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
CHUK	1147	broad.mit.edu	37	10	101982738	101982738	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101982738C>A	uc001kqp.2	-	c.201_splice	c.e3-1	p.K67_splice		NM_001278	NP_001269			conserved helix-loop-helix ubiquitous kinase						I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus	ATP binding|identical protein binding|IkappaB kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1)	7		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)		Ovarian(159;52 1904 10536 35305 37148)				415				0.217391	42.14404	48.92484	20	72	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	101982738	101982738	3550	10	C	A	A	A	312	24	CHUK	5	2
SEC23IP	11196	broad.mit.edu	37	10	121691670	121691671	+	Nonsense_Mutation	DNP	GG	CT	CT			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:121691670_121691671GG>CT	uc001leu.1	+	c.2598_2599GG>CT	c.(2596-2601)ATGGGA>ATCTGA	p.866_867MG>I*	SEC23IP_uc010qtc.1_Nonsense_Mutation_p.655_656MG>I*|SEC23IP_uc009xzk.1_Non-coding_Transcript	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	866_867	DDHD.				Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding			ovary(3)	3		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)										0.114865	30.462373	52.094514	17	131	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	121691670	121691671	14479	10	GG	CT	CT	CT	611	47	SEC23IP	5	3
CUBN	8029	broad.mit.edu	37	10	16867009	16867009	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:16867009G>T	uc001ioo.2	-	c.10837C>A	c.(10837-10839)CGT>AGT	p.R3613S		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	3613	CUB 27.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.26087	30.978412	33.359726	12	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16867009	16867009	4211	10	G	T	T	T	494	38	CUBN	1	1
ARHGAP21	57584	broad.mit.edu	37	10	24884819	24884819	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:24884819C>A	uc001isb.2	-	c.3631G>T	c.(3631-3633)GAT>TAT	p.D1211Y	ARHGAP21_uc010qdb.1_Non-coding_Transcript	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1210	Rho-GAP.				signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8														0.086207	0.125869	10.193636	5	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24884819	24884819	882	10	C	A	A	A	377	29	ARHGAP21	2	2
ZEB1	6935	broad.mit.edu	37	10	31809806	31809806	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:31809806A>C	uc001ivu.3	+	c.1546A>C	c.(1546-1548)AAG>CAG	p.K516Q	ZEB1_uc001ivr.3_Missense_Mutation_p.K297Q|ZEB1_uc010qee.1_Missense_Mutation_p.K297Q|ZEB1_uc010qef.1_Missense_Mutation_p.K297Q|ZEB1_uc009xlj.1_Missense_Mutation_p.K441Q|ZEB1_uc010qeg.1_Missense_Mutation_p.K374Q|ZEB1_uc009xlk.1_Missense_Mutation_p.K297Q|ZEB1_uc001ivs.3_Missense_Mutation_p.K515Q|ZEB1_uc001ivt.3_Missense_Mutation_p.K297Q|ZEB1_uc001ivv.3_Missense_Mutation_p.K495Q|ZEB1_uc010qeh.1_Missense_Mutation_p.K448Q|ZEB1_uc009xlo.1_Missense_Mutation_p.K498Q|ZEB1_uc009xlp.2_Missense_Mutation_p.K499Q	NM_030751	NP_001121600	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	515					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter	cytoplasm	sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				Ovarian(40;423 959 14296 36701 49589)								0.252632	74.660446	79.934943	24	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31809806	31809806	18211	10	A	C	C	C	169	13	ZEB1	4	4
CUL2	8453	broad.mit.edu	37	10	35333791	35333791	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:35333791C>A	uc010qer.1	-	c.569G>T	c.(568-570)CGT>CTT	p.R190L	CUL2_uc009xma.2_Missense_Mutation_p.R40L|CUL2_uc001ixv.2_Missense_Mutation_p.R171L|CUL2_uc001ixw.2_Missense_Mutation_p.R171L|CUL2_uc010qes.1_Missense_Mutation_p.R108L	NM_003591	NP_003582	Q13617	CUL2_HUMAN	cullin 2	171					cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3														0.138889	17.2023	26.274506	10	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35333791	35333791	4215	10	C	A	A	A	247	19	CUL2	1	1
CUL2	8453	broad.mit.edu	37	10	35333797	35333797	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:35333797C>A	uc010qer.1	-	c.564_splice	c.e7-1	p.N188_splice	CUL2_uc009xma.2_Splice_Site_SNP_p.N38_splice|CUL2_uc001ixv.2_Splice_Site_SNP_p.N169_splice|CUL2_uc001ixw.2_Splice_Site_SNP_p.N169_splice|CUL2_uc010qes.1_Splice_Site_SNP_p.S106_splice	NM_003591	NP_003582			cullin 2						cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3														0.126984	9.050794	17.607999	8	55	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	35333797	35333797	4215	10	C	A	A	A	260	20	CUL2	5	2
CSTF2T	23283	broad.mit.edu	37	10	53458658	53458658	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:53458658C>A	uc001jjp.2	-	c.652G>T	c.(652-654)GGC>TGC	p.G218C	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	218					mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)										0.180328	20.692551	26.551341	11	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53458658	53458658	4126	10	C	A	A	A	273	21	CSTF2T	2	2
PRKG1	5592	broad.mit.edu	37	10	53822338	53822338	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:53822338C>A	uc001jjo.2	+	c.882C>A	c.(880-882)GTC>GTA	p.V294V	PRKG1_uc001jjm.2_Silent_p.V279V|PRKG1_uc001jjn.2_Silent_p.V294V|PRKG1_uc009xow.1_5'UTR	NM_006258	NP_006249	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I isoform	279	cGMP 2.				actin cytoskeleton organization|platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)						1247				0.160714	12.723531	18.88789	9	47	KEEP	---	---	---	---	capture		Silent	SNP	53822338	53822338	12965	10	C	A	A	A	405	32	PRKG1	2	2
JMJD1C	221037	broad.mit.edu	37	10	64945331	64945331	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:64945331C>A	uc001jmn.2	-	c.6822G>T	c.(6820-6822)ATG>ATT	p.M2274I	JMJD1C_uc001jml.2_Missense_Mutation_p.M2037I|JMJD1C_uc001jmm.2_Missense_Mutation_p.M1986I|JMJD1C_uc010qiq.1_Missense_Mutation_p.M2092I|JMJD1C_uc009xpi.2_Missense_Mutation_p.M2092I|JMJD1C_uc009xpj.1_Non-coding_Transcript|JMJD1C_uc001jmo.2_Missense_Mutation_p.M181I	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	2274	JmjC.				blood coagulation|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)	5	Prostate(12;0.0119)|all_hematologic(501;0.191)													0.131579	13.694731	23.723405	10	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64945331	64945331	8254	10	C	A	A	A	325	25	JMJD1C	2	2
JMJD1C	221037	broad.mit.edu	37	10	64952769	64952769	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:64952769G>A	uc001jmn.2	-	c.6005C>T	c.(6004-6006)CCT>CTT	p.P2002L	JMJD1C_uc001jml.2_Missense_Mutation_p.P1765L|JMJD1C_uc001jmm.2_Missense_Mutation_p.P1714L|JMJD1C_uc010qiq.1_Missense_Mutation_p.P1820L|JMJD1C_uc009xpi.2_Missense_Mutation_p.P1820L|JMJD1C_uc009xpj.1_Non-coding_Transcript|JMJD1C_uc001jmo.2_5'Flank|JMJD1C_uc009xpk.1_Missense_Mutation_p.P900L	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	2002					blood coagulation|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)	5	Prostate(12;0.0119)|all_hematologic(501;0.191)													0.167139	120.91805	157.977647	59	294	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64952769	64952769	8254	10	G	A	A	A	455	35	JMJD1C	2	2
KIAA1274	27143	broad.mit.edu	37	10	72291088	72291088	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:72291088C>A	uc001jrd.3	+	c.511C>A	c.(511-513)CTG>ATG	p.L171M		NM_014431	NP_055246	Q9ULE6	PALD_HUMAN	KIAA1274	171										ovary(2)|central_nervous_system(1)	3														0.192825	80.872042	100.546414	43	180	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72291088	72291088	8529	10	C	A	A	A	311	24	KIAA1274	2	2
NRG3	10718	broad.mit.edu	37	10	84498364	84498364	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:84498364G>A	uc001kco.2	+	c.985G>A	c.(985-987)GAT>AAT	p.D329N	NRG3_uc010qlz.1_Missense_Mutation_p.D329N|NRG3_uc001kcp.2_Missense_Mutation_p.D108N|NRG3_uc001kcq.2_5'UTR	NM_001010848	NP_001010848	P56975	NRG3_HUMAN	neuregulin 3 isoform 1	329	EGF-like.|Extracellular (Potential).				regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity				0				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)										0.189024	58.114463	72.968429	31	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84498364	84498364	11054	10	G	A	A	A	585	45	NRG3	2	2
MMRN2	79812	broad.mit.edu	37	10	88703608	88703608	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:88703608C>A	uc001kea.2	-	c.933G>T	c.(931-933)GTG>GTT	p.V311V	MMRN2_uc010qmn.1_Intron|MMRN2_uc009xtb.2_Silent_p.V268V	NM_024756	NP_079032	Q9H8L6	MMRN2_HUMAN	multimerin 2 precursor	311	Potential.					extracellular space				large_intestine(1)	1														0.037383	-18.093443	6.708787	4	103	KEEP	---	---	---	---	capture		Silent	SNP	88703608	88703608	10062	10	C	A	A	A	262	21	MMRN2	2	2
PDE6C	5146	broad.mit.edu	37	10	95380423	95380423	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:95380423C>A	uc001kiu.3	+	c.515C>A	c.(514-516)ACT>AAT	p.T172N		NM_006204	NP_006195	P51160	PDE6C_HUMAN	phosphodiesterase 6C	172	cGMP (By similarity).|GAF 1.				visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)	3		Colorectal(252;0.123)												0.142857	32.124577	51.093113	22	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95380423	95380423	12068	10	C	A	A	A	260	20	PDE6C	2	2
PDE6C	5146	broad.mit.edu	37	10	95394518	95394518	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:95394518G>T	uc001kiu.3	+	c.1123G>T	c.(1123-1125)GGA>TGA	p.G375*		NM_006204	NP_006195	P51160	PDE6C_HUMAN	phosphodiesterase 6C	375	GAF 2.				visual perception	plasma membrane	3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|metal ion binding			ovary(2)|kidney(1)	3		Colorectal(252;0.123)												0.173913	21.655117	28.583545	12	57	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	95394518	95394518	12068	10	G	T	T	T	455	35	PDE6C	5	2
C10orf28	27291	broad.mit.edu	37	10	99991416	99991416	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:99991416G>T	uc001kox.3	+	c.1975G>T	c.(1975-1977)GAC>TAC	p.D659Y	C10orf28_uc001kow.3_Missense_Mutation_p.D645Y|C10orf28_uc001koy.3_Missense_Mutation_p.D645Y|C10orf28_uc009xvx.2_Missense_Mutation_p.D645Y|C10orf28_uc009xvy.2_Missense_Mutation_p.D51Y|C10orf28_uc001koz.3_Non-coding_Transcript	NM_014472	NP_055287	Q4KMY3	Q4KMY3_HUMAN	growth inhibition and differentiation related	645							nucleotide binding			large_intestine(1)	1		Colorectal(252;0.234)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)										0.164384	17.242037	25.069842	12	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99991416	99991416	1638	10	G	T	T	T	429	33	C10orf28	2	2
PGR	5241	broad.mit.edu	37	11	100999187	100999187	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:100999187C>A	uc001pgh.2	-	c.615G>T	c.(613-615)TGG>TGT	p.W205C	PGR_uc001pgi.2_Missense_Mutation_p.W205C|PGR_uc009yww.1_Non-coding_Transcript|PGR_uc001pgj.2_Non-coding_Transcript|PGR_uc009ywx.1_Non-coding_Transcript	NM_000926	NP_000917	P06401	PRGR_HUMAN	progesterone receptor	205	Modulating, Pro-Rich.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			lung(1)|liver(1)|central_nervous_system(1)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	Pancreas(124;2271 2354 21954 22882)				429				0.285714	18.289803	19.443078	8	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100999187	100999187	12228	11	C	A	A	A	234	18	PGR	2	2
TRPC6	7225	broad.mit.edu	37	11	101353723	101353723	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101353723G>T	uc001pgk.3	-	c.1467C>A	c.(1465-1467)TCC>TCA	p.S489S	TRPC6_uc009ywy.2_Silent_p.S373S|TRPC6_uc009ywz.1_Silent_p.S434S	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	489	Helical; (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		Colon(166;1315 1927 11094 12848 34731)								0.17284	25.139594	33.298909	14	67	KEEP	---	---	---	---	capture		Silent	SNP	101353723	101353723	17134	11	G	T	T	T	444	35	TRPC6	2	2
MMP27	64066	broad.mit.edu	37	11	102576439	102576439	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102576439G>T	uc001phd.1	-	c.7C>A	c.(7-9)CGC>AGC	p.R3S		NM_022122	NP_071405	Q9H306	MMP27_HUMAN	matrix metalloproteinase 27 precursor	3					collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)	2	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)										0.204082	43.549266	51.511594	20	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102576439	102576439	10055	11	G	T	T	T	494	38	MMP27	1	1
MMP13	4322	broad.mit.edu	37	11	102818698	102818698	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102818698T>C	uc001phl.2	-	c.1133A>G	c.(1132-1134)GAA>GGA	p.E378G		NM_002427	NP_002418	P45452	MMP13_HUMAN	matrix metalloproteinase 13 preproprotein	378					collagen catabolic process|proteolysis	extracellular space	metalloendopeptidase activity|zinc ion binding			ovary(2)	2		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)										0.085714	5.515061	17.673421	6	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102818698	102818698	10042	11	T	C	C	C	806	62	MMP13	4	4
GUCY1A2	2977	broad.mit.edu	37	11	106810239	106810239	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:106810239G>A	uc009yxn.1	-	c.1153C>T	c.(1153-1155)CCG>TCG	p.P385S	GUCY1A2_uc001pjg.1_Missense_Mutation_p.P385S|GUCY1A2_uc010rvo.1_Missense_Mutation_p.P385S	NM_000855	NP_000846	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	385					intracellular signal transduction|platelet activation	cytoplasm	GTP binding|guanylate cyclase activity|heme binding			large_intestine(3)|pancreas(2)|ovary(1)	6		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)						248				0.12	15.826526	29.99445	12	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106810239	106810239	7173	11	G	A	A	A	559	43	GUCY1A2	2	2
RDX	5962	broad.mit.edu	37	11	110108242	110108242	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:110108242T>A	uc009yxy.2	-	c.1226A>T	c.(1225-1227)GAC>GTC	p.D409V	RDX_uc009yxx.1_Non-coding_Transcript|RDX_uc009yxz.2_Missense_Mutation_p.D62V|RDX_uc009yya.2_Intron|RDX_uc001pks.2_5'Flank|RDX_uc001pkt.2_Missense_Mutation_p.D63V|RDX_uc001pku.2_Missense_Mutation_p.D409V|RDX_uc010rwe.1_Missense_Mutation_p.D273V	NM_002906	NP_002897	P35241	RADI_HUMAN	radixin	409	Glu-rich.				actin filament capping	cleavage furrow|cytoskeleton|extrinsic to membrane|Golgi apparatus|nucleolus|plasma membrane	actin binding				0		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		Esophageal Squamous(55;25 1062 11040 28755 44273)								0.244681	53.401572	58.969211	23	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110108242	110108242	13667	11	T	A	A	A	754	58	RDX	3	3
HTR3B	9177	broad.mit.edu	37	11	113803683	113803683	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:113803683G>T	uc001pok.2	+	c.564G>T	c.(562-564)CTG>CTT	p.L188L	HTR3B_uc001pol.2_Silent_p.L177L	NM_006028	NP_006019	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B	188	Extracellular (Potential).				synaptic transmission	integral to plasma membrane|postsynaptic membrane	serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)										0.190476	36.334264	45.745294	20	85	KEEP	---	---	---	---	capture		Silent	SNP	113803683	113803683	7745	11	G	T	T	T	574	45	HTR3B	2	2
IL10RA	3587	broad.mit.edu	37	11	117864126	117864126	+	Splice_Site_SNP	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117864126G>C	uc001prv.2	+	c.537_splice	c.e4+1	p.T179_splice	IL10RA_uc010rxl.1_Splice_Site_SNP_p.T159_splice|IL10RA_uc010rxm.1_Splice_Site_SNP_p.T159_splice|IL10RA_uc010rxn.1_Splice_Site_SNP_p.T30_splice|IL10RA_uc001prw.2_Splice_Site_SNP_p.T30_splice	NM_001558	NP_001549			interleukin 10 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)										0.226804	69.601578	76.244568	22	75	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	117864126	117864126	7921	11	G	C	C	C	572	44	IL10RA	5	3
OR8B8	26493	broad.mit.edu	37	11	124310583	124310583	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:124310583C>A	uc010sal.1	-	c.399G>T	c.(397-399)ATG>ATT	p.M133I		NM_012378	NP_036510	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B,	133	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)										0.122222	10.553586	23.152635	11	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124310583	124310583	11641	11	C	A	A	A	273	21	OR8B8	2	2
IGSF9B	22997	broad.mit.edu	37	11	133790344	133790344	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:133790344C>A	uc001qgx.3	-	c.3276G>T	c.(3274-3276)CCG>CCT	p.P1092P		NM_014987	NP_055802	Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1092	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)										0.290323	42.827122	45.269152	18	44	KEEP	---	---	---	---	capture		Silent	SNP	133790344	133790344	7907	11	C	A	A	A	288	23	IGSF9B	1	1
INSC	387755	broad.mit.edu	37	11	15198682	15198682	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:15198682G>C	uc001mly.2	+	c.569G>C	c.(568-570)TGC>TCC	p.C190S	INSC_uc001mlz.2_Missense_Mutation_p.C143S|INSC_uc001mma.2_Missense_Mutation_p.C143S|INSC_uc010rcs.1_Missense_Mutation_p.C143S|INSC_uc001mmb.2_Missense_Mutation_p.C143S|INSC_uc001mmc.2_Missense_Mutation_p.C143S	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	190					cell differentiation|nervous system development	cytoplasm	binding			ovary(2)|central_nervous_system(1)	3														0.116883	29.953365	52.17209	18	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15198682	15198682	8065	11	G	C	C	C	598	46	INSC	3	3
IFITM5	387733	broad.mit.edu	37	11	299433	299433	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:299433C>A	uc001low.1	-	c.58G>T	c.(58-60)GCC>TCC	p.A20S		NM_001025295	NP_001020466	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	20	Extracellular (Potential).				multicellular organismal development|regulation of bone mineralization|response to biotic stimulus	integral to membrane|plasma membrane					0		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)										0.1875	5.314149	6.779326	3	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	299433	299433	7830	11	C	A	A	A	325	25	IFITM5	2	2
STIM1	6786	broad.mit.edu	37	11	4103493	4103493	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4103493G>T	uc001lyv.2	+	c.1049G>T	c.(1048-1050)TGG>TTG	p.W350L	STIM1_uc009yef.2_Missense_Mutation_p.W350L|STIM1_uc009yeg.2_Missense_Mutation_p.W177L	NM_003156	NP_003147	Q13586	STIM1_HUMAN	stromal interaction molecule 1 precursor	350	Cytoplasmic (Potential).|Potential.				activation of store-operated calcium channel activity|calcium ion transport|detection of calcium ion|platelet activation	integral to endoplasmic reticulum membrane|integral to plasma membrane|microtubule	calcium ion binding|microtubule plus-end binding			pancreas(1)	1		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)										0.309091	41.950222	43.739063	17	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4103493	4103493	15803	11	G	T	T	T	611	47	STIM1	2	2
OR52I2	143502	broad.mit.edu	37	11	4608223	4608223	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4608223C>A	uc010qyh.1	+	c.181C>A	c.(181-183)CTG>ATG	p.L61M		NM_001005170	NP_001005170	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I,	61	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.181185	104.628595	132.049353	52	235	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4608223	4608223	11531	11	C	A	A	A	259	20	OR52I2	2	2
OR4A16	81327	broad.mit.edu	37	11	55111191	55111191	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55111191T>C	uc010rie.1	+	c.515T>C	c.(514-516)ATT>ACT	p.I172T		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3														0.258824	130.431314	139.381525	44	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55111191	55111191	11447	11	T	C	C	C	676	52	OR4A16	4	4
OR52H1	390067	broad.mit.edu	37	11	5566115	5566115	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5566115C>A	uc010qzh.1	-	c.639G>T	c.(637-639)ATG>ATT	p.M213I	HBG2_uc001mak.1_Intron	NM_001005289	NP_001005289	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H,	213	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.168539	23.360773	32.632236	15	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5566115	5566115	11529	11	C	A	A	A	377	29	OR52H1	2	2
OR5AS1	219447	broad.mit.edu	37	11	55798258	55798258	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55798258C>T	uc010riw.1	+	c.364C>T	c.(364-366)CGC>TGC	p.R122C		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	122	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)	4	Esophageal squamous(21;0.00693)													0.14	11.091876	17.348975	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55798258	55798258	11556	11	C	T	T	T	299	23	OR5AS1	1	1
OR9G9	504191	broad.mit.edu	37	11	56468505	56468505	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56468505G>T	uc010rjn.1	+	c.642G>T	c.(640-642)CTG>CTT	p.L214L		NM_001013358	NP_001013376	P0C7N8	OR9G9_HUMAN	olfactory receptor, family 9, subfamily G,	214	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.12749	36.099539	70.113271	32	219	KEEP	---	---	---	---	capture		Silent	SNP	56468505	56468505	11663	11	G	T	T	T	600	47	OR9G9	2	2
OR52N4	390072	broad.mit.edu	37	11	5776387	5776387	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5776387C>A	uc001mbu.2	+	c.417C>A	c.(415-417)ACC>ACA	p.T139T	TRIM5_uc001mbq.1_Intron|TRIM22_uc009yet.1_Intron	NM_001005175	NP_001005175	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N,	139	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)										0.184615	46.413972	58.550914	24	106	KEEP	---	---	---	---	capture		Silent	SNP	5776387	5776387	11539	11	C	A	A	A	262	21	OR52N4	2	2
CNTF	1270	broad.mit.edu	37	11	58391556	58391556	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58391556G>T	uc001nna.3	+	c.164G>T	c.(163-165)GGG>GTG	p.G55V	ZFP91-CNTF_uc010rkm.1_Non-coding_Transcript	NM_000614	NP_000605	P26441	CNTF_HUMAN	ciliary neurotrophic factor	55					ciliary neurotrophic factor-mediated signaling pathway|growth|negative regulation of neuron apoptosis|positive regulation of tyrosine phosphorylation of Stat3 protein	extracellular space	ciliary neurotrophic factor receptor binding|growth factor activity|interleukin-6 receptor binding			ovary(1)	1		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)												0.214286	34.09498	40.437769	18	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58391556	58391556	3775	11	G	T	T	T	559	43	CNTF	2	2
OR4D6	219983	broad.mit.edu	37	11	59224871	59224871	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59224871G>A	uc010rku.1	+	c.438G>A	c.(436-438)GTG>GTA	p.V146V		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	146	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.131356	44.057052	75.239732	31	205	KEEP	---	---	---	---	capture		Silent	SNP	59224871	59224871	11465	11	G	A	A	A	600	47	OR4D6	2	2
OR56A3	390083	broad.mit.edu	37	11	5969347	5969347	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5969347C>A	uc010qzt.1	+	c.771C>A	c.(769-771)ACC>ACA	p.T257T		NM_001003443	NP_001003443	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A,	257	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.197628	100.205754	121.750564	50	203	KEEP	---	---	---	---	capture		Silent	SNP	5969347	5969347	11544	11	C	A	A	A	262	21	OR56A3	2	2
FAM160A2	84067	broad.mit.edu	37	11	6239874	6239874	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6239874T>A	uc001mck.3	-	c.1391A>T	c.(1390-1392)CAC>CTC	p.H464L	FAM160A2_uc001mcl.3_Missense_Mutation_p.H464L|FAM160A2_uc001mcm.2_Missense_Mutation_p.H464L	NM_032127	NP_115503	Q8N612	F16A2_HUMAN	hypothetical protein LOC84067 isoform 1	464					early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|protein transport	FHF complex	protein binding				0														0.16	90.159286	125.908693	52	273	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6239874	6239874	5673	11	T	A	A	A	767	59	FAM160A2	3	3
SLC22A6	9356	broad.mit.edu	37	11	62751813	62751813	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62751813G>T	uc001nwk.2	-	c.350C>A	c.(349-351)CCA>CAA	p.P117Q	SLC22A6_uc001nwl.2_Missense_Mutation_p.P117Q|SLC22A6_uc001nwj.2_Missense_Mutation_p.P117Q|SLC22A6_uc001nwm.2_Missense_Mutation_p.P117Q	NM_004790	NP_004781	Q4U2R8	S22A6_HUMAN	solute carrier family 22 member 6 isoform a	117	Extracellular (Potential).				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding				0														0.129187	36.467616	64.472268	27	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62751813	62751813	14955	11	G	T	T	T	611	47	SLC22A6	2	2
NRXN2	9379	broad.mit.edu	37	11	64390552	64390552	+	Splice_Site_SNP	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64390552T>A	uc001oar.2	-	c.3848_splice	c.e22-1	p.G1283_splice	NRXN2_uc001oas.2_Splice_Site_SNP_p.G1213_splice|NRXN2_uc001oao.2_De_novo_Start_OutOfFrame|NRXN2_uc001oap.2_Splice_Site_SNP_p.G237_splice|NRXN2_uc001oaq.2_Splice_Site_SNP_p.G950_splice	NM_015080	NP_055895			neurexin 2 isoform alpha-1 precursor						cell adhesion	integral to membrane				ovary(2)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	6														0.210526	8.690823	10.162845	4	15	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	64390552	64390552	11071	11	T	A	A	A	728	56	NRXN2	5	3
NRXN2	9379	broad.mit.edu	37	11	64418893	64418893	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64418893C>A	uc001oar.2	-	c.2752G>T	c.(2752-2754)GAT>TAT	p.D918Y	NRXN2_uc001oas.2_Missense_Mutation_p.D878Y|NRXN2_uc001oaq.2_Missense_Mutation_p.D585Y	NM_015080	NP_055895	P58401	NRX2B_HUMAN	neurexin 2 isoform alpha-1 precursor	Error:Variant_position_missing_in_P58401_after_alignment					cell adhesion	integral to membrane				ovary(2)|pancreas(1)|kidney(1)|central_nervous_system(1)|skin(1)	6												OREG0021057	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.131148	10.160039	18.229068	8	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64418893	64418893	11071	11	C	A	A	A	403	31	NRXN2	1	1
OR2AG1	144125	broad.mit.edu	37	11	6806979	6806979	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6806979C>A	uc001mer.1	+	c.711C>A	c.(709-711)GCC>GCA	p.A237A		NM_001004489	NP_001004489	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG,	237	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.212121	39.419372	47.014637	21	78	KEEP	---	---	---	---	capture		Silent	SNP	6806979	6806979	11390	11	C	A	A	A	275	22	OR2AG1	2	2
MYEOV	26579	broad.mit.edu	37	11	69063537	69063537	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:69063537G>T	uc001oov.2	+	c.620G>T	c.(619-621)GGG>GTG	p.G207V	MYEOV_uc001oox.2_Intron|MYEOV_uc009ysl.2_Missense_Mutation_p.G207V|MYEOV_uc001oow.2_Missense_Mutation_p.G149V	NM_138768	NP_620123	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	207											0	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)										0.179039	70.291549	92.458904	41	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69063537	69063537	10420	11	G	T	T	T	559	43	MYEOV	2	2
PPFIA1	8500	broad.mit.edu	37	11	70118299	70118299	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:70118299G>T	uc001opo.2	+	c.21G>T	c.(19-21)CCG>CCT	p.P7P	PPFIA1_uc001opn.1_Silent_p.P7P|PPFIA1_uc001opp.2_Non-coding_Transcript	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	7					cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)											0.17847	109.959541	144.393814	63	290	KEEP	---	---	---	---	capture		Silent	SNP	70118299	70118299	12739	11	G	T	T	T	470	37	PPFIA1	1	1
