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_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
GBP1	2633	broad.mit.edu	37	1	89520410	89520410	+	Silent	SNP	G	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:89520410G>C	uc001dmx.2	-	10	1840	c.1620C>G	c.(1618-1620)GTC>GTG	p.V540V		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	540					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)|skin(1)	2		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		TCAGCAACTGGACCCTGTCGT	0.433													86	281					0	0	0.870114	0	0
RSBN1	54665	broad.mit.edu	37	1	114310931	114310931	+	Missense_Mutation	SNP	C	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:114310931C>G	uc001edq.2	-	5	1775	c.1739G>C	c.(1738-1740)AGA>ACA	p.R580T	RSBN1_uc001edr.2_RNA	NM_018364	NP_060834	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	580						nucleus				ovary(1)	1	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCATGAGCTCTAGTCCTATC	0.433													45	67					0	0	0.859065	0	0
NBPF10	100132406	broad.mit.edu	37	1	145367739	145367739	+	Silent	SNP	A	G	G	rs146714035	by1000genomes	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:145367739A>G	uc001end.3	+	85	10595	c.10560A>G	c.(10558-10560)AAA>AAG	p.K3520K	NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406	3445											0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ggaaggggaaaaaaagaaggg	0.244													5	125					0	0	0.184627	0	0
GABPB2	126626	broad.mit.edu	37	1	151070440	151070440	+	Missense_Mutation	SNP	C	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr1:151070440C>A	uc001ewr.2	+	5	915	c.584C>A	c.(583-585)GCA>GAA	p.A195E	GABPB2_uc010pcp.1_Missense_Mutation_p.A211E|GABPB2_uc001ews.2_Missense_Mutation_p.A155E|GABPB2_uc001ewt.2_Missense_Mutation_p.A94E	NM_144618	NP_653219	Q8TAK5	GABP2_HUMAN	GA repeat binding protein, beta 2	195					positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	protein heterodimerization activity|transcription regulatory region DNA binding				0				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		GTTAACCTCGCAAGCCTTATT	0.413													8	52					2.27111e-07	2.4945e-07	0.411799	1	0
GLYAT	10249	broad.mit.edu	37	11	58477535	58477535	+	Missense_Mutation	SNP	G	A	A	rs138125182		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:58477535G>A	uc001nnb.2	-	6	750	c.595C>T	c.(595-597)CGC>TGC	p.R199C		NM_201648	NP_964011	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase isoform a	199					acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process	mitochondrial matrix	glycine N-acyltransferase activity|glycine N-benzoyltransferase activity				0		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TGAATGCAGCGCTCAATGAAT	0.502													62	78					0	0	0.870114	0	0
C2CD3	26005	broad.mit.edu	37	11	73829328	73829328	+	Missense_Mutation	SNP	C	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:73829328C>G	uc001ouu.2	-	9	1692	c.1465G>C	c.(1465-1467)GTT>CTT	p.V489L	C2CD3_uc001ouv.2_Missense_Mutation_p.V489L	NM_015531	NP_056346	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	489						centrosome				ovary(4)|pancreas(2)|skin(1)	7	Breast(11;4.16e-06)					GACTCCAGAACCTTAGATGAT	0.413													50	75					0	0	0.870114	0	0
BCL9L	283149	broad.mit.edu	37	11	118772822	118772822	+	Missense_Mutation	SNP	G	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:118772822G>C	uc001pug.2	-	6	2595	c.1630C>G	c.(1630-1632)CGT>GGT	p.R544G	BCL9L_uc009zal.2_Missense_Mutation_p.R539G	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	544					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TGCAGAGGACGGCTCCCATGC	0.632													3	93					0	0	0.115264	0	0
ST14	6768	broad.mit.edu	37	11	130069892	130069892	+	Silent	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr11:130069892C>T	uc001qfw.2	+	16	2047	c.1854C>T	c.(1852-1854)GGC>GGT	p.G618G		NM_021978	NP_068813	Q9Y5Y6	ST14_HUMAN	matriptase	618	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to plasma membrane	serine-type endopeptidase activity			ovary(2)|skin(2)|central_nervous_system(1)	5	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	TTGTTGGGGGCACGGATGCGG	0.617													6	119					0	0	0.248553	0	0
