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
PNLIP	5406	broad.mit.edu	37	10	118314956	118314956	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118314956G>T	uc001lcm.2	+	c.748G>T	c.(748-750)GAA>TAA	p.E250*		NM_000936	NP_000927	P16233	LIPP_HUMAN	pancreatic lipase precursor	250					lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)	2				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)									0.220833	110.55998	127.781131	53	187	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	118314956	118314956	12575	10	G	T	T	T	533	41	PNLIP	5	2
PDZD8	118987	broad.mit.edu	37	10	119044815	119044815	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:119044815C>A	uc001lde.1	-	c.1429G>T	c.(1429-1431)GGT>TGT	p.G477C		NM_173791	NP_776152	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	477					intracellular signal transduction		metal ion binding				0		Colorectal(252;0.19)		all cancers(201;0.0121)										0.210797	171.438055	201.537171	82	307	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119044815	119044815	12126	10	C	A	A	A	286	22	PDZD8	2	2
TACC2	10579	broad.mit.edu	37	10	123969979	123969979	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:123969979C>T	uc001lfv.2	+	c.6039C>T	c.(6037-6039)TTC>TTT	p.F2013F	TACC2_uc001lfw.2_Silent_p.F159F|TACC2_uc009xzx.2_Silent_p.F1968F|TACC2_uc010qtv.1_Silent_p.F2017F|TACC2_uc001lfx.2_5'UTR|TACC2_uc001lfy.2_5'UTR|TACC2_uc001lfz.2_Silent_p.F91F|TACC2_uc001lga.2_Silent_p.F91F|TACC2_uc009xzy.2_Silent_p.F91F|TACC2_uc001lgb.2_Silent_p.F48F|TACC2_uc010qtw.1_Silent_p.F108F	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	2013	Pro-rich.					microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|central_nervous_system(1)	8		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)												0.189655	22.790572	28.015794	11	47	KEEP	---	---	---	---	capture		Silent	SNP	123969979	123969979	16023	10	C	T	T	T	389	30	TACC2	2	2
MKX	283078	broad.mit.edu	37	10	27964308	27964308	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27964308C>T	uc001ity.3	-	c.909G>A	c.(907-909)ACG>ACA	p.T303T	MKX_uc001itx.3_Silent_p.T303T	NM_173576	NP_775847	Q8IYA7	MKX_HUMAN	mohawk homeobox	303					muscle organ development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.067568	-9.945084	33.028473	15	207	KEEP	---	---	---	---	capture		Silent	SNP	27964308	27964308	10000	10	C	T	T	T	236	19	MKX	1	1
KIAA1462	57608	broad.mit.edu	37	10	30317994	30317994	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:30317994C>T	uc009xle.1	-	c.1083G>A	c.(1081-1083)ACG>ACA	p.T361T	KIAA1462_uc001iux.2_Silent_p.T361T|KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_Silent_p.T223T	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	361	Pro-rich.									ovary(4)	4														0.04878	-17.699173	17.744955	8	156	KEEP	---	---	---	---	capture		Silent	SNP	30317994	30317994	8543	10	C	T	T	T	288	23	KIAA1462	1	1
ERCC6	2074	broad.mit.edu	37	10	50740774	50740774	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:50740774C>G	uc001jhs.3	-	c.237G>C	c.(235-237)CAG>CAC	p.Q79H	PGBD3_uc009xoe.2_Missense_Mutation_p.Q79H|PGBD3_uc001jhu.2_Missense_Mutation_p.Q79H	NM_000124	NP_000115	Q03468	ERCC6_HUMAN	excision repair cross-complementing rodent	79					base-excision repair|positive regulation of transcription elongation, DNA-dependent|transcription from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair	nucleolus|soluble fraction|transcription elongation factor complex	ATP binding|chromatin binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein C-terminus binding|protein complex binding|protein N-terminus binding|transcription elongation regulator activity			breast(5)|ovary(2)|large_intestine(2)|lung(1)	10										738				0.089552	4.896419	16.291752	6	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50740774	50740774	5410	10	C	G	G	G	415	32	ERCC6	3	3
PCDH15	65217	broad.mit.edu	37	10	55566686	55566686	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55566686C>A	uc010qhq.1	-	c.4702G>T	c.(4702-4704)GCT>TCT	p.A1568S	PCDH15_uc010qhr.1_Missense_Mutation_p.A1563S	NM_001142771	NP_001136243	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD3-1 precursor	421	Cadherin 4.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.204778	130.351759	153.969068	60	233	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55566686	55566686	11931	10	C	A	A	A	325	25	PCDH15	2	2
PCDH15	65217	broad.mit.edu	37	10	55913025	55913025	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55913025G>T	uc010qhy.1	-	c.1634C>A	c.(1633-1635)TCA>TAA	p.S545*	PCDH15_uc010qhq.1_Nonsense_Mutation_p.S545*|PCDH15_uc010qhr.1_Nonsense_Mutation_p.S540*|PCDH15_uc010qhs.1_Nonsense_Mutation_p.S552*|PCDH15_uc010qht.1_Nonsense_Mutation_p.S547*|PCDH15_uc010qhu.1_Nonsense_Mutation_p.S540*|PCDH15_uc001jjv.1_Nonsense_Mutation_p.S518*|PCDH15_uc010qhv.1_Nonsense_Mutation_p.S540*|PCDH15_uc010qhw.1_Nonsense_Mutation_p.S503*|PCDH15_uc010qhx.1_Nonsense_Mutation_p.S540*|PCDH15_uc010qhz.1_Nonsense_Mutation_p.S540*|PCDH15_uc010qia.1_Nonsense_Mutation_p.S518*|PCDH15_uc001jju.1_Nonsense_Mutation_p.S540*|PCDH15_uc010qib.1_Nonsense_Mutation_p.S518*|PCDH15_uc001jjw.2_Nonsense_Mutation_p.S540*	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	540	Cadherin 5.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.194539	109.380312	134.917045	57	236	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	55913025	55913025	11931	10	G	T	T	T	585	45	PCDH15	5	2
ANK3	288	broad.mit.edu	37	10	61898827	61898827	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:61898827C>A	uc001jky.2	-	c.2633G>T	c.(2632-2634)GGG>GTG	p.G878V	ANK3_uc001jkw.2_Missense_Mutation_p.G12V|ANK3_uc009xpa.2_Missense_Mutation_p.G12V|ANK3_uc001jkx.2_Missense_Mutation_p.G56V|ANK3_uc010qih.1_Missense_Mutation_p.G879V|ANK3_uc001jkz.3_Missense_Mutation_p.G872V|ANK3_uc001jlb.1_Missense_Mutation_p.G386V|ANK3_uc001jlc.1_Missense_Mutation_p.G518V	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	878					establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			ovary(6)|pancreas(2)|central_nervous_system(1)|skin(1)	10														0.058642	-28.721099	37.392674	19	305	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61898827	61898827	625	10	C	A	A	A	286	22	ANK3	2	2
HERC4	26091	broad.mit.edu	37	10	69714447	69714447	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:69714447C>T	uc001jng.3	-	c.2266G>A	c.(2266-2268)GAA>AAA	p.E756K	HERC4_uc009xpq.2_Missense_Mutation_p.E289K|HERC4_uc001jnf.3_Non-coding_Transcript|HERC4_uc001jnh.3_Missense_Mutation_p.E748K|HERC4_uc009xpr.2_Missense_Mutation_p.E756K|HERC4_uc001jni.3_Missense_Mutation_p.E492K	NM_022079	NP_071362	Q5GLZ8	HERC4_HUMAN	hect domain and RLD 4 isoform a	756	HECT.				cell differentiation|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|spermatogenesis	cytosol	ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3														0.193548	66.25641	79.845927	30	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69714447	69714447	7343	10	C	T	T	T	416	32	HERC4	2	2
PSAP	5660	broad.mit.edu	37	10	73590956	73590956	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73590956T>G	uc001jsm.2	-	c.302A>C	c.(301-303)AAC>ACC	p.N101T		NM_002778	NP_002769	P07602	SAP_HUMAN	prosaposin isoform a preproprotein	101	Saposin B-type 1.				glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding			ovary(1)	1														0.243243	24.761056	26.981285	9	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73590956	73590956	13096	10	T	G	G	G	780	60	PSAP	4	4
SFMBT2	57713	broad.mit.edu	37	10	7409776	7409776	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7409776A>T	uc009xio.1	-	c.271T>A	c.(271-273)TAC>AAC	p.Y91N	SFMBT2_uc001ijn.1_Missense_Mutation_p.Y91N|SFMBT2_uc010qay.1_Missense_Mutation_p.Y91N|SFMBT2_uc001ijo.1_Missense_Mutation_p.Y91N	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	91	MBT 1.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6														0.22	24.096467	27.710884	11	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7409776	7409776	14647	10	A	T	T	T	182	14	SFMBT2	3	3
KIAA1377	57562	broad.mit.edu	37	11	101833351	101833351	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101833351C>T	uc001pgm.2	+	c.1585C>T	c.(1585-1587)CAC>TAC	p.H529Y	KIAA1377_uc001pgn.2_Missense_Mutation_p.H485Y|KIAA1377_uc010run.1_Missense_Mutation_p.H330Y|KIAA1377_uc009yxa.1_Missense_Mutation_p.H330Y	NM_020802	NP_065853	Q9P2H0	K1377_HUMAN	hypothetical protein LOC57562	529							protein binding			breast(2)|ovary(1)|central_nervous_system(1)	4	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)										0.1375	15.577081	25.743906	11	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101833351	101833351	8536	11	C	T	T	T	377	29	KIAA1377	2	2
ATM	472	broad.mit.edu	37	11	108196179	108196179	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108196179A>G	uc001pkb.1	+	c.6715A>G	c.(6715-6717)ATG>GTG	p.M2239V	ATM_uc009yxr.1_Missense_Mutation_p.M2239V|C11orf65_uc010rvx.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.M891V|ATM_uc001pkg.1_Missense_Mutation_p.M596V	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2239	FAT.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			haematopoietic_and_lymphoid_tissue(174)|lung(24)|breast(14)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	238		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)						1073	TSP Lung(14;0.12)			0.041009	-39.69069	32.149707	13	304	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108196179	108196179	1128	11	A	G	G	G	52	4	ATM	4	4
BCO2	83875	broad.mit.edu	37	11	112072759	112072759	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:112072759G>C	uc001pnf.2	+	c.1040G>C	c.(1039-1041)AGA>ACA	p.R347T	BCO2_uc001pne.1_Missense_Mutation_p.R174T|BCO2_uc001png.2_Missense_Mutation_p.R274T|BCO2_uc001pnh.2_Missense_Mutation_p.R313T|BCO2_uc010rwt.1_Missense_Mutation_p.R242T|BCO2_uc009yyn.2_Missense_Mutation_p.R313T|BCO2_uc001pni.2_Missense_Mutation_p.R313T	NM_031938	NP_114144	Q9BYV7	BCDO2_HUMAN	beta-carotene dioxygenase 2 isoform a	347					carotene metabolic process|oxidation-reduction process|retinal metabolic process|retinoic acid metabolic process	intracellular	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0						GBM(177;1916 2099 21049 29541 39946)								0.036232	-20.551513	11.653402	5	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112072759	112072759	1406	11	G	C	C	C	429	33	BCO2	3	3
DSCAML1	57453	broad.mit.edu	37	11	117310559	117310559	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117310559G>T	uc001prh.1	-	c.4136C>A	c.(4135-4137)CCT>CAT	p.P1379H		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1319	Extracellular (Potential).|Ig-like C2-type 10.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)										0.046667	-20.289547	12.572086	7	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117310559	117310559	4953	11	G	T	T	T	455	35	DSCAML1	2	2
HYOU1	10525	broad.mit.edu	37	11	118926013	118926013	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118926013C>A	uc001puu.2	-	c.303G>T	c.(301-303)CAG>CAT	p.Q101H	HYOU1_uc001put.2_Missense_Mutation_p.Q66H|HYOU1_uc010ryu.1_Missense_Mutation_p.Q121H|HYOU1_uc010ryv.1_Intron|HYOU1_uc001pux.3_Missense_Mutation_p.Q101H|HYOU1_uc010ryw.1_Non-coding_Transcript|HYOU1_uc001puw.1_Missense_Mutation_p.Q101H	NM_006389	NP_006380	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1 precursor	101						endoplasmic reticulum lumen	ATP binding|protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)										0.044776	-31.089054	13.524099	9	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118926013	118926013	7770	11	C	A	A	A	363	28	HYOU1	2	2
TRIM29	23650	broad.mit.edu	37	11	120007970	120007970	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:120007970G>A	uc001pwz.2	-	c.770C>T	c.(769-771)ACC>ATC	p.T257I	TRIM29_uc001pxa.2_Non-coding_Transcript	NM_012101	NP_036233	Q14134	TRI29_HUMAN	tripartite motif protein TRIM29	257	B box-type.				transcription from RNA polymerase II promoter	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)|kidney(1)	3		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)										0.15	18.953725	28.347855	12	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120007970	120007970	17047	11	G	A	A	A	572	44	TRIM29	2	2
OR6X1	390260	broad.mit.edu	37	11	123624624	123624624	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123624624G>T	uc010rzy.1	-	c.603C>A	c.(601-603)ACC>ACA	p.T201T		NM_001005188	NP_001005188	Q8NH79	OR6X1_HUMAN	olfactory receptor, family 6, subfamily X,	201	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)										0.052419	-26.610017	25.888554	13	235	KEEP	---	---	---	---	capture		Silent	SNP	123624624	123624624	11623	11	G	T	T	T	600	47	OR6X1	2	2
OR6M1	390261	broad.mit.edu	37	11	123676203	123676203	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123676203A>G	uc010rzz.1	-	c.855T>C	c.(853-855)TTT>TTC	p.F285F		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)										0.131105	93.880597	145.327433	51	338	KEEP	---	---	---	---	capture		Silent	SNP	123676203	123676203	11615	11	A	G	G	G	167	13	OR6M1	4	4
OR10G8	219869	broad.mit.edu	37	11	123900769	123900769	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123900769C>A	uc001pzp.1	+	c.440C>A	c.(439-441)ACT>AAT	p.T147N		NM_001004464	NP_001004464	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G,	147	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)										0.108635	40.972389	95.449111	39	320	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123900769	123900769	11309	11	C	A	A	A	260	20	OR10G8	2	2
USH1C	10083	broad.mit.edu	37	11	17519711	17519711	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:17519711C>A	uc001mne.2	-	c.2488G>T	c.(2488-2490)GGG>TGG	p.G830W	USH1C_uc001mnf.2_Missense_Mutation_p.G530W|USH1C_uc009yhb.2_Missense_Mutation_p.G511W|USH1C_uc001mng.2_Non-coding_Transcript|USH1C_uc001mnd.2_Missense_Mutation_p.G494W	NM_153676	NP_710142	Q9Y6N9	USH1C_HUMAN	harmonin isoform b3	530	PDZ 3.				equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1														0.153061	28.071856	39.34732	15	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17519711	17519711	17596	11	C	A	A	A	299	23	USH1C	1	1