FAT3	120114	broad.mit.edu	37	11	92086706	92086706	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92086706G>T	uc001pdj.3	+	c.1428G>T	c.(1426-1428)CTG>CTT	p.L476L		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	476	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.230769	14.034916	15.763268	6	20	KEEP	---	---	---	---	capture		Silent	SNP	92086706	92086706	5927	11	G	T	T	T	613	48	FAT3	2	2
FAT3	120114	broad.mit.edu	37	11	92616483	92616483	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92616483C>G	uc001pdj.3	+	c.12861C>G	c.(12859-12861)CCC>CCG	p.P4287P	FAT3_uc001pdi.3_Silent_p.P727P	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	4287	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.106061	7.708668	17.853106	7	59	KEEP	---	---	---	---	capture		Silent	SNP	92616483	92616483	5927	11	C	G	G	G	262	21	FAT3	3	3
ZNF143	7702	broad.mit.edu	37	11	9534020	9534020	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:9534020G>T	uc001mhr.2	+	c.1401G>T	c.(1399-1401)GGG>GGT	p.G467G	ZNF143_uc009yfu.2_Silent_p.G466G|ZNF143_uc010rby.1_Silent_p.G436G	NM_003442	NP_003433	P52747	ZN143_HUMAN	zinc finger protein 143	467					regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding|RNA polymerase III transcription factor activity|specific RNA polymerase II transcription factor activity|zinc ion binding				0				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)										0.201681	107.09127	126.755848	48	190	KEEP	---	---	---	---	capture		Silent	SNP	9534020	9534020	18323	11	G	T	T	T	561	44	ZNF143	2	2
ANO4	121601	broad.mit.edu	37	12	101436171	101436171	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:101436171T>A	uc010svm.1	+	c.1079T>A	c.(1078-1080)ATG>AAG	p.M360K	ANO4_uc001thw.2_Missense_Mutation_p.M325K|ANO4_uc001thx.2_Missense_Mutation_p.M360K	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	360	Helical; (Potential).					chloride channel complex	chloride channel activity			ovary(4)	4														0.216216	60.154904	68.39001	24	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101436171	101436171	707	12	T	A	A	A	663	51	ANO4	3	3
NUP37	79023	broad.mit.edu	37	12	102512147	102512147	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:102512147C>A	uc001tjc.2	-	c.150G>T	c.(148-150)ACG>ACT	p.T50T	NUP37_uc009zub.1_Silent_p.T50T|C12orf48_uc001tjd.2_5'Flank|C12orf48_uc001tje.2_5'Flank|C12orf48_uc001tjg.2_5'Flank|C12orf48_uc010swa.1_5'Flank|C12orf48_uc001tjf.2_5'Flank|C12orf48_uc001tjh.2_5'Flank|C12orf48_uc010swb.1_5'Flank|C12orf48_uc001tji.2_5'Flank	NM_024057	NP_076962	Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	50					carbohydrate metabolic process|cell division|chromosome segregation|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	protein binding			ovary(1)	1														0.185185	78.812835	96.375389	35	154	KEEP	---	---	---	---	capture		Silent	SNP	102512147	102512147	11169	12	C	A	A	A	236	19	NUP37	1	1
PAH	5053	broad.mit.edu	37	12	103238194	103238194	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:103238194C>A	uc001tjq.1	-	c.985G>T	c.(985-987)GTG>TTG	p.V329L		NM_000277	NP_000268	P00439	PH4H_HUMAN	phenylalanine hydroxylase	329					catecholamine biosynthetic process|L-phenylalanine catabolic process|neurotransmitter biosynthetic process|oxidation-reduction process	cytosol	phenylalanine 4-monooxygenase activity			ovary(4)	4					Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Levodopa(DB01235)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)									0.219512	19.750153	22.72369	9	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103238194	103238194	11810	12	C	A	A	A	221	17	PAH	2	2
RFX4	5992	broad.mit.edu	37	12	107075814	107075814	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107075814G>T	uc001tlt.2	+	c.386G>T	c.(385-387)GGG>GTG	p.G129V	RFX4_uc001tlr.2_Missense_Mutation_p.G120V|RFX4_uc010swv.1_Non-coding_Transcript|RFX4_uc001tls.2_Missense_Mutation_p.G129V|RFX4_uc001tlv.2_5'Flank	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	120	|RFX-type winged-helix.				transcription, DNA-dependent	nucleus	DNA binding				0														0.133929	18.741089	33.311104	15	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107075814	107075814	13737	12	G	T	T	T	559	43	RFX4	2	2
BTBD11	121551	broad.mit.edu	37	12	107914368	107914368	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107914368G>T	uc001tmk.1	+	c.1240G>T	c.(1240-1242)GAG>TAG	p.E414*	BTBD11_uc009zut.1_Nonsense_Mutation_p.E414*|BTBD11_uc001tmj.2_Nonsense_Mutation_p.E414*	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	414						integral to membrane	DNA binding			ovary(1)	1														0.18797	43.830789	55.9354	25	108	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	107914368	107914368	1571	12	G	T	T	T	481	37	BTBD11	5	1
TAS2R19	259294	broad.mit.edu	37	12	11174543	11174543	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:11174543G>A	uc010shj.1	-	c.628C>T	c.(628-630)CGG>TGG	p.R210W	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Intron|PRH1_uc001qzc.2_Intron|PRB4_uc001qzf.1_Intron|PRH1_uc001qzj.2_Intron	NM_176888	NP_795369	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	210	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0														0.230159	62.691258	71.12205	29	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11174543	11174543	16092	12	G	A	A	A	493	38	TAS2R19	1	1
TMEM132D	121256	broad.mit.edu	37	12	129566310	129566310	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:129566310G>T	uc009zyl.1	-	c.1917C>A	c.(1915-1917)ACC>ACA	p.T639T	TMEM132D_uc001uia.2_Silent_p.T177T	NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D precursor	639	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.144737	14.67147	23.910593	11	65	KEEP	---	---	---	---	capture		Silent	SNP	129566310	129566310	16579	12	G	T	T	T	600	47	TMEM132D	2	2
STX2	2054	broad.mit.edu	37	12	131285836	131285836	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:131285836C>A	uc001uio.2	-	c.538_splice	c.e8-1	p.I180_splice	STX2_uc001uip.2_Splice_Site_SNP_p.I180_splice|STX2_uc010tbj.1_Splice_Site_SNP_p.I180_splice	NM_194356	NP_919337			syntaxin 2 isoform 2						acrosome reaction|ectoderm development|intracellular protein transport|organ morphogenesis|signal transduction	basolateral plasma membrane|integral to membrane|microsome|soluble fraction	calcium-dependent protein binding|SNAP receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)										0.171053	21.021769	28.805685	13	63	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	131285836	131285836	15865	12	C	A	A	A	416	32	STX2	5	2
KIAA1467	57613	broad.mit.edu	37	12	13232874	13232874	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:13232874C>G	uc001rbi.2	+	c.1794C>G	c.(1792-1794)ACC>ACG	p.T598T	KIAA1467_uc009zhx.1_Non-coding_Transcript	NM_020853	NP_065904	A2RU67	K1467_HUMAN	hypothetical protein LOC57613	598						integral to membrane				central_nervous_system(2)|skin(1)	3		Prostate(47;0.184)		BRCA - Breast invasive adenocarcinoma(232;0.157)										0.169231	25.48317	32.214984	11	54	KEEP	---	---	---	---	capture		Silent	SNP	13232874	13232874	8544	12	C	G	G	G	275	22	KIAA1467	3	3
SLCO1B1	10599	broad.mit.edu	37	12	21370190	21370190	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21370190A>C	uc001req.3	+	c.1635A>C	c.(1633-1635)TTA>TTC	p.L545F		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	545	Helical; Name=10; (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.22449	32.803541	36.217718	11	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21370190	21370190	15220	12	A	C	C	C	206	16	SLCO1B1	4	4
PKP2	5318	broad.mit.edu	37	12	32949210	32949210	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:32949210C>G	uc001rlj.3	-	c.2322G>C	c.(2320-2322)TTG>TTC	p.L774F	PKP2_uc001rlk.3_Missense_Mutation_p.L730F|PKP2_uc010skj.1_Missense_Mutation_p.L727F	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b	774	ARM 7.				cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)													0.138889	16.98972	26.085561	10	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32949210	32949210	12410	12	C	G	G	G	272	21	PKP2	3	3
PRMT8	56341	broad.mit.edu	37	12	3677879	3677879	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:3677879C>A	uc001qmf.2	+	c.489C>A	c.(487-489)ACC>ACA	p.T163T	PRMT8_uc009zed.2_Silent_p.T154T|PRMT8_uc009zee.1_Non-coding_Transcript|PRMT8_uc001qmg.2_5'UTR	NM_019854	NP_062828	Q9NR22	ANM8_HUMAN	HMT1 hnRNP methyltransferase-like 4	163					regulation of protein binding	cytoplasm|plasma membrane	histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity			ovary(3)	3			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)											0.163265	26.931689	37.497599	16	82	KEEP	---	---	---	---	capture		Silent	SNP	3677879	3677879	12985	12	C	A	A	A	262	21	PRMT8	2	2
C12orf40	283461	broad.mit.edu	37	12	40076706	40076707	+	Missense_Mutation	DNP	TG	AT	AT			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:40076706_40076707TG>AT	uc001rmc.2	+	c.980_981TG>AT	c.(979-981)ATG>AAT	p.M327N	C12orf40_uc009zjv.1_Non-coding_Transcript	NM_001031748	NP_001026918	Q86WS4	CL040_HUMAN	hypothetical protein LOC283461	327										ovary(6)	6														0.14	10.296525	16.550258	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	40076706	40076707	1730	12	TG	AT	AT	AT	663	51	C12orf40	3	3
ADAMTS20	80070	broad.mit.edu	37	12	43862482	43862482	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43862482C>A	uc010skx.1	-	c.1144G>T	c.(1144-1146)GAT>TAT	p.D382Y		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	382	Peptidase M12B.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.107143	2.602374	6.892338	3	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43862482	43862482	267	12	C	A	A	A	377	29	ADAMTS20	2	2
OR8S1	341568	broad.mit.edu	37	12	48920047	48920047	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:48920047C>T	uc010slu.1	+	c.633C>T	c.(631-633)TTC>TTT	p.F211F		NM_001005203	NP_001005203	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.216374	82.378336	95.072588	37	134	KEEP	---	---	---	---	capture		Silent	SNP	48920047	48920047	11657	12	C	T	T	T	389	30	OR8S1	2	2
ACCN2	41	broad.mit.edu	37	12	50472281	50472281	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50472281C>T	uc001rvv.2	+	c.915C>T	c.(913-915)TAC>TAT	p.Y305Y	ACCN2_uc001rvw.2_Silent_p.Y305Y|ACCN2_uc009zln.2_Silent_p.Y96Y|ACCN2_uc009zlo.2_Silent_p.Y305Y	NM_020039	NP_064423	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	305	Extracellular (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)									0.033898	-67.183489	16.667493	12	342	KEEP	---	---	---	---	capture		Silent	SNP	50472281	50472281	130	12	C	T	T	T	220	17	ACCN2	2	2
SLC11A2	4891	broad.mit.edu	37	12	51382191	51382191	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:51382191T>C	uc001rxk.1	-	c.1690A>G	c.(1690-1692)ATG>GTG	p.M564V	SLC11A2_uc001rxe.3_Missense_Mutation_p.M535V|SLC11A2_uc001rxd.3_Missense_Mutation_p.M384V|SLC11A2_uc001rxc.3_Missense_Mutation_p.M535V|SLC11A2_uc001rxf.2_Non-coding_Transcript|SLC11A2_uc001rxg.1_Missense_Mutation_p.M148V|SLC11A2_uc010smx.1_Missense_Mutation_p.M531V|SLC11A2_uc001rxh.1_Missense_Mutation_p.M535V|SLC11A2_uc001rxj.1_Missense_Mutation_p.M535V|SLC11A2_uc001rxi.2_Missense_Mutation_p.M535V|SLC11A2_uc010smy.1_Missense_Mutation_p.M498V	NM_000617	NP_000608	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled	535	Cytoplasmic (Potential).				activation of caspase activity|cellular iron ion homeostasis|cellular response to oxidative stress|detection of oxygen|ferrous iron import|multicellular organismal iron ion homeostasis|response to hypoxia|response to iron ion	apical plasma membrane|basal part of cell|cell surface|cytoplasmic vesicle|early endosome|late endosome|late endosome membrane|lysosomal membrane|lysosome|nucleus|paraferritin complex|perinuclear region of cytoplasm|perinuclear region of cytoplasm|plasma membrane|recycling endosome|trans-Golgi network	cadmium ion transmembrane transporter activity|cadmium ion transmembrane transporter activity|cobalt ion transmembrane transporter activity|copper ion transmembrane transporter activity|ferrous iron transmembrane transporter activity|ferrous iron transmembrane transporter activity|lead ion transmembrane transporter activity|lead ion transmembrane transporter activity|manganese ion transmembrane transporter activity|manganese ion transmembrane transporter activity|nickel ion transmembrane transporter activity|protein binding|solute:hydrogen symporter activity|vanadium ion transmembrane transporter activity|zinc ion transmembrane transporter activity			large_intestine(1)	1														0.22619	48.104418	53.870567	19	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51382191	51382191	14876	12	T	C	C	C	663	51	SLC11A2	4	4
KRT82	3888	broad.mit.edu	37	12	52793777	52793777	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52793777G>T	uc001sai.1	-	c.934C>A	c.(934-936)CAG>AAG	p.Q312K		NM_033033	NP_149022	Q9NSB4	KRT82_HUMAN	keratin 82	312	Coil 2.|Rod.					keratin filament	protein binding|structural constituent of epidermis			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.193)										0.181159	38.401523	51.744527	25	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52793777	52793777	8811	12	G	T	T	T	611	47	KRT82	2	2
KRT1	3848	broad.mit.edu	37	12	53069297	53069297	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53069297A>T	uc001sau.1	-	c.1615T>A	c.(1615-1617)TAT>AAT	p.Y539N	KRT1_uc001sav.1_Missense_Mutation_p.Y539N	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	539	Gly/Ser-rich.|Tail.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)	1														0.27027	24.438951	26.197307	10	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53069297	53069297	8762	12	A	T	T	T	195	15	KRT1	3	3
IGFBP6	3489	broad.mit.edu	37	12	53494882	53494882	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53494882C>A	uc001sbu.1	+	c.538C>A	c.(538-540)CGA>AGA	p.R180R	SOAT2_uc001sbv.2_5'Flank|SOAT2_uc009zms.2_5'Flank	NM_002178	NP_002169	P24592	IBP6_HUMAN	insulin-like growth factor binding protein 6	180	Thyroglobulin type-1.				negative regulation of cell proliferation|regulation of cell growth|signal transduction					ovary(1)	1						Esophageal Squamous(83;1656 1718 30141 34380)								0.179104	47.826686	60.805381	24	110	KEEP	---	---	---	---	capture		Silent	SNP	53494882	53494882	7884	12	C	A	A	A	295	23	IGFBP6	1	1
OR10A7	121364	broad.mit.edu	37	12	55615132	55615132	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55615132C>A	uc010spf.1	+	c.324C>A	c.(322-324)GGC>GGA	p.G108G		NM_001005280	NP_001005280	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4														0.132275	33.532839	58.369982	25	164	KEEP	---	---	---	---	capture		Silent	SNP	55615132	55615132	11301	12	C	A	A	A	314	25	OR10A7	2	2
NTF3	4908	broad.mit.edu	37	12	5603704	5603704	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5603704C>A	uc001qnk.3	+	c.363C>A	c.(361-363)GAC>GAA	p.D121E	NTF3_uc001qnl.3_Missense_Mutation_p.D108E	NM_001102654	NP_001096124	P20783	NTF3_HUMAN	neurotrophin 3 isoform 1 preproprotein	108					signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding			pancreas(1)	1						GBM(194;1104 2182 8339 9578 18493)								0.183099	51.193863	64.562859	26	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5603704	5603704	11101	12	C	A	A	A	220	17	NTF3	2	2
LRRC10	376132	broad.mit.edu	37	12	70004184	70004184	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70004184G>T	uc001svc.2	-	c.435C>A	c.(433-435)CTC>CTA	p.L145L		NM_201550	NP_963844	Q5BKY1	LRC10_HUMAN	leucine rich repeat containing 10	145	LRR 5.					nucleus					0	all_cancers(2;2.83e-105)|Breast(13;9.83e-07)|Esophageal squamous(21;0.187)		Epithelial(6;1.98e-18)|GBM - Glioblastoma multiforme(2;7.43e-12)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)											0.144578	14.938903	25.039675	12	71	KEEP	---	---	---	---	capture		Silent	SNP	70004184	70004184	9340	12	G	T	T	T	522	41	LRRC10	2	2
BEST3	144453	broad.mit.edu	37	12	70087526	70087526	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70087526G>T	uc001svg.2	-	c.409C>A	c.(409-411)CTG>ATG	p.L137M	BEST3_uc001svd.1_Missense_Mutation_p.L137M|BEST3_uc001sve.1_Non-coding_Transcript|BEST3_uc010stm.1_Missense_Mutation_p.L31M|BEST3_uc001svh.2_De_novo_Start_OutOfFrame|BEST3_uc001svi.1_Non-coding_Transcript	NM_032735	NP_116124	Q8N1M1	BEST3_HUMAN	vitelliform macular dystrophy 2-like 3 isoform	137	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	chloride channel activity				0	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)											0.164706	24.191605	33.268355	14	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70087526	70087526	1429	12	G	T	T	T	451	35	BEST3	2	2
CD163L1	283316	broad.mit.edu	37	12	7531644	7531644	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7531644C>A	uc010sge.1	-	c.2331G>T	c.(2329-2331)TGG>TGT	p.W777C	CD163L1_uc001qsy.2_Missense_Mutation_p.W767C	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	767	SRCR 7.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.169014	18.448121	25.82368	12	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7531644	7531644	3095	12	C	A	A	A	286	22	CD163L1	2	2
LRRIQ1	84125	broad.mit.edu	37	12	85521630	85521630	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:85521630A>T	uc001tac.2	+	c.4028A>T	c.(4027-4029)CAG>CTG	p.Q1343L		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1343	IQ 2.									ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.340426	44.686706	45.744031	16	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85521630	85521630	9405	12	A	T	T	T	91	7	LRRIQ1	3	3
HAL	3034	broad.mit.edu	37	12	96387882	96387882	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:96387882G>A	uc001tem.1	-	c.397C>T	c.(397-399)CGC>TGC	p.R133C	HAL_uc009zti.1_Non-coding_Transcript|HAL_uc010suw.1_De_novo_Start_InFrame|HAL_uc010sux.1_Missense_Mutation_p.R133C	NM_002108	NP_002099	P42357	HUTH_HUMAN	histidine ammonia-lyase	133					biosynthetic process|histidine catabolic process	cytosol	histidine ammonia-lyase activity			ovary(2)	2					L-Histidine(DB00117)	NSCLC(169;943 2815 23563 30031)								0.218978	308.036723	357.942627	150	535	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96387882	96387882	7229	12	G	A	A	A	520	40	HAL	1	1
FLT1	2321	broad.mit.edu	37	13	29005449	29005449	+	Splice_Site_SNP	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:29005449T>C	uc001usb.3	-	c.814_splice	c.e7-1	p.K272_splice	FLT1_uc010aar.1_Splice_Site_SNP_p.K272_splice|FLT1_uc001usc.3_Splice_Site_SNP_p.K272_splice|FLT1_uc010tdp.1_Splice_Site_SNP_p.K272_splice	NM_002019	NP_002010			fms-related tyrosine kinase 1 isoform 1						cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(6)|central_nervous_system(5)|ovary(2)|urinary_tract(1)|breast(1)	15	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)					738				0.148148	9.485327	12.690675	4	23	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	29005449	29005449	6183	13	T	C	C	C	689	53	FLT1	5	4
PCDH17	27253	broad.mit.edu	37	13	58207776	58207776	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:58207776C>T	uc001vhq.1	+	c.1096C>T	c.(1096-1098)CCT>TCT	p.P366S	PCDH17_uc010aec.1_Missense_Mutation_p.P366S	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	366	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)|pancreas(2)	4		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		Melanoma(72;952 1291 1619 12849 33676)								0.109091	4.235345	12.540997	6	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58207776	58207776	11932	13	C	T	T	T	286	22	PCDH17	2	2
LMO7	4008	broad.mit.edu	37	13	76427505	76427505	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:76427505G>T	uc001vjv.2	+	c.3943G>T	c.(3943-3945)GGC>TGC	p.G1315C	LMO7_uc010thv.1_Missense_Mutation_p.G1266C|LMO7_uc010thw.1_Missense_Mutation_p.G1192C	NM_015842	NP_056667	Q8WWI1	LMO7_HUMAN	LIM domain only 7 isoform 2	1600						cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding			large_intestine(2)	2		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)										0.233333	31.915461	35.824057	14	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76427505	76427505	9184	13	G	T	T	T	455	35	LMO7	2	2
SLITRK1	114798	broad.mit.edu	37	13	84454311	84454311	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:84454311C>A	uc001vlk.2	-	c.1332G>T	c.(1330-1332)GCG>GCT	p.A444A		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	444	LRR 9.|Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)										0.220183	101.385815	117.105392	48	170	KEEP	---	---	---	---	capture		Silent	SNP	84454311	84454311	15240	13	C	A	A	A	288	23	SLITRK1	1	1
SLITRK1	114798	broad.mit.edu	37	13	84455094	84455094	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:84455094G>C	uc001vlk.2	-	c.549C>G	c.(547-549)GAC>GAG	p.D183E		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor	183	Extracellular (Potential).|LRR 6.					integral to membrane				ovary(2)|central_nervous_system(1)	3	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)										0.181818	69.58062	83.165461	26	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84455094	84455094	15240	13	G	C	C	C	568	44	SLITRK1	3	3
CYP46A1	10858	broad.mit.edu	37	14	100182493	100182493	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:100182493C>T	uc001ygo.2	+	c.864C>T	c.(862-864)GAC>GAT	p.D288D	CYP46A1_uc001ygp.2_Silent_p.D135D	NM_006668	NP_006659	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46	288					bile acid biosynthetic process|cholesterol catabolic process|nervous system development|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol 24-hydroxylase activity|electron carrier activity|heme binding|steroid hydroxylase activity				0		Melanoma(154;0.0866)|all_epithelial(191;0.179)												0.162651	42.733534	60.688673	27	139	KEEP	---	---	---	---	capture		Silent	SNP	100182493	100182493	4347	14	C	T	T	T	246	19	CYP46A1	1	1
BRF1	2972	broad.mit.edu	37	14	105692627	105692627	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105692627G>A	uc001yqp.2	-	c.916C>T	c.(916-918)CTT>TTT	p.L306F	BRF1_uc010tyo.1_Missense_Mutation_p.L191F|BRF1_uc010typ.1_Missense_Mutation_p.L191F|BRF1_uc001yql.2_Missense_Mutation_p.L102F|BRF1_uc001yqo.2_Missense_Mutation_p.L68F|BRF1_uc010axg.1_Missense_Mutation_p.L279F|BRF1_uc001yqn.2_Non-coding_Transcript|BRF1_uc010axh.1_Non-coding_Transcript	NM_001519	NP_001510	Q92994	TF3B_HUMAN	transcription initiation factor IIIB isoform 1	306					regulation of transcription, DNA-dependent|rRNA transcription|transcription initiation from RNA polymerase III promoter|tRNA transcription	transcription factor TFIIIB complex	RNA polymerase III transcription factor activity|transcription activator activity|translation initiation factor activity|zinc ion binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)										0.293173	189.062558	198.606996	73	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105692627	105692627	1541	14	G	A	A	A	442	34	BRF1	2	2
OR4K17	390436	broad.mit.edu	37	14	20586080	20586080	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20586080G>A	uc001vwo.1	+	c.515G>A	c.(514-516)TGT>TAT	p.C172Y		NM_001004715	NP_001004715	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K,	144	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)										0.132231	17.60935	33.520082	16	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20586080	20586080	11481	14	G	A	A	A	624	48	OR4K17	2	2
RPGRIP1	57096	broad.mit.edu	37	14	21790024	21790024	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21790024G>A	uc001wag.2	+	c.1623G>A	c.(1621-1623)GAG>GAA	p.E541E	RPGRIP1_uc001wah.2_Silent_p.E183E|RPGRIP1_uc001wai.2_Silent_p.E183E|RPGRIP1_uc001waj.1_Silent_p.E17E|RPGRIP1_uc001wak.2_Silent_p.E16E|RPGRIP1_uc010aim.2_5'UTR|RPGRIP1_uc001wal.2_5'UTR|RPGRIP1_uc001wam.2_5'Flank	NM_020366	NP_065099	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator	541	Potential.				response to stimulus|visual perception	cilium				ovary(4)|breast(2)|pancreas(1)	7	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)						1408				0.119048	6.642218	12.629547	5	37	KEEP	---	---	---	---	capture		Silent	SNP	21790024	21790024	14028	14	G	A	A	A	451	35	RPGRIP1	2	2
RTN1	6252	broad.mit.edu	37	14	60213093	60213093	+	Silent	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:60213093A>G	uc001xen.1	-	c.348T>C	c.(346-348)CCT>CCC	p.P116P		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	116					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)										0.036697	-16.394601	8.974084	4	105	KEEP	---	---	---	---	capture		Silent	SNP	60213093	60213093	14205	14	A	G	G	G	132	11	RTN1	4	4
KCNH5	27133	broad.mit.edu	37	14	63246542	63246542	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63246542G>T	uc001xfx.2	-	c.1923C>A	c.(1921-1923)ATC>ATA	p.I641I	KCNH5_uc001xfy.2_Intron|KCNH5_uc001xfz.1_Silent_p.I583I	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	641	cNMP.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)										0.325581	69.462039	71.787758	28	58	KEEP	---	---	---	---	capture		Silent	SNP	63246542	63246542	8340	14	G	T	T	T	577	45	KCNH5	2	2
TMEM63C	57156	broad.mit.edu	37	14	77709294	77709294	+	Silent	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77709294A>T	uc001xtf.2	+	c.1236A>T	c.(1234-1236)GCA>GCT	p.A412A	TMEM63C_uc010asq.1_Silent_p.A412A	NM_020431	NP_065164	Q9P1W3	TM63C_HUMAN	transmembrane protein 63C	412	Helical; (Potential).					integral to membrane					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)										0.156716	33.304178	48.380156	21	113	KEEP	---	---	---	---	capture		Silent	SNP	77709294	77709294	16731	14	A	T	T	T	54	5	TMEM63C	3	3
KCNK10	54207	broad.mit.edu	37	14	88729781	88729781	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:88729781A>T	uc001xwm.2	-	c.167T>A	c.(166-168)GTG>GAG	p.V56E	KCNK10_uc001xwn.2_Missense_Mutation_p.V56E|KCNK10_uc001xwo.2_Missense_Mutation_p.V51E	NM_138318	NP_612191	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	51	Cytoplasmic (Potential).				signal transduction	integral to membrane	potassium channel activity|voltage-gated ion channel activity			ovary(2)|pancreas(1)	3														0.151042	46.05177	68.471199	29	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88729781	88729781	8364	14	A	T	T	T	78	6	KCNK10	3	3
OCA2	4948	broad.mit.edu	37	15	28171326	28171326	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28171326T>C	uc001zbh.3	-	c.2026A>G	c.(2026-2028)AGA>GGA	p.R676G	OCA2_uc010ayv.2_Missense_Mutation_p.R652G	NM_000275	NP_000266	Q04671	P_HUMAN	oculocutaneous albinism II	676	Cytoplasmic (Potential).				eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding			ovary(3)|breast(1)|pancreas(1)	5		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)										0.234043	59.203823	65.2864	22	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28171326	28171326	11220	15	T	C	C	C	713	55	OCA2	4	4