HOXC13	3229	broad.mit.edu	37	12	54338833	54338833	+	Silent	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr12:54338833G>A	uc001sei.2	+	2	901	c.786G>A	c.(784-786)AAG>AAA	p.K262K	HOXC13_uc010sop.1_RNA	NM_017410	NP_059106	P31276	HXC13_HUMAN	homeobox C13	262	Homeobox.					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)	1						GCGGGCGCAAGAAACGCGTGC	0.612			T	NUP98	AML								86	144					0	0	0.870114	0	0
TBC1D4	9882	broad.mit.edu	37	13	75873512	75873512	+	Missense_Mutation	SNP	T	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr13:75873512T>A	uc001vjl.1	-	17	3457	c.3110A>T	c.(3109-3111)GAC>GTC	p.D1037V	TBC1D4_uc010tht.1_Missense_Mutation_p.D247V|TBC1D4_uc010thu.1_Missense_Mutation_p.D194V|TBC1D4_uc010aer.2_Missense_Mutation_p.D1029V|TBC1D4_uc010aes.2_Missense_Mutation_p.D974V	NM_014832	NP_055647	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1037	Rab-GAP TBC.					cytoplasm	Rab GTPase activator activity			ovary(4)|central_nervous_system(1)|skin(1)	6		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GAAGCCGAGGTCATACATGAG	0.512													3	43					0	0	0.150653	0	0
PLCG2	5336	broad.mit.edu	37	16	81969947	81969947	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr16:81969947G>A	uc002fgt.2	+	27	3168	c.3016G>A	c.(3016-3018)GGT>AGT	p.G1006S		NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	1006	PI-PLC Y-box.				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8						CTGGCTGTGCGGTTCTCAGAT	0.572													51	55					0	0	0.870114	0	0
TP53	7157	broad.mit.edu	37	17	7577548	7577548	+	Missense_Mutation	SNP	C	T	T	rs28934575		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7577548C>T	uc002gim.2	-	7	927	c.733G>A	c.(733-735)GGC>AGC	p.G245S	TP53_uc002gig.1_Missense_Mutation_p.G245S|TP53_uc002gih.2_Missense_Mutation_p.G245S|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.G113S|TP53_uc010cng.1_Missense_Mutation_p.G113S|TP53_uc002gii.1_Missense_Mutation_p.G113S|TP53_uc010cnh.1_Missense_Mutation_p.G245S|TP53_uc010cni.1_Missense_Mutation_p.G245S|TP53_uc002gij.2_Missense_Mutation_p.G245S|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.G152S|TP53_uc002gio.2_Missense_Mutation_p.G113S	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	245	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		G -> N (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> A (in sporadic cancers; somatic mutation).|G -> V (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> F (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> R (in sporadic cancers; somatic mutation).|G -> E (in a sporadic cancer; somatic mutation).|G -> D (in LFS; germline mutation and in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> L (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|G -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.G245S(274)|p.G245D(93)|p.G245V(50)|p.G245C(47)|p.G245R(10)|p.G245A(8)|p.0?(7)|p.G245G(3)|p.G245fs*2(3)|p.G245N(2)|p.G245H(1)|p.G245L(1)|p.G244fs*17(1)|p.G245F(1)|p.G245E(1)|p.C242_M246>L(1)|p.C238_M246delCNSSCMGGM(1)|p.S241_G245delSCMGG(1)|p.C242fs*98(1)|p.G245fs*22(1)|p.M243fs*18(1)|p.G245del(1)|p.G245fs*14(1)|p.G245fs*17(1)|p.G245fs*16(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CGGTTCATGCCGCCCATGCAG	0.577	G245S(SKLMS1_SOFT_TISSUE)|G245S(LS1034_LARGE_INTESTINE)|G245S(NUGC2_STOMACH)|G245S(PANC0403_PANCREAS)|G245S(SKMEL2_SKIN)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			4	90					0	0	0.150653	0	0