NAV2	89797	broad.mit.edu	37	11	19967974	19967974	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:19967974G>A	uc001mpr.3	+	c.2174G>A	c.(2173-2175)CGG>CAG	p.R725Q	NAV2_uc001mpp.2_Missense_Mutation_p.R661Q|NAV2_uc010rdm.1_Missense_Mutation_p.R748Q	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	748	Potential.					nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.266667	9.40013	10.133873	4	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19967974	19967974	10580	11	G	A	A	A	507	39	NAV2	1	1
ANO5	203859	broad.mit.edu	37	11	22249096	22249096	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22249096G>T	uc001mqi.2	+	c.612G>T	c.(610-612)CAG>CAT	p.Q204H	ANO5_uc001mqj.2_Missense_Mutation_p.Q203H	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	204	Cytoplasmic (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.037879	-44.737744	16.334793	10	254	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22249096	22249096	708	11	G	T	T	T	451	35	ANO5	2	2
SLC17A6	57084	broad.mit.edu	37	11	22384370	22384370	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22384370C>T	uc001mqk.2	+	c.747C>T	c.(745-747)TAC>TAT	p.Y249Y		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	249	Helical; (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.151079	35.086551	51.304447	21	118	KEEP	---	---	---	---	capture		Silent	SNP	22384370	22384370	14917	11	C	T	T	T	246	19	SLC17A6	1	1
SLC17A6	57084	broad.mit.edu	37	11	22399127	22399127	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22399127C>A	uc001mqk.2	+	c.1590C>A	c.(1588-1590)GAC>GAA	p.D530E		NM_020346	NP_065079	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (sodium-dependent	530	Cytoplasmic (Potential).				sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)|breast(1)	4														0.109244	14.484314	32.481422	13	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22399127	22399127	14917	11	C	A	A	A	220	17	SLC17A6	2	2
ANO3	63982	broad.mit.edu	37	11	26463526	26463526	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:26463526C>A	uc001mqt.3	+	c.108C>A	c.(106-108)TCC>TCA	p.S36S	ANO3_uc010rdr.1_Silent_p.S20S	NM_031418	NP_113606	Q9BYT9	ANO3_HUMAN	transmembrane protein 16C	36	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.126984	62.270462	122.017797	56	385	KEEP	---	---	---	---	capture		Silent	SNP	26463526	26463526	706	11	C	A	A	A	275	22	ANO3	2	2
CCDC73	493860	broad.mit.edu	37	11	32724418	32724418	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:32724418C>A	uc001mtv.2	-	c.279_splice	c.e4+1	p.Q93_splice	CCDC73_uc001mtw.1_Splice_Site_SNP_p.Q93_splice|CCDC73_uc009yjt.2_Splice_Site_SNP_p.Q93_splice	NM_001008391	NP_001008392			sarcoma antigen NY-SAR-79											ovary(1)	1	Breast(20;0.112)													0.129412	48.728059	82.813184	33	222	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	32724418	32724418	2969	11	C	A	A	A	234	18	CCDC73	5	2
TRAF6	7189	broad.mit.edu	37	11	36511491	36511491	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36511491T>A	uc001mwr.1	-	c.1466A>T	c.(1465-1467)AAG>ATG	p.K489M	TRAF6_uc001mws.1_Missense_Mutation_p.K489M	NM_145803	NP_665802	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6	489	MATH.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|ossification|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of osteoclast differentiation|positive regulation of T cell activation|positive regulation of T cell cytokine production|protein autoubiquitination|protein K63-linked ubiquitination|response to interleukin-1|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cell cortex|cytosol|endosome membrane|internal side of plasma membrane|nuclear membrane	histone deacetylase binding|mitogen-activated protein kinase kinase kinase binding|protein kinase B binding|protein N-terminus binding|transcription repressor activity|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)	1	all_lung(20;0.211)	all_hematologic(20;0.107)								148				0.047414	-58.738665	42.492744	22	442	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36511491	36511491	16989	11	T	A	A	A	728	56	TRAF6	3	3
LRRC4C	57689	broad.mit.edu	37	11	40137279	40137279	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40137279G>T	uc001mxa.1	-	c.564C>A	c.(562-564)ATC>ATA	p.I188I	LRRC4C_uc001mxc.1_Silent_p.I184I|LRRC4C_uc001mxd.1_Silent_p.I184I|LRRC4C_uc001mxb.1_Silent_p.I184I	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	188	LRR 5.				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)												0.037975	-40.222532	14.513757	9	228	KEEP	---	---	---	---	capture		Silent	SNP	40137279	40137279	9383	11	G	T	T	T	421	33	LRRC4C	2	2
TTC17	55761	broad.mit.edu	37	11	43423014	43423014	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:43423014G>T	uc001mxi.2	+	c.1238G>T	c.(1237-1239)CGA>CTA	p.R413L	TTC17_uc001mxh.2_Missense_Mutation_p.R413L|TTC17_uc010rfj.1_Missense_Mutation_p.R356L|TTC17_uc001mxj.2_Missense_Mutation_p.R183L	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	413							binding			ovary(5)	5														0.216667	34.346565	38.785617	13	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43423014	43423014	17238	11	G	T	T	T	481	37	TTC17	1	1
CHST1	8534	broad.mit.edu	37	11	45672159	45672159	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:45672159G>T	uc001mys.1	-	c.315C>A	c.(313-315)ACC>ACA	p.T105T		NM_003654	NP_003645	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6)	105	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)										0.209677	23.027712	27.892283	13	49	KEEP	---	---	---	---	capture		Silent	SNP	45672159	45672159	3531	11	G	T	T	T	548	43	CHST1	2	2
HBG1	3047	broad.mit.edu	37	11	5269700	5269701	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5269700_5269701CA>AG	uc001mah.1	-	c.332_333TG>CT	c.(331-333)CTG>CCT	p.L111P	HBG2_uc001mai.1_Missense_Mutation_p.L111P	NM_000559	NP_000550	P69891	HBG1_HUMAN	A-gamma globin	111					blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity|protein binding				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		Ovarian(117;2080 2193 33416 49679)								0.091954	5.528786	20.119702	8	79	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	5269700	5269701	7264	11	CA	AG	AG	AG	262	21	HBG1	2	2
OR4C11	219429	broad.mit.edu	37	11	55371502	55371502	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55371502C>A	uc010rii.1	-	c.348G>T	c.(346-348)ATG>ATT	p.M116I		NM_001004700	NP_001004700	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C,	116	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.057471	-14.475291	21.265452	10	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55371502	55371502	11451	11	C	A	A	A	273	21	OR4C11	2	2
OR4P4	81300	broad.mit.edu	37	11	55406718	55406718	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55406718C>A	uc010rij.1	+	c.885C>A	c.(883-885)GCC>GCA	p.A295A		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	295	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.178862	44.504561	56.421037	22	101	KEEP	---	---	---	---	capture		Silent	SNP	55406718	55406718	11490	11	C	A	A	A	262	21	OR4P4	2	2
OR4S2	219431	broad.mit.edu	37	11	55418706	55418706	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55418706G>C	uc001nhs.1	+	c.327G>C	c.(325-327)GAG>GAC	p.E109D		NM_001004059	NP_001004059	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S,	109	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)												0.045307	-70.78851	65.687917	28	590	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55418706	55418706	11493	11	G	C	C	C	425	33	OR4S2	3	3
OR5D13	390142	broad.mit.edu	37	11	55541459	55541459	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55541459C>A	uc010ril.1	+	c.546C>A	c.(544-546)GAC>GAA	p.D182E		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		all_epithelial(135;0.196)												0.091912	11.563174	57.190439	25	247	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55541459	55541459	11564	11	C	A	A	A	233	18	OR5D13	2	2
OR5D14	219436	broad.mit.edu	37	11	55563697	55563697	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55563697C>G	uc010rim.1	+	c.666C>G	c.(664-666)TTC>TTG	p.F222L		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	222	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)												0.069519	-2.277829	33.514421	13	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55563697	55563697	11565	11	C	G	G	G	376	29	OR5D14	3	3
OR5L2	26338	broad.mit.edu	37	11	55595053	55595053	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55595053A>G	uc001nhy.1	+	c.359A>G	c.(358-360)TAT>TGT	p.Y120C		NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L,	120	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)												0.154867	140.512576	192.137879	70	382	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55595053	55595053	11581	11	A	G	G	G	208	16	OR5L2	4	4
OR5I1	10798	broad.mit.edu	37	11	55703819	55703819	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55703819G>T	uc010ris.1	-	c.58C>A	c.(58-60)CCA>ACA	p.P20T		NM_006637	NP_006628	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.124224	22.596706	44.81784	20	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55703819	55703819	11574	11	G	T	T	T	533	41	OR5I1	2	2
OR8K1	390157	broad.mit.edu	37	11	56113826	56113826	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56113826C>A	uc010rjg.1	+	c.312C>A	c.(310-312)GCC>GCA	p.A104A		NM_001002907	NP_001002907	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K,	104	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)													0.05277	-39.88963	40.173667	20	359	KEEP	---	---	---	---	capture		Silent	SNP	56113826	56113826	11654	11	C	A	A	A	262	21	OR8K1	2	2
OR5M1	390168	broad.mit.edu	37	11	56380109	56380109	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56380109A>G	uc001nja.1	-	c.870T>C	c.(868-870)TAT>TAC	p.Y290Y		NM_001004740	NP_001004740	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M,	290	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.07967	15.617505	81.206155	29	335	KEEP	---	---	---	---	capture		Silent	SNP	56380109	56380109	11582	11	A	G	G	G	206	16	OR5M1	4	4
SSRP1	6749	broad.mit.edu	37	11	57102589	57102589	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57102589C>T	uc001njt.2	-	c.7G>A	c.(7-9)GAG>AAG	p.E3K	SSRP1_uc010rjq.1_Missense_Mutation_p.E3K	NM_003146	NP_003137	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	3					DNA repair|DNA replication|positive regulation of viral transcription|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|viral reproduction	chromosome|cytoplasm|nucleoplasm	DNA binding|protein binding			ovary(2)	2						Colon(89;1000 1340 6884 23013 41819)								0.065574	-11.353533	24.511473	12	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57102589	57102589	15710	11	C	T	T	T	416	32	SSRP1	2	2
OR9Q2	219957	broad.mit.edu	37	11	57958874	57958874	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57958874C>A	uc010rka.1	+	c.912C>A	c.(910-912)GCC>GCA	p.A304A		NM_001005283	NP_001005283	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q,	304	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|breast(1)|central_nervous_system(1)	4		Breast(21;0.0589)												0.15	23.274882	35.008781	15	85	KEEP	---	---	---	---	capture		Silent	SNP	57958874	57958874	11667	11	C	A	A	A	275	22	OR9Q2	2	2
OR10Q1	219960	broad.mit.edu	37	11	57995801	57995801	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57995801G>A	uc010rkd.1	-	c.547C>T	c.(547-549)CTC>TTC	p.L183F		NM_001004471	NP_001004471	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(21;0.0589)												0.095238	4.62401	18.475339	8	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57995801	57995801	11322	11	G	A	A	A	455	35	OR10Q1	2	2
GLYAT	10249	broad.mit.edu	37	11	58477334	58477334	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58477334C>A	uc001nnb.2	-	c.796G>T	c.(796-798)GAC>TAC	p.D266Y		NM_201648	NP_964011	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase isoform a	266					acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process	mitochondrial matrix	glycine N-acyltransferase activity|glycine N-benzoyltransferase activity				0		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)					191				0.115385	11.433891	26.582841	12	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58477334	58477334	6747	11	C	A	A	A	416	32	GLYAT	2	2
OR4D9	390199	broad.mit.edu	37	11	59282816	59282816	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59282816T>A	uc010rkv.1	+	c.431T>A	c.(430-432)CTC>CAC	p.L144H		NM_001004711	NP_001004711	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D,	144	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.134752	25.726462	43.972048	19	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59282816	59282816	11466	11	T	A	A	A	702	54	OR4D9	3	3
MS4A3	932	broad.mit.edu	37	11	59828682	59828682	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59828682C>A	uc001nom.2	+	c.49C>A	c.(49-51)CAT>AAT	p.H17N	MS4A3_uc001non.2_Missense_Mutation_p.H17N|MS4A3_uc001noo.2_Intron	NM_006138	NP_006129	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member	17	Cytoplasmic (Potential).					endomembrane system|integral to membrane|perinuclear region of cytoplasm	protein binding|receptor activity			ovary(2)	2		all_epithelial(135;0.245)												0.136364	54.125016	87.852289	36	228	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59828682	59828682	10254	11	C	A	A	A	273	21	MS4A3	2	2
MS4A12	54860	broad.mit.edu	37	11	60269496	60269496	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60269496A>T	uc001npr.2	+	c.455A>T	c.(454-456)GAG>GTG	p.E152V		NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member	152	Cytoplasmic (Potential).					integral to membrane	receptor activity				0														0.138776	98.250369	160.084919	68	422	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60269496	60269496	10249	11	A	T	T	T	143	11	MS4A12	3	3
TMEM132A	54972	broad.mit.edu	37	11	60698117	60698117	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60698117A>T	uc001nqi.2	+	c.1002A>T	c.(1000-1002)ACA>ACT	p.T334T	TMEM132A_uc001nqj.2_Silent_p.T334T|TMEM132A_uc001nqk.2_Silent_p.T347T|TMEM132A_uc001nql.1_Silent_p.T347T	NM_017870	NP_060340	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform a	334	Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0														0.193548	11.737429	14.451578	6	25	KEEP	---	---	---	---	capture		Silent	SNP	60698117	60698117	16576	11	A	T	T	T	80	7	TMEM132A	3	3