CDAN1	146059	broad.mit.edu	37	15	43027805	43027805	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43027805C>G	uc001zql.2	-	c.846G>C	c.(844-846)CGG>CGC	p.R282R	CDAN1_uc001zqk.2_5'Flank|CDAN1_uc010bcx.1_5'Flank	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	282						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)										0.22093	52.406149	58.551208	19	67	KEEP	---	---	---	---	capture		Silent	SNP	43027805	43027805	3182	15	C	G	G	G	379	30	CDAN1	3	3
DMXL2	23312	broad.mit.edu	37	15	51780775	51780775	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51780775T>C	uc010ufy.1	-	c.5021A>G	c.(5020-5022)AAG>AGG	p.K1674R	DMXL2_uc002abf.2_Missense_Mutation_p.K1674R|DMXL2_uc010bfa.2_Missense_Mutation_p.K1038R	NM_015263	NP_056078	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1674						cell junction|synaptic vesicle membrane	Rab GTPase binding			ovary(6)	6				all cancers(107;0.00494)										0.031915	-15.960178	6.566494	3	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51780775	51780775	4777	15	T	C	C	C	728	56	DMXL2	4	4
ANXA2	302	broad.mit.edu	37	15	60641388	60641388	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:60641388C>T	uc002agm.2	-	c.900G>A	c.(898-900)GGG>GGA	p.G300G	ANXA2_uc002agn.2_Silent_p.G282G|ANXA2_uc002agk.2_Silent_p.G282G|ANXA2_uc002agl.2_Silent_p.G282G|ANXA2_uc010uhd.1_Intron	NM_001002858	NP_001002858	P07355	ANXA2_HUMAN	annexin A2 isoform 1	282	Annexin 4.				angiogenesis|positive regulation of vesicle fusion|skeletal system development	basement membrane|melanosome|midbody|soluble fraction	calcium ion binding|calcium-dependent phospholipid binding|cytoskeletal protein binding|phospholipase inhibitor activity			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Tenecteplase(DB00031)									0.272727	46.91829	49.992707	18	48	KEEP	---	---	---	---	capture		Silent	SNP	60641388	60641388	726	15	C	T	T	T	379	30	ANXA2	2	2
VPS13C	54832	broad.mit.edu	37	15	62174899	62174899	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62174899G>T	uc002agz.2	-	c.9520C>A	c.(9520-9522)CCT>ACT	p.P3174T	VPS13C_uc002aha.2_Missense_Mutation_p.P3131T|VPS13C_uc002ahb.1_Missense_Mutation_p.P3174T|VPS13C_uc002ahc.1_Missense_Mutation_p.P3131T	NM_020821	NP_065872	Q709C8	VP13C_HUMAN	vacuolar protein sorting 13C protein isoform 2A	3174					protein localization					ovary(2)	2														0.263158	44.501557	48.336232	20	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62174899	62174899	17758	15	G	T	T	T	559	43	VPS13C	2	2
GRIN2A	2903	broad.mit.edu	37	16	10031897	10031897	+	Missense_Mutation	SNP	T	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:10031897T>G	uc002czo.3	-	c.926A>C	c.(925-927)AAG>ACG	p.K309T	GRIN2A_uc010uym.1_Missense_Mutation_p.K309T|GRIN2A_uc010uyn.1_Missense_Mutation_p.K152T|GRIN2A_uc002czr.3_Missense_Mutation_p.K309T	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	309	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.109375	6.483145	16.149867	7	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10031897	10031897	7058	16	T	G	G	G	728	56	GRIN2A	4	4
CIITA	4261	broad.mit.edu	37	16	11016071	11016071	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:11016071G>T	uc002daj.3	+	c.3200G>T	c.(3199-3201)CGT>CTT	p.R1067L	CIITA_uc002dai.3_Missense_Mutation_p.R1066L|CIITA_uc002dak.3_Missense_Mutation_p.R482L	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	1066	LRR 3.				interferon-gamma-mediated signaling pathway|negative regulation of collagen biosynthetic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of MHC class II biosynthetic process|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|promoter binding|protein C-terminus binding|protein complex binding|RNA polymerase II transcription factor activity|transcription activator activity|transcription coactivator activity|transcription repressor activity			central_nervous_system(1)	1										532				0.176119	127.12155	160.165612	59	276	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11016071	11016071	3562	16	G	T	T	T	520	40	CIITA	1	1
PDILT	204474	broad.mit.edu	37	16	20370695	20370695	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20370695C>A	uc002dhc.1	-	c.1701G>T	c.(1699-1701)AAG>AAT	p.K567N		NM_174924	NP_777584	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis	567					cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis	endoplasmic reticulum	isomerase activity			large_intestine(1)	1														0.252788	162.061506	176.999227	68	201	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20370695	20370695	12095	16	C	A	A	A	363	28	PDILT	2	2
SEZ6L2	26470	broad.mit.edu	37	16	29909285	29909285	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:29909285C>A	uc010vec.1	-	c.100G>T	c.(100-102)GAG>TAG	p.E34*	BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_Nonsense_Mutation_p.E34*|SEZ6L2_uc002dur.3_Nonsense_Mutation_p.E34*|SEZ6L2_uc002duq.3_Nonsense_Mutation_p.E34*|SEZ6L2_uc002dus.3_Nonsense_Mutation_p.E34*|SEZ6L2_uc010ved.1_Intron|ASPHD1_uc002dut.2_5'Flank|ASPHD1_uc002duu.3_5'Flank|ASPHD1_uc010bzi.2_5'Flank	NM_201575	NP_963869	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2 isoform	34	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane|plasma membrane				ovary(1)	1														0.104167	4.585575	19.553639	10	86	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	29909285	29909285	14633	16	C	A	A	A	390	30	SEZ6L2	5	2
HYDIN	54768	broad.mit.edu	37	16	71007834	71007834	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71007834G>T	uc002ezr.2	-	c.5124C>A	c.(5122-5124)GCC>GCA	p.A1708A		NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	1709										ovary(1)	1		Ovarian(137;0.0654)												0.139073	28.862897	47.883486	21	130	KEEP	---	---	---	---	capture		Silent	SNP	71007834	71007834	7767	16	G	T	T	T	600	47	HYDIN	2	2
CNTNAP4	85445	broad.mit.edu	37	16	76573654	76573654	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:76573654G>T	uc002fex.1	+	c.3268G>T	c.(3268-3270)GAG>TAG	p.E1090*	CNTNAP4_uc002feu.1_Nonsense_Mutation_p.E1087*|CNTNAP4_uc002fev.1_Nonsense_Mutation_p.E951*|CNTNAP4_uc010chb.1_Nonsense_Mutation_p.E1014*	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	1087	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2														0.263158	11.764892	12.729895	5	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	76573654	76573654	3787	16	G	T	T	T	429	33	CNTNAP4	5	2
ADAMTS18	170692	broad.mit.edu	37	16	77331205	77331205	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:77331205C>A	uc002ffc.3	-	c.2782G>T	c.(2782-2784)GCT>TCT	p.A928S	ADAMTS18_uc010chc.1_Missense_Mutation_p.A516S|ADAMTS18_uc002ffe.1_Missense_Mutation_p.A624S	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	928					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|kidney(4)|skin(2)|pancreas(1)|ovary(1)	12										1451				0.164384	46.510443	62.125793	24	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77331205	77331205	264	16	C	A	A	A	351	27	ADAMTS18	1	1
MYH13	8735	broad.mit.edu	37	17	10253943	10253943	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10253943C>T	uc002gmk.1	-	c.1074G>A	c.(1072-1074)GTG>GTA	p.V358V	MYH13_uc010vvf.1_Silent_p.V33V	NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	358	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.248322	77.473281	86.086422	37	112	KEEP	---	---	---	---	capture		Silent	SNP	10253943	10253943	10427	17	C	T	T	T	366	29	MYH13	2	2
MYH1	4619	broad.mit.edu	37	17	10408603	10408603	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10408603G>T	uc002gmo.2	-	c.2312C>A	c.(2311-2313)GCT>GAT	p.A771D		NM_005963	NP_005954	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	771	Myosin head-like.|Actin-binding (By similarity).					muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(10)|breast(3)|kidney(1)|skin(1)	15										585				0.073684	-3.455703	14.294618	7	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10408603	10408603	10424	17	G	T	T	T	442	34	MYH1	2	2
DPH1	1801	broad.mit.edu	37	17	1936926	1936926	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:1936926G>T	uc010vqs.1	+	c.234G>T	c.(232-234)AGG>AGT	p.R78S	DPH1_uc002ftr.1_Non-coding_Transcript|DPH1_uc002fts.2_Missense_Mutation_p.R68S|DPH1_uc002ftt.2_Missense_Mutation_p.R63S|DPH1_uc010cjx.2_5'UTR	NM_001383	NP_001374	Q9BZG8	DPH1_HUMAN	diptheria toxin resistance protein required for	68					peptidyl-diphthamide biosynthetic process from peptidyl-histidine|translation	cytoplasm|nucleus				pancreas(1)	1														0.157895	28.482142	43.346025	21	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1936926	1936926	4903	17	G	T	T	T	529	41	DPH1	2	2
FOXN1	8456	broad.mit.edu	37	17	26851543	26851543	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:26851543C>T	uc010crm.2	+	c.146C>T	c.(145-147)TCG>TTG	p.S49L	FOXN1_uc002hbj.2_Missense_Mutation_p.S49L	NM_003593	NP_003584	O15353	FOXN1_HUMAN	forkhead box N1	49					defense response|embryo development|epithelial cell proliferation|keratinocyte differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ morphogenesis|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|thymus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			skin(1)	1	Lung NSC(42;0.00431)													0.04142	-26.318276	11.904192	7	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26851543	26851543	6265	17	C	T	T	T	403	31	FOXN1	1	1
LIG3	3980	broad.mit.edu	37	17	33319679	33319679	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33319679G>T	uc002hik.1	+	c.1423G>T	c.(1423-1425)GCC>TCC	p.A475S	LIG3_uc002hij.2_Missense_Mutation_p.A475S|LIG3_uc010cth.1_Missense_Mutation_p.A484S	NM_013975	NP_039269	P49916	DNLI3_HUMAN	ligase III, DNA, ATP-dependent isoform alpha	475					base-excision repair|cell division|DNA ligation involved in DNA repair|DNA replication|reciprocal meiotic recombination|spermatogenesis	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|protein binding|zinc ion binding			ovary(2)|large_intestine(1)|pancreas(1)	4		Ovarian(249;0.17)			Bleomycin(DB00290)									0.194444	25.503897	31.928709	14	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33319679	33319679	9108	17	G	T	T	T	546	42	LIG3	2	2
MYO19	80179	broad.mit.edu	37	17	34859855	34859855	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34859855C>A	uc010wcy.1	-	c.1911G>T	c.(1909-1911)CTG>CTT	p.L637L	MYO19_uc002hmw.2_Intron|MYO19_uc010cuu.2_Non-coding_Transcript	NM_001163735	NP_001157207	Q96H55	MYO19_HUMAN	myosin XIX isoform 2	637	Myosin head-like.					mitochondrial outer membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)	1		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)										0.1875	5.314536	6.779043	3	13	KEEP	---	---	---	---	capture		Silent	SNP	34859855	34859855	10462	17	C	A	A	A	366	29	MYO19	2	2
C17orf78	284099	broad.mit.edu	37	17	35742976	35742976	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:35742976G>C	uc002hns.2	+	c.421G>C	c.(421-423)GTC>CTC	p.V141L	ACACA_uc002hnn.2_Intron|ACACA_uc002hno.2_Intron|ACACA_uc002hnq.2_Intron|C17orf78_uc010cva.1_Intron	NM_173625	NP_775896	Q8N4C9	CQ078_HUMAN	hypothetical protein LOC284099	141						integral to membrane					0		Breast(25;0.00295)|Ovarian(249;0.15)												0.148148	8.782567	11.990299	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35742976	35742976	1941	17	G	C	C	C	468	36	C17orf78	3	3
FKBP10	60681	broad.mit.edu	37	17	39974501	39974501	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39974501C>A	uc002hxv.2	+	c.552C>A	c.(550-552)ACC>ACA	p.T184T	FKBP10_uc002hxw.1_5'Flank	NM_021939	NP_068758	Q96AY3	FKB10_HUMAN	FK506 binding protein 10 precursor	184	PPIase FKBP-type 2.				protein folding	endoplasmic reticulum lumen|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)										0.181818	26.177027	34.533831	16	72	KEEP	---	---	---	---	capture		Silent	SNP	39974501	39974501	6140	17	C	A	A	A	275	22	FKBP10	2	2
PSMB6	5694	broad.mit.edu	37	17	4701416	4701416	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4701416C>A	uc002fzb.2	+	c.545C>A	c.(544-546)ACC>AAC	p.T182N		NM_002798	NP_002789	P28072	PSB6_HUMAN	proteasome beta 6 subunit precursor	182					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity			ovary(2)	2														0.092896	5.419048	35.867289	17	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4701416	4701416	13134	17	C	A	A	A	234	18	PSMB6	2	2
CACNA1G	8913	broad.mit.edu	37	17	48680470	48680470	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:48680470A>G	uc002irk.1	+	c.4079A>G	c.(4078-4080)GAC>GGC	p.D1360G	CACNA1G_uc002iri.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irj.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irl.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irm.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irn.1_Missense_Mutation_p.D1337G|CACNA1G_uc002iro.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irp.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irq.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irr.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irs.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irt.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irv.1_Missense_Mutation_p.D1360G|CACNA1G_uc002irw.1_Missense_Mutation_p.D1337G|CACNA1G_uc002iru.1_Missense_Mutation_p.D1337G|CACNA1G_uc002irx.1_Missense_Mutation_p.D1273G|CACNA1G_uc002iry.1_Missense_Mutation_p.D1273G|CACNA1G_uc002irz.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isa.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isb.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isc.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isd.1_Missense_Mutation_p.D1273G|CACNA1G_uc002ise.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isf.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isg.1_Missense_Mutation_p.D1273G|CACNA1G_uc002ish.1_Missense_Mutation_p.D1273G|CACNA1G_uc002isi.1_Missense_Mutation_p.D1250G|CACNA1G_uc002isj.2_Missense_Mutation_p.D84G	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	1360	III.|Helical; Name=S3 of repeat III; (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)									0.057554	-8.103821	20.429944	8	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48680470	48680470	2660	17	A	G	G	G	130	10	CACNA1G	4	4
MKS1	54903	broad.mit.edu	37	17	56283513	56283513	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56283513C>A	uc002ivr.1	-	c.1607G>T	c.(1606-1608)CGG>CTG	p.R536L	MKS1_uc010wnq.1_Missense_Mutation_p.R333L|MKS1_uc002ivs.1_3'UTR	NM_017777	NP_060247	Q9NXB0	MKS1_HUMAN	Meckel syndrome type 1 protein isoform 1	536					cilium assembly	centrosome|cilium|microtubule basal body	protein binding			ovary(1)	1														0.213333	32.661401	38.355362	16	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56283513	56283513	9999	17	C	A	A	A	299	23	MKS1	1	1
SOX9	6662	broad.mit.edu	37	17	70120440	70120440	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:70120440C>G	uc002jiw.2	+	c.1442C>G	c.(1441-1443)GCC>GGC	p.A481G		NM_000346	NP_000337	P48436	SOX9_HUMAN	transcription factor SOX9	481					negative regulation of gene-specific transcription|positive regulation of branching involved in ureteric bud morphogenesis|renal vesicle induction|signal transduction	nucleus	specific RNA polymerase II transcription factor activity|transcription repressor activity				0		Colorectal(1115;0.245)	STAD - Stomach adenocarcinoma(260;0.119)			Pancreas(42;83 1041 2320 35205 39456)								0.120219	34.82898	60.708289	22	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70120440	70120440	15458	17	C	G	G	G	338	26	SOX9	3	3
TP53	7157	broad.mit.edu	37	17	7578492	7578492	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578492C>T	uc002gim.2	-	c.438G>A	c.(436-438)TGG>TGA	p.W146*	TP53_uc002gig.1_Nonsense_Mutation_p.W146*|TP53_uc002gih.2_Nonsense_Mutation_p.W146*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.W14*|TP53_uc010cng.1_Nonsense_Mutation_p.W14*|TP53_uc002gii.1_Nonsense_Mutation_p.W14*|TP53_uc010cnh.1_Nonsense_Mutation_p.W146*|TP53_uc010cni.1_Nonsense_Mutation_p.W146*|TP53_uc002gij.2_Nonsense_Mutation_p.W146*|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Nonsense_Mutation_p.W53*|TP53_uc002gio.2_Nonsense_Mutation_p.W14*|TP53_uc010vug.1_Nonsense_Mutation_p.W107*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	146	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		W -> S (in sporadic cancers; somatic mutation).|W -> C (in a sporadic cancer; somatic mutation).|W -> G (in sporadic cancers; somatic mutation).|W -> R (in sporadic cancers; somatic mutation).|W -> L (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 gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|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|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	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|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|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.W146*(30)|p.0?(6)|p.W146C(2)|p.Q144_G154del11(1)|p.W146_V147insXXXXXXX(1)|p.W146_S149>C(1)|p.Q144fs*32(1)|p.W146fs*1(1)|p.L137_W146del10(1)|p.W53fs*1(1)|p.W146fs*22(1)|p.W146fs*23(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|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)	21904		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)		Pancreas(47;798 1329 9957 10801)		111	p.W146*(NCIH520-Tumor)|p.W146*(BICR16-Tumor)|p.146_149WVDS>C(YKG1-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.293578	80.357769	84.515559	32	77	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7578492	7578492	16923	17	C	T	T	T	286	22	TP53	5	2
CCDC40	55036	broad.mit.edu	37	17	78021138	78021138	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:78021138C>A	uc010dht.2	+	c.613C>A	c.(613-615)CGG>AGG	p.R205R	CCDC40_uc010wub.1_Silent_p.R205R|CCDC40_uc002jxm.3_5'Flank	NM_017950	NP_060420	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	205					axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)											0.041096	-9.907042	6.601316	3	70	KEEP	---	---	---	---	capture		Silent	SNP	78021138	78021138	2934	17	C	A	A	A	295	23	CCDC40	1	1
ARL16	339231	broad.mit.edu	37	17	79650818	79650818	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79650818G>T	uc002kbf.2	-	c.38C>A	c.(37-39)GCC>GAC	p.A13D	ARL16_uc002kbe.2_5'Flank|HGS_uc010wus.1_5'Flank|HGS_uc002kbg.2_5'Flank	NM_001040025	NP_001035114	Q0P5N6	ARL16_HUMAN	ADP-ribosylation factor-like 16	13							GTP binding				0	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)											0.121212	3.682052	8.319524	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79650818	79650818	947	17	G	T	T	T	546	42	ARL16	2	2
NDEL1	81565	broad.mit.edu	37	17	8350154	8350154	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8350154A>G	uc002glj.2	+	c.323A>G	c.(322-324)AAG>AGG	p.K108R	NDEL1_uc002gli.2_Missense_Mutation_p.K108R	NM_030808	NP_110435	Q9GZM8	NDEL1_HUMAN	nudE nuclear distribution gene E homolog (A.	108	Interaction with KATNB1 (By similarity).|Potential.|Self-association (By similarity).				chromosome segregation|mitotic prometaphase	condensed chromosome kinetochore|cytosol|microtubule|spindle					0														0.285714	65.272419	68.155651	20	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8350154	8350154	10643	17	A	G	G	G	39	3	NDEL1	4	4
LAMA3	3909	broad.mit.edu	37	18	21441624	21441624	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:21441624G>A	uc002kuq.2	+	c.4437G>A	c.(4435-4437)CTG>CTA	p.L1479L	LAMA3_uc002kur.2_Silent_p.L1479L	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1479	Laminin IV type A.				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|central_nervous_system(1)	9	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.168675	23.20248	31.830416	14	69	KEEP	---	---	---	---	capture		Silent	SNP	21441624	21441624	8930	18	G	A	A	A	600	47	LAMA3	2	2
DSG4	147409	broad.mit.edu	37	18	28979469	28979469	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:28979469A>G	uc002kwr.2	+	c.1240A>G	c.(1240-1242)ATA>GTA	p.I414V	DSG4_uc002kwq.2_Missense_Mutation_p.I414V	NM_001134453	NP_001127925	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 1 preproprotein	414	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8			OV - Ovarian serous cystadenocarcinoma(10;0.00504)											0.195122	38.656846	45.760246	16	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28979469	28979469	4963	18	A	G	G	G	104	8	DSG4	4	4
MCART2	147407	broad.mit.edu	37	18	29340603	29340603	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:29340603C>A	uc002kxa.2	-	c.22G>T	c.(22-24)GAA>TAA	p.E8*		NM_001034172	NP_001029344	Q3SY17	MCAR2_HUMAN	mitochondrial carrier triple repeat 2	8					transport	integral to membrane|mitochondrial inner membrane					0			OV - Ovarian serous cystadenocarcinoma(10;0.0539)											0.145833	49.248442	78.224892	35	205	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	29340603	29340603	9759	18	C	A	A	A	377	29	MCART2	5	2
SETBP1	26040	broad.mit.edu	37	18	42530189	42530189	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:42530189G>T	uc010dni.2	+	c.884G>T	c.(883-885)AGC>ATC	p.S295I		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	295						nucleus	DNA binding			large_intestine(1)	1				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										0.217822	41.888383	49.311446	22	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42530189	42530189	14617	18	G	T	T	T	442	34	SETBP1	2	2
SERPINB3	6317	broad.mit.edu	37	18	61323052	61323052	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61323052C>G	uc002lji.2	-	c.1012G>C	c.(1012-1014)GAG>CAG	p.E338Q	SERPINB4_uc002ljg.2_Intron|SERPINB3_uc010dqa.2_Missense_Mutation_p.E286Q	NM_006919	NP_008850	P29508	SPB3_HUMAN	serine (or cysteine) proteinase inhibitor, clade	338					regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|central_nervous_system(1)	2														0.183333	27.888536	33.535434	11	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61323052	61323052	14590	18	C	G	G	G	416	32	SERPINB3	3	3
ZNF407	55628	broad.mit.edu	37	18	72346333	72346333	+	Nonsense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:72346333A>T	uc002llw.2	+	c.3358A>T	c.(3358-3360)AAA>TAA	p.K1120*	ZNF407_uc010xfc.1_Nonsense_Mutation_p.K1120*|ZNF407_uc010dqu.1_Nonsense_Mutation_p.K1120*|ZNF407_uc002llu.2_Nonsense_Mutation_p.K1119*	NM_017757	NP_060227	Q9C0G0	ZN407_HUMAN	zinc finger protein 407 isoform 1	1120					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)										0.166667	11.301886	15.725482	7	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	72346333	72346333	18480	18	A	T	T	T	169	13	ZNF407	5	3
RDH8	50700	broad.mit.edu	37	19	10132321	10132321	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10132321G>T	uc002mmr.2	+	c.832G>T	c.(832-834)GTG>TTG	p.V278L		NM_015725	NP_056540	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	278					estrogen biosynthetic process|oxidation-reduction process|response to stimulus|visual perception	cytoplasm|integral to plasma membrane	binding|estradiol 17-beta-dehydrogenase activity|NADP-retinol dehydrogenase activity|retinol dehydrogenase activity			ovary(3)|pancreas(1)	4			Epithelial(33;4.24e-05)		Vitamin A(DB00162)									0.322917	81.992824	84.664952	31	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10132321	10132321	13665	19	G	T	T	T	624	48	RDH8	2	2
CYP4F3	4051	broad.mit.edu	37	19	15769365	15769365	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15769365G>A	uc002nbj.2	+	c.1314G>A	c.(1312-1314)GAG>GAA	p.E438E	CYP4F3_uc010xok.1_Silent_p.E438E|CYP4F3_uc010xol.1_Silent_p.E438E|CYP4F3_uc010xom.1_Silent_p.E289E|CYP4F3_uc002nbk.2_Silent_p.E438E|CYP4F3_uc010xon.1_Silent_p.E148E	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,	438					leukotriene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3														0.182635	128.570875	160.090924	61	273	KEEP	---	---	---	---	capture		Silent	SNP	15769365	15769365	4355	19	G	A	A	A	451	35	CYP4F3	2	2
CHERP	10523	broad.mit.edu	37	19	16640580	16640580	+	Silent	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16640580T>C	uc002nei.1	-	c.1008A>G	c.(1006-1008)CAA>CAG	p.Q336Q	MED26_uc002nee.2_Intron	NM_006387	NP_006378	Q8IWX8	CHERP_HUMAN	calcium homeostasis endoplasmic reticulum	336	Gln-rich.				cellular calcium ion homeostasis|negative regulation of cell proliferation|nervous system development|RNA processing	endoplasmic reticulum|perinuclear region of cytoplasm	RNA binding			ovary(2)	2														0.25	6.048327	6.5013	2	6	KEEP	---	---	---	---	capture		Silent	SNP	16640580	16640580	3470	19	T	C	C	C	777	60	CHERP	4	4
LRRC25	126364	broad.mit.edu	37	19	18507413	18507413	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18507413C>G	uc002niw.2	-	c.361G>C	c.(361-363)GAG>CAG	p.E121Q	LRRC25_uc002nix.2_Missense_Mutation_p.E121Q	NM_145256	NP_660299	Q8N386	LRC25_HUMAN	leucine rich repeat containing 25 precursor	121	Extracellular (Potential).					integral to membrane					0														0.234375	42.692276	46.823353	15	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18507413	18507413	9354	19	C	G	G	G	390	30	LRRC25	3	3
NCAN	1463	broad.mit.edu	37	19	19334856	19334856	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19334856C>A	uc002nlz.2	+	c.502C>A	c.(502-504)CGG>AGG	p.R168R	NCAN_uc010ecc.1_5'Flank	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	168	Link 1.				axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)											0.170543	43.672497	56.914249	22	107	KEEP	---	---	---	---	capture		Silent	SNP	19334856	19334856	10603	19	C	A	A	A	295	23	NCAN	1	1
ZNF208	7757	broad.mit.edu	37	19	22157392	22157392	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22157392G>T	uc002nqp.2	-	c.444C>A	c.(442-444)GGC>GGA	p.G148G	ZNF208_uc002nqo.1_Intron|ZNF208_uc010ecw.1_5'Flank	NM_007153	NP_009084			zinc finger protein 208											ovary(5)	5		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.269231	17.512138	18.762537	7	19	KEEP	---	---	---	---	capture		Silent	SNP	22157392	22157392	18357	19	G	T	T	T	587	46	ZNF208	2	2
ZNF536	9745	broad.mit.edu	37	19	31040159	31040159	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31040159C>T	uc002nsu.1	+	c.3633C>T	c.(3631-3633)CCC>CCT	p.P1211P	ZNF536_uc010edd.1_Silent_p.P1211P	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	1211					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.108333	6.391913	24.647392	13	107	KEEP	---	---	---	---	capture		Silent	SNP	31040159	31040159	18568	19	C	T	T	T	262	21	ZNF536	2	2
TSHZ3	57616	broad.mit.edu	37	19	31767880	31767880	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31767880C>A	uc002nsy.3	-	c.2819G>T	c.(2818-2820)GGG>GTG	p.G940V		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	940	Homeobox; atypical.				regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.13253	12.37892	23.259496	11	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31767880	31767880	17176	19	C	A	A	A	286	22	TSHZ3	2	2
RYR1	6261	broad.mit.edu	37	19	38939038	38939038	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38939038C>T	uc002oit.2	+	c.844C>T	c.(844-846)CGG>TGG	p.R282W	RYR1_uc002oiu.2_Missense_Mutation_p.R282W	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	282	MIR 4.|Cytoplasmic.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)									0.173729	81.731271	105.449573	41	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38939038	38939038	14248	19	C	T	T	T	295	23	RYR1	1	1
