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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
MYPN	84665	broad.mit.edu	37	10	69934146	69934146	+	Missense_Mutation	SNP	C	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:69934146C>G	uc001jnm.3	+	c.2297C>G	c.(2296-2298)TCT>TGT	p.S766C	MYPN_uc001jnn.3_Missense_Mutation_p.S491C|MYPN_uc001jno.3_Missense_Mutation_p.S766C|MYPN_uc009xpt.2_Missense_Mutation_p.S766C|MYPN_uc010qit.1_Missense_Mutation_p.S472C|MYPN_uc010qiu.1_Non-coding_Transcript	NM_032578	NP_115967	Q86TC9	MYPN_HUMAN	myopalladin	766						nucleus|sarcomere	actin binding			ovary(3)	3														0.542857	269.606136	269.829061	76	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69934146	69934146	10493	10	C	G	G	G	416	32	MYPN	3	3
DYNC2H1	79659	broad.mit.edu	37	11	102999641	102999641	+	Silent	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102999641G>T	uc001phn.1	+	c.1860G>T	c.(1858-1860)GTG>GTT	p.V620V	DYNC2H1_uc001pho.2_Silent_p.V620V|DYNC2H1_uc009yxe.1_Silent_p.V620V	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	620	Stem (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.375	58.057283	58.826903	21	35	KEEP	---	---	---	---	capture		Silent	SNP	102999641	102999641	5032	11	G	T	T	T	600	47	DYNC2H1	2	2
IGSF9B	22997	broad.mit.edu	37	11	133790096	133790096	+	Missense_Mutation	SNP	G	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:133790096G>C	uc001qgx.3	-	c.3524C>G	c.(3523-3525)CCC>CGC	p.P1175R		NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1175	Pro-rich.|Cytoplasmic (Potential).					integral to membrane|plasma membrane					0	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)										0.169014	20.053953	27.441629	12	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133790096	133790096	7907	11	G	C	C	C	559	43	IGSF9B	3	3
HIPK3	10114	broad.mit.edu	37	11	33373334	33373334	+	Silent	SNP	G	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:33373334G>C	uc001mul.1	+	c.2988G>C	c.(2986-2988)GTG>GTC	p.V996V	HIPK3_uc001mum.1_Silent_p.V975V|HIPK3_uc009yjv.1_Silent_p.V975V	NM_005734	NP_005725	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3 isoform	996					anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)|ovary(1)|pancreas(1)	3										376				0.42	71.137688	71.422712	21	29	KEEP	---	---	---	---	capture		Silent	SNP	33373334	33373334	7403	11	G	C	C	C	587	46	HIPK3	3	3
NR1H3	10062	broad.mit.edu	37	11	47283259	47283259	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47283259G>A	uc001nel.2	+	c.735G>A	c.(733-735)CTG>CTA	p.L245L	NR1H3_uc009yll.1_Silent_p.L296L|NR1H3_uc010rhk.1_Silent_p.L296L|NR1H3_uc001nek.2_Silent_p.L245L|NR1H3_uc001nej.2_Intron|NR1H3_uc009ylm.2_Silent_p.L290L|NR1H3_uc001nen.3_Intron|NR1H3_uc001nem.2_Silent_p.L290L|NR1H3_uc001nep.2_Intron	NM_001130102	NP_001123574	Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	290	Ligand-binding (Potential).				apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of macrophage derived foam cell differentiation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis	nuclear chromatin|nucleoplasm	cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding			ovary(2)|lung(1)	3										119				0.426471	79.065004	79.38493	29	39	KEEP	---	---	---	---	capture		Silent	SNP	47283259	47283259	11023	11	G	A	A	A	574	45	NR1H3	2	2
INTS5	80789	broad.mit.edu	37	11	62416429	62416429	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62416429G>A	uc001nud.2	-	c.1123C>T	c.(1123-1125)CAC>TAC	p.H375Y	GANAB_uc001nua.2_5'Flank|GANAB_uc001nub.2_5'Flank|GANAB_uc001nuc.2_5'Flank|GANAB_uc010rma.1_5'Flank|GANAB_uc010rmb.1_5'Flank	NM_030628	NP_085131	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	375					snRNA processing	integral to membrane|integrator complex	protein binding			ovary(2)	2														0.211268	27.277149	32.761934	15	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62416429	62416429	8082	11	G	A	A	A	624	48	INTS5	2	2
DCHS1	8642	broad.mit.edu	37	11	6647528	6647528	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6647528C>T	uc001mem.1	-	c.6448G>A	c.(6448-6450)GGA>AGA	p.G2150R		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	2150	Cadherin 20.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.166667	7.685971	10.213602	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6647528	6647528	4458	11	C	T	T	T	312	24	DCHS1	2	2
IGHMBP2	3508	broad.mit.edu	37	11	68682465	68682465	+	Missense_Mutation	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:68682465A>G	uc001ook.1	+	c.886A>G	c.(886-888)ATC>GTC	p.I296V	IGHMBP2_uc001ooj.1_Non-coding_Transcript	NM_002180	NP_002171	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	296	Leu-rich.				cell death|DNA recombination|DNA repair|DNA replication|protein homooligomerization|transcription, DNA-dependent|translation	axon|growth cone|nucleus|ribonucleoprotein complex	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' RNA helicase activity|ribosome binding|single-stranded DNA binding|transcription factor binding|tRNA binding|zinc ion binding				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)											0.345455	60.612591	61.77056	19	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68682465	68682465	7892	11	A	G	G	G	208	16	IGHMBP2	4	4
OR10A6	390093	broad.mit.edu	37	11	7949674	7949674	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7949674C>T	uc010rbh.1	-	c.536G>A	c.(535-537)TGT>TAT	p.C179Y		NM_001004461	NP_001004461	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A,	179	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.5	63.645074	63.645074	22	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7949674	7949674	11300	11	C	T	T	T	221	17	OR10A6	2	2
ARID2	196528	broad.mit.edu	37	12	46231201	46231201	+	Splice_Site_SNP	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:46231201G>A	uc001ros.1	+	c.1120_splice	c.e9+1	p.G374_splice	ARID2_uc001ror.2_Splice_Site_SNP_p.G374_splice|ARID2_uc009zkg.1_Splice_Site_SNP|ARID2_uc009zkh.1_Splice_Site_SNP_p.G20_splice|ARID2_uc001rot.1_Splice_Site_SNP_p.G20_splice	NM_152641	NP_689854			AT rich interactive domain 2 (ARID, RFX-like)						chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(1)	7	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)										0.407407	62.837153	63.242368	22	32	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	46231201	46231201	930	12	G	A	A	A	572	44	ARID2	5	2
