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
CPN1	1369	broad.mit.edu	37	10	101816798	101816798	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101816798C>A	uc001kql.2	-	c.983G>T	c.(982-984)CGG>CTG	p.R328L		NM_001308	NP_001299	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1 precursor	328	Catalytic.				proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			central_nervous_system(3)|pancreas(1)	4		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)										0.136546	53.292573	85.129031	34	215	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101816798	101816798	3947	10	C	A	A	A	299	23	CPN1	1	1
MGEA5	10724	broad.mit.edu	37	10	103550754	103550754	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:103550754C>A	uc001ktv.2	-	c.2353G>T	c.(2353-2355)GAT>TAT	p.D785Y	MGEA5_uc001ktu.2_Non-coding_Transcript|MGEA5_uc010qqe.1_Missense_Mutation_p.D732Y|MGEA5_uc009xws.2_Missense_Mutation_p.D718Y	NM_012215	NP_036347	O60502	NCOAT_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	785	Histone acetyltransferase activity (By similarity).|Required for histone H4 binding (By similarity).				glycoprotein catabolic process	cytoplasm|nucleus	beta-N-acetylhexosaminidase activity|histone acetyltransferase activity|hyalurononglucosaminidase activity			ovary(2)	2		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)										0.235294	25.369421	28.642332	12	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103550754	103550754	9945	10	C	A	A	A	416	32	MGEA5	2	2
NRAP	4892	broad.mit.edu	37	10	115349505	115349505	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115349505G>C	uc001lal.3	-	c.5008C>G	c.(5008-5010)CCT>GCT	p.P1670A	NRAP_uc009xyb.2_Missense_Mutation_p.P423A|NRAP_uc001laj.2_Missense_Mutation_p.P1670A|NRAP_uc001lak.2_Missense_Mutation_p.P1635A	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1670						fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)	9		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)										0.288889	40.861696	42.656408	13	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115349505	115349505	11043	10	G	C	C	C	533	41	NRAP	3	3
SEC23IP	11196	broad.mit.edu	37	10	121658365	121658365	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:121658365C>T	uc001leu.1	+	c.590C>T	c.(589-591)GCA>GTA	p.A197V	SEC23IP_uc010qtc.1_Intron	NM_007190	NP_009121	Q9Y6Y8	S23IP_HUMAN	Sec23-interacting protein p125	197	Interaction with SEC23A.|Pro-rich.				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)										0.255319	84.429717	92.090856	36	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121658365	121658365	14479	10	C	T	T	T	325	25	SEC23IP	2	2
MCM10	55388	broad.mit.edu	37	10	13237238	13237238	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:13237238C>A	uc001ima.2	+	c.1946C>A	c.(1945-1947)CCA>CAA	p.P649Q	MCM10_uc001imb.2_Missense_Mutation_p.P648Q|MCM10_uc001imc.2_Missense_Mutation_p.P648Q	NM_182751	NP_877428	Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	649					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	metal ion binding|protein binding			ovary(2)|central_nervous_system(1)	3														0.081081	0.243079	6.81613	3	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13237238	13237238	9774	10	C	A	A	A	273	21	MCM10	2	2
ITGA8	8516	broad.mit.edu	37	10	15730022	15730022	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:15730022C>A	uc001ioc.1	-	c.359G>T	c.(358-360)AGA>ATA	p.R120I	ITGA8_uc010qcb.1_Missense_Mutation_p.R120I	NM_003638	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8 precursor	120	Extracellular (Potential).				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity			ovary(3)|lung(3)	6														0.152778	17.073076	25.386831	11	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15730022	15730022	8186	10	C	A	A	A	416	32	ITGA8	2	2
ARHGAP21	57584	broad.mit.edu	37	10	24909728	24909728	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:24909728C>T	uc001isb.2	-	c.1096G>A	c.(1096-1098)GTG>ATG	p.V366M	ARHGAP21_uc010qdb.1_Non-coding_Transcript|ARHGAP21_uc009xkl.1_Missense_Mutation_p.V366M|ARHGAP21_uc010qdc.1_Missense_Mutation_p.V201M|ARHGAP21_uc001isc.1_Missense_Mutation_p.V356M	NM_020824	NP_065875	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	365					signal transduction	cell junction|cytoplasmic vesicle membrane|cytoskeleton|Golgi membrane	GTPase activator activity|protein binding			ovary(7)|pancreas(1)	8														0.253165	47.659791	52.032148	20	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24909728	24909728	882	10	C	T	T	T	221	17	ARHGAP21	2	2
KIAA1462	57608	broad.mit.edu	37	10	30315636	30315636	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:30315636G>T	uc009xle.1	-	c.3441C>A	c.(3439-3441)GGC>GGA	p.G1147G	KIAA1462_uc001iux.2_Silent_p.G1147G|KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Silent_p.G1009G	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	1147										ovary(4)	4														0.259843	83.811172	90.447758	33	94	KEEP	---	---	---	---	capture		Silent	SNP	30315636	30315636	8543	10	G	T	T	T	587	46	KIAA1462	2	2
ZNF485	220992	broad.mit.edu	37	10	44112694	44112694	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:44112694G>C	uc010qfc.1	+	c.1203G>C	c.(1201-1203)CAG>CAC	p.Q401H	ZNF485_uc010qfd.1_Missense_Mutation_p.Q310H	NM_145312	NP_660355	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	401	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.395349	58.767415	59.179201	17	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44112694	44112694	18532	10	G	C	C	C	425	33	ZNF485	3	3
RBP3	5949	broad.mit.edu	37	10	48388966	48388966	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:48388966C>T	uc001jez.2	-	c.1912G>A	c.(1912-1914)GCC>ACC	p.A638T		NM_002900	NP_002891	P10745	RET3_HUMAN	retinol-binding protein 3 precursor	638	4 X approximate tandem repeats.|3.				lipid metabolic process|proteolysis|transport|visual perception	interphotoreceptor matrix	retinal binding|serine-type peptidase activity			large_intestine(1)|central_nervous_system(1)	2					Vitamin A(DB00162)									0.227273	11.46277	12.96537	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48388966	48388966	13626	10	C	T	T	T	338	26	RBP3	2	2
ANK3	288	broad.mit.edu	37	10	61832647	61832647	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:61832647C>T	uc001jky.2	-	c.7992G>A	c.(7990-7992)GAG>GAA	p.E2664E	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	2664					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			ovary(6)|pancreas(2)|central_nervous_system(1)|skin(1)	10														0.074074	-0.943169	9.11914	4	50	KEEP	---	---	---	---	capture		Silent	SNP	61832647	61832647	625	10	C	T	T	T	415	32	ANK3	2	2
LRRTM3	347731	broad.mit.edu	37	10	68686880	68686880	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:68686880G>A	uc001jmz.1	+	c.206G>A	c.(205-207)CGC>CAC	p.R69H	CTNNA3_uc009xpn.1_Intron|CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmy.2_Missense_Mutation_p.R69H	NM_178011	NP_821079	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	69	Extracellular (Potential).|LRR 1.					integral to membrane				ovary(1)	1														0.357798	108.603369	110.540553	39	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68686880	68686880	9417	10	G	A	A	A	494	38	LRRTM3	1	1
CYP26A1	1592	broad.mit.edu	37	10	94836933	94836933	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:94836933A>G	uc001kil.2	+	c.1366A>G	c.(1366-1368)ACA>GCA	p.T456A	CYP26A1_uc001kik.1_Missense_Mutation_p.T387A|CYP26A1_uc001kim.1_Missense_Mutation_p.T354A	NM_000783	NP_000774	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A,	456					negative regulation of retinoic acid receptor signaling pathway|oxidation-reduction process|retinoic acid catabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|oxygen binding|retinoic acid 4-hydroxylase activity|retinoic acid binding			ovary(1)|breast(1)	2		Colorectal(252;0.122)												0.190476	8.989259	10.869715	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94836933	94836933	4320	10	A	G	G	G	182	14	CYP26A1	4	4
TRPC6	7225	broad.mit.edu	37	11	101375222	101375222	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101375222G>T	uc001pgk.3	-	c.478C>A	c.(478-480)CGA>AGA	p.R160R	TRPC6_uc009ywy.2_Silent_p.R160R|TRPC6_uc009ywz.1_Silent_p.R160R	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	160	Cytoplasmic (Potential).|ANK 2.				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)								0.285714	45.780077	48.085614	16	40	KEEP	---	---	---	---	capture		Silent	SNP	101375222	101375222	17134	11	G	T	T	T	480	37	TRPC6	1	1
MMP8	4317	broad.mit.edu	37	11	102584511	102584511	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:102584511T>G	uc001phe.2	-	c.1268A>C	c.(1267-1269)AAA>ACA	p.K423T	MMP8_uc010rut.1_3'UTR|MMP8_uc010ruu.1_Missense_Mutation_p.K400T	NM_002424	NP_002415	P22894	MMP8_HUMAN	matrix metalloproteinase 8 preproprotein	423					collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)						426				0.176471	30.758893	37.464896	12	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102584511	102584511	10059	11	T	G	G	G	832	64	MMP8	4	4
DYNC2H1	79659	broad.mit.edu	37	11	103090682	103090682	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103090682G>A	uc001phn.1	+	c.8871G>A	c.(8869-8871)AAG>AAA	p.K2957K	DYNC2H1_uc001pho.2_Silent_p.K2957K|DYNC2H1_uc009yxe.1_Intron	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2957	Potential.|Stalk (By similarity).				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity				0		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)										0.363636	23.893695	24.253771	8	14	KEEP	---	---	---	---	capture		Silent	SNP	103090682	103090682	5032	11	G	A	A	A	438	34	DYNC2H1	2	2
TECTA	7007	broad.mit.edu	37	11	121000540	121000540	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:121000540C>T	uc010rzo.1	+	c.2561C>T	c.(2560-2562)GCC>GTC	p.A854V		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	854	VWFD 2.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)	8	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)										0.116883	9.316609	20.439726	9	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121000540	121000540	16274	11	C	T	T	T	338	26	TECTA	2	2
SPATA19	219938	broad.mit.edu	37	11	133715076	133715076	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:133715076C>A	uc001qgv.1	-	c.88G>T	c.(88-90)GTT>TTT	p.V30F		NM_174927	NP_777587	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19 precursor	30					cell differentiation|multicellular organismal development|spermatogenesis	mitochondrial outer membrane					0	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)										0.261905	31.533986	33.670102	11	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133715076	133715076	15512	11	C	A	A	A	247	19	SPATA19	1	1
KCNA4	3739	broad.mit.edu	37	11	30033380	30033380	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:30033380C>G	uc001msk.2	-	c.846G>C	c.(844-846)AGG>AGC	p.R282S		NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	282						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.133333	26.191508	45.775831	20	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30033380	30033380	8310	11	C	G	G	G	285	22	KCNA4	3	3
C11orf74	119710	broad.mit.edu	37	11	36680708	36680708	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36680708G>T	uc001mwy.1	+	c.638G>T	c.(637-639)AGC>ATC	p.S213I	C11orf74_uc010rfd.1_Non-coding_Transcript|C11orf74_uc001mww.1_Missense_Mutation_p.S139I|C11orf74_uc001mwx.1_Intron|C11orf74_uc001mwz.1_Missense_Mutation_p.S139I|C11orf74_uc010rfe.1_Intron	NM_138787	NP_620142	Q86VG3	CK074_HUMAN	hypothetical protein LOC119710	213											0	all_lung(20;0.226)	all_hematologic(20;0.0118)												0.089744	-0.563433	12.793728	7	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36680708	36680708	1701	11	G	T	T	T	442	34	C11orf74	2	2
LRRC4C	57689	broad.mit.edu	37	11	40136613	40136613	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40136613C>A	uc001mxa.1	-	c.1230G>T	c.(1228-1230)ACG>ACT	p.T410T	LRRC4C_uc001mxc.1_Silent_p.T406T|LRRC4C_uc001mxd.1_Silent_p.T406T|LRRC4C_uc001mxb.1_Silent_p.T406T	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	410	Ig-like C2-type.				regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.125	29.599637	51.57323	20	140	KEEP	---	---	---	---	capture		Silent	SNP	40136613	40136613	9383	11	C	A	A	A	236	19	LRRC4C	1	1
CHST1	8534	broad.mit.edu	37	11	45671313	45671313	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45671313G>A	uc001mys.1	-	c.1161C>T	c.(1159-1161)ATC>ATT	p.I387I		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	387	Lumenal (Potential).				galactose metabolic process|inflammatory response|keratan sulfate metabolic process	Golgi membrane|integral to membrane	keratan sulfotransferase activity			pancreas(1)	1				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)										0.125	7.718763	14.311878	6	42	KEEP	---	---	---	---	capture		Silent	SNP	45671313	45671313	3531	11	G	A	A	A	473	37	CHST1	1	1
OR5W2	390148	broad.mit.edu	37	11	55681285	55681285	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55681285C>T	uc010rir.1	-	c.774G>A	c.(772-774)ATG>ATA	p.M258I		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	258	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						Melanoma(48;171 1190 15239 43886 49348)								0.38	109.121506	110.386335	38	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55681285	55681285	11595	11	C	T	T	T	221	17	OR5W2	2	2
TMEM132A	54972	broad.mit.edu	37	11	60699470	60699470	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60699470G>A	uc001nqi.2	+	c.1230G>A	c.(1228-1230)GTG>GTA	p.V410V	TMEM132A_uc001nqj.2_Silent_p.V409V|TMEM132A_uc001nqk.2_Silent_p.V422V|TMEM132A_uc001nql.1_3'UTR|TMEM132A_uc001nqm.2_5'Flank	NM_017870	NP_060340	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform a	409	Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0														0.217391	11.761848	13.456083	5	18	KEEP	---	---	---	---	capture		Silent	SNP	60699470	60699470	16576	11	G	A	A	A	574	45	TMEM132A	2	2
CHRM1	1128	broad.mit.edu	37	11	62677713	62677713	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62677713G>T	uc001nwi.2	-	c.860C>A	c.(859-861)TCC>TAC	p.S287Y		NM_000738	NP_000729	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	287	Cytoplasmic (Potential).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell proliferation|nervous system development|positive regulation of cell proliferation|protein modification process	cell junction|integral to plasma membrane|membrane fraction|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity|protein binding				0					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Benztropine(DB00245)|Bethanechol(DB01019)|Biperiden(DB00810)|Buclizine(DB00354)|Carbachol(DB00411)|Carbinoxamine(DB00748)|Cevimeline(DB00185)|Clidinium(DB00771)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Doxylamine(DB00366)|Ethopropazine(DB00392)|Flavoxate(DB01148)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quinacrine(DB01103)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trospium(DB00209)									0.348485	123.227561	125.893745	46	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62677713	62677713	3510	11	G	T	T	T	533	41	CHRM1	2	2
SYT9	143425	broad.mit.edu	37	11	7334892	7334892	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7334892C>A	uc001mfe.2	+	c.764C>A	c.(763-765)ACT>AAT	p.T255N	SYT9_uc001mfd.2_Non-coding_Transcript|SYT9_uc009yfi.2_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX	255	Cytoplasmic (Potential).|C2 1.					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)										0.107527	11.382674	25.589596	10	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7334892	7334892	16002	11	C	A	A	A	260	20	SYT9	2	2
DLG2	1740	broad.mit.edu	37	11	83183817	83183817	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:83183817C>T	uc001pak.2	-	c.2297G>A	c.(2296-2298)GGA>GAA	p.G766E	DLG2_uc001pai.2_Missense_Mutation_p.G540E|DLG2_uc010rsy.1_Missense_Mutation_p.G610E|DLG2_uc001paj.2_Missense_Mutation_p.G661E|DLG2_uc010rsz.1_Missense_Mutation_p.G657E|DLG2_uc010rta.1_Missense_Mutation_p.G643E|DLG2_uc010rtb.1_Missense_Mutation_p.G628E|DLG2_uc010rsw.1_Missense_Mutation_p.G125E|DLG2_uc010rsx.1_Missense_Mutation_p.G138E	NM_001142699	NP_001136171	Q15700	DLG2_HUMAN	chapsyn-110 isoform 1	661						cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)	5		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)												0.461538	57.246887	57.297067	18	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83183817	83183817	4735	11	C	T	T	T	390	30	DLG2	2	2
RPLP0	6175	broad.mit.edu	37	12	120636435	120636435	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120636435C>A	uc001txp.2	-	c.573G>T	c.(571-573)CAG>CAT	p.Q191H	RPLP0_uc001txq.2_Missense_Mutation_p.Q191H|RPLP0_uc001txr.2_Intron	NM_053275	NP_444505	P05388	RLA0_HUMAN	ribosomal protein P0	191					endocrine pancreas development|interspecies interaction between organisms|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.391304	27.36946	27.607612	9	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120636435	120636435	14083	12	C	A	A	A	311	24	RPLP0	2	2
KDM2B	84678	broad.mit.edu	37	12	121878958	121878958	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121878958G>A	uc001uat.2	-	c.3363C>T	c.(3361-3363)ATC>ATT	p.I1121I	KDM2B_uc001uaq.2_Silent_p.I561I|KDM2B_uc010szy.1_Silent_p.I561I|KDM2B_uc001uar.2_Silent_p.I712I|KDM2B_uc001uas.2_Silent_p.I1052I|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Silent_p.I369I|KDM2B_uc010szx.1_Silent_p.I369I|KDM2B_uc001uap.2_Non-coding_Transcript	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	1121					oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)	1														0.075758	-2.180095	10.001797	5	61	KEEP	---	---	---	---	capture		Silent	SNP	121878958	121878958	8431	12	G	A	A	A	577	45	KDM2B	2	2
