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	init_n_lod
EYA3	2140	broad.mit.edu	37	1	28339654	28339654	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr1:28339654G>A	uc001bpi.1	-	9	902	c.737C>T	c.(736-738)GCG>GTG	p.A246V	EYA3_uc010ofs.1_Missense_Mutation_p.A193V|EYA3_uc010oft.1_Missense_Mutation_p.A200V|EYA3_uc001bpj.2_Missense_Mutation_p.A200V|EYA3_uc001bpk.1_RNA|EYA3_uc010ofu.1_RNA	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	246					anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)|skin(1)	3		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		AGGTGCAGGCGCCATGACACT	0.512													28	68					0	0	0.116897	0	0	
RCSD1	92241	broad.mit.edu	37	1	167666869	167666869	+	Silent	SNP	A	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr1:167666869A>C	uc001gem.2	+	6	1195	c.1008A>C	c.(1006-1008)ACA>ACC	p.T336T	RCSD1_uc010pli.1_Silent_p.T306T	NM_052862	NP_443094	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	336										ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)					GCCAAGAAACAAAGAAGCTGG	0.557													5	17					0	0	0.184627	0	0	
HMCN1	83872	broad.mit.edu	37	1	186107009	186107009	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr1:186107009C>T	uc001grq.1	+	89	14058	c.13829C>T	c.(13828-13830)ACC>ATC	p.T4610I	HMCN1_uc001grs.1_Missense_Mutation_p.T179I	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4610	TSP type-1 2.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						CAAACCAGGACCAGGACTTGC	0.502													25	78					0	0	0.091800	0	0	
PRKCQ	5588	broad.mit.edu	37	10	6525445	6525445	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr10:6525445T>C	uc001ijj.1	-	11	1211	c.1136A>G	c.(1135-1137)GAT>GGT	p.D379G	PRKCQ_uc009xim.1_Missense_Mutation_p.D379G|PRKCQ_uc001iji.1_Missense_Mutation_p.D412G|PRKCQ_uc009xin.1_Missense_Mutation_p.D343G|PRKCQ_uc010qax.1_Missense_Mutation_p.D254G	NM_006257	NP_006248	Q04759	KPCT_HUMAN	protein kinase C, theta	379					axon guidance|cellular component disassembly involved in apoptosis|intracellular signal transduction|membrane protein ectodomain proteolysis|platelet activation|regulation of cell growth|T cell receptor signaling pathway	cytosol	ATP binding|metal ion binding|protein binding|protein kinase C activity			ovary(3)|lung(2)|large_intestine(1)	6						CAAGATAAAATCCTCAATTTT	0.433													33	36					0	0	0.183431	0	0	
ST8SIA6	338596	broad.mit.edu	37	10	17365124	17365124	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr10:17365124C>T	uc001ipd.2	-	7	668	c.668G>A	c.(667-669)AGT>AAT	p.S223N	ST8SIA6_uc010qce.1_RNA	NM_001004470	NP_001004470	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide	223	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			ovary(1)	1						AACATCTTTACTAACATCTCC	0.313													17	9					0	0	0.175082	0	0	
KCNJ11	3767	broad.mit.edu	37	11	17408516	17408516	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr11:17408516T>C	uc001mna.2	-	1	1691	c.1123A>G	c.(1123-1125)ATG>GTG	p.M375V	KCNJ11_uc001mnb.3_Missense_Mutation_p.M288V	NM_000525	NP_000516	B4DWI4	B4DWI4_HUMAN	potassium inwardly-rectifying channel J11	375						integral to membrane	ATP-activated inward rectifier potassium channel activity			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)		GCCTTGGCCATGGGCACGCTG	0.652											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	64					0	0	0.047766	0	0	
NOP2	4839	broad.mit.edu	37	12	6675951	6675951	+	Silent	SNP	A	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr12:6675951A>G	uc001qpk.1	-	2	185	c.141T>C	c.(139-141)GCT>GCC	p.A47A	NOP2_uc001qph.1_Silent_p.A47A|NOP2_uc001qpi.1_Silent_p.A47A|NOP2_uc001qpj.1_Intron|NOP2_uc001qpl.1_Silent_p.A47A|NOP2_uc001qpm.1_Silent_p.A47A			P46087	NOP2_HUMAN	Homo sapiens cDNA FLJ31646 fis, clone NT2RI2003921, highly similar to PROLIFERATING-CELL NUCLEOLAR ANTIGEN P120.	47					positive regulation of cell proliferation|rRNA processing	nucleolus	protein binding|RNA binding|S-adenosylmethionine-dependent methyltransferase activity			ovary(2)	2						ACCTCTTTCGAGCACGACTAG	0.393													4	15					0	0	0.150653	0	0	
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr13:115047559C>T	uc001vup.2	+	2	308	c.271C>T	c.(271-273)CTG>TTG	p.L91L	UPF3A_uc010tkn.1_Silent_p.L91L|UPF3A_uc001vuq.2_Silent_p.L91L|UPF3A_uc001vus.2_RNA|UPF3A_uc001vur.2_RNA	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	91	Required for interaction with UPF2.				mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding			skin(1)	1	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCTGCGCCCGCTGCCAGCACA	0.731													3	6					0	0	0.115264	0	0	