NFATC4	4776	broad.mit.edu	37	14	24839714	24839714	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24839714G>A	uc010tol.1	+	c.1299G>A	c.(1297-1299)AAG>AAA	p.K433K	NFATC4_uc010tok.1_Silent_p.K433K|NFATC4_uc010alr.2_Silent_p.K433K|NFATC4_uc010als.2_Silent_p.K383K|NFATC4_uc010tom.1_Silent_p.K383K|NFATC4_uc010ton.1_Silent_p.K383K|NFATC4_uc010too.1_Silent_p.K383K|NFATC4_uc010alt.2_Silent_p.K402K|NFATC4_uc010top.1_Silent_p.K402K|NFATC4_uc010toq.1_Silent_p.K402K|NFATC4_uc010alu.2_Intron|NFATC4_uc001wpc.2_Silent_p.K370K|NFATC4_uc010tor.1_Silent_p.K370K|NFATC4_uc010tos.1_Silent_p.K300K|NFATC4_uc010tot.1_Silent_p.K358K|NFATC4_uc010tou.1_Silent_p.K300K|NFATC4_uc010tov.1_Silent_p.K358K|NFATC4_uc010tow.1_Silent_p.K300K|NFATC4_uc010alv.2_Silent_p.K358K|NFATC4_uc010tox.1_Silent_p.K300K|NFATC4_uc001wpd.2_5'Flank|NFATC4_uc010toy.1_5'Flank|NFATC4_uc010toz.1_5'Flank	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	370					cell differentiation|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.018)										0.140845	17.198848	26.03944	10	61	KEEP	---	---	---	---	capture		Silent	SNP	24839714	24839714	10765	14	G	A	A	A	451	35	NFATC4	2	2
NFATC4	4776	broad.mit.edu	37	14	24839725	24839725	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24839725G>A	uc010tol.1	+	c.1310G>A	c.(1309-1311)GGC>GAC	p.G437D	NFATC4_uc010tok.1_Missense_Mutation_p.G437D|NFATC4_uc010alr.2_Missense_Mutation_p.G437D|NFATC4_uc010als.2_Missense_Mutation_p.G387D|NFATC4_uc010tom.1_Missense_Mutation_p.G387D|NFATC4_uc010ton.1_Missense_Mutation_p.G387D|NFATC4_uc010too.1_Missense_Mutation_p.G387D|NFATC4_uc010alt.2_Missense_Mutation_p.G406D|NFATC4_uc010top.1_Missense_Mutation_p.G406D|NFATC4_uc010toq.1_Missense_Mutation_p.G406D|NFATC4_uc010alu.2_Intron|NFATC4_uc001wpc.2_Missense_Mutation_p.G374D|NFATC4_uc010tor.1_Missense_Mutation_p.G374D|NFATC4_uc010tos.1_Missense_Mutation_p.G304D|NFATC4_uc010tot.1_Missense_Mutation_p.G362D|NFATC4_uc010tou.1_Missense_Mutation_p.G304D|NFATC4_uc010tov.1_Missense_Mutation_p.G362D|NFATC4_uc010tow.1_Missense_Mutation_p.G304D|NFATC4_uc010alv.2_Missense_Mutation_p.G362D|NFATC4_uc010tox.1_Missense_Mutation_p.G304D|NFATC4_uc001wpd.2_5'Flank|NFATC4_uc010toy.1_5'Flank|NFATC4_uc010toz.1_5'Flank	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	374					cell differentiation|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.018)										0.148649	15.373545	24.145088	11	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24839725	24839725	10765	14	G	A	A	A	546	42	NFATC4	2	2
FAM179B	23116	broad.mit.edu	37	14	45431925	45431925	+	Missense_Mutation	SNP	C	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45431925C>G	uc001wvw.2	+	c.301C>G	c.(301-303)CAA>GAA	p.Q101E	FAM179B_uc001wvv.2_Missense_Mutation_p.Q101E|FAM179B_uc010anc.2_Non-coding_Transcript|KLHL28_uc001wvq.2_5'Flank|KLHL28_uc001wvr.2_5'Flank|FAM179B_uc010anb.1_Missense_Mutation_p.Q101E|FAM179B_uc001wvu.2_Missense_Mutation_p.Q101E	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	101							binding				0														0.396825	167.129116	168.301106	50	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45431925	45431925	5712	14	C	G	G	G	377	29	FAM179B	3	3
ITPKA	3706	broad.mit.edu	37	15	41793911	41793911	+	Missense_Mutation	SNP	T	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:41793911T>G	uc001znz.2	+	c.665T>G	c.(664-666)CTG>CGG	p.L222R		NM_002220	NP_002211	P23677	IP3KA_HUMAN	1D-myo-inositol-trisphosphate 3-kinase A	222					signal transduction		ATP binding|calmodulin binding|inositol trisphosphate 3-kinase activity				0		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;7.63e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)										0.157895	4.511775	6.637617	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41793911	41793911	8221	15	T	G	G	G	715	55	ITPKA	4	4
LBXCOR1	390598	broad.mit.edu	37	15	68125572	68125572	+	Missense_Mutation	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68125572A>G	uc002aqy.1	+	c.2648A>G	c.(2647-2649)TAT>TGT	p.Y883C		NM_001031807	NP_001026977	P84550	SKOR1_HUMAN	transcriptional corepressor Corl1	927					negative regulation of BMP signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	cytoplasm|dendrite|neuronal cell body|nucleus	nucleotide binding|SMAD binding|transcription repressor activity				0														0.40625	42.774877	43.018832	13	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68125572	68125572	8978	15	A	G	G	G	208	16	LBXCOR1	4	4
AKAP13	11214	broad.mit.edu	37	15	86286756	86286756	+	Missense_Mutation	SNP	C	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:86286756C>G	uc002blu.1	+	c.8104C>G	c.(8104-8106)CCA>GCA	p.P2702A	AKAP13_uc002blv.1_Missense_Mutation_p.P2698A|AKAP13_uc002blw.1_Missense_Mutation_p.P1163A|AKAP13_uc002blx.1_Missense_Mutation_p.P943A	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	2698	Interaction with ESR1.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.059172	-12.370418	21.991683	10	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86286756	86286756	452	15	C	G	G	G	286	22	AKAP13	3	3
KIAA0182	23199	broad.mit.edu	37	16	85704643	85704643	+	Missense_Mutation	SNP	G	A	A	rs2303203	byFrequency	TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85704643G>A	uc002fix.2	+	c.3458G>A	c.(3457-3459)CGA>CAA	p.R1153Q	KIAA0182_uc002fiw.2_Missense_Mutation_p.R1049Q|KIAA0182_uc002fiy.2_Missense_Mutation_p.R1080Q|KIAA0182_uc002fiz.2_Missense_Mutation_p.R295Q|KIAA0182_uc010cho.2_Missense_Mutation_p.R333Q	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	1153	Potential.						protein binding			large_intestine(3)|ovary(1)|skin(1)	5														0.389831	63.111292	63.738497	23	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85704643	85704643	8466	16	G	A	A	A	481	37	KIAA0182	1	1
CCDC55	84081	broad.mit.edu	37	17	28511752	28511752	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28511752C>T	uc002heu.2	+	c.737C>T	c.(736-738)GCA>GTA	p.A246V	CCDC55_uc002hev.2_Missense_Mutation_p.A192V|CCDC55_uc010wbl.1_Missense_Mutation_p.A192V|CCDC55_uc010wbm.1_Missense_Mutation_p.A192V|CCDC55_uc002hex.2_Missense_Mutation_p.A192V	NM_032141	NP_115517	Q9H0G5	CCD55_HUMAN	coiled-coil domain containing 55 isoform 1	246						nuclear speck				ovary(1)	1														0.365591	88.415244	89.896671	34	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28511752	28511752	2948	17	C	T	T	T	325	25	CCDC55	2	2
ARHGAP27	201176	broad.mit.edu	37	17	43473891	43473891	+	Missense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:43473891C>A	uc002iix.2	-	c.1112G>T	c.(1111-1113)CGC>CTC	p.R371L	ARHGAP27_uc010dak.2_Missense_Mutation_p.R344L	NM_199282	NP_954976	Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27 isoform a	712	Rho-GAP.				positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction	cytoplasm|membrane	Rac GTPase activator activity|SH3 domain binding				0	Renal(3;0.0405)													0.388889	19.520269	19.715129	7	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43473891	43473891	888	17	C	A	A	A	351	27	ARHGAP27	1	1