CACNA1C	775	broad.mit.edu	37	12	2775889	2775889	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:2775889C>A	uc009zdu.1	+	c.4708C>A	c.(4708-4710)CGG>AGG	p.R1570R	CACNA1C_uc009zdv.1_Silent_p.R1519R|CACNA1C_uc001qkb.2_Silent_p.R1522R|CACNA1C_uc001qkc.2_Silent_p.R1522R|CACNA1C_uc001qke.2_Silent_p.R1511R|CACNA1C_uc001qkf.2_Silent_p.R1511R|CACNA1C_uc001qjz.2_Silent_p.R1522R|CACNA1C_uc001qkd.2_Silent_p.R1522R|CACNA1C_uc001qkg.2_Silent_p.R1509R|CACNA1C_uc009zdw.1_Silent_p.R1544R|CACNA1C_uc001qkh.2_Silent_p.R1511R|CACNA1C_uc001qkl.2_Silent_p.R1570R|CACNA1C_uc001qkn.2_Silent_p.R1522R|CACNA1C_uc001qko.2_Silent_p.R1542R|CACNA1C_uc001qkp.2_Silent_p.R1522R|CACNA1C_uc001qkr.2_Silent_p.R1539R|CACNA1C_uc001qku.2_Silent_p.R1522R|CACNA1C_uc001qkq.2_Silent_p.R1550R|CACNA1C_uc001qks.2_Silent_p.R1522R|CACNA1C_uc001qkt.2_Silent_p.R1522R|CACNA1C_uc001qki.1_Silent_p.R1258R|CACNA1C_uc001qkj.1_Silent_p.R1258R|CACNA1C_uc001qkk.1_Silent_p.R1258R|CACNA1C_uc001qkm.1_Silent_p.R1247R|CACNA1C_uc010sea.1_Silent_p.R213R	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	1570	Cytoplasmic (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.3125	14.569868	15.070225	5	11	KEEP	---	---	---	---	capture		Silent	SNP	2775889	2775889	2656	12	C	A	A	A	295	23	CACNA1C	1	1
KIF21A	55605	broad.mit.edu	37	12	39725586	39725586	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:39725586C>G	uc001rly.2	-	c.3059G>C	c.(3058-3060)GGT>GCT	p.G1020A	KIF21A_uc001rlv.2_Missense_Mutation_p.G32A|KIF21A_uc001rlw.2_Missense_Mutation_p.G337A|KIF21A_uc001rlx.2_Missense_Mutation_p.G1007A|KIF21A_uc001rlz.2_Missense_Mutation_p.G984A|KIF21A_uc010skl.1_Missense_Mutation_p.G1007A	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1020					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|lung(1)|pancreas(1)	6		Lung NSC(34;0.179)|all_lung(34;0.213)												0.193798	63.001243	74.285043	25	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39725586	39725586	8599	12	C	G	G	G	234	18	KIF21A	3	3
GPR84	53831	broad.mit.edu	37	12	54756620	54756620	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54756620T>C	uc001sfu.2	-	c.1016A>G	c.(1015-1017)AAC>AGC	p.N339S		NM_020370	NP_065103	Q9NQS5	GPR84_HUMAN	G protein-coupled receptor 84	339	Helical; Name=6; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0														0.258929	85.326221	91.219572	29	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54756620	54756620	6989	12	T	C	C	C	780	60	GPR84	4	4
LRP1	4035	broad.mit.edu	37	12	57602924	57602924	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57602924C>T	uc001snd.2	+	c.12204C>T	c.(12202-12204)GTC>GTT	p.V4068V		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	4068	LDL-receptor class B 34.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.205128	14.870356	18.025915	8	31	KEEP	---	---	---	---	capture		Silent	SNP	57602924	57602924	9324	12	C	T	T	T	366	29	LRP1	2	2
PTPRB	5787	broad.mit.edu	37	12	70949687	70949687	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70949687G>T	uc001swc.3	-	c.4956C>A	c.(4954-4956)AGC>AGA	p.S1652R	PTPRB_uc001swb.3_Missense_Mutation_p.S1434R|PTPRB_uc010sto.1_Missense_Mutation_p.S1344R|PTPRB_uc010stp.1_Missense_Mutation_p.S1344R|PTPRB_uc001swa.3_Missense_Mutation_p.S1564R	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1434	Fibronectin type-III 16.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)											0.209459	75.049696	86.608545	31	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70949687	70949687	13253	12	G	T	T	T	490	38	PTPRB	1	1
NALCN	259232	broad.mit.edu	37	13	101728244	101728244	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101728244A>G	uc001vox.1	-	c.3934T>C	c.(3934-3936)TTC>CTC	p.F1312L		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1312	Helical; Voltage-sensor; Name=S4 of repeat IV; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.322917	100.093606	102.76518	31	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101728244	101728244	10544	13	A	G	G	G	13	1	NALCN	4	4
N6AMT2	221143	broad.mit.edu	37	13	21306050	21306050	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:21306050C>T	uc001uno.1	-	c.438G>A	c.(436-438)TCG>TCA	p.S146S	N6AMT2_uc009zzr.1_Silent_p.S146S|N6AMT2_uc001unp.2_Non-coding_Transcript	NM_174928	NP_777588	Q8WVE0	N6MT2_HUMAN	N-6 adenine-specific DNA methyltransferase 2	146							methyltransferase activity|nucleic acid binding				0		all_cancers(29;5.91e-19)|all_epithelial(30;1.42e-15)|all_lung(29;5.9e-14)|Lung SC(185;0.0367)		all cancers(112;0.000234)|Epithelial(112;0.000471)|OV - Ovarian serous cystadenocarcinoma(117;0.0111)|Lung(94;0.0161)|LUSC - Lung squamous cell carcinoma(192;0.0431)										0.111111	3.906603	7.942028	3	24	KEEP	---	---	---	---	capture		Silent	SNP	21306050	21306050	10510	13	C	T	T	T	288	23	N6AMT2	1	1
AHNAK2	113146	broad.mit.edu	37	14	105418309	105418309	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105418309T>A	uc010axc.1	-	c.3479A>T	c.(3478-3480)GAC>GTC	p.D1160V	AHNAK2_uc001ypx.2_Missense_Mutation_p.D1060V	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1160						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.303571	44.353669	46.282235	17	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105418309	105418309	418	14	T	A	A	A	754	58	AHNAK2	3	3
LRFN5	145581	broad.mit.edu	37	14	42356187	42356187	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:42356187G>T	uc001wvm.2	+	c.359G>T	c.(358-360)AGT>ATT	p.S120I	LRFN5_uc010ana.2_Missense_Mutation_p.S120I	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	120	Extracellular (Potential).|LRR 3.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)										0.186047	16.274891	20.247282	8	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42356187	42356187	9314	14	G	T	T	T	468	36	LRFN5	2	2
SLC35F4	341880	broad.mit.edu	37	14	58033246	58033246	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:58033246G>T	uc001xdb.1	-	c.1271C>A	c.(1270-1272)ACA>AAA	p.T424K	SLC35F4_uc010aoz.1_Non-coding_Transcript|SLC35F4_uc010apa.1_Missense_Mutation_p.T265K	NM_001080455	NP_001073924	A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	424	Helical; (Potential).				transport	integral to membrane				ovary(2)	2														0.217391	12.561874	14.256053	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58033246	58033246	15088	14	G	T	T	T	624	48	SLC35F4	2	2
GALNTL1	57452	broad.mit.edu	37	14	69798189	69798189	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:69798189C>A	uc010aqu.1	+	c.699C>A	c.(697-699)ACC>ACA	p.T233T	GALNTL1_uc001xla.1_Silent_p.T233T|GALNTL1_uc001xlb.1_Silent_p.T233T	NM_020692	NP_065743	Q8N428	GLTL1_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	233	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)	2				all cancers(60;0.00793)|BRCA - Breast invasive adenocarcinoma(234;0.0174)|OV - Ovarian serous cystadenocarcinoma(108;0.0656)										0.197452	67.846822	81.223309	31	126	KEEP	---	---	---	---	capture		Silent	SNP	69798189	69798189	6485	14	C	A	A	A	275	22	GALNTL1	2	2
ANGEL1	23357	broad.mit.edu	37	14	77272897	77272897	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77272897C>A	uc001xsv.2	-	c.1242G>T	c.(1240-1242)GTG>GTT	p.V414V	ANGEL1_uc010tvf.1_Intron	NM_015305	NP_056120	Q9UNK9	ANGE1_HUMAN	angel homolog 1	414										ovary(2)|central_nervous_system(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)										0.296296	42.479351	44.483215	16	38	KEEP	---	---	---	---	capture		Silent	SNP	77272897	77272897	611	14	C	A	A	A	262	21	ANGEL1	2	2
SPTBN5	51332	broad.mit.edu	37	15	42147101	42147101	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42147101C>A	uc001zos.2	-	c.9392G>T	c.(9391-9393)AGG>ATG	p.R3131M		NM_016642	NP_057726	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3166	Spectrin 28.				actin cytoskeleton organization|actin filament capping|axon guidance	cytosol|membrane|spectrin				ovary(1)|central_nervous_system(1)	2		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)										0.206897	12.832934	15.142848	6	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42147101	42147101	15636	15	C	A	A	A	312	24	SPTBN5	2	2
DUOX2	50506	broad.mit.edu	37	15	45388110	45388110	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:45388110G>T	uc010bea.2	-	c.3996C>A	c.(3994-3996)CAC>CAA	p.H1332Q	DUOX2_uc001zun.2_Missense_Mutation_p.H1332Q	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1332	Cytoplasmic (Potential).|FAD-binding FR-type.				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|pancreas(1)	3		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)										0.153846	19.928716	28.907369	12	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45388110	45388110	4986	15	G	T	T	T	620	48	DUOX2	2	2
SLC24A5	283652	broad.mit.edu	37	15	48426633	48426633	+	Silent	SNP	T	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48426633T>C	uc001zwe.2	+	c.387T>C	c.(385-387)GGT>GGC	p.G129G	SLC24A5_uc010bel.2_Silent_p.G69G	NM_205850	NP_995322	Q71RS6	NCKX5_HUMAN	solute carrier family 24, member 5 precursor	129	Helical; Name=2; (Potential).				response to stimulus	integral to membrane|melanosome|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity				0		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)										0.168675	25.982982	34.644118	14	69	KEEP	---	---	---	---	capture		Silent	SNP	48426633	48426633	14966	15	T	C	C	C	756	59	SLC24A5	4	4
XYLT1	64131	broad.mit.edu	37	16	17294464	17294464	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:17294464T>A	uc002dfa.2	-	c.961A>T	c.(961-963)ATG>TTG	p.M321L		NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	321	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4														0.313008	231.691235	239.34424	77	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17294464	17294464	18046	16	T	A	A	A	663	51	XYLT1	3	3
GP2	2813	broad.mit.edu	37	16	20329668	20329668	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20329668G>A	uc002dgv.2	-	c.1101C>T	c.(1099-1101)TAC>TAT	p.Y367Y	GP2_uc002dgw.2_Silent_p.Y364Y|GP2_uc002dgx.2_Silent_p.Y220Y|GP2_uc002dgy.2_Silent_p.Y217Y	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	367	ZP.					anchored to membrane|extracellular region|plasma membrane				ovary(3)	3														0.223529	183.5382	207.419077	76	264	KEEP	---	---	---	---	capture		Silent	SNP	20329668	20329668	6856	16	G	A	A	A	516	40	GP2	1	1
ABCC12	94160	broad.mit.edu	37	16	48174704	48174704	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48174704C>T	uc002efc.1	-	c.551G>A	c.(550-552)TGG>TAG	p.W184*	ABCC12_uc002eey.1_Non-coding_Transcript|ABCC12_uc002eez.1_Non-coding_Transcript|ABCC12_uc002efa.1_Non-coding_Transcript|ABCC12_uc002efb.1_Non-coding_Transcript|ABCC12_uc002efd.1_Non-coding_Transcript|ABCC12_uc002efe.1_Nonsense_Mutation_p.W184*|ABCC12_uc010vgj.1_Non-coding_Transcript	NM_033226	NP_150229	Q96J65	MRP9_HUMAN	ATP-binding cassette protein C12	184	ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(2)	2		all_cancers(37;0.0474)|all_lung(18;0.047)												0.136585	40.550383	66.774055	28	177	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	48174704	48174704	53	16	C	T	T	T	273	21	ABCC12	5	2
ABCC11	85320	broad.mit.edu	37	16	48204061	48204061	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:48204061C>T	uc002eff.1	-	c.3846G>A	c.(3844-3846)GAG>GAA	p.E1282E	ABCC11_uc002efg.1_Silent_p.E1282E|ABCC11_uc002efh.1_Intron|ABCC11_uc010cbg.1_Non-coding_Transcript	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	1282	ABC transporter 2.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|central_nervous_system(1)	4		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												0.188525	99.798675	121.960096	46	198	KEEP	---	---	---	---	capture		Silent	SNP	48204061	48204061	52	16	C	T	T	T	415	32	ABCC11	2	2
NOD2	64127	broad.mit.edu	37	16	50745449	50745449	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:50745449C>T	uc002egm.1	+	c.1627C>T	c.(1627-1629)CGC>TGC	p.R543C	NOD2_uc010cbk.1_Missense_Mutation_p.R516C|NOD2_uc002egl.1_Missense_Mutation_p.R321C|NOD2_uc010cbl.1_Missense_Mutation_p.R321C|NOD2_uc010cbm.1_Missense_Mutation_p.R321C|NOD2_uc010cbn.1_Non-coding_Transcript|NOD2_uc010cbo.1_Non-coding_Transcript|NOD2_uc010cbp.1_5'Flank|NOD2_uc010cbq.1_5'Flank|NOD2_uc010cbr.1_5'Flank	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	543	NACHT.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)	3		all_cancers(37;0.0156)												0.105263	2.578308	8.461045	4	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50745449	50745449	10920	16	C	T	T	T	299	23	NOD2	1	1
SDR42E1	93517	broad.mit.edu	37	16	82033761	82033761	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:82033761G>C	uc002fgu.2	-	c.137C>G	c.(136-138)ACC>AGC	p.T46S		NM_145168	NP_660151	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E,	46					oxidation-reduction process|steroid biosynthetic process	integral to membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding				0														0.14554	60.642983	86.330744	31	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82033761	82033761	14459	16	G	C	C	C	572	44	SDR42E1	3	3
MYH2	4620	broad.mit.edu	37	17	10430315	10430315	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10430315G>T	uc010coi.2	-	c.3930C>A	c.(3928-3930)GGC>GGA	p.G1310G	MYH2_uc002gmp.3_Silent_p.G1310G|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1310	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.090909	2.274367	9.689989	4	40	KEEP	---	---	---	---	capture		Silent	SNP	10430315	10430315	10430	17	G	T	T	T	587	46	MYH2	2	2
MYO1D	4642	broad.mit.edu	37	17	31107692	31107692	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:31107692C>A	uc002hho.1	-	c.206G>T	c.(205-207)CGT>CTT	p.R69L	MYO1D_uc002hhp.1_Missense_Mutation_p.R69L|MYO1D_uc010wcb.1_Missense_Mutation_p.R69L	NM_015194	NP_056009	O94832	MYO1D_HUMAN	myosin ID	69	Myosin head-like.					myosin complex	actin binding|ATP binding|calmodulin binding			large_intestine(1)|ovary(1)|central_nervous_system(1)	3			BRCA - Breast invasive adenocarcinoma(9;0.0362)											0.20339	30.871528	35.686388	12	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31107692	31107692	10466	17	C	A	A	A	247	19	MYO1D	1	1
UNC45B	146862	broad.mit.edu	37	17	33496891	33496891	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33496891C>G	uc002hja.2	+	c.1488C>G	c.(1486-1488)GAC>GAG	p.D496E	UNC45B_uc002hjb.2_Missense_Mutation_p.D496E|UNC45B_uc002hjc.2_Missense_Mutation_p.D496E|UNC45B_uc010cto.2_Intron	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	496			D -> H (in a breast cancer sample; somatic mutation).		cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.318182	43.13334	44.426818	14	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33496891	33496891	17547	17	C	G	G	G	259	20	UNC45B	3	3
KRTAP1-3	81850	broad.mit.edu	37	17	39190779	39190779	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39190779T>C	uc002hvv.2	-	c.295A>G	c.(295-297)AGT>GGT	p.S99G		NM_030966	NP_112228	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	109						extracellular region|keratin filament	structural constituent of epidermis				0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)											0.078947	0.902317	7.775129	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39190779	39190779	8818	17	T	C	C	C	715	55	KRTAP1-3	4	4
MEOX1	4222	broad.mit.edu	37	17	41738663	41738663	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:41738663G>T	uc002idz.2	-	c.240C>A	c.(238-240)ATC>ATA	p.I80I	MEOX1_uc002iea.2_Silent_p.I80I|MEOX1_uc002ieb.2_5'UTR	NM_004527	NP_004518	P50221	MEOX1_HUMAN	mesenchyme homeobox 1 isoform 1	80						nucleus	sequence-specific DNA binding|transcription regulator activity				0		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0753)										0.175	13.398771	17.385704	7	33	KEEP	---	---	---	---	capture		Silent	SNP	41738663	41738663	9862	17	G	T	T	T	421	33	MEOX1	2	2
MYCBPAP	84073	broad.mit.edu	37	17	48586035	48586035	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:48586035C>T	uc010wmr.1	+	c.129C>T	c.(127-129)ACC>ACT	p.T43T	MYCBPAP_uc002iqx.2_Silent_p.T43T|MYCBPAP_uc002iqz.2_Non-coding_Transcript	NM_032133	NP_115509	Q8TBZ2	MYBPP_HUMAN	Myc-binding protein-associated protein	6					cell differentiation|multicellular organismal development|spermatogenesis|synaptic transmission	cytoplasm|membrane	protein binding			urinary_tract(2)|ovary(1)|pancreas(1)	4	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)											0.421053	21.183042	21.288849	8	11	KEEP	---	---	---	---	capture		Silent	SNP	48586035	48586035	10414	17	C	T	T	T	262	21	MYCBPAP	2	2
MARCH10	162333	broad.mit.edu	37	17	60813722	60813722	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60813722C>T	uc010dds.2	-	c.1621G>A	c.(1621-1623)GGA>AGA	p.G541R	MARCH10_uc010ddr.2_Missense_Mutation_p.G503R|MARCH10_uc002jag.3_Missense_Mutation_p.G503R|MARCH10_uc002jah.2_Missense_Mutation_p.G502R	NM_152598	NP_689811	Q8NA82	MARHA_HUMAN	ring finger protein 190	503							ligase activity|zinc ion binding				0														0.255814	58.012698	62.661214	22	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60813722	60813722	9682	17	C	T	T	T	286	22	MARCH10	2	2
TP53	7157	broad.mit.edu	37	17	7578550	7578550	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578550G>A	uc002gim.2	-	c.380C>T	c.(379-381)TCC>TTC	p.S127F	TP53_uc002gig.1_Missense_Mutation_p.S127F|TP53_uc002gih.2_Missense_Mutation_p.S127F|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'UTR|TP53_uc010cng.1_5'UTR|TP53_uc002gii.1_5'UTR|TP53_uc010cnh.1_Missense_Mutation_p.S127F|TP53_uc010cni.1_Missense_Mutation_p.S127F|TP53_uc002gij.2_Missense_Mutation_p.S127F|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.S34F|TP53_uc002gio.2_5'UTR|TP53_uc010vug.1_Missense_Mutation_p.S88F	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	127	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		S -> C (in a sporadic cancer; somatic mutation).|S -> F (in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).|S -> P (in sporadic cancers; somatic mutation).|S -> T (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.S127F(18)|p.S127Y(8)|p.0?(6)|p.Y126_K132delYSPALNK(6)|p.Y126_N131delYSPALN(3)|p.P128fs*42(2)|p.V73fs*9(1)|p.S127fs*36(1)|p.P128fs*18(1)|p.Y126fs*11(1)|p.S127C(1)|p.S127_Q136del10(1)|p.P13fs*18(1)|p.?(1)|p.S127fs*42(1)|p.Y126fs*18(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	(CORL279-Tumor)|p.S127F(SNU410-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.32	44.180991	45.621066	16	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7578550	7578550	16923	17	G	A	A	A	533	41	TP53	2	2
PIK3R6	146850	broad.mit.edu	37	17	8730560	8730560	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:8730560C>A	uc002glq.1	-	c.1444G>T	c.(1444-1446)GGC>TGC	p.G482C	PIK3R6_uc002glr.1_Non-coding_Transcript|PIK3R6_uc002gls.1_Non-coding_Transcript	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	482					platelet activation	cytosol					0														0.347826	19.491566	19.962115	8	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8730560	8730560	12347	17	C	A	A	A	286	22	PIK3R6	2	2