PGA3	643834	broad.mit.edu	37	11	60971721	60971721	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60971721C>A	uc001nqx.2	+	c.199C>A	c.(199-201)CCC>ACC	p.P67T	PGA3_uc010rld.1_Missense_Mutation_p.P67T	NM_001079807	NP_001073275			pepsinogen 3, group I precursor											ovary(1)	1														0.133929	17.949643	32.436226	15	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60971721	60971721	12193	11	C	A	A	A	338	26	PGA3	2	2
CNGA4	1262	broad.mit.edu	37	11	6260936	6260936	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6260936C>A	uc001mco.2	+	c.187C>A	c.(187-189)CAC>AAC	p.H63N	CNGA4_uc010raa.1_Missense_Mutation_p.H23N|CNGA4_uc001mcn.2_Missense_Mutation_p.H23N	NM_001037329	NP_001032406	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	63	Extracellular (Potential).				response to stimulus|sensory perception of smell		cAMP binding				0		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.129032	9.144597	17.483549	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6260936	6260936	3737	11	C	A	A	A	325	25	CNGA4	2	2
SLC22A8	9376	broad.mit.edu	37	11	62782097	62782097	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62782097C>T	uc001nwo.2	-	c.333_splice	c.e2+1	p.E111_splice	SLC22A8_uc001nwp.2_Intron|SLC22A8_uc009yom.2_Intron|SLC22A8_uc010rmm.1_Splice_Site_SNP_p.E20_splice|SLC22A8_uc009yon.2_Splice_Site_SNP_p.E111_splice	NM_004254	NP_004245			solute carrier family 22 member 8						response to toxin	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|organic anion transmembrane transporter activity			ovary(1)	1														0.067485	-8.850233	22.6757	11	152	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	62782097	62782097	14957	11	C	T	T	T	234	18	SLC22A8	5	2
RCOR2	283248	broad.mit.edu	37	11	63681923	63681923	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:63681923G>A	uc001nyc.2	-	c.571C>T	c.(571-573)CGG>TGG	p.R191W		NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	191					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1														0.25	12.767214	13.902223	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63681923	63681923	13652	11	G	A	A	A	506	39	RCOR2	1	1
RIN1	9610	broad.mit.edu	37	11	66100057	66100057	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66100057T>A	uc001ohn.1	-	c.2042A>T	c.(2041-2043)TAC>TTC	p.Y681F	RIN1_uc010roy.1_Missense_Mutation_p.Y312F|RIN1_uc009yrd.1_Missense_Mutation_p.Y374F|RIN1_uc010roz.1_Missense_Mutation_p.Y576F|RIN1_uc010rpa.1_Missense_Mutation_p.Y515F	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	681	Ras and 14-3-3 protein binding region.|Ras-associating.				endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(1)	1														0.164179	19.499901	26.663594	11	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66100057	66100057	13848	11	T	A	A	A	741	57	RIN1	3	3
NUMA1	4926	broad.mit.edu	37	11	71716300	71716300	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:71716300G>T	uc001orl.1	-	c.5808C>A	c.(5806-5808)ACC>ACA	p.T1936T	IL18BP_uc009ysu.1_Intron|NUMA1_uc001orj.2_Silent_p.T118T|NUMA1_uc009ysw.1_Silent_p.T1503T|NUMA1_uc001ork.1_Silent_p.T800T|NUMA1_uc001orm.1_Silent_p.T1922T	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1936					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8										525				0.086957	0.661931	8.609979	4	42	KEEP	---	---	---	---	capture		Silent	SNP	71716300	71716300	11155	11	G	T	T	T	444	35	NUMA1	2	2
OR5P3	120066	broad.mit.edu	37	11	7846762	7846763	+	Missense_Mutation	DNP	CC	AT	AT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7846762_7846763CC>AT	uc010rbg.1	-	c.757_758GG>AT	c.(757-759)GGG>ATG	p.G253M		NM_153445	NP_703146	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.12069	16.179411	32.53674	14	102	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	7846762	7846763	11589	11	CC	AT	AT	AT	286	22	OR5P3	2	2
CCDC83	220047	broad.mit.edu	37	11	85597313	85597313	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:85597313G>T	uc001pbg.1	+	c.414G>T	c.(412-414)GAG>GAT	p.E138D	CCDC83_uc001pbh.1_Missense_Mutation_p.E138D|CCDC83_uc001pbi.1_Non-coding_Transcript|CCDC83_uc001pbj.1_Intron	NM_173556	NP_775827	Q8IWF9	CCD83_HUMAN	coiled-coil domain containing 83	138	Potential.										0		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)												0.077922	-0.414219	13.615271	6	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85597313	85597313	2981	11	G	T	T	T	451	35	CCDC83	2	2
FAT3	120114	broad.mit.edu	37	11	92533659	92533659	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92533659C>A	uc001pdj.3	+	c.7480C>A	c.(7480-7482)CCT>ACT	p.P2494T		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	2494	Cadherin 22.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.112903	2.939301	12.23432	7	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92533659	92533659	5927	11	C	A	A	A	286	22	FAT3	2	2
PIWIL4	143689	broad.mit.edu	37	11	94301943	94301943	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94301943C>T	uc001pfa.2	+	c.135C>T	c.(133-135)GGC>GGT	p.G45G	PIWIL4_uc010rue.1_Non-coding_Transcript|PIWIL4_uc009ywk.1_Non-coding_Transcript	NM_152431	NP_689644	Q7Z3Z4	PIWL4_HUMAN	piwi-like 4	45					cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|meiosis|multicellular organismal development|piRNA metabolic process|regulation of translation|spermatogenesis	nucleus|piP-body	piRNA binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.043103	-14.921945	11.039318	5	111	KEEP	---	---	---	---	capture		Silent	SNP	94301943	94301943	12384	11	C	T	T	T	353	28	PIWIL4	2	2
LHX5	64211	broad.mit.edu	37	12	113909175	113909175	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113909175G>A	uc001tvj.1	-	c.129C>T	c.(127-129)TGC>TGT	p.C43C		NM_022363	NP_071758	Q9H2C1	LHX5_HUMAN	LIM homeobox protein 5	43	LIM zinc-binding 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding				0														0.226415	27.278204	30.916768	12	41	KEEP	---	---	---	---	capture		Silent	SNP	113909175	113909175	9100	12	G	A	A	A	438	34	LHX5	2	2
OASL	8638	broad.mit.edu	37	12	121461898	121461898	+	Silent	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121461898T>A	uc001tzj.1	-	c.942A>T	c.(940-942)GCA>GCT	p.A314A	OASL_uc001tzk.1_Nonsense_Mutation_p.R234*	NM_003733	NP_003724	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like isoform a	314					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nucleolus	ATP binding|DNA binding|double-stranded RNA binding|thyroid hormone receptor binding|transferase activity				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					Colon(192;517 2041 31392 31913 39966)								0.163636	34.886457	46.706381	18	92	KEEP	---	---	---	---	capture		Silent	SNP	121461898	121461898	11207	12	T	A	A	A	713	55	OASL	3	3
P2RX7	5027	broad.mit.edu	37	12	121592673	121592673	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121592673G>T	uc001tzm.2	+	c.211G>T	c.(211-213)GTG>TTG	p.V71L	P2RX7_uc001tzn.2_5'UTR|P2RX7_uc001tzo.2_Non-coding_Transcript|P2RX7_uc001tzp.2_5'UTR|P2RX7_uc001tzq.2_5'UTR	NM_002562	NP_002553	A8K2Z0	A8K2Z0_HUMAN	purinergic receptor P2X7	71						integral to membrane	ATP binding|ion channel activity|receptor activity			large_intestine(2)|lung(1)|breast(1)	4	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)									719				0.067925	-12.557996	38.659647	18	247	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121592673	121592673	11758	12	G	T	T	T	572	44	P2RX7	2	2
TMTC1	83857	broad.mit.edu	37	12	29709922	29709922	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29709922C>A	uc001rjb.2	-	c.1220G>T	c.(1219-1221)CGC>CTC	p.R407L	TMTC1_uc001riz.2_Missense_Mutation_p.R164L|TMTC1_uc001rja.2_Missense_Mutation_p.R251L|TMTC1_uc001rjc.1_Missense_Mutation_p.R469L	NM_175861	NP_787057	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat	407	TPR 1.					integral to membrane	binding				0	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)													0.172093	80.000346	101.79901	37	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29709922	29709922	16801	12	C	A	A	A	351	27	TMTC1	1	1
TEAD4	7004	broad.mit.edu	37	12	3129934	3129934	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:3129934G>T	uc010sej.1	+	c.715G>T	c.(715-717)GAC>TAC	p.D239Y	TEAD4_uc010sek.1_Missense_Mutation_p.D196Y|TEAD4_uc001qln.2_Missense_Mutation_p.D111Y	NM_003213	NP_003204	Q15561	TEAD4_HUMAN	TEA domain family member 4 isoform 1	240					hippo signaling cascade|muscle organ development|skeletal system development		DNA binding|protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0	Ovarian(42;0.211)		OV - Ovarian serous cystadenocarcinoma(31;0.000563)|COAD - Colon adenocarcinoma(12;0.0831)											0.09434	0.878458	9.611768	5	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3129934	3129934	16268	12	G	T	T	T	533	41	TEAD4	2	2
KIF21A	55605	broad.mit.edu	37	12	39734124	39734124	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:39734124C>A	uc001rly.2	-	c.2153G>T	c.(2152-2154)AGG>ATG	p.R718M	KIF21A_uc001rlw.2_Missense_Mutation_p.R35M|KIF21A_uc001rlx.2_Missense_Mutation_p.R705M|KIF21A_uc001rlz.2_Missense_Mutation_p.R705M|KIF21A_uc010skl.1_Missense_Mutation_p.R705M	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	718					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)												0.192308	20.417081	25.017434	10	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39734124	39734124	8599	12	C	A	A	A	312	24	KIF21A	2	2
PRICKLE1	144165	broad.mit.edu	37	12	42853951	42853951	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:42853951C>A	uc010skv.1	-	c.2156G>T	c.(2155-2157)CGG>CTG	p.R719L	PRICKLE1_uc001rnl.2_Missense_Mutation_p.R719L|PRICKLE1_uc010skw.1_Missense_Mutation_p.R719L|PRICKLE1_uc001rnm.2_Missense_Mutation_p.R719L|PRICKLE1_uc001rnk.1_5'Flank	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	719					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination	cytosol|nuclear membrane	zinc ion binding			ovary(3)	3	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)										0.21	95.930297	111.43427	42	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42853951	42853951	12929	12	C	A	A	A	299	23	PRICKLE1	1	1
ADAMTS20	80070	broad.mit.edu	37	12	43769219	43769219	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43769219G>C	uc010skx.1	-	c.5409C>G	c.(5407-5409)AGC>AGG	p.S1803R		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1803	GON.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.126984	40.95042	66.530671	24	165	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43769219	43769219	267	12	G	C	C	C	594	46	ADAMTS20	3	3
NELL2	4753	broad.mit.edu	37	12	45173531	45173531	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:45173531C>T	uc010skz.1	-	c.671G>A	c.(670-672)AGG>AAG	p.R224K	NELL2_uc001rof.3_Missense_Mutation_p.R173K|NELL2_uc001rog.2_Missense_Mutation_p.R174K|NELL2_uc001roh.2_Missense_Mutation_p.R174K|NELL2_uc009zkd.2_Missense_Mutation_p.R173K|NELL2_uc010sla.1_Missense_Mutation_p.R197K|NELL2_uc001roi.1_Missense_Mutation_p.R174K|NELL2_uc010slb.1_Missense_Mutation_p.R173K|NELL2_uc001roj.2_Missense_Mutation_p.R174K	NM_001145107	NP_001138579	Q99435	NELL2_HUMAN	NEL-like protein 2 isoform a	174	TSP N-terminal.				cell adhesion	extracellular region	calcium ion binding|protein binding|structural molecule activity			central_nervous_system(1)	1	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)										0.177515	65.742402	82.298373	30	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45173531	45173531	10733	12	C	T	T	T	312	24	NELL2	2	2
SLC38A4	55089	broad.mit.edu	37	12	47172453	47172453	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:47172453G>C	uc001rpi.2	-	c.824C>G	c.(823-825)CCC>CGC	p.P275R	SLC38A4_uc001rpj.2_Missense_Mutation_p.P275R	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	275	Extracellular (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)	3	Lung SC(27;0.192)|Renal(347;0.236)													0.082759	2.434973	28.063006	12	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47172453	47172453	15103	12	G	C	C	C	559	43	SLC38A4	3	3
NCKAP5L	57701	broad.mit.edu	37	12	50190474	50190474	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50190474C>A	uc009zlk.2	-	c.1169G>T	c.(1168-1170)AGG>ATG	p.R390M	NCKAP5L_uc001rvc.3_5'Flank|NCKAP5L_uc001rvb.2_De_novo_Start_InFrame	NM_001037806	NP_001032895	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	386	Pro-rich.										0														0.181818	12.861352	17.068245	8	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50190474	50190474	10623	12	C	A	A	A	312	24	NCKAP5L	2	2
LARP4	113251	broad.mit.edu	37	12	50867819	50867819	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50867819T>C	uc001rwo.1	+	c.1723T>C	c.(1723-1725)TCT>CCT	p.S575P	LARP4_uc001rwp.1_Missense_Mutation_p.S569P|LARP4_uc001rwq.1_Missense_Mutation_p.S498P|LARP4_uc001rwr.1_Missense_Mutation_p.S498P|LARP4_uc001rws.1_Missense_Mutation_p.S568P|LARP4_uc009zlr.1_Missense_Mutation_p.S388P|LARP4_uc001rwt.1_Missense_Mutation_p.S160P	NM_199188	NP_954658	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform b	569							nucleotide binding|RNA binding			ovary(1)	1														0.117647	26.700204	46.243231	16	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50867819	50867819	8953	12	T	C	C	C	702	54	LARP4	4	4
LARP4	113251	broad.mit.edu	37	12	50867905	50867905	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50867905A>G	uc001rwo.1	+	c.1809A>G	c.(1807-1809)TCA>TCG	p.S603S	LARP4_uc001rwp.1_Silent_p.S597S|LARP4_uc001rwq.1_Silent_p.S526S|LARP4_uc001rwr.1_Silent_p.S526S|LARP4_uc001rws.1_Silent_p.S596S|LARP4_uc009zlr.1_Intron|LARP4_uc001rwt.1_Silent_p.S188S	NM_199188	NP_954658	Q71RC2	LARP4_HUMAN	c-Mpl binding protein isoform b	597							nucleotide binding|RNA binding			ovary(1)	1														0.163265	43.709461	59.553428	24	123	KEEP	---	---	---	---	capture		Silent	SNP	50867905	50867905	8953	12	A	G	G	G	67	6	LARP4	4	4