PRKD1	5587	broad.mit.edu	37	14	30066697	30066697	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr14:30066697C>A	uc001wqh.2	-	16	2615	c.2434G>T	c.(2434-2436)GCC>TCC	p.A812S		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	812	Protein kinase.				cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		AAGATATTACCTTCATGAGAT	0.279													12	39					1.61879e-10	1.70872e-10	0.093190	1	0	
PAX9	5083	broad.mit.edu	37	14	37132197	37132197	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr14:37132197C>T	uc001wty.3	+	3	817	c.100C>T	c.(100-102)CAA>TAA	p.Q34*		NM_006194	NP_006185	P55771	PAX9_HUMAN	paired box 9	34	Paired.				multicellular organismal development|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		GGAACTGGCCCAACTGGGCAT	0.642													18	69					0	0	0.189662	0	0	
KCNK13	56659	broad.mit.edu	37	14	90651085	90651085	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr14:90651085G>A	uc001xye.1	+	2	1407	c.965G>A	c.(964-966)CGC>CAC	p.R322H		NM_022054	NP_071337	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	322	Cytoplasmic (Potential).					integral to membrane	potassium channel activity|voltage-gated ion channel activity			skin(1)	1		all_cancers(154;0.186)				GTCCGGAACCGCTGCAACATC	0.612													37	100					0	0	0.214465	0	0	
TDRD9	122402	broad.mit.edu	37	14	104481153	104481153	+	Missense_Mutation	SNP	T	C	C	rs148349259	byFrequency	TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr14:104481153T>C	uc001yom.3	+	21	2228	c.2198T>C	c.(2197-2199)ATA>ACA	p.I733T	TDRD9_uc001yon.3_Missense_Mutation_p.I471T	NM_153046	NP_694591	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	733					cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				CAAGAGTATATATATAAGCAG	0.393													4	53					0	0	0.184627	0	0	
ADAM6	8755	broad.mit.edu	37	14	107218778	107218778	+	RNA	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr14:107218778C>T	uc010tyt.1	-	12		c.936G>A								Parts of antibodies, mostly variable regions.												0						ATCGGCCCTTCACGGAGTCCG	0.547													13	234					0	0	0.105934	0	0	
MYEF2	50804	broad.mit.edu	37	15	48441243	48441243	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr15:48441243T>A	uc001zwi.3	-	16	1749	c.1625A>T	c.(1624-1626)AAA>ATA	p.K542I	MYEF2_uc001zwg.3_Missense_Mutation_p.K80I|MYEF2_uc001zwh.3_Missense_Mutation_p.K130I|MYEF2_uc001zwj.3_Missense_Mutation_p.K518I	NM_016132	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	542	RRM 3.				transcription, DNA-dependent	Golgi apparatus|nucleus	DNA binding|nucleotide binding|RNA binding			lung(2)|ovary(1)	3		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		CTGACTGAATTTCTCTTTTAG	0.299													20	52					0	0	0.062417	0	0	
THSD4	79875	broad.mit.edu	37	15	72040794	72040794	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr15:72040794G>A	uc002atb.1	+	13	2355	c.2276G>A	c.(2275-2277)CGT>CAT	p.R759H	THSD4_uc002ate.2_Missense_Mutation_p.R399H	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	759	TSP type-1 3.					proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2						CAGAGGACCCGTGATGTGAAG	0.557													17	42					0	0	0.160694	0	0	
SCAMP5	192683	broad.mit.edu	37	15	75308977	75308977	+	Silent	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr15:75308977G>A	uc002azk.1	+	4	342	c.180G>A	c.(178-180)GCG>GCA	p.A60A	SCAMP5_uc002azl.1_Silent_p.A60A|SCAMP5_uc002azm.1_Silent_p.A60A|SCAMP5_uc002azn.1_Silent_p.A60A|SCAMP5_uc010uly.1_Intron	NM_138967	NP_620417	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	60	Helical; (Potential).				exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1						GCTGTCTCGCGTGGCTGATCG	0.607													29	82					0	0	0.116897	0	0	
CHRNB4	1143	broad.mit.edu	37	15	78921738	78921738	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr15:78921738C>T	uc002bed.1	-	5	1021	c.909G>A	c.(907-909)ATG>ATA	p.M303I	CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Missense_Mutation_p.M121I	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4	303	Helical; (Potential).				regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0						TGACCAGCACCATGGTGAACA	0.592													22	61					0	0	0.069288	0	0	