GH2	2689	broad.mit.edu	37	17	61958402	61958402	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61958402G>A	uc002jcl.1	-	c.278C>T	c.(277-279)ACG>ATG	p.T93M	GH2_uc002jcj.2_Missense_Mutation_p.T93M|CSH2_uc002jck.2_Intron|GH2_uc002jcm.1_Missense_Mutation_p.T93M|GH2_uc002jcn.1_Missense_Mutation_p.T78M|GH2_uc002jco.1_Missense_Mutation_p.T93M	NM_022557	NP_072051	P01242	SOM2_HUMAN	growth hormone 2 isoform 2	93						extracellular region	hormone activity			pancreas(1)	1														0.363636	417.467648	424.4917	156	273	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61958402	61958402	6636	17	G	A	A	A	520	40	GH2	1	1
CSH1	1442	broad.mit.edu	37	17	61972557	61972557	+	Silent	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61972557C>A	uc002jcu.1	-	c.732G>T	c.(730-732)CCG>CCT	p.P244P	CSH2_uc002jck.2_Intron|CSH1_uc002jcp.1_Silent_p.P150P|CSH1_uc002jcq.1_Missense_Mutation_p.R121L|CSH1_uc002jcr.1_3'UTR|CSH1_uc002jcs.1_Missense_Mutation_p.R160L|CSH1_uc002jct.1_Missense_Mutation_p.R126L|CSH1_uc002jcv.1_Missense_Mutation_p.R65L|CSH1_uc002jcw.2_Silent_p.P159P|CSH1_uc002jcy.2_3'UTR	NM_022640	NP_072166	P01243	CSH_HUMAN	chorionic somatomammotropin hormone 1 isoform 2	Error:Variant_position_missing_in_P01243_after_alignment					female pregnancy|signal transduction	extracellular region	hormone activity|metal ion binding				0														0.365385	150.193765	152.694184	57	99	KEEP	---	---	---	---	capture		Silent	SNP	61972557	61972557	4081	17	C	A	A	A	299	23	CSH1	1	1
AIPL1	23746	broad.mit.edu	37	17	6328905	6328905	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:6328905C>T	uc002gcp.2	-	c.1030G>A	c.(1030-1032)GCA>ACA	p.A344T	AIPL1_uc002gcq.2_Missense_Mutation_p.A284T|AIPL1_uc002gcr.2_Missense_Mutation_p.A281T|AIPL1_uc010clk.2_Missense_Mutation_p.A322T|AIPL1_uc010cll.2_Missense_Mutation_p.A320T|AIPL1_uc002gcs.2_3'UTR	NM_014336	NP_055151	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting	344					protein farnesylation|protein folding|visual perception	cytoplasm|nucleus	farnesylated protein binding|unfolded protein binding				0				COAD - Colon adenocarcinoma(228;0.141)										0.35443	141.06423	144.009851	56	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6328905	6328905	439	17	C	T	T	T	351	27	AIPL1	1	1
LLGL2	3993	broad.mit.edu	37	17	73566508	73566508	+	Nonsense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:73566508C>T	uc002joh.2	+	c.1954C>T	c.(1954-1956)CAG>TAG	p.Q652*	LLGL2_uc002joi.2_Nonsense_Mutation_p.Q652*|LLGL2_uc010dgg.1_Nonsense_Mutation_p.Q652*|LLGL2_uc002joj.2_Nonsense_Mutation_p.Q641*|LLGL2_uc010wsd.1_Nonsense_Mutation_p.Q279*	NM_001031803	NP_001026973	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 isoform c	652	WD 10.				cell cycle|cell division|exocytosis|regulation of establishment or maintenance of cell polarity	cytoplasm|intracellular membrane-bounded organelle	PDZ domain binding			ovary(2)	2	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)											0.315789	12.63596	13.213613	6	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	73566508	73566508	9163	17	C	T	T	T	377	29	LLGL2	5	2
EPHX3	79852	broad.mit.edu	37	19	15338342	15338342	+	Missense_Mutation	SNP	T	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15338342T>C	uc002nap.2	-	c.989A>G	c.(988-990)CAC>CGC	p.H330R	EPHX3_uc002naq.2_Missense_Mutation_p.H330R	NM_024794	NP_079070	Q9H6B9	EPHX3_HUMAN	abhydrolase domain containing 9 precursor	330						extracellular region	hydrolase activity				0														0.430556	91.158696	91.469992	31	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15338342	15338342	5374	19	T	C	C	C	767	59	EPHX3	4	4
HKR1	284459	broad.mit.edu	37	19	37853120	37853120	+	Missense_Mutation	SNP	T	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37853120T>G	uc002ogb.2	+	c.423T>G	c.(421-423)AGT>AGG	p.S141R	HKR1_uc002ofx.2_5'UTR|HKR1_uc002ofy.2_5'UTR|HKR1_uc002oga.2_Missense_Mutation_p.S123R|HKR1_uc010xto.1_Missense_Mutation_p.S123R|HKR1_uc002ogc.2_Missense_Mutation_p.S122R|HKR1_uc010xtp.1_Missense_Mutation_p.S80R|HKR1_uc002ogd.2_Missense_Mutation_p.S80R	NM_181786	NP_861451	P10072	HKR1_HUMAN	GLI-Kruppel family member HKR1	141					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.374269	210.959875	213.33238	64	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37853120	37853120	7485	19	T	G	G	G	777	60	HKR1	4	4
PSG1	5669	broad.mit.edu	37	19	43382252	43382252	+	Silent	SNP	T	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43382252T>C	uc010eio.1	-	c.243A>G	c.(241-243)TCA>TCG	p.S81S	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Silent_p.S81S|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Non-coding_Transcript|PSG1_uc002our.1_Silent_p.S81S|PSG1_uc002oux.1_Silent_p.S10S|PSG1_uc002ouy.1_Silent_p.S81S|PSG1_uc002ouz.1_Silent_p.S81S|PSG1_uc002ova.1_Silent_p.S81S|PSG1_uc002ovb.2_Silent_p.S81S|PSG1_uc002ovc.2_Silent_p.S81S|PSG1_uc002ovd.1_Silent_p.S81S	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	81	Ig-like V-type.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)												0.396057	668.155471	673.429757	221	337	KEEP	---	---	---	---	capture		Silent	SNP	43382252	43382252	13106	19	T	C	C	C	652	51	PSG1	4	4
SHANK1	50944	broad.mit.edu	37	19	51165489	51165489	+	Silent	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51165489C>T	uc002psx.1	-	c.6219G>A	c.(6217-6219)TCG>TCA	p.S2073S	SHANK1_uc002psw.1_Silent_p.S1457S	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2073					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)										0.15	8.828856	13.523553	6	34	KEEP	---	---	---	---	capture		Silent	SNP	51165489	51165489	14756	19	C	T	T	T	340	27	SHANK1	1	1
KLK15	55554	broad.mit.edu	37	19	51330321	51330321	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51330321G>A	uc002ptl.2	-	c.294C>T	c.(292-294)TAC>TAT	p.Y98Y	KLK15_uc002ptm.2_Silent_p.Y98Y|KLK15_uc002ptn.2_Silent_p.Y98Y|KLK15_uc002pto.2_Silent_p.Y97Y|KLK15_uc010ych.1_Non-coding_Transcript|KLK15_uc010yci.1_Silent_p.Y97Y|KLK15_uc010eod.2_Non-coding_Transcript	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	98	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		Pancreas(140;10 2513 7143 9246)								0.4	110.013493	110.934665	42	63	KEEP	---	---	---	---	capture		Silent	SNP	51330321	51330321	8717	19	G	A	A	A	516	40	KLK15	1	1