LGALS13	29124	broad.mit.edu	37	19	40097972	40097972	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40097972G>T	uc002omb.2	+	c.413G>T	c.(412-414)TGC>TTC	p.C138F		NM_013268	NP_037400	Q9UHV8	PP13_HUMAN	galectin-13	138	Galectin.				lipid catabolic process|phospholipid metabolic process		lysophospholipase activity|sugar binding			ovary(1)	1	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)											0.291139	60.389169	63.478777	23	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40097972	40097972	9065	19	G	T	T	T	598	46	LGALS13	2	2
PSG9	5678	broad.mit.edu	37	19	43763160	43763160	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43763160G>T	uc002owd.3	-	c.837C>A	c.(835-837)AGC>AGA	p.S279R	PSG9_uc002owe.3_Intron|PSG9_uc010xwm.1_Missense_Mutation_p.S186R|PSG9_uc002owf.3_Intron|PSG9_uc002owg.2_Intron|PSG9_uc002owh.2_Intron	NM_002784	NP_002775	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	279	Ig-like C2-type 2.				female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.21174	198.718902	235.385108	101	376	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43763160	43763160	13115	19	G	T	T	T	542	42	PSG9	2	2
CEACAM16	388551	broad.mit.edu	37	19	45206812	45206812	+	Silent	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45206812T>A	uc002ozq.2	+	c.408T>A	c.(406-408)CCT>CCA	p.P136P	CEACAM16_uc010xxd.1_Silent_p.P77P	NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	77										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)												0.230769	20.95699	23.546339	9	30	KEEP	---	---	---	---	capture		Silent	SNP	45206812	45206812	3321	19	T	A	A	A	704	55	CEACAM16	3	3
MUC16	94025	broad.mit.edu	37	19	9048356	9048356	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9048356G>T	uc002mkp.2	-	c.33275C>A	c.(33274-33276)CCT>CAT	p.P11092H		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11094	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														0.197531	31.34733	38.255345	16	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9048356	9048356	10367	19	G	T	T	T	455	35	MUC16	2	2
OR7G1	125962	broad.mit.edu	37	19	9225999	9225999	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9225999G>T	uc002mks.1	-	c.441C>A	c.(439-441)CTC>CTA	p.L147L		NM_001005192	NP_001005192	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.342466	62.945123	64.549327	25	48	KEEP	---	---	---	---	capture		Silent	SNP	9225999	9225999	11633	19	G	T	T	T	418	33	OR7G1	2	2
HIAT1	64645	broad.mit.edu	37	1	100533603	100533603	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:100533603G>A	uc001dst.2	+	c.557G>A	c.(556-558)GGG>GAG	p.G186E		NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	186	Cytoplasmic (Potential).				response to antibiotic	integral to membrane	tetracycline:hydrogen antiporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)										0.122066	34.790903	64.593471	26	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100533603	100533603	7382	1	G	A	A	A	559	43	HIAT1	2	2
CDC14A	8556	broad.mit.edu	37	1	100964529	100964529	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:100964529A>G	uc001dtf.2	+	c.1466A>G	c.(1465-1467)AAT>AGT	p.N489S	CDC14A_uc010oui.1_Missense_Mutation_p.N431S|CDC14A_uc009wed.1_Missense_Mutation_p.N196S|CDC14A_uc001dtg.3_Missense_Mutation_p.N489S|CDC14A_uc009wee.2_Missense_Mutation_p.N489S	NM_033312	NP_201569	Q9UNH5	CC14A_HUMAN	CDC14 homolog A isoform 2	489					cell cycle|cell division|cell proliferation	microtubule organizing center|nucleus|spindle	protein binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			large_intestine(1)	1		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)										0.065934	-1.82114	15.961925	6	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100964529	100964529	3184	1	A	G	G	G	52	4	CDC14A	4	4
EPS8L3	79574	broad.mit.edu	37	1	110293311	110293311	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110293311G>A	uc001dyq.1	-	c.1744C>T	c.(1744-1746)CGG>TGG	p.R582W	EPS8L3_uc001dys.1_Missense_Mutation_p.R551W|EPS8L3_uc001dyr.1_Missense_Mutation_p.R581W|EPS8L3_uc009wfm.1_Missense_Mutation_p.R518W	NM_139053	NP_620641	Q8TE67	ES8L3_HUMAN	epidermal growth factor receptor pathway	581						cytoplasm	protein binding			ovary(2)|skin(1)	3		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)										0.261905	52.81211	57.121157	22	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110293311	110293311	5390	1	G	A	A	A	506	39	EPS8L3	1	1
RBM15	64783	broad.mit.edu	37	1	110882449	110882449	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:110882449G>T	uc001dzl.1	+	c.422G>T	c.(421-423)CGC>CTC	p.R141L	RBM15_uc001dzm.1_Missense_Mutation_p.R141L	NM_022768	NP_073605	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	141	Gly/Ser-rich.				interspecies interaction between organisms	nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)						100		OREG0013656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.28169	49.171121	52.211594	20	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110882449	110882449	13577	1	G	T	T	T	494	38	RBM15	1	1
MTOR	2475	broad.mit.edu	37	1	11270888	11270888	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11270888T>C	uc001asd.2	-	c.3637A>G	c.(3637-3639)ATC>GTC	p.I1213V		NM_004958	NP_004949	P42345	MTOR_HUMAN	FK506 binding protein 12-rapamycin associated	1213					cell growth|cellular response to hypoxia|insulin receptor signaling pathway|nerve growth factor receptor signaling pathway|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|protein autophosphorylation|protein catabolic process|response to amino acid stimulus|response to nutrient|T cell costimulation|TOR signaling cascade	endoplasmic reticulum membrane|Golgi membrane|lysosome|mitochondrial outer membrane|phosphatidylinositol 3-kinase complex|PML body|TORC1 complex|TORC2 complex	ATP binding|phosphoprotein binding|protein serine/threonine kinase activity			central_nervous_system(7)|ovary(4)|kidney(3)|large_intestine(2)|skin(2)|lung(1)	19										1389				0.196262	55.022422	64.213311	21	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11270888	11270888	10347	1	T	C	C	C	663	51	MTOR	4	4
NRAS	4893	broad.mit.edu	37	1	115256530	115256530	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:115256530G>T	uc009wgu.2	-	c.181C>A	c.(181-183)CAA>AAA	p.Q61K		NM_002524	NP_002515	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61	GTP.		Q -> K (in neuroblastoma cell).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.Q61K(511)|p.Q61R(40)|p.Q61H(10)|p.Q61E(9)|p.Q61L(7)|p.Q61?(4)		haematopoietic_and_lymphoid_tissue(994)|skin(911)|thyroid(325)|NS(60)|large_intestine(52)|lung(29)|upper_aerodigestive_tract(25)|soft_tissue(25)|urinary_tract(12)|liver(10)|adrenal_gland(9)|autonomic_ganglia(8)|testis(8)|central_nervous_system(8)|prostate(8)|breast(7)|biliary_tract(6)|ovary(6)|stomach(5)|pancreas(5)|endometrium(2)|kidney(2)|cervix(2)|eye(1)	2520	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)			Q61K(HT1080_SOFT_TISSUE)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(TYKNU_OVARY)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH2087_LUNG)|Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HS944T_SKIN)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(HS936T_SKIN)|Q61K(NCIH1299_LUNG)	50	p.Q61K(HCC15-Tumor)|p.Q61K(SKNSH-Tumor)|p.Q61K(HS944.T-Tumor)|p.Q61K(HS936.T-Tumor)|p.Q61K(JJN3-Tumor)|p.Q61K(SJSA1-Tumor)|p.Q61K(NCIH1299-Tumor)|p.Q61K(NCIH1573-Tumor)|p.Q61K(SKNAS-Tumor)|p.Q61K(CHP212-Tumor)|p.Q61K(HUT78-Tumor)|p.Q61K(TYKNU-Tumor)|p.Q61K(HT1080-Tumor)|p.Q61K(SKMEL30-Tumor)|p.Q61K(M07E-Tumor)|p.Q61K(SNU387-Tumor)|p.Q61K(OCILY19-Tumor)	128	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			0.313084	181.029376	187.694832	67	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115256530	115256530	11045	1	G	T	T	T	624	48	NRAS	2	2
CD101	9398	broad.mit.edu	37	1	117561104	117561104	+	Silent	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117561104A>C	uc010oxb.1	+	c.1939A>C	c.(1939-1941)AGA>CGA	p.R647R	CD101_uc009whd.2_Silent_p.R647R|CD101_uc010oxc.1_Silent_p.R647R|CD101_uc010oxd.1_Silent_p.R585R	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	647	Extracellular (Potential).|Ig-like C2-type 5.				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			ovary(1)	1														0.335404	151.604576	155.463097	54	107	KEEP	---	---	---	---	capture		Silent	SNP	117561104	117561104	3089	1	A	C	C	C	88	7	CD101	4	4
PRAMEF2	65122	broad.mit.edu	37	1	12919588	12919588	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12919588G>T	uc001aum.1	+	c.328G>T	c.(328-330)GAG>TAG	p.E110*		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	110											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)										0.202586	183.141504	221.316141	94	370	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	12919588	12919588	12872	1	G	T	T	T	585	45	PRAMEF2	5	2
ENSA	2029	broad.mit.edu	37	1	150601933	150601933	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150601933T>C	uc009wly.2	-	c.14A>G	c.(13-15)CAA>CGA	p.Q5R	ENSA_uc001evd.2_Missense_Mutation_p.Q5R|ENSA_uc001eve.2_Missense_Mutation_p.Q5R|ENSA_uc001evg.2_Missense_Mutation_p.Q5R|ENSA_uc001evh.2_Missense_Mutation_p.Q5R|ENSA_uc009wlz.1_Missense_Mutation_p.Q5R|ENSA_uc001evi.2_Missense_Mutation_p.Q5R	NM_207043	NP_997051	O43768	ENSA_HUMAN	endosulfine alpha isoform 2	5				Q -> R (in Ref. 8; CAG38815).	cell division|G2/M transition of mitotic cell cycle|mitosis|response to nutrient|transport	cytoplasm	ion channel inhibitor activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity|receptor binding			central_nervous_system(1)	1	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			Esophageal Squamous(188;763 2078 3002 3411 26027)								0.108696	13.695519	34.751684	15	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150601933	150601933	5329	1	T	C	C	C	819	63	ENSA	4	4
FLG	2312	broad.mit.edu	37	1	152284188	152284188	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152284188G>T	uc001ezu.1	-	c.3174C>A	c.(3172-3174)GTC>GTA	p.V1058V		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1058	Filaggrin 6.|Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.321429	642.886649	665.941062	261	551	KEEP	---	---	---	---	capture		Silent	SNP	152284188	152284188	6160	1	G	T	T	T	574	45	FLG	2	2
OR6Y1	391112	broad.mit.edu	37	1	158517140	158517140	+	Silent	SNP	G	C	C	rs114824139	by1000genomes	TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158517140G>C	uc010pil.1	-	c.756C>G	c.(754-756)GTC>GTG	p.V252V		NM_001005189	NP_001005189	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y,	252	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.09375	23.129902	60.267963	21	203	KEEP	---	---	---	---	capture		Silent	SNP	158517140	158517140	11624	1	G	C	C	C	470	37	OR6Y1	3	3
SPTA1	6708	broad.mit.edu	37	1	158636191	158636191	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158636191G>C	uc001fst.1	-	c.2135C>G	c.(2134-2136)TCT>TGT	p.S712C		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	712	Spectrin 8.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.288889	41.986587	43.766612	13	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158636191	158636191	15630	1	G	C	C	C	429	33	SPTA1	3	3
OR6N2	81442	broad.mit.edu	37	1	158746816	158746816	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158746816C>T	uc010pir.1	-	c.610G>A	c.(610-612)GCT>ACT	p.A204T		NM_001005278	NP_001005278	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N,	204	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_hematologic(112;0.0378)													0.118644	5.478311	13.915055	7	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158746816	158746816	11617	1	C	T	T	T	325	25	OR6N2	2	2
ATP1A4	480	broad.mit.edu	37	1	160136342	160136342	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160136342C>A	uc001fve.3	+	c.1072C>A	c.(1072-1074)CGC>AGC	p.R358S	ATP1A4_uc001fvf.3_Non-coding_Transcript|ATP1A4_uc001fvg.2_5'UTR	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	358	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)	2	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.111111	14.289659	35.828498	16	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160136342	160136342	1150	1	C	A	A	A	351	27	ATP1A4	1	1
UFC1	51506	broad.mit.edu	37	1	161123809	161123809	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161123809C>T	uc001fyd.3	+	c.22C>T	c.(22-24)CGT>TGT	p.R8C		NM_016406	NP_057490	Q9Y3C8	UFC1_HUMAN	ubiquitin-fold modifier conjugating enzyme 1	8					protein ufmylation		protein binding|UFM1 conjugating enzyme activity				0	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)											0.16129	38.167588	55.100303	25	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161123809	161123809	17492	1	C	T	T	T	247	19	UFC1	1	1
DDR2	4921	broad.mit.edu	37	1	162748381	162748381	+	Silent	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:162748381T>A	uc001gcf.2	+	c.2295T>A	c.(2293-2295)ACT>ACA	p.T765T	DDR2_uc001gcg.2_Silent_p.T765T	NM_001014796	NP_001014796	Q16832	DDR2_HUMAN	discoidin domain receptor family, member 2	765	Cytoplasmic (Potential).|Protein kinase.				cell adhesion|protein phosphorylation	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(2)|central_nervous_system(2)|ovary(1)|kidney(1)	6	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)			NSCLC(161;314 2006 8283 19651 23192)				497				0.150538	88.762383	132.302464	56	316	KEEP	---	---	---	---	capture		Silent	SNP	162748381	162748381	4508	1	T	A	A	A	678	53	DDR2	3	3
GPA33	10223	broad.mit.edu	37	1	167038228	167038228	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167038228C>T	uc001gea.1	-	c.346G>A	c.(346-348)GAG>AAG	p.E116K		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	116	Ig-like V-type.|Extracellular (Potential).					integral to plasma membrane	receptor activity				0														0.356436	96.568596	98.40364	36	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167038228	167038228	6860	1	C	T	T	T	403	31	GPA33	1	1
NBPF1	55672	broad.mit.edu	37	1	16902974	16902974	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16902974T>A	uc009vos.1	-	c.1907A>T	c.(1906-1908)CAA>CTA	p.Q636L	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Missense_Mutation_p.Q94L|NBPF1_uc010oce.1_Missense_Mutation_p.Q365L	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	636	Potential.					cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)										0.017621	-105.182852	13.966845	8	446	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16902974	16902974	10588	1	T	A	A	A	819	63	NBPF1	3	3
GORAB	92344	broad.mit.edu	37	1	170508612	170508612	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:170508612A>G	uc001gha.2	+	c.398A>G	c.(397-399)AAG>AGG	p.K133R	GORAB_uc009wvw.2_3'UTR|GORAB_uc001ggz.3_Missense_Mutation_p.K133R|GORAB_uc009wvx.2_5'UTR|GORAB_uc001ghb.2_5'UTR|GORAB_uc001ghc.2_5'UTR	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting isoform a	133						Golgi apparatus|nucleus					0														0.318841	75.127569	77.138934	22	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170508612	170508612	6847	1	A	G	G	G	39	3	GORAB	4	4
GORAB	92344	broad.mit.edu	37	1	170513848	170513848	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:170513848C>T	uc001gha.2	+	c.599C>T	c.(598-600)TCC>TTC	p.S200F	GORAB_uc001ggz.3_Missense_Mutation_p.S200F|GORAB_uc009wvx.2_Missense_Mutation_p.S20F|GORAB_uc001ghb.2_Missense_Mutation_p.S20F|GORAB_uc001ghc.2_Missense_Mutation_p.S20F|GORAB_uc001ghd.2_5'UTR	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting isoform a	200	Potential.					Golgi apparatus|nucleus					0														0.101124	5.514236	19.642148	9	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170513848	170513848	6847	1	C	T	T	T	390	30	GORAB	2	2
PADI6	353238	broad.mit.edu	37	1	17723578	17723578	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17723578A>G	uc001bak.1	+	c.1630A>G	c.(1630-1632)AAA>GAA	p.K544E		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	536					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)									0.15	8.072765	12.894099	6	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17723578	17723578	11797	1	A	G	G	G	65	5	PADI6	4	4
PADI6	353238	broad.mit.edu	37	1	17723626	17723626	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17723626G>C	uc001bak.1	+	c.1678G>C	c.(1678-1680)GAA>CAA	p.E560Q		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	552					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)									0.2	30.102111	34.699909	11	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17723626	17723626	11797	1	G	C	C	C	585	45	PADI6	3	3
ARHGEF10L	55160	broad.mit.edu	37	1	17983154	17983154	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17983154G>A	uc001ban.2	+	c.2811G>A	c.(2809-2811)CTG>CTA	p.L937L	ARHGEF10L_uc009vpe.1_Silent_p.L898L|ARHGEF10L_uc001bao.2_Silent_p.L898L|ARHGEF10L_uc001bap.2_Silent_p.L893L|ARHGEF10L_uc001baq.2_Silent_p.L698L|ARHGEF10L_uc010ocs.1_Silent_p.L710L|ARHGEF10L_uc001bar.2_Silent_p.L640L|ARHGEF10L_uc009vpf.2_Non-coding_Transcript	NM_018125	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF)	937					regulation of Rho protein signal transduction	cytoplasm	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)|ovary(1)|pancreas(1)	3		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)										0.183486	33.624363	43.890806	20	89	KEEP	---	---	---	---	capture		Silent	SNP	17983154	17983154	909	1	G	A	A	A	587	46	ARHGEF10L	2	2
KIAA1751	85452	broad.mit.edu	37	1	1897854	1897854	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1897854G>T	uc009vkz.1	-	c.1357C>A	c.(1357-1359)CCC>ACC	p.P453T	KIAA1751_uc001aim.1_Missense_Mutation_p.P453T	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN	hypothetical protein LOC85452	453										pancreas(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)										0.054795	-8.758854	6.498694	4	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1897854	1897854	8567	1	G	T	T	T	546	42	KIAA1751	2	2
UBR4	23352	broad.mit.edu	37	1	19444381	19444381	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19444381A>C	uc001bbi.2	-	c.10565T>G	c.(10564-10566)TTT>TGT	p.F3522C	UBR4_uc001bbj.1_5'UTR	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	3522					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.201493	74.656372	85.745751	27	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19444381	19444381	17462	1	A	C	C	C	13	1	UBR4	4	4
PTPRC	5788	broad.mit.edu	37	1	198665956	198665956	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198665956C>A	uc001gur.1	+	c.210C>A	c.(208-210)ACC>ACA	p.T70T	PTPRC_uc001gus.1_Silent_p.T70T|PTPRC_uc001gut.1_Intron|PTPRC_uc009wze.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron|PTPRC_uc001guu.1_Silent_p.T113T|PTPRC_uc001guv.1_Intron|PTPRC_uc001guw.1_Intron	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	70	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.17931	49.156564	63.192791	26	119	KEEP	---	---	---	---	capture		Silent	SNP	198665956	198665956	13254	1	C	A	A	A	262	21	PTPRC	2	2
CACNA1S	779	broad.mit.edu	37	1	201043678	201043678	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201043678G>T	uc001gvv.2	-	c.2019C>A	c.(2017-2019)GCC>GCA	p.A673A		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	673	Cytoplasmic (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.137255	8.822726	15.291482	7	44	KEEP	---	---	---	---	capture		Silent	SNP	201043678	201043678	2663	1	G	T	T	T	548	43	CACNA1S	2	2
LRRN2	10446	broad.mit.edu	37	1	204588373	204588373	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204588373C>A	uc001hbe.1	-	c.748G>T	c.(748-750)GCC>TCC	p.A250S	MDM4_uc001hbd.1_Intron|LRRN2_uc001hbf.1_Missense_Mutation_p.A250S|LRRN2_uc009xbf.1_Missense_Mutation_p.A250S|MDM4_uc001hbc.2_Intron	NM_006338	NP_006329	O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2 precursor	250	Extracellular (Potential).|LRR 8.				cell adhesion	integral to membrane	receptor activity			central_nervous_system(2)	2	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)											0.159722	35.658043	51.527095	23	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204588373	204588373	9411	1	C	A	A	A	338	26	LRRN2	2	2
KCNH1	3756	broad.mit.edu	37	1	211093022	211093022	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:211093022G>T	uc001hib.2	-	c.1422C>A	c.(1420-1422)GAC>GAA	p.D474E	KCNH1_uc001hic.2_Missense_Mutation_p.D447E	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,	474	Extracellular (Potential).				myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)										0.034826	-36.37155	11.083985	7	194	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	211093022	211093022	8336	1	G	T	T	T	620	48	KCNH1	2	2
ALPL	249	broad.mit.edu	37	1	21902329	21902329	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:21902329C>A	uc001bet.2	+	c.1101C>A	c.(1099-1101)TCC>TCA	p.S367S	ALPL_uc010odn.1_Silent_p.S315S|ALPL_uc010odo.1_Silent_p.S312S|ALPL_uc010odp.1_Silent_p.S290S|ALPL_uc001beu.3_Silent_p.S367S	NM_000478	NP_000469	P05186	PPBT_HUMAN	tissue-nonspecific alkaline phosphatase	367					response to vitamin D|skeletal system development	anchored to membrane|cytoplasm|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(2)|central_nervous_system(2)	4		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)									0.171348	93.906799	130.334292	61	295	KEEP	---	---	---	---	capture		Silent	SNP	21902329	21902329	550	1	C	A	A	A	301	24	ALPL	2	2
OBSCN	84033	broad.mit.edu	37	1	228482094	228482094	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228482094C>T	uc009xez.1	+	c.11373C>T	c.(11371-11373)ACC>ACT	p.T3791T	OBSCN_uc001hsn.2_Silent_p.T3791T|OBSCN_uc001hsq.1_Silent_p.T1047T	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	3791	Ig-like 38.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.173184	61.319354	79.37253	31	148	KEEP	---	---	---	---	capture		Silent	SNP	228482094	228482094	11217	1	C	T	T	T	301	24	OBSCN	2	2
TTC13	79573	broad.mit.edu	37	1	231052046	231052046	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:231052046C>A	uc001huf.3	-	c.1986G>T	c.(1984-1986)CAG>CAT	p.Q662H	TTC13_uc009xfi.2_Missense_Mutation_p.Q609H|TTC13_uc009xfj.2_Non-coding_Transcript|TTC13_uc001hug.3_Splice_Site_SNP_p.F609_splice|TTC13_uc009xfk.1_Splice_Site_SNP_p.F552_splice	NM_024525	NP_078801	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13 isoform a	662							binding			ovary(1)|skin(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)		COAD - Colon adenocarcinoma(196;0.243)										0.151961	47.975559	71.652157	31	173	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231052046	231052046	17234	1	C	A	A	A	260	20	TTC13	2	2
NID1	4811	broad.mit.edu	37	1	236195839	236195839	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236195839C>T	uc001hxo.2	-	c.1399G>A	c.(1399-1401)GGG>AGG	p.G467R	NID1_uc009xgd.2_Missense_Mutation_p.G467R	NM_002508	NP_002499	P14543	NID1_HUMAN	nidogen 1 precursor	467	Nidogen G2 beta-barrel.				bioluminescence|cell-matrix adhesion|protein-chromophore linkage	basement membrane|membrane	calcium ion binding			large_intestine(1)|pancreas(1)	2	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Becaplermin(DB00102)|Urokinase(DB00013)									0.172131	36.896974	49.295451	21	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	236195839	236195839	10815	1	C	T	T	T	299	23	NID1	1	1
EDARADD	128178	broad.mit.edu	37	1	236645937	236645937	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:236645937C>T	uc001hxu.1	+	c.636C>T	c.(634-636)TCC>TCT	p.S212S	EDARADD_uc001hxv.1_Silent_p.S202S	NM_145861	NP_665860	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain isoform A	212					cell differentiation|signal transduction	cytoplasm					0	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)											0.167347	65.407193	91.129403	41	204	KEEP	---	---	---	---	capture		Silent	SNP	236645937	236645937	5093	1	C	T	T	T	262	21	EDARADD	2	2
RYR2	6262	broad.mit.edu	37	1	237895400	237895400	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237895400C>T	uc001hyl.1	+	c.10990C>T	c.(10990-10992)CTA>TTA	p.L3664L	RYR2_uc010pya.1_Silent_p.L60L	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3664					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.121212	5.378866	10.017242	4	29	KEEP	---	---	---	---	capture		Silent	SNP	237895400	237895400	14249	1	C	T	T	T	415	32	RYR2	2	2
MAP1LC3C	440738	broad.mit.edu	37	1	242161853	242161853	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:242161853G>A	uc001hzk.2	-	c.184C>T	c.(184-186)CAG>TAG	p.Q62*		NM_001004343	NP_001004343	Q9BXW4	MLP3C_HUMAN	microtubule-associated protein 1 light chain 3	62					autophagy	autophagic vacuole membrane|cytoplasmic vesicle|endomembrane system|microtubule	protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(106;0.0188)									OREG0014354	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.091549	1.183019	25.047837	13	129	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	242161853	242161853	9616	1	G	A	A	A	598	46	MAP1LC3C	5	2
NLRP3	114548	broad.mit.edu	37	1	247588096	247588096	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247588096C>T	uc001icr.2	+	c.1351C>T	c.(1351-1353)CTG>TTG	p.L451L	NLRP3_uc001ics.2_Silent_p.L451L|NLRP3_uc001icu.2_Silent_p.L451L|NLRP3_uc001icw.2_Silent_p.L451L|NLRP3_uc001icv.2_Silent_p.L451L|NLRP3_uc010pyw.1_Silent_p.L449L|NLRP3_uc001ict.1_Silent_p.L449L	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	451	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)							412				0.184211	29.901686	37.014092	14	62	KEEP	---	---	---	---	capture		Silent	SNP	247588096	247588096	10881	1	C	T	T	T	363	28	NLRP3	2	2
OR2L8	391190	broad.mit.edu	37	1	248112520	248112520	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248112520C>T	uc001idt.1	+	c.361C>T	c.(361-363)CGT>TGT	p.R121C	OR2L13_uc001ids.2_Intron	NM_001001963	NP_001001963	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)											0.183673	86.026901	109.038226	45	200	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248112520	248112520	11415	1	C	T	T	T	403	31	OR2L8	1	1
OR2T33	391195	broad.mit.edu	37	1	248436623	248436623	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248436623G>T	uc010pzi.1	-	c.494C>A	c.(493-495)CCA>CAA	p.P165Q		NM_001004695	NP_001004695	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(1)|ovary(1)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)											0.127517	21.311898	41.482009	19	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248436623	248436623	11430	1	G	T	T	T	611	47	OR2T33	2	2
CSMD2	114784	broad.mit.edu	37	1	33992844	33992844	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:33992844C>A	uc001bxm.1	-	c.10186G>T	c.(10186-10188)GGG>TGG	p.G3396W	CSMD2_uc001bxn.1_Missense_Mutation_p.G3252W	NM_052896	NP_443128	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3252	Extracellular (Potential).					integral to membrane|plasma membrane	protein binding			ovary(5)|pancreas(1)	6		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)												0.153846	28.269733	41.680778	18	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33992844	33992844	4086	1	C	A	A	A	273	21	CSMD2	2	2