SCN8A	6334	broad.mit.edu	37	12	52159593	52159593	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52159593C>G	uc001ryw.2	+	c.2683C>G	c.(2683-2685)CAA>GAA	p.Q895E	SCN8A_uc010snl.1_Missense_Mutation_p.Q760E|SCN8A_uc001ryy.2_Missense_Mutation_p.Q760E	NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	895	Helical; Name=S5 of repeat II; (Potential).|ATP (Potential).|II.				axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier|voltage-gated sodium channel complex	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)									0.092486	11.31014	40.190719	16	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52159593	52159593	14406	12	C	G	G	G	325	25	SCN8A	3	3
SCN8A	6334	broad.mit.edu	37	12	52200939	52200939	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52200939T>A	uc001ryw.2	+	c.5669T>A	c.(5668-5670)CTG>CAG	p.L1890Q		NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	1890					axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier|voltage-gated sodium channel complex	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)									0.214724	84.269527	96.491694	35	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52200939	52200939	14406	12	T	A	A	A	715	55	SCN8A	3	3
CALCOCO1	57658	broad.mit.edu	37	12	54109682	54109682	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54109682C>A	uc001sef.2	-	c.1155G>T	c.(1153-1155)CTG>CTT	p.L385L	CALCOCO1_uc001see.2_5'Flank|CALCOCO1_uc010som.1_Silent_p.L300L|CALCOCO1_uc010son.1_Silent_p.L262L|CALCOCO1_uc001seh.2_Silent_p.L385L|CALCOCO1_uc009znd.2_Silent_p.L385L|CALCOCO1_uc001seg.2_Silent_p.L210L|CALCOCO1_uc010soo.1_Silent_p.L378L	NM_020898	NP_065949	Q9P1Z2	CACO1_HUMAN	coiled-coil transcriptional coactivator isoform	385					steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm	armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding			ovary(1)	1														0.131313	18.513543	31.59378	13	86	KEEP	---	---	---	---	capture		Silent	SNP	54109682	54109682	2693	12	C	A	A	A	262	21	CALCOCO1	2	2
OR6C68	403284	broad.mit.edu	37	12	55886576	55886576	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55886576T>A	uc010spo.1	+	c.430T>A	c.(430-432)TGC>AGC	p.C144S		NM_001005519	NP_001005519	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C,	139	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.102564	24.442057	61.256877	24	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55886576	55886576	11606	12	T	A	A	A	767	59	OR6C68	3	3
GEFT	115557	broad.mit.edu	37	12	58008761	58008761	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:58008761G>T	uc009zpy.2	+	c.1038G>T	c.(1036-1038)AAG>AAT	p.K346N	GEFT_uc001soz.1_Missense_Mutation_p.K181N|GEFT_uc001spb.2_Missense_Mutation_p.K307N|GEFT_uc001spa.2_Missense_Mutation_p.K201N|GEFT_uc001spd.2_Missense_Mutation_p.K12N	NM_001111270	NP_001104740	Q86VW2	ARHGP_HUMAN	RhoA/RAC/CDC42 exchange factor isoform 3	307	DH.				regulation of Rho protein signal transduction	cytosol|plasma membrane|sarcomere	Rho guanyl-nucleotide exchange factor activity				0	Melanoma(17;0.122)													0.155556	10.083255	15.206748	7	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58008761	58008761	6596	12	G	T	T	T	464	36	GEFT	2	2
OS9	10956	broad.mit.edu	37	12	58114582	58114582	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:58114582G>T	uc001spj.2	+	c.1894G>T	c.(1894-1896)GAG>TAG	p.E632*	OS9_uc010srx.1_Nonsense_Mutation_p.E371*|OS9_uc001spk.2_Nonsense_Mutation_p.E617*|OS9_uc001spl.2_Nonsense_Mutation_p.E577*|OS9_uc001spm.2_Nonsense_Mutation_p.E562*|OS9_uc001spn.2_Nonsense_Mutation_p.E578*|OS9_uc010sry.1_Nonsense_Mutation_p.E545*|OS9_uc010srz.1_Nonsense_Mutation_p.E503*	NM_006812	NP_006803	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum	632					ER-associated protein catabolic process|protein retention in ER lumen|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to endoplasmic reticulum stress	endoplasmic reticulum lumen|Hrd1p ubiquitin ligase complex	glycoprotein binding|protein binding|sugar binding			ovary(1)	1	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)											0.142857	15.167402	24.640085	11	66	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	58114582	58114582	11683	12	G	T	T	T	429	33	OS9	5	2
ANO2	57101	broad.mit.edu	37	12	6031944	6031944	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6031944G>A	uc001qnm.2	-	c.37C>T	c.(37-39)CGC>TGC	p.R13C		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	17	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.179487	13.707827	17.472449	7	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6031944	6031944	705	12	G	A	A	A	520	40	ANO2	1	1
SRGAP1	57522	broad.mit.edu	37	12	64488712	64488712	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:64488712G>T	uc010ssp.1	+	c.1540G>T	c.(1540-1542)GAC>TAC	p.D514Y	SRGAP1_uc001srv.2_Missense_Mutation_p.D451Y	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	514	Rho-GAP.				axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)										0.15914	118.767813	170.263532	74	391	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64488712	64488712	15659	12	G	T	T	T	533	41	SRGAP1	2	2
PTPRB	5787	broad.mit.edu	37	12	70953392	70953393	+	Missense_Mutation	DNP	GG	TC	TC			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70953392_70953393GG>TC	uc001swc.3	-	c.4444_4445CC>GA	c.(4444-4446)CCC>GAC	p.P1482D	PTPRB_uc001swb.3_Missense_Mutation_p.P1264D|PTPRB_uc010sto.1_Missense_Mutation_p.P1174D|PTPRB_uc010stp.1_Missense_Mutation_p.P1174D|PTPRB_uc001swa.3_Missense_Mutation_p.P1394D|PTPRB_uc001swd.3_Missense_Mutation_p.P1481D|PTPRB_uc009zrr.1_Missense_Mutation_p.P1361D	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1264	Fibronectin type-III 15.|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)											0.067901	-11.329706	20.294848	11	151	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	70953392	70953393	13253	12	GG	TC	TC	TC	559	43	PTPRB	2	2
PTPRB	5787	broad.mit.edu	37	12	70970274	70970274	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70970274C>T	uc001swc.3	-	c.2730G>A	c.(2728-2730)AAG>AAA	p.K910K	PTPRB_uc001swb.3_Silent_p.K692K|PTPRB_uc010sto.1_Silent_p.K692K|PTPRB_uc010stp.1_Silent_p.K602K|PTPRB_uc001swa.3_Intron|PTPRB_uc001swd.3_Silent_p.K909K|PTPRB_uc009zrr.1_Silent_p.K789K	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	692	Fibronectin type-III 8.|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)											0.235294	9.390492	10.480756	4	13	KEEP	---	---	---	---	capture		Silent	SNP	70970274	70970274	13253	12	C	T	T	T	259	20	PTPRB	2	2
LGR5	8549	broad.mit.edu	37	12	71977686	71977686	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:71977686G>T	uc001swl.2	+	c.1896G>T	c.(1894-1896)GAG>GAT	p.E632D	LGR5_uc001swm.2_Missense_Mutation_p.E608D|LGR5_uc001swn.1_Non-coding_Transcript	NM_003667	NP_003658	O75473	LGR5_HUMAN	leucine-rich repeat-containing G protein-coupled	632	Extracellular (Potential).					integral to plasma membrane	protein-hormone receptor activity			ovary(1)|pancreas(1)	2										516				0.111111	14.666568	41.600035	20	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71977686	71977686	9083	12	G	T	T	T	425	33	LGR5	2	2
ZFC3H1	196441	broad.mit.edu	37	12	72004520	72004520	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72004520C>A	uc001swo.2	-	c.5787G>T	c.(5785-5787)CAG>CAT	p.Q1929H		NM_144982	NP_659419	O60293	ZC3H1_HUMAN	proline/serine-rich coiled-coil 2	1929	HAT 6.				RNA processing	intracellular	metal ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4														0.073394	-3.892279	16.508845	8	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72004520	72004520	18221	12	C	A	A	A	415	32	ZFC3H1	2	2
CD163L1	283316	broad.mit.edu	37	12	7522158	7522158	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7522158G>T	uc010sge.1	-	c.3864C>A	c.(3862-3864)GCC>GCA	p.A1288A	CD163L1_uc001qsy.2_Silent_p.A1278A	NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	1278	SRCR 12.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.184116	112.081261	137.922442	51	226	KEEP	---	---	---	---	capture		Silent	SNP	7522158	7522158	3095	12	G	T	T	T	496	39	CD163L1	1	1
NAV3	89795	broad.mit.edu	37	12	78400688	78400688	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78400688G>T	uc001syp.2	+	c.1370G>T	c.(1369-1371)AGC>ATC	p.S457I	NAV3_uc001syo.2_Missense_Mutation_p.S457I	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	457						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.220339	91.628566	104.376079	39	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78400688	78400688	10581	12	G	T	T	T	442	34	NAV3	2	2
NAV3	89795	broad.mit.edu	37	12	78515929	78515929	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78515929C>T	uc001syp.2	+	c.3959C>T	c.(3958-3960)ACA>ATA	p.T1320I	NAV3_uc001syo.2_Missense_Mutation_p.T1320I|NAV3_uc010sub.1_Missense_Mutation_p.T820I|NAV3_uc009zsf.2_Intron	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	1320	Ser-rich.					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.189189	40.909046	50.943399	21	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78515929	78515929	10581	12	C	T	T	T	221	17	NAV3	2	2
MYF6	4618	broad.mit.edu	37	12	81101521	81101521	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:81101521C>G	uc001szf.1	+	c.23C>G	c.(22-24)ACT>AGT	p.T8S		NM_002469	NP_002460	P23409	MYF6_HUMAN	myogenic factor 6	8					muscle cell fate commitment|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(1)	1														0.096154	11.387764	28.378348	10	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81101521	81101521	10423	12	C	G	G	G	260	20	MYF6	3	3
PPFIA2	8499	broad.mit.edu	37	12	81693091	81693091	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:81693091C>G	uc001szo.1	-	c.2713G>C	c.(2713-2715)GCA>CCA	p.A905P	PPFIA2_uc010sue.1_Intron|PPFIA2_uc010sug.1_Non-coding_Transcript|PPFIA2_uc010suh.1_Non-coding_Transcript|PPFIA2_uc010sui.1_Non-coding_Transcript|PPFIA2_uc010suj.1_Non-coding_Transcript|PPFIA2_uc009zsi.1_Non-coding_Transcript|PPFIA2_uc010suf.1_Non-coding_Transcript|PPFIA2_uc009zsh.2_Non-coding_Transcript	NM_003625	NP_003616	O75334	LIPA2_HUMAN	PTPRF interacting protein alpha 2	905	SAM 1.				cell-matrix adhesion	cell surface|cytoplasm	protein binding			ovary(3)|lung(2)|pancreas(1)	6														0.111111	5.974235	11.355578	4	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81693091	81693091	12740	12	C	G	G	G	351	27	PPFIA2	3	3
CCDC38	120935	broad.mit.edu	37	12	96288796	96288796	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:96288796G>T	uc001tek.1	-	c.743C>A	c.(742-744)GCA>GAA	p.A248E		NM_182496	NP_872302	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	248											0														0.181818	83.793618	105.787427	42	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96288796	96288796	2932	12	G	T	T	T	598	46	CCDC38	2	2
TMTC4	84899	broad.mit.edu	37	13	101316583	101316583	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101316583T>G	uc001vot.2	-	c.227A>C	c.(226-228)CAA>CCA	p.Q76P	TMTC4_uc001vou.2_Missense_Mutation_p.Q57P|TMTC4_uc010tja.1_Intron	NM_032813	NP_116202	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat	57						integral to membrane	binding			ovary(2)|breast(1)	3	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)													0.121951	7.745549	13.486023	5	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101316583	101316583	16804	13	T	G	G	G	819	63	TMTC4	4	4
PSPC1	55269	broad.mit.edu	37	13	20346466	20346466	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:20346466C>T	uc001uml.2	-	c.590G>A	c.(589-591)GGA>GAA	p.G197E	PSPC1_uc001umj.1_Non-coding_Transcript|PSPC1_uc001umk.1_Non-coding_Transcript	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1	197	RRM 2.|Sufficient for paraspeckles localization.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)										0.126126	12.84838	28.078553	14	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20346466	20346466	13170	13	C	T	T	T	390	30	PSPC1	2	2
SPATA13	221178	broad.mit.edu	37	13	24864909	24864909	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:24864909G>T	uc001upd.1	+	c.2967G>T	c.(2965-2967)CTG>CTT	p.L989L	C1QTNF9_uc001upe.2_Non-coding_Transcript|SPATA13_uc001upg.1_Silent_p.L364L|SPATA13_uc010tcy.1_Silent_p.L310L|SPATA13_uc010tcz.1_Silent_p.L248L|SPATA13_uc010tda.1_Silent_p.L308L|SPATA13_uc001uph.2_Silent_p.L286L|SPATA13_uc010tdb.1_Silent_p.L224L|SPATA13_uc009zzz.1_Silent_p.L89L	NM_153023	NP_694568	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	364	DH.				cell migration|filopodium assembly|lamellipodium assembly|regulation of cell migration|regulation of Rho protein signal transduction	cytoplasm|filopodium|lamellipodium|ruffle membrane	protein binding|Rac guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)	3		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)										0.107143	5.43711	13.989089	6	50	KEEP	---	---	---	---	capture		Silent	SNP	24864909	24864909	15508	13	G	T	T	T	587	46	SPATA13	2	2
NAA16	79612	broad.mit.edu	37	13	41941683	41941683	+	Silent	SNP	A	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:41941683A>C	uc001uyf.2	+	c.1648A>C	c.(1648-1650)AGA>CGA	p.R550R	NAA16_uc010tfg.1_Non-coding_Transcript	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform	550					N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1														0.18254	45.04353	56.975287	23	103	KEEP	---	---	---	---	capture		Silent	SNP	41941683	41941683	10514	13	A	C	C	C	36	3	NAA16	4	4
CCDC70	83446	broad.mit.edu	37	13	52439952	52439953	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:52439952_52439953CC>AA	uc001vfu.3	+	c.438_439CC>AA	c.(436-441)GACCGG>GAAAGG	p.D146E		NM_031290	NP_112580	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70 precursor	146	Potential.					extracellular region|plasma membrane					0		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)										0.093366	20.718134	88.327876	38	369	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	52439952	52439953	2966	13	CC	AA	AA	AA	233	18	CCDC70	2	2
PCDH9	5101	broad.mit.edu	37	13	67477676	67477676	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:67477676G>A	uc001vik.2	-	c.3098C>T	c.(3097-3099)ACG>ATG	p.T1033M	PCDH9_uc010aei.2_Non-coding_Transcript|PCDH9_uc001vil.2_Intron|PCDH9_uc010thl.1_Missense_Mutation_p.T1033M	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	1033	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)										0.041667	-25.018342	12.918277	7	161	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67477676	67477676	11938	13	G	A	A	A	520	40	PCDH9	1	1