ALPK2	115701	broad.mit.edu	37	18	56247641	56247641	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:56247641T>A	uc002lhj.3	-	c.367A>T	c.(367-369)AGG>TGG	p.R123W		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	123					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11										343				0.049505	-10.513273	11.246938	5	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56247641	56247641	548	18	T	A	A	A	713	55	ALPK2	3	3
SERPINB5	5268	broad.mit.edu	37	18	61170670	61170670	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61170670G>T	uc002liz.3	+	c.843G>T	c.(841-843)ATG>ATT	p.M281I		NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	281					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1														0.1	3.134602	11.12983	5	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61170670	61170670	14592	18	G	T	T	T	585	45	SERPINB5	2	2
SERPINB4	6318	broad.mit.edu	37	18	61305029	61305029	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61305029T>C	uc002ljf.2	-	c.1097A>G	c.(1096-1098)AAT>AGT	p.N366S	SERPINB4_uc002lje.2_Missense_Mutation_p.N345S|SERPINB4_uc002ljg.2_Missense_Mutation_p.N366S	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	366					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.266055	87.630153	93.016424	29	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61305029	61305029	14591	18	T	C	C	C	676	52	SERPINB4	4	4
KEAP1	9817	broad.mit.edu	37	19	10602334	10602334	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10602334C>T	uc002moq.1	-	c.1244G>A	c.(1243-1245)CGC>CAC	p.R415H	KEAP1_uc002mop.1_Missense_Mutation_p.R133H|KEAP1_uc002mor.1_Missense_Mutation_p.R415H	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	415	Kelch 2.			R->A: Loss of interaction with NFE2L2. Abolishes repression of NFE2L2-dependent gene expression. Loss of interaction with PGAM5.	regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)											0.588235	31.851046	31.96661	10	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10602334	10602334	8447	19	C	T	T	T	351	27	KEAP1	1	1
RGL3	57139	broad.mit.edu	37	19	11507974	11507974	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11507974G>A	uc002mro.2	-	c.1978C>T	c.(1978-1980)CCC>TCC	p.P660S	RGL3_uc002mrn.2_Missense_Mutation_p.P418S|RGL3_uc002mrm.2_Missense_Mutation_p.P418S|RGL3_uc002mrp.2_Missense_Mutation_p.P654S	NM_001161616	NP_001155088	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	654	Interaction with HRAS, MRAS and RIT1 (By similarity).|Ras-associating.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						GBM(174;751 2067 17998 27979 33959)				120				0.403846	59.077435	59.493404	21	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11507974	11507974	13751	19	G	A	A	A	546	42	RGL3	2	2
OR7A17	26333	broad.mit.edu	37	19	14991763	14991763	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14991763G>T	uc010xob.1	-	c.405C>A	c.(403-405)ATC>ATA	p.I135I		NM_030901	NP_112163	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A,	135	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	Ovarian(108;0.203)													0.36	97.263965	98.992867	36	64	KEEP	---	---	---	---	capture		Silent	SNP	14991763	14991763	11626	19	G	T	T	T	577	45	OR7A17	2	2
UPF1	5976	broad.mit.edu	37	19	18971211	18971211	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18971211A>T	uc002nkg.2	+	c.2297A>T	c.(2296-2298)GAG>GTG	p.E766V	UPF1_uc002nkf.2_Missense_Mutation_p.E755V|UPF1_uc002nkh.2_Missense_Mutation_p.E10V	NM_002911	NP_002902	Q92900	RENT1_HUMAN	regulator of nonsense transcripts 1	766					cell cycle|DNA repair|DNA replication|histone mRNA catabolic process|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translational termination	chromatin|cytoplasmic mRNA processing body|exon-exon junction complex	ATP binding|ATP-dependent RNA helicase activity|chromatin binding|DNA binding|protein binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1														0.304348	38.731415	40.303294	14	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18971211	18971211	17563	19	A	T	T	T	143	11	UPF1	3	3
ZNF382	84911	broad.mit.edu	37	19	37117340	37117340	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37117340C>T	uc002oek.2	+	c.541C>T	c.(541-543)CCT>TCT	p.P181S	ZNF382_uc010efa.2_Missense_Mutation_p.P132S|ZNF382_uc010efb.2_Missense_Mutation_p.P180S|ZNF382_uc002oel.2_Missense_Mutation_p.P180S	NM_032825	NP_116214	Q96SR6	ZN382_HUMAN	zinc finger protein 382	181	Represses transcription (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)											0.252336	66.368634	72.33401	27	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37117340	37117340	18465	19	C	T	T	T	390	30	ZNF382	2	2
SIRT2	22933	broad.mit.edu	37	19	39372103	39372103	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:39372103C>A	uc002ojt.1	-	c.660G>T	c.(658-660)AAG>AAT	p.K220N	SIRT2_uc010egh.1_Missense_Mutation_p.K183N|SIRT2_uc010egi.1_Missense_Mutation_p.K183N|SIRT2_uc002ojs.1_Missense_Mutation_p.K200N|SIRT2_uc002oju.1_Missense_Mutation_p.K183N|SIRT2_uc010egj.1_Missense_Mutation_p.K183N|SIRT2_uc002ojv.1_Missense_Mutation_p.K218N	NM_012237	NP_036369	Q8IXJ6	SIRT2_HUMAN	sirtuin 2 isoform 1	220	Deacetylase sirtuin-type.				cell division|chromatin silencing at rDNA|chromatin silencing at telomere|mitosis|negative regulation of striated muscle tissue development|protein ADP-ribosylation|regulation of exit from mitosis|regulation of phosphorylation|response to redox state	chromatin silencing complex|cytoplasm|microtubule	histone acetyltransferase binding|histone deacetylase binding|NAD+ binding|NAD-dependent histone deacetylase activity|transcription factor binding|tubulin deacetylase activity|ubiquitin binding|zinc ion binding				0	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)											0.365854	45.114781	45.763354	15	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39372103	39372103	14833	19	C	A	A	A	259	20	SIRT2	2	2
PSG1	5669	broad.mit.edu	37	19	43376074	43376074	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43376074T>A	uc010eio.1	-	c.554A>T	c.(553-555)CAG>CTG	p.Q185L	PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.Q185L|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_Non-coding_Transcript|PSG1_uc002our.1_Missense_Mutation_p.Q185L|PSG1_uc002oux.1_Missense_Mutation_p.Q114L|PSG1_uc002ouy.1_Missense_Mutation_p.Q185L|PSG1_uc002ouz.1_Missense_Mutation_p.Q185L|PSG1_uc002ova.1_Intron|PSG1_uc002ovb.2_Missense_Mutation_p.Q185L|PSG1_uc002ovc.2_Intron|PSG1_uc002ovd.1_Missense_Mutation_p.Q185L	NM_006905	NP_008836	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	185	Ig-like C2-type 1.				female pregnancy	extracellular region				ovary(2)	2		Prostate(69;0.00682)												0.354402	478.655929	486.929516	157	286	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43376074	43376074	13106	19	T	A	A	A	715	55	PSG1	3	3
ZNF285	26974	broad.mit.edu	37	19	44892196	44892196	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44892196G>C	uc010xxa.1	-	c.232C>G	c.(232-234)CTT>GTT	p.L78V	ZFP112_uc010xwz.1_Intron|ZNF285_uc002ozd.3_Missense_Mutation_p.L71V	NM_152354	NP_689567	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	71	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.298246	52.152449	54.226414	17	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44892196	44892196	18414	19	G	C	C	C	442	34	ZNF285	3	3
SIGLEC6	946	broad.mit.edu	37	19	52031475	52031475	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52031475C>A	uc002pwy.2	-	c.1045G>T	c.(1045-1047)GGA>TGA	p.G349*	SIGLEC6_uc002pwz.2_Nonsense_Mutation_p.G333*|SIGLEC6_uc002pxa.2_Intron|SIGLEC6_uc010ydb.1_Nonsense_Mutation_p.G286*|SIGLEC6_uc010ydc.1_Nonsense_Mutation_p.G349*|SIGLEC6_uc010eoz.1_Intron	NM_001245	NP_001236	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6 isoform 1	349	Helical; (Potential).				cell adhesion|cell-cell signaling	cytoplasm|extracellular region|integral to plasma membrane|membrane fraction|nucleus				ovary(1)	1		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)										0.36	51.334998	52.19828	18	32	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52031475	52031475	14807	19	C	A	A	A	286	22	SIGLEC6	5	2
FPR2	2358	broad.mit.edu	37	19	52272462	52272462	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52272462G>T	uc002pxr.2	+	c.551G>T	c.(550-552)GGT>GTT	p.G184V	FPR2_uc002pxs.3_Missense_Mutation_p.G184V|FPR2_uc010epf.2_Missense_Mutation_p.G184V	NM_001005738	NP_001005738	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	184	Extracellular (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.287234	70.165952	73.997863	27	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52272462	52272462	6285	19	G	T	T	T	572	44	FPR2	2	2
MCOLN1	57192	broad.mit.edu	37	19	7593514	7593514	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:7593514G>T	uc002mgo.2	+	c.909G>T	c.(907-909)GTG>GTT	p.V303V	MCOLN1_uc002mgp.2_Silent_p.V268V	NM_020533	NP_065394	Q9GZU1	MCLN1_HUMAN	mucolipin 1	303	Helical; (Potential).				calcium ion transport|cellular iron ion homeostasis|transferrin transport	integral to plasma membrane|late endosome membrane|lysosomal membrane	cation channel activity|iron ion transmembrane transporter activity			breast(1)	1														0.441176	46.119946	46.222562	15	19	KEEP	---	---	---	---	capture		Silent	SNP	7593514	7593514	9784	19	G	T	T	T	600	47	MCOLN1	2	2
KCNA2	3737	broad.mit.edu	37	1	111146103	111146103	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:111146103G>A	uc001dzu.2	-	c.1302C>T	c.(1300-1302)AGC>AGT	p.S434S	KCNA2_uc009wfv.1_Intron|KCNA2_uc009wfw.2_Silent_p.S434S	NM_004974	NP_004965	P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related	434						juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(1)	1		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)		Pancreas(18;568 735 10587 23710 36357)								0.183099	27.829073	34.525667	13	58	KEEP	---	---	---	---	capture		Silent	SNP	111146103	111146103	8308	1	G	A	A	A	438	34	KCNA2	2	2
WNT2B	7482	broad.mit.edu	37	1	113033704	113033704	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:113033704G>T	uc001eca.2	+	c.125_splice	c.e2+1	p.R42_splice	WNT2B_uc009wgg.2_Intron	NM_004185	NP_004176			wingless-type MMTV integration site family,						chondrocyte differentiation|cornea development in camera-type eye|dorsal/ventral axis specification|forebrain regionalization|hemopoietic stem cell proliferation|iris morphogenesis|lens development in camera-type eye|lung induction|male gonad development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	frizzled-2 binding|signal transducer activity			ovary(1)	1	Lung SC(450;0.246)	all_cancers(81;7.31e-07)|all_epithelial(167;4.59e-06)|all_lung(203;2.56e-05)|Lung NSC(69;4.38e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.214286	7.717545	8.772595	3	11	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	113033704	113033704	17961	1	G	T	T	T	572	44	WNT2B	5	2
PTCHD2	57540	broad.mit.edu	37	1	11585275	11585275	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:11585275G>T	uc001ash.3	+	c.2519G>T	c.(2518-2520)GGC>GTC	p.G840V	PTCHD2_uc001asi.1_Missense_Mutation_p.G840V	NM_020780	NP_065831	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	840	Extracellular (Potential).				cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway	endoplasmic reticulum|integral to membrane|nuclear membrane	hedgehog receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)										0.243243	18.982742	21.196309	9	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11585275	11585275	13187	1	G	T	T	T	546	42	PTCHD2	2	2
NOTCH2	4853	broad.mit.edu	37	1	120466412	120466412	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120466412C>A	uc001eik.2	-	c.4707G>T	c.(4705-4707)CTG>CTT	p.L1569L		NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	1569	Negative regulatory region (NRR).|Extracellular (Potential).				anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(7)|ovary(4)|lung(3)|central_nervous_system(2)|kidney(2)|breast(1)	19	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)						581				0.264151	36.027738	38.692026	14	39	KEEP	---	---	---	---	capture		Silent	SNP	120466412	120466412	10951	1	C	A	A	A	262	21	NOTCH2	2	2
PRUNE	58497	broad.mit.edu	37	1	150998086	150998086	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:150998086C>G	uc001ewh.1	+	c.616C>G	c.(616-618)CCA>GCA	p.P206A	PRUNE_uc001ewi.1_Missense_Mutation_p.P24A|PRUNE_uc010pco.1_Intron|PRUNE_uc001ewj.1_Intron|PRUNE_uc001ewk.1_Missense_Mutation_p.P24A	NM_021222	NP_067045	Q86TP1	PRUNE_HUMAN	prune	206						cytoplasm|focal adhesion|nucleus	inorganic diphosphatase activity|manganese ion binding|protein binding			ovary(1)	1	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)											0.144928	48.608531	73.725191	30	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150998086	150998086	13091	1	C	G	G	G	286	22	PRUNE	3	3
SEMA6C	10500	broad.mit.edu	37	1	151107786	151107786	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:151107786C>A	uc001ewv.2	-	c.1434_splice	c.e15-1	p.R478_splice	SEMA6C_uc001ewu.2_Splice_Site_SNP_p.R478_splice|SEMA6C_uc001eww.2_Splice_Site_SNP_p.R438_splice|SEMA6C_uc010pcq.1_Splice_Site_SNP_p.R478_splice	NM_030913	NP_112175			semaphorin Y precursor							integral to membrane	receptor activity			ovary(1)	1	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)											0.328358	59.825952	61.576746	22	45	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	151107786	151107786	14527	1	C	A	A	A	312	24	SEMA6C	5	2
HRNR	388697	broad.mit.edu	37	1	152191897	152191897	+	Silent	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152191897T>A	uc001ezt.1	-	c.2208A>T	c.(2206-2208)TCA>TCT	p.S736S		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	736	7.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.15873	20.710364	27.701535	10	53	KEEP	---	---	---	---	capture		Silent	SNP	152191897	152191897	7653	1	T	A	A	A	652	51	HRNR	3	3
DCST1	149095	broad.mit.edu	37	1	155011886	155011886	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155011886G>T	uc001fgn.1	+	c.270G>T	c.(268-270)GGG>GGT	p.G90G	DCST1_uc010per.1_Silent_p.G115G|DCST1_uc010pes.1_Silent_p.G65G	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	90	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)											0.080808	0.120254	17.85334	8	91	KEEP	---	---	---	---	capture		Silent	SNP	155011886	155011886	4473	1	G	T	T	T	548	43	DCST1	2	2
IGSF9	57549	broad.mit.edu	37	1	159912758	159912758	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:159912758T>A	uc001fur.2	-	c.242A>T	c.(241-243)TAC>TTC	p.Y81F	IGSF9_uc001fuq.2_Missense_Mutation_p.Y81F	NM_001135050	NP_001128522	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9 isoform a	81	Ig-like 1.|Extracellular (Potential).					cell junction|integral to membrane|synapse				ovary(2)|central_nervous_system(2)|large_intestine(1)	5	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)											0.392157	60.490174	61.009096	20	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159912758	159912758	7906	1	T	A	A	A	741	57	IGSF9	3	3
LY9	4063	broad.mit.edu	37	1	160783558	160783558	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160783558C>A	uc001fwu.2	+	c.587C>A	c.(586-588)CCC>CAC	p.P196H	LY9_uc010pjs.1_Missense_Mutation_p.P196H|LY9_uc001fwv.2_Missense_Mutation_p.P196H|LY9_uc001fww.2_Missense_Mutation_p.P196H|LY9_uc001fwx.2_Missense_Mutation_p.P196H|LY9_uc001fwy.1_Missense_Mutation_p.P98H|LY9_uc001fwz.2_5'Flank	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	196	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)											0.239362	113.976084	125.639243	45	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160783558	160783558	9478	1	C	A	A	A	286	22	LY9	2	2
CDC42BPA	8476	broad.mit.edu	37	1	227381578	227381578	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:227381578C>A	uc001hqr.2	-	c.508G>T	c.(508-510)GAA>TAA	p.E170*	CDC42BPA_uc001hqs.2_Nonsense_Mutation_p.E170*|CDC42BPA_uc009xes.2_Nonsense_Mutation_p.E170*|CDC42BPA_uc010pvs.1_Nonsense_Mutation_p.E170*	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	170	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction|protein phosphorylation	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(6)|breast(2)|ovary(1)|pancreas(1)	10		all_cancers(173;0.156)|Prostate(94;0.0792)								1574				0.372093	45.786501	46.405422	16	27	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	227381578	227381578	3200	1	C	A	A	A	377	29	CDC42BPA	5	2
GUK1	2987	broad.mit.edu	37	1	228335158	228335158	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228335158C>A	uc001hsi.2	+	c.366C>A	c.(364-366)GAC>GAA	p.D122E	GUK1_uc001hsh.2_Missense_Mutation_p.D101E|GUK1_uc001hsj.2_Missense_Mutation_p.D41E|GUK1_uc010pvv.1_Missense_Mutation_p.D101E|GJC2_uc001hsk.2_5'Flank	NM_001159390	NP_001152862	Q16774	KGUA_HUMAN	guanylate kinase 1 isoform a	101	Guanylate kinase-like.				nucleobase, nucleoside and nucleotide interconversion|purine nucleotide metabolic process	cytosol	ATP binding|guanylate kinase activity				0		Prostate(94;0.0405)												0.069767	-0.809632	7.407493	3	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228335158	228335158	7180	1	C	A	A	A	246	19	GUK1	1	1
URB2	9816	broad.mit.edu	37	1	229772543	229772543	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:229772543G>T	uc001hts.1	+	c.2183G>T	c.(2182-2184)GGG>GTG	p.G728V	URB2_uc009xfd.1_Missense_Mutation_p.G728V	NM_014777	NP_055592	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog	728						nucleolus				central_nervous_system(2)|ovary(1)	3										340				0.132231	23.618146	39.515657	16	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	229772543	229772543	17587	1	G	T	T	T	559	43	URB2	2	2
RYR2	6262	broad.mit.edu	37	1	237947956	237947956	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237947956G>T	uc001hyl.1	+	c.12944G>T	c.(12943-12945)GGG>GTG	p.G4315V	RYR2_uc010pya.1_Missense_Mutation_p.G730V	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4315					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)											0.376344	99.618368	100.8601	35	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237947956	237947956	14249	1	G	T	T	T	559	43	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237993849	237993849	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237993849G>T	uc001hyl.1	+	c.14675G>T	c.(14674-14676)GGG>GTG	p.G4892V	RYR2_uc010pyb.1_Intron	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4892					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)											0.0563	-34.648565	42.558282	21	352	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237993849	237993849	14249	1	G	T	T	T	559	43	RYR2	2	2