ZNF614	80110	broad.mit.edu	37	19	52519939	52519939	+	Silent	SNP	A	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52519939A>C	uc002pyj.2	-	c.912T>G	c.(910-912)GCT>GCG	p.A304A	ZNF614_uc002pyi.3_Intron|ZNF614_uc010epj.2_Silent_p.A7A	NM_025040	NP_079316	Q8N883	ZN614_HUMAN	zinc finger protein 614	304	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)										0.100529	17.58014	47.697283	19	170	KEEP	---	---	---	---	capture		Silent	SNP	52519939	52519939	18634	19	A	C	C	C	132	11	ZNF614	4	4
PEG3	5178	broad.mit.edu	37	19	57327010	57327010	+	Nonsense_Mutation	SNP	T	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57327010T>A	uc002qnu.2	-	c.2800A>T	c.(2800-2802)AAG>TAG	p.K934*	ZIM2_uc010ygq.1_Intron|ZIM2_uc010ygr.1_Intron|ZIM2_uc002qnr.2_Intron|ZIM2_uc002qnq.2_Intron|ZIM2_uc010etp.2_Intron|ZIM2_uc010ygs.1_Intron|PEG3_uc002qnt.2_Nonsense_Mutation_p.K905*|PEG3_uc002qnv.2_Nonsense_Mutation_p.K934*|PEG3_uc002qnw.2_Nonsense_Mutation_p.K810*|PEG3_uc002qnx.2_Nonsense_Mutation_p.K808*|PEG3_uc010etr.2_Nonsense_Mutation_p.K934*	NM_001146186	NP_001139658	Q9GZU2	PEG3_HUMAN	paternally expressed 3 isoform 1	934					apoptosis|regulation of transcription, DNA-dependent|viral reproduction	cytoplasm|nucleus	nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(7)|large_intestine(1)|pancreas(1)	9		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)										0.331658	164.375076	169.375573	66	133	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	57327010	57327010	12141	19	T	A	A	A	806	62	PEG3	5	3
FBN3	84467	broad.mit.edu	37	19	8191468	8191468	+	Missense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8191468C>A	uc002mjf.2	-	c.2438G>T	c.(2437-2439)TGG>TTG	p.W813L		NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	813	TB 4.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.328125	52.152601	53.829393	21	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8191468	8191468	5940	19	C	A	A	A	273	21	FBN3	2	2
MUC16	94025	broad.mit.edu	37	19	9073701	9073701	+	Nonsense_Mutation	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9073701G>T	uc002mkp.2	-	c.13745C>A	c.(13744-13746)TCA>TAA	p.S4582*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4584	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.21519	34.125303	40.047167	17	62	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9073701	9073701	10367	19	G	T	T	T	585	45	MUC16	5	2
KIF1B	23095	broad.mit.edu	37	1	10292474	10292474	+	Missense_Mutation	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10292474A>G	uc001aqz.2	+	c.88A>G	c.(88-90)ATG>GTG	p.M30V	KIF1B_uc001aqv.3_Missense_Mutation_p.M30V|KIF1B_uc001aqw.3_Missense_Mutation_p.M30V|KIF1B_uc001aqx.3_Missense_Mutation_p.M30V|KIF1B_uc001aqy.2_Missense_Mutation_p.M30V|KIF1B_uc001ara.2_Missense_Mutation_p.M30V|KIF1B_uc001arb.2_Missense_Mutation_p.M30V|KIF1B_uc009vmt.2_Non-coding_Transcript	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	30	Kinesin-motor.				anterograde axon cargo transport|apoptosis|nerve-nerve synaptic transmission|neuromuscular synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)	2	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)										0.416667	52.320965	52.538694	15	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10292474	10292474	8595	1	A	G	G	G	156	12	KIF1B	4	4
FCGR3B	2215	broad.mit.edu	37	1	161599819	161599819	+	Missense_Mutation	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161599819A>G	uc009wul.2	-	c.68T>C	c.(67-69)CTC>CCC	p.L23P		NM_000570	NP_000561	O75015	FCG3B_HUMAN	low affinity immunoglobulin gamma Fc region	23					immune response	anchored to membrane|extracellular region|plasma membrane	IgG binding|receptor activity				0	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)									0.40625	88.740044	89.231102	26	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161599819	161599819	6022	1	A	G	G	G	143	11	FCGR3B	4	4
SMG7	9887	broad.mit.edu	37	1	183486889	183486889	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:183486889G>A	uc001gqf.2	+	c.246G>A	c.(244-246)CCG>CCA	p.P82P	SMG7_uc010pob.1_Silent_p.P111P|SMG7_uc001gqh.2_Silent_p.P82P|SMG7_uc001gqg.2_Silent_p.P82P|SMG7_uc001gqi.2_Silent_p.P40P|SMG7_uc010poc.1_Silent_p.P40P	NM_201568	NP_963862	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 2	82					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			central_nervous_system(1)	1														0.109375	22.917954	61.602729	28	228	KEEP	---	---	---	---	capture		Silent	SNP	183486889	183486889	15296	1	G	A	A	A	470	37	SMG7	1	1
TPR	7175	broad.mit.edu	37	1	186329117	186329117	+	Silent	SNP	A	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186329117A>C	uc001grv.2	-	c.1203T>G	c.(1201-1203)GCT>GCG	p.A401A	TPR_uc010pop.1_Silent_p.A477A	NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	401					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)						1949				0.361111	73.626851	74.850667	26	46	KEEP	---	---	---	---	capture		Silent	SNP	186329117	186329117	16960	1	A	C	C	C	28	3	TPR	4	4
NAV1	89796	broad.mit.edu	37	1	201777624	201777624	+	Silent	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201777624G>T	uc001gwu.2	+	c.3915G>T	c.(3913-3915)TCG>TCT	p.S1305S	NAV1_uc001gwx.2_Silent_p.S914S|MIR1231_hsa-mir-1231|MI0006321_5'Flank	NM_020443	NP_065176	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1308	Potential.				cell differentiation|nervous system development	cytoplasm|microtubule	nucleoside-triphosphatase activity|nucleotide binding			central_nervous_system(2)|ovary(1)	3														0.324324	97.759106	100.800865	36	75	KEEP	---	---	---	---	capture		Silent	SNP	201777624	201777624	10579	1	G	T	T	T	496	39	NAV1	1	1
MIA3	375056	broad.mit.edu	37	1	222801788	222801788	+	Missense_Mutation	SNP	A	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222801788A>T	uc001hnl.2	+	c.1226A>T	c.(1225-1227)GAG>GTG	p.E409V	MIA3_uc009xea.1_Missense_Mutation_p.E245V	NM_198551	NP_940953	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	409	Extracellular (Potential).				exocytosis|negative regulation of cell adhesion|negative regulation of cell migration|positive regulation of leukocyte migration|protein transport|wound healing	endoplasmic reticulum membrane|integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(131;0.0199)										0.34104	155.166644	159.032573	59	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	222801788	222801788	9955	1	A	T	T	T	143	11	MIA3	3	3