OR4Q3	441669	broad.mit.edu	37	14	20216386	20216386	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20216386C>G	uc010tkt.1	+	c.800C>G	c.(799-801)TCT>TGT	p.S267C		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	267	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.096606	38.864411	101.357263	37	346	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20216386	20216386	11491	14	C	G	G	G	416	32	OR4Q3	3	3
OR4M1	441670	broad.mit.edu	37	14	20249408	20249408	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20249408G>T	uc010tku.1	+	c.927G>T	c.(925-927)TTG>TTT	p.L309F		NM_001005500	NP_001005500	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M,	309	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.196429	26.791537	31.600826	11	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20249408	20249408	11485	14	G	T	T	T	620	48	OR4M1	2	2
OR4N5	390437	broad.mit.edu	37	14	20611943	20611943	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20611943C>A	uc010tla.1	+	c.49C>A	c.(49-51)CTG>ATG	p.L17M		NM_001004724	NP_001004724	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N,	17	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)										0.216772	294.215994	341.005021	137	495	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20611943	20611943	11489	14	C	A	A	A	415	32	OR4N5	2	2
CHD8	57680	broad.mit.edu	37	14	21859724	21859724	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21859724C>A	uc001was.1	-	c.6126G>T	c.(6124-6126)GTG>GTT	p.V2042V	CHD8_uc001war.1_Silent_p.V1938V	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2321					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|chromatin assembly or disassembly|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	chromatin|MLL1 complex	ATP binding|beta-catenin binding|chromatin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding|transcription activator activity|transcription repressor activity			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)						886				0.073171	-0.90939	6.772626	3	38	KEEP	---	---	---	---	capture		Silent	SNP	21859724	21859724	3465	14	C	A	A	A	262	21	CHD8	2	2
HECTD1	25831	broad.mit.edu	37	14	31576778	31576778	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:31576778G>C	uc001wrc.1	-	c.6613C>G	c.(6613-6615)CGT>GGT	p.R2205G	HECTD1_uc001wra.1_Missense_Mutation_p.R331G|HECTD1_uc001wrb.1_Missense_Mutation_p.R331G	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	2205	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(2)|large_intestine(1)	3	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)										0.154639	34.096359	45.122683	15	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31576778	31576778	7322	14	G	C	C	C	481	37	HECTD1	3	3
MLH3	27030	broad.mit.edu	37	14	75498773	75498773	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75498773T>A	uc001xrd.1	-	c.3825A>T	c.(3823-3825)TTA>TTT	p.L1275F	MLH3_uc001xre.1_Missense_Mutation_p.L1251F|MLH3_uc010tuy.1_Non-coding_Transcript	NM_001040108	NP_001035197	Q9UHC1	MLH3_HUMAN	mutL homolog 3 isoform 1	1275					mismatch repair|reciprocal meiotic recombination	chiasma|MutLbeta complex|synaptonemal complex	ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00688)										0.163043	32.670551	42.59298	15	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75498773	75498773	10008	14	T	A	A	A	634	49	MLH3	3	3
ESRRB	2103	broad.mit.edu	37	14	76905848	76905848	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:76905848C>A	uc001xsr.2	+	c.152C>A	c.(151-153)ACC>AAC	p.T51N	ESRRB_uc001xso.2_Non-coding_Transcript|ESRRB_uc001xsq.1_Missense_Mutation_p.T51N	NM_004452	NP_004443	A2VDJ2	A2VDJ2_HUMAN	estrogen-related receptor beta	51					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.0213)										0.159091	9.59361	14.476351	7	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76905848	76905848	5454	14	C	A	A	A	234	18	ESRRB	2	2
ISM2	145501	broad.mit.edu	37	14	77948824	77948824	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77948824C>G	uc001xtz.2	-	c.814G>C	c.(814-816)GAC>CAC	p.D272H	ISM2_uc001xua.2_Intron|ISM2_uc001xty.2_Missense_Mutation_p.D184H|ISM2_uc010tvl.1_Missense_Mutation_p.D191H	NM_199296	NP_954993	Q6H9L7	ISM2_HUMAN	isthmin 2 homolog isoform 1	272						extracellular region					0														0.323529	74.738272	76.611831	22	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77948824	77948824	8165	14	C	G	G	G	416	32	ISM2	3	3
STON2	85439	broad.mit.edu	37	14	81744495	81744495	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:81744495T>G	uc001xvk.1	-	c.1160A>C	c.(1159-1161)CAA>CCA	p.Q387P	STON2_uc010tvu.1_Missense_Mutation_p.Q387P|STON2_uc010tvt.1_Missense_Mutation_p.Q184P	NM_033104	NP_149095	Q8WXE9	STON2_HUMAN	stonin 2	387					endocytosis|intracellular protein transport|regulation of endocytosis	clathrin adaptor complex|nucleolus	protein binding			pancreas(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.0348)										0.057471	-7.398817	10.494415	5	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81744495	81744495	15838	14	T	G	G	G	819	63	STON2	4	4
SERPINA1	5265	broad.mit.edu	37	14	94849303	94849303	+	Missense_Mutation	SNP	C	A	A	rs28931568		TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94849303C>A	uc001ycx.3	-	c.272G>T	c.(271-273)GGG>GTG	p.G91V	SERPINA1_uc001ycw.3_Non-coding_Transcript|SERPINA1_uc010auw.2_Missense_Mutation_p.G91V|SERPINA1_uc010aux.2_Missense_Mutation_p.G91V|SERPINA1_uc001ycy.3_Missense_Mutation_p.G91V|SERPINA1_uc010auy.2_Missense_Mutation_p.G91V|SERPINA1_uc001ycz.3_Missense_Mutation_p.G91V|SERPINA1_uc010auz.2_Missense_Mutation_p.G91V|SERPINA1_uc010ava.2_Missense_Mutation_p.G91V|SERPINA1_uc001ydb.3_Missense_Mutation_p.G91V|SERPINA1_uc010avb.2_Missense_Mutation_p.G91V|SERPINA1_uc001ydc.3_Missense_Mutation_p.G91V|SERPINA1_uc001yda.1_Missense_Mutation_p.G91V	NM_000295	NP_000286	P01009	A1AT_HUMAN	serine proteinase inhibitor, clade A, member 1	91					acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis	extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix	protease binding|serine-type endopeptidase inhibitor activity			skin(1)	1		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)	Alpha-1-proteinase inhibitor(DB00058)									0.195402	30.852168	38.394998	17	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94849303	94849303	14574	14	C	A	A	A	286	22	SERPINA1	2	2
C15orf2	23742	broad.mit.edu	37	15	24922505	24922505	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24922505C>T	uc001ywo.2	+	c.1491C>T	c.(1489-1491)CCC>CCT	p.P497P		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	497	Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)					p.P497P(MEWO-Tumor)	443				0.034188	-85.093989	25.850773	16	452	KEEP	---	---	---	---	capture		Silent	SNP	24922505	24922505	1834	15	C	T	T	T	275	22	C15orf2	2	2
HERC2	8924	broad.mit.edu	37	15	28375308	28375308	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:28375308C>T	uc001zbj.2	-	c.12802_splice	c.e83+1	p.G4268_splice		NM_004667	NP_004658			hect domain and RLD 2						DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(2)|central_nervous_system(1)	11		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)						1580				0.061947	-8.891317	13.657197	7	106	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	28375308	28375308	7341	15	C	T	T	T	234	18	HERC2	5	2
MTMR15	22909	broad.mit.edu	37	15	31198066	31198066	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31198066G>T	uc001zff.2	+	c.1200G>T	c.(1198-1200)GAG>GAT	p.E400D	MTMR15_uc001zfc.3_Missense_Mutation_p.E400D|MTMR15_uc010azw.2_Missense_Mutation_p.E400D|MTMR15_uc001zfd.3_Missense_Mutation_p.E400D|MTMR15_uc001zfe.2_5'UTR	NM_014967	NP_055782	Q9Y2M0	FAN1_HUMAN	myotubularin related protein 15 isoform a	400					double-strand break repair via homologous recombination|nucleotide-excision repair, DNA incision	nucleus	5'-3' exonuclease activity|5'-flap endonuclease activity|DNA binding|magnesium ion binding|phosphodiesterase I activity|ubiquitin binding				0		all_lung(180;2.23e-09)		all cancers(64;4.72e-15)|Epithelial(43;5.4e-11)|GBM - Glioblastoma multiforme(186;0.000136)|BRCA - Breast invasive adenocarcinoma(123;0.00402)|Lung(196;0.168)										0.05	-12.010692	9.473352	5	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31198066	31198066	10336	15	G	T	T	T	425	33	MTMR15	2	2
RYR3	6263	broad.mit.edu	37	15	33855076	33855076	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:33855076C>A	uc001zhi.2	+	c.1011C>A	c.(1009-1011)GAC>GAA	p.D337E	RYR3_uc010bar.2_Missense_Mutation_p.D337E	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	337	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.0625	-6.856478	15.481175	7	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33855076	33855076	14250	15	C	A	A	A	220	17	RYR3	2	2
FSIP1	161835	broad.mit.edu	37	15	40034009	40034009	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:40034009T>A	uc001zki.2	-	c.652A>T	c.(652-654)AAA>TAA	p.K218*		NM_152597	NP_689810	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	218										ovary(2)	2		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)										0.080645	-0.16727	10.941799	5	57	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	40034009	40034009	6325	15	T	A	A	A	793	61	FSIP1	5	3
TGM7	116179	broad.mit.edu	37	15	43574190	43574190	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:43574190G>T	uc001zrf.1	-	c.1203C>A	c.(1201-1203)AAC>AAA	p.N401K		NM_052955	NP_443187	Q96PF1	TGM7_HUMAN	transglutaminase 7	401		Calcium (By similarity).			peptide cross-linking		acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity			ovary(2)	2		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)									0.132075	5.625426	12.755702	7	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43574190	43574190	16363	15	G	T	T	T	516	40	TGM7	1	1
FRMD5	84978	broad.mit.edu	37	15	44166263	44166263	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:44166263G>T	uc001ztl.2	-	c.1533C>A	c.(1531-1533)CTC>CTA	p.L511L	FRMD5_uc001ztj.1_Intron|FRMD5_uc001ztk.1_Intron|FRMD5_uc010uef.1_Silent_p.L184L|FRMD5_uc001ztm.2_Silent_p.L184L|FRMD5_uc001ztn.2_Silent_p.L277L	NM_032892	NP_116281	Q7Z6J6	FRMD5_HUMAN	FERM domain containing 5 isoform 2	511	Helical; (Potential).					cytoplasm|cytoskeleton|extrinsic to membrane|integral to membrane	cytoskeletal protein binding			ovary(1)	1		all_cancers(109;2.29e-15)|all_epithelial(112;9.98e-13)|Lung NSC(122;4.89e-08)|all_lung(180;5.08e-07)|Melanoma(134;0.0275)		all cancers(107;8.63e-20)|GBM - Glioblastoma multiforme(94;3.63e-06)										0.052632	-10.95765	8.998531	5	90	KEEP	---	---	---	---	capture		Silent	SNP	44166263	44166263	6303	15	G	T	T	T	522	41	FRMD5	2	2
SLC12A1	6557	broad.mit.edu	37	15	48559802	48559802	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48559802G>A	uc001zwn.3	+	c.2199G>A	c.(2197-2199)GCG>GCA	p.A733A	SLC12A1_uc010uew.1_Silent_p.A539A|SLC12A1_uc010bem.2_Silent_p.A733A|SLC12A1_uc001zwq.3_Silent_p.A504A|SLC12A1_uc001zwr.3_Silent_p.A460A	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2	733					potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)									0.15873	17.713508	24.704377	10	53	KEEP	---	---	---	---	capture		Silent	SNP	48559802	48559802	14877	15	G	A	A	A	470	37	SLC12A1	1	1
DUT	1854	broad.mit.edu	37	15	48624496	48624496	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:48624496C>T	uc001zws.2	+	c.312C>T	c.(310-312)GCC>GCT	p.A104A	DUT_uc001zwt.2_5'UTR|DUT_uc001zwu.2_Non-coding_Transcript|DUT_uc001zwv.2_Silent_p.A16A|DUT_uc001zww.2_Silent_p.A16A	NM_001025248	NP_001020419	P33316	DUT_HUMAN	deoxyuridine triphosphatase isoform 1 precursor	104					DNA replication|dUTP metabolic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process	mitochondrion|nucleoplasm	dUTP diphosphatase activity|protein binding				0		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)										0.142857	5.480053	8.929694	4	24	KEEP	---	---	---	---	capture		Silent	SNP	48624496	48624496	5018	15	C	T	T	T	275	22	DUT	2	2
ALDH1A2	8854	broad.mit.edu	37	15	58258026	58258026	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:58258026C>A	uc002aex.2	-	c.799_splice	c.e8-1	p.V267_splice	ALDH1A2_uc002aey.2_Splice_Site_SNP_p.V229_splice|ALDH1A2_uc010ugv.1_Splice_Site_SNP_p.V246_splice|ALDH1A2_uc010ugw.1_Splice_Site_SNP_p.V238_splice|ALDH1A2_uc002aew.2_Splice_Site_SNP_p.V171_splice	NM_003888	NP_003879			aldehyde dehydrogenase 1A2 isoform 1						negative regulation of cell proliferation|neural tube development|oxidation-reduction process|response to cytokine stimulus	nucleus	3-chloroallyl aldehyde dehydrogenase activity|retinal binding|retinal dehydrogenase activity			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)									0.045977	-11.57762	7.569129	4	83	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	58258026	58258026	494	15	C	A	A	A	312	24	ALDH1A2	5	2
PPIB	5479	broad.mit.edu	37	15	64448275	64448275	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:64448275C>A	uc002and.2	-	c.598G>T	c.(598-600)GCA>TCA	p.A200S	SNX22_uc002anc.1_3'UTR	NM_000942	NP_000933	P23284	PPIB_HUMAN	peptidylprolyl isomerase B precursor	200	PPIase cyclophilin-type.				protein folding	endoplasmic reticulum lumen|melanosome	peptide binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding				0					L-Proline(DB00172)	GBM(105;399 1481 32889 33051 36637)								0.056075	-8.326422	13.829517	6	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64448275	64448275	12754	15	C	A	A	A	351	27	PPIB	1	1
ITGA11	22801	broad.mit.edu	37	15	68596157	68596157	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68596157G>A	uc010bib.2	-	c.3451C>T	c.(3451-3453)CTG>TTG	p.L1151L	ITGA11_uc002ari.2_Silent_p.L1150L	NM_001004439	NP_001004439	Q9UKX5	ITA11_HUMAN	integrin, alpha 11 precursor	1150	Helical; (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|muscle organ development	integrin complex	collagen binding|receptor activity			kidney(2)|pancreas(1)	3					Tirofiban(DB00775)									0.070175	-4.276871	17.4489	8	106	KEEP	---	---	---	---	capture		Silent	SNP	68596157	68596157	8178	15	G	A	A	A	451	35	ITGA11	2	2