C1orf94	84970	broad.mit.edu	37	1	34663245	34663245	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:34663245C>A	uc001bxt.2	+	c.740C>A	c.(739-741)TCC>TAC	p.S247Y	C1orf94_uc001bxs.3_Missense_Mutation_p.S57Y	NM_001134734	NP_001128206	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform a	57							protein binding				0		Myeloproliferative disorder(586;0.0393)												0.17094	30.324815	42.31562	20	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34663245	34663245	2147	1	C	A	A	A	390	30	C1orf94	2	2
TPRG1L	127262	broad.mit.edu	37	1	3542012	3542012	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3542012G>C	uc001akm.2	+	c.226G>C	c.(226-228)GAG>CAG	p.E76Q	TPRG1L_uc009vlj.2_Missense_Mutation_p.E76Q	NM_182752	NP_877429	Q5T0D9	TPRGL_HUMAN	tumor protein p63 regulated 1-like	76						cell junction|synaptic vesicle					0	all_cancers(77;0.0119)|all_epithelial(69;0.00481)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.41e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.83e-22)|GBM - Glioblastoma multiforme(42;4.77e-14)|Colorectal(212;1.12e-05)|COAD - Colon adenocarcinoma(227;5.61e-05)|Kidney(185;0.000351)|BRCA - Breast invasive adenocarcinoma(365;0.000688)|KIRC - Kidney renal clear cell carcinoma(229;0.00553)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.201)										0.333333	13.796162	14.091288	4	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3542012	3542012	16963	1	G	C	C	C	533	41	TPRG1L	3	3
NASP	4678	broad.mit.edu	37	1	46081054	46081054	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46081054C>G	uc001coh.1	+	c.1939C>G	c.(1939-1941)CTG>GTG	p.L647V	NASP_uc001coi.1_Missense_Mutation_p.L645V|NASP_uc001coj.1_Missense_Mutation_p.L306V|NASP_uc010olr.1_Missense_Mutation_p.L581V|NASP_uc001col.1_Missense_Mutation_p.L153V	NM_172164	NP_751896	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein isoform 1	645	Potential.|Glu-rich (acidic).				blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)													0.167883	57.13537	71.452592	23	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46081054	46081054	10568	1	C	G	G	G	259	20	NASP	3	3
TMEM69	51249	broad.mit.edu	37	1	46159007	46159007	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46159007G>C	uc001cor.1	+	c.174G>C	c.(172-174)ATG>ATC	p.M58I		NM_016486	NP_057570	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	58						integral to membrane				ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.181303	342.058194	409.44314	128	578	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46159007	46159007	16737	1	G	C	C	C	585	45	TMEM69	3	3
DMBX1	127343	broad.mit.edu	37	1	46978111	46978112	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:46978111_46978112GG>TT	uc001cpx.2	+	c.1094_1095GG>TT	c.(1093-1095)CGG>CTT	p.R365L	DMBX1_uc001cpw.2_Missense_Mutation_p.R360L	NM_147192	NP_671725	Q8NFW5	DMBX1_HUMAN	diencephalon/mesencephalon homeobox 1 isoform b	365	OAR.				brain development|developmental growth|negative regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.124088	22.901316	41.811036	17	120	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	46978111	46978112	4758	1	GG	TT	TT	TT	507	39	DMBX1	1	1
USP1	7398	broad.mit.edu	37	1	62913035	62913035	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62913035C>G	uc001daj.1	+	c.1273C>G	c.(1273-1275)CTA>GTA	p.L425V	USP1_uc001dak.1_Missense_Mutation_p.L425V|USP1_uc001dal.1_Missense_Mutation_p.L425V	NM_001017415	NP_001017415	O94782	UBP1_HUMAN	ubiquitin specific protease 1	425					DNA repair|monoubiquitinated protein deubiquitination|regulation of DNA repair|response to UV|ubiquitin-dependent protein catabolic process	nucleoplasm	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		Ovarian(122;1846 2315 3982 19504)								0.034091	-13.656602	7.150789	3	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62913035	62913035	17602	1	C	G	G	G	363	28	USP1	3	3
C1orf173	127254	broad.mit.edu	37	1	75065534	75065534	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75065534T>C	uc001dgg.2	-	c.1571A>G	c.(1570-1572)AAT>AGT	p.N524S	C1orf173_uc001dgi.3_Missense_Mutation_p.N318S	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	524	Glu-rich.									ovary(3)|central_nervous_system(1)	4														0.155844	29.151708	37.856919	12	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75065534	75065534	2081	1	T	C	C	C	676	52	C1orf173	4	4
SLC44A3	126969	broad.mit.edu	37	1	95360466	95360466	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:95360466C>T	uc001dqv.3	+	c.1950C>T	c.(1948-1950)GCC>GCT	p.A650A	SLC44A3_uc001dqx.3_Silent_p.A649A|SLC44A3_uc010otq.1_Silent_p.A582A|SLC44A3_uc010otr.1_Silent_p.A614A|SLC44A3_uc001dqw.3_Silent_p.A602A|SLC44A3_uc010ots.1_Silent_p.A570A|SLC44A3_uc009wds.2_Silent_p.A553A|SLC44A3_uc010ott.1_Silent_p.A569A	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1	650						integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)									0.092593	0.129012	9.159085	5	49	KEEP	---	---	---	---	capture		Silent	SNP	95360466	95360466	15134	1	C	T	T	T	262	21	SLC44A3	2	2
SIRPG	55423	broad.mit.edu	37	20	1617103	1617103	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:1617103G>T	uc002wfm.1	-	c.479C>A	c.(478-480)CCT>CAT	p.P160H	SIRPG_uc002wfn.1_Missense_Mutation_p.P160H|SIRPG_uc002wfo.1_Intron	NM_018556	NP_061026	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma isoform 1	160	Extracellular (Potential).|Ig-like C1-type 1.				blood coagulation|cell adhesion|cell junction assembly|cell-cell signaling|intracellular signal transduction|leukocyte migration|negative regulation of cell proliferation|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to membrane|plasma membrane	protein binding			ovary(1)	1														0.226891	57.561967	65.713334	27	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1617103	1617103	14831	20	G	T	T	T	455	35	SIRPG	2	2
C20orf26	26074	broad.mit.edu	37	20	20177420	20177420	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20177420G>T	uc002wru.2	+	c.1797G>T	c.(1795-1797)AAG>AAT	p.K599N	C20orf26_uc010zse.1_Missense_Mutation_p.K579N	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	599										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)										0.160494	21.819393	30.711508	13	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20177420	20177420	2186	20	G	T	T	T	451	35	C20orf26	2	2
SSTR4	6754	broad.mit.edu	37	20	23016165	23016165	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23016165G>T	uc002wsr.2	+	c.45G>T	c.(43-45)CTG>CTT	p.L15L		NM_001052	NP_001043	P31391	SSR4_HUMAN	somatostatin receptor 4	15	Extracellular (Potential).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation	integral to plasma membrane	somatostatin receptor activity				0	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					Esophageal Squamous(15;850 1104 16640)								0.111111	3.571429	8.957392	4	32	KEEP	---	---	---	---	capture		Silent	SNP	23016165	23016165	15716	20	G	T	T	T	600	47	SSTR4	2	2
BPIL1	80341	broad.mit.edu	37	20	31608184	31608184	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:31608184G>T	uc002wyj.2	+	c.1131G>T	c.(1129-1131)GGG>GGT	p.G377G		NM_025227	NP_079503	Q8N4F0	BPIL1_HUMAN	bactericidal/permeability-increasing	377						extracellular region	lipid binding			large_intestine(1)|ovary(1)	2														0.148936	19.183526	30.307318	14	80	KEEP	---	---	---	---	capture		Silent	SNP	31608184	31608184	1519	20	G	T	T	T	522	41	BPIL1	2	2
ITCH	83737	broad.mit.edu	37	20	33001615	33001615	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33001615G>T	uc010geu.1	+	c.405G>T	c.(403-405)TTG>TTT	p.L135F	ITCH_uc002xak.2_Missense_Mutation_p.L135F|ITCH_uc010zuj.1_Missense_Mutation_p.L25F	NM_031483	NP_113671	Q96J02	ITCH_HUMAN	itchy homolog E3 ubiquitin protein ligase	135					apoptosis|entry of virus into host cell|inflammatory response|innate immune response|negative regulation of apoptosis|negative regulation of defense response to virus|negative regulation of JNK cascade|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K29-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cell growth|regulation of protein deubiquitination|response to virus	cytosol|nucleus|plasma membrane	CXCR chemokine receptor binding|ribonucleoprotein binding|ubiquitin-protein ligase activity				0														0.180851	36.113975	45.117221	17	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33001615	33001615	8172	20	G	T	T	T	620	48	ITCH	2	2
ADAM33	80332	broad.mit.edu	37	20	3655230	3655230	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3655230G>T	uc002wit.2	-	c.521C>A	c.(520-522)ACC>AAC	p.T174N	ADAM33_uc002wir.1_Missense_Mutation_p.T174N|ADAM33_uc002wis.2_5'Flank|ADAM33_uc002wiu.2_Missense_Mutation_p.T174N|ADAM33_uc002wiw.1_Intron|ADAM33_uc010gba.1_Intron|ADAM33_uc010gbb.1_Intron|ADAM33_uc002wix.1_Intron|ADAM33_uc010zqg.1_Missense_Mutation_p.T186N|ADAM33_uc010zqh.1_Missense_Mutation_p.T174N	NM_025220	NP_079496	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33 isoform alpha	174	Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			large_intestine(2)|ovary(1)|skin(1)	4														0.206897	121.270903	144.34469	60	230	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3655230	3655230	251	20	G	T	T	T	572	44	ADAM33	2	2
SULF2	55959	broad.mit.edu	37	20	46311847	46311847	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:46311847C>G	uc002xto.2	-	c.955G>C	c.(955-957)GGT>CGT	p.G319R	SULF2_uc002xtr.2_Missense_Mutation_p.G319R|SULF2_uc002xtq.2_Missense_Mutation_p.G319R	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	319					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)	5										709				0.236842	46.211272	51.022261	18	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46311847	46311847	15891	20	C	G	G	G	299	23	SULF2	3	3
PREX1	57580	broad.mit.edu	37	20	47292735	47292735	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47292735G>A	uc002xtw.1	-	c.1661C>T	c.(1660-1662)GCT>GTT	p.A554V		NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	554	DEP 2.				actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)											0.134259	44.450443	72.458806	29	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47292735	47292735	12919	20	G	A	A	A	442	34	PREX1	2	2
KCNB1	3745	broad.mit.edu	37	20	47990014	47990014	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47990014G>T	uc002xur.1	-	c.2083C>A	c.(2083-2085)CTC>ATC	p.L695I	KCNB1_uc002xus.1_Missense_Mutation_p.L695I	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	695	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)											0.15534	22.423312	34.125109	16	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47990014	47990014	8317	20	G	T	T	T	429	33	KCNB1	2	2
CBR3	874	broad.mit.edu	37	21	37518591	37518591	+	Silent	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:37518591G>C	uc002yve.2	+	c.615G>C	c.(613-615)TCG>TCC	p.S205S		NM_001236	NP_001227	O75828	CBR3_HUMAN	carbonyl reductase 3	205					oxidation-reduction process	cytosol|nucleus	carbonyl reductase (NADPH) activity|NADPH binding				0														0.166667	35.80411	44.645746	14	70	KEEP	---	---	---	---	capture		Silent	SNP	37518591	37518591	2828	21	G	C	C	C	470	37	CBR3	3	3
DOPEY2	9980	broad.mit.edu	37	21	37617641	37617641	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:37617641C>T	uc002yvg.2	+	c.3363C>T	c.(3361-3363)GAC>GAT	p.D1121D	DOPEY2_uc011aeb.1_Silent_p.D1070D|DOPEY2_uc002yvh.2_5'UTR	NM_005128	NP_005119	Q9Y3R5	DOP2_HUMAN	pad-1-like	1121					endoplasmic reticulum organization|Golgi to endosome transport|multicellular organismal development|protein transport	Golgi membrane				ovary(1)|central_nervous_system(1)	2														0.170213	36.396381	50.926303	24	117	KEEP	---	---	---	---	capture		Silent	SNP	37617641	37617641	4892	21	C	T	T	T	220	17	DOPEY2	2	2
TRPM2	7226	broad.mit.edu	37	21	45825878	45825878	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:45825878C>A	uc010gpt.1	+	c.2748C>A	c.(2746-2748)ATC>ATA	p.I916I	TRPM2_uc002zet.1_Silent_p.I916I|TRPM2_uc002zeu.1_Silent_p.I916I|TRPM2_uc002zew.1_Silent_p.I916I|TRPM2_uc002zex.1_Silent_p.I702I|TRPM2_uc002zey.1_Silent_p.I429I	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	916	Helical; (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.19708	149.590055	184.781862	81	330	KEEP	---	---	---	---	capture		Silent	SNP	45825878	45825878	17137	21	C	A	A	A	369	29	TRPM2	2	2
FTCD	10841	broad.mit.edu	37	21	47570097	47570097	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47570097G>A	uc002zif.2	-	c.842C>T	c.(841-843)GCG>GTG	p.A281V	FTCD_uc002zig.2_Missense_Mutation_p.A281V|FTCD_uc002zih.2_Missense_Mutation_p.A281V|FTCD_uc010gqf.2_Missense_Mutation_p.A281V|FTCD_uc010gqg.1_Missense_Mutation_p.A150V	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	281	Formiminotransferase C-subdomain (By similarity).				folic acid-containing compound metabolic process|histidine catabolic process	centriole|cytosol|Golgi apparatus	folic acid binding|formimidoyltetrahydrofolate cyclodeaminase activity|glutamate formimidoyltransferase activity			pancreas(1)	1	Breast(49;0.214)			Colorectal(79;0.235)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)									0.190476	7.787275	9.668859	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47570097	47570097	6332	21	G	A	A	A	494	38	FTCD	1	1
DIP2A	23181	broad.mit.edu	37	21	47954024	47954024	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:47954024G>T	uc002zjo.2	+	c.1537G>T	c.(1537-1539)GAG>TAG	p.E513*	DIP2A_uc011afy.1_Nonsense_Mutation_p.E449*|DIP2A_uc011afz.1_Nonsense_Mutation_p.E509*|DIP2A_uc002zjl.2_Nonsense_Mutation_p.E513*|DIP2A_uc002zjm.2_Nonsense_Mutation_p.E513*|DIP2A_uc010gql.2_Nonsense_Mutation_p.E470*|DIP2A_uc002zjn.2_Nonsense_Mutation_p.E513*|DIP2A_uc002zjp.1_Nonsense_Mutation_p.E258*	NM_015151	NP_055966	Q14689	DIP2A_HUMAN	disco-interacting protein 2A isoform a	513					multicellular organismal development	nucleus	catalytic activity|transcription factor binding			ovary(2)	2	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)										0.084746	-3.536389	7.039013	5	54	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47954024	47954024	4706	21	G	T	T	T	585	45	DIP2A	5	2
CCT8L2	150160	broad.mit.edu	37	22	17072677	17072677	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:17072677G>T	uc002zlp.1	-	c.764C>A	c.(763-765)GCA>GAA	p.A255E		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	255					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)												0.232877	113.479779	127.822679	51	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17072677	17072677	3088	22	G	T	T	T	598	46	CCT8L2	2	2
CECR1	51816	broad.mit.edu	37	22	17669245	17669245	+	Missense_Mutation	SNP	G	T	T	rs116020027	by1000genomes	TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:17669245G>T	uc002zmk.1	-	c.1065C>A	c.(1063-1065)TTC>TTA	p.F355L	CECR1_uc010gqu.1_Missense_Mutation_p.F355L|CECR1_uc011agi.1_Missense_Mutation_p.F313L|CECR1_uc002zmj.1_Missense_Mutation_p.F114L	NM_017424	NP_059120	Q9NZK5	CECR1_HUMAN	cat eye syndrome critical region protein 1	355					adenosine catabolic process|multicellular organismal development|purine ribonucleoside monophosphate biosynthetic process	extracellular space|Golgi apparatus	adenosine deaminase activity|adenosine receptor binding|growth factor activity|heparin binding|protein homodimerization activity|proteoglycan binding|zinc ion binding			ovary(1)	1		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)												0.223684	34.932081	40.270169	17	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17669245	17669245	3338	22	G	T	T	T	529	41	CECR1	2	2
PLA2G3	50487	broad.mit.edu	37	22	31534744	31534744	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:31534744G>T	uc003aka.2	-	c.556C>A	c.(556-558)CGC>AGC	p.R186S		NM_015715	NP_056530	Q9NZ20	PA2G3_HUMAN	phospholipase A2, group III precursor	186	Phospholipase A2-like.				cilium morphogenesis|lipid catabolic process|phospholipid metabolic process	centriole|extracellular space|plasma membrane	calcium ion binding|calcium-dependent phospholipase A2 activity				0														0.224044	88.807994	101.599639	41	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31534744	31534744	12426	22	G	T	T	T	507	39	PLA2G3	1	1
SFI1	9814	broad.mit.edu	37	22	32011186	32011186	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:32011186C>A	uc003ale.2	+	c.3221C>A	c.(3220-3222)CCG>CAG	p.P1074Q	SFI1_uc003alf.2_Missense_Mutation_p.P1043Q|SFI1_uc003alg.2_Missense_Mutation_p.P992Q|SFI1_uc011alp.1_Missense_Mutation_p.P980Q|SFI1_uc011alq.1_Missense_Mutation_p.P1019Q|SFI1_uc003alh.2_Non-coding_Transcript|SFI1_uc010gwi.2_Non-coding_Transcript|SFI1_uc003ali.2_Missense_Mutation_p.P166Q|SFI1_uc003alj.2_Missense_Mutation_p.P208Q	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	1074					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1														0.096774	1.327178	6.357969	3	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32011186	32011186	14645	22	C	A	A	A	299	23	SFI1	1	1
ANKRD54	129138	broad.mit.edu	37	22	38229004	38229004	+	Silent	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:38229004A>G	uc003auc.2	-	c.681T>C	c.(679-681)CAT>CAC	p.H227H	ANKRD54_uc003aud.2_Silent_p.H104H	NM_138797	NP_620152	Q6NXT1	ANR54_HUMAN	ankyrin repeat domain 54	227	ANK 4.										0	Melanoma(58;0.045)													0.235849	68.335561	75.087722	25	81	KEEP	---	---	---	---	capture		Silent	SNP	38229004	38229004	688	22	A	G	G	G	102	8	ANKRD54	4	4
SLC9A2	6549	broad.mit.edu	37	2	103274287	103274287	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:103274287G>T	uc002tca.2	+	c.554G>T	c.(553-555)GGG>GTG	p.G185V		NM_003048	NP_003039	Q9UBY0	SL9A2_HUMAN	solute carrier family 9 (sodium/hydrogen	185	Helical; Name=E/M5; (Potential).					integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			central_nervous_system(3)|breast(2)	5														0.125773	65.827868	132.093972	61	424	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103274287	103274287	15209	2	G	T	T	T	559	43	SLC9A2	2	2
CNTNAP5	129684	broad.mit.edu	37	2	125281898	125281898	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125281898G>T	uc010flu.2	+	c.1346G>T	c.(1345-1347)GGC>GTC	p.G449V	CNTNAP5_uc002tno.2_Missense_Mutation_p.G448V	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	448	Laminin G-like 2.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.329787	80.687934	83.104535	31	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125281898	125281898	3788	2	G	T	T	T	546	42	CNTNAP5	2	2
FAM123C	205147	broad.mit.edu	37	2	131519727	131519727	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131519727G>T	uc002trw.2	+	c.82G>T	c.(82-84)GCT>TCT	p.A28S	FAM123C_uc010fmv.2_Missense_Mutation_p.A28S|FAM123C_uc010fms.1_Missense_Mutation_p.A28S|FAM123C_uc010fmt.1_Missense_Mutation_p.A28S|FAM123C_uc010fmu.1_Missense_Mutation_p.A28S	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)										0.157895	4.812373	6.933647	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131519727	131519727	5621	2	G	T	T	T	546	42	FAM123C	2	2
POTEE	445582	broad.mit.edu	37	2	132021567	132021567	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:132021567C>A	uc002tsn.2	+	c.2539C>A	c.(2539-2541)CGT>AGT	p.R847S	PLEKHB2_uc002tsh.2_Intron|POTEE_uc002tsk.2_Missense_Mutation_p.R447S|POTEE_uc002tsl.2_Missense_Mutation_p.R429S|POTEE_uc010fmy.1_Missense_Mutation_p.R311S	NM_001083538	NP_001077007	Q6S8J3	POTEE_HUMAN	protein expressed in prostate, ovary, testis,	847	Actin-like.						ATP binding				0														0.305913	325.64802	338.679873	119	270	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132021567	132021567	12694	2	C	A	A	A	299	23	POTEE	1	1
ZRANB3	84083	broad.mit.edu	37	2	136261918	136261918	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:136261918C>A	uc002tum.2	-	c.142G>T	c.(142-144)GCC>TCC	p.A48S	ZRANB3_uc002tuk.2_5'UTR|ZRANB3_uc002tul.2_Missense_Mutation_p.A48S|ZRANB3_uc002tun.1_Intron	NM_032143	NP_115519	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	48	Helicase ATP-binding.					intracellular	ATP binding|DNA binding|endonuclease activity|helicase activity|zinc ion binding				0				BRCA - Breast invasive adenocarcinoma(221;0.135)										0.077922	-0.81544	13.215888	6	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136261918	136261918	18828	2	C	A	A	A	325	25	ZRANB3	2	2
LRP1B	53353	broad.mit.edu	37	2	141643727	141643727	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141643727C>T	uc002tvj.1	-	c.3944G>A	c.(3943-3945)GGA>GAA	p.G1315E	LRP1B_uc010fnl.1_Missense_Mutation_p.G497E	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1315	Extracellular (Potential).|LDL-receptor class B 9.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		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)		Colon(99;50 2074 2507 20106)			p.G1315V(LCLC103H-Tumor)	2546	TSP Lung(27;0.18)			0.088889	1.062546	8.749234	4	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141643727	141643727	9328	2	C	T	T	T	390	30	LRP1B	2	2
EPC2	26122	broad.mit.edu	37	2	149542282	149542282	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:149542282G>T	uc010zbt.1	+	c.2063G>T	c.(2062-2064)AGC>ATC	p.S688I		NM_015630	NP_056445	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2	688					chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)										0.163934	50.943604	70.575521	30	153	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149542282	149542282	5354	2	G	T	T	T	442	34	EPC2	2	2
SCN3A	6328	broad.mit.edu	37	2	165986747	165986747	+	Silent	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165986747A>T	uc002ucx.2	-	c.2625T>A	c.(2623-2625)ATT>ATA	p.I875I	SCN3A_uc002ucy.2_Silent_p.I826I|SCN3A_uc002ucz.2_Silent_p.I826I|SCN3A_uc002uda.1_Silent_p.I695I|SCN3A_uc002udb.1_Silent_p.I695I	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	875						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.203125	50.676739	61.156127	26	102	KEEP	---	---	---	---	capture		Silent	SNP	165986747	165986747	14400	2	A	T	T	T	60	5	SCN3A	3	3
SCN9A	6335	broad.mit.edu	37	2	167085307	167085307	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:167085307C>A	uc010fpl.2	-	c.4067G>T	c.(4066-4068)CGT>CTT	p.R1356L		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1367	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.03413	-48.914698	20.348909	10	283	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167085307	167085307	14407	2	C	A	A	A	247	19	SCN9A	1	1
SP3	6670	broad.mit.edu	37	2	174820756	174820756	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:174820756T>C	uc002uig.2	-	c.484A>G	c.(484-486)AAT>GAT	p.N162D	SP3_uc002uie.2_Missense_Mutation_p.N94D|SP3_uc002uif.2_Missense_Mutation_p.N109D|SP3_uc010zel.1_Missense_Mutation_p.N159D	NM_003111	NP_003102	Q02447	SP3_HUMAN	Sp3 transcription factor isoform 1	162	Transactivation domain (Gln-rich).				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	protein binding|transcription activator activity|transcription repressor activity|zinc ion binding		EWSR1/SP3(3)	soft_tissue(3)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.185)											0.230126	166.804366	182.755934	55	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	174820756	174820756	15465	2	T	C	C	C	832	64	SP3	4	4
TTN	7273	broad.mit.edu	37	2	179429587	179429587	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179429587A>G	uc010zfg.1	-	c.73568T>C	c.(73567-73569)GTG>GCG	p.V24523A	TTN_uc010zfh.1_Missense_Mutation_p.V18218A|TTN_uc010zfi.1_Missense_Mutation_p.V18151A|TTN_uc010zfj.1_Missense_Mutation_p.V18026A	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	2297										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				0.202703	34.189338	40.259296	15	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179429587	179429587	17290	2	A	G	G	G	78	6	TTN	4	4
TTN	7273	broad.mit.edu	37	2	179449825	179449825	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179449825G>T	uc010zfg.1	-	c.56942C>A	c.(56941-56943)ACT>AAT	p.T18981N	TTN_uc010zfh.1_Missense_Mutation_p.T12676N|TTN_uc010zfi.1_Missense_Mutation_p.T12609N|TTN_uc010zfj.1_Missense_Mutation_p.T12484N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1922										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				0.173804	129.5114	169.426874	69	328	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179449825	179449825	17290	2	G	T	T	T	468	36	TTN	2	2
ZNF804A	91752	broad.mit.edu	37	2	185801222	185801222	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185801222A>T	uc002uph.2	+	c.1099A>T	c.(1099-1101)AAT>TAT	p.N367Y		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	367						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.147059	7.655981	11.722621	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185801222	185801222	18768	2	A	T	T	T	169	13	ZNF804A	3	3
FAM171B	165215	broad.mit.edu	37	2	187626438	187626438	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:187626438C>A	uc002ups.2	+	c.1369C>A	c.(1369-1371)CGG>AGG	p.R457R	FAM171B_uc002upr.1_Silent_p.R424R|FAM171B_uc002upt.2_5'Flank	NM_177454	NP_803237	Q6P995	F171B_HUMAN	KIAA1946	457	Cytoplasmic (Potential).					integral to membrane	DNA binding			ovary(6)|breast(3)|central_nervous_system(1)	10														0.096154	3.236411	11.74014	5	47	KEEP	---	---	---	---	capture		Silent	SNP	187626438	187626438	5697	2	C	A	A	A	399	31	FAM171B	1	1
PMS1	5378	broad.mit.edu	37	2	190719014	190719014	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190719014C>T	uc002urh.3	+	c.1016C>T	c.(1015-1017)CCA>CTA	p.P339L	PMS1_uc010zga.1_Missense_Mutation_p.P300L|PMS1_uc010zgb.1_Missense_Mutation_p.P278L|PMS1_uc002urk.3_Missense_Mutation_p.P300L|PMS1_uc002uri.3_Missense_Mutation_p.P339L|PMS1_uc010zgc.1_Missense_Mutation_p.P163L|PMS1_uc010zgd.1_Missense_Mutation_p.P163L|PMS1_uc002urj.2_Non-coding_Transcript|PMS1_uc010fry.1_Missense_Mutation_p.P300L|PMS1_uc010frz.2_Intron|PMS1_uc002url.2_Missense_Mutation_p.P124L|PMS1_uc002urm.2_Non-coding_Transcript|PMS1_uc002urn.1_Missense_Mutation_p.P7L	NM_000534	NP_000525	P54277	PMS1_HUMAN	postmeiotic segregation 1 isoform a	339					mismatch repair|reciprocal meiotic recombination	MutLalpha complex	ATP binding|ATPase activity|mismatched DNA binding			ovary(2)|kidney(1)|central_nervous_system(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)							236				0.133333	6.878793	10.793296	4	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190719014	190719014	12568	2	C	T	T	T	273	21	PMS1	2	2
MYT1L	23040	broad.mit.edu	37	2	1926245	1926245	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1926245G>T	uc002qxe.2	-	c.1296C>A	c.(1294-1296)ACC>ACA	p.T432T	MYT1L_uc002qxd.2_Silent_p.T432T|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	432					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)										0.208955	85.669232	101.524276	42	159	KEEP	---	---	---	---	capture		Silent	SNP	1926245	1926245	10502	2	G	T	T	T	548	43	MYT1L	2	2
TMEFF2	23671	broad.mit.edu	37	2	193049172	193049172	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:193049172C>A	uc002utc.2	-	c.320G>T	c.(319-321)GGG>GTG	p.G107V	TMEFF2_uc002utd.1_Missense_Mutation_p.G107V	NM_016192	NP_057276	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two	107	Kazal-like 1.|Extracellular (Potential).					extracellular region|integral to membrane				pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			Pancreas(50;1277 1381 28487 47072)								0.210526	7.787961	9.262497	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	193049172	193049172	16544	2	C	A	A	A	286	22	TMEFF2	2	2