ZSCAN2	54993	broad.mit.edu	37	15	85164300	85164300	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr15:85164300A>C	uc002bkr.2	+	3	1100	c.874A>C	c.(874-876)AAC>CAC	p.N292H	ZSCAN2_uc010bmz.1_Missense_Mutation_p.N290H|ZSCAN2_uc010bna.2_Missense_Mutation_p.N142H|ZSCAN2_uc010uox.1_Intron|ZSCAN2_uc010uoy.1_Intron|ZSCAN2_uc010uoz.1_Intron	NM_181877	NP_870992	Q7Z7L9	ZSCA2_HUMAN	zinc finger protein 29 isoform 1	292	C2H2-type 3.				cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		CCGGAGTGCCAACCTCATAAC	0.522													12	42					0	0	0.080935	0	0	
ITGAM	3684	broad.mit.edu	37	16	31283290	31283290	+	Silent	SNP	G	A	A	rs41499844		TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr16:31283290G>A	uc002ebq.2	+	7	779	c.681G>A	c.(679-681)ACG>ACA	p.T227T	ITGAM_uc002ebr.2_Silent_p.T227T	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M isoform 2 precursor	227	VWFA.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1						GGACACACACGGCCACGGGCA	0.522													28	80					0	0	0.144211	0	0	
HYDIN	54768	broad.mit.edu	37	16	71218824	71218824	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr16:71218824T>G	uc002ezr.2	-	3	333	c.205A>C	c.(205-207)ATG>CTG	p.M69L	HYDIN_uc010cfz.1_5'UTR|HYDIN_uc002ezv.2_Missense_Mutation_p.M69L|HYDIN_uc010vmc.1_Missense_Mutation_p.M86L|HYDIN_uc010vmd.1_Missense_Mutation_p.M96L|HYDIN_uc002ezw.3_Missense_Mutation_p.M86L	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	69										ovary(1)|skin(1)	2		Ovarian(137;0.0654)				GGTCGGCACATCAAACGTGTT	0.453													5	61					0	0	0.021553	0	0	
ZZEF1	23140	broad.mit.edu	37	17	3977531	3977531	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr17:3977531C>T	uc002fxe.2	-	24	3662	c.3598G>A	c.(3598-3600)GTG>ATG	p.V1200M		NM_015113	NP_055928	O43149	ZZEF1_HUMAN	zinc finger, ZZ type with EF hand domain 1	1200							calcium ion binding|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4						CCCCAAGACACGGCAACATCG	0.592													11	219					0	0	0.080935	0	0	
TNFRSF13B	23495	broad.mit.edu	37	17	16852283	16852283	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr17:16852283G>A	uc002gqs.1	-	3	227	c.214C>T	c.(214-216)CGC>TGC	p.R72C	TNFRSF13B_uc010vwt.1_RNA|TNFRSF13B_uc002gqt.1_Missense_Mutation_p.R26C|TNFRSF13B_uc010vwu.1_Missense_Mutation_p.R72C	NM_012452	NP_036584	O14836	TR13B_HUMAN	tumor necrosis factor receptor 13B	72	Extracellular (Potential).|TNFR-Cys 2.				cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding|receptor activity			kidney(2)	2						TGCTCCTTGCGGCAGCTGAGT	0.498									IgA_Deficiency_Selective				7	57					0	0	0.038147	0	0	
NEK8	284086	broad.mit.edu	37	17	27062001	27062001	+	Silent	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr17:27062001C>T	uc002hcp.2	+	3	465	c.465C>T	c.(463-465)AGC>AGT	p.S155S		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	155	Protein kinase.					cytoplasm|primary cilium	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|pancreas(1)|liver(1)|skin(1)	6	Lung NSC(42;0.0158)					AGATCCTTAGCAGCAAGAGCA	0.582													23	72					0	0	0.069288	0	0	
FAM117A	81558	broad.mit.edu	37	17	47788765	47788765	+	Missense_Mutation	SNP	G	C	C	rs138923537		TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr17:47788765G>C	uc002ipk.2	-	8	1283	c.1214C>G	c.(1213-1215)CCG>CGG	p.P405R	FAM117A_uc010wlz.1_Missense_Mutation_p.P133R	NM_030802	NP_110429	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	405	Pro-rich.									ovary(1)	1						GGGAGATCCCGGGTTTGAGGG	0.647													29	23					0	0	0.108266	0	0	
POTEC	388468	broad.mit.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr18:14513764C>T	uc010dln.2	-	10	1884	c.1430G>A	c.(1429-1431)CGG>CAG	p.R477Q	POTEC_uc010xaj.1_RNA	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	ANKRD26-like family B, member 2	477										skin(3)	3						AAGTTGTTTCCGGGTATCATT	0.358													3	25					0	0	0.115264	0	0	
GMIP	51291	broad.mit.edu	37	19	19746378	19746378	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr19:19746378T>G	uc002nnd.2	-	15	1523	c.1406A>C	c.(1405-1407)GAC>GCC	p.D469A	GMIP_uc010xrb.1_Missense_Mutation_p.D443A|GMIP_uc010xrc.1_Missense_Mutation_p.D440A	NM_016573	NP_057657	Q9P107	GMIP_HUMAN	GEM interacting protein	469					negative regulation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	metal ion binding|protein binding|Rho GTPase activator activity			ovary(1)	1						GTCTCCCAGGTCTGCAGGGAG	0.552													45	71					0	0	0.111260	0	0	