TP53	7157	broad.mit.edu	37	17	7578190	7578190	+	Missense_Mutation	SNP	T	C	C	rs121912666		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:7578190T>C	uc002gim.2	-	6	853	c.659A>G	c.(658-660)TAT>TGT	p.Y220C	TP53_uc002gig.1_Missense_Mutation_p.Y220C|TP53_uc002gih.2_Missense_Mutation_p.Y220C|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.Y88C|TP53_uc010cng.1_Missense_Mutation_p.Y88C|TP53_uc002gii.1_Missense_Mutation_p.Y88C|TP53_uc010cnh.1_Missense_Mutation_p.Y220C|TP53_uc010cni.1_Missense_Mutation_p.Y220C|TP53_uc002gij.2_Missense_Mutation_p.Y220C|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.Y127C|TP53_uc002gio.2_Missense_Mutation_p.Y88C|TP53_uc010vug.1_Missense_Mutation_p.Y181C	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	220	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		Y -> N (in sporadic cancers; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.Y220C(205)|p.Y220N(12)|p.Y220H(9)|p.Y220S(9)|p.0?(7)|p.Y220fs*27(4)|p.Y220*(3)|p.Y220D(2)|p.Y127C(2)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.?(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*1(1)|p.Y220fs*2(1)|p.V218fs*26(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		AGGCGGCTCATAGGGCACCAC	0.557		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			45	8					0	0	0.870114	0	0
CDRT1	374286	broad.mit.edu	37	17	15496762	15496762	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:15496762C>T	uc002gov.3	-	11	2087	c.1895G>A	c.(1894-1896)TGT>TAT	p.C632Y	TRIM16_uc002gor.1_Intron|CDRT1_uc010vvy.1_Missense_Mutation_p.C36Y|CDRT1_uc010vvz.1_Intron|CDRT1_uc002gou.2_3'UTR	NM_006382	NP_006373	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	632	WD 7.										0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GCCATCTGCACAGGCGCTGAT	0.498													15	308					0	0	0.500413	0	0
DDX5	1655	broad.mit.edu	37	17	62498302	62498302	+	Missense_Mutation	SNP	T	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:62498302T>G	uc002jek.2	-	10	1381	c.1134A>C	c.(1132-1134)CAA>CAC	p.Q378H	DDX5_uc010deh.2_Missense_Mutation_p.Q378H|DDX5_uc002jej.2_Missense_Mutation_p.Q273H|DDX5_uc010wqa.1_Missense_Mutation_p.Q299H	NM_004396	NP_004387	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5	378	Helicase C-terminal.				cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA helicase activity|transcription cofactor activity			ovary(2)|lung(1)	3	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			AGTCACGCTCTTGTTGACTCT	0.378			T	ETV4	prostate								10	51					0	0	0.435327	0	0
LRRC37A3	374819	broad.mit.edu	37	17	62856449	62856449	+	Missense_Mutation	SNP	C	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:62856449C>G	uc002jey.2	-	11	4346	c.3815G>C	c.(3814-3816)TGG>TCG	p.W1272S	LRRC37A3_uc010wqg.1_Missense_Mutation_p.W390S|LRRC37A3_uc002jex.1_Missense_Mutation_p.W249S|LRRC37A3_uc010wqf.1_Missense_Mutation_p.W310S|LRRC37A3_uc010dek.1_Missense_Mutation_p.W278S	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1272	Extracellular (Potential).					integral to membrane					0						TAAGTCTTTCCATCTGTCTCT	0.458													5	135					0	0	0.278610	0	0
RYR1	6261	broad.mit.edu	37	19	39070725	39070725	+	Missense_Mutation	SNP	C	T	T	rs148540135		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39070725C>T	uc002oit.2	+	100	14598	c.14468C>T	c.(14467-14469)ACG>ATG	p.T4823M	RYR1_uc002oiu.2_Missense_Mutation_p.T4818M	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4823					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GGGGTCAAGACGCTGCGCACC	0.597													43	52					0	0	0.859065	0	0
RYR1	6261	broad.mit.edu	37	19	39071043	39071043	+	Missense_Mutation	SNP	G	T	T	rs118192168		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr19:39071043G>T	uc002oit.2	+	101	14675	c.14545G>T	c.(14545-14547)GTC>TTC	p.V4849F	RYR1_uc002oiu.2_Missense_Mutation_p.V4844F	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	4849	Helical; Name=M8; (Potential).		V -> I (in MHS1 and CCD; autosomal recessive form).		muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1)	12	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	GGCGGTGGTCGTCTACCTGTA	0.602													22	25					6.44725e-10	7.19943e-10	0.624587	1	0