FMN2	56776	broad.mit.edu	37	1	240635683	240635683	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:240635683C>A	uc010pye.1	+	c.5084C>A	c.(5083-5085)GCC>GAC	p.A1695D	FMN2_uc010pyd.1_Missense_Mutation_p.A1691D|FMN2_uc010pyg.1_Missense_Mutation_p.A287D|FMN2_uc001hyr.2_Non-coding_Transcript	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	1691	Potential.|FH2.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)							1289				0.358209	69.291902	70.47355	24	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	240635683	240635683	6192	1	C	A	A	A	338	26	FMN2	2	2
WDTC1	23038	broad.mit.edu	37	1	27614294	27614294	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:27614294G>T	uc009vst.2	+	c.421G>T	c.(421-423)GCC>TCC	p.A141S	WDTC1_uc001bno.2_Missense_Mutation_p.A141S|WDTC1_uc001bnp.1_Non-coding_Transcript	NM_015023	NP_055838	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	141	WD 3.						protein binding			ovary(1)|central_nervous_system(1)	2		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)										0.217391	13.063733	14.756404	5	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27614294	27614294	17916	1	G	T	T	T	494	38	WDTC1	1	1
SNRNP40	9410	broad.mit.edu	37	1	31740734	31740734	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:31740734C>A	uc010oge.1	-	c.904G>T	c.(904-906)GCT>TCT	p.A302S	SNRNP40_uc009vtt.2_5'UTR|SNRNP40_uc001bso.2_Missense_Mutation_p.A302S	NM_004814	NP_004805	Q96DI7	SNR40_HUMAN	WD repeat domain 57 (U5 snRNP specific)	302	WD 6.				nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|cytoplasm|nucleoplasm|small nucleolar ribonucleoprotein complex|U5 snRNP	protein binding				0														0.216667	30.241791	34.685007	13	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31740734	31740734	15356	1	C	A	A	A	364	28	SNRNP40	2	2
TIE1	7075	broad.mit.edu	37	1	43774757	43774757	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43774757G>A	uc001ciu.2	+	c.1143G>A	c.(1141-1143)GTG>GTA	p.V381V	TIE1_uc010okd.1_Silent_p.V381V|TIE1_uc010oke.1_Silent_p.V336V|TIE1_uc009vwq.2_Silent_p.V337V|TIE1_uc010okf.1_Silent_p.V26V|TIE1_uc010okg.1_Silent_p.V26V|TIE1_uc010okc.1_Intron	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	381	Ig-like C2-type 2.|Extracellular (Potential).				mesoderm development|protein phosphorylation	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			stomach(1)|salivary_gland(1)|lung(1)|ovary(1)	4	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)								488				0.219048	46.786808	54.413821	23	82	KEEP	---	---	---	---	capture		Silent	SNP	43774757	43774757	16421	1	G	A	A	A	587	46	TIE1	2	2
DMRTB1	63948	broad.mit.edu	37	1	53927147	53927147	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53927147G>T	uc001cvq.1	+	c.579G>T	c.(577-579)GTG>GTT	p.V193V		NM_033067	NP_149056	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal,	193	Pro-rich.				regulation of transcription, DNA-dependent|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity				0														0.076923	-0.343807	9.186764	4	48	KEEP	---	---	---	---	capture		Silent	SNP	53927147	53927147	4770	1	G	T	T	T	587	46	DMRTB1	2	2
ASB17	127247	broad.mit.edu	37	1	76397586	76397586	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:76397586G>A	uc001dhe.1	-	c.391C>T	c.(391-393)CTG>TTG	p.L131L	ASB17_uc001dhf.1_Non-coding_Transcript	NM_080868	NP_543144	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box-containing 17	131					intracellular signal transduction					ovary(1)	1														0.290323	25.961985	27.183425	9	22	KEEP	---	---	---	---	capture		Silent	SNP	76397586	76397586	1039	1	G	A	A	A	464	36	ASB17	2	2
DNASE2B	58511	broad.mit.edu	37	1	84880404	84880404	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:84880404G>A	uc001djt.1	+	c.939G>A	c.(937-939)AAG>AAA	p.K313K	DNASE2B_uc001dju.1_Silent_p.K105K|DNASE2B_uc009wch.1_Silent_p.K105K	NM_021233	NP_067056	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta isoform 1 precursor	313					DNA metabolic process	lysosome	deoxyribonuclease II activity				0				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		Pancreas(54;788 1175 11852 16034 30034)								0.117647	6.174822	11.060918	4	30	KEEP	---	---	---	---	capture		Silent	SNP	84880404	84880404	4848	1	G	A	A	A	451	35	DNASE2B	2	2
RERE	473	broad.mit.edu	37	1	8674657	8674657	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:8674657G>A	uc001ape.2	-	c.485C>T	c.(484-486)CCA>CTA	p.P162L	RERE_uc001apf.2_Missense_Mutation_p.P162L|RERE_uc001aph.1_Missense_Mutation_p.P162L	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	162	BAH.				multicellular organismal development|NLS-bearing substrate import into nucleus|regulation of transcription, DNA-dependent	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)										0.092308	7.801774	29.551737	12	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8674657	8674657	13700	1	G	A	A	A	611	47	RERE	2	2
GBP5	115362	broad.mit.edu	37	1	89732239	89732239	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:89732239G>C	uc001dnc.2	-	c.658C>G	c.(658-660)CCC>GCC	p.P220A	GBP5_uc001dnd.2_Missense_Mutation_p.P220A|GBP5_uc001dne.1_Missense_Mutation_p.P220A	NM_052942	NP_443174	Q96PP8	GBP5_HUMAN	guanylate-binding protein 5	220						plasma membrane	GTP binding|GTPase activity			ovary(1)	1				all cancers(265;0.00784)|Epithelial(280;0.0286)										0.16129	20.307009	27.078084	10	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89732239	89732239	6543	1	G	C	C	C	546	42	GBP5	3	3
BRDT	676	broad.mit.edu	37	1	92447221	92447221	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:92447221G>A	uc010osz.1	+	c.1923G>A	c.(1921-1923)CTG>CTA	p.L641L	BRDT_uc001dok.3_Silent_p.L637L|BRDT_uc001dol.3_Silent_p.L637L|BRDT_uc009wdf.2_Silent_p.L564L|BRDT_uc010ota.1_Silent_p.L591L|BRDT_uc010otb.1_Silent_p.L591L|BRDT_uc001dom.3_Silent_p.L637L	NM_207189	NP_997072	Q58F21	BRDT_HUMAN	testis-specific bromodomain protein	637	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity			stomach(1)|ovary(1)|lung(1)	3		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)						576				0.164384	20.953418	28.763231	12	61	KEEP	---	---	---	---	capture		Silent	SNP	92447221	92447221	1539	1	G	A	A	A	574	45	BRDT	2	2
JAG1	182	broad.mit.edu	37	20	10621877	10621877	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:10621877G>A	uc002wnw.2	-	c.2932C>T	c.(2932-2934)CAC>TAC	p.H978Y		NM_000214	NP_000205	P78504	JAG1_HUMAN	jagged 1 precursor	978	Extracellular (Potential).				angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation	extracellular region|integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding|structural molecule activity			lung(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5										587				0.324324	32.084999	33.099607	12	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10621877	10621877	8238	20	G	A	A	A	598	46	JAG1	2	2
ADNP	23394	broad.mit.edu	37	20	49518564	49518564	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49518564G>C	uc002xvt.1	-	c.191C>G	c.(190-192)ACG>AGG	p.T64R	ADNP_uc002xvu.1_Missense_Mutation_p.T64R	NM_015339	NP_056154	Q9H2P0	ADNP_HUMAN	activity-dependent neuroprotector	64					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2														0.257426	79.806987	85.190023	26	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49518564	49518564	324	20	G	C	C	C	520	40	ADNP	3	3
KRTAP13-1	140258	broad.mit.edu	37	21	31768824	31768824	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31768824G>T	uc002yoa.2	+	c.420G>T	c.(418-420)CTG>CTT	p.L140L		NM_181599	NP_853630	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	140						intermediate filament				ovary(1)	1														0.282051	28.669742	30.298232	11	28	KEEP	---	---	---	---	capture		Silent	SNP	31768824	31768824	8837	21	G	T	T	T	600	47	KRTAP13-1	2	2
SFRS15	57466	broad.mit.edu	37	21	33073388	33073388	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:33073388G>A	uc002ypd.2	-	c.697C>T	c.(697-699)CAG>TAG	p.Q233*	SFRS15_uc002ype.2_Nonsense_Mutation_p.Q233*|SFRS15_uc010glu.2_Nonsense_Mutation_p.Q218*|SFRS15_uc002ypf.1_5'UTR|SFRS15_uc002ypg.2_Nonsense_Mutation_p.Q233*	NM_020706	NP_065757	O95104	SFR15_HUMAN	splicing factor, arginine/serine-rich 15 isoform	233						nucleus	nucleotide binding|RNA binding				0														0.310345	46.82587	48.685871	18	40	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	33073388	33073388	14661	21	G	A	A	A	585	45	SFRS15	5	2
PRAME	23532	broad.mit.edu	37	22	22890729	22890729	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22890729G>T	uc002zwf.2	-	c.1290C>A	c.(1288-1290)CTC>CTA	p.L430L	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Silent_p.L414L|PRAME_uc010gtr.2_Silent_p.L430L|PRAME_uc002zwg.2_Silent_p.L430L|PRAME_uc002zwh.2_Silent_p.L430L|PRAME_uc002zwi.2_Silent_p.L430L|PRAME_uc002zwj.2_Silent_p.L430L|PRAME_uc002zwk.2_Silent_p.L430L	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	430	Mediates interaction with RARA.				apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.254545	33.120838	36.130349	14	41	KEEP	---	---	---	---	capture		Silent	SNP	22890729	22890729	12860	22	G	T	T	T	574	45	PRAME	2	2
PRR5	55615	broad.mit.edu	37	22	45132724	45132724	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45132724A>T	uc010gzt.1	+	c.833A>T	c.(832-834)TAC>TTC	p.Y278F	PRR5_uc003bew.1_Missense_Mutation_p.Y246F|PRR5_uc003bex.1_Missense_Mutation_p.Y160F|PRR5_uc010gzu.1_Missense_Mutation_p.Y219F|PRR5_uc003bey.1_Missense_Mutation_p.Y246F|PRR5_uc003bez.1_Missense_Mutation_p.Y160F|PRR5-ARHGAP8_uc003bfc.2_Intron|PRR5-ARHGAP8_uc003bfd.2_Intron|PRR5-ARHGAP8_uc011aqi.1_Intron|PRR5-ARHGAP8_uc011aqj.1_Intron|PRR5_uc003bfa.1_Missense_Mutation_p.Y148F|PRR5_uc003bfb.1_Missense_Mutation_p.Y255F|PRR5_uc003bfe.1_Non-coding_Transcript|PRR5-ARHGAP8_uc003bfg.1_Intron|PRR5_uc003bfh.1_Missense_Mutation_p.Y154F	NM_001017530	NP_001017530	P85299	PRR5_HUMAN	proline rich 5 (renal) isoform 3	255					cell cycle						0		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)										0.333333	14.570914	14.939466	5	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45132724	45132724	13049	22	A	T	T	T	182	14	PRR5	3	3
CREG2	200407	broad.mit.edu	37	2	101971757	101971757	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:101971757G>T	uc002tba.2	-	c.683C>A	c.(682-684)TCT>TAT	p.S228Y		NM_153836	NP_722578	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	228						extracellular region	FMN binding			ovary(1)	1														0.296296	20.187133	21.190684	8	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101971757	101971757	4004	2	G	T	T	T	429	33	CREG2	2	2
RANBP2	5903	broad.mit.edu	37	2	109380884	109380884	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:109380884A>T	uc002tem.3	+	c.3889A>T	c.(3889-3891)AAG>TAG	p.K1297*		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	1297	RanBD1 1.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(14)	soft_tissue(14)|pancreas(1)	15														0.314286	61.024127	63.172693	22	48	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	109380884	109380884	13488	2	A	T	T	T	65	5	RANBP2	5	3
CNTNAP5	129684	broad.mit.edu	37	2	125521610	125521610	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125521610A>G	uc010flu.2	+	c.2419A>G	c.(2419-2421)ACC>GCC	p.T807A	CNTNAP5_uc002tno.2_Missense_Mutation_p.T806A	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	806	Laminin G-like 3.|Extracellular (Potential).				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.205479	77.563998	89.320498	30	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125521610	125521610	3788	2	A	G	G	G	182	14	CNTNAP5	4	4
MYO7B	4648	broad.mit.edu	37	2	128394193	128394193	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128394193C>A	uc002top.2	+	c.6119C>A	c.(6118-6120)CCC>CAC	p.P2040H	MYO7B_uc002tos.1_Missense_Mutation_p.P150H|MYO7B_uc002tot.2_Missense_Mutation_p.P150H	NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB	2040	FERM 2.					apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)										0.333333	11.695875	11.991145	4	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128394193	128394193	10478	2	C	A	A	A	286	22	MYO7B	2	2
LRP1B	53353	broad.mit.edu	37	2	141242937	141242937	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141242937C>A	uc002tvj.1	-	c.9400G>T	c.(9400-9402)GAC>TAC	p.D3134Y		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	3134	Extracellular (Potential).|LDL-receptor class B 29.				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)				2546	TSP Lung(27;0.18)			0.14	10.088121	16.348919	7	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141242937	141242937	9328	2	C	A	A	A	416	32	LRP1B	2	2
LRP1B	53353	broad.mit.edu	37	2	141625751	141625751	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141625751G>T	uc002tvj.1	-	c.4251C>A	c.(4249-4251)ATC>ATA	p.I1417I	LRP1B_uc010fnl.1_Silent_p.I599I	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1417	Extracellular (Potential).|LDL-receptor class B 11.				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)				2546	TSP Lung(27;0.18)			0.28169	50.266174	53.309398	20	51	KEEP	---	---	---	---	capture		Silent	SNP	141625751	141625751	9328	2	G	T	T	T	421	33	LRP1B	2	2
HOXD8	3234	broad.mit.edu	37	2	176995617	176995617	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:176995617C>A	uc002uko.2	+	c.523C>A	c.(523-525)CAC>AAC	p.H175N	HOXD8_uc002ukn.2_5'UTR|HOXD8_uc002ukp.2_Missense_Mutation_p.H175N	NM_019558	NP_062458	P13378	HXD8_HUMAN	homeobox D8	175					anterior/posterior axis specification, embryo	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)										0.242991	67.594084	74.038723	26	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176995617	176995617	7617	2	C	A	A	A	273	21	HOXD8	2	2
ZNF804A	91752	broad.mit.edu	37	2	185798372	185798372	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185798372G>T	uc002uph.2	+	c.298G>T	c.(298-300)GCA>TCA	p.A100S		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	100						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.236364	31.444873	34.941091	13	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185798372	185798372	18768	2	G	T	T	T	442	34	ZNF804A	2	2
CCDC150	284992	broad.mit.edu	37	2	197521518	197521518	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:197521518C>T	uc002utp.1	+	c.338C>T	c.(337-339)TCC>TTC	p.S113F	CCDC150_uc002uto.1_Missense_Mutation_p.S113F|CCDC150_uc010zgq.1_Non-coding_Transcript|CCDC150_uc010zgr.1_Intron|CCDC150_uc010zgs.1_Intron	NM_001080539	NP_001074008	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	113	Potential.										0														0.247312	58.778067	64.1828	23	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197521518	197521518	2905	2	C	T	T	T	390	30	CCDC150	2	2
CFLAR	8837	broad.mit.edu	37	2	202000805	202000805	+	Silent	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:202000805A>G	uc002uxb.3	+	c.498A>G	c.(496-498)ACA>ACG	p.T166T	CFLAR_uc002uwy.2_Silent_p.T166T|CFLAR_uc002uwz.2_Silent_p.T166T|CFLAR_uc002uxa.3_Silent_p.T166T|CFLAR_uc010zhk.1_Silent_p.T70T|CFLAR_uc002uxc.3_Silent_p.T166T|CFLAR_uc010zhl.1_Silent_p.T70T|CFLAR_uc010fsw.1_Non-coding_Transcript|CFLAR_uc002uxd.3_Silent_p.T166T|CFLAR_uc002uxe.2_Silent_p.T166T|CFLAR_uc002uxf.2_Silent_p.T166T|CFLAR_uc010fsy.2_Non-coding_Transcript|CFLAR_uc010fsx.2_Silent_p.T166T|CFLAR_uc010zhm.1_Silent_p.T70T|CFLAR_uc010fsz.2_5'UTR	NM_003879	NP_003870	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator isoform	166	Interaction with FADD.|Interaction with caspase-8.|DED 2.|Not proteolytically processed and involved in apoptosis inhibition.|Interaction with caspase-8 propeptide.				anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis		cysteine-type endopeptidase activity|protein binding				0						Pancreas(16;548 657 22190 32864 42338)								0.275	59.714164	63.362463	22	58	KEEP	---	---	---	---	capture		Silent	SNP	202000805	202000805	3425	2	A	G	G	G	54	5	CFLAR	4	4
APOB	338	broad.mit.edu	37	2	21255315	21255315	+	Silent	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21255315G>C	uc002red.2	-	c.1263C>G	c.(1261-1263)CCC>CCG	p.P421P		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	421	Vitellogenin.				cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.270677	89.336198	95.649026	36	97	KEEP	---	---	---	---	capture		Silent	SNP	21255315	21255315	796	2	G	C	C	C	444	35	APOB	3	3
SPHKAP	80309	broad.mit.edu	37	2	228883645	228883645	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228883645G>A	uc002vpq.2	-	c.1925C>T	c.(1924-1926)TCC>TTC	p.S642F	SPHKAP_uc002vpp.2_Missense_Mutation_p.S642F|SPHKAP_uc010zlx.1_Missense_Mutation_p.S642F	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	642						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.285714	43.375131	45.683671	16	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228883645	228883645	15560	2	G	A	A	A	533	41	SPHKAP	2	2
CXCR7	57007	broad.mit.edu	37	2	237489382	237489382	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:237489382T>A	uc010fyq.2	+	c.274T>A	c.(274-276)TGG>AGG	p.W92R	CXCR7_uc002vwd.2_Missense_Mutation_p.W92R	NM_020311	NP_064707	P25106	CXCR7_HUMAN	chemokine orphan receptor 1	92	Helical; Name=2; (Potential).				interspecies interaction between organisms	integral to membrane|plasma membrane	G-protein coupled receptor activity|protein binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3		Breast(86;0.000182)|Renal(207;0.00339)|all_hematologic(139;0.0048)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|all_lung(227;0.147)|all_neural(83;0.223)		Epithelial(121;8.35e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.09e-11)|Kidney(56;1.11e-07)|KIRC - Kidney renal clear cell carcinoma(57;3.03e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000176)|Lung(119;0.00468)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.118)						49				0.218978	70.979661	80.945978	30	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237489382	237489382	4256	2	T	A	A	A	767	59	CXCR7	3	3