STRN	6801	broad.mit.edu	37	2	37082457	37082457	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:37082457C>T	uc002rpn.2	-	15	1885	c.1876G>A	c.(1876-1878)GAC>AAC	p.D626N	STRN_uc010ezx.2_Missense_Mutation_p.D589N	NM_003162	NP_003153	O43815	STRN_HUMAN	striatin, calmodulin binding protein	626					dendrite development|locomotory behavior|negative regulation of cell proliferation|tight junction assembly|Wnt receptor signaling pathway	cytoplasm|dendritic spine|neuronal cell body|postsynaptic density|postsynaptic membrane|tight junction	armadillo repeat domain binding|calmodulin binding|estrogen receptor binding|protein complex binding|protein phosphatase 2A binding			skin(1)	1		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TGGCTCGGGTCACTGCTCACT	0.393													11	24					0	0	0.093190	0	0	
SNRNP200	23020	broad.mit.edu	37	2	96950142	96950142	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:96950142T>C	uc002svu.2	-	31	4432	c.4346A>G	c.(4345-4347)AAC>AGC	p.N1449S	SNRNP200_uc002svt.2_Missense_Mutation_p.N59S|SNRNP200_uc010yuj.1_RNA|SNRNP200_uc002svv.1_5'UTR	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1449	Helicase ATP-binding 2.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|skin(4)|large_intestine(1)	10						CACGAAGAGGTTGATGTTCTG	0.557													21	55					0	0	0.076483	0	0	
LRP1B	53353	broad.mit.edu	37	2	141128795	141128795	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:141128795A>G	uc002tvj.1	-	70	11800	c.10828T>C	c.(10828-10830)TCT>CCT	p.S3610P		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3610	Extracellular (Potential).|LDL-receptor class A 28.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CATTTCAAAGATGCTGAAATA	0.294										TSP Lung(27;0.18)			4	4					0	0	0.184627	0	0	
SCN1A	6323	broad.mit.edu	37	2	166900312	166900312	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:166900312G>A	uc010zcz.1	-	11	1928	c.1910C>T	c.(1909-1911)GCG>GTG	p.A637V	SCN1A_uc002udo.3_Missense_Mutation_p.A506V|SCN1A_uc010fpk.2_Missense_Mutation_p.A506V	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	637						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	CTTCCCATTCGCTGGAAACAC	0.542													22	52					0	0	0.062417	0	0	
PPIG	9360	broad.mit.edu	37	2	170493840	170493840	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:170493840A>G	uc002uez.2	+	14	2292	c.2072A>G	c.(2071-2073)AAA>AGA	p.K691R	PPIG_uc010fpx.2_Missense_Mutation_p.K676R|PPIG_uc010fpy.2_Missense_Mutation_p.K684R|PPIG_uc002ufb.2_Missense_Mutation_p.K691R|PPIG_uc002ufd.2_Missense_Mutation_p.K688R	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	691					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)	CCCTTCTCAAAAATAAAACAA	0.353													4	27					0	0	0.150653	0	0	
STAT1	6772	broad.mit.edu	37	2	191851578	191851578	+	Splice_Site	SNP	A	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:191851578A>G	uc002usj.2	-	14	1609	c.1221_splice	c.e14+1	p.L407_splice	STAT1_uc010fse.1_Splice_Site_p.L407_splice|STAT1_uc002usk.2_Splice_Site_p.L407_splice|STAT1_uc002usl.2_Splice_Site_p.L409_splice|STAT1_uc010fsf.1_Splice_Site_p.L219_splice	NM_007315	NP_009330	P42224	STAT1_HUMAN	signal transducer and activator of transcription						activation of caspase activity|I-kappaB kinase/NF-kappaB cascade|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway|tyrosine phosphorylation of STAT protein	cytosol|nucleolus|nucleoplasm	calcium ion binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity|signal transducer activity			lung(3)|breast(3)|central_nervous_system(2)|upper_aerodigestive_tract(1)|ovary(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)		Fludarabine(DB01073)	TGATGTCCCTACCAGGTGCCG	0.483													15	212					0	0	0.146539	0	0	
DNPEP	23549	broad.mit.edu	37	2	220251022	220251022	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr2:220251022G>A	uc010zlg.1	-	5	551	c.469C>T	c.(469-471)CGC>TGC	p.R157C	DNPEP_uc010zlf.1_5'Flank|DNPEP_uc002vle.2_Missense_Mutation_p.R149C|DNPEP_uc002vlf.1_Missense_Mutation_p.R135C|DNPEP_uc002vlh.2_Missense_Mutation_p.R96C|DNPEP_uc002vli.1_Missense_Mutation_p.R96C|DNPEP_uc002vlj.2_Missense_Mutation_p.R139C|uc002vlk.1_5'Flank	NM_012100	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	139					peptide metabolic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|protein binding|zinc ion binding				0		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	L-Glutamic Acid(DB00142)	ACAATGACGCGTCCAGCCAGA	0.627													26	105					0	0	0.108266	0	0	
