160137299 160137299 + Missense_Mutation SNP T T A TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr3:160137299T>A ENST00000357388.3 + 12 2276 c.1825T>A c.(1825-1827)Tct>Act p.S609T SMC4_ENST00000469762.1_Missense_Mutation_p.S584T|SMC4_ENST00000344722.5_Missense_Mutation_p.S609T|SMC4_ENST00000360111.2_Missense_Mutation_p.S609T|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000462787.1_Missense_Mutation_p.S609T NM_001002800.1 NP_001002800.1 Q9NTJ3 SMC4_HUMAN structural maintenance of chromosomes 4 609 Flexible hinge. cell division|mitotic chromosome condensation condensin complex|cytoplasm|nucleus ATP binding|protein heterodimerization activity breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 48 Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523) AGAAAAAAAATCTGGCAGGAT 0.343000 35 53 0 0 1 0 0 NPAS3 64067 broad.mit.edu 37 14 34263252 34263252 + Splice_Site SNP T T G TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr14:34263252T>G ENST00000346562.2 + 9 1279 c.e9+2 NPAS3_ENST00000551492.1_Splice_Site|NPAS3_ENST00000548645.1_Splice_Site|NPAS3_ENST00000357798.5_Splice_Site|NPAS3_ENST00000356141.4_Splice_Site NM_001164749.1|NM_001165893.1|NM_022123.2|NM_173159.2 NP_001158221.1|NP_001159365.1|NP_071406.1|NP_775182.1 Q8IXF0 NPAS3_HUMAN neuronal PAS domain protein 3 regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|signal transducer activity breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 40 Breast(36;0.0102)|Hepatocellular(127;0.133) LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968) GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115) CCTTCTTAGGTATATTTTCTA 0.333000 25 39 0 0 1 0 0 FUBP1 8880 broad.mit.edu 37 1 78433848 78433851 + Splice_Site DEL CAGT CAGT - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr1:78433848_78433851delCAGT ENST00000370767.1 - 3 335_338 c.250_splice c.e3+1 p.83_splice FUBP1_ENST00000436586.2_Splice_Site_p.104_splice|FUBP1_ENST00000370768.2_Splice_Site_p.83_splice Q96AE4 FUBP1_HUMAN far upstream element (FUSE) binding protein 1 83 transcription from RNA polymerase II promoter nucleus protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding p.?(1) central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3) 17 GGAATACTTACAGTCATTTTGAGG 0.319 """F, N""" oligodendroglioma 20 11 --- --- --- --- HGD 3081 broad.mit.edu 37 3 120357338 120357338 + Frame_Shift_Del DEL C C - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr3:120357338delC ENST00000283871.5 - 12 1429 c.970delG c.(970-972)ttfs p.V324fs NM_000187.3 NP_000178.2 Q93099 HGD_HUMAN homogentisate 1,2-dioxygenase 324 L-phenylalanine catabolic process|tyrosine catabolic process cytosol homogentisate 1,2-dioxygenase activity|metal ion binding cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2) 25 GBM - Glioblastoma multiforme(114;0.158) TTATCAGCAACCCCCCATCGA 0.483 23 94 --- --- --- --- WDFY3 23001 broad.mit.edu 37 4 85731329 85731331 + In_Frame_Del DEL GAA GAA - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr4:85731329_85731331delGAA ENST00000322366.6 - 14 2461_2463 c.2054_2056delTTC c.(2053-2058)cac>c p.LH685del WDFY3-AS1_ENST00000510449.1_RNA|WDFY3_ENST00000295888.4_In_Frame_Del_p.LH685del Q8IZQ1 WDFY3_HUMAN WD repeat and FYVE domain containing 3 685 cytoplasmic part|extrinsic to membrane|nuclear envelope 1-phosphatidylinositol binding|metal ion binding|protein binding breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 134 Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000808) AACACAGTGTGAAGAAGTTCAAA 0.448 28 51 --- --- --- --- FAM149A 25854 broad.mit.edu 37 4 187084676 187084678 + In_Frame_Del DEL CTT CTT - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr4:187084676_187084678delCTT ENST00000356371.5 + 10 1805_1807 c.1805_1807delCTT c.