WDR64	128025	broad.mit.edu	37	1	241929587	241929587	+	Missense_Mutation	SNP	T	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241929587T>C	uc001hzf.1	+	c.1145T>C	c.(1144-1146)ATA>ACA	p.I382T	WDR64_uc001hzg.1_Missense_Mutation_p.I128T	NM_144625	NP_653226	B1ANS9	WDR64_HUMAN	WD repeat domain 64	662	WD 9.										0	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)											0.273437	115.287989	121.195735	35	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241929587	241929587	17888	1	T	C	C	C	637	49	WDR64	4	4
HECTD3	79654	broad.mit.edu	37	1	45471493	45471493	+	Missense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:45471493C>A	uc009vxk.2	-	c.1908G>T	c.(1906-1908)AAG>AAT	p.K636N	HECTD3_uc001cmx.3_5'Flank|HECTD3_uc001cmy.3_Missense_Mutation_p.K246N|HECTD3_uc010olh.1_Missense_Mutation_p.K352N	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3	636	HECT.				proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex|perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)													0.37234	94.215914	95.555285	35	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45471493	45471493	7324	1	C	A	A	A	311	24	HECTD3	2	2
FAF1	11124	broad.mit.edu	37	1	50941262	50941262	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:50941262G>A	uc009vyx.1	-	c.1743C>T	c.(1741-1743)CCC>CCT	p.P581P	FAF1_uc009vyw.1_Non-coding_Transcript|FAF1_uc001cse.1_Silent_p.P581P|FAF1_uc010onc.1_Silent_p.P339P	NM_007051	NP_008982	Q9UNN5	FAF1_HUMAN	FAS-associated factor 1	581	UBX.				apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)										0.446154	89.774419	89.93704	29	36	KEEP	---	---	---	---	capture		Silent	SNP	50941262	50941262	5566	1	G	A	A	A	600	47	FAF1	2	2
C20orf185	359710	broad.mit.edu	37	20	31651454	31651454	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31651454G>A	uc002wym.1	+	c.625G>A	c.(625-627)GTG>ATG	p.V209M		NM_182658	NP_872599	P59826	LPLC3_HUMAN	antimicrobial peptide RYA3 precursor	209	Leu-rich.				innate immune response	cytoplasm|extracellular region	lipid binding|protein binding			ovary(4)	4														0.241071	121.422411	135.139037	54	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31651454	31651454	2175	20	G	A	A	A	572	44	C20orf185	2	2
ITGB2	3689	broad.mit.edu	37	21	46313397	46313397	+	Silent	SNP	G	A	A	rs61737080		TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46313397G>A	uc002zgd.2	-	c.1146C>T	c.(1144-1146)TAC>TAT	p.Y382Y	ITGB2_uc002zge.2_Silent_p.Y382Y|ITGB2_uc002zgf.3_Silent_p.Y382Y|ITGB2_uc011afl.1_Silent_p.Y304Y|ITGB2_uc010gpw.2_Silent_p.Y325Y|ITGB2_uc002zgg.2_Silent_p.Y382Y	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	382	Extracellular (Potential).				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(2)	8				Colorectal(79;0.0669)	Simvastatin(DB00641)							OREG0026255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.176744	69.212894	90.391289	38	177	KEEP	---	---	---	---	capture		Silent	SNP	46313397	46313397	8198	21	G	A	A	A	516	40	ITGB2	1	1
FAM123C	205147	broad.mit.edu	37	2	131519728	131519728	+	Missense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131519728C>A	uc002trw.2	+	c.83C>A	c.(82-84)GCT>GAT	p.A28D	FAM123C_uc010fmv.2_Missense_Mutation_p.A28D|FAM123C_uc010fms.1_Missense_Mutation_p.A28D|FAM123C_uc010fmt.1_Missense_Mutation_p.A28D|FAM123C_uc010fmu.1_Missense_Mutation_p.A28D	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	28										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.13)										0.333333	10.702915	10.994682	4	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131519728	131519728	5621	2	C	A	A	A	364	28	FAM123C	2	2
OSBPL6	114880	broad.mit.edu	37	2	179248905	179248905	+	Splice_Site_SNP	SNP	T	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179248905T>C	uc002uly.2	+	c.2088_splice	c.e19+2	p.Q696_splice	OSBPL6_uc002ulx.2_Splice_Site_SNP_p.Q671_splice|OSBPL6_uc010zfe.1_Splice_Site_SNP_p.Q640_splice|OSBPL6_uc002ulz.2_Splice_Site_SNP_p.Q635_splice|OSBPL6_uc002uma.2_Splice_Site_SNP_p.Q675_splice	NM_145739	NP_665682			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)											0.081633	22.843319	92.649847	32	360	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	179248905	179248905	11692	2	T	C	C	C	741	57	OSBPL6	5	4
TTN	7273	broad.mit.edu	37	2	179640620	179640620	+	Missense_Mutation	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179640620G>T	uc010zfg.1	-	c.5971C>A	c.(5971-5973)CCT>ACT	p.P1991T	TTN_uc010zfh.1_Missense_Mutation_p.P1945T|TTN_uc010zfi.1_Missense_Mutation_p.P1945T|TTN_uc010zfj.1_Missense_Mutation_p.P1945T|TTN_uc002unb.2_Missense_Mutation_p.P1991T	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1991										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.088136	3.82987	54.428095	26	269	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179640620	179640620	17290	2	G	T	T	T	546	42	TTN	2	2
ITGAV	3685	broad.mit.edu	37	2	187540632	187540632	+	Missense_Mutation	SNP	A	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:187540632A>T	uc002upq.2	+	c.2906A>T	c.(2905-2907)GAG>GTG	p.E969V	ITGAV_uc010frs.2_Missense_Mutation_p.E933V|ITGAV_uc010zfv.1_Missense_Mutation_p.E923V	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor	969	Extracellular (Potential).				angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		Melanoma(58;108 1995 6081)				606				0.369565	46.461043	47.149557	17	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187540632	187540632	8192	2	A	T	T	T	143	11	ITGAV	3	3
WDR35	57539	broad.mit.edu	37	2	20135266	20135266	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:20135266G>A	uc002rdi.2	-	c.2546C>T	c.(2545-2547)GCC>GTC	p.A849V	WDR35_uc002rdj.2_Missense_Mutation_p.A838V|WDR35_uc010ext.2_Non-coding_Transcript|WDR35_uc002rdh.2_Missense_Mutation_p.A414V|WDR35_uc002rdk.3_Missense_Mutation_p.A414V	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	849										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.275	56.51576	60.163043	22	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20135266	20135266	17862	2	G	A	A	A	546	42	WDR35	2	2
EPT1	85465	broad.mit.edu	37	2	26607932	26607932	+	Missense_Mutation	SNP	G	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26607932G>C	uc010ykz.1	+	c.837G>C	c.(835-837)TGG>TGC	p.W279C	EPT1_uc010eyl.1_Non-coding_Transcript	NM_033505	NP_277040	Q9C0D9	EPT1_HUMAN	selenoprotein I	279					phospholipid biosynthetic process	integral to membrane	ethanolaminephosphotransferase activity|metal ion binding				0														0.097561	4.06677	10.718325	4	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26607932	26607932	5392	2	G	C	C	C	572	44	EPT1	3	3