NEO1	4756	broad.mit.edu	37	15	73566308	73566308	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:73566308G>T	uc002avm.3	+	c.3122G>T	c.(3121-3123)GGA>GTA	p.G1041V	NEO1_uc010ukx.1_Missense_Mutation_p.G1041V|NEO1_uc010uky.1_Missense_Mutation_p.G1041V|NEO1_uc010ukz.1_Missense_Mutation_p.G465V|NEO1_uc002avn.3_Missense_Mutation_p.G690V	NM_002499	NP_002490	Q92859	NEO1_HUMAN	neogenin homolog 1 precursor	1041	Extracellular (Potential).|Fibronectin type-III 6.				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus				pancreas(1)	1														0.05618	-8.574998	9.833378	5	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73566308	73566308	10735	15	G	T	T	T	533	41	NEO1	2	2
CHRNA3	1136	broad.mit.edu	37	15	78894042	78894042	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:78894042A>T	uc002bec.2	-	c.942T>A	c.(940-942)TTT>TTA	p.F314L	CHRNA3_uc002bea.2_Non-coding_Transcript|CHRNA3_uc002beb.2_Missense_Mutation_p.F314L	NM_000743	NP_000734	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3	314	Helical; (Potential).				activation of transmembrane receptor protein tyrosine kinase activity|behavioral response to nicotine|locomotory behavior|regulation of acetylcholine secretion|regulation of dendrite morphogenesis|regulation of excitatory postsynaptic membrane potential|regulation of smooth muscle contraction|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|dendrite|neuronal cell body|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic density|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			central_nervous_system(3)|ovary(1)	4										173				0.054687	-13.481232	13.263872	7	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78894042	78894042	3518	15	A	T	T	T	63	5	CHRNA3	3	3
MKL2	57496	broad.mit.edu	37	16	14345718	14345718	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:14345718G>A	uc010uza.1	+	c.2404_splice	c.e14-1	p.V802_splice	MKL2_uc002dcg.2_Splice_Site_SNP_p.V752_splice|MKL2_uc002dcj.2_Splice_Site_SNP_p.V47_splice	NM_014048	NP_054767			megakaryoblastic leukemia 2 protein						cell differentiation|muscle organ development|positive regulation of striated muscle tissue development|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	identical protein binding|nucleic acid binding|transcription coactivator activity			ovary(3)|kidney(1)|pancreas(1)	5														0.115385	36.450654	70.547663	27	207	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	14345718	14345718	9992	16	G	A	A	A	455	35	MKL2	5	2
ERN2	10595	broad.mit.edu	37	16	23716211	23716211	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23716211G>T	uc002dma.3	-	c.991C>A	c.(991-993)CAG>AAG	p.Q331K	ERN2_uc010bxp.2_Missense_Mutation_p.Q331K|ERN2_uc010bxq.1_Missense_Mutation_p.Q139K	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	283	Lumenal (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|protein phosphorylation|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)						225				0.132353	13.229973	22.156787	9	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23716211	23716211	5431	16	G	T	T	T	611	47	ERN2	2	2
XPO6	23214	broad.mit.edu	37	16	28112854	28112854	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28112854T>C	uc002dpa.1	-	c.3201A>G	c.(3199-3201)CCA>CCG	p.P1067P	XPO6_uc002dpb.1_Silent_p.P1053P|XPO6_uc010vcp.1_Silent_p.P1066P	NM_015171	NP_055986	Q96QU8	XPO6_HUMAN	exportin 6	1067					protein export from nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			ovary(1)|skin(1)	2														0.111111	5.580324	10.957019	4	32	KEEP	---	---	---	---	capture		Silent	SNP	28112854	28112854	18031	16	T	C	C	C	704	55	XPO6	4	4
SALL1	6299	broad.mit.edu	37	16	51175198	51175198	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:51175198C>A	uc010vgs.1	-	c.935G>T	c.(934-936)GGT>GTT	p.G312V	SALL1_uc010vgr.1_Missense_Mutation_p.G215V|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	312					adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription repressor activity|zinc ion binding			ovary(3)	3		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GBM(103;1352 1446 1855 4775 8890)								0.096774	8.545637	38.828208	18	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51175198	51175198	14290	16	C	A	A	A	234	18	SALL1	2	2
FTSJD1	55783	broad.mit.edu	37	16	71319117	71319117	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71319117C>A	uc010cga.2	-	c.707G>T	c.(706-708)GGG>GTG	p.G236V	FTSJD1_uc002ezy.3_Missense_Mutation_p.G236V|FTSJD1_uc002ezz.3_Missense_Mutation_p.G236V	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	236						integral to membrane	methyltransferase activity|nucleic acid binding				0														0.133803	24.774549	43.217754	19	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71319117	71319117	6341	16	C	A	A	A	286	22	FTSJD1	2	2
CHST5	23563	broad.mit.edu	37	16	75563211	75563211	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:75563211C>A	uc002fej.1	-	c.1090G>T	c.(1090-1092)GCG>TCG	p.A364S	CHST5_uc002fei.2_Missense_Mutation_p.A358S	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	358	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0														0.108108	2.728167	8.317	4	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75563211	75563211	3541	16	C	A	A	A	351	27	CHST5	1	1
A2BP1	54715	broad.mit.edu	37	16	7759057	7759057	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:7759057G>C	uc010uxz.1	+	c.1125_splice	c.e15-1	p.S375_splice	A2BP1_uc002cys.2_Splice_Site_SNP_p.S332_splice|A2BP1_uc002cyt.2_Splice_Site_SNP_p.S305_splice|A2BP1_uc010uya.1_Splice_Site_SNP_p.V307_splice|A2BP1_uc010uyb.1_Splice_Site_SNP_p.S332_splice|A2BP1_uc002cyw.2_Splice_Site_SNP_p.V371_splice|A2BP1_uc002cyy.2_Splice_Site_SNP_p.S353_splice|A2BP1_uc002cyx.2_Splice_Site_SNP_p.S353_splice|A2BP1_uc010uyc.1_Splice_Site_SNP_p.S326_splice	NM_018723	NP_061193			ataxin 2-binding protein 1 isoform 4						mRNA processing|RNA splicing|RNA transport	nucleus|trans-Golgi network	nucleotide binding|protein C-terminus binding|RNA binding				0		all_cancers(2;4.54e-52)|Colorectal(2;6.95e-44)|all_epithelial(2;1.15e-37)|Lung NSC(2;0.000289)|all_lung(2;0.00148)|Myeloproliferative disorder(2;0.0122)|Medulloblastoma(2;0.0354)|all_neural(2;0.0381)|all_hematologic(2;0.0749)|Renal(2;0.0758)|Melanoma(2;0.211)		Colorectal(1;3.55e-51)|COAD - Colon adenocarcinoma(2;1.92e-46)|all cancers(1;5.36e-16)|Epithelial(1;3.98e-15)|READ - Rectum adenocarcinoma(2;3.71e-05)|GBM - Glioblastoma multiforme(1;0.0499)										0.074803	1.845296	48.946426	19	235	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	7759057	7759057	3	16	G	C	C	C	468	36	A2BP1	5	3
VAT1L	57687	broad.mit.edu	37	16	77910358	77910358	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:77910358T>A	uc002ffg.1	+	c.814T>A	c.(814-816)TAC>AAC	p.Y272N		NM_020927	NP_065978	Q9HCJ6	VAT1L_HUMAN	vesicle amine transport protein 1 homolog (T.	272					oxidation-reduction process		oxidoreductase activity|zinc ion binding			central_nervous_system(1)	1														0.141388	90.590031	138.825393	55	334	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77910358	77910358	17695	16	T	A	A	A	689	53	VAT1L	3	3
FOXC2	2303	broad.mit.edu	37	16	86602418	86602418	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:86602418C>A	uc002fjq.2	+	c.1477C>A	c.(1477-1479)CCC>ACC	p.P493T		NM_005251	NP_005242	Q99958	FOXC2_HUMAN	forkhead box C2	493					anti-apoptosis|artery morphogenesis|blood vessel remodeling|camera-type eye development|cardiac muscle cell proliferation|collagen fibril organization|embryonic heart tube development|embryonic viscerocranium morphogenesis|insulin receptor signaling pathway|lymphangiogenesis|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neural crest cell fate commitment|Notch signaling pathway|ossification|paraxial mesodermal cell fate commitment|patterning of blood vessels|positive regulation of cell adhesion mediated by integrin|positive regulation of cell migration involved in sprouting angiogenesis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of vascular wound healing|regulation of blood vessel size|regulation of organ growth|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|ureteric bud development|vascular endothelial growth factor receptor signaling pathway|vasculogenesis|ventricular cardiac muscle tissue morphogenesis	transcription factor complex	chromatin DNA binding|DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0														0.25	8.019958	8.701246	3	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86602418	86602418	6237	16	C	A	A	A	286	22	FOXC2	2	2
GRIN2A	2903	broad.mit.edu	37	16	9858108	9858108	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9858108C>A	uc002czo.3	-	c.3293G>T	c.(3292-3294)TGT>TTT	p.C1098F	GRIN2A_uc010uym.1_Missense_Mutation_p.C1098F|GRIN2A_uc010uyn.1_Missense_Mutation_p.C941F|GRIN2A_uc002czr.3_Missense_Mutation_p.C1098F	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1098	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.038356	-56.366167	27.716452	14	351	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9858108	9858108	7058	16	C	A	A	A	221	17	GRIN2A	2	2
MYH13	8735	broad.mit.edu	37	17	10206756	10206756	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10206756C>T	uc002gmk.1	-	c.5526G>A	c.(5524-5526)AAG>AAA	p.K1842K		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1842	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.129032	53.125069	86.360864	32	216	KEEP	---	---	---	---	capture		Silent	SNP	10206756	10206756	10427	17	C	T	T	T	311	24	MYH13	2	2
MYH13	8735	broad.mit.edu	37	17	10214506	10214506	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10214506C>A	uc002gmk.1	-	c.4570G>T	c.(4570-4572)GGC>TGC	p.G1524C		NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	1524	Potential.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)	4														0.081081	-0.209657	13.024359	6	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10214506	10214506	10427	17	C	A	A	A	273	21	MYH13	2	2
MYH8	4626	broad.mit.edu	37	17	10296518	10296518	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10296518G>T	uc002gmm.2	-	c.5176C>A	c.(5176-5178)CTC>ATC	p.L1726I		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1726	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														0.087977	5.768053	64.331921	30	311	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10296518	10296518	10436	17	G	T	T	T	429	33	MYH8	2	2
UNC45B	146862	broad.mit.edu	37	17	33475407	33475407	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33475407T>A	uc002hja.2	+	c.125T>A	c.(124-126)CTG>CAG	p.L42Q	UNC45B_uc002hjb.2_Missense_Mutation_p.L42Q|UNC45B_uc002hjc.2_Missense_Mutation_p.L42Q|UNC45B_uc010cto.2_Missense_Mutation_p.L42Q	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	42					cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.2	14.535038	17.044382	6	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33475407	33475407	17547	17	T	A	A	A	715	55	UNC45B	3	3
GAS2L2	246176	broad.mit.edu	37	17	34072118	34072118	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34072118C>A	uc002hjv.1	-	c.2398G>T	c.(2398-2400)GCC>TCC	p.A800S		NM_139285	NP_644814	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	800					cell cycle arrest	cytoplasm|cytoskeleton				ovary(1)|skin(1)	2		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.065574	-3.244842	8.700533	4	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34072118	34072118	6511	17	C	A	A	A	338	26	GAS2L2	2	2
C17orf98	388381	broad.mit.edu	37	17	36997587	36997587	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:36997587C>A	uc002hqv.2	-	c.56G>T	c.(55-57)GGG>GTG	p.G19V		NM_001080465	NP_001073934	A8MV24	CQ098_HUMAN	hypothetical protein LOC388381	19											0														0.111111	6.422235	18.535174	9	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36997587	36997587	1953	17	C	A	A	A	286	22	C17orf98	2	2
RAPGEFL1	51195	broad.mit.edu	37	17	38349661	38349661	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:38349661G>T	uc010cwu.1	+	c.1238G>T	c.(1237-1239)CGG>CTG	p.R413L	RAPGEFL1_uc010wfd.1_Missense_Mutation_p.R349L	NM_016339	NP_057423	Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor	619	Ras-GEF.				G-protein coupled receptor protein signaling pathway|nervous system development|small GTPase mediated signal transduction	intracellular|membrane fraction	guanyl-nucleotide exchange factor activity			ovary(1)|central_nervous_system(1)	2						Esophageal Squamous(28;274 750 6870 14218 42203)								0.166667	25.989122	34.879472	14	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38349661	38349661	13509	17	G	T	T	T	507	39	RAPGEFL1	1	1
KRTAP4-12	83755	broad.mit.edu	37	17	39280289	39280289	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39280289G>T	uc002hwa.2	-	c.86C>A	c.(85-87)ACC>AAC	p.T29N		NM_031854	NP_114060	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	29	3.|31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)											0.211864	56.64291	65.606049	25	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39280289	39280289	8872	17	G	T	T	T	572	44	KRTAP4-12	2	2
GAST	2520	broad.mit.edu	37	17	39871692	39871692	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39871692C>A	uc002hxl.2	+	c.4C>A	c.(4-6)CAG>AAG	p.Q2K	JUP_uc010wfs.1_Intron	NM_000805	NP_000796	P01350	GAST_HUMAN	gastrin preproprotein	2						extracellular region	hormone activity				0		Breast(137;0.000307)	BRCA - Breast invasive adenocarcinoma(4;0.0677)											0.071839	-11.526851	54.112483	25	323	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39871692	39871692	6516	17	C	A	A	A	325	25	GAST	2	2
WNK4	65266	broad.mit.edu	37	17	40939444	40939444	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40939444C>G	uc002ibj.2	+	c.1625C>G	c.(1624-1626)GCA>GGA	p.A542G	WNK4_uc010wgx.1_Missense_Mutation_p.A206G|WNK4_uc002ibk.1_Missense_Mutation_p.A314G|WNK4_uc010wgy.1_5'UTR	NM_032387	NP_115763	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	542					intracellular protein kinase cascade|protein phosphorylation	tight junction	ATP binding|protein serine/threonine kinase activity			ovary(3)|skin(3)|stomach(1)	7		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		Esophageal Squamous(6;201 374 4964 23855 42828)				263				0.21	53.975734	61.716963	21	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40939444	40939444	17954	17	C	G	G	G	325	25	WNK4	3	3