(1804-1809)cct>c p.PS602del FAM149A_ENST00000514153.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000503432.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000502970.1_In_Frame_Del_p.PS311del|FAM149A_ENST00000389354.5_In_Frame_Del_p.PS311del|FAM149A_ENST00000227065.4_In_Frame_Del_p.PS311del A5PLN7 F149A_HUMAN family with sequence similarity 149, member A 602 breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2) 25 all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243) OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166) GGATTATCACCTTCTGCAAAGAA 0.532 10 76 --- --- --- --- PIK3R1 5295 broad.mit.edu 37 5 67591105 67591107 + In_Frame_Del DEL TAA TAA - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr5:67591105_67591107delTAA ENST00000521381.1 + 13 2314_2316 c.1698_1700delTAA c.(1696-1701)ata>at p.IK566del PIK3R1_ENST00000521657.1_In_Frame_Del_p.IK566del|PIK3R1_ENST00000396611.1_In_Frame_Del_p.IK566del|PIK3R1_ENST00000320694.8_In_Frame_Del_p.IK266del|PIK3R1_ENST00000523872.1_In_Frame_Del_p.IK203del|PIK3R1_ENST00000336483.5_In_Frame_Del_p.IK296del|PIK3R1_ENST00000274335.5_In_Frame_Del_p.IK566del NM_181523.2 NP_852664.1 P27986 P85A_HUMAN phosphoinositide-3-kinase, regulatory subunit 1 (alpha) 566 epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway 1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex 1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297E(1)|p.K567_L570delKPDL(1)|p.K567E(1)|p.K267E(1)|p.K297_L300delKPDL(1) breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2) 178 Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176) OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211) Isoproterenol(DB01064) TGAACAGCATTAAACCAGACCTT 0.369 """Mis, F, O""" """gliobastoma, ovarian, colorectal""" TCGA GBM(4;<1E-08) 16 108 --- --- --- --- MAN2A1 4124 broad.mit.edu 37 5 109049430 109049433 + Frame_Shift_Del DEL CTGT CTGT - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr5:109049430_109049433delCTGT ENST00000261483.4 + 2 1397_1400 c.345_348delCTGT c.(343-348)gafs p.DC115fs NM_002372.2 NP_002363.2 Q16706 MA2A1_HUMAN mannosidase, alpha, class 2A, member 1 115 mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine Golgi membrane|integral to membrane alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 55 all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244) OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141) ACACTGCAGACTGTCTGTTTGCTT 0.407 38 135 --- --- --- --- COL11A2 1302 broad.mit.edu 37 6 33159977 33159979 + In_Frame_Del DEL AGG AGG - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:33159977_33159979delAGG ENST00000341947.2 - 1 266_268 c.39_41delCCT c.(37-42)cta>ct p.LL13del COL11A2_ENST00000357486.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000361917.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000395194.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374713.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374714.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374712.1_In_Frame_Del_p.LL13del|COL11A2_ENST00000374708.4_In_Frame_Del_p.LL13del|COL11A2_ENST00000395197.1_In_Frame_Del_p.LL13del NM_080680.2 NP_542411.2 P13942 COBA2_HUMAN collagen, type XI, alpha 2 13 cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development collagen type XI extracellular matrix structural constituent conferring tensile strength|protein binding, bridging biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6) 68 CACCAGAGGTAGGAGGAGGAGGA 0.675 3 3 --- --- --- --- HDAC2 3066 broad.mit.edu 37 6 114277842 114277844 + In_Frame_Del DEL TCT TCT - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr6:114277842_114277844delTCT ENST00000519065.1 - 4 673_675 c.297_299delAGA c.