CGREF1	10669	broad.mit.edu	37	2	27324165	27324165	+	Missense_Mutation	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27324165G>T	uc010eyr.1	-	c.1249C>A	c.(1249-1251)CAA>AAA	p.Q417K	CGREF1_uc010ylf.1_Intron|CGREF1_uc002rip.1_Intron|CGREF1_uc002riq.2_Missense_Mutation_p.Q312K|CGREF1_uc010eys.1_Missense_Mutation_p.Q295K|CGREF1_uc002rir.1_Missense_Mutation_p.Q295K|CGREF1_uc002ris.2_Missense_Mutation_p.F295L	NM_006569	NP_006560	Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	295					cell adhesion|cell cycle arrest|negative regulation of cell proliferation|response to stress	extracellular region	calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.346154	318.852779	325.925236	117	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27324165	27324165	3438	2	G	T	T	T	585	45	CGREF1	2	2
RPS7	6201	broad.mit.edu	37	2	3627799	3627799	+	Silent	SNP	G	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:3627799G>C	uc002qxw.2	+	c.456G>C	c.(454-456)CGG>CGC	p.R152R	RPS7_uc002qxy.2_Non-coding_Transcript	NM_001011	NP_001002	P62081	RS7_HUMAN	ribosomal protein S7	152					endocrine pancreas development|ribosomal small subunit biogenesis|rRNA processing|translational elongation|translational termination|viral transcription	90S preribosome|cytosolic small ribosomal subunit|nucleolus|small-subunit processome	protein binding|RNA binding|structural constituent of ribosome				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0963)|Epithelial(75;0.208)										0.328947	81.803494	83.747472	25	51	KEEP	---	---	---	---	capture		Silent	SNP	3627799	3627799	14140	2	G	C	C	C	535	42	RPS7	3	3
MECOM	2122	broad.mit.edu	37	3	168833635	168833635	+	Silent	SNP	T	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:168833635T>A	uc011bpj.1	-	c.2025A>T	c.(2023-2025)TCA>TCT	p.S675S	MECOM_uc010hwk.1_Silent_p.S510S|MECOM_uc003ffj.3_Silent_p.S552S|MECOM_uc003ffi.3_Silent_p.S487S|MECOM_uc011bpi.1_Silent_p.S488S|MECOM_uc003ffn.3_Silent_p.S487S|MECOM_uc003ffk.2_Silent_p.S487S|MECOM_uc003ffl.2_Silent_p.S647S|MECOM_uc011bpk.1_Silent_p.S477S|MECOM_uc010hwn.2_Silent_p.S675S	NM_004991	NP_004982	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus isoform c	Error:Variant_position_missing_in_Q13465_after_alignment							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8										646				0.223077	67.814071	76.9768	29	101	KEEP	---	---	---	---	capture		Silent	SNP	168833635	168833635	9811	3	T	A	A	A	808	63	MECOM	3	3
DVL3	1857	broad.mit.edu	37	3	183884764	183884764	+	Splice_Site_SNP	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:183884764G>T	uc003fms.2	+	c.1198_splice	c.e11+1	p.R400_splice	DVL3_uc011bqw.1_Splice_Site_SNP_p.R383_splice|DVL3_uc003fmt.2_Splice_Site_SNP_p.R71_splice|DVL3_uc003fmu.2_Splice_Site_SNP_p.R232_splice	NM_004423	NP_004414			dishevelled 3						canonical Wnt receptor signaling pathway|intracellular signal transduction|positive regulation of JUN kinase activity|positive regulation of protein phosphorylation|positive regulation of transcription, DNA-dependent	cytoplasm	beta-catenin binding|frizzled binding|protease binding|protein heterodimerization activity|signal transducer activity			ovary(1)|breast(1)	2	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)											0.176829	61.393784	77.517614	29	135	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	183884764	183884764	5023	3	G	T	T	T	520	40	DVL3	5	1
STAC	6769	broad.mit.edu	37	3	36527665	36527665	+	Missense_Mutation	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36527665G>T	uc003cgh.1	+	c.611G>T	c.(610-612)CGC>CTC	p.R204L	STAC_uc010hgd.1_Non-coding_Transcript|STAC_uc011aya.1_Missense_Mutation_p.R143L	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	204					intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			ovary(1)|pancreas(1)	2														0.20438	122.947772	145.09931	56	218	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36527665	36527665	15757	3	G	T	T	T	494	38	STAC	1	1
LAMB2	3913	broad.mit.edu	37	3	49167754	49167754	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49167754G>A	uc003cwe.2	-	c.1135C>T	c.(1135-1137)CAT>TAT	p.H379Y	LAMB2_uc003cwf.1_Missense_Mutation_p.H379Y	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	379	Laminin EGF-like 2.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.552941	127.404649	127.608975	47	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49167754	49167754	8934	3	G	A	A	A	598	46	LAMB2	2	2
LAMB2	3913	broad.mit.edu	37	3	49170269	49170269	+	Missense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49170269C>A	uc003cwe.2	-	c.32G>T	c.(31-33)GGA>GTA	p.G11V	LAMB2_uc003cwf.1_Missense_Mutation_p.G11V	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	11					cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.5	51.159529	51.159529	21	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49170269	49170269	8934	3	C	A	A	A	390	30	LAMB2	2	2
FSTL5	56884	broad.mit.edu	37	4	162577480	162577480	+	Silent	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:162577480A>G	uc003iqh.2	-	c.894T>C	c.(892-894)AAT>AAC	p.N298N	FSTL5_uc003iqi.2_Silent_p.N297N|FSTL5_uc010iqv.2_Silent_p.N297N	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN	follistatin-like 5 isoform a	298	Ig-like 1.					extracellular region	calcium ion binding			ovary(2)|pancreas(2)|large_intestine(1)|central_nervous_system(1)	6	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)										0.428571	18.74834	18.810513	6	8	KEEP	---	---	---	---	capture		Silent	SNP	162577480	162577480	6331	4	A	G	G	G	102	8	FSTL5	4	4
PPP2R2C	5522	broad.mit.edu	37	4	6380272	6380272	+	Nonsense_Mutation	SNP	C	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6380272C>A	uc003gja.2	-	c.196G>T	c.(196-198)GAA>TAA	p.E66*	PPP2R2C_uc003gjb.2_Nonsense_Mutation_p.E49*|PPP2R2C_uc003gjc.2_Nonsense_Mutation_p.E66*|PPP2R2C_uc011bwd.1_Nonsense_Mutation_p.E59*|PPP2R2C_uc011bwe.1_Nonsense_Mutation_p.E59*|PPP2R2C_uc003gjd.1_Nonsense_Mutation_p.E154*	NM_181876	NP_870991	Q9Y2T4	2ABG_HUMAN	gamma isoform of regulatory subunit B55, protein	66				E -> D (in Ref. 2; AAG39636).	signal transduction	protein phosphatase type 2A complex	protein phosphatase type 2A regulator activity			ovary(1)|kidney(1)|central_nervous_system(1)	3														0.48125	226.560012	226.608995	77	83	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	6380272	6380272	12822	4	C	A	A	A	403	31	PPP2R2C	5	1
EPB41L4A	64097	broad.mit.edu	37	5	111519749	111519749	+	Missense_Mutation	SNP	T	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:111519749T>A	uc003kpv.1	-	c.1586A>T	c.(1585-1587)GAC>GTC	p.D529V	EPB41L4A_uc003kpp.1_Missense_Mutation_p.D156V	NM_022140	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte protein band 4.1-like 4	529						cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135)		OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791)										0.327869	95.159237	98.364395	40	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111519749	111519749	5348	5	T	A	A	A	754	58	EPB41L4A	3	3