SPEG	10290	broad.mit.edu	37	2	220354241	220354241	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220354241C>A	uc010fwg.2	+	c.8501C>A	c.(8500-8502)TCG>TAG	p.S2834*		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2834	Pro-rich.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)						482				0.219895	83.725136	97.676161	42	149	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	220354241	220354241	15548	2	C	A	A	A	403	31	SPEG	5	1
TM4SF20	79853	broad.mit.edu	37	2	228243815	228243815	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228243815C>G	uc002vpb.2	-	c.170G>C	c.(169-171)GGA>GCA	p.G57A		NM_024795	NP_079071	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	57	Helical; (Potential).					integral to membrane|plasma membrane					0		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)										0.163043	38.163981	48.090646	15	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228243815	228243815	16499	2	C	G	G	G	390	30	TM4SF20	3	3
FBXO36	130888	broad.mit.edu	37	2	230861624	230861624	+	Silent	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:230861624A>T	uc010fxi.1	+	c.363A>T	c.(361-363)TCA>TCT	p.S121S	FBXO36_uc002vqa.2_Silent_p.S121S|FBXO36_uc002vqb.2_Silent_p.S90S|FBXO36_uc002vqc.2_Non-coding_Transcript	NM_174899	NP_777559	Q8NEA4	FBX36_HUMAN	F-box protein 36	121	F-box.									ovary(1)	1		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)										0.155844	61.058065	87.184206	36	195	KEEP	---	---	---	---	capture		Silent	SNP	230861624	230861624	5982	2	A	T	T	T	67	6	FBXO36	3	3
NGEF	25791	broad.mit.edu	37	2	233834989	233834989	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:233834989G>T	uc002vts.2	-	c.318C>A	c.(316-318)ATC>ATA	p.I106I		NM_019850	NP_062824	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	106	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42 (By similarity).				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|growth cone|plasma membrane	Rho guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)|skin(1)	7		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)										0.158228	35.258282	52.876281	25	133	KEEP	---	---	---	---	capture		Silent	SNP	233834989	233834989	10794	2	G	T	T	T	525	41	NGEF	2	2
DNMT3A	1788	broad.mit.edu	37	2	25469539	25469539	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:25469539G>A	uc002rgc.2	-	c.1229C>T	c.(1228-1230)GCC>GTC	p.A410V	DNMT3A_uc002rgd.2_Missense_Mutation_p.A410V|DNMT3A_uc010eyi.2_Non-coding_Transcript|DNMT3A_uc002rgb.2_Missense_Mutation_p.A221V	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	410					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(107)|ovary(3)	110	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.025316	-51.330929	7.898457	6	231	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25469539	25469539	4859	2	G	A	A	A	546	42	DNMT3A	2	2
CAD	790	broad.mit.edu	37	2	27465587	27465587	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27465587A>C	uc002rji.2	+	c.6322A>C	c.(6322-6324)AGC>CGC	p.S2108R	CAD_uc010eyw.2_Missense_Mutation_p.S2045R	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	2108	ATCase (Aspartate transcarbamylase).				'de novo' pyrimidine base biosynthetic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|nuclear matrix	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)					653				0.126126	24.530149	39.623494	14	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27465587	27465587	2681	2	A	C	C	C	91	7	CAD	4	4
LTBP1	4052	broad.mit.edu	37	2	33590483	33590483	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33590483G>C	uc002ros.2	+	c.4627G>C	c.(4627-4629)GGC>CGC	p.G1543R	LTBP1_uc002rot.2_Missense_Mutation_p.G1217R|LTBP1_uc002rou.2_Missense_Mutation_p.G1216R|LTBP1_uc002rov.2_Missense_Mutation_p.G1163R|LTBP1_uc010ymz.1_Missense_Mutation_p.G1174R|LTBP1_uc010yna.1_Missense_Mutation_p.G1121R|LTBP1_uc010ynb.1_Missense_Mutation_p.G440R	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	1542	TB 4.				negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity	p.G1543S(1)		ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)												0.179245	41.767145	52.024375	19	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33590483	33590483	9449	2	G	C	C	C	559	43	LTBP1	3	3
SLC8A1	6546	broad.mit.edu	37	2	40656817	40656817	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:40656817G>T	uc002rrx.2	-	c.604C>A	c.(604-606)CGT>AGT	p.R202S	SLC8A1_uc002rry.2_Missense_Mutation_p.R202S|SLC8A1_uc002rrz.2_Missense_Mutation_p.R202S|SLC8A1_uc002rsa.2_Missense_Mutation_p.R202S|SLC8A1_uc002rsd.3_Missense_Mutation_p.R202S|SLC8A1_uc002rsb.1_Missense_Mutation_p.R202S|SLC8A1_uc010fan.1_Missense_Mutation_p.R202S|SLC8A1_uc002rsc.1_Missense_Mutation_p.R202S	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	202	Cytoplasmic (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)									0.235294	29.373492	32.642152	12	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40656817	40656817	15203	2	G	T	T	T	494	38	SLC8A1	1	1
ABCG8	64241	broad.mit.edu	37	2	44079961	44079961	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44079961C>A	uc002rtq.2	+	c.918C>A	c.(916-918)GCC>GCA	p.A306A	ABCG8_uc010yoa.1_Silent_p.A306A	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	306	ABC transporter.|Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|intestinal cholesterol absorption|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)												0.03871	-25.064836	10.551894	6	149	KEEP	---	---	---	---	capture		Silent	SNP	44079961	44079961	73	2	C	A	A	A	262	21	ABCG8	2	2
SOCS5	9655	broad.mit.edu	37	2	46986062	46986062	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:46986062G>T	uc002rvf.2	+	c.393G>T	c.(391-393)AAG>AAT	p.K131N	SOCS5_uc010yoe.1_Missense_Mutation_p.K100N|SOCS5_uc002rvg.2_Missense_Mutation_p.K131N	NM_014011	NP_054730	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	131					cell growth|cytokine-mediated signaling pathway|intracellular signal transduction|negative regulation of signal transduction|negative regulation of T-helper 2 cell differentiation|positive regulation of T-helper 1 cell differentiation|regulation of growth					ovary(1)|central_nervous_system(1)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)											0.243243	37.906596	42.359643	18	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46986062	46986062	15417	2	G	T	T	T	425	33	SOCS5	2	2
MSH6	2956	broad.mit.edu	37	2	48032810	48032810	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48032810G>C	uc002rwd.3	+	c.3610G>C	c.(3610-3612)GCA>CCA	p.A1204P	MSH6_uc010fbj.2_Missense_Mutation_p.A902P|MSH6_uc010yoi.1_Missense_Mutation_p.A1074P|MSH6_uc010yoj.1_Missense_Mutation_p.A902P	NM_000179	NP_000170	P52701	MSH6_HUMAN	mutS homolog 6	1204					determination of adult lifespan|DNA damage response, signal transduction resulting in induction of apoptosis|isotype switching|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|response to UV|somatic hypermutation of immunoglobulin genes	MutSalpha complex	ATP binding|DNA-dependent ATPase activity|protein binding			large_intestine(53)|endometrium(28)|central_nervous_system(27)|stomach(21)|haematopoietic_and_lymphoid_tissue(9)|skin(6)|urinary_tract(5)|lung(5)|ovary(3)|breast(2)|thyroid(1)	160		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)							517				0.223214	71.113195	79.004199	25	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48032810	48032810	10267	2	G	C	C	C	598	46	MSH6	3	3
ANKRD53	79998	broad.mit.edu	37	2	71206297	71206297	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71206297G>A	uc002shl.3	+	c.241G>A	c.(241-243)GCC>ACC	p.A81T	ANKRD53_uc002shk.3_Missense_Mutation_p.A81T|ANKRD53_uc002shm.3_Intron	NM_001115116	NP_001108588	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53 isoform a	81											0														0.085937	-4.459582	17.817038	11	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71206297	71206297	687	2	G	A	A	A	598	46	ANKRD53	2	2
SLC4A5	57835	broad.mit.edu	37	2	74452074	74452074	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74452074G>T	uc002sko.1	-	c.3187C>A	c.(3187-3189)CAG>AAG	p.Q1063K	SLC4A5_uc002skl.2_Non-coding_Transcript|SLC4A5_uc002skn.2_Missense_Mutation_p.Q1047K|SLC4A5_uc010ffc.1_Missense_Mutation_p.Q966K|SLC4A5_uc002skp.1_Missense_Mutation_p.Q945K|SLC4A5_uc002sks.1_Silent_p.P954P	NM_021196	NP_067019	Q9BY07	S4A5_HUMAN	sodium bicarbonate transporter 4 isoform a	1063	Extracellular (Potential).					apical plasma membrane|integral to membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			ovary(5)|central_nervous_system(1)|skin(1)	7														0.128492	24.799749	48.881683	23	156	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74452074	74452074	15154	2	G	T	T	T	611	47	SLC4A5	2	2
POLR1A	25885	broad.mit.edu	37	2	86271325	86271325	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86271325C>T	uc002sqs.2	-	c.3072G>A	c.(3070-3072)CTG>CTA	p.L1024L	POLR1A_uc010ytb.1_Silent_p.L390L|POLR1A_uc002sqt.1_Silent_p.L47L	NM_015425	NP_056240	O95602	RPA1_HUMAN	DNA-directed RNA polymerase I A	1024					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)	2														0.159292	28.131056	40.590268	18	95	KEEP	---	---	---	---	capture		Silent	SNP	86271325	86271325	12637	2	C	T	T	T	262	21	POLR1A	2	2
GOLGB1	2804	broad.mit.edu	37	3	121411082	121411082	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:121411082T>A	uc010hrc.2	-	c.7129A>T	c.(7129-7131)AGG>TGG	p.R2377W	GOLGB1_uc003eei.3_Missense_Mutation_p.R2372W|GOLGB1_uc003eej.3_Missense_Mutation_p.R2338W	NM_004487	NP_004478	Q14789	GOGB1_HUMAN	golgi autoantigen, golgin subfamily b,	2372	Cytoplasmic (Potential).|Potential.				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding			ovary(6)|breast(2)	8				GBM - Glioblastoma multiforme(114;0.0989)										0.196078	42.348875	51.12463	20	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121411082	121411082	6838	3	T	A	A	A	687	53	GOLGB1	3	3
CSTA	1475	broad.mit.edu	37	3	122060408	122060408	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122060408C>T	uc003eex.2	+	c.291C>T	c.(289-291)GGC>GGT	p.G97G		NM_005213	NP_005204	P01040	CYTA_HUMAN	cystatin A	97					keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|nucleus	cysteine-type endopeptidase inhibitor activity|protease binding|protein binding, bridging|structural molecule activity				0				GBM - Glioblastoma multiforme(114;0.155)		Pancreas(26;157 1503 12440)								0.20155	57.515577	68.169823	26	103	KEEP	---	---	---	---	capture		Silent	SNP	122060408	122060408	4122	3	C	T	T	T	353	28	CSTA	2	2
ZXDC	79364	broad.mit.edu	37	3	126180752	126180752	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:126180752C>A	uc003eiv.2	-	c.1753G>T	c.(1753-1755)GGG>TGG	p.G585W	ZXDC_uc010hsh.2_Non-coding_Transcript|ZXDC_uc003eix.2_Missense_Mutation_p.G585W	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	585	Required for transcriptional activation.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)										0.03268	-27.97645	8.451399	5	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126180752	126180752	18857	3	C	A	A	A	299	23	ZXDC	1	1
CPNE4	131034	broad.mit.edu	37	3	131293942	131293942	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:131293942G>C	uc011blq.1	-	c.954C>G	c.(952-954)ATC>ATG	p.I318M	CPNE4_uc003eok.2_Missense_Mutation_p.I300M|CPNE4_uc003eol.2_Missense_Mutation_p.I318M|CPNE4_uc003eom.2_Missense_Mutation_p.I300M	NM_130808	NP_570720	Q96A23	CPNE4_HUMAN	copine IV	300										central_nervous_system(1)	1														0.279279	101.676538	106.539634	31	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131293942	131293942	3952	3	G	C	C	C	577	45	CPNE4	3	3
SHOX2	6474	broad.mit.edu	37	3	157815836	157815836	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:157815836C>T	uc003fbs.2	-	c.1048G>A	c.(1048-1050)GCC>ACC	p.A350T	SHOX2_uc010hvw.2_Missense_Mutation_p.A314T|SHOX2_uc003fbr.2_Missense_Mutation_p.A326T	NM_003030	NP_003021	O60902	SHOX2_HUMAN	short stature homeobox 2 isoform b	326	OAR.				nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0			Lung(72;0.00318)|LUSC - Lung squamous cell carcinoma(72;0.0043)											0.046192	-115.280708	60.707704	37	764	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157815836	157815836	14784	3	C	T	T	T	351	27	SHOX2	1	1
SERPINI2	5276	broad.mit.edu	37	3	167183287	167183287	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:167183287G>T	uc003fes.1	-	c.683C>A	c.(682-684)GCT>GAT	p.A228D	SERPINI2_uc003fer.1_Missense_Mutation_p.A218D|SERPINI2_uc003fet.1_Missense_Mutation_p.A218D	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	218					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			urinary_tract(1)	1														0.236842	20.353287	22.76065	9	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167183287	167183287	14607	3	G	T	T	T	442	34	SERPINI2	2	2
MASP1	5648	broad.mit.edu	37	3	186953530	186953530	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186953530C>A	uc003fri.2	-	c.2129G>T	c.(2128-2130)TGG>TTG	p.W710L	MASP1_uc003frh.1_Intron|MASP1_uc003frj.2_Missense_Mutation_p.W679L	NM_139125	NP_624302	P48740	MASP1_HUMAN	mannan-binding lectin serine protease 1 isoform	690	Peptidase S1.				complement activation, lectin pathway|negative regulation of complement activation|proteolysis	extracellular space	calcium ion binding|calcium-dependent protein binding|protein binding|protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|breast(1)|liver(1)	4	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)										0.066667	-10.0914	13.287737	8	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186953530	186953530	9706	3	C	A	A	A	273	21	MASP1	2	2
ZNF385D	79750	broad.mit.edu	37	3	21552501	21552501	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:21552501G>T	uc003cce.2	-	c.291C>A	c.(289-291)GCC>GCA	p.A97A	ZNF385D_uc010hfb.1_Non-coding_Transcript	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	97	Matrin-type 1.					nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(1)	3														0.179104	21.255301	27.752169	12	55	KEEP	---	---	---	---	capture		Silent	SNP	21552501	21552501	18470	3	G	T	T	T	548	43	ZNF385D	2	2
CHL1	10752	broad.mit.edu	37	3	383704	383704	+	Silent	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:383704T>A	uc003bot.2	+	c.618T>A	c.(616-618)GCT>GCA	p.A206A	CHL1_uc003bou.2_Silent_p.A206A|CHL1_uc003bow.1_Silent_p.A206A|CHL1_uc011asi.1_Silent_p.A206A	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	206	Ig-like C2-type 2.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)						659				0.166667	10.058449	13.21697	5	25	KEEP	---	---	---	---	capture		Silent	SNP	383704	383704	3483	3	T	A	A	A	704	55	CHL1	3	3
CACNA1D	776	broad.mit.edu	37	3	53531424	53531424	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:53531424G>A	uc003dgu.3	+	c.313G>A	c.(313-315)GCC>ACC	p.A105T	CACNA1D_uc003dgv.3_Missense_Mutation_p.A105T|CACNA1D_uc003dgy.3_Missense_Mutation_p.A105T	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	105	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Verapamil(DB00661)									0.248521	91.214123	100.916789	42	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53531424	53531424	2657	3	G	A	A	A	494	38	CACNA1D	1	1
SHQ1	55164	broad.mit.edu	37	3	72890283	72890283	+	Silent	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:72890283G>C	uc003dpf.2	-	c.399C>G	c.(397-399)CCC>CCG	p.P133P	SHQ1_uc010hod.2_Silent_p.P44P	NM_018130	NP_060600	Q6PI26	SHQ1_HUMAN	SHQ1 homolog	133					ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)										0.217391	99.501516	113.049836	40	144	KEEP	---	---	---	---	capture		Silent	SNP	72890283	72890283	14787	3	G	C	C	C	444	35	SHQ1	3	3
PDZRN3	23024	broad.mit.edu	37	3	73433091	73433091	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:73433091G>T	uc003dpl.1	-	c.2626C>A	c.(2626-2628)CAC>AAC	p.H876N	PDZRN3_uc011bgh.1_Missense_Mutation_p.H533N|PDZRN3_uc010hoe.1_Missense_Mutation_p.H574N|PDZRN3_uc011bgf.1_Missense_Mutation_p.H593N|PDZRN3_uc011bgg.1_Missense_Mutation_p.H596N	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	876							ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|pancreas(2)|large_intestine(1)	5		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)										0.178571	56.642105	72.988726	30	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73433091	73433091	12130	3	G	T	T	T	598	46	PDZRN3	2	2
GRM7	2917	broad.mit.edu	37	3	7620535	7620535	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:7620535G>A	uc003bql.2	+	c.1942G>A	c.(1942-1944)GCC>ACC	p.A648T	GRM7_uc011ata.1_Non-coding_Transcript|GRM7_uc011atb.1_Non-coding_Transcript|GRM7_uc010hcf.2_Non-coding_Transcript|GRM7_uc011atc.1_Non-coding_Transcript|GRM7_uc010hcg.2_Missense_Mutation_p.A648T|GRM7_uc003bqm.2_Missense_Mutation_p.A648T|GRM7_uc003bqn.1_Missense_Mutation_p.A231T|GRM7_uc010hch.1_Missense_Mutation_p.A159T	NM_181874	NP_870989	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7 isoform b	648	Helical; Name=2; (Potential).				negative regulation of adenylate cyclase activity|negative regulation of cAMP biosynthetic process|negative regulation of glutamate secretion|sensory perception of smell|sensory perception of sound|synaptic transmission	asymmetric synapse|axon|cell cortex|dendritic shaft|integral to plasma membrane|postsynaptic membrane|presynaptic active zone	adenylate cyclase inhibitor activity|calcium ion binding|glutamate binding|group III metabotropic glutamate receptor activity|PDZ domain binding|serine binding			ovary(4)	4					L-Glutamic Acid(DB00142)									0.060302	-18.271507	21.961907	12	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7620535	7620535	7081	3	G	A	A	A	598	46	GRM7	2	2
SRGAP3	9901	broad.mit.edu	37	3	9055137	9055137	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9055137C>T	uc003brf.1	-	c.2002G>A	c.(2002-2004)GAT>AAT	p.D668N	SRGAP3_uc003brg.1_Missense_Mutation_p.D644N	NM_014850	NP_055665	O43295	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	668	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding		SRGAP3/RAF1(4)	central_nervous_system(4)|urinary_tract(1)|breast(1)	6				OV - Ovarian serous cystadenocarcinoma(96;0.0563)										0.202247	35.292209	42.630878	18	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9055137	9055137	15661	3	C	T	T	T	377	29	SRGAP3	2	2
OR5H2	79310	broad.mit.edu	37	3	98002178	98002178	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:98002178G>T	uc003dsj.1	+	c.447G>T	c.(445-447)CTG>CTT	p.L149L		NM_001005482	NP_001005482	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H,	149	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3														0.209302	21.249896	24.614346	9	34	KEEP	---	---	---	---	capture		Silent	SNP	98002178	98002178	11572	3	G	T	T	T	613	48	OR5H2	2	2
C4orf21	55345	broad.mit.edu	37	4	113541279	113541279	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113541279C>A	uc003iau.2	-	c.230G>T	c.(229-231)GGA>GTA	p.G77V	C4orf21_uc003iaw.2_Missense_Mutation_p.G77V	NM_018392	NP_060862	Q6ZU11	YD002_HUMAN	prematurely terminated mRNA decay factor-like	Error:Variant_position_missing_in_Q6ZU11_after_alignment						integral to membrane	zinc ion binding				0		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)										0.135135	11.493252	21.050677	10	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113541279	113541279	2349	4	C	A	A	A	390	30	C4orf21	2	2
SPATA5	166378	broad.mit.edu	37	4	123850195	123850195	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:123850195G>T	uc003iez.3	+	c.289G>T	c.(289-291)GTG>TTG	p.V97L	SPATA5_uc003iey.2_Missense_Mutation_p.V96L	NM_145207	NP_660208	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	97					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrion	ATP binding|nucleoside-triphosphatase activity				0														0.130435	3.52816	6.568906	3	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123850195	123850195	15521	4	G	T	T	T	572	44	SPATA5	2	2
INTU	27152	broad.mit.edu	37	4	128637582	128637582	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:128637582A>T	uc003ifk.1	+	c.2820A>T	c.(2818-2820)TTA>TTT	p.L940F	INTU_uc011cgq.1_Non-coding_Transcript	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6	940										ovary(1)	1														0.222222	20.92792	24.121676	10	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128637582	128637582	8087	4	A	T	T	T	167	13	INTU	3	3
PCDH10	57575	broad.mit.edu	37	4	134073607	134073607	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:134073607G>C	uc003iha.2	+	c.2312G>C	c.(2311-2313)TGT>TCT	p.C771S	PCDH10_uc003igz.2_Missense_Mutation_p.C771S	NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	771	Cys-rich.|Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(193;0.227)										0.15	6.911633	9.26011	3	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134073607	134073607	11927	4	G	C	C	C	624	48	PCDH10	3	3
PPID	5481	broad.mit.edu	37	4	159638256	159638256	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:159638256C>A	uc003iqc.2	-	c.430G>T	c.(430-432)GGG>TGG	p.G144W		NM_005038	NP_005029	Q08752	PPID_HUMAN	peptidylprolyl isomerase D	144	PPIase cyclophilin-type.				protein folding	cytoplasm|intermediate filament cytoskeleton	cyclosporin A binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)										0.02907	-33.585455	8.37917	5	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159638256	159638256	12756	4	C	A	A	A	273	21	PPID	2	2
TRIM60	166655	broad.mit.edu	37	4	165961743	165961743	+	Silent	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:165961743A>G	uc003iqy.1	+	c.519A>G	c.(517-519)AAA>AAG	p.K173K	TRIM60_uc010iqx.1_Silent_p.K173K	NM_152620	NP_689833	Q495X7	TRI60_HUMAN	ring finger protein 129	173	Potential.					intracellular	zinc ion binding			skin(1)	1	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)										0.128205	18.331536	28.806194	10	68	KEEP	---	---	---	---	capture		Silent	SNP	165961743	165961743	17081	4	A	G	G	G	11	1	TRIM60	4	4
KLB	152831	broad.mit.edu	37	4	39439587	39439587	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:39439587C>A	uc003gua.2	+	c.1577C>A	c.(1576-1578)TCC>TAC	p.S526Y	KLB_uc011byj.1_Missense_Mutation_p.S526Y	NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta	526	Extracellular (Potential).|Glycosyl hydrolase-1 2.				carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1														0.192308	19.341805	23.923976	10	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39439587	39439587	8644	4	C	A	A	A	390	30	KLB	2	2
GABRA2	2555	broad.mit.edu	37	4	46390663	46390663	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46390663C>A	uc003gxc.3	-	c.61G>T	c.(61-63)GAC>TAC	p.D21Y	GABRA2_uc010igc.2_Missense_Mutation_p.D21Y|GABRA2_uc011bzc.1_5'UTR|GABRA2_uc003gxe.2_Missense_Mutation_p.D21Y|GABRA2_uc010igd.1_Missense_Mutation_p.D21Y	NM_001114175	NP_001107647	P47869	GBRA2_HUMAN	gamma-aminobutyric acid A receptor, alpha 2	21					gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels	cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)									0.114035	10.285659	27.044233	13	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46390663	46390663	6412	4	C	A	A	A	390	30	GABRA2	2	2
CEP135	9662	broad.mit.edu	37	4	56878095	56878095	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:56878095A>T	uc003hbi.2	+	c.2746A>T	c.(2746-2748)ACT>TCT	p.T916S	CEP135_uc003hbj.2_Missense_Mutation_p.T622S	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	916	Potential.				centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Glioma(25;0.08)|all_neural(26;0.101)													0.134146	15.572908	26.216256	11	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56878095	56878095	3380	4	A	T	T	T	78	6	CEP135	3	3
JAKMIP1	152789	broad.mit.edu	37	4	6086641	6086641	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:6086641C>A	uc010idb.1	-	c.886G>T	c.(886-888)GAA>TAA	p.E296*	JAKMIP1_uc010idc.1_Nonsense_Mutation_p.E131*|JAKMIP1_uc010idd.1_Nonsense_Mutation_p.E296*|JAKMIP1_uc003giu.3_Nonsense_Mutation_p.E296*|JAKMIP1_uc011bwc.1_Nonsense_Mutation_p.E131*|JAKMIP1_uc003giv.3_Nonsense_Mutation_p.E296*|JAKMIP1_uc010ide.2_Nonsense_Mutation_p.E296*	NM_001099433	NP_001092903	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein	296	Potential.|Mediates association with microtubules.				protein transport	cytoplasm|membrane|microtubule|peripheral to membrane of membrane fraction|ribonucleoprotein complex	GABA receptor binding|RNA binding	p.E296K(1)		large_intestine(1)|ovary(1)|pancreas(1)	3														0.197002	187.400796	227.369546	92	375	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	6086641	6086641	8244	4	C	A	A	A	377	29	JAKMIP1	5	2
TMPRSS11D	9407	broad.mit.edu	37	4	68699042	68699042	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68699042G>T	uc003hdq.2	-	c.572C>A	c.(571-573)ACT>AAT	p.T191N	LOC550112_uc003hdl.3_Intron|TMPRSS11D_uc003hdp.2_De_novo_Start_OutOfFrame|TMPRSS11D_uc011caj.1_Missense_Mutation_p.T74N	NM_004262	NP_004253	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	191	Peptidase S1.|Extracellular (Potential).				proteolysis|respiratory gaseous exchange	extracellular region|integral to plasma membrane	serine-type endopeptidase activity			ovary(1)	1														0.122449	26.116149	53.435823	24	172	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68699042	68699042	16782	4	G	T	T	T	468	36	TMPRSS11D	2	2
UGT2B28	54490	broad.mit.edu	37	4	70156378	70156378	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70156378G>T	uc003hej.2	+	c.1159G>T	c.(1159-1161)GGG>TGG	p.G387W	UGT2B28_uc010ihr.2_Intron	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	387					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0					Flunitrazepam(DB01544)									0.119565	11.95466	25.028269	11	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70156378	70156378	17518	4	G	T	T	T	611	47	UGT2B28	2	2
EREG	2069	broad.mit.edu	37	4	75246765	75246765	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:75246765G>A	uc003hie.1	+	c.189G>A	c.(187-189)GTG>GTA	p.V63V	EREG_uc003hid.2_Silent_p.V57V	NM_001432	NP_001423	O14944	EREG_HUMAN	epiregulin preproprotein	63	Extracellular (Potential).				angiogenesis|cell-cell signaling|cytokine-mediated signaling pathway|epidermal growth factor receptor signaling pathway|female meiosis|keratinocyte differentiation|keratinocyte proliferation|luteinizing hormone signaling pathway|mRNA transcription|negative regulation of epithelial cell proliferation|negative regulation of smooth muscle cell differentiation|negative regulation of transcription, DNA-dependent|oocyte maturation|organ morphogenesis|ovarian cumulus expansion|ovulation|positive regulation of cell division|positive regulation of cytokine production|positive regulation of DNA replication|positive regulation of epidermal growth factor receptor activity|positive regulation of fibroblast proliferation|positive regulation of innate immune response|positive regulation of interleukin-6 biosynthetic process|positive regulation of mitosis|positive regulation of phosphorylation|positive regulation of smooth muscle cell proliferation|primary follicle stage|wound healing	extracellular space|integral to plasma membrane	epidermal growth factor receptor binding|growth factor activity			breast(1)	1			Lung(101;0.196)											0.216783	63.638001	74.227186	31	112	KEEP	---	---	---	---	capture		Silent	SNP	75246765	75246765	5413	4	G	A	A	A	613	48	EREG	2	2