ALK	238	broad.mit.edu	37	2	29474042	29474042	+	Missense_Mutation	SNP	G	T	T	rs77102810	by1000genomes	TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:29474042G>T	uc002rmy.2	-	c.2133C>A	c.(2131-2133)AGC>AGA	p.S711R		NM_004304	NP_004295	Q9UM73	ALK_HUMAN	anaplastic lymphoma kinase precursor	711	Extracellular (Potential).				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		NPM1/ALK(632)|EML4/ALK(191)|CLTC/ALK(44)|TPM3/ALK(33)|ATIC/ALK(24)|RANBP2/ALK(14)|TPM4/ALK(12)|TFG/ALK(7)|MSN/ALK(6)|CARS/ALK(5)|VCL/ALK(4)|KIF5B/ALK(4)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|SQSTM1/ALK(2)	haematopoietic_and_lymphoid_tissue(726)|lung(200)|autonomic_ganglia(95)|soft_tissue(59)|kidney(4)|large_intestine(3)|ovary(3)|central_nervous_system(1)|breast(1)|pancreas(1)	1093	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)					777				0.185185	10.859274	13.368002	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29474042	29474042	528	2	G	T	T	T	490	38	ALK	1	1
BIRC6	57448	broad.mit.edu	37	2	32658763	32658763	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:32658763G>T	uc010ezu.2	+	c.3300G>T	c.(3298-3300)ATG>ATT	p.M1100I		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	1100					anti-apoptosis|apoptosis|post-translational protein modification	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					Pancreas(94;175 1509 16028 18060 45422)				1555				0.156863	14.864728	20.596569	8	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32658763	32658763	1463	2	G	T	T	T	611	47	BIRC6	2	2
VIT	5212	broad.mit.edu	37	2	37041396	37041396	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37041396C>T	uc002rpl.2	+	c.1974C>T	c.(1972-1974)CCC>CCT	p.P658P	VIT_uc002rpm.2_Silent_p.P636P|VIT_uc010ezv.2_Silent_p.P614P|VIT_uc010ezw.2_Silent_p.P615P	NM_053276	NP_444506	Q6UXI7	VITRN_HUMAN	vitrin	643	VWFA 2.					proteinaceous extracellular matrix				ovary(1)|pancreas(1)	2		all_hematologic(82;0.248)												0.408163	62.993507	63.353812	20	29	KEEP	---	---	---	---	capture		Silent	SNP	37041396	37041396	17738	2	C	T	T	T	288	23	VIT	1	1
ABCG8	64241	broad.mit.edu	37	2	44071702	44071702	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:44071702C>G	uc002rtq.2	+	c.120C>G	c.(118-120)TAC>TAG	p.Y40*	ABCG8_uc010yoa.1_Nonsense_Mutation_p.Y40*	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	40	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)												0.175439	22.212809	27.876821	10	47	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	44071702	44071702	73	2	C	G	G	G	220	17	ABCG8	5	3
NRXN1	9378	broad.mit.edu	37	2	50699567	50699567	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50699567G>C	uc010fbq.2	-	c.3233C>G	c.(3232-3234)TCC>TGC	p.S1078C	NRXN1_uc002rxb.3_Missense_Mutation_p.S710C|NRXN1_uc002rxe.3_Missense_Mutation_p.S1038C|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	223	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.166667	28.653509	36.238119	12	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50699567	50699567	11070	2	G	C	C	C	533	41	NRXN1	3	3
C2orf86	51057	broad.mit.edu	37	2	63631702	63631702	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63631702C>T	uc002sch.2	-	c.916G>A	c.(916-918)GTA>ATA	p.V306I	C2orf86_uc002sce.2_Non-coding_Transcript|C2orf86_uc002scf.2_Missense_Mutation_p.V147I|C2orf86_uc010ypu.1_Non-coding_Transcript|C2orf86_uc002scg.2_Missense_Mutation_p.V114I|C2orf86_uc002sci.1_Missense_Mutation_p.V282I|C2orf86_uc010fcr.1_Missense_Mutation_p.V196I	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	306					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0														0.125	26.877867	49.943895	21	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63631702	63631702	2293	2	C	T	T	T	247	19	C2orf86	1	1
ALMS1	7840	broad.mit.edu	37	2	73835701	73835701	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:73835701G>T	uc002sje.1	+	c.12465G>T	c.(12463-12465)AAG>AAT	p.K4155N	ALMS1_uc002sjf.1_Missense_Mutation_p.K4111N	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4153					G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.194444	15.803116	18.939068	7	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73835701	73835701	538	2	G	T	T	T	451	35	ALMS1	2	2
ARID5A	10865	broad.mit.edu	37	2	97217015	97217015	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:97217015G>A	uc002swe.2	+	c.750G>A	c.(748-750)GGG>GGA	p.G250G	ARID5A_uc010yuq.1_Silent_p.G198G|ARID5A_uc002swf.2_Silent_p.G86G|ARID5A_uc002swg.2_Silent_p.G198G	NM_212481	NP_997646	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A	250					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|transcription repressor activity				0														0.192308	10.559256	12.858645	5	21	KEEP	---	---	---	---	capture		Silent	SNP	97217015	97217015	936	2	G	A	A	A	522	41	ARID5A	2	2
GAP43	2596	broad.mit.edu	37	3	115395284	115395284	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:115395284C>G	uc003ebr.2	+	c.563C>G	c.(562-564)CCG>CGG	p.P188R	GAP43_uc003ebq.2_Missense_Mutation_p.P152R	NM_001130064	NP_001123536	P17677	NEUM_HUMAN	growth associated protein 43 isoform 1	152					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell differentiation|nervous system development|regulation of growth|response to wounding	cell junction|growth cone membrane|synapse	calmodulin binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.164)										0.183673	14.635478	19.254267	9	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115395284	115395284	6499	3	C	G	G	G	299	23	GAP43	3	3
PLOD2	5352	broad.mit.edu	37	3	145796987	145796987	+	Silent	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:145796987G>C	uc003evr.1	-	c.1416C>G	c.(1414-1416)CTC>CTG	p.L472L	PLOD2_uc003evq.1_Silent_p.L132L|PLOD2_uc011bnm.1_Silent_p.L417L|PLOD2_uc003evs.1_Silent_p.L472L	NM_182943	NP_891988	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	472					oxidation-reduction process|protein modification process|response to hypoxia	rough endoplasmic reticulum membrane	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding			ovary(1)	1					Vitamin C(DB00126)									0.133333	19.497726	29.282765	10	65	KEEP	---	---	---	---	capture		Silent	SNP	145796987	145796987	12528	3	G	C	C	C	522	41	PLOD2	3	3
MED12L	116931	broad.mit.edu	37	3	151085515	151085515	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151085515G>A	uc003eyp.2	+	c.3304G>A	c.(3304-3306)GTC>ATC	p.V1102I	MED12L_uc011bnz.1_Missense_Mutation_p.V962I|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.V265I	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1102					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex	RNA polymerase II transcription mediator activity			ovary(4)|large_intestine(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							59				0.446667	207.912686	208.283091	67	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151085515	151085515	9818	3	G	A	A	A	520	40	MED12L	1	1
AADAC	13	broad.mit.edu	37	3	151545721	151545721	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151545721C>T	uc003eze.2	+	c.961C>T	c.(961-963)CCT>TCT	p.P321S		NM_001086	NP_001077	P22760	AAAD_HUMAN	arylacetamide deacetylase	321	Lumenal (Potential).				positive regulation of triglyceride catabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	deacetylase activity|serine hydrolase activity|triglyceride lipase activity				0		Myeloproliferative disorder(1037;0.0255)|all_neural(597;0.112)	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			Ovarian(30;839 841 2699 32801 46334)								0.467532	115.293985	115.364598	36	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151545721	151545721	11	3	C	T	T	T	286	22	AADAC	2	2
PLCL2	23228	broad.mit.edu	37	3	17056392	17056392	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:17056392A>T	uc011awc.1	+	c.2983A>T	c.(2983-2985)ACT>TCT	p.T995S	PLCL2_uc011awd.1_Missense_Mutation_p.T877S	NM_001144382	NP_001137854	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2 isoform 1	1003					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)|lung(1)	2														0.166667	34.812364	47.480809	20	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17056392	17056392	12466	3	A	T	T	T	26	2	PLCL2	3	3
NLGN1	22871	broad.mit.edu	37	3	173997312	173997312	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:173997312C>A	uc003fio.1	+	c.1521C>A	c.(1519-1521)GAC>GAA	p.D507E	NLGN1_uc010hww.1_Missense_Mutation_p.D547E|NLGN1_uc003fip.1_Missense_Mutation_p.D507E	NM_014932	NP_055747	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	524	Extracellular (Potential).				calcium-dependent cell-cell adhesion|neuron cell-cell adhesion|neuronal signal transduction|positive regulation of dendritic spine development|positive regulation of intracellular protein kinase cascade|positive regulation of synaptogenesis|protein targeting|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|regulation of excitatory postsynaptic membrane potential|regulation of N-methyl-D-aspartate selective glutamate receptor activity|regulation of synaptic transmission|synapse assembly|synaptic vesicle targeting	cell junction|cell surface|dendrite|integral to plasma membrane|postsynaptic density|postsynaptic membrane	carboxylesterase activity|cell adhesion molecule binding|neurexin binding|receptor activity			lung(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	6	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)											0.173077	18.943405	24.191401	9	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	173997312	173997312	10864	3	C	A	A	A	246	19	NLGN1	1	1
EFHB	151651	broad.mit.edu	37	3	19921148	19921148	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:19921148C>A	uc003cbl.3	-	c.2477G>T	c.(2476-2478)CGG>CTG	p.R826L	EFHB_uc003cbm.2_Missense_Mutation_p.R696L	NM_144715	NP_653316	Q8N7U6	EFHB_HUMAN	EF hand domain family, member B	826					signal transduction	proteinaceous extracellular matrix	calcium ion binding				0														0.079545	0.956897	16.832383	7	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19921148	19921148	5133	3	C	A	A	A	299	23	EFHB	1	1
SLC22A14	9389	broad.mit.edu	37	3	38355272	38355272	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38355272C>T	uc010hhc.1	+	c.1218C>T	c.(1216-1218)GGC>GGT	p.G406G	SLC22A14_uc003cib.2_Silent_p.G406G|SLC22A14_uc011ayo.1_Non-coding_Transcript	NM_004803	NP_004794	Q9Y267	S22AE_HUMAN	organic cation transporter like 4	406	Extracellular (Potential).					integral to plasma membrane	organic cation transmembrane transporter activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)										0.173228	41.543426	54.294927	22	105	KEEP	---	---	---	---	capture		Silent	SNP	38355272	38355272	14941	3	C	T	T	T	340	27	SLC22A14	1	1
CCR1	1230	broad.mit.edu	37	3	46245043	46245043	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:46245043G>T	uc003cph.1	-	c.762C>A	c.(760-762)CCC>CCA	p.P254P	CCR3_uc003cpg.1_Intron	NM_001295	NP_001286	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1	254	Helical; Name=6; (Potential).				cell adhesion|cell-cell signaling|cytokine-mediated signaling pathway|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cyclic nucleotide second messenger|immune response|inflammatory response	integral to plasma membrane	C-C chemokine receptor activity			skin(2)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)						20				0.247059	51.729733	56.681867	21	64	KEEP	---	---	---	---	capture		Silent	SNP	46245043	46245043	3066	3	G	T	T	T	444	35	CCR1	2	2
PRICKLE2	166336	broad.mit.edu	37	3	64142982	64142982	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:64142982G>T	uc003dmf.2	-	c.456C>A	c.(454-456)GGC>GGA	p.G152G		NM_198859	NP_942559	Q7Z3G6	PRIC2_HUMAN	prickle-like 2	152	LIM zinc-binding 1.					cytoplasm|nuclear membrane	zinc ion binding			ovary(4)	4		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)										0.235294	20.783073	22.961502	8	26	KEEP	---	---	---	---	capture		Silent	SNP	64142982	64142982	12930	3	G	T	T	T	483	38	PRICKLE2	1	1
ROBO2	6092	broad.mit.edu	37	3	77147176	77147176	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:77147176C>A	uc003dpz.2	+	c.73C>A	c.(73-75)CGC>AGC	p.R25S	ROBO2_uc003dpy.3_Missense_Mutation_p.R25S|ROBO2_uc011bgj.1_Non-coding_Transcript|ROBO2_uc011bgk.1_Missense_Mutation_p.R25S	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	25	Extracellular (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|ovary(1)|large_intestine(1)|liver(1)	8				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)						1049				0.5	12.399783	12.399783	4	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77147176	77147176	13993	3	C	A	A	A	403	31	ROBO2	1	1
MTTP	4547	broad.mit.edu	37	4	100532328	100532328	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100532328A>G	uc011cej.1	+	c.1879A>G	c.(1879-1881)ATG>GTG	p.M627V	MTTP_uc003hvc.3_Missense_Mutation_p.M600V	NM_000253	NP_000244	P55157	MTP_HUMAN	microsomal triglyceride transfer protein large	600	Vitellogenin.				lipid metabolic process|lipoprotein metabolic process	endoplasmic reticulum lumen	lipid binding|lipid transporter activity			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)									0.208955	34.31176	39.56709	14	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100532328	100532328	10357	4	A	G	G	G	52	4	MTTP	4	4
EGF	1950	broad.mit.edu	37	4	110902110	110902110	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:110902110G>T	uc003hzy.3	+	c.2350G>T	c.(2350-2352)GAT>TAT	p.D784Y	EGF_uc011cfu.1_Missense_Mutation_p.D742Y|EGF_uc011cfv.1_Missense_Mutation_p.D784Y|EGF_uc010imk.2_Missense_Mutation_p.D13Y	NM_001963	NP_001954	P01133	EGF_HUMAN	epidermal growth factor precursor	784	Extracellular (Potential).				angiogenesis|DNA replication|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of secretion|platelet activation|platelet degranulation|positive regulation of catenin import into nucleus|positive regulation of epidermal growth factor receptor activity|positive regulation of MAP kinase activity|positive regulation of mitosis|regulation of calcium ion import|regulation of protein localization at cell surface	integral to membrane|plasma membrane|platelet alpha granule lumen	calcium ion binding|epidermal growth factor receptor binding|growth factor activity|transmembrane receptor protein tyrosine kinase activator activity			central_nervous_system(1)	1		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sulindac(DB00605)					724				0.263158	109.290884	117.971375	45	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110902110	110902110	5151	4	G	T	T	T	533	41	EGF	2	2
ANK2	287	broad.mit.edu	37	4	114232510	114232510	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114232510G>T	uc003ibe.3	+	c.2648G>T	c.(2647-2649)GGT>GTT	p.G883V	ANK2_uc003ibd.3_Missense_Mutation_p.G862V|ANK2_uc003ibf.3_Missense_Mutation_p.G883V|ANK2_uc011cgc.1_Missense_Mutation_p.G92V|ANK2_uc003ibc.2_Missense_Mutation_p.G859V|ANK2_uc011cgb.1_Missense_Mutation_p.G898V	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	883					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.060241	-4.896825	11.883253	5	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114232510	114232510	624	4	G	T	T	T	572	44	ANK2	2	2
DCHS2	54798	broad.mit.edu	37	4	155180879	155180879	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155180879G>T	uc003inw.2	-	c.5242C>A	c.(5242-5244)CTT>ATT	p.L1748I		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1748	Cadherin 15.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)										0.188406	26.831017	33.10404	13	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155180879	155180879	4459	4	G	T	T	T	429	33	DCHS2	2	2
FAM149A	25854	broad.mit.edu	37	4	187088124	187088124	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187088124C>G	uc003iyt.3	+	c.1167C>G	c.(1165-1167)TAC>TAG	p.Y389*	FAM149A_uc011cla.1_Nonsense_Mutation_p.Y389*|FAM149A_uc003iyu.3_Nonsense_Mutation_p.Y389*|FAM149A_uc010isl.2_Nonsense_Mutation_p.Y389*|FAM149A_uc011clb.1_Nonsense_Mutation_p.Y389*	NM_015398	NP_056213	A5PLN7	F149A_HUMAN	hypothetical protein LOC25854	680										breast(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)										0.131579	9.747532	14.760306	5	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	187088124	187088124	5652	4	C	G	G	G	220	17	FAM149A	5	3
C4orf19	55286	broad.mit.edu	37	4	37591710	37591710	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:37591710C>T	uc003gsw.3	+	c.33C>T	c.(31-33)AGC>AGT	p.S11S	C4orf19_uc003gsy.3_Silent_p.S11S	NM_001104629	NP_001098099	Q8IY42	CD019_HUMAN	hypothetical protein LOC55286	11											0														0.20398	93.854851	110.207902	41	160	KEEP	---	---	---	---	capture		Silent	SNP	37591710	37591710	2348	4	C	T	T	T	363	28	C4orf19	2	2
DCUN1D4	23142	broad.mit.edu	37	4	52740525	52740525	+	Silent	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:52740525A>G	uc011bzo.1	+	c.357A>G	c.(355-357)TTA>TTG	p.L119L	DCUN1D4_uc003gze.2_Silent_p.L75L|DCUN1D4_uc003gzf.2_Silent_p.L75L|DCUN1D4_uc011bzn.1_Silent_p.L15L|DCUN1D4_uc003gzg.2_Non-coding_Transcript|DCUN1D4_uc003gzh.2_Non-coding_Transcript	NM_001040402	NP_001035492	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain	75										ovary(2)	2			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)											0.075949	0.28958	14.845907	6	73	KEEP	---	---	---	---	capture		Silent	SNP	52740525	52740525	4487	4	A	G	G	G	206	16	DCUN1D4	4	4
EPHA5	2044	broad.mit.edu	37	4	66361218	66361218	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:66361218G>C	uc011cah.1	-	c.954C>G	c.(952-954)AGC>AGG	p.S318R	EPHA5_uc003hcx.2_Missense_Mutation_p.S249R|EPHA5_uc003hcy.2_Missense_Mutation_p.S318R|EPHA5_uc003hcz.2_Missense_Mutation_p.S318R|EPHA5_uc011cai.1_Missense_Mutation_p.S318R|EPHA5_uc003hda.2_Missense_Mutation_p.S318R	NM_004439	NP_004430	P54756	EPHA5_HUMAN	ephrin receptor EphA5 isoform a precursor	318	Extracellular (Potential).|Cys-rich.				cAMP-mediated signaling|ephrin receptor signaling pathway|neuron development|protein phosphorylation	dendrite|external side of plasma membrane|integral to plasma membrane|neuronal cell body|perinuclear region of cytoplasm|rough endoplasmic reticulum	ATP binding|transmembrane-ephrin receptor activity			lung(12)|ovary(2)|central_nervous_system(1)	15										537	TSP Lung(17;0.13)			0.094828	10.031492	29.156653	11	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66361218	66361218	5363	4	G	C	C	C	438	34	EPHA5	3	3