TMEM173	340061	broad.mit.edu	37	5	138861279	138861279	+	Missense_Mutation	SNP	G	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:138861279G>C	uc003lep.2	-	c.11C>G	c.(10-12)TCC>TGC	p.S4C		NM_198282	NP_938023	Q86WV6	TM173_HUMAN	transmembrane protein 173	4	Cytoplasmic (Potential).				activation of innate immune response|apoptosis|cellular response to exogenous dsRNA|defense response to virus|innate immune response|interferon-beta production|positive regulation of defense response to virus by host|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of protein binding|positive regulation of protein import into nucleus, translocation|positive regulation of transcription factor import into nucleus	endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane|perinuclear region of cytoplasm|plasma membrane	protein homodimerization activity|protein kinase binding|transcription factor binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											0.26	41.451906	44.059268	13	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138861279	138861279	16623	5	G	C	C	C	533	41	TMEM173	3	3
C7	730	broad.mit.edu	37	5	40937762	40937762	+	Silent	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:40937762G>T	uc003jmh.2	+	c.537G>T	c.(535-537)CTG>CTT	p.L179L	C7_uc011cpn.1_Intron	NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	179	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)												0.611111	29.816289	30.008508	11	7	KEEP	---	---	---	---	capture		Silent	SNP	40937762	40937762	2482	5	G	T	T	T	574	45	C7	2	2
BAT2	7916	broad.mit.edu	37	6	31599748	31599748	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31599748C>T	uc003nvb.3	+	c.3298C>T	c.(3298-3300)CGG>TGG	p.R1100W	BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.R1100W	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1100	4 X 57 AA type A repeats.					cytoplasm|nucleus	protein binding				0														0.116667	6.281703	14.958753	7	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31599748	31599748	1340	6	C	T	T	T	347	27	BAT2	1	1
TBX18	9096	broad.mit.edu	37	6	85446869	85446869	+	Missense_Mutation	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:85446869C>T	uc003pkl.1	-	c.1358G>A	c.(1357-1359)AGG>AAG	p.R453K	TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	453					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)						300				0.480519	116.054864	116.080198	37	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85446869	85446869	16179	6	C	T	T	T	312	24	TBX18	2	2
SLC13A1	6561	broad.mit.edu	37	7	122768953	122768953	+	Missense_Mutation	SNP	A	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:122768953A>C	uc003vkm.2	-	c.1079T>G	c.(1078-1080)CTA>CGA	p.L360R	SLC13A1_uc010lks.2_Missense_Mutation_p.L236R	NM_022444	NP_071889	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate	360	Helical; (Potential).					integral to membrane|plasma membrane	sodium:sulfate symporter activity			ovary(2)	2					Succinic acid(DB00139)									0.272727	43.118783	45.66803	15	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122768953	122768953	14886	7	A	C	C	C	195	15	SLC13A1	4	4
STK31	56164	broad.mit.edu	37	7	23751905	23751905	+	Missense_Mutation	SNP	G	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:23751905G>T	uc003sws.3	+	c.150G>T	c.(148-150)CAG>CAT	p.Q50H	STK31_uc003swt.3_Missense_Mutation_p.Q27H|STK31_uc011jze.1_Missense_Mutation_p.Q50H|STK31_uc010kuq.2_Missense_Mutation_p.Q27H	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	50					protein phosphorylation		ATP binding|nucleic acid binding|protein serine/threonine kinase activity			ovary(2)|lung(2)	4										598				0.333333	107.583474	110.695465	42	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23751905	23751905	15816	7	G	T	T	T	451	35	STK31	2	2
KLHL38	340359	broad.mit.edu	37	8	124659239	124659239	+	Missense_Mutation	SNP	T	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124659239T>C	uc003yqs.1	-	c.1366A>G	c.(1366-1368)AGA>GGA	p.R456G		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	456	Kelch 4.										0														0.302857	143.807888	149.879765	53	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124659239	124659239	8704	8	T	C	C	C	713	55	KLHL38	4	4
RNF139	11236	broad.mit.edu	37	8	125498172	125498172	+	Silent	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:125498172G>A	uc003yrc.2	+	c.282G>A	c.(280-282)TTG>TTA	p.L94L		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	94	Helical; (Potential).				regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	ligase activity|protein binding|receptor activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)											0.29927	106.72201	111.655149	41	96	KEEP	---	---	---	---	capture		Silent	SNP	125498172	125498172	13919	8	G	A	A	A	607	47	RNF139	2	2
ADCY8	114	broad.mit.edu	37	8	132051638	132051638	+	Silent	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:132051638C>T	uc003ytd.3	-	c.942G>A	c.(940-942)GCG>GCA	p.A314A	ADCY8_uc010mds.2_Silent_p.A314A	NM_001115	NP_001106	P40145	ADCY8_HUMAN	adenylate cyclase 8	314	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|membrane fraction|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|metal ion binding			large_intestine(1)|central_nervous_system(1)	2	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)											0.258621	72.526435	78.631635	30	86	KEEP	---	---	---	---	capture		Silent	SNP	132051638	132051638	301	8	C	T	T	T	288	23	ADCY8	1	1
FAM135B	51059	broad.mit.edu	37	8	139151255	139151255	+	Missense_Mutation	SNP	A	G	G			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139151255A>G	uc003yuy.2	-	c.3875T>C	c.(3874-3876)TTC>TCC	p.F1292S	FAM135B_uc003yux.2_Missense_Mutation_p.F1193S|FAM135B_uc003yuz.2_Non-coding_Transcript	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	1292										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.322835	134.988538	138.498813	41	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139151255	139151255	5646	8	A	G	G	G	117	9	FAM135B	4	4