FRAS1	80144	broad.mit.edu	37	4	79343066	79343066	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79343066G>A	uc003hlb.2	+	c.4590G>A	c.(4588-4590)ACG>ACA	p.T1530T	FRAS1_uc003hkw.2_Silent_p.T1530T|FRAS1_uc010ijj.1_Intron	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	1529	CSPG 4.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.133094	45.490117	81.823656	37	241	KEEP	---	---	---	---	capture		Silent	SNP	79343066	79343066	6288	4	G	A	A	A	483	38	FRAS1	1	1
LOX	4015	broad.mit.edu	37	5	121413408	121413408	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:121413408G>A	uc003ksu.2	-	c.273C>T	c.(271-273)ATC>ATT	p.I91I	LOX_uc010jcq.2_5'Flank|LOX_uc011cwk.1_5'Flank|LOX_uc010jcr.2_5'Flank	NM_002317	NP_002308	P28300	LYOX_HUMAN	lysyl oxidase preproprotein	91					oxidation-reduction process|protein modification process	extracellular space	copper ion binding|protein-lysine 6-oxidase activity			lung(1)	1		all_cancers(142;0.0124)|Prostate(80;0.0322)|Ovarian(225;0.0814)|Breast(839;0.143)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;2.14e-11)|OV - Ovarian serous cystadenocarcinoma(64;7.87e-10)|all cancers(49;2.49e-09)|COAD - Colon adenocarcinoma(49;0.02)										0.266667	9.291864	10.030634	4	11	KEEP	---	---	---	---	capture		Silent	SNP	121413408	121413408	9270	5	G	A	A	A	525	41	LOX	2	2
DNAH5	1767	broad.mit.edu	37	5	13885124	13885124	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:13885124T>A	uc003jfd.2	-	c.2957A>T	c.(2956-2958)CAT>CTT	p.H986L		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	986	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.114679	33.532003	65.415368	25	193	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13885124	13885124	4787	5	T	A	A	A	663	51	DNAH5	3	3
PCDHB11	56125	broad.mit.edu	37	5	140581684	140581684	+	Silent	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140581684T>C	uc003liy.2	+	c.2337T>C	c.(2335-2337)CTT>CTC	p.L779L	PCDHB11_uc011daj.1_Silent_p.L414L	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	779	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.21519	82.973828	94.797682	34	124	KEEP	---	---	---	---	capture		Silent	SNP	140581684	140581684	11956	5	T	C	C	C	808	63	PCDHB11	4	4
PCDHB12	56124	broad.mit.edu	37	5	140590616	140590616	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140590616C>A	uc003liz.2	+	c.2137C>A	c.(2137-2139)CTG>ATG	p.L713M	PCDHB12_uc011dak.1_Missense_Mutation_p.L376M|PCDHB13_uc003lja.1_5'Flank	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	713	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.467626	341.185394	341.447864	130	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140590616	140590616	11957	5	C	A	A	A	363	28	PCDHB12	2	2
FAT2	2196	broad.mit.edu	37	5	150946774	150946774	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150946774G>A	uc003lue.3	-	c.1719C>T	c.(1717-1719)ATC>ATT	p.I573I	GM2A_uc011dcs.1_Intron|FAT2_uc010jhx.1_Silent_p.I573I	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	573	Extracellular (Potential).|Cadherin 5.				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.336207	101.464181	104.229616	39	77	KEEP	---	---	---	---	capture		Silent	SNP	150946774	150946774	5926	5	G	A	A	A	525	41	FAT2	2	2
G3BP1	10146	broad.mit.edu	37	5	151179556	151179556	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:151179556G>T	uc003lun.2	+	c.950G>T	c.(949-951)AGA>ATA	p.R317I	G3BP1_uc003lum.2_Missense_Mutation_p.R317I|G3BP1_uc011dcu.1_Missense_Mutation_p.R135I|G3BP1_uc010jhz.2_Missense_Mutation_p.R135I|G3BP1_uc003luq.2_5'UTR	NM_005754	NP_005745	Q13283	G3BP1_HUMAN	Ras-GTPase-activating protein SH3-domain-binding	317					Ras protein signal transduction|transport	cytosol|nucleus|plasma membrane	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|endonuclease activity|protein binding|RNA binding			ovary(1)	1		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)											0.157895	4.210658	6.334138	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151179556	151179556	6392	5	G	T	T	T	429	33	G3BP1	2	2
SGCD	6444	broad.mit.edu	37	5	155935668	155935668	+	Nonsense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:155935668G>T	uc003lwc.3	+	c.250G>T	c.(250-252)GAA>TAA	p.E84*	SGCD_uc003lwa.1_Nonsense_Mutation_p.E84*|SGCD_uc003lwb.2_Nonsense_Mutation_p.E84*|SGCD_uc003lwd.3_Nonsense_Mutation_p.E83*	NM_000337	NP_000328	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 1	83	Extracellular (Potential).				cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.28	17.313086	18.401898	7	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	155935668	155935668	14692	5	G	T	T	T	585	45	SGCD	5	2
HAVCR1	26762	broad.mit.edu	37	5	156469690	156469690	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156469690C>A	uc010jij.1	-	c.785G>T	c.(784-786)GGG>GTG	p.G262V	HAVCR1_uc011ddl.1_Missense_Mutation_p.G93V|HAVCR1_uc003lwi.2_Missense_Mutation_p.G262V	NM_001099414	NP_001092884	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	257	Extracellular (Potential).				interspecies interaction between organisms	integral to membrane	receptor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.262295	72.716185	78.97685	32	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156469690	156469690	7255	5	C	A	A	A	286	22	HAVCR1	2	2
RGS14	10636	broad.mit.edu	37	5	176799028	176799028	+	Silent	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176799028C>T	uc003mgf.2	+	c.1653C>T	c.(1651-1653)GCC>GCT	p.A551A	RGS14_uc003mgh.2_Silent_p.A399A|RGS14_uc003mgi.2_Silent_p.A322A|RGS14_uc003mgj.2_Non-coding_Transcript	NM_006480	NP_006471	O43566	RGS14_HUMAN	regulator of G-protein signalling 14	551					chromosome segregation|long-term memory|long-term synaptic potentiation|negative regulation of ERK1 and ERK2 cascade|negative regulation of MAP kinase activity|negative regulation of synaptic plasticity|nucleocytoplasmic transport|platelet-derived growth factor receptor signaling pathway|positive regulation of neurogenesis|regulation of G-protein coupled receptor protein signaling pathway|regulation of transcription in response to stress|response to oxidative stress|spindle organization|visual learning|zygote asymmetric cell division	centrosome|dendritic spine|nuclear body|plasma membrane|postsynaptic density|spindle pole	GDP-dissociation inhibitor activity|GTPase activator activity|microtubule binding|receptor signaling complex scaffold activity|receptor signaling protein activity			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			NSCLC(47;353 1896 28036)								0.021113	-117.9298	15.780828	11	510	KEEP	---	---	---	---	capture		Silent	SNP	176799028	176799028	13771	5	C	T	T	T	275	22	RGS14	2	2
NPR3	4883	broad.mit.edu	37	5	32739117	32739117	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32739117G>T	uc003jhv.2	+	c.1040G>T	c.(1039-1041)GGG>GTG	p.G347V	NPR3_uc010iuo.2_Missense_Mutation_p.G131V|NPR3_uc011cnz.1_Missense_Mutation_p.G131V|NPR3_uc003jhu.2_Missense_Mutation_p.G347V	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase	347	Extracellular (Potential).				diuresis|osteoclast proliferation|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)									0.141667	21.287762	36.160962	17	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32739117	32739117	11001	5	G	T	T	T	559	43	NPR3	2	2
C5orf34	375444	broad.mit.edu	37	5	43509410	43509410	+	Missense_Mutation	SNP	T	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43509410T>C	uc003jnz.1	-	c.32A>G	c.(31-33)GAA>GGA	p.E11G	C5orf34_uc011cpx.1_Intron	NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444	11										breast(1)	1	Lung NSC(6;2.07e-05)													0.15942	26.993208	34.605611	11	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43509410	43509410	2391	5	T	C	C	C	806	62	C5orf34	4	4
EXOC3	11336	broad.mit.edu	37	5	458042	458042	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:458042G>C	uc003jba.2	+	c.1192G>C	c.(1192-1194)GCG>CCG	p.A398P		NM_007277	NP_009208	O60645	EXOC3_HUMAN	Sec6 protein	409					exocytosis|protein transport						0		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)											0.185185	13.058107	15.56726	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	458042	458042	5496	5	G	C	C	C	442	34	EXOC3	3	3
ADCY2	108	broad.mit.edu	37	5	7709407	7709407	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7709407C>A	uc003jdz.1	+	c.1485C>A	c.(1483-1485)ACC>ACA	p.T495T	ADCY2_uc011cmo.1_Silent_p.T315T	NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	495	Cytoplasmic (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	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)	6														0.107143	4.208413	12.786669	6	50	KEEP	---	---	---	---	capture		Silent	SNP	7709407	7709407	295	5	C	A	A	A	275	22	ADCY2	2	2
DDO	8528	broad.mit.edu	37	6	110714106	110714106	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:110714106C>A	uc003puc.2	-	c.982G>T	c.(982-984)GTA>TTA	p.V328L	C6orf186_uc003pub.2_Intron|DDO_uc003pud.2_Missense_Mutation_p.V269L	NM_003649	NP_003640	Q99489	OXDD_HUMAN	D-aspartate oxidase isoform a	300					aspartate catabolic process|oxidation-reduction process	peroxisome	binding|D-amino-acid oxidase activity|D-aspartate oxidase activity			ovary(2)|breast(1)	3		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)										0.190476	54.233442	65.512359	24	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110714106	110714106	4505	6	C	A	A	A	221	17	DDO	2	2
GJA1	2697	broad.mit.edu	37	6	121768009	121768009	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:121768009G>A	uc003pyr.2	+	c.16G>A	c.(16-18)GCC>ACC	p.A6T	GJA1_uc011ebo.1_5'UTR|GJA1_uc011ebp.1_5'UTR	NM_000165	NP_000156	P17302	CXA1_HUMAN	connexin 43	6	Cytoplasmic (Potential).				cell-cell signaling|cellular membrane organization|gap junction assembly|heart development|muscle contraction|positive regulation of I-kappaB kinase/NF-kappaB cascade	connexon complex|Golgi-associated vesicle membrane|integral to plasma membrane|membrane raft	ion transmembrane transporter activity|signal transducer activity			ovary(2)	2				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)									0.028169	-42.804119	9.418162	6	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121768009	121768009	6668	6	G	A	A	A	494	38	GJA1	1	1
THEMIS	387357	broad.mit.edu	37	6	128134714	128134714	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:128134714C>A	uc011ebt.1	-	c.1072G>T	c.(1072-1074)GCT>TCT	p.A358S	THEMIS_uc010kfa.2_Missense_Mutation_p.A261S|THEMIS_uc003qbi.2_Missense_Mutation_p.A358S|THEMIS_uc010kfb.2_Missense_Mutation_p.A323S	NM_001010923	NP_001010923	Q8N1K5	THMS1_HUMAN	thymocyte selection pathway associated isoform	358	CABIT 2.				negative T cell selection|positive T cell selection|T cell receptor signaling pathway	cytoplasm|nucleus				ovary(2)	2														0.22	51.69203	58.917605	22	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128134714	128134714	16388	6	C	A	A	A	351	27	THEMIS	1	1
TAAR5	9038	broad.mit.edu	37	6	132910429	132910429	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:132910429G>T	uc003qdk.2	-	c.397C>A	c.(397-399)CAC>AAC	p.H133N		NM_003967	NP_003958	O14804	TAAR5_HUMAN	trace amine associated receptor 5	133	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity				0	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)										0.346667	71.123702	72.682086	26	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132910429	132910429	16012	6	G	T	T	T	611	47	TAAR5	2	2
C6orf118	168090	broad.mit.edu	37	6	165715670	165715670	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165715670C>A	uc003qum.3	-	c.141G>T	c.(139-141)CGG>CGT	p.R47R	C6orf118_uc011egi.1_Non-coding_Transcript	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	47											0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)										0.310976	124.853644	130.079395	51	113	KEEP	---	---	---	---	capture		Silent	SNP	165715670	165715670	2425	6	C	A	A	A	327	26	C6orf118	2	2
PDE10A	10846	broad.mit.edu	37	6	165808673	165808673	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165808673G>C	uc003quo.2	-	c.1502C>G	c.(1501-1503)TCC>TGC	p.S501C	PDE10A_uc011egj.1_Non-coding_Transcript|PDE10A_uc011egk.1_Missense_Mutation_p.S421C|PDE10A_uc003qun.2_Missense_Mutation_p.S491C	NM_001130690	NP_001124162	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 1	491					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)	3		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	Esophageal Squamous(22;308 615 5753 12038 40624)								0.208333	14.260961	16.151895	5	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165808673	165808673	12051	6	G	C	C	C	533	41	PDE10A	3	3
KIF13A	63971	broad.mit.edu	37	6	17817465	17817465	+	Splice_Site_SNP	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:17817465C>A	uc003ncg.3	-	c.1787_splice	c.e17-1	p.D596_splice	KIF13A_uc003ncf.2_Splice_Site_SNP_p.D596_splice|KIF13A_uc003nch.3_Splice_Site_SNP_p.D596_splice|KIF13A_uc003nci.3_Splice_Site_SNP_p.D596_splice|KIF13A_uc003ncj.2_Splice_Site_SNP_p.D272_splice	NM_022113	NP_071396			kinesin family member 13A isoform a						cargo loading into vesicle|cell cycle|cytokinesis|endosome to lysosome transport|Golgi to plasma membrane protein transport|melanosome organization|plus-end-directed vesicle transport along microtubule	centrosome|endosome membrane|microtubule|midbody|trans-Golgi network membrane	ATP binding|microtubule motor activity|protein binding			large_intestine(2)|ovary(2)	4	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)											0.204225	57.985724	69.524835	29	113	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	17817465	17817465	8585	6	C	A	A	A	416	32	KIF13A	5	2
IRF4	3662	broad.mit.edu	37	6	394900	394900	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:394900G>A	uc003msz.3	+	c.296G>A	c.(295-297)TGC>TAC	p.C99Y	IRF4_uc010jne.1_Missense_Mutation_p.C99Y|IRF4_uc003mta.3_Non-coding_Transcript|IRF4_uc003mtb.3_Missense_Mutation_p.C99Y|IRF4_uc003mtc.1_5'Flank	NM_002460	NP_002451	Q15306	IRF4_HUMAN	interferon regulatory factor 4	99	IRF tryptophan pentad repeat.				interferon-gamma-mediated signaling pathway|positive regulation of interleukin-10 biosynthetic process|positive regulation of interleukin-13 biosynthetic process|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|regulation of T-helper cell differentiation|T cell activation|type I interferon-mediated signaling pathway	cytoplasm	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding			ovary(1)	1		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)						223				0.123894	26.22938	57.515738	28	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	394900	394900	8135	6	G	A	A	A	598	46	IRF4	2	2
C6orf138	442213	broad.mit.edu	37	6	47846409	47846409	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:47846409A>T	uc011dwm.1	-	c.2120T>A	c.(2119-2121)TTC>TAC	p.F707Y	C6orf138_uc011dwn.1_Missense_Mutation_p.F471Y	NM_001013732	NP_001013754	Q6ZW05	CF138_HUMAN	hypothetical protein LOC442213	724	Helical; (Potential).					integral to membrane	hedgehog receptor activity			central_nervous_system(1)	1														0.276596	29.553197	31.666109	13	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47846409	47846409	2435	6	A	T	T	T	117	9	C6orf138	3	3
HUS1B	135458	broad.mit.edu	37	6	656684	656684	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:656684C>G	uc003mtg.2	-	c.261G>C	c.(259-261)CTG>CTC	p.L87L	EXOC2_uc003mtd.2_Intron|EXOC2_uc003mte.2_Intron|EXOC2_uc011dho.1_Intron	NM_148959	NP_683762	Q8NHY5	HUS1B_HUMAN	HUS1 checkpoint protein B	87											0	Ovarian(93;0.0733)	Breast(5;0.00139)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.041)|BRCA - Breast invasive adenocarcinoma(62;0.0965)										0.25	13.264786	14.401561	5	15	KEEP	---	---	---	---	capture		Silent	SNP	656684	656684	7760	6	C	G	G	G	210	17	HUS1B	3	3
EYS	346007	broad.mit.edu	37	6	66205086	66205086	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:66205086G>T	uc011dxu.1	-	c.218C>A	c.(217-219)GCT>GAT	p.A73D	EYS_uc003peq.2_Missense_Mutation_p.A73D|EYS_uc003per.1_Missense_Mutation_p.A73D|EYS_uc010kaj.1_Non-coding_Transcript	NM_001142800	NP_001136272	Q5T1H1	EYS_HUMAN	eyes shut homolog isoform 1	73					response to stimulus|visual perception	extracellular region	calcium ion binding			ovary(1)	1														0.230769	59.756215	67.535077	27	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66205086	66205086	5526	6	G	T	T	T	442	34	EYS	2	2
RELN	5649	broad.mit.edu	37	7	103193923	103193923	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103193923G>A	uc003vca.2	-	c.6057C>T	c.(6055-6057)ACC>ACT	p.T2019T	RELN_uc010liz.2_Silent_p.T2019T	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	2019					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.252525	56.2184	61.732279	25	74	KEEP	---	---	---	---	capture		Silent	SNP	103193923	103193923	13689	7	G	A	A	A	600	47	RELN	2	2
SRPK2	6733	broad.mit.edu	37	7	104767464	104767464	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:104767464C>A	uc003vcv.2	-	c.1798G>T	c.(1798-1800)GGG>TGG	p.G600W	SRPK2_uc003vct.2_Missense_Mutation_p.G589W|SRPK2_uc003vcu.2_Missense_Mutation_p.G589W|SRPK2_uc003vcs.1_Non-coding_Transcript	NM_182692	NP_872634	P78362	SRPK2_HUMAN	serine/arginine-rich protein-specific kinase 2	589	Protein kinase.				angiogenesis|cell differentiation|innate immune response|intracellular protein kinase cascade|negative regulation of viral genome replication|nuclear speck organization|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene expression|positive regulation of neuron apoptosis|positive regulation of viral genome replication|protein phosphorylation|spliceosome assembly	cytoplasm|nucleolus	14-3-3 protein binding|ATP binding|magnesium ion binding|protein serine/threonine kinase activity			central_nervous_system(3)|ovary(2)	5										326				0.098361	9.898946	39.451914	18	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104767464	104767464	15674	7	C	A	A	A	273	21	SRPK2	2	2
LRRN3	54674	broad.mit.edu	37	7	110764808	110764808	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:110764808C>A	uc003vft.3	+	c.1980C>A	c.(1978-1980)AGC>AGA	p.S660R	IMMP2L_uc003vfq.1_Intron|IMMP2L_uc010ljr.1_Intron|IMMP2L_uc003vfr.2_Intron|LRRN3_uc003vfu.3_Missense_Mutation_p.S660R|LRRN3_uc003vfs.3_Missense_Mutation_p.S660R	NM_001099660	NP_001093130	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3 precursor	660	Cytoplasmic (Potential).					integral to membrane				ovary(2)|pancreas(2)|central_nervous_system(1)	5				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)										0.274336	74.959918	80.155828	31	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110764808	110764808	9412	7	C	A	A	A	363	28	LRRN3	2	2
PLXNA4	91584	broad.mit.edu	37	7	131908295	131908295	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:131908295C>A	uc003vra.3	-	c.2088G>T	c.(2086-2088)AAG>AAT	p.K696N		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	696	PSI 2.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.179487	13.425775	17.176503	7	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131908295	131908295	12548	7	C	A	A	A	363	28	PLXNA4	2	2
CHRM2	1129	broad.mit.edu	37	7	136700630	136700630	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136700630A>C	uc003vtf.1	+	c.1018A>C	c.(1018-1020)ACT>CCT	p.T340P	CHRM2_uc003vtg.1_Missense_Mutation_p.T340P|CHRM2_uc003vtj.1_Missense_Mutation_p.T340P|CHRM2_uc003vtk.1_Missense_Mutation_p.T340P|CHRM2_uc003vtl.1_Missense_Mutation_p.T340P|CHRM2_uc003vtm.1_Missense_Mutation_p.T340P|CHRM2_uc003vti.1_Missense_Mutation_p.T340P|CHRM2_uc003vto.1_Missense_Mutation_p.T340P|CHRM2_uc003vtn.1_Missense_Mutation_p.T340P	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	340	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)									0.057851	-6.666294	18.129223	7	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136700630	136700630	3511	7	A	C	C	C	26	2	CHRM2	4	4
EPHB6	2051	broad.mit.edu	37	7	142563342	142563342	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142563342C>G	uc011kst.1	+	c.1059C>G	c.(1057-1059)GGC>GGG	p.G353G	EPHB6_uc011ksu.1_Silent_p.G353G|EPHB6_uc003wbs.2_Silent_p.G61G|EPHB6_uc003wbt.2_5'UTR|EPHB6_uc003wbu.2_Silent_p.G61G|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	353	Extracellular (Potential).|Cys-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|large_intestine(4)|central_nervous_system(3)|ovary(1)|pancreas(1)	14	Melanoma(164;0.059)									313				0.081081	-3.418102	9.867224	6	68	KEEP	---	---	---	---	capture		Silent	SNP	142563342	142563342	5371	7	C	G	G	G	353	28	EPHB6	3	3
SSPO	23145	broad.mit.edu	37	7	149475980	149475980	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149475980T>A	uc010lpk.2	+	c.946T>A	c.(946-948)TGG>AGG	p.W316R	SSPO_uc010lpl.1_5'UTR	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	SCO-spondin precursor	316	VWFD 1.				cell adhesion	extracellular space	peptidase inhibitor activity				0	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)											0.15625	58.087987	83.360169	35	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149475980	149475980	15705	7	T	A	A	A	715	55	SSPO	3	3
MLL3	58508	broad.mit.edu	37	7	151945162	151945162	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:151945162G>T	uc003wla.2	-	c.2357C>A	c.(2356-2358)ACA>AAA	p.T786K		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	786					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		Colon(68;14 1149 1884 27689 34759)			p.T786K(CORL47-Tumor)	1780				0.024768	-66.905752	14.059888	8	315	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151945162	151945162	10012	7	G	T	T	T	624	48	MLL3	2	2
MLL3	58508	broad.mit.edu	37	7	151962128	151962128	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:151962128G>T	uc003wla.2	-	c.1179C>A	c.(1177-1179)AAC>AAA	p.N393K		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	393	PHD-type 2.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		Colon(68;14 1149 1884 27689 34759)			p.N393N(NCIH1568-Tumor)|p.N393N(UACC257-Tumor)|p.N393N(CORL51-Tumor)|p.N393N(SKOV3-Tumor)|p.N393N(SF295-Tumor)|p.N393N(HCC4006-Tumor)|p.N393N(COLO829-Tumor)|p.N393N(MHHCALL3-Tumor)|p.N393N(SJRH30-Tumor)|p.N393N(ASPC1-Tumor)|p.N393N(U266B1-Tumor)|p.N393N(SW1088-Tumor)|p.N393N(SKES1-Tumor)|p.N393N(SH4-Tumor)|p.N393N(NCIH460-Tumor)|p.N393N(LS123-Tumor)|p.N393N(MOLT13-Tumor)|p.N393N(MV411-Tumor)|p.N393N(HS840.T-Tumor)|p.N393N(HT115-Tumor)|p.N393N(MELHO-Tumor)|p.N393N(NCIH2029-Tumor)|p.N393N(S117-Tumor)|p.N393N(NCIH1573-Tumor)|p.N393K(JHUEM7-Tumor)|p.N393N(CAL62-Tumor)|p.N393N(MELJUSO-Tumor)|p.N393K(NAMALWA-Tumor)|p.N393N(U138MG-Tumor)|p.N393N(OCILY3-Tumor)|p.N393N(H4-Tumor)|p.N393N(U87MG-Tumor)	1780				0.031646	-60.941308	14.955684	10	306	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151962128	151962128	10012	7	G	T	T	T	464	36	MLL3	2	2
VIPR2	7434	broad.mit.edu	37	7	158835748	158835748	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:158835748C>A	uc003woh.2	-	c.575G>T	c.(574-576)TGC>TTC	p.C192F	VIPR2_uc010lqx.2_Non-coding_Transcript|VIPR2_uc010lqy.2_Non-coding_Transcript	NM_003382	NP_003373	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	192	Extracellular (Potential).				cell-cell signaling	integral to plasma membrane				lung(1)|central_nervous_system(1)	2	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		Pancreas(154;1876 1931 2329 17914 20079)								0.095238	0.976378	14.772698	8	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158835748	158835748	17737	7	C	A	A	A	325	25	VIPR2	2	2
AGR3	155465	broad.mit.edu	37	7	16900155	16900155	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:16900155C>A	uc003sts.2	-	c.420G>T	c.(418-420)TTG>TTT	p.L140F		NM_176813	NP_789783	Q8TD06	AGR3_HUMAN	breast cancer membrane protein 11 precursor	140						extracellular region					0	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)										0.127907	14.657605	26.27394	11	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16900155	16900155	399	7	C	A	A	A	220	17	AGR3	2	2
HDAC9	9734	broad.mit.edu	37	7	18705968	18705968	+	Missense_Mutation	SNP	A	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:18705968A>T	uc003sui.2	+	c.1600A>T	c.(1600-1602)AGC>TGC	p.S534C	HDAC9_uc003sue.2_Missense_Mutation_p.S531C|HDAC9_uc011jyd.1_Missense_Mutation_p.S531C|HDAC9_uc003suh.2_Missense_Mutation_p.S531C|HDAC9_uc003suj.2_Missense_Mutation_p.S490C|HDAC9_uc011jya.1_Missense_Mutation_p.S528C|HDAC9_uc003sua.1_Missense_Mutation_p.S509C|HDAC9_uc011jyb.1_Missense_Mutation_p.S487C|HDAC9_uc003sud.1_Missense_Mutation_p.S531C|HDAC9_uc011jyc.1_Missense_Mutation_p.S490C|HDAC9_uc003suf.1_Missense_Mutation_p.S562C|HDAC9_uc010kud.1_Missense_Mutation_p.S534C|HDAC9_uc011jye.1_Missense_Mutation_p.S503C|HDAC9_uc011jyf.1_Missense_Mutation_p.S454C|HDAC9_uc010kue.1_Intron	NM_178425	NP_848512	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 5	531					B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|specific transcriptional repressor activity|transcription corepressor activity|transcription repressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)							OREG0017877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.13	16.10255	29.429328	13	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18705968	18705968	7297	7	A	T	T	T	91	7	HDAC9	3	3
SP4	6671	broad.mit.edu	37	7	21470206	21470206	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:21470206C>A	uc003sva.2	+	c.1423C>A	c.(1423-1425)CAG>AAG	p.Q475K	SP4_uc003svb.2_Missense_Mutation_p.Q162K	NM_003112	NP_003103	Q02446	SP4_HUMAN	Sp4 transcription factor	475					regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|transcription coactivator activity|zinc ion binding			ovary(3)	3														0.101828	23.314714	83.903012	39	344	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21470206	21470206	15466	7	C	A	A	A	377	29	SP4	2	2
POLD2	5425	broad.mit.edu	37	7	44156543	44156543	+	Missense_Mutation	SNP	A	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44156543A>C	uc010kxz.2	-	c.653T>G	c.(652-654)CTG>CGG	p.L218R	POLD2_uc003tke.3_Missense_Mutation_p.L218R|POLD2_uc010kya.2_Missense_Mutation_p.L218R|POLD2_uc003tkf.3_Missense_Mutation_p.L218R	NM_006230	NP_006221	P49005	DPOD2_HUMAN	DNA-directed DNA polymerase delta 2	218					base-excision repair|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	DNA binding|DNA-directed DNA polymerase activity|protein binding			ovary(2)	2														0.162791	13.699785	18.345822	7	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44156543	44156543	12619	7	A	C	C	C	91	7	POLD2	4	4
MYO1G	64005	broad.mit.edu	37	7	45005450	45005450	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:45005450C>A	uc003tmh.2	-	c.2167G>T	c.(2167-2169)GGC>TGC	p.G723C	MYO1G_uc003tmf.2_Missense_Mutation_p.G166C|MYO1G_uc003tmg.2_Missense_Mutation_p.G485C|MYO1G_uc010kym.2_Missense_Mutation_p.G608C	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	723	IQ.					myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|pancreas(1)	3														0.305556	25.106434	26.323587	11	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45005450	45005450	10469	7	C	A	A	A	286	22	MYO1G	2	2