KCNB1	3745	broad.mit.edu	37	20	47990303	47990303	+	Silent	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr20:47990303G>A	uc002xur.1	-	2	1958	c.1794C>T	c.(1792-1794)TTC>TTT	p.F598F	KCNB1_uc002xus.1_Silent_p.F598F	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	598	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TGGCCTCAGGGAAGTCTGTGG	0.592													40	41					0	0	0.214465	0	0	
KCNB1	3745	broad.mit.edu	37	20	47990462	47990462	+	Silent	SNP	G	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr20:47990462G>C	uc002xur.1	-	2	1799	c.1635C>G	c.(1633-1635)CTC>CTG	p.L545L	KCNB1_uc002xus.1_Silent_p.L545L	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	545	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CCTTGGTATTGAGGATGGGTT	0.517													106	113					0	0	0.139131	0	0	
MYT1	4661	broad.mit.edu	37	20	62850293	62850293	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr20:62850293G>T	uc002yii.2	+	12	2240	c.1876G>T	c.(1876-1878)GCA>TCA	p.A626S	MYT1_uc002yih.2_Missense_Mutation_p.A328S|MYT1_uc002yij.2_Missense_Mutation_p.A285S	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	626					cell differentiation|nervous system development	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CGCCGAGGCTGCACACATGGC	0.602													33	277					3.80469e-20	4.13081e-20	0.144211	1	0	
WDR6	11180	broad.mit.edu	37	3	49051915	49051915	+	Silent	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr3:49051915G>A	uc003cvj.2	+	4	2994	c.2856G>A	c.(2854-2856)GAG>GAA	p.E952E	WDR6_uc011bby.1_Silent_p.E400E|WDR6_uc010hkn.2_Silent_p.E896E|WDR6_uc011bbz.1_Silent_p.E871E	NM_018031	NP_060501	Q9NNW5	WDR6_HUMAN	WD repeat domain 6 protein	922	WD 14.				cell cycle arrest|negative regulation of cell proliferation	cytoplasm				central_nervous_system(1)	1				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		TTACACACGAGGCACCCAACC	0.552											OREG0015565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	39	39					0	0	0.092188	0	0	
STAG1	10274	broad.mit.edu	37	3	136096591	136096591	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr3:136096591C>T	uc003era.1	-	23	2573	c.2281G>A	c.(2281-2283)GAT>AAT	p.D761N	STAG1_uc003erb.1_Missense_Mutation_p.D761N|STAG1_uc003erc.1_Missense_Mutation_p.D535N	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN	stromal antigen 1	761					cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(2)	2						ACCAACAAATCCTCCTGTAAG	0.368													19	11					0	0	0.204396	0	0	
ADD1	118	broad.mit.edu	37	4	2896323	2896323	+	Silent	SNP	A	G	G			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr4:2896323A>G	uc003gfr.2	+	6	794	c.606A>G	c.(604-606)CTA>CTG	p.L202L	ADD1_uc003gfn.2_Intron|ADD1_uc010ico.1_Silent_p.L202L|ADD1_uc003gfo.2_Silent_p.L202L|ADD1_uc003gfp.2_Silent_p.L202L|ADD1_uc003gfq.2_Silent_p.L202L|ADD1_uc003gfs.2_Silent_p.L202L|ADD1_uc003gft.3_Silent_p.L202L|ADD1_uc003gfu.2_5'UTR	NM_001119	NP_001110	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform a	202					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGATCAATCTACAAGGAGATA	0.323													5	34					0	0	0.021553	0	0	
IL13	3596	broad.mit.edu	37	5	131995159	131995159	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr5:131995159G>A	uc003kxj.1	+	2	238	c.224G>A	c.(223-225)GGC>GAC	p.G75D		NM_002188	NP_002179	P35225	IL13_HUMAN	interleukin 13 precursor	75					cellular component movement|immune response|inflammatory response|signal transduction	extracellular space|soluble fraction	cytokine activity			ovary(1)|skin(1)	2		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTGACAGCTGGCATGGTAAGG	0.592													3	12					0	0	0.150653	0	0	
PKHD1	5314	broad.mit.edu	37	6	51900507	51900507	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr6:51900507G>T	uc003pah.1	-	28	3386	c.3110C>A	c.(3109-3111)GCC>GAC	p.A1037D	PKHD1_uc003pai.2_Missense_Mutation_p.A1037D	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1037	IPT/TIG 5.|Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					TCGGATGGTGGCCCAGAGCCC	0.408													7	30					2.74318e-10	2.85591e-10	0.058154	1	0	