ROCK2	9475	broad.mit.edu	37	2	11355517	11355517	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:11355517A>T	uc002rbd.1	-	15	2068	c.1619T>A	c.(1618-1620)CTT>CAT	p.L540H		NM_004850	NP_004841	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein	540	REM.|Potential.|Interaction with PPP1R12A.				axon guidance|cytokinesis|intracellular signal transduction	cytosol|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity			stomach(2)|skin(2)	4	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CAAATCTTCAAGTTGATCTTT	0.308													33	40					0	0	0.740014	0	0
WASH2P	375260	broad.mit.edu	37	2	114356239	114356239	+	Silent	SNP	T	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:114356239T>C	uc002tkh.2	+	6	775	c.717T>C	c.(715-717)CGT>CGC	p.R239R	WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						CCTTTGCCCGTGTGTCAGACT	0.642													3	11					0	0	0.184627	0	0
LIMS2	55679	broad.mit.edu	37	2	128399630	128399630	+	Silent	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:128399630G>A	uc002tpa.2	-	6	820	c.654C>T	c.(652-654)CAC>CAT	p.H218H	LIMS2_uc002tou.2_Silent_p.H26H|LIMS2_uc002tov.2_Silent_p.H66H|LIMS2_uc002tow.2_Silent_p.H66H|LIMS2_uc002tox.2_Silent_p.H242H|LIMS2_uc010fmb.2_Silent_p.H128H|LIMS2_uc002toy.2_Silent_p.H213H|LIMS2_uc010yzm.1_Silent_p.H240H|LIMS2_uc002toz.2_Silent_p.H213H|LIMS2_uc002tpb.2_Silent_p.H213H	NM_001161403	NP_001154875	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	218	LIM zinc-binding 4.				cell junction assembly	cytosol|focal adhesion|nucleus	zinc ion binding				0	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		TCACCTCCACGTGCCACTGCT	0.677													15	26					0	0	0.539581	0	0
CALCRL	10203	broad.mit.edu	37	2	188225389	188225389	+	Silent	SNP	T	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:188225389T>G	uc002upv.3	-	10	1265	c.717A>C	c.(715-717)ACA>ACC	p.T239T	CALCRL_uc010frt.2_Silent_p.T239T	NM_005795	NP_005786	Q16602	CALRL_HUMAN	calcitonin receptor-like precursor	239	Cytoplasmic (Potential).					integral to plasma membrane				lung(3)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			CCACAATGAGTGTGTGTAGGT	0.403													36	42					0	0	0.796494	0	0
ALS2	57679	broad.mit.edu	37	2	202609063	202609063	+	Silent	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:202609063G>A	uc002uyo.2	-	10	2444	c.2088C>T	c.(2086-2088)CAC>CAT	p.H696H	ALS2_uc002uyp.3_Silent_p.H696H|ALS2_uc002uyq.2_Silent_p.H696H|ALS2_uc010ftl.2_RNA	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	696	DH.				cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						TAGCTAACTCGTGGAGACTGG	0.398													31	35					0	0	0.740014	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|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).|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 -> 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).		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(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma 								41	48					0	0	0.840704	0	0
SIRPA	140885	broad.mit.edu	37	20	1902301	1902301	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:1902301G>A	uc002wfq.2	+	4	1057	c.697G>A	c.(697-699)GTC>ATC	p.V233I	SIRPA_uc010zps.1_Missense_Mutation_p.V213I|SIRPA_uc002wfr.2_Missense_Mutation_p.V233I|SIRPA_uc002wfs.2_Missense_Mutation_p.V233I|SIRPA_uc002wft.2_Missense_Mutation_p.V233I	NM_001040022	NP_001035111	P78324	SHPS1_HUMAN	signal-regulatory protein alpha precursor	233	Ig-like C1-type 1.|Extracellular (Potential).				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding			ovary(1)	1				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GGTGGCCCACGTCACCTTGCA	0.617													5	120					0	0	0.184627	0	0