(295-300)gat>ga p.ED99del HDAC2_ENST00000398283.2_In_Frame_Del_p.ED193del|HDAC2_ENST00000519108.1_In_Frame_Del_p.ED69del|HDAC2_ENST00000368632.2_In_Frame_Del_p.ED69del Q92769 HDAC2_HUMAN histone deacetylase 2 99 Histone deacetylase. blood coagulation|dendrite development|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|maintenance of chromatin silencing|negative regulation of apoptosis|negative regulation of cell cycle|negative regulation of neuron projection development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of proteolysis|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter cytoplasm|ESC/E(Z) complex|NuRD complex|Sin3 complex chromatin binding|enzyme binding|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)|sequence-specific DNA binding|transcription factor binding biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2) 27 all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24) all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832) Vorinostat(DB02546) CACTGGACAATCTTCTCCAACAT 0.350 15 16 --- --- --- --- ZAN 7455 broad.mit.edu 37 7 100369720 100369721 + RNA INS - - T TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr7:100369720_100369721insT ENST00000542585.1 + 0 5573 ZAN_ENST00000443370.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000348028.3_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546292.1_RNA NM_003386.1 NP_003377.1 Q9Y493 ZAN_HUMAN zonadhesin (gene/pseudogene) binding of sperm to zona pellucida|cell-cell adhesion integral to membrane|plasma membrane NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3) 139 Lung NSC(181;0.041)|all_lung(186;0.0581) STAD - Stomach adenocarcinoma(171;0.19) cctctaaattcttttttttttt 0.535 4 7 --- --- --- --- MAPK15 225689 broad.mit.edu 37 8 144801230 144801230 + Frame_Shift_Del DEL T T - rs139710965 byFrequency TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr8:144801230delT ENST00000338033.4 + 6 604 c.485delT c.(484-486)cgfs p.L162fs MAPK15_ENST00000395108.2_Frame_Shift_Del_p.L162fs|MAPK15_ENST00000395107.4_Frame_Shift_Del_p.L179fs NM_139021.2 NP_620590.2 Q8TD08 MK15_HUMAN mitogen-activated protein kinase 15 162 Protein kinase. protein autophosphorylation extracellular region ATP binding|MAP kinase activity|SH3 domain binding endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1) 12 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) GCCCGCTCCCTGGGCGACCTC 0.667 2 4 --- --- --- --- NOTCH1 4851 broad.mit.edu 37 9 139391997 139391998 + Frame_Shift_Del DEL AG AG - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr9:139391997_139391998delAG ENST00000277541.6 - 34 6268_6269 c.6193_6194delCT c.(6193-6195)gfs p.L2065fs NM_017617.3 NP_060087.3 P46531 NOTC1_HUMAN notch 1 2065 aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3) 1359 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) GGCCAGAAACAGGGGTGTCTCC 0.683 """T, Mis, O""" TRB@ T-ALL HNSCC(8;0.001) 17 14 --- --- --- --- NOTCH1 4851 broad.mit.edu 37 9 139395163 139395166 + Frame_Shift_Del DEL GTCT GTCT - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr9:139395163_139395166delGTCT ENST00000277541.6 - 31 5847_5850 c.5772_5775delAGAC c.