UGT2B10	7365	broad.mit.edu	37	4	69682436	69682436	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:69682436G>C	uc003hee.2	+	c.699G>C	c.(697-699)CAG>CAC	p.Q233H	UGT2B10_uc011cam.1_Intron	NM_001075	NP_001066	P36537	UDB10_HUMAN	UDP glucuronosyltransferase 2B10 isoform 1	233					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			ovary(2)	2						Melanoma(133;755 1763 25578 26334 46021)								0.272727	36.780991	38.829003	12	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69682436	69682436	17514	4	G	C	C	C	464	36	UGT2B10	3	3
SH3TC1	54436	broad.mit.edu	37	4	8217932	8217932	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:8217932T>A	uc003gkv.3	+	c.576T>A	c.(574-576)CAT>CAA	p.H192Q	SH3TC1_uc003gkw.3_Missense_Mutation_p.H116Q|SH3TC1_uc003gkx.3_Non-coding_Transcript	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	192							binding			large_intestine(2)|pancreas(1)	3						NSCLC(145;2298 2623 35616 37297)								0.227273	13.263764	14.765289	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8217932	8217932	14753	4	T	A	A	A	660	51	SH3TC1	3	3
C4orf37	285555	broad.mit.edu	37	4	98762072	98762072	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:98762072C>A	uc003htt.1	-	c.1056G>T	c.(1054-1056)GCG>GCT	p.A352A		NM_174952	NP_777612	Q8N412	CD037_HUMAN	hypothetical protein LOC285555	352											0				OV - Ovarian serous cystadenocarcinoma(123;2.27e-08)										0.346939	53.666171	54.676804	17	32	KEEP	---	---	---	---	capture		Silent	SNP	98762072	98762072	2362	4	C	A	A	A	340	27	C4orf37	1	1
APC	324	broad.mit.edu	37	5	112175871	112175871	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112175871C>T	uc010jby.2	+	c.4580C>T	c.(4579-4581)CCA>CTA	p.P1527L	APC_uc011cvt.1_Missense_Mutation_p.P1509L|APC_uc003kpz.3_Missense_Mutation_p.P1527L|APC_uc003kpy.3_Missense_Mutation_p.P1527L|APC_uc010jbz.2_Missense_Mutation_p.P1244L|APC_uc010jca.2_Missense_Mutation_p.P827L	NM_001127511	NP_001120983	P25054	APC_HUMAN	adenomatous polyposis coli	1527	Ser-rich.				canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of protein catabolic process|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	p.K1192fs*3(1)|p.?(1)		large_intestine(2012)|stomach(123)|soft_tissue(55)|small_intestine(34)|pancreas(25)|breast(23)|urinary_tract(20)|lung(18)|thyroid(18)|liver(13)|central_nervous_system(10)|ovary(9)|upper_aerodigestive_tract(6)|adrenal_gland(6)|NS(5)|bone(5)|skin(4)|prostate(4)|endometrium(3)|kidney(1)|oesophagus(1)|biliary_tract(1)	2396		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		12		629	TSP Lung(16;0.13)			0.345679	80.872336	82.577072	28	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112175871	112175871	773	5	C	T	T	T	273	21	APC	2	2
CTNND2	1501	broad.mit.edu	37	5	11236884	11236884	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:11236884C>A	uc003jfa.1	-	c.1680G>T	c.(1678-1680)CAG>CAT	p.Q560H	CTNND2_uc010itt.2_Missense_Mutation_p.Q469H|CTNND2_uc011cmy.1_Missense_Mutation_p.Q223H|CTNND2_uc011cmz.1_Missense_Mutation_p.Q127H|CTNND2_uc010itu.1_Non-coding_Transcript|CTNND2_uc011cmx.1_Missense_Mutation_p.Q127H	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	560	ARM 2.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7														0.236453	116.78993	129.683992	48	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11236884	11236884	4179	5	C	A	A	A	363	28	CTNND2	2	2
FBN2	2201	broad.mit.edu	37	5	127636547	127636547	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127636547C>A	uc003kuu.2	-	c.6128G>T	c.(6127-6129)TGT>TTT	p.C2043F		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	2043	EGF-like 34; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.295775	58.344701	60.995003	21	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	127636547	127636547	5939	5	C	A	A	A	221	17	FBN2	2	2
PCDHGA2	56113	broad.mit.edu	37	5	140719887	140719887	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140719887C>G	uc003ljk.1	+	c.1349C>G	c.(1348-1350)CCC>CGC	p.P450R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.P450R	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	450	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.323529	88.535481	91.357411	33	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140719887	140719887	11974	5	C	G	G	G	286	22	PCDHGA2	3	3
SLIT3	6586	broad.mit.edu	37	5	168123402	168123402	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:168123402A>T	uc010jjg.2	-	c.2998T>A	c.(2998-3000)TGT>AGT	p.C1000S	SLIT3_uc003mab.2_Missense_Mutation_p.C993S	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	993	EGF-like 2.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			Ovarian(29;311 847 10864 17279 24903)								0.403846	59.965438	60.385234	21	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168123402	168123402	15239	5	A	T	T	T	78	6	SLIT3	3	3
CDH18	1016	broad.mit.edu	37	5	19612586	19612586	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19612586G>C	uc003jgc.2	-	c.768C>G	c.(766-768)ATC>ATG	p.I256M	CDH18_uc003jgd.2_Missense_Mutation_p.I256M|CDH18_uc011cnm.1_Missense_Mutation_p.I256M	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	256	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.107143	7.00833	15.584085	6	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19612586	19612586	3232	5	G	C	C	C	577	45	CDH18	3	3
CDH9	1007	broad.mit.edu	37	5	26881506	26881506	+	Silent	SNP	A	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:26881506A>T	uc003jgs.1	-	c.2109T>A	c.(2107-2109)ACT>ACA	p.T703T	CDH9_uc011cnv.1_Silent_p.T296T	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	703	Cytoplasmic (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.223404	55.425879	62.036683	21	73	KEEP	---	---	---	---	capture		Silent	SNP	26881506	26881506	3246	5	A	T	T	T	80	7	CDH9	3	3
CRHBP	1393	broad.mit.edu	37	5	76251567	76251567	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:76251567T>G	uc003ker.2	+	c.423T>G	c.(421-423)TGT>TGG	p.C141W	CRHBP_uc010izx.2_Missense_Mutation_p.C141W	NM_001882	NP_001873	P24387	CRHBP_HUMAN	corticotropin releasing hormone binding protein	141					female pregnancy|learning or memory|signal transduction	soluble fraction					0		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-51)|Epithelial(54;8.79e-46)|all cancers(79;2.49e-41)										0.357143	65.886761	66.892435	20	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76251567	76251567	4009	5	T	G	G	G	764	59	CRHBP	4	4
MTRR	4552	broad.mit.edu	37	5	7878268	7878268	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:7878268G>A	uc003jed.2	+	c.694G>A	c.(694-696)GAG>AAG	p.E232K	MTRR_uc010itn.1_Non-coding_Transcript|MTRR_uc003jee.3_Missense_Mutation_p.E205K|MTRR_uc003jef.3_Non-coding_Transcript|MTRR_uc003jeg.3_Non-coding_Transcript|MTRR_uc010ito.2_Non-coding_Transcript	NM_024010	NP_076915	Q9UBK8	MTRR_HUMAN	methionine synthase reductase isoform 2	232	Hinge.				methionine biosynthetic process|oxidation-reduction process	cytosol	[methionine synthase] reductase activity|flavin adenine dinucleotide binding|FMN binding|iron ion binding|NADP binding			ovary(1)	1					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)									0.184783	34.116575	42.693393	17	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7878268	7878268	10354	5	G	A	A	A	585	45	MTRR	2	2
EDIL3	10085	broad.mit.edu	37	5	83433157	83433157	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:83433157T>G	uc003kio.1	-	c.371A>C	c.(370-372)GAA>GCA	p.E124A	EDIL3_uc003kip.1_Missense_Mutation_p.E114A	NM_005711	NP_005702	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like	124	EGF-like 3.				cell adhesion|multicellular organismal development	extracellular region	calcium ion binding|integrin binding			skin(2)	2		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)										0.307692	61.077181	63.219139	20	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83433157	83433157	5102	5	T	G	G	G	806	62	EDIL3	4	4
ZDHHC11	79844	broad.mit.edu	37	5	843743	843743	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:843743C>A	uc011cma.1	-	c.600G>T	c.(598-600)GGG>GGT	p.G200G	ZDHHC11_uc003jbj.2_Non-coding_Transcript|ZDHHC11_uc010itd.1_5'Flank|ZDHHC11_uc003jbk.2_5'UTR	NM_024786	NP_079062	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	200						integral to membrane	acyltransferase activity|zinc ion binding			pancreas(1)	1			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)											0.189189	13.501918	16.848476	7	30	KEEP	---	---	---	---	capture		Silent	SNP	843743	843743	18189	5	C	A	A	A	275	22	ZDHHC11	2	2
SEMA5A	9037	broad.mit.edu	37	5	9154783	9154783	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9154783C>T	uc003jek.2	-	c.1298G>A	c.(1297-1299)CGG>CAG	p.R433Q		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	433	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.157303	27.308651	37.26601	14	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9154783	9154783	14523	5	C	T	T	T	299	23	SEMA5A	1	1
GRIK2	2898	broad.mit.edu	37	6	102503456	102503456	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:102503456G>A	uc003pqp.3	+	c.2562_splice	c.e15+1	p.K854_splice	GRIK2_uc003pqo.3_Splice_Site_SNP_p.K854_splice|GRIK2_uc010kcw.2_Splice_Site_SNP_p.K854_splice	NM_021956	NP_068775			glutamate receptor, ionotropic, kainate 2						glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|breast(1)|pancreas(1)	4		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)									0.072289	-2.316947	13.312738	6	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	102503456	102503456	7053	6	G	A	A	A	572	44	GRIK2	5	2
CLVS2	134829	broad.mit.edu	37	6	123319300	123319300	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:123319300G>A	uc003pzi.1	+	c.378G>A	c.(376-378)TGG>TGA	p.W126*		NM_001010852	NP_001010852	Q5SYC1	CLVS2_HUMAN	retinaldehyde binding protein 1-like 2	126	CRAL-TRIO.				lysosome organization	clathrin-coated vesicle|early endosome membrane|trans-Golgi network	phosphatidylinositol-3,5-bisphosphate binding|transporter activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.24359	51.886172	56.559732	19	59	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123319300	123319300	3710	6	G	A	A	A	559	43	CLVS2	5	2
LAMA2	3908	broad.mit.edu	37	6	129634156	129634156	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:129634156T>A	uc003qbn.2	+	c.3325T>A	c.(3325-3327)TTC>ATC	p.F1109I	LAMA2_uc003qbo.2_Missense_Mutation_p.F1109I	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	1109	Laminin EGF-like 13.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)	9				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)										0.093023	3.531327	17.867002	8	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129634156	129634156	8929	6	T	A	A	A	728	56	LAMA2	3	3
SLC2A12	154091	broad.mit.edu	37	6	134350827	134350827	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:134350827T>A	uc003qem.1	-	c.136A>T	c.(136-138)ACT>TCT	p.T46S		NM_145176	NP_660159	Q8TD20	GTR12_HUMAN	solute carrier family 2 (facilitated glucose	46	Helical; (Potential).					endomembrane system|integral to membrane|perinuclear region of cytoplasm|plasma membrane	D-glucose transmembrane transporter activity			ovary(1)	1	Breast(56;0.214)|Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0101)|GBM - Glioblastoma multiforme(68;0.0123)		Melanoma(122;1663 1672 14489 35294 41228)								0.111111	11.691525	25.141623	10	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134350827	134350827	15038	6	T	A	A	A	767	59	SLC2A12	3	3
GRM1	2911	broad.mit.edu	37	6	146350745	146350745	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146350745G>C	uc010khw.1	+	c.92G>C	c.(91-93)GGA>GCA	p.G31A	GRM1_uc010khu.1_Missense_Mutation_p.G31A|GRM1_uc010khv.1_Missense_Mutation_p.G31A|GRM1_uc003qll.2_Missense_Mutation_p.G31A|GRM1_uc011edz.1_Missense_Mutation_p.G31A|GRM1_uc011eea.1_Missense_Mutation_p.G31A	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	31	Extracellular (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.29927	118.396304	123.346142	41	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146350745	146350745	7075	6	G	C	C	C	533	41	GRM1	3	3
SASH1	23328	broad.mit.edu	37	6	148808849	148808849	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:148808849A>G	uc003qme.1	+	c.727A>G	c.(727-729)AAT>GAT	p.N243D		NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	243							protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)										0.151899	21.345267	30.516845	12	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148808849	148808849	14329	6	A	G	G	G	65	5	SASH1	4	4
SYNE1	23345	broad.mit.edu	37	6	152770719	152770719	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152770719C>A	uc010kiw.2	-	c.3453G>T	c.(3451-3453)AAG>AAT	p.K1151N	SYNE1_uc003qot.3_Missense_Mutation_p.K1158N|SYNE1_uc003qou.3_Missense_Mutation_p.K1151N|SYNE1_uc010kjb.1_Missense_Mutation_p.K1134N|SYNE1_uc003qow.2_Missense_Mutation_p.K446N|SYNE1_uc003qox.1_Missense_Mutation_p.K667N	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1151	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.068182	-4.624957	12.357568	6	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152770719	152770719	15966	6	C	A	A	A	311	24	SYNE1	2	2
IPCEF1	26034	broad.mit.edu	37	6	154544347	154544347	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:154544347G>A	uc003qpw.2	-	c.277C>T	c.(277-279)CCT>TCT	p.P93S	OPRM1_uc003qpt.1_Intron|IPCEF1_uc003qpx.2_Missense_Mutation_p.P92S|IPCEF1_uc010kjh.2_Missense_Mutation_p.P93S	NM_001130699	NP_001124171	Q8WWN9	ICEF1_HUMAN	phosphoinositide-binding protein PIP3-E isoform	92	PH.				response to oxidative stress	cytoplasm|plasma membrane	oxygen transporter activity|peroxidase activity				0														0.328358	60.625529	62.376542	22	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154544347	154544347	8092	6	G	A	A	A	546	42	IPCEF1	2	2
PHF3	23469	broad.mit.edu	37	6	64408494	64408494	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:64408494A>G	uc003pep.1	+	c.2981A>G	c.(2980-2982)AAT>AGT	p.N994S	PHF3_uc010kah.1_Missense_Mutation_p.N808S|PHF3_uc003pen.2_Missense_Mutation_p.N906S|PHF3_uc011dxs.1_Missense_Mutation_p.N263S	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	994	TFIIS central.				multicellular organismal development	nucleus	zinc ion binding			ovary(2)|lung(1)|skin(1)	4	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GBM(135;136 1820 29512 34071 46235)				350				0.358974	43.437564	44.121182	14	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64408494	64408494	12259	6	A	G	G	G	52	4	PHF3	4	4
TSC22D4	81628	broad.mit.edu	37	7	100075243	100075243	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100075243G>C	uc003uva.2	-	c.419C>G	c.(418-420)CCA>CGA	p.P140R	TSC22D4_uc003uvb.2_Intron|TSC22D4_uc011kjv.1_Intron|TSC22D4_uc010lgx.2_Missense_Mutation_p.P140R|TSC22D4_uc003uvc.3_Missense_Mutation_p.P140R	NM_030935	NP_112197	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	140					regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			breast(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.357143	13.870497	14.122409	5	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100075243	100075243	17161	7	G	C	C	C	611	47	TSC22D4	3	3
ZAN	7455	broad.mit.edu	37	7	100350349	100350349	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100350349C>A	uc003uwj.2	+	c.2621C>A	c.(2620-2622)CCC>CAC	p.P874H	ZAN_uc003uwk.2_Missense_Mutation_p.P874H|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	874	66 X heptapeptide repeats (approximate) (mucin-like domain).|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.380952	23.894853	24.155962	8	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100350349	100350349	18096	7	C	A	A	A	286	22	ZAN	2	2
MUC17	140453	broad.mit.edu	37	7	100677005	100677005	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100677005A>C	uc003uxp.1	+	c.2308A>C	c.(2308-2310)ACT>CCT	p.T770P	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	770	Extracellular (Potential).|Ser-rich.|10.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.086614	7.632381	51.690688	22	232	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100677005	100677005	10368	7	A	C	C	C	26	2	MUC17	4	4
MUC17	140453	broad.mit.edu	37	7	100683857	100683857	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100683857A>G	uc003uxp.1	+	c.9160A>G	c.(9160-9162)AGC>GGC	p.S3054G	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3054	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|49.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.258427	112.662536	122.07924	46	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100683857	100683857	10368	7	A	G	G	G	91	7	MUC17	4	4
FOXP2	93986	broad.mit.edu	37	7	114282499	114282499	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:114282499G>T	uc003vgz.2	+	c.885G>T	c.(883-885)TGG>TGT	p.W295C	FOXP2_uc003vgu.2_Non-coding_Transcript|FOXP2_uc003vha.2_Missense_Mutation_p.W178C|FOXP2_uc003vhb.2_Missense_Mutation_p.W270C|FOXP2_uc011kmu.1_Missense_Mutation_p.W287C|FOXP2_uc011kmv.1_Missense_Mutation_p.W269C|FOXP2_uc010ljz.1_Missense_Mutation_p.W178C|FOXP2_uc003vgx.2_Missense_Mutation_p.W270C|FOXP2_uc003vhd.2_Missense_Mutation_p.W270C|FOXP2_uc003vhc.2_Missense_Mutation_p.W295C	NM_148898	NP_683696	O15409	FOXP2_HUMAN	forkhead box P2 isoform II	270					camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|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|zinc ion binding			ovary(4)|lung(1)|breast(1)|pancreas(1)	7														0.223881	34.493076	39.186542	15	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114282499	114282499	6273	7	G	T	T	T	533	41	FOXP2	2	2
CCDC136	64753	broad.mit.edu	37	7	128449627	128449627	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:128449627G>T	uc003vnv.1	+	c.1729G>T	c.(1729-1731)GAG>TAG	p.E577*	CCDC136_uc003vnu.1_Intron|CCDC136_uc003vnw.1_Intron|CCDC136_uc003vnx.1_Nonsense_Mutation_p.E393*|CCDC136_uc010llq.1_5'UTR|CCDC136_uc003vny.1_Nonsense_Mutation_p.E187*	NM_022742	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	577						integral to membrane	protein binding			ovary(2)	2														0.363636	10.896443	11.076631	4	7	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	128449627	128449627	2890	7	G	T	T	T	533	41	CCDC136	5	2