FRG1B	284802	broad.mit.edu	37	20	29628243	29628243	+	Missense_Mutation	SNP	T	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:29628243T>C	uc010ztl.1	+	3	187	c.155T>C	c.(154-156)TTG>TCG	p.L52S	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.L4S					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						ATGGCTTTGTTGGCCTCAAAT	0.353													3	102					0	0	0.115264	0	0
SULF2	55959	broad.mit.edu	37	20	46291893	46291893	+	Missense_Mutation	SNP	T	C	C	rs145371797		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr20:46291893T>C	uc002xto.2	-	17	2621	c.2291A>G	c.(2290-2292)AAT>AGT	p.N764S	SULF2_uc002xtr.2_Missense_Mutation_p.N764S|SULF2_uc002xtq.2_Missense_Mutation_p.N764S|SULF2_uc010zyd.1_Missense_Mutation_p.N43S	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	764					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						GTGAGTCTCATTGATGGTCCT	0.517											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	102					0	0	0.184627	0	0
USP25	29761	broad.mit.edu	37	21	17238647	17238647	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr21:17238647A>G	uc002yjy.1	+	20	2796	c.2579A>G	c.(2578-2580)AAC>AGC	p.N860S	USP25_uc011aby.1_Missense_Mutation_p.N930S|USP25_uc002yjz.1_Missense_Mutation_p.N892S|USP25_uc010gla.1_Intron	NM_013396	NP_037528	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	860					protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(3)|liver(2)	5				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		GAAGAAGTAAACTTGGAGGAA	0.303													16	51					0	0	0.539581	0	0
RTDR1	27156	broad.mit.edu	37	22	23404005	23404005	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:23404005C>T	uc002zwt.2	-	6	930	c.772G>A	c.(772-774)GCC>ACC	p.A258T		NM_014433	NP_055248	Q9UHP6	RTDR1_HUMAN	rhabdoid tumor deletion region protein 1	258							binding			ovary(1)	1	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		ATCACTGTGGCGAACATCAGG	0.587													12	24					0	0	0.435327	0	0
FBXO7	25793	broad.mit.edu	37	22	32879927	32879927	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr22:32879927A>G	uc003amq.2	+	3	744	c.461A>G	c.(460-462)AAT>AGT	p.N154S	FBXO7_uc003amp.1_Missense_Mutation_p.N40S|FBXO7_uc003amr.2_Missense_Mutation_p.N40S|FBXO7_uc003ams.2_5'UTR|FBXO7_uc003amt.2_Missense_Mutation_p.N75S|FBXO7_uc003amu.2_Missense_Mutation_p.N40S	NM_012179	NP_036311	Q9Y3I1	FBX7_HUMAN	F-box only protein 7 isoform 1	154					cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1						ATTCAAGATAATGCGCATATG	0.383													26	47					0	0	0.681144	0	0
KCNH8	131096	broad.mit.edu	37	3	19575087	19575087	+	Silent	SNP	C	T	T	rs151258565	by1000genomes	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:19575087C>T	uc003cbk.1	+	16	3015	c.2820C>T	c.(2818-2820)GGC>GGT	p.G940G	KCNH8_uc010hex.1_Silent_p.G401G	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	940	Cytoplasmic (Potential).					integral to membrane	two-component sensor activity			lung(4)|ovary(1)	5						TGCAAACAGGCGGGGCTGCTT	0.542													50	76					0	0	0.870114	0	0
MCM2	4171	broad.mit.edu	37	3	127337890	127337890	+	Silent	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:127337890C>T	uc003ejp.2	+	13	2091	c.2034C>T	c.(2032-2034)TTC>TTT	p.F678F	MCM2_uc011bkm.1_Silent_p.F548F|MCM2_uc010hsl.2_RNA|MCM2_uc011bkn.1_Silent_p.F631F	NM_004526	NP_004517	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	678	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|helicase activity|metal ion binding			ovary(3)|skin(1)	4						TGGCCCGCTTCGTGGTGGGCA	0.632													5	24					0	0	0.217242	0	0
CP	1356	broad.mit.edu	37	3	148930358	148930358	+	Missense_Mutation	SNP	A	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:148930358A>G	uc003ewy.3	-	2	527	c.274T>C	c.(274-276)TTT>CTT	p.F92L	CP_uc011bnr.1_RNA|CP_uc003ewz.2_Missense_Mutation_p.F92L	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	92	F5/8 type A 1.|Plastocyanin-like 1.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GGGCCTAAAAACCCAAGCCAG	0.398													6	88					0	0	0.217242	0	0