CARD11	84433	broad.mit.edu	37	7	2956965	2956965	+	Missense_Mutation	SNP	G	A	A	rs142828146		TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:2956965G>A	uc003smv.2	-	20	3066	c.2662C>T	c.(2662-2664)CGT>TGT	p.R888C		NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	888					positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity	p.R881C(1)		haematopoietic_and_lymphoid_tissue(43)|ovary(2)|kidney(2)|skin(2)|central_nervous_system(1)	50		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGCGAGAGACGGGGGCTGACC	0.557			Mis		DLBCL								9	17					0	0	0.069234	0	0	
HOXA6	3203	broad.mit.edu	37	7	27185319	27185319	+	Silent	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:27185319C>T	uc003syo.1	-	2	660	c.660G>A	c.(658-660)ACG>ACA	p.T220T	HOXA5_uc003syn.1_5'Flank|uc003syp.1_5'Flank	NM_024014	NP_076919	P31267	HXA6_HUMAN	homeobox A6	220						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)	2						CGCTGGGCTGCGTGGAATTGA	0.612													13	131					0	0	0.105934	0	0	
GTF2IRD1	9569	broad.mit.edu	37	7	73922530	73922530	+	Silent	SNP	C	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:73922530C>A	uc003uaq.2	+	2	513	c.120C>A	c.(118-120)TCC>TCA	p.S40S	GTF2IRD1_uc010lbq.2_Silent_p.S40S|GTF2IRD1_uc003uap.2_Silent_p.S40S|GTF2IRD1_uc003uar.1_Silent_p.S40S	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	40						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CCTTAGACTCCATGGTGAGTG	0.612													30	96					1.06801e-11	1.14322e-11	0.144211	1	0	
GTF2IRD1	9569	broad.mit.edu	37	7	73933930	73933930	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:73933930C>T	uc003uaq.2	+	6	1190	c.797C>T	c.(796-798)GCC>GTC	p.A266V	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.A298V|GTF2IRD1_uc003uap.2_Missense_Mutation_p.A266V|GTF2IRD1_uc003uar.1_Missense_Mutation_p.A266V	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	266						nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CCCAACCACGCCATCCGAGAG	0.692													29	88					0	0	0.116897	0	0	
PCLO	27445	broad.mit.edu	37	7	82582618	82582618	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:82582618C>T	uc003uhx.2	-	5	7940	c.7651G>A	c.(7651-7653)GAT>AAT	p.D2551N	PCLO_uc003uhv.2_Missense_Mutation_p.D2551N|PCLO_uc010lec.2_5'Flank	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	2482					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						AATTTATAATCTGCTGAAGTC	0.398													12	49					0	0	0.080935	0	0	
AKAP9	10142	broad.mit.edu	37	7	91709233	91709233	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:91709233G>C	uc003ulg.2	+	31	8011	c.7786G>C	c.(7786-7788)GAG>CAG	p.E2596Q	AKAP9_uc003ulf.2_Missense_Mutation_p.E2588Q|AKAP9_uc003uli.2_Missense_Mutation_p.E2219Q|AKAP9_uc003ulj.2_Missense_Mutation_p.E366Q	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	2608	Potential.|Glu-rich.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAGAGAAGATGAGTTGGGGTC	0.318			T	BRAF	papillary thyroid								12	23					0	0	0.080935	0	0	
ZNF3	7551	broad.mit.edu	37	7	99672845	99672845	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:99672845G>A	uc003usq.2	-	5	491	c.184C>T	c.(184-186)CGG>TGG	p.R62W	ZNF3_uc003usp.2_Missense_Mutation_p.R62W|ZNF3_uc003usr.2_Missense_Mutation_p.R62W|ZNF3_uc010lgj.2_Missense_Mutation_p.R26W|ZNF3_uc003uss.2_Missense_Mutation_p.R69W|ZNF3_uc003ust.3_Missense_Mutation_p.R62W	NM_032924	NP_116313	P17036	ZNF3_HUMAN	zinc finger protein 3 isoform 2	62	KRAB.				cell differentiation|leukocyte activation|multicellular organismal development	nucleus	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			CACTCCTTCCGGATGAAGTAC	0.488													35	95					0	0	0.080422	0	0	
SND1	27044	broad.mit.edu	37	7	127326707	127326707	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:127326707G>T	uc003vmi.2	+	2	345	c.119G>T	c.(118-120)CGT>CTT	p.R40L		NM_014390	NP_055205	Q7KZF4	SND1_HUMAN	staphylococcal nuclease domain containing 1	40	TNase-like 1.				gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity			ovary(2)|central_nervous_system(1)	3						GGTCAGCCTCGTGGTGGGCCT	0.567													25	79					3.01185e-09	3.09325e-09	0.091800	1	0	
OR2A12	346525	broad.mit.edu	37	7	143792959	143792959	+	Silent	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr7:143792959C>T	uc011kty.1	+	1	759	c.759C>T	c.(757-759)AGC>AGT	p.S253S		NM_001004135	NP_001004135	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	Melanoma(164;0.0783)					TCTTTGGCAGCGCCATTGTCA	0.562													18	203					0	0	0.175082	0	0	