HOXB13	10481	broad.mit.edu	37	17	46804191	46804191	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46804191C>T	uc002ioa.2	-	c.816G>A	c.(814-816)AAG>AAA	p.K272K		NM_006361	NP_006352	Q92826	HXB13_HUMAN	homeobox B13	272	Homeobox.				angiogenesis|epidermis development|regulation of transcription, DNA-dependent|response to wounding		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0														0.210526	53.526858	62.37834	24	90	KEEP	---	---	---	---	capture		Silent	SNP	46804191	46804191	7592	17	C	T	T	T	415	32	HOXB13	2	2
KIF2B	84643	broad.mit.edu	37	17	51902347	51902347	+	Silent	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:51902347T>A	uc002iua.2	+	c.1953T>A	c.(1951-1953)GCT>GCA	p.A651A		NM_032559	NP_115948	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	651	Potential.				blood coagulation|cell division|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|microtubule|microtubule organizing center|nucleolus|spindle	ATP binding|microtubule motor activity			ovary(5)	5														0.130081	19.512422	35.896922	16	107	KEEP	---	---	---	---	capture		Silent	SNP	51902347	51902347	8609	17	T	A	A	A	691	54	KIF2B	3	3
BZRAP1	9256	broad.mit.edu	37	17	56385038	56385038	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56385038C>A	uc002ivx.3	-	c.4917G>T	c.(4915-4917)GTG>GTT	p.V1639V	BZRAP1_uc002ivv.2_5'Flank|BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Silent_p.V1579V|BZRAP1_uc010wnt.1_Silent_p.V1639V	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1639	SH3 2.					mitochondrion	benzodiazepine receptor binding				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.111111	3.804159	7.841824	3	24	KEEP	---	---	---	---	capture		Silent	SNP	56385038	56385038	1611	17	C	A	A	A	210	17	BZRAP1	2	2
BZRAP1	9256	broad.mit.edu	37	17	56385040	56385040	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56385040C>A	uc002ivx.3	-	c.4915G>T	c.(4915-4917)GTG>TTG	p.V1639L	BZRAP1_uc002ivv.2_5'Flank|BZRAP1_uc002ivw.2_5'Flank|BZRAP1_uc010dcs.2_Missense_Mutation_p.V1579L|BZRAP1_uc010wnt.1_Missense_Mutation_p.V1639L	NM_004758	NP_004749	O95153	RIMB1_HUMAN	peripheral benzodiazepine receptor-associated	1639	SH3 2.					mitochondrion	benzodiazepine receptor binding				0	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.111111	2.814383	6.846527	3	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56385040	56385040	1611	17	C	A	A	A	247	19	BZRAP1	1	1
C17orf64	124773	broad.mit.edu	37	17	58506878	58506878	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:58506878C>A	uc002iyq.2	+	c.585C>A	c.(583-585)CCC>CCA	p.P195P		NM_181707	NP_859058	Q86WR6	CQ064_HUMAN	hypothetical protein LOC124773	195										breast(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)											0.134328	11.255386	19.927537	9	58	KEEP	---	---	---	---	capture		Silent	SNP	58506878	58506878	1929	17	C	A	A	A	275	22	C17orf64	2	2
MRC2	9902	broad.mit.edu	37	17	60744809	60744809	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60744809C>T	uc002jad.2	+	c.1032C>T	c.(1030-1032)GGC>GGT	p.G344G	MRC2_uc002jac.2_Silent_p.G344G	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	344	Extracellular (Potential).|C-type lectin 1.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.085714	1.633152	7.689743	3	32	KEEP	---	---	---	---	capture		Silent	SNP	60744809	60744809	10150	17	C	T	T	T	340	27	MRC2	1	1
MARCH10	162333	broad.mit.edu	37	17	60821890	60821890	+	Splice_Site_SNP	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60821890C>G	uc010dds.2	-	c.497_splice	c.e6-1	p.A166_splice	MARCH10_uc010ddr.2_Splice_Site_SNP_p.A128_splice|MARCH10_uc002jag.3_Splice_Site_SNP_p.A128_splice|MARCH10_uc002jah.2_Intron	NM_152598	NP_689811			ring finger protein 190								ligase activity|zinc ion binding				0														0.159091	30.5906	40.33625	14	74	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	60821890	60821890	9682	17	C	G	G	G	364	28	MARCH10	5	3
GNA13	10672	broad.mit.edu	37	17	63052483	63052483	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:63052483C>G	uc002jfc.2	-	c.229G>C	c.(229-231)GAC>CAC	p.D77H	GNA13_uc010wqh.1_5'Flank	NM_006572	NP_006563	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein),	77					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase D activity|cellular component movement|platelet activation|Rho protein signal transduction	brush border membrane|heterotrimeric G-protein complex|melanosome	D5 dopamine receptor binding|G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|signal transducer activity|type 1 angiotensin receptor binding				0														0.153846	7.120759	11.798589	6	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63052483	63052483	6770	17	C	G	G	G	403	31	GNA13	3	3
CACNG5	27091	broad.mit.edu	37	17	64875163	64875163	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:64875163G>A	uc002jfr.2	+	c.270G>A	c.(268-270)ACG>ACA	p.T90T	CACNG5_uc010wqi.1_Silent_p.T90T|CACNG5_uc010wqj.1_Silent_p.T90T	NM_014404	NP_055219	Q9UF02	CCG5_HUMAN	voltage-dependent calcium channel gamma-5	90					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|postsynaptic density	voltage-gated calcium channel activity			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)											0.102273	7.412822	21.288469	9	79	KEEP	---	---	---	---	capture		Silent	SNP	64875163	64875163	2676	17	G	A	A	A	496	39	CACNG5	1	1
ABCA9	10350	broad.mit.edu	37	17	67016539	67016539	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:67016539G>T	uc002jhu.2	-	c.2590C>A	c.(2590-2592)CTG>ATG	p.L864M	ABCA9_uc010dez.2_Missense_Mutation_p.L864M	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	864	Helical; (Potential).				transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.082759	-0.389634	25.263979	12	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67016539	67016539	40	17	G	T	T	T	451	35	ABCA9	2	2
TP53	7157	broad.mit.edu	37	17	7579377	7579377	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7579377G>A	uc002gim.2	-	c.310C>T	c.(310-312)CAG>TAG	p.Q104*	TP53_uc002gig.1_Nonsense_Mutation_p.Q104*|TP53_uc002gih.2_Nonsense_Mutation_p.Q104*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Nonsense_Mutation_p.Q104*|TP53_uc010cni.1_Nonsense_Mutation_p.Q104*|TP53_uc002gij.2_Nonsense_Mutation_p.Q104*|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Nonsense_Mutation_p.Q65*|TP53_uc010cnk.1_Nonsense_Mutation_p.Q119*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	104	Interaction with HIPK1 (By similarity).||Interaction with WWOX.		Q -> H (in sporadic cancers; somatic mutation).|Q -> L (in a sporadic cancer; 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.0?(6)|p.Q104*(5)|p.G59fs*23(3)|p.V73fs*9(1)|p.Y103_Q104>**(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y103_L111>L(1)|p.Y103fs*15(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		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.172414	61.132802	78.792161	30	144	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7579377	7579377	16923	17	G	A	A	A	611	47	TP53	5	2
CANT1	124583	broad.mit.edu	37	17	76989810	76989810	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:76989810C>T	uc002jwn.2	-	c.1028G>A	c.(1027-1029)GGC>GAC	p.G343D	CANT1_uc002jwk.2_Missense_Mutation_p.G343D|CANT1_uc002jwj.2_Missense_Mutation_p.G343D|CANT1_uc002jwl.2_Intron|CANT1_uc002jwm.1_Non-coding_Transcript	NM_001159772	NP_001153244	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	343	Lumenal (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to membrane	calcium ion binding|nucleoside-diphosphatase activity|signal transducer activity				0			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)											0.071429	-1.208284	6.740112	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76989810	76989810	2734	17	C	T	T	T	338	26	CANT1	2	2
MYL12B	103910	broad.mit.edu	37	18	3277806	3277806	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:3277806G>T	uc010dkl.2	+	c.390G>T	c.(388-390)ATG>ATT	p.M130I	MYL12B_uc002klt.3_Missense_Mutation_p.M108I|MYL12B_uc010wyv.1_Missense_Mutation_p.M130I	NM_001144944	NP_001138416	O14950	ML12B_HUMAN	myosin regulatory light chain MRCL2 isoform A	130	EF-hand 2.				axon guidance|muscle contraction	cytosol|myosin complex	calcium ion binding|motor activity				0														0.050633	-8.541078	8.340125	4	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3277806	3277806	10441	18	G	T	T	T	611	47	MYL12B	2	2
PIK3C3	5289	broad.mit.edu	37	18	39584342	39584342	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:39584342G>T	uc002lap.2	+	c.1007G>T	c.(1006-1008)TGT>TTT	p.C336F	PIK3C3_uc010xcl.1_Missense_Mutation_p.C273F	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3	336				FLKCVN -> ILTSVI (in Ref. 1; CAA87094).	cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(7)|ovary(1)	8						NSCLC(37;552 1060 2683 16430 37914)				441	TSP Lung(28;0.18)			0.094017	6.829994	26.213837	11	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39584342	39584342	12336	18	G	T	T	T	624	48	PIK3C3	2	2
SETBP1	26040	broad.mit.edu	37	18	42530885	42530885	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:42530885C>A	uc010dni.2	+	c.1580C>A	c.(1579-1581)GCT>GAT	p.A527D		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	527						nucleus	DNA binding			large_intestine(1)	1				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										0.108014	26.41881	70.064596	31	256	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42530885	42530885	14617	18	C	A	A	A	364	28	SETBP1	2	2
SLC14A2	8170	broad.mit.edu	37	18	43262343	43262343	+	Silent	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:43262343G>C	uc010dnj.2	+	c.2622G>C	c.(2620-2622)CTG>CTC	p.L874L	SLC14A2_uc002lbe.2_Silent_p.L874L	NM_007163	NP_009094	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter),	874	Helical; (Potential).					apical plasma membrane|integral to membrane|membrane fraction	protein binding|urea transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2														0.040268	-38.916925	28.895493	12	286	KEEP	---	---	---	---	capture		Silent	SNP	43262343	43262343	14892	18	G	C	C	C	574	45	SLC14A2	3	3
ALPK2	115701	broad.mit.edu	37	18	56191220	56191220	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:56191220C>G	uc002lhj.3	-	c.5576G>C	c.(5575-5577)TGC>TCC	p.C1859S		NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1859	Ig-like 2.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11										343				0.072727	0.454263	10.784168	4	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56191220	56191220	548	18	C	G	G	G	325	25	ALPK2	3	3
SERPINB4	6318	broad.mit.edu	37	18	61306561	61306561	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61306561G>T	uc002ljf.2	-	c.626C>A	c.(625-627)TCT>TAT	p.S209Y	SERPINB4_uc002lje.2_Intron|SERPINB4_uc002ljg.2_Intron	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	209					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.068966	-8.104343	14.206315	8	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61306561	61306561	14591	18	G	T	T	T	429	33	SERPINB4	2	2
HMSD	284293	broad.mit.edu	37	18	61620724	61620724	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61620724T>A	uc010dqj.2	+	c.35T>A	c.(34-36)ATG>AAG	p.M12K		NM_001123366	NP_001116838	A8MTL9	HMSD_HUMAN	histocompatibility (minor) serpin domain	12						extracellular region	serine-type endopeptidase inhibitor activity				0														0.051948	-6.96109	9.382419	4	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61620724	61620724	7538	18	T	A	A	A	663	51	HMSD	3	3
CDH7	1005	broad.mit.edu	37	18	63491946	63491946	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:63491946C>T	uc002ljz.2	+	c.860C>T	c.(859-861)GCT>GTT	p.A287V	CDH7_uc002lka.2_Missense_Mutation_p.A287V|CDH7_uc002lkb.2_Missense_Mutation_p.A287V	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	287	Extracellular (Potential).|Cadherin 3.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.129)												0.110048	23.085331	54.535779	23	186	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63491946	63491946	3244	18	C	T	T	T	364	28	CDH7	2	2
RTTN	25914	broad.mit.edu	37	18	67776792	67776792	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:67776792T>A	uc002lkp.2	-	c.3845A>T	c.(3844-3846)CAC>CTC	p.H1282L	RTTN_uc002lko.2_Non-coding_Transcript|RTTN_uc010xfb.1_Missense_Mutation_p.H370L	NM_173630	NP_775901	Q86VV8	RTTN_HUMAN	rotatin	1282							binding			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Esophageal squamous(42;0.129)												0.101266	12.703985	37.756085	16	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67776792	67776792	14217	18	T	A	A	A	767	59	RTTN	3	3
LAMA1	284217	broad.mit.edu	37	18	7037598	7037598	+	Silent	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7037598G>C	uc002knm.2	-	c.1716C>G	c.(1714-1716)CCC>CCG	p.P572P	LAMA1_uc010wzj.1_Silent_p.P48P	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	572	Laminin IV type A 1.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.146341	23.084803	37.891449	18	105	KEEP	---	---	---	---	capture		Silent	SNP	7037598	7037598	8928	18	G	C	C	C	496	39	LAMA1	3	3
YES1	7525	broad.mit.edu	37	18	756705	756705	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:756705T>C	uc002kky.2	-	c.123A>G	c.(121-123)CCA>CCG	p.P41P	YES1_uc002kkz.2_Silent_p.P41P	NM_005433	NP_005424	P07947	YES_HUMAN	viral oncogene yes-1 homolog 1	41					blood coagulation|leukocyte migration|protein phosphorylation|regulation of vascular permeability|T cell costimulation	cytosol|plasma membrane	ATP binding|ion channel binding|non-membrane spanning protein tyrosine kinase activity			lung(2)|ovary(1)	3					Dasatinib(DB01254)					156				0.099071	27.473882	79.37565	32	291	KEEP	---	---	---	---	capture		Silent	SNP	756705	756705	18057	18	T	C	C	C	652	51	YES1	4	4
ZNF69	7620	broad.mit.edu	37	19	12014497	12014498	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12014497_12014498GG>TT	uc002mst.3	+	c.131_132GG>TT	c.(130-132)AGG>ATT	p.R44I		NM_021915	NP_068734	Q9UC07	ZNF69_HUMAN	zinc finger protein 69	58	KRAB.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				Lung(535;0.011)										0.047945	-16.902383	14.847534	7	139	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	12014497	12014498	18690	19	GG	TT	TT	TT	455	35	ZNF69	2	2