SDHAP1	255812	broad.mit.edu	37	3	195692347	195692347	+	Missense_Mutation	SNP	G	A	A	rs62282794	by1000genomes	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr3:195692347G>A	uc003fvy.2	-	3	310	c.196C>T	c.(196-198)CAC>TAC	p.H66Y	SDHAP1_uc003fvx.3_RNA					Homo sapiens full length insert cDNA clone ZC24D06.												0						TTCCTCCAGTGCTCCTCAAAG	0.572													5	26					0	0	0.278610	0	0
ADAM29	11086	broad.mit.edu	37	4	175898936	175898936	+	Missense_Mutation	SNP	G	T	T	rs139608576		TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr4:175898936G>T	uc003iuc.2	+	5	2930	c.2260G>T	c.(2260-2262)GTG>TTG	p.V754L	ADAM29_uc003iud.2_Missense_Mutation_p.V754L|ADAM29_uc010irr.2_Missense_Mutation_p.V754L|ADAM29_uc011cki.1_Missense_Mutation_p.V754L	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	754	Cytoplasmic (Potential).|9 X 9 AA approximate repeats.|2.				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TCATCCTCAGGTGATGCCTTC	0.557													3	17					3.59834e-05	3.88852e-05	0.217242	1	0
AQPEP	206338	broad.mit.edu	37	5	115351039	115351039	+	Silent	SNP	T	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr5:115351039T>C	uc003kro.2	+	17	2705	c.2541T>C	c.(2539-2541)ACT>ACC	p.T847T	AQPEP_uc003krp.2_RNA|AQPEP_uc003krq.2_RNA|AQPEP_uc003krr.2_RNA|AQPEP_uc003krs.2_RNA	NM_173800	NP_776161	Q6Q4G3	AMPQ_HUMAN	laeverin	847	Lumenal (Potential).				proteolysis	integral to membrane	metallopeptidase activity|zinc ion binding				0						ATACTTACACTAATACAACAA	0.348													6	86					0	0	0.217242	0	0
GFPT2	9945	broad.mit.edu	37	5	179740844	179740844	+	Missense_Mutation	SNP	A	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr5:179740844A>T	uc003mlw.1	-	14	1492	c.1394T>A	c.(1393-1395)ATC>AAC	p.I465N		NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	465	SIS 1.				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CCCTGCGTTGATGTGGACGCC	0.701													6	10					0	0	0.335167	0	0
ROS1	6098	broad.mit.edu	37	6	117609712	117609712	+	Silent	SNP	A	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:117609712A>G	uc003pxp.1	-	43	7186	c.6987T>C	c.(6985-6987)CCT>CCC	p.P2329P	ROS1_uc011ebi.1_RNA	NM_002944	NP_002935	P08922	ROS_HUMAN	proto-oncogene c-ros-1 protein precursor	2329	Cytoplasmic (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TCAGGCCTTCAGGCTTGCCAG	0.438			T	GOPC|ROS1	glioblastoma|NSCLC								43	69					0	0	0.853193	0	0
NKAIN2	154215	broad.mit.edu	37	6	124979504	124979504	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr6:124979504C>T	uc003pzo.2	+	4	723	c.446C>T	c.(445-447)GCT>GTT	p.A149V	NKAIN2_uc003pzn.1_Missense_Mutation_p.A149V|NKAIN2_uc003pzp.2_Missense_Mutation_p.A148V|NKAIN2_uc010keq.2_Intron|NKAIN2_uc010ker.2_Missense_Mutation_p.A59V	NM_001040214	NP_001035304	Q5VXU1	NKAI2_HUMAN	T-cell lymphoma breakpoint-associated target 1	149						integral to membrane|plasma membrane					0				GBM - Glioblastoma multiforme(226;0.104)		ATAGAAGTGGCTCATAGTTCC	0.542													38	50					0	0	0.819951	0	0
EIF3B	8662	broad.mit.edu	37	7	2404028	2404028	+	Missense_Mutation	SNP	C	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr7:2404028C>T	uc003slx.2	+	6	1104	c.1021C>T	c.(1021-1023)CGT>TGT	p.R341C	EIF3B_uc003sly.2_Missense_Mutation_p.R341C|EIF3B_uc003slz.1_Missense_Mutation_p.R302C|EIF3B_uc003sma.2_Missense_Mutation_p.R69C	NM_003751	NP_003742	P55884	EIF3B_HUMAN	eukaryotic translation initiation factor 3,	341	Sufficient for interaction with EIF3E.|WD 1.				regulation of translational initiation	cytosol|eukaryotic translation initiation factor 3 complex	nucleotide binding|protein complex scaffold|translation initiation factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		GACGTATGTGCGTTGGTCTCC	0.458													88	107					0	0	0.870114	0	0