EXOC4	60412	broad.mit.edu	37	7	133059673	133059673	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:133059673G>T	uc003vrk.2	+	c.1099G>T	c.(1099-1101)GTA>TTA	p.V367L	EXOC4_uc011kpo.1_Missense_Mutation_p.V266L|EXOC4_uc003vri.2_Missense_Mutation_p.V367L|EXOC4_uc003vrj.2_Missense_Mutation_p.V367L	NM_021807	NP_068579	Q96A65	EXOC4_HUMAN	SEC8 protein isoform a	367					vesicle docking involved in exocytosis	exocyst	protein N-terminus binding			ovary(4)|large_intestine(3)	7		Esophageal squamous(399;0.129)												0.243243	23.655502	25.879719	9	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133059673	133059673	5499	7	G	T	T	T	624	48	EXOC4	2	2
PRSS1	5644	broad.mit.edu	37	7	142460823	142460823	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142460823C>T	uc003wak.2	+	c.696C>T	c.(694-696)GTC>GTT	p.V232V	TRY6_uc011ksn.1_Intron|PRSS1_uc003wam.2_Silent_p.V172V	NM_002769	NP_002760	P07477	TRY1_HUMAN	protease, serine, 1 preproprotein	232	Peptidase S1.				digestion|proteolysis	extracellular space	metal ion binding|protein binding|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)											0.228916	45.979221	51.575527	19	64	KEEP	---	---	---	---	capture		Silent	SNP	142460823	142460823	13064	7	C	T	T	T	405	32	PRSS1	2	2
CNTNAP2	26047	broad.mit.edu	37	7	148080944	148080944	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148080944G>A	uc003weu.1	+	c.3679G>A	c.(3679-3681)GCC>ACC	p.A1227T	CNTNAP2_uc003wev.1_Missense_Mutation_p.A4T	NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	1227	Extracellular (Potential).		A -> T.		behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)											0.36	25.47014	25.900619	9	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148080944	148080944	3785	7	G	A	A	A	494	38	CNTNAP2	1	1
ZNF746	155061	broad.mit.edu	37	7	149191294	149191294	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149191294C>T	uc010lpi.2	-	c.324_splice	c.e2+1	p.K108_splice	ZNF746_uc003wfw.2_Splice_Site_SNP_p.K108_splice	NM_001163474	NP_001156946			zinc finger protein 746 isoform 1						neuron death|regulation of cell death|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	promoter binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding			ovary(2)|breast(1)	3	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)											0.284153	126.809226	134.476235	52	131	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	149191294	149191294	18727	7	C	T	T	T	234	18	ZNF746	5	2
GLI3	2737	broad.mit.edu	37	7	42005508	42005508	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:42005508C>A	uc011kbh.1	-	c.3163G>T	c.(3163-3165)GGC>TGC	p.G1055C	GLI3_uc011kbg.1_Missense_Mutation_p.G996C	NM_000168	NP_000159	P10071	GLI3_HUMAN	GLI-Kruppel family member GLI3	1055					negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|thymocyte apoptosis	cilium|cytosol|nucleolus	beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			large_intestine(2)|ovary(2)|central_nervous_system(1)|lung(1)|kidney(1)|pancreas(1)	8										806				0.371429	37.068225	37.575484	13	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42005508	42005508	6707	7	C	A	A	A	299	23	GLI3	1	1
FOXK1	221937	broad.mit.edu	37	7	4800711	4800711	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4800711C>T	uc003snc.1	+	c.1713C>T	c.(1711-1713)CCC>CCT	p.P571P	FOXK1_uc003sna.1_Silent_p.P408P	NM_001037165	NP_001032242	P85037	FOXK1_HUMAN	forkhead box K1	571					cell differentiation|embryo development|muscle organ development|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|magnesium ion 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				0		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)										0.111111	3.573365	8.957709	4	32	KEEP	---	---	---	---	capture		Silent	SNP	4800711	4800711	6260	7	C	T	T	T	262	21	FOXK1	2	2
GRB10	2887	broad.mit.edu	37	7	50684045	50684045	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:50684045C>A	uc003tpi.2	-	c.847_splice	c.e8-1	p.N283_splice	GRB10_uc003tph.3_Splice_Site_SNP_p.N225_splice|GRB10_uc003tpj.2_Intron|GRB10_uc003tpk.2_Splice_Site_SNP_p.N283_splice|GRB10_uc010kzb.2_Splice_Site_SNP_p.N225_splice|GRB10_uc003tpl.2_Splice_Site_SNP_p.N277_splice|GRB10_uc003tpm.2_Splice_Site_SNP_p.N225_splice|GRB10_uc003tpn.2_Splice_Site_SNP_p.N225_splice	NM_005311	NP_005302			growth factor receptor-bound protein 10 isoform						insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|ovary(1)	2	Glioma(55;0.08)|all_neural(89;0.245)													0.318182	18.916358	19.56327	7	15	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	50684045	50684045	7033	7	C	A	A	A	416	32	GRB10	5	2
WBSCR17	64409	broad.mit.edu	37	7	71130408	71130408	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:71130408G>A	uc003tvy.2	+	c.1093G>A	c.(1093-1095)GGG>AGG	p.G365R	WBSCR17_uc003tvz.2_Missense_Mutation_p.G64R	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	365	Catalytic subdomain B.|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)												0.222222	59.539868	67.207721	24	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71130408	71130408	17836	7	G	A	A	A	611	47	WBSCR17	2	2
FKBP6	8468	broad.mit.edu	37	7	72755322	72755322	+	Silent	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:72755322A>G	uc003tya.2	+	c.834A>G	c.(832-834)CGA>CGG	p.R278R	FKBP6_uc003twz.2_Silent_p.R248R|FKBP6_uc011kew.1_Silent_p.R273R|FKBP6_uc010lbe.1_Non-coding_Transcript	NM_003602	NP_003593	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform a	278	TPR 3.				protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.235294	104.913244	115.920239	40	130	KEEP	---	---	---	---	capture		Silent	SNP	72755322	72755322	6150	7	A	G	G	G	132	11	FKBP6	4	4
STX1A	6804	broad.mit.edu	37	7	73118706	73118706	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73118706C>A	uc003tyx.2	-	c.331G>T	c.(331-333)GCT>TCT	p.A111S	WBSCR22_uc003tyw.1_3'UTR|STX1A_uc003tyy.2_Missense_Mutation_p.A111S|STX1A_uc010lbj.1_Missense_Mutation_p.A111S	NM_004603	NP_004594	Q16623	STX1A_HUMAN	syntaxin 1A isoform 1	111	Cytoplasmic (Potential).				energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.290909	42.978631	45.132438	16	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73118706	73118706	15863	7	C	A	A	A	351	27	STX1A	1	1
STX1A	6804	broad.mit.edu	37	7	73118711	73118711	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:73118711G>C	uc003tyx.2	-	c.326C>G	c.(325-327)TCC>TGC	p.S109C	WBSCR22_uc003tyw.1_3'UTR|STX1A_uc003tyy.2_Missense_Mutation_p.S109C|STX1A_uc010lbj.1_Missense_Mutation_p.S109C	NM_004603	NP_004594	Q16623	STX1A_HUMAN	syntaxin 1A isoform 1	109	Potential.|Cytoplasmic (Potential).				energy reserve metabolic process|glutamate secretion|intracellular protein transport|regulation of insulin secretion	cell junction|extracellular region|integral to membrane|neuron projection|synaptic vesicle membrane|synaptosome	SNAP receptor activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)												0.259259	41.625375	44.459392	14	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73118711	73118711	15863	7	G	C	C	C	533	41	STX1A	3	3
CSMD3	114788	broad.mit.edu	37	8	113364659	113364659	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113364659C>A	uc003ynu.2	-	c.6241G>T	c.(6241-6243)GGA>TGA	p.G2081*	CSMD3_uc003yns.2_Nonsense_Mutation_p.G1283*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.G2041*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.G1977*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2081	Extracellular (Potential).|Sushi 11.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.25	34.548775	37.503641	13	39	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	113364659	113364659	4087	8	C	A	A	A	312	24	CSMD3	5	2
WDR67	93594	broad.mit.edu	37	8	124140704	124140704	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124140704C>G	uc003ypp.1	+	c.2068C>G	c.(2068-2070)CAG>GAG	p.Q690E	WDR67_uc011lig.1_Missense_Mutation_p.Q690E|WDR67_uc011lih.1_Missense_Mutation_p.Q580E|WDR67_uc003ypq.1_Non-coding_Transcript|WDR67_uc003yps.1_Intron|WDR67_uc003ypt.1_Missense_Mutation_p.Q147E|WDR67_uc003ypu.1_Missense_Mutation_p.Q147E	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	WD repeat domain 67 isoform 1	690						intracellular	Rab GTPase activator activity			skin(1)	1	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)											0.173913	28.855059	35.781045	12	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124140704	124140704	17891	8	C	G	G	G	221	17	WDR67	3	3
FAM135B	51059	broad.mit.edu	37	8	139209862	139209862	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139209862C>G	uc003yuy.2	-	c.720G>C	c.(718-720)TGG>TGC	p.W240C	FAM135B_uc003yux.2_Missense_Mutation_p.W141C|FAM135B_uc003yuz.2_Non-coding_Transcript	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	240										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.32	46.34935	47.754394	16	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139209862	139209862	5646	8	C	G	G	G	338	26	FAM135B	3	3
XPO7	23039	broad.mit.edu	37	8	21860756	21860756	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:21860756C>T	uc010lti.2	+	c.2997C>T	c.(2995-2997)ATC>ATT	p.I999I	XPO7_uc003xaa.3_Silent_p.I990I|XPO7_uc010ltk.2_Silent_p.I991I	NM_001100161	NP_001093631	Q9UIA9	XPO7_HUMAN	exportin 7 isoform a	990					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)										0.388889	20.820548	21.015371	7	11	KEEP	---	---	---	---	capture		Silent	SNP	21860756	21860756	18032	8	C	T	T	T	369	29	XPO7	2	2
CDCA2	157313	broad.mit.edu	37	8	25346185	25346185	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:25346185G>A	uc003xep.1	+	c.1651G>A	c.(1651-1653)GCA>ACA	p.A551T	PPP2R2A_uc003xek.2_Intron|CDCA2_uc011lae.1_Missense_Mutation_p.A551T|CDCA2_uc003xeq.1_Missense_Mutation_p.A536T|CDCA2_uc003xer.1_Missense_Mutation_p.A214T	NM_152562	NP_689775	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	551	Lys-rich.				cell division|mitosis	cytoplasm|nucleus					0		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)										0.163636	16.436906	22.35157	9	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25346185	25346185	3215	8	G	A	A	A	442	34	CDCA2	2	2
CSMD1	64478	broad.mit.edu	37	8	2830776	2830776	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:2830776C>T	uc011kwk.1	-	c.8789G>A	c.(8788-8790)GGG>GAG	p.G2930E	CSMD1_uc011kwj.1_Missense_Mutation_p.G2259E|CSMD1_uc010lrg.2_Missense_Mutation_p.G940E	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2930	Extracellular (Potential).|Sushi 22.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)										0.371429	118.997287	120.522556	39	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2830776	2830776	4085	8	C	T	T	T	286	22	CSMD1	2	2
RAB11FIP1	80223	broad.mit.edu	37	8	37732582	37732582	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:37732582G>A	uc003xkm.1	-	c.1073C>T	c.(1072-1074)ACA>ATA	p.T358I	RAB11FIP1_uc010lvz.1_Missense_Mutation_p.T206I|RAB11FIP1_uc003xkn.1_Missense_Mutation_p.T358I|RAB11FIP1_uc003xkl.1_5'Flank|RAB11FIP1_uc003xko.1_5'Flank|RAB11FIP1_uc003xkp.1_Missense_Mutation_p.T206I	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	358					protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)	1		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)											0.315789	76.708915	79.580148	30	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37732582	37732582	13352	8	G	A	A	A	624	48	RAB11FIP1	2	2
ADRB3	155	broad.mit.edu	37	8	37823585	37823585	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:37823585G>T	uc003xkr.1	-	c.403C>A	c.(403-405)CGC>AGC	p.R135S		NM_000025	NP_000016	P13945	ADRB3_HUMAN	adrenergic, beta-3-, receptor	135	Cytoplasmic (By similarity).				carbohydrate metabolic process|energy reserve metabolic process|positive regulation of MAPKKK cascade	integral to plasma membrane|receptor complex	beta3-adrenergic receptor activity|protein homodimerization activity				0	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		Norepinephrine(DB00368)|Pindolol(DB00960)|Propranolol(DB00571)									0.470588	24.803814	24.816032	8	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37823585	37823585	343	8	G	T	T	T	507	39	ADRB3	1	1
PLAT	5327	broad.mit.edu	37	8	42048920	42048920	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42048920G>T	uc003xos.2	-	c.85C>A	c.(85-87)CGA>AGA	p.R29R	PLAT_uc010lxf.1_Silent_p.R29R|PLAT_uc010lxg.1_Silent_p.R29R|PLAT_uc003xot.2_Silent_p.R29R|PLAT_uc011lcm.1_Silent_p.R29R|PLAT_uc011lcn.1_Silent_p.R29R	NM_000930	NP_000921	P00750	TPA_HUMAN	plasminogen activator, tissue isoform 1	29					blood coagulation|fibrinolysis|negative regulation of proteolysis|protein modification process|proteolysis	cell surface|cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			breast(1)|skin(1)	2	all_cancers(6;3.84e-26)|all_epithelial(6;9.61e-28)|all_lung(13;7.2e-13)|Lung NSC(13;1.18e-11)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000378)|Lung NSC(58;0.00145)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00135)|Colorectal(10;0.00165)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)		Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Iloprost(DB01088)|Reteplase(DB00015)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)					176				0.26087	67.57708	72.326296	24	68	KEEP	---	---	---	---	capture		Silent	SNP	42048920	42048920	12447	8	G	T	T	T	506	39	PLAT	1	1
HOOK3	84376	broad.mit.edu	37	8	42823316	42823316	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42823316G>T	uc003xpr.2	+	c.1081G>T	c.(1081-1083)GCC>TCC	p.A361S	HOOK3_uc010lxq.1_Missense_Mutation_p.A361S	NM_032410	NP_115786	Q86VS8	HOOK3_HUMAN	golgi-associated microtubule-binding protein	361	Potential.				cytoplasmic microtubule organization|early endosome to late endosome transport|endosome organization|endosome to lysosome transport|Golgi localization|interkinetic nuclear migration|lysosome organization|microtubule anchoring|negative regulation of neurogenesis|protein localization to centrosome|protein transport	cis-Golgi network|FHF complex|microtubule|pericentriolar material	identical protein binding|microtubule binding			ovary(1)|breast(1)	2	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)											0.163043	28.463904	38.392949	15	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42823316	42823316	7576	8	G	T	T	T	546	42	HOOK3	2	2
GEM	2669	broad.mit.edu	37	8	95262780	95262780	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95262780A>G	uc003ygj.2	-	c.649T>C	c.(649-651)TTC>CTC	p.F217L	GEM_uc003ygi.2_Missense_Mutation_p.F217L	NM_005261	NP_005252	P55040	GEM_HUMAN	GTP-binding mitogen-induced T-cell protein	217					cell surface receptor linked signaling pathway|immune response|small GTPase mediated signal transduction	internal side of plasma membrane	calmodulin binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding				0	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)								0.260274	53.689771	57.490938	19	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95262780	95262780	6597	8	A	G	G	G	26	2	GEM	4	4
COL15A1	1306	broad.mit.edu	37	9	101748343	101748343	+	Silent	SNP	C	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101748343C>T	uc004azb.1	+	c.597C>T	c.(595-597)AGC>AGT	p.S199S	COL15A1_uc004aza.2_Silent_p.S199S	NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	199	TSP N-terminal.				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)												0.081081	1.097274	14.322969	6	68	KEEP	---	---	---	---	capture		Silent	SNP	101748343	101748343	3810	9	C	T	T	T	350	27	COL15A1	1	1
SPTAN1	6709	broad.mit.edu	37	9	131348057	131348057	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131348057A>G	uc004bvm.3	+	c.2591A>G	c.(2590-2592)AAG>AGG	p.K864R	SPTAN1_uc011mbg.1_Missense_Mutation_p.K864R|SPTAN1_uc011mbh.1_Missense_Mutation_p.K876R|SPTAN1_uc004bvl.3_Missense_Mutation_p.K864R|SPTAN1_uc004bvn.3_Missense_Mutation_p.K864R	NM_001130438	NP_001123910	Q13813	SPTA2_HUMAN	spectrin, alpha, non-erythrocytic 1	864	Spectrin 9.				actin filament capping|axon guidance|cellular component disassembly involved in apoptosis	cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin	actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton			breast(5)|ovary(4)|pancreas(1)	10						NSCLC(120;833 1744 2558 35612 37579)				1105				0.297297	136.34338	141.779487	44	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131348057	131348057	15631	9	A	G	G	G	39	3	SPTAN1	4	4
ACO1	48	broad.mit.edu	37	9	32436254	32436254	+	Silent	SNP	T	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:32436254T>C	uc003zqw.3	+	c.2106T>C	c.(2104-2106)ACT>ACC	p.T702T	ACO1_uc010mjh.1_3'UTR|ACO1_uc003zqx.3_Silent_p.T702T|ACO1_uc003zqy.3_Non-coding_Transcript	NM_002197	NP_002188	P21399	ACOC_HUMAN	aconitase 1	702					citrate metabolic process|response to iron(II) ion|tricarboxylic acid cycle	cytosol|endoplasmic reticulum|Golgi apparatus	4 iron, 4 sulfur cluster binding|aconitate hydratase activity|citrate hydro-lyase (cis-aconitate-forming) activity|iron-responsive element binding|isocitrate hydro-lyase (cis-aconitate-forming) activity|metal ion binding|protein binding				0			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)										0.1	6.043619	14.028405	5	45	KEEP	---	---	---	---	capture		Silent	SNP	32436254	32436254	147	9	T	C	C	C	691	54	ACO1	4	4
TMEM8B	51754	broad.mit.edu	37	9	35853738	35853738	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35853738G>T	uc003zym.2	+	c.1320G>T	c.(1318-1320)CGG>CGT	p.R440R	TMEM8B_uc003zyo.2_Silent_p.R440R	NM_001042589	NP_001036054	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B isoform a	440	Cytoplasmic (Potential).				cell-matrix adhesion|regulation of growth|regulation of mitotic cell cycle	cell surface|endoplasmic reticulum|integral to membrane|mitochondrion|nucleus|plasma membrane	protein binding			ovary(1)	1														0.357143	26.90273	27.380188	10	18	KEEP	---	---	---	---	capture		Silent	SNP	35853738	35853738	16755	9	G	T	T	T	548	43	TMEM8B	2	2
PRUNE2	158471	broad.mit.edu	37	9	79322001	79322001	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:79322001G>T	uc010mpk.2	-	c.5189C>A	c.(5188-5190)GCT>GAT	p.A1730D	PRUNE2_uc004akj.3_5'Flank|PRUNE2_uc010mpl.1_5'Flank	NM_015225	NP_056040	Q8WUY3	PRUN2_HUMAN	prune homolog 2	1730					apoptosis|G1 phase|induction of apoptosis	cytoplasm	metal ion binding|pyrophosphatase activity				0														0.266667	41.471417	44.423115	16	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79322001	79322001	13092	9	G	T	T	T	442	34	PRUNE2	2	2
C9orf79	286234	broad.mit.edu	37	9	90502663	90502663	+	Silent	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:90502663A>G	uc004app.3	+	c.3261A>G	c.(3259-3261)CCA>CCG	p.P1087P		NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	1087						integral to membrane				ovary(3)	3														0.054795	-5.963018	9.278749	4	69	KEEP	---	---	---	---	capture		Silent	SNP	90502663	90502663	2613	9	A	G	G	G	80	7	C9orf79	4	4