TNRC18	84629	broad.mit.edu	37	7	5360180	5360180	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5360180G>A	uc003soi.3	-	c.6619C>T	c.(6619-6621)CAG>TAG	p.Q2207*		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2207							DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)										0.21875	13.003047	15.340631	7	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	5360180	5360180	16880	7	G	A	A	A	598	46	TNRC18	5	2
FBXL18	80028	broad.mit.edu	37	7	5540694	5540694	+	Silent	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5540694G>A	uc003soo.2	-	c.1206C>T	c.(1204-1206)GGC>GGT	p.G402G	FBXL18_uc003son.3_Silent_p.G402G	NM_024963	NP_079239	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	402	LRR 7.									central_nervous_system(2)|ovary(1)	3		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)										0.26087	25.995264	28.366991	12	34	KEEP	---	---	---	---	capture		Silent	SNP	5540694	5540694	5951	7	G	A	A	A	535	42	FBXL18	2	2
WBSCR17	64409	broad.mit.edu	37	7	70853322	70853322	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:70853322C>A	uc003tvy.2	+	c.524C>A	c.(523-525)GCC>GAC	p.A175D	WBSCR17_uc003tvz.2_5'UTR	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	175	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.267717	75.401051	81.590782	34	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70853322	70853322	17836	7	C	A	A	A	338	26	WBSCR17	2	2
DTX2	113878	broad.mit.edu	37	7	76112259	76112259	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76112259G>T	uc011kgk.1	+	c.430G>T	c.(430-432)GCT>TCT	p.A144S	DTX2_uc003uff.3_Missense_Mutation_p.A235S|DTX2_uc003ufg.3_Missense_Mutation_p.A235S|DTX2_uc003ufh.3_Missense_Mutation_p.A235S|DTX2_uc003ufj.3_Missense_Mutation_p.A235S	NM_020892	NP_065943	Q86UW9	DTX2_HUMAN	deltex 2 isoform a	235					Notch signaling pathway	cytoplasm|nucleus	protein binding|zinc ion binding			ovary(1)	1														0.057398	-74.612041	86.704015	45	739	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76112259	76112259	4979	7	G	T	T	T	494	38	DTX2	1	1
SEMA3E	9723	broad.mit.edu	37	7	83016314	83016314	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:83016314C>T	uc003uhy.1	-	c.1720G>A	c.(1720-1722)GGA>AGA	p.G574R		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	574					axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)												0.142857	6.379794	9.822655	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83016314	83016314	14514	7	C	T	T	T	273	21	SEMA3E	2	2
FZD1	8321	broad.mit.edu	37	7	90895971	90895971	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:90895971G>T	uc003ula.2	+	c.1776G>T	c.(1774-1776)CCG>CCT	p.P592P		NM_003505	NP_003496	Q9UP38	FZD1_HUMAN	frizzled 1 precursor	592	Extracellular (Potential).				autocrine signaling|axonogenesis|brain development|canonical Wnt receptor signaling pathway involved in mesenchymal stem cell differentiation|canonical Wnt receptor signaling pathway involved in osteoblast differentiation|embryo development|epithelial cell differentiation|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|lung alveolus development|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|regulation of gene-specific transcription from RNA polymerase II promoter|response to drug|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cell surface|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|receptor binding|Wnt receptor activity|Wnt-protein binding				0	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)						p.P592P(REH-Tumor)|p.P592P(NCIH1651-Tumor)	79				0.457627	73.444845	73.530908	27	32	KEEP	---	---	---	---	capture		Silent	SNP	90895971	90895971	6379	7	G	T	T	T	483	38	FZD1	1	1
CCDC132	55610	broad.mit.edu	37	7	92921085	92921085	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92921085G>T	uc003umo.2	+	c.1013G>T	c.(1012-1014)AGC>ATC	p.S338I	CCDC132_uc003umq.2_Non-coding_Transcript|CCDC132_uc003ump.2_Missense_Mutation_p.S308I|CCDC132_uc003umr.2_Non-coding_Transcript|CCDC132_uc011khz.1_Missense_Mutation_p.S58I	NM_017667	NP_060137	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132 isoform a	338											0	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)											0.217391	10.360238	12.056333	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92921085	92921085	2887	7	G	T	T	T	442	34	CCDC132	2	2
LMTK2	22853	broad.mit.edu	37	7	97821047	97821047	+	Nonsense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:97821047C>T	uc003upd.1	+	c.1270C>T	c.(1270-1272)CAG>TAG	p.Q424*		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	424					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(8)|pancreas(2)|large_intestine(1)	11	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)									547				0.357143	73.120675	74.632796	30	54	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	97821047	97821047	9188	7	C	T	T	T	221	17	LMTK2	5	2
ZKSCAN5	23660	broad.mit.edu	37	7	99110112	99110112	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99110112G>T	uc003uqv.2	+	c.451G>T	c.(451-453)GCA>TCA	p.A151S	ZKSCAN5_uc010lfx.2_Missense_Mutation_p.A151S|ZKSCAN5_uc003uqw.2_Missense_Mutation_p.A151S|ZKSCAN5_uc003uqx.2_Missense_Mutation_p.A151S|ZKSCAN5_uc003uqy.2_5'UTR	NM_145102	NP_659570	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	151					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)													0.130252	36.845624	68.574199	31	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99110112	99110112	18281	7	G	T	T	T	546	42	ZKSCAN5	2	2
GPC2	221914	broad.mit.edu	37	7	99773222	99773222	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99773222C>G	uc003utv.2	-	c.621G>C	c.(619-621)GGG>GGC	p.G207G	GPC2_uc010lgr.2_Non-coding_Transcript|GPC2_uc003utw.1_Silent_p.G207G|STAG3_uc010lgs.1_5'Flank|STAG3_uc003utx.1_5'Flank|STAG3_uc011kjk.1_5'Flank	NM_152742	NP_689955	Q8N158	GPC2_HUMAN	glypican 2 precursor	207						anchored to membrane|endoplasmic reticulum|extracellular space|plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)|pancreas(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.176471	13.133557	16.484108	6	28	KEEP	---	---	---	---	capture		Silent	SNP	99773222	99773222	6872	7	C	G	G	G	275	22	GPC2	3	3
PKHD1L1	93035	broad.mit.edu	37	8	110457421	110457421	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110457421G>C	uc003yne.2	+	c.5323G>C	c.(5323-5325)GTT>CTT	p.V1775L		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	1775	Extracellular (Potential).|IPT/TIG 10.				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.089286	5.529345	15.068719	5	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110457421	110457421	12397	8	G	C	C	C	624	48	PKHD1L1	3	3
TRPS1	7227	broad.mit.edu	37	8	116427219	116427219	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:116427219C>G	uc003yny.2	-	c.2917G>C	c.(2917-2919)GCT>CCT	p.A973P	TRPS1_uc011lhy.1_Missense_Mutation_p.A964P|TRPS1_uc010mcy.2_Missense_Mutation_p.A960P|TRPS1_uc003ynz.2_Missense_Mutation_p.A960P	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	960					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)							312				0.346405	171.023437	174.258586	53	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116427219	116427219	17144	8	C	G	G	G	338	26	TRPS1	3	3
FER1L6	654463	broad.mit.edu	37	8	124998416	124998416	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124998416G>T	uc003yqw.2	+	c.1519G>T	c.(1519-1521)GGT>TGT	p.G507C		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	507	Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)											0.14433	19.587245	31.400049	14	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124998416	124998416	6052	8	G	T	T	T	611	47	FER1L6	2	2
MYOM2	9172	broad.mit.edu	37	8	2057240	2057240	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:2057240G>A	uc003wpx.3	+	c.3098G>A	c.(3097-3099)CGC>CAC	p.R1033H	MYOM2_uc011kwi.1_Missense_Mutation_p.R458H	NM_003970	NP_003961	P54296	MYOM2_HUMAN	myomesin 2	1033					muscle contraction	myosin filament	structural constituent of muscle			ovary(4)|central_nervous_system(1)	5		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)										0.4	63.783938	64.309568	24	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2057240	2057240	10487	8	G	A	A	A	494	38	MYOM2	1	1
TM2D2	83877	broad.mit.edu	37	8	38851131	38851131	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:38851131G>A	uc003xmk.2	-	c.364C>T	c.(364-366)CAT>TAT	p.H122Y	TM2D2_uc003xml.2_Missense_Mutation_p.H79Y|TM2D2_uc003xmm.2_Missense_Mutation_p.H79Y|TM2D2_uc003xmn.2_Missense_Mutation_p.H79Y	NM_078473	NP_510882	Q9BX73	TM2D2_HUMAN	TM2 domain containing 2 isoform a	122						integral to membrane					0		all_lung(54;0.00338)|Lung NSC(58;0.0133)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;1.5e-07)											0.053333	-8.466266	7.335017	4	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38851131	38851131	16494	8	G	A	A	A	611	47	TM2D2	2	2
POTEA	340441	broad.mit.edu	37	8	43211932	43211932	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:43211932C>A	uc003xpz.1	+	c.1391C>A	c.(1390-1392)GCA>GAA	p.A464E	POTEA_uc003xqa.1_Missense_Mutation_p.A418E	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	464										ovary(1)	1														0.092105	3.080206	15.80048	7	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43211932	43211932	12690	8	C	A	A	A	325	25	POTEA	2	2
ZFHX4	79776	broad.mit.edu	37	8	77765131	77765131	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77765131C>T	uc003yav.2	+	c.5839C>T	c.(5839-5841)CTT>TTT	p.L1947F	ZFHX4_uc003yau.1_Missense_Mutation_p.L1992F|ZFHX4_uc003yaw.1_Missense_Mutation_p.L1947F	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1947					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.302326	36.357375	37.858158	13	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77765131	77765131	18223	8	C	T	T	T	364	28	ZFHX4	2	2
ZFHX4	79776	broad.mit.edu	37	8	77766327	77766327	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77766327C>A	uc003yav.2	+	c.7035C>A	c.(7033-7035)CCC>CCA	p.P2345P	ZFHX4_uc003yau.1_Silent_p.P2390P|ZFHX4_uc003yaw.1_Silent_p.P2345P	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2345	Pro-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.21374	57.25683	67.154068	28	103	KEEP	---	---	---	---	capture		Silent	SNP	77766327	77766327	18223	8	C	A	A	A	275	22	ZFHX4	2	2
MMP16	4325	broad.mit.edu	37	8	89053848	89053848	+	Silent	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:89053848C>A	uc003yeb.3	-	c.1665G>T	c.(1663-1665)CTG>CTT	p.L555L		NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	555	Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|kidney(1)|central_nervous_system(1)	5														0.385965	114.056456	115.36098	44	70	KEEP	---	---	---	---	capture		Silent	SNP	89053848	89053848	10045	8	C	A	A	A	262	21	MMP16	2	2
PDP1	54704	broad.mit.edu	37	8	94935757	94935758	+	Nonsense_Mutation	DNP	CG	TT	TT			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:94935757_94935758CG>TT	uc011lgn.1	+	c.1647_1648CG>TT	c.(1645-1650)AACGAG>AATTAG	p.E550*	PDP1_uc003yge.2_Nonsense_Mutation_p.E491*|PDP1_uc003ygf.2_Nonsense_Mutation_p.E516*|PDP1_uc010max.2_Nonsense_Mutation_p.E516*|PDP1_uc011lgm.1_Nonsense_Mutation_p.E491*	NM_001161778	NP_001155250	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic	491					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.287234	145.871803	153.505992	54	134	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	94935757	94935758	12106	8	CG	TT	TT	TT	246	19	PDP1	5	1
CDH17	1015	broad.mit.edu	37	8	95188777	95188777	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95188777G>T	uc003ygh.2	-	c.416C>A	c.(415-417)TCT>TAT	p.S139Y	CDH17_uc011lgo.1_Missense_Mutation_p.S139Y|CDH17_uc011lgp.1_Missense_Mutation_p.S139Y	NM_004063	NP_004054	Q12864	CAD17_HUMAN	cadherin 17 precursor	139	Extracellular (Potential).|Cadherin 2.					integral to membrane	calcium ion binding			ovary(5)	5	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)											0.257143	97.870263	107.245911	45	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95188777	95188777	3231	8	G	T	T	T	429	33	CDH17	2	2
COL15A1	1306	broad.mit.edu	37	9	101807041	101807041	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101807041C>T	uc004azb.1	+	c.2668C>T	c.(2668-2670)CCA>TCA	p.P890S		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	890	Triple-helical region 5 (COL5).				angiogenesis|cell adhesion|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding|extracellular matrix structural constituent			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)												0.155556	11.994468	17.095568	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101807041	101807041	3810	9	C	T	T	T	286	22	COL15A1	2	2
OR13C2	392376	broad.mit.edu	37	9	107367587	107367587	+	Missense_Mutation	SNP	C	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107367587C>T	uc011lvq.1	-	c.322G>A	c.(322-324)GGG>AGG	p.G108R		NM_001004481	NP_001004481	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C,	108	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.100917	6.244985	23.583061	11	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107367587	107367587	11340	9	C	T	T	T	286	22	OR13C2	2	2
AKNA	80709	broad.mit.edu	37	9	117139109	117139109	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:117139109C>G	uc004biq.3	-	c.978G>C	c.(976-978)CGG>CGC	p.R326R	AKNA_uc004bio.3_5'UTR|AKNA_uc004bip.3_Silent_p.R245R|AKNA_uc004bir.3_Silent_p.R326R|AKNA_uc004bis.3_Silent_p.R326R|AKNA_uc010mve.2_Silent_p.R207R|AKNA_uc004biu.1_Silent_p.R67R|AKNA_uc004biv.1_Silent_p.R326R|AKNA_uc004biw.1_Silent_p.R326R	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	326					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6														0.2	17.208763	20.135734	7	28	KEEP	---	---	---	---	capture		Silent	SNP	117139109	117139109	466	9	C	G	G	G	327	26	AKNA	3	3
ANGPTL2	23452	broad.mit.edu	37	9	129851286	129851286	+	Nonsense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:129851286G>A	uc004bqr.1	-	c.1414C>T	c.(1414-1416)CGA>TGA	p.R472*	RALGPS1_uc004bqo.1_Intron|RALGPS1_uc011mab.1_Intron|RALGPS1_uc011mac.1_Intron|RALGPS1_uc004bqq.3_Intron|ANGPTL2_uc010mxg.1_Nonsense_Mutation_p.R170*	NM_012098	NP_036230	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2 precursor	472	Fibrinogen C-terminal.				multicellular organismal development|signal transduction	extracellular space	receptor binding				0														0.221122	153.37036	175.057824	67	236	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	129851286	129851286	617	9	G	A	A	A	506	39	ANGPTL2	5	1
DBH	1621	broad.mit.edu	37	9	136501597	136501597	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:136501597C>A	uc004cel.2	+	c.104C>A	c.(103-105)GCC>GAC	p.A35D		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta hydroxylase precursor	35	Helical; Signal-anchor for type II membrane protein; (Potential).				hormone biosynthetic process|oxidation-reduction process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)									0.08547	-1.528177	18.855596	10	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136501597	136501597	4421	9	C	A	A	A	338	26	DBH	2	2
CAMSAP1	157922	broad.mit.edu	37	9	138714662	138714662	+	Silent	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138714662C>G	uc004cgr.3	-	c.1845G>C	c.(1843-1845)CGG>CGC	p.R615R	CAMSAP1_uc004cgq.3_Silent_p.R505R|CAMSAP1_uc010nbg.2_Silent_p.R337R	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	615						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)										0.052632	-13.59106	14.539841	7	126	KEEP	---	---	---	---	capture		Silent	SNP	138714662	138714662	2728	9	C	G	G	G	275	22	CAMSAP1	3	3
FREM1	158326	broad.mit.edu	37	9	14859286	14859287	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:14859286_14859287CC>AA	uc003zlm.2	-	c.525_526GG>TT	c.(523-528)CTGGAC>CTTTAC	p.D176Y	FREM1_uc010mic.2_Non-coding_Transcript	NM_144966	NP_659403	Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1 precursor	176					cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(50;3.53e-06)										0.166667	27.874576	39.264828	18	90	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	14859286	14859287	6291	9	CC	AA	AA	AA	390	30	FREM1	2	2
SMU1	55234	broad.mit.edu	37	9	33073725	33073725	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:33073725C>G	uc010mjo.1	-	c.106G>C	c.(106-108)GTG>CTG	p.V36L	SMU1_uc003zsf.1_Missense_Mutation_p.V36L|SMU1_uc010mjp.1_Missense_Mutation_p.V36L|SMU1_uc011lnu.1_Intron	NM_018225	NP_060695	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog	36	LisH.					cytoplasm|nucleus				ovary(1)	1			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)										0.131148	32.209406	48.349485	16	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33073725	33073725	15317	9	C	G	G	G	221	17	SMU1	3	3
FBXO10	26267	broad.mit.edu	37	9	37516063	37516063	+	Missense_Mutation	SNP	T	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37516063T>A	uc004aac.2	-	c.2582A>T	c.(2581-2583)CAC>CTC	p.H861L	FBXO10_uc004aab.2_Missense_Mutation_p.H845L|FBXO10_uc004aad.2_Missense_Mutation_p.H395L	NM_012166	NP_036298	Q9UK96	FBX10_HUMAN	F-box protein 10	845	PbH1 17.					ubiquitin ligase complex	ubiquitin-protein ligase activity				0				GBM - Glioblastoma multiforme(29;0.0107)										0.222222	48.178956	54.549225	20	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37516063	37516063	5963	9	T	A	A	A	767	59	FBXO10	3	3
FRMPD1	22844	broad.mit.edu	37	9	37733495	37733495	+	Missense_Mutation	SNP	A	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37733495A>G	uc004aag.1	+	c.1021A>G	c.(1021-1023)ATA>GTA	p.I341V	FRMPD1_uc004aah.1_Missense_Mutation_p.I341V|FRMPD1_uc011lqm.1_Missense_Mutation_p.I163V|FRMPD1_uc011lqn.1_Missense_Mutation_p.I210V	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	341	FERM.					cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|breast(1)	7				GBM - Glioblastoma multiforme(29;0.00655)										0.096296	11.106825	33.139507	13	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37733495	37733495	6307	9	A	G	G	G	208	16	FRMPD1	4	4
FAM75A3	727830	broad.mit.edu	37	9	40702715	40702715	+	Silent	SNP	T	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:40702715T>G	uc010mmj.2	+	c.372T>G	c.(370-372)GGT>GGG	p.G124G		NM_001083124	NP_001076593	Q5VYP0	F75A3_HUMAN	hypothetical protein LOC727830	124	Pro-rich.					integral to membrane				ovary(2)	2				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.041451	-25.137591	18.528875	8	185	KEEP	---	---	---	---	capture		Silent	SNP	40702715	40702715	5845	9	T	G	G	G	756	59	FAM75A3	4	4
KDM4C	23081	broad.mit.edu	37	9	7049120	7049120	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:7049120G>C	uc003zkh.2	+	c.2344G>C	c.(2344-2346)GTC>CTC	p.V782L	KDM4C_uc010mhu.2_Missense_Mutation_p.V804L|KDM4C_uc011lmi.1_Missense_Mutation_p.V782L|KDM4C_uc011lmj.1_Intron|KDM4C_uc003zkg.2_Missense_Mutation_p.V782L|KDM4C_uc011lmk.1_Missense_Mutation_p.V527L|KDM4C_uc011lml.1_Missense_Mutation_p.V469L	NM_015061	NP_055876	Q9H3R0	KDM4C_HUMAN	jumonji domain containing 2C isoform 1	782					oxidation-reduction process|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	nuclear chromatin	androgen receptor binding|enzyme binding|histone demethylase activity (H3-K9 specific)|nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			ovary(1)	1														0.160714	23.44263	29.573895	9	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7049120	7049120	8436	9	G	C	C	C	572	44	KDM4C	3	3
CHRDL1	91851	broad.mit.edu	37	X	109919536	109919536	+	Missense_Mutation	SNP	T	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:109919536T>G	uc004eou.3	-	c.1300A>C	c.(1300-1302)AGT>CGT	p.S434R	CHRDL1_uc004eov.2_Missense_Mutation_p.S423R|CHRDL1_uc004eow.2_Missense_Mutation_p.S432R|CHRDL1_uc010nps.2_Missense_Mutation_p.S433R|CHRDL1_uc004eot.2_Missense_Mutation_p.S353R|CHRDL1_uc011mss.1_Missense_Mutation_p.S348R	NM_001143981	NP_001137453	Q9BU40	CRDL1_HUMAN	chordin-like 1 isoform 1 precursor	426					BMP signaling pathway|cell differentiation|nervous system development|ossification	extracellular region					0														0.079365	1.423856	12.802923	5	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109919536	109919536	3507	23	T	G	G	G	728	56	CHRDL1	4	4
SLC6A14	11254	broad.mit.edu	37	X	115582710	115582710	+	Missense_Mutation	SNP	C	G	G			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:115582710C>G	uc004eqi.2	+	c.1034C>G	c.(1033-1035)TCT>TGT	p.S345C		NM_007231	NP_009162	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid	345					cellular amino acid metabolic process|response to toxin	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)|pancreas(1)	3					L-Proline(DB00172)									0.188679	27.518088	32.324546	10	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115582710	115582710	15174	23	C	G	G	G	416	32	SLC6A14	3	3
GRIA3	2892	broad.mit.edu	37	X	122319800	122319800	+	Missense_Mutation	SNP	G	C	C			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:122319800G>C	uc004etq.3	+	c.226G>C	c.(226-228)GAT>CAT	p.D76H	GRIA3_uc004etr.3_Missense_Mutation_p.D76H|GRIA3_uc004ets.3_Non-coding_Transcript|GRIA3_uc011muf.1_Missense_Mutation_p.D60H|GRIA3_uc010nqs.1_Missense_Mutation_p.D76H	NM_007325	NP_015564	P42263	GRIA3_HUMAN	glutamate receptor, ionotrophic, AMPA 3 isoform	76	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|pancreas(1)	4					L-Glutamic Acid(DB00142)					217				0.128571	17.123974	26.531829	9	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122319800	122319800	7047	23	G	C	C	C	429	33	GRIA3	3	3
GPR50	9248	broad.mit.edu	37	X	150348520	150348520	+	Missense_Mutation	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:150348520G>T	uc010ntg.1	+	c.465G>T	c.(463-465)ATG>ATT	p.M155I	GPR50_uc011myc.1_Missense_Mutation_p.M155I	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	155	Helical; Name=4; (Potential).				cell-cell signaling	integral to plasma membrane	melatonin receptor activity	p.M155I(1)		large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)													0.460432	182.86781	183.05893	64	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150348520	150348520	6972	23	G	T	T	T	585	45	GPR50	2	2
CETN2	1069	broad.mit.edu	37	X	151997692	151997693	+	Missense	DNP	CC	AA	AA			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:151997692C>A	uc004fgq.2	-	c.291_splice	c.e3+1	p.M97_splice	CETN2_uc004fgr.2_Splice_Site_SNP_p.M26_splice|NSDHL_uc004fgt.1_5'Flank|NSDHL_uc004fgs.1_5'Flank	NM_004344	NP_004335			caltractin						cell division|centriole replication|G2/M transition of mitotic cell cycle|mitosis|nucleotide-excision repair|regulation of cytokinesis	centriole|cytosol|XPC complex	ATP binding|ATP-dependent helicase activity|calcium ion binding|nucleic acid binding				0	Acute lymphoblastic leukemia(192;6.56e-05)													0.357143	102.087927	103.853619	35	63	KEEP	---	---	---	---	capture		Missense	DNP	151997692	151997693	3408	23	CC	AA	AA	A	234	18	CETN2	2	2
FAM48B1	100130302	broad.mit.edu	37	X	24383507	24383507	+	Missense_Mutation	SNP	G	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24383507G>A	uc011mjx.1	+	c.2630G>A	c.(2629-2631)AGG>AAG	p.R877K		NM_001136234	NP_001129706			hypothetical protein LOC100130302											kidney(1)	1														0.169492	19.509575	25.612644	10	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24383507	24383507	5795	23	G	A	A	A	455	35	FAM48B1	2	2
ARSH	347527	broad.mit.edu	37	X	2947341	2947341	+	Missense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:2947341C>A	uc011mhj.1	+	c.1253C>A	c.(1252-1254)TCC>TAC	p.S418Y		NM_001011719	NP_001011719	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	418						integral to membrane	arylsulfatase activity|metal ion binding			lung(1)	1		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)												0.244681	46.806505	52.372967	23	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2947341	2947341	1011	23	C	A	A	A	390	30	ARSH	2	2
ARSF	416	broad.mit.edu	37	X	3002330	3002330	+	Nonsense_Mutation	SNP	C	A	A			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3002330C>A	uc004cre.1	+	c.453C>A	c.(451-453)TGC>TGA	p.C151*	ARSF_uc004crf.1_Nonsense_Mutation_p.C151*	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	151						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.37931	59.094067	59.813484	22	36	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	3002330	3002330	1009	23	C	A	A	A	337	26	ARSF	5	2
BCOR	54880	broad.mit.edu	37	X	39933725	39933726	+	Missense_Mutation	DNP	CC	AT	AT			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:39933725_39933726CC>AT	uc004den.3	-	c.873_874GG>AT	c.(871-876)ATGGGC>ATATGC	p.291_292MG>IC	BCOR_uc004dep.3_Missense_Mutation_p.291_292MG>IC|BCOR_uc004deo.3_Missense_Mutation_p.291_292MG>IC|BCOR_uc004dem.3_Missense_Mutation_p.291_292MG>IC|BCOR_uc004deq.3_Missense_Mutation_p.291_292MG>IC	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	291_292					chromatin modification|heart development|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|odontogenesis|palate development|protein ubiquitination|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|promoter binding|transcription corepressor activity|transcription factor binding			ovary(2)|kidney(1)|central_nervous_system(1)	4														0.148148	5.480221	8.691827	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	39933725	39933726	1407	23	CC	AT	AT	AT	286	22	BCOR	2	2
ATP7A	538	broad.mit.edu	37	X	77254174	77254174	+	Silent	SNP	G	T	T			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77254174G>T	uc004ecx.3	+	c.1536G>T	c.(1534-1536)CGG>CGT	p.R512R	ATP7A_uc004ecw.2_Silent_p.R512R	NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	512	HMA 5.|Cytoplasmic (Potential).				ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0														0.235294	34.459721	38.822503	16	52	KEEP	---	---	---	---	capture		Silent	SNP	77254174	77254174	1209	23	G	T	T	T	548	43	ATP7A	2	2
CACNA2D3	55799	broad.mit.edu	37	3	54354528	54354528	+	Frame_Shift_Del	DEL	A	-	-			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:54354528_54354528delA	uc003dhf.2	+	c.264_264delA	c.(262-264)GTAfs	p.V88fs	CACNA2D3_uc011beu.1_Non-coding_Transcript|CACNA2D3_uc003dhg.1_5'UTR|CACNA2D3_uc003dhh.1_Non-coding_Transcript|CACNA2D3_uc010hmv.1_5'UTR|CACNA2D3_uc003dhi.2_Non-coding_Transcript	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	88	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	54354528	54354528	2666	3	A	-	-	-	158	13	CACNA2D3	5	5
TMEM31	203562	broad.mit.edu	37	X	102968916	102968918	+	In_Frame_Del	DEL	TCT	-	-			TCGA-35-4123-01	TCGA-35-4123-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:102968916_102968918delTCT	uc004elh.2	+	c.497_499delTCT	c.(496-501)ATCTTC>ATC	p.F168del	GLRA4_uc011mse.1_Intron	NM_182541	NP_872347	Q5JXX7	TMM31_HUMAN	transmembrane protein 31	168	Helical; (Potential).					integral to membrane					0														0.31			5	11		---	---	---	---	capture_indel		In_Frame_Del	DEL	102968916	102968918	16694	23	TCT	-	-	-	650	50	TMEM31	5	5