PKD1L1	168507	broad.mit.edu	37	7	47876598	47876598	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr7:47876598G>A	uc003tny.1	-	37	5864	c.5864C>T	c.(5863-5865)CCG>CTG	p.P1955L		NM_138295	NP_612152	Q8TDX9	PK1L1_HUMAN	polycystin-1L1	1955	Cytoplasmic (Potential).				cell-cell adhesion	integral to membrane				ovary(8)|upper_aerodigestive_tract(2)|breast(1)	11						GGTGAGGCGCGGCGTGTGCAG	0.582													3	41					0	0	0.150653	0	0
CDKN2A	1029	broad.mit.edu	37	9	21974684	21974684	+	Missense_Mutation	SNP	G	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:21974684G>C	uc003zpk.2	-	1	355	c.143C>G	c.(142-144)CCG>CGG	p.P48R	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_Missense_Mutation_p.P48R|CDKN2A_uc010miu.2_RNA|CDKN2A_uc003zpl.2_Intron	NM_000077	NP_000068	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 1	48	ANK 2.		P -> L (in CMM2 and a head and neck tumor; somatic mutation).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(1112)|p.?(25)|p.P48L(9)|p.P48P(1)|p.P48R(1)|p.V28_V51del(1)		haematopoietic_and_lymphoid_tissue(647)|skin(419)|upper_aerodigestive_tract(414)|central_nervous_system(381)|lung(325)|pancreas(244)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|soft_tissue(79)|bone(77)|ovary(76)|biliary_tract(71)|stomach(46)|breast(46)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|salivary_gland(10)|large_intestine(9)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3678		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CACCTGGATCGGCCTCCGACC	0.677		17							Uveal_Melanoma_Familial|Familial_Malignant_Melanoma_and_Tumors_of_the_Nervous_System|Hereditary_Melanoma	HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)			10	21					0	0	0.387290	0	0
WNK2	65268	broad.mit.edu	37	9	96080327	96080327	+	Missense_Mutation	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:96080327G>A	uc011lud.1	+	29	6646	c.6646G>A	c.(6646-6648)GCC>ACC	p.A2216T	WNK2_uc004atj.2_Intron|WNK2_uc004atk.2_3'UTR	NM_006648	NP_006639	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	Error:Variant_position_missing_in_Q9Y3S1_after_alignment					intracellular protein kinase cascade		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|stomach(3)|ovary(2)|large_intestine(1)|central_nervous_system(1)|breast(1)	12						TGGTCCACGCGCCGTCTCCAC	0.582													7	104					0	0	0.387290	0	0
XPA	7507	broad.mit.edu	37	9	100459509	100459509	+	Silent	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:100459509G>A	uc004axr.3	-	1	183	c.66C>T	c.(64-66)GCC>GCT	p.A22A	XPA_uc004axs.3_RNA	NM_000380	NP_000371	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	22	Interaction with CEP164 and required for UV resistance.				nucleotide-excision repair, DNA damage removal	nucleoplasm	damaged DNA binding|metal ion binding|nucleotide binding|protein domain specific binding|protein homodimerization activity			breast(1)	1		Acute lymphoblastic leukemia(62;0.158)				CCCGCACCGAGGCAGGCAGCT	0.736			Mis|N|F|S			skin basal cell|skin squamous cell|melanoma		NER	Xeroderma_Pigmentosum				4	12					0	0	0.184627	0	0
NUP214	8021	broad.mit.edu	37	9	134073213	134073213	+	Silent	SNP	A	G	G			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr9:134073213A>G	uc004cag.2	+	29	4443	c.4332A>G	c.(4330-4332)CAA>CAG	p.Q1444Q	NUP214_uc004cah.2_Silent_p.Q1434Q|NUP214_uc004cai.2_Silent_p.Q874Q|NUP214_uc010mzg.2_RNA|NUP214_uc011mcg.1_Silent_p.Q270Q|NUP214_uc011mcf.1_Silent_p.Q221Q|NUP214_uc010mzh.1_5'UTR|NUP214_uc010mzi.1_5'UTR	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	1444	Pro/Ser/Thr-rich.|11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(7)|lung(3)|skin(3)|ovary(2)|central_nervous_system(1)	16	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTGGAAGCCAACAGACCAATA	0.522			T	DEK|SET|ABL1	AML|T-ALL								20	98					0	0	0.592651	0	0
Unknown	0	broad.mit.edu	37	MT	6762	6762	+	Translation_Start_Site	SNP	G	A	A			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:6762G>A	uc011mfh.1	+	1	909	c.-139G>A	c.(-141--137)TCGTG>TCATG		uc004cou.3_5'Flank|uc011mfi.1_5'Flank					Homo sapiens cDNA: FLJ22894 fis, clone KAT04907.																		TAGGGTTTATCGTGTGAGCAC	0.418													19	37					0	0	0.750413	0	0