PRPS1	5631	broad.mit.edu	37	X	106884176	106884176	+	Silent	SNP	T	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:106884176T>A	uc004ene.3	+	c.351T>A	c.(349-351)TCT>TCA	p.S117S	PRPS1_uc010npg.2_Intron|PRPS1_uc011msj.1_Intron	NM_002764	NP_002755	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	117					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|large_intestine(1)	4														0.118644	21.263545	38.118224	14	104	KEEP	---	---	---	---	capture		Silent	SNP	106884176	106884176	13021	23	T	A	A	A	704	55	PRPS1	3	3
ODZ1	10178	broad.mit.edu	37	X	123785893	123785893	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123785893G>C	uc010nqy.2	-	c.1450C>G	c.(1450-1452)CGG>GGG	p.R484G	ODZ1_uc011muj.1_Missense_Mutation_p.R483G|ODZ1_uc004euj.2_Missense_Mutation_p.R484G	NM_001163278	NP_001156750	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 1	484	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	22										623				0.064516	-2.52367	15.80333	6	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123785893	123785893	11239	23	G	C	C	C	480	37	ODZ1	3	3
SMARCA1	6594	broad.mit.edu	37	X	128649931	128649931	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:128649931G>C	uc011muk.1	-	c.469C>G	c.(469-471)CTA>GTA	p.L157V	SMARCA1_uc004eun.3_Missense_Mutation_p.L157V|SMARCA1_uc004eup.3_Missense_Mutation_p.L157V|SMARCA1_uc011mul.1_Missense_Mutation_p.L157V	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	157					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of gene-specific transcription|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding|transcription regulator activity			ovary(3)|skin(1)	4														0.25974	59.164316	63.188991	20	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128649931	128649931	15266	23	G	C	C	C	438	34	SMARCA1	3	3
AIFM1	9131	broad.mit.edu	37	X	129264138	129264138	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129264138G>T	uc004evg.2	-	c.1577C>A	c.(1576-1578)ACT>AAT	p.T526N	AIFM1_uc011mur.1_Missense_Mutation_p.T174N|AIFM1_uc011mus.1_3'UTR|AIFM1_uc004evh.2_Missense_Mutation_p.T522N|AIFM1_uc004evi.2_Missense_Mutation_p.T239N|AIFM1_uc004evk.2_Non-coding_Transcript	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	526					activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change|oxidation-reduction process	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5										210				0.092199	7.86568	31.473755	13	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129264138	129264138	429	23	G	T	T	T	468	36	AIFM1	2	2
AFF2	2334	broad.mit.edu	37	X	147743992	147743992	+	Silent	SNP	G	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:147743992G>A	uc004fcp.2	+	c.744G>A	c.(742-744)GCG>GCA	p.A248A	AFF2_uc004fco.2_Silent_p.A244A|AFF2_uc004fcq.2_Silent_p.A244A|AFF2_uc004fcr.2_Silent_p.A244A|AFF2_uc011mxb.1_Silent_p.A248A|AFF2_uc004fcs.2_Silent_p.A244A	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	248					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.05305	-40.208761	39.324299	20	357	KEEP	---	---	---	---	capture		Silent	SNP	147743992	147743992	358	23	G	A	A	A	483	38	AFF2	1	1
MAGEA11	4110	broad.mit.edu	37	X	148797640	148797640	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:148797640C>A	uc004fdq.2	+	c.494C>A	c.(493-495)GCT>GAT	p.A165D	HSFX2_uc004fdl.2_Intron|HSFX1_uc004fdm.2_Intron|MAGEA11_uc004fdr.2_Missense_Mutation_p.A136D	NM_005366	NP_005357	P43364	MAGAB_HUMAN	melanoma antigen family A, 11 isoform a	165						cytoplasm|nucleus	protein binding			ovary(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)													0.068966	-2.749258	8.391906	4	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148797640	148797640	9542	23	C	A	A	A	364	28	MAGEA11	2	2
MAMLD1	10046	broad.mit.edu	37	X	149639223	149639223	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:149639223C>A	uc004fee.1	+	c.1378C>A	c.(1378-1380)CCA>ACA	p.P460T	MAMLD1_uc011mxt.1_Missense_Mutation_p.P422T|MAMLD1_uc011mxu.1_Missense_Mutation_p.P435T|MAMLD1_uc011mxv.1_Missense_Mutation_p.P435T|MAMLD1_uc011mxw.1_Missense_Mutation_p.P387T	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	460					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)													0.310924	99.371907	103.138932	37	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149639223	149639223	9591	23	C	A	A	A	286	22	MAMLD1	2	2
L1CAM	3897	broad.mit.edu	37	X	153133300	153133300	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153133300G>T	uc004fjb.2	-	c.1894C>A	c.(1894-1896)CGC>AGC	p.R632S	L1CAM_uc004fjc.2_Missense_Mutation_p.R632S|L1CAM_uc010nuo.2_Missense_Mutation_p.R627S	NM_000425	NP_000416	P32004	L1CAM_HUMAN	L1 cell adhesion molecule isoform 1 precursor	632	Fibronectin type-III 1.|Extracellular (Potential).		R -> P (in MASA).		axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane				ovary(8)|central_nervous_system(1)	9	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.178571	11.359512	14.080898	5	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	153133300	153133300	8911	23	G	T	T	T	494	38	L1CAM	1	1
MTCP1NB	100272147	broad.mit.edu	37	X	154292295	154292295	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:154292295G>T	uc004fmy.2	-	c.4C>A	c.(4-6)CCG>ACG	p.P2T		NM_001018024	NP_001018024	P56277	MTCNB_HUMAN	mature T-cell proliferation 1 neighbor	2					cell proliferation	mitochondrion					0									(EFM19-Tumor)					0.049505	-11.914451	9.849628	5	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154292295	154292295	10309	23	G	T	T	T	546	42	MTCP1NB	2	2
PHKA2	5256	broad.mit.edu	37	X	18915323	18915323	+	Silent	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:18915323G>T	uc004cyv.3	-	c.3240C>A	c.(3238-3240)GTC>GTA	p.V1080V	PHKA2_uc004cyu.3_Silent_p.V386V|PHKA2_uc010nfe.1_Silent_p.V112V|PHKA2_uc010nff.1_Non-coding_Transcript	NM_000292	NP_000283	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	1080	Calmodulin-binding (Potential).				glucose metabolic process|glycogen catabolic process|protein modification process	cytosol|phosphorylase kinase complex|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(1)|central_nervous_system(1)	2	Hepatocellular(33;0.183)													0.153846	10.761289	16.729649	8	44	KEEP	---	---	---	---	capture		Silent	SNP	18915323	18915323	12268	23	G	T	T	T	522	41	PHKA2	2	2
ZNF645	158506	broad.mit.edu	37	X	22291637	22291637	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:22291637C>A	uc004dai.1	+	c.529C>A	c.(529-531)CTA>ATA	p.L177I		NM_152577	NP_689790	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	177						intracellular	zinc ion binding			lung(1)|pancreas(1)	2														0.103586	16.847968	56.140461	26	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22291637	22291637	18656	23	C	A	A	A	415	32	ZNF645	2	2
MAGEB18	286514	broad.mit.edu	37	X	26157999	26157999	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:26157999C>A	uc004dbq.1	+	c.897C>A	c.(895-897)TTC>TTA	p.F299L		NM_173699	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	299	MAGE.						protein binding			central_nervous_system(1)	1														0.111111	3.673048	9.057005	4	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26157999	26157999	9556	23	C	A	A	A	389	30	MAGEB18	2	2
IL1RAPL1	11141	broad.mit.edu	37	X	29301284	29301284	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:29301284G>T	uc004dby.2	+	c.312G>T	c.(310-312)TGG>TGT	p.W104C		NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	104	Ig-like C2-type 1.|Extracellular (Potential).				innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5														0.272727	72.981226	77.590425	27	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29301284	29301284	7962	23	G	T	T	T	572	44	IL1RAPL1	2	2
MAGEB4	4115	broad.mit.edu	37	X	30260301	30260301	+	Silent	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30260301C>A	uc004dcb.2	+	c.49C>A	c.(49-51)CGG>AGG	p.R17R	MAGEB1_uc004dcc.2_5'Flank|MAGEB1_uc004dcd.2_5'Flank	NM_002367	NP_002358	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	17										ovary(1)	1														0.166667	19.542385	25.229394	9	45	KEEP	---	---	---	---	capture		Silent	SNP	30260301	30260301	9559	23	C	A	A	A	347	27	MAGEB4	1	1
MXRA5	25878	broad.mit.edu	37	X	3238059	3238059	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3238059C>A	uc004crg.3	-	c.5667G>T	c.(5665-5667)AAG>AAT	p.K1889N		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1889	Ig-like C2-type 3.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.205882	16.129754	18.839477	7	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3238059	3238059	10397	23	C	A	A	A	311	24	MXRA5	2	2
RP2	6102	broad.mit.edu	37	X	46713150	46713150	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46713150C>A	uc004dgw.3	+	c.342C>A	c.(340-342)TGC>TGA	p.C114*		NM_006915	NP_008846	O75695	XRP2_HUMAN	XRP2 protein	114	C-CAP/cofactor C-like.				cell morphogenesis|CTP biosynthetic process|GTP biosynthetic process|protein folding|response to stimulus|UTP biosynthetic process|visual perception	cytoplasm|plasma membrane	ATP binding|GTP binding|GTPase activator activity|nucleoside diphosphate kinase activity|unfolded protein binding				0														0.088889	3.446593	18.798848	8	82	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	46713150	46713150	14013	23	C	A	A	A	337	26	RP2	5	2
ZNF157	7712	broad.mit.edu	37	X	47272470	47272470	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47272470G>T	uc004dhr.1	+	c.998G>T	c.(997-999)GGT>GTT	p.G333V		NM_003446	NP_003437	P51786	ZN157_HUMAN	zinc finger protein 157	333	C2H2-type 7.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.333333	39.635139	40.668795	14	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47272470	47272470	18328	23	G	T	T	T	572	44	ZNF157	2	2
BMP15	9210	broad.mit.edu	37	X	50658984	50658984	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:50658984A>G	uc011mnw.1	+	c.556A>G	c.(556-558)ATC>GTC	p.I186V		NM_005448	NP_005439	O95972	BMP15_HUMAN	bone morphogenetic protein 15 precursor	186					female gamete generation|granulosa cell development|ovarian follicle development	extracellular space	cytokine activity|growth factor activity			ovary(2)	2	Ovarian(276;0.236)													0.182796	41.323094	50.105109	17	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50658984	50658984	1483	23	A	G	G	G	208	16	BMP15	4	4
NLGN4X	57502	broad.mit.edu	37	X	5821878	5821878	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:5821878C>A	uc010ndi.2	-	c.952G>T	c.(952-954)GGC>TGC	p.G318C	NLGN4X_uc004crp.2_Missense_Mutation_p.G301C|NLGN4X_uc010ndh.2_Missense_Mutation_p.G281C|NLGN4X_uc004crq.2_Missense_Mutation_p.G281C|NLGN4X_uc004crr.2_Missense_Mutation_p.G281C|NLGN4X_uc010ndj.2_Missense_Mutation_p.G281C	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor	281	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|regulation of synaptic transmission|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	carboxylesterase activity|chloride ion binding|neurexin binding|protein homodimerization activity			large_intestine(1)|skin(1)	2														0.111111	5.744371	12.471099	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5821878	5821878	10867	23	C	A	A	A	299	23	NLGN4X	1	1
ZC3H12B	340554	broad.mit.edu	37	X	64722025	64722025	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:64722025G>C	uc010nko.2	+	c.1414G>C	c.(1414-1416)GGT>CGT	p.G472R		NM_001010888	NP_001010888	Q5HYM0	ZC12B_HUMAN	zinc finger CCCH-type containing 12B	472							endonuclease activity|nucleic acid binding|zinc ion binding			lung(1)|kidney(1)|pancreas(1)	3														0.083636	7.026803	55.455672	23	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64722025	64722025	18150	23	G	C	C	C	559	43	ZC3H12B	3	3
RGAG4	340526	broad.mit.edu	37	X	71350439	71350439	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:71350439G>T	uc010nlh.1	-	c.952C>A	c.(952-954)CCG>ACG	p.P318T	NHSL2_uc011mqa.1_Intron|RGAG4_uc004eaj.1_Non-coding_Transcript	NM_001024455	NP_001019626	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	318										ovary(2)|skin(1)	3	Renal(35;0.156)													0.132911	29.259209	49.93891	21	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71350439	71350439	13748	23	G	T	T	T	559	43	RGAG4	2	2
TBX22	50945	broad.mit.edu	37	X	79282220	79282220	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79282220G>T	uc010nmg.1	+	c.651G>T	c.(649-651)ATG>ATT	p.M217I	TBX22_uc004edi.1_Missense_Mutation_p.M97I|TBX22_uc004edj.1_Missense_Mutation_p.M217I	NM_001109878	NP_001103348	Q9Y458	TBX22_HUMAN	T-box 22 isoform 1	217	T-box.				multicellular organismal development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			large_intestine(3)|central_nervous_system(2)|lung(1)|ovary(1)	7										298				0.159574	29.4613	39.839431	15	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79282220	79282220	16184	23	G	T	T	T	598	46	TBX22	2	2
PCDH11X	27328	broad.mit.edu	37	X	91642767	91642767	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91642767G>T	uc004efk.1	+	c.3178G>T	c.(3178-3180)GGC>TGC	p.G1060C	PCDH11X_uc004efl.1_Missense_Mutation_p.G1050C|PCDH11X_uc004efo.1_Missense_Mutation_p.G1023C|PCDH11X_uc010nmv.1_Intron|PCDH11X_uc004efm.1_Missense_Mutation_p.G1060C|PCDH11X_uc004efn.1_Missense_Mutation_p.G1050C	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1060	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.311475	50.199618	52.132	19	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91642767	91642767	11928	23	G	T	T	T	455	35	PCDH11X	2	2
DNHD1	144132	broad.mit.edu	37	11	6567895	6567896	+	In_Frame_Ins	INS	-	TGCCCTACTGCA	TGCCCTACTGCA	rs35369957		TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6567895_6567896insTGCCCTACTGCA	uc001mdw.3	+	c.5726_5727insTGCCCTACTGCA	c.(5725-5727)GCT>GCTGCCCTACTGCAT	p.1909_1910insALLH	DNHD1_uc001mds.1_3'UTR	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	1909_1910					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)										0.43			3	4		---	---	---	---	capture_indel		In_Frame_Ins	INS	6567895	6567896	4851	11	-	TGCCCTACTGCA	TGCCCTACTGCA	TGCCCTACTGCA	364	28	DNHD1	5	5
MYH8	4626	broad.mit.edu	37	17	10303998	10304000	+	In_Frame_Del	DEL	CTC	-	-			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10303998_10304000delCTC	uc002gmm.2	-	c.3442_3444delGAG	c.(3442-3444)GAGdel	p.E1148del		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1148	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.41			53	76		---	---	---	---	capture_indel		In_Frame_Del	DEL	10303998	10304000	10436	17	CTC	-	-	-	415	32	MYH8	5	5
CRLF3	51379	broad.mit.edu	37	17	29151659	29151660	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29151659_29151660insC	uc002hfr.3	-	c.10_11insG	c.(10-12)GCGfs	p.A4fs	CRLF3_uc010wbr.1_5'UTR	NM_015986	NP_057070	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	4					negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of cell cycle arrest|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of JAK-STAT cascade	cytoplasm	transcription activator activity				0		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				Pancreas(30;346 881 29244 33464 41299)								0.33			3	6		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	29151659	29151660	4027	17	-	C	C	C	494	38	CRLF3	5	5
TGIF1	7050	broad.mit.edu	37	18	3452223	3452223	+	Frame_Shift_Del	DEL	T	-	-			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:3452223_3452223delT	uc002klz.2	+	c.246_246delT	c.(244-246)CCTfs	p.P82fs	TGIF1_uc002klu.2_Intron|TGIF1_uc002klv.2_Intron|TGIF1_uc002klx.2_Intron|TGIF1_uc002klw.2_Intron|TGIF1_uc010dkm.1_Intron|TGIF1_uc002kly.2_Intron|TGIF1_uc002kma.2_Intron|TGIF1_uc002kmb.2_5'Flank	NM_170695	NP_733796	Q15583	TGIF1_HUMAN	TG-interacting factor isoform a	82					negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity			ovary(1)	1	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)												0.50			6	6		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	3452223	3452223	16353	18	T	-	-	-	691	54	TGIF1	5	5
ZSCAN1	284312	broad.mit.edu	37	19	58565207	58565207	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58565207_58565207delG	uc002qrc.1	+	c.1015_1015delG	c.(1015-1017)GGCfs	p.G339fs		NM_182572	NP_872378	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	339	C2H2-type 2.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)										0.46			18	21		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	58565207	58565207	18830	19	G	-	-	-	611	47	ZSCAN1	5	5
AFF3	3899	broad.mit.edu	37	2	100210335	100210340	+	In_Frame_Del	DEL	GGCTGA	-	-			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:100210335_100210340delGGCTGA	uc002taf.2	-	c.1858_1863delTCAGCC	c.(1858-1863)TCAGCCdel	p.SA620del	AFF3_uc002tag.2_In_Frame_Del_p.SA595del|AFF3_uc010fiq.1_In_Frame_Del_p.SA595del|AFF3_uc010yvr.1_In_Frame_Del_p.SA748del|AFF3_uc002tah.1_In_Frame_Del_p.SA620del	NM_001025108	NP_001020279	P51826	AFF3_HUMAN	AF4/FMR2 family, member 3 isoform 2	595_596					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6										693				0.36			4	7		---	---	---	---	capture_indel		In_Frame_Del	DEL	100210335	100210340	359	2	GGCTGA	-	-	-	496	39	AFF3	5	5
PRR21	643905	broad.mit.edu	37	2	240982117	240982144	+	Frame_Shift_Del	DEL	GTGGGTGAAGAGGCATGGATGAAGGACT	-	-	rs112308001;rs79839275;rs74754936;rs79314166		TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:240982117_240982144delGTGGGTGAAGAGGCATGGATGAAGGACT	uc010zod.1	-	c.256_283delAGTCCTTCATCCATGCCTCTTCACCCAC	c.(256-285)AGTCCTTCATCCATGCCTCTTCACCCACGGfs	p.S86fs		NM_001080835	NP_001074304	Q8WXC7	PRR21_HUMAN	proline rich 21	86_95	Pro-rich.									ovary(1)	1														0.69			24	11		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	240982117	240982144	13040	2	GTGGGTGAAGAGGCATGGATGAAGGACT	-	-	-	519	40	PRR21	5	5
CCDC54	84692	broad.mit.edu	37	3	107096304	107096308	+	De_novo_Start_OutOfFrame	DEL	TTCCA	-	-			TCGA-17-Z001-01	TCGA-17-Z001-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:107096304_107096308delTTCCA	uc003dwi.1	+	c.-130_-126delTTCCA	c.(-132--124)ATTTCCAGA>ATGA			NM_032600	NP_115989			coiled-coil domain containing 54												0														0.49			18	19		---	---	---	---	capture_indel		De_novo_Start_OutOfFrame	DEL	107096304	107096308	2947	3	TTCCA	-	-	-	820	64	CCDC54	5	5