(5770-5775)acfs p.TD1924fs NM_017617.3 NP_060087.3 P46531 NOTC1_HUMAN notch 1 1924 aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane calcium ion binding|protein binding|receptor activity breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3) 1359 all_cancers(76;0.223) Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06) CGCCCGTGCGGTCTGTCTGGTTGT 0.686 """T, Mis, O""" TRB@ T-ALL HNSCC(8;0.001) 41 137 --- --- --- --- PHLPP2 23035 broad.mit.edu 37 16 71692597 71692599 + In_Frame_Del DEL TGT TGT - rs145938775 TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr16:71692597_71692599delTGT ENST00000393524.2 - 12 2637_2639 c.1904_1906delACA c.(1903-1908)atc>a p.NI635del PHLPP2_ENST00000568954.1_In_Frame_Del_p.NI702del|PHLPP2_ENST00000567016.1_In_Frame_Del_p.NI737del|RP11-432I5.6_ENST00000567077.1_RNA|PHLPP2_ENST00000356272.3_In_Frame_Del_p.NI702del|PHLPP2_ENST00000540628.1_5'UTR|PHLPP2_ENST00000360429.3_In_Frame_Del_p.NI702del Q6ZVD8 PHLP2_HUMAN PH domain and leucine rich repeat protein phosphatase 2 702 cytoplasm|membrane|nucleus metal ion binding|phosphoprotein phosphatase activity central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1) 37 AAAATGCTGATGTTGTTGGAGTG 0.458 25 135 --- --- --- --- NF1 4763 broad.mit.edu 37 17 29546036 29546037 + Frame_Shift_Del DEL AG AG - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:29546036_29546037delAG ENST00000358273.4 + 14 1924_1925 c.1541_1542delAG c.(1540-1542)cfs p.Q514fs NF1_ENST00000356175.3_Frame_Shift_Del_p.Q514fs|NF1_ENST00000431387.4_Frame_Shift_Del_p.Q514fs NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 514 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.?(6)|p.Q514fs*43(2)|p.N510_E547del(1) 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) CCAAGAAAACAGGGGCCCGAAA 0.426 """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) 7 13 --- --- --- --- NF1 4763 broad.mit.edu 37 17 29652976 29652979 + Frame_Shift_Del DEL TCTC TCTC - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr17:29652976_29652979delTCTC ENST00000358273.4 + 37 5357_5360 c.4974_4977delTCTC c.(4972-4977)ttfs p.FL1658fs NF1_ENST00000356175.3_Frame_Shift_Del_p.FL1637fs|NF1_ENST00000581113.2_3'UTR NM_001042492.2 NP_001035957.1 P21359 NF1_HUMAN neurofibromin 1 1658 CRAL-TRIO. 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.?(3)|p.S1660fs*37(2) 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) AAACAGACTTTCTCTCTAAGTGGT 0.422 """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) 11 168 --- --- --- --- PLIN4 729359 broad.mit.edu 37 19 4510914 4510916 + In_Frame_Del DEL TGG TGG - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chr19:4510914_4510916delTGG ENST00000301286.3 - 3 3013_3015 c.3014_3016delCCA c.(3013-3018)aag>a p.TK1005del NM_001080400.1 NP_001073869.1 Q96Q06 PLIN4_HUMAN perilipin 4 1005 lipid particle|plasma membrane NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2) 41 AGCACTGTCTTGGTGGTGTCCAG 0.626 22 28 --- --- --- --- BCORL1 63035 broad.mit.edu 37 X 129147257 129147259 + In_Frame_Del DEL AGA AGA - TCGA-DU-6394-01A-11D-1705-08 TCGA-DU-6394-10A-01D-1705-08 Untested Somatic Phase_I WXS none Illumina GAIIx 611b0bd5-fb3a-4c10-999c-e4b3f6980d0b d7371b5d-ee62-450e-bc22-082b1de3911b g.chrX:129147257_129147259delAGA ENST00000540052.1 + 3 553_555 c.509_511delAGA c.(508-513)gag>g p.EK170del BCORL1_ENST00000218147.7_In_Frame_Del_p.EK170del|BCORL1_ENST00000359304.2_In_Frame_Del_p.EK170del|BCORL1_ENST00000303743.5_In_Frame_Del_p.EK170del NM_021946.4 NP_068765.3 Q5H9F3 BCORL_HUMAN BCL6 corepressor-like 1 170 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 75 GGTGTTGGAGAGAAGAATACTTT 0.552 9 21 --- --- --- ---