ORM1	5004	broad.mit.edu	37	9	117087068	117087068	+	Splice_Site	SNP	A	T	T	rs112963597		TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr9:117087068A>T	uc004bik.3	+	4	440	c.329_splice	c.e4-2	p.V110_splice	ORM1_uc011lxo.1_Splice_Site_p.V110_splice	NM_000607	NP_000598	P02763	A1AG1_HUMAN	orosomucoid 1 precursor						acute-phase response|regulation of immune system process|transport	extracellular space	protein binding				0		Myeloproliferative disorder(63;0.163)			Acenocoumarol(DB01418)|Alfentanil(DB00802)|Aprindine(DB01429)|Disopyramide(DB00280)|Penbutolol(DB01359)|Phenprocoumon(DB00946)|Quinidine(DB00908)|Tamsulosin(DB00706)	TTTCTCTTCCAGTGGGAGGCC	0.537													14	27					0	0	0.160694	0	0	
SARDH	1757	broad.mit.edu	37	9	136531865	136531865	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr9:136531865C>T	uc004cep.3	-	20	2757	c.2623G>A	c.(2623-2625)GGT>AGT	p.G875S	SARDH_uc004ceo.2_Missense_Mutation_p.G875S|SARDH_uc011mdn.1_Missense_Mutation_p.G875S|SARDH_uc011mdo.1_Missense_Mutation_p.G707S|SARDH_uc004cen.2_Missense_Mutation_p.G325S	NM_001134707	NP_001128179	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase precursor	875					glycine catabolic process	mitochondrial matrix	aminomethyltransferase activity|sarcosine dehydrogenase activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		ACCGGCCCACCGCTGGGGTCA	0.632													4	10					0	0	0.150653	0	0	
ARHGAP6	395	broad.mit.edu	37	X	11157185	11157185	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:11157185G>A	uc004cup.1	-	13	3596	c.2723C>T	c.(2722-2724)ACG>ATG	p.T908M	ARHGAP6_uc004cuo.1_RNA|ARHGAP6_uc004cum.1_Missense_Mutation_p.T705M|ARHGAP6_uc004cun.1_Missense_Mutation_p.T728M	NM_013427	NP_038286	O43182	RHG06_HUMAN	Rho GTPase activating protein 6 isoform 1	908					actin filament polymerization|activation of phospholipase C activity|negative regulation of focal adhesion assembly|negative regulation of stress fiber assembly|Rho protein signal transduction	actin filament|cytosol	phospholipase activator activity|phospholipase binding|Rho GTPase activator activity|SH3 domain binding|SH3/SH2 adaptor activity			urinary_tract(1)|lung(1)	2						TCCCTGGTCCGTGGGTGTCTC	0.706													8	18					0	0	0.047766	0	0	
ATP6AP2	10159	broad.mit.edu	37	X	40450529	40450529	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:40450529G>A	uc004det.2	+	3	314	c.212G>A	c.(211-213)CGT>CAT	p.R71H	ATP6AP2_uc010nhc.2_RNA|ATP6AP2_uc011mkl.1_5'UTR|ATP6AP2_uc011mkm.1_Missense_Mutation_p.R71H|ATP6AP2_uc011mkn.1_Missense_Mutation_p.R71H	NM_005765	NP_005756	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory	71	Extracellular (Potential).				angiotensin maturation|positive regulation of transforming growth factor-beta1 production|regulation of MAPKKK cascade	external side of plasma membrane|integral to membrane	protein binding|receptor activity				0						CTGTTTCATCGTCCTCGGGCT	0.493													14	93					0	0	0.146539	0	0	
CHST7	56548	broad.mit.edu	37	X	46433919	46433919	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:46433919G>A	uc004dgt.2	+	1	728	c.553G>A	c.(553-555)GCC>ACC	p.A185T		NM_019886	NP_063939	Q9NS84	CHST7_HUMAN	chondroitin 6-sulfotransferase 7	185	Lumenal (Potential).				chondroitin sulfate biosynthetic process|N-acetylglucosamine metabolic process	Golgi membrane|integral to membrane	chondroitin 6-sulfotransferase activity|N-acetylglucosamine 6-O-sulfotransferase activity			breast(3)	3						cccggACACGGCCAATCTTAC	0.562													15	47					0	0	0.119110	0	0	
HEPH	9843	broad.mit.edu	37	X	65392442	65392442	+	Splice_Site	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:65392442G>A	uc011moz.1	+	3	481	c.421_splice	c.e3+1	p.G141_splice	HEPH_uc004dwn.2_Splice_Site_p.G141_splice|HEPH_uc004dwo.2_Splice_Site|HEPH_uc010nkr.2_Splice_Site_p.G141_splice|HEPH_uc011mpa.1_Splice_Site_p.G141_splice	NM_138737	NP_620074	Q9BQS7	HEPH_HUMAN	hephaestin isoform a						cellular iron ion homeostasis|copper ion transport|transmembrane transport	integral to membrane|plasma membrane	copper ion binding|oxidoreductase activity			lung(5)|ovary(4)	9						GACTCTGAAGGTAAACCATTC	0.443													22	126					0	0	0.062417	0	0	