PTGS1	5742	broad.mit.edu	37	9	125148924	125148924	+	Silent	SNP	C	T	T			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125148924C>T	uc004bmg.1	+	c.1209C>T	c.(1207-1209)TAC>TAT	p.Y403Y	PTGS1_uc011lys.1_Intron|PTGS1_uc010mwb.1_Intron|PTGS1_uc004bmf.1_Intron|PTGS1_uc004bmh.1_Silent_p.Y294Y|PTGS1_uc011lyt.1_Silent_p.Y294Y	NM_000962	NP_000953	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 isoform 1	403					cyclooxygenase pathway|hormone biosynthetic process|oxidation-reduction process|regulation of blood pressure|response to oxidative stress|xenobiotic metabolic process	endoplasmic reticulum membrane|Golgi apparatus|microsome|plasma membrane	heme binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peroxidase activity|prostaglandin-endoperoxide synthase activity			ovary(1)	1					Acetaminophen(DB00316)|Aspirin(DB00945)|Balsalazide(DB01014)|Bromfenac(DB00963)|Ciclopirox(DB01188)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dipyrone(DB04817)|Etodolac(DB00749)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|gamma-Homolinolenic acid(DB00154)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lumiracoxib(DB01283)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Mesalazine(DB00244)|Minoxidil(DB00350)|Nabumetone(DB00461)|Naproxen(DB00788)|Phenacetin(DB03783)|Piroxicam(DB00554)|Rofecoxib(DB00533)|Salicyclic acid(DB00936)|Salsalate(DB01399)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Tolmetin(DB00500)									0.101449	6.652588	28.535713	14	124	KEEP	---	---	---	---	capture		Silent	SNP	125148924	125148924	13210	9	C	T	T	T	246	19	PTGS1	1	1
GTF3C5	9328	broad.mit.edu	37	9	135917627	135917627	+	Missense_Mutation	SNP	G	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135917627G>A	uc004ccj.3	+	c.307G>A	c.(307-309)GCC>ACC	p.A103T	GTF3C5_uc010mzz.2_Intron|GTF3C5_uc004cci.3_Missense_Mutation_p.A103T	NM_001122823	NP_001116295	Q9Y5Q8	TF3C5_HUMAN	general transcription factor IIIC, polypeptide 5	103					5S class rRNA transcription from RNA polymerase III type 1 promoter|tRNA transcription from RNA polymerase III promoter	transcription factor TFIIIC complex	DNA binding|protein binding				0				OV - Ovarian serous cystadenocarcinoma(145;4.01e-06)|Epithelial(140;4e-05)										0.216216	65.113739	76.117955	32	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135917627	135917627	7156	9	G	A	A	A	546	42	GTF3C5	2	2
NDP	4693	broad.mit.edu	37	X	43817761	43817761	+	Missense_Mutation	SNP	T	C	C	rs104894870		TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:43817761T>C	uc004dga.3	-	c.131A>G	c.(130-132)TAT>TGT	p.Y44C		NM_000266	NP_000257	Q00604	NDP_HUMAN	norrin precursor	44	CTCK.		Y -> C (in ND).		cell proliferation|cell-cell signaling|nervous system development|positive regulation of transcription, DNA-dependent|sensory perception of sound|vacuole organization|visual perception|Wnt receptor signaling pathway	extracellular matrix|extracellular space	cell surface binding|frizzled binding|growth factor activity|protein homodimerization activity				0														0.073684	1.958212	19.688915	7	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43817761	43817761	10649	23	T	C	C	C	637	49	NDP	4	4
NLRC5	84166	broad.mit.edu	37	16	57073747	57073747	+	Frame_Shift_Del	DEL	G	-	-			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57073747_57073747delG	uc002ekk.1	+	c.2856_2856delG	c.(2854-2856)AAGfs	p.K952fs	NLRC5_uc010ccq.1_Non-coding_Transcript|NLRC5_uc002ekn.2_Frame_Shift_Del_p.K701fs|NLRC5_uc002ekl.2_Frame_Shift_Del_p.K757fs|NLRC5_uc002ekm.2_Frame_Shift_Del_p.K757fs|NLRC5_uc010ccr.1_Non-coding_Transcript|NLRC5_uc010ccs.1_Non-coding_Transcript|NLRC5_uc002eko.1_5'Flank|NLRC5_uc002ekp.1_5'Flank	NM_032206	NP_115582	Q86WI3	NLRC5_HUMAN	nucleotide-binding oligomerization domains 27	952	LRR 7.				defense response to virus|innate immune response|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|negative regulation of type I interferon-mediated signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of interferon-gamma-mediated signaling pathway|positive regulation of MHC class I biosynthetic process|positive regulation of type I interferon-mediated signaling pathway|regulation of kinase activity	cytosol|nucleus	ATP binding|protein binding|RNA polymerase II core promoter sequence-specific DNA binding			ovary(4)|breast(1)|skin(1)	6		all_neural(199;0.225)												0.38			80	132		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	57073747	57073747	10873	16	G	-	-	-	451	35	NLRC5	5	5
TMCO7	79613	broad.mit.edu	37	16	68894367	68894367	+	Frame_Shift_Del	DEL	A	-	-			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68894367_68894367delA	uc002ewi.3	+	c.675_675delA	c.(673-675)GCAfs	p.A225fs	TMCO7_uc002ewh.2_Frame_Shift_Del_p.A225fs	NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	225						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)										0.38			71	118		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	68894367	68894367	16531	16	A	-	-	-	80	7	TMCO7	5	5
RIT1	6016	broad.mit.edu	37	1	155874278	155874283	+	In_Frame_Del	DEL	TGGCTG	-	-			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155874278_155874283delTGGCTG	uc001fmh.1	-	c.248_253delCAGCCA	c.(247-255)ACAGCCATG>ATG	p.TA83del	RIT1_uc010pgr.1_In_Frame_Del_p.TA47del	NM_006912	NP_008843	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	83_84					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity				0	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)											0.50			35	35		---	---	---	---	capture_indel		In_Frame_Del	DEL	155874278	155874283	13863	1	TGGCTG	-	-	-	663	51	RIT1	5	5
EDEM3	80267	broad.mit.edu	37	1	184690453	184690454	+	Frame_Shift_Ins	INS	-	C	C			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:184690453_184690454insC	uc010pom.1	-	c.920_921insG	c.(919-921)GGAfs	p.G307fs	EDEM3_uc010pok.1_Frame_Shift_Ins_p.G307fs|EDEM3_uc010pol.1_Non-coding_Transcript|EDEM3_uc001gqy.2_Frame_Shift_Ins_p.G230fs	NM_025191	NP_079467	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like	307					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			skin(1)	1														0.62			60	37		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	184690453	184690454	5100	1	-	C	C	C	691	54	EDEM3	5	5
RBM16	22828	broad.mit.edu	37	6	155114064	155114065	+	Frame_Shift_Ins	INS	-	A	A			TCGA-73-4675-01	TCGA-73-4675-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:155114064_155114065insA	uc011efj.1	+	c.627_628insA	c.(625-630)GTCACAfs	p.V209fs	RBM16_uc011efk.1_Frame_Shift_Ins_p.V188fs|RBM16_uc003qqa.2_Frame_Shift_Ins_p.V143fs|RBM16_uc003qpz.2_Frame_Shift_Ins_p.V143fs|RBM16_uc010kji.2_Frame_Shift_Ins_p.V164fs	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	143_144					mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)										0.44			18	23		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	155114064	155114065	13579	6	-	A	A	A	366	29	RBM16	5	5