Unknown	0	broad.mit.edu	37	MT	13133	13133	+	RNA	SNP	T	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:13133T>C	uc004cox.3	+	1		c.797T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CTTCCACCCCCTAGCAGAAAA	0.502													7	186					0	0	0.248553	0	0
Unknown	0	broad.mit.edu	37	MT	13143	13143	+	RNA	SNP	T	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrM:13143T>C	uc004cox.3	+	1		c.807T>C			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CTAGCAGAAAATAGCCCACTA	0.483													113	85					0	0	0.870114	0	0
ATRX	546	broad.mit.edu	37	X	76829760	76829760	+	Nonsense_Mutation	SNP	G	C	C			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76829760G>C	uc004ecp.3	-	28	6513	c.6281C>G	c.(6280-6282)TCA>TGA	p.S2094*	ATRX_uc004ecq.3_Nonsense_Mutation_p.S2056*|ATRX_uc004eco.3_Nonsense_Mutation_p.S1879*	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2094	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			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	CTTCTTCCTTGACTGTGCAGT	0.313			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						69	12					0	0	0.870114	0	0
PCDH11Y	83259	broad.mit.edu	37	Y	5369105	5369105	+	Missense_Mutation	SNP	G	T	T			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrY:5369105G>T	uc004fqo.2	+	3	3871	c.3137G>T	c.(3136-3138)CGG>CTG	p.R1046L		NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	1046	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0						CAGTCCCAGCGGCGTGTCACA	0.473													3	59					0.00909568	0.00952204	0.150653	1	0
DOC2A	8448	broad.mit.edu	37	16	30018527	30018529	+	In_Frame_Del	DEL	CTT	-	-	rs139431507	byFrequency	TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr16:30018527_30018529delCTT	uc002dvm.2	-	6	719_721	c.619_621delAAG	c.(619-621)AAGdel	p.K207del	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|DOC2A_uc002dvl.2_In_Frame_Del_p.K207del|DOC2A_uc002dvn.2_In_Frame_Del_p.K207del|DOC2A_uc010vef.1_RNA|DOC2A_uc002dvo.2_In_Frame_Del_p.K207del|DOC2A_uc002dvp.2_In_Frame_Del_p.K207del|DOC2A_uc002dvq.2_In_Frame_Del_p.K207del	NM_003586	NP_003577	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	207					nervous system development|regulation of calcium ion-dependent exocytosis	cell junction|lysosome|synaptic vesicle membrane|synaptosome	calcium-dependent phospholipid binding|protein binding|transporter activity			ovary(2)	2						TGTTAAAATGCTTCTTCTGCGAA	0.635													45	75	---	---	---	---					
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chr17:45219612delA	uc002ild.3	-	11	1488	c.1361delT	c.(1360-1362)CTAfs	p.L454fs	CDC27_uc002ile.3_Frame_Shift_Del_p.L460fs|CDC27_uc002ilf.3_Frame_Shift_Del_p.L454fs|CDC27_uc010wkp.1_Frame_Shift_Del_p.L393fs|CDC27_uc010wkq.1_Intron	NM_001256	NP_001247	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 2	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding			lung(2)|breast(2)|ovary(1)	5						TGCTTTTTGTAGATTAAAGGC	0.308													8	52	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76938044	76938044	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CS-4943-01A-01D-1468-08	TCGA-CS-4943-10A-01D-1468-08									Somatic	Phase_I	Capture				Illumina GAIIx	14627ffd-642c-42b5-9d95-ad436c9b1d35	0d4a92bf-0624-4dfa-9d95-8f91a693ea3f	g.chrX:76938044delT	uc004ecp.3	-	9	2936	c.2704delA	c.(2704-2706)ATGfs	p.M902fs	ATRX_uc004ecq.3_Frame_Shift_Del_p.M864fs|ATRX_uc004eco.3_Frame_Shift_Del_p.M687fs|ATRX_uc004ecr.2_Frame_Shift_Del_p.M834fs|ATRX_uc010nlx.1_Frame_Shift_Del_p.M873fs|ATRX_uc010nly.1_Frame_Shift_Del_p.M847fs	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	902					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			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	CTTAATTCCATGATGGTCGTG	0.428			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						7	207	---	---	---	---					