PCDH11X	27328	broad.mit.edu	37	X	91873740	91873740	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:91873740G>C	uc004efk.1	+	7	4690	c.3845G>C	c.(3844-3846)TGG>TCG	p.W1282S	PCDH11X_uc004efl.1_Missense_Mutation_p.W1272S|PCDH11X_uc004efo.1_Missense_Mutation_p.W1245S|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.W1274S|PCDH11X_uc004efn.1_Missense_Mutation_p.W1264S	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1282	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CAGCAAGGTTGGGTGCAAGGT	0.507													24	333					0	0	0.083992	0	0	
PGRMC1	10857	broad.mit.edu	37	X	118370534	118370534	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:118370534C>T	uc004erb.2	+	1	324	c.208C>T	c.(208-210)CGG>TGG	p.R70W	PGRMC1_uc011mts.1_Missense_Mutation_p.R70W	NM_006667	NP_006658	O00264	PGRC1_HUMAN	progesterone receptor membrane component 1	70	Cytoplasmic (Potential).					cell surface|endoplasmic reticulum membrane|integral to membrane|microsome|nucleolus	heme binding|protein binding|receptor activity|steroid binding				0						CCGCCTCAAGCGGCGCGACTT	0.687													10	59					0	0	0.069234	0	0	
UPF3B	65109	broad.mit.edu	37	X	118972014	118972014	+	Silent	SNP	T	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:118972014T>C	uc004erz.1	-	10	1085	c.1008A>G	c.(1006-1008)AGA>AGG	p.R336R	UPF3B_uc004esa.1_Silent_p.R323R	NM_080632	NP_542199	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B	336	Sufficient for association with EJC core.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|termination of RNA polymerase II transcription	cytosol|exon-exon junction complex|nucleoplasm	mRNA binding|nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(2)|kidney(1)	3						CATCTTCAGGTCTGCATGAAA	0.478													11	178					0	0	0.069234	0	0	
ODZ1	10178	broad.mit.edu	37	X	123556374	123556374	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:123556374C>T	uc004euj.2	-	23	4262	c.4198G>A	c.(4198-4200)GCA>ACA	p.A1400T	ODZ1_uc011muj.1_Missense_Mutation_p.A1406T|ODZ1_uc010nqy.2_Missense_Mutation_p.A1407T	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1400	NHL 3.|Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						GGGCGTCCTGCGATGATCCGA	0.493													44	98					0	0	0.117977	0	0	
GPC4	2239	broad.mit.edu	37	X	132548987	132548987	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:132548987G>A	uc004exc.1	-	1	219	c.7C>T	c.(7-9)CGG>TGG	p.R3W	GPC4_uc011mvg.1_5'Flank	NM_001448	NP_001439	O75487	GPC4_HUMAN	glypican 4 precursor	3					anatomical structure morphogenesis|cell proliferation	anchored to membrane|external side of plasma membrane|extracellular space|insoluble fraction|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	Acute lymphoblastic leukemia(192;0.000127)					AAGCCGAACCGTGCCATGGTG	0.701													9	81					0	0	0.058154	0	0	
MTM1	4534	broad.mit.edu	37	X	149787547	149787547	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chrX:149787547G>T	uc004fef.3	+	6	455	c.379G>T	c.(379-381)GGC>TGC	p.G127C	MTM1_uc011mxx.1_RNA|MTM1_uc011mxy.1_Missense_Mutation_p.G90C|MTM1_uc011mxz.1_Missense_Mutation_p.G12C|MTM1_uc010nte.2_Intron	NM_000252	NP_000243	Q13496	MTM1_HUMAN	myotubularin	127					endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					GAAACAGGAAGGCCACAGCAG	0.468													8	86					0.000978159	0.000991201	0.080935	1	0	
TP53	7157	broad.mit.edu	37	17	7579395	7579396	+	Frame_Shift_Ins	INS	-	C	C			TCGA-BR-8486-01A-31D-2394-08	TCGA-BR-8486-10A-01D-2394-08									Somatic	Phase_I	Capture				Illumina GAIIx	6a7cdaf6-211e-4eb8-a70e-1153d69c45e4	0fa8cee4-2d26-4caf-9da2-96047854f29f	g.chr17:7579395_7579396insC	uc002gim.2	-	4	485_486	c.291_292insG	c.(289-294)GTCCCTfs	p.V97fs	TP53_uc002gig.1_Frame_Shift_Ins_p.V97fs|TP53_uc002gih.2_Frame_Shift_Ins_p.V97fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Frame_Shift_Ins_p.V97fs|TP53_uc010cni.1_Frame_Shift_Ins_p.V97fs|TP53_uc002gij.2_Frame_Shift_Ins_p.V97fs|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Frame_Shift_Ins_p.V58fs|TP53_uc010cnk.1_Frame_Shift_Ins_p.V112fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	97_98	Interaction with WWOX.		P -> L (in sporadic cancers; somatic mutation).|P -> S (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.0?(7)|p.P98S(4)|p.S99fs*48(3)|p.G59fs*23(3)|p.V73fs*9(1)|p.V97A(1)|p.V97I(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(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)		TTCTGGGAAGGGACAGAAGATG	0.639		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)			55	56	---	---	---	---						.