ZNF676	163223	broad.mit.edu	37	19	22363326	22363326	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22363326C>A	uc002nqs.1	-	c.1193G>T	c.(1192-1194)TGT>TTT	p.C398F		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	398	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.060403	-10.05414	20.043146	9	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22363326	22363326	18678	19	C	A	A	A	221	17	ZNF676	2	2
ZNF676	163223	broad.mit.edu	37	19	22363351	22363351	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22363351C>A	uc002nqs.1	-	c.1168G>T	c.(1168-1170)GAG>TAG	p.E390*		NM_001001411	NP_001001411	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	390					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)												0.077465	-4.792336	21.159027	11	131	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22363351	22363351	18678	19	C	A	A	A	416	32	ZNF676	5	2
ZNF98	148198	broad.mit.edu	37	19	22586189	22586189	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22586189C>A	uc002nqt.2	-	c.156G>T	c.(154-156)GTG>GTT	p.V52V		NM_001098626	NP_001092096	A6NK75	ZNF98_HUMAN	zinc finger protein 98	52	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)												0.168675	26.6033	35.228193	14	69	KEEP	---	---	---	---	capture		Silent	SNP	22586189	22586189	18807	19	C	A	A	A	262	21	ZNF98	2	2
ZNF254	9534	broad.mit.edu	37	19	24309224	24309224	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:24309224G>C	uc002nru.2	+	c.422G>C	c.(421-423)GGA>GCA	p.G141A	ZNF254_uc010xrk.1_Missense_Mutation_p.G56A	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	141					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)												0.066667	-0.961617	19.472784	7	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24309224	24309224	18389	19	G	C	C	C	533	41	ZNF254	3	3
TSHZ3	57616	broad.mit.edu	37	19	31768670	31768670	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:31768670C>A	uc002nsy.3	-	c.2029G>T	c.(2029-2031)GGG>TGG	p.G677W		NM_020856	NP_065907	Q63HK5	TSH3_HUMAN	zinc finger protein 537	677					regulation of respiratory gaseous exchange by neurological system process|regulation of transcription, DNA-dependent	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(4)|pancreas(1)|lung(1)|skin(1)	7	Esophageal squamous(110;0.226)													0.081633	-0.036641	8.695439	4	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31768670	31768670	17176	19	C	A	A	A	273	21	TSHZ3	2	2
RBM42	79171	broad.mit.edu	37	19	36122121	36122121	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36122121G>T	uc002oan.2	+	c.362G>T	c.(361-363)GGC>GTC	p.G121V	RBM42_uc010xsx.1_Missense_Mutation_p.G121V|RBM42_uc010eef.2_Missense_Mutation_p.G121V|RBM42_uc002oao.2_Missense_Mutation_p.G121V|RBM42_uc002oap.2_Missense_Mutation_p.G121V|RBM42_uc002oaq.2_Missense_Mutation_p.G121V|RBM42_uc010eeg.2_Missense_Mutation_p.G121V	NM_024321	NP_077297	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	121						cytoplasm|nucleus	nucleotide binding|RNA binding				0	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)											0.051724	-30.870365	18.435007	12	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36122121	36122121	13598	19	G	T	T	T	546	42	RBM42	2	2
ZNF585A	199704	broad.mit.edu	37	19	37644059	37644059	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37644059C>A	uc002ofo.1	-	c.742G>T	c.(742-744)GGC>TGC	p.G248C	ZNF585A_uc002ofm.1_Missense_Mutation_p.G193C|ZNF585A_uc002ofn.1_Missense_Mutation_p.G193C	NM_199126	NP_954577	Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	248	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.135647	63.893869	104.685064	43	274	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37644059	37644059	18612	19	C	A	A	A	273	21	ZNF585A	2	2
ZNF569	148266	broad.mit.edu	37	19	37917230	37917230	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37917230C>T	uc002ogj.2	-	c.138G>A	c.(136-138)TGG>TGA	p.W46*	ZNF569_uc002ogh.2_Intron|ZNF569_uc002ogi.2_Nonsense_Mutation_p.W22*	NM_152484	NP_689697	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	22	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.049645	-16.597302	13.759962	7	134	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	37917230	37917230	18595	19	C	T	T	T	390	30	ZNF569	5	2
CIC	23152	broad.mit.edu	37	19	42794391	42794391	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42794391G>T	uc002otf.1	+	c.1471G>T	c.(1471-1473)GGT>TGT	p.G491C		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	491					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)	8		Prostate(69;0.00682)								241				0.081967	2.97879	35.530209	15	168	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42794391	42794391	3558	19	G	T	T	T	611	47	CIC	2	2
MEGF8	1954	broad.mit.edu	37	19	42839471	42839471	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42839471G>T	uc002otl.3	+	c.762G>T	c.(760-762)CTG>CTT	p.L254L	MEGF8_uc002otm.3_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	254	Extracellular (Potential).|Kelch 1.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.111111	9.817918	21.927208	9	72	KEEP	---	---	---	---	capture		Silent	SNP	42839471	42839471	9852	19	G	T	T	T	600	47	MEGF8	2	2
PSG3	5671	broad.mit.edu	37	19	43233937	43233937	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43233937A>T	uc010eil.2	-	c.1047T>A	c.(1045-1047)AAT>AAA	p.N349K	PSG3_uc002ouf.2_Non-coding_Transcript|PSG1_uc002oug.1_Intron|PSG3_uc002oue.2_Missense_Mutation_p.N327K	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	327	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.064103	-7.064238	23.747293	10	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43233937	43233937	13109	19	A	T	T	T	102	8	PSG3	3	3
PSG3	5671	broad.mit.edu	37	19	43233974	43233974	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43233974C>T	uc010eil.2	-	c.1010G>A	c.(1009-1011)CGA>CAA	p.R337Q	PSG3_uc002ouf.2_Non-coding_Transcript|PSG1_uc002oug.1_Intron|PSG3_uc002oue.2_Missense_Mutation_p.R315Q	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	315	Ig-like C2-type 2.				defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.09058	9.837975	56.430529	25	251	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43233974	43233974	13109	19	C	T	T	T	403	31	PSG3	1	1
PSG3	5671	broad.mit.edu	37	19	43243222	43243222	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43243222C>A	uc010eil.2	-	c.150G>T	c.(148-150)TGG>TGT	p.W50C	PSG3_uc002ouf.2_Non-coding_Transcript|PSG1_uc002oug.1_Intron|PSG3_uc002oue.2_Missense_Mutation_p.W28C	NM_021016	NP_066296	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	28					defense response|female pregnancy	extracellular region				ovary(1)	1		Prostate(69;0.00682)												0.16129	107.08813	151.05171	65	338	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43243222	43243222	13109	19	C	A	A	A	390	30	PSG3	2	2
PSG7	5676	broad.mit.edu	37	19	43441197	43441197	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43441197T>A	uc002ovl.3	-	c.32A>T	c.(31-33)CAG>CTG	p.Q11L	PSG3_uc002ouf.2_5'Flank|PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG7_uc010xwl.1_Missense_Mutation_p.Q11L	NM_002783	NP_002774	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7	11					female pregnancy	extracellular region					0		Prostate(69;0.00682)												0.036036	-36.791393	15.08296	8	214	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43441197	43441197	13113	19	T	A	A	A	715	55	PSG7	3	3
USP29	57663	broad.mit.edu	37	19	57641436	57641436	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57641436C>A	uc002qny.2	+	c.1393C>A	c.(1393-1395)CTT>ATT	p.L465I		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	465					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			ovary(2)|breast(2)|pancreas(1)	5		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.037838	-28.077853	14.615445	7	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57641436	57641436	17623	19	C	A	A	A	260	20	USP29	2	2
USP29	57663	broad.mit.edu	37	19	57641688	57641688	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57641688C>G	uc002qny.2	+	c.1645C>G	c.(1645-1647)CTT>GTT	p.L549V		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	549					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			ovary(2)|breast(2)|pancreas(1)	5		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)										0.055556	-18.031777	30.632676	13	221	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57641688	57641688	17623	19	C	G	G	G	416	32	USP29	3	3
MUC16	94025	broad.mit.edu	37	19	9048299	9048299	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9048299G>T	uc002mkp.2	-	c.33332C>A	c.(33331-33333)ACA>AAA	p.T11111K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11113	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.033708	-46.461629	16.833101	9	258	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9048299	9048299	10367	19	G	T	T	T	624	48	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9063443	9063443	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9063443C>A	uc002mkp.2	-	c.24003G>T	c.(24001-24003)GTG>GTT	p.V8001V		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8003	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.070707	-4.856939	13.967559	7	92	KEEP	---	---	---	---	capture		Silent	SNP	9063443	9063443	10367	19	C	A	A	A	366	29	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9090970	9090970	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9090970G>T	uc002mkp.2	-	c.845C>A	c.(844-846)GCG>GAG	p.A282E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	282	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.097046	25.735351	102.746338	46	428	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9090970	9090970	10367	19	G	T	T	T	494	38	MUC16	1	1
OR7G2	390882	broad.mit.edu	37	19	9213879	9213879	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9213879A>T	uc010xkk.1	-	c.104T>A	c.(103-105)CTC>CAC	p.L35H		NM_001005193	NP_001005193	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G,	14	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						Esophageal Squamous(67;143 1448 28637 40648)								0.057143	-9.717638	11.890861	6	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9213879	9213879	11634	19	A	T	T	T	143	11	OR7G2	3	3
OLFM3	118427	broad.mit.edu	37	1	102302572	102302572	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:102302572T>A	uc001duf.2	-	c.139A>T	c.(139-141)AGT>TGT	p.S47C	OLFM3_uc001dug.2_Missense_Mutation_p.S27C|OLFM3_uc001duh.2_Non-coding_Transcript|OLFM3_uc001dui.2_Non-coding_Transcript|OLFM3_uc001duj.2_5'UTR|OLFM3_uc001due.2_Non-coding_Transcript	NM_058170	NP_477518	Q96PB7	NOE3_HUMAN	olfactomedin 3	47						extracellular region				ovary(2)|skin(1)	3		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)										0.051948	-7.559406	8.783536	4	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102302572	102302572	11259	1	T	A	A	A	689	53	OLFM3	3	3
COL11A1	1301	broad.mit.edu	37	1	103352456	103352456	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103352456C>A	uc001dum.2	-	c.4801G>T	c.(4801-4803)GAC>TAC	p.D1601Y	COL11A1_uc001duk.2_Missense_Mutation_p.D785Y|COL11A1_uc001dul.2_Missense_Mutation_p.D1589Y|COL11A1_uc001dun.2_Missense_Mutation_p.D1550Y|COL11A1_uc009weh.2_Missense_Mutation_p.D1473Y	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	1589	Fibrillar collagen NC1.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)										0.072816	-8.528219	30.139901	15	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103352456	103352456	3805	1	C	A	A	A	416	32	COL11A1	2	2
VAV3	10451	broad.mit.edu	37	1	108247587	108247587	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:108247587G>A	uc010ouw.1	-	c.1599C>T	c.(1597-1599)CTC>CTT	p.L533L	VAV3_uc001dvk.1_Silent_p.L533L|VAV3_uc001dvl.1_Silent_p.L357L|VAV3_uc010oux.1_Silent_p.L533L	NM_006113	NP_006104	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor isoform	533	Phorbol-ester/DAG-type.				angiogenesis|apoptosis|B cell receptor signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of B cell proliferation|regulation of Rho protein signal transduction|response to DNA damage stimulus|response to drug|small GTPase mediated signal transduction	cytosol	GTPase activator activity|metal ion binding|SH3/SH2 adaptor activity			ovary(4)|lung(2)|breast(2)	8		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)										0.118644	8.416336	16.815675	7	52	KEEP	---	---	---	---	capture		Silent	SNP	108247587	108247587	17698	1	G	A	A	A	522	41	VAV3	2	2
CD53	963	broad.mit.edu	37	1	111437624	111437625	+	Missense_Mutation	DNP	CG	AC	AC			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:111437624_111437625CG>AC	uc001dzw.2	+	c.370_371CG>AC	c.(370-372)CGT>ACT	p.R124T	CD53_uc001dzx.2_Missense_Mutation_p.R124T|CD53_uc010owa.1_Intron|CD53_uc001dzy.2_Missense_Mutation_p.R124T	NM_001040033	NP_001035122	P19397	CD53_HUMAN	CD53 antigen	124	Extracellular (Potential).				signal transduction	integral to membrane|plasma membrane					0		all_cancers(81;1.06e-05)|all_epithelial(167;1.95e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0264)|Colorectal(144;0.0375)|all cancers(265;0.11)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.141)|LUSC - Lung squamous cell carcinoma(189;0.144)										0.097222	6.971318	30.26344	14	130	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	111437624	111437625	3151	1	CG	AC	AC	AC	299	23	CD53	1	1
DDX20	11218	broad.mit.edu	37	1	112309029	112309029	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:112309029A>T	uc001ebs.2	+	c.1983A>T	c.(1981-1983)TCA>TCT	p.S661S	DDX20_uc010owf.1_Silent_p.S423S|DDX20_uc001ebt.2_Silent_p.S269S	NM_007204	NP_009135	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	661					assembly of spliceosomal tri-snRNP|ncRNA metabolic process	Cajal body|cytoskeleton|cytosol|spliceosomal complex	ATP binding|ATP-dependent RNA helicase activity|DNA binding|protein binding			lung(1)|kidney(1)	2		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.132948	35.512252	58.135414	23	150	KEEP	---	---	---	---	capture		Silent	SNP	112309029	112309029	4519	1	A	T	T	T	54	5	DDX20	3	3
MOV10	4343	broad.mit.edu	37	1	113232258	113232258	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:113232258G>C	uc001eck.2	+	c.563G>C	c.(562-564)TGT>TCT	p.C188S	MOV10_uc001ecl.2_Missense_Mutation_p.C188S|MOV10_uc001ecn.2_Missense_Mutation_p.C188S|MOV10_uc001ecm.2_Missense_Mutation_p.C128S|MOV10_uc009wgj.1_Missense_Mutation_p.C128S	NM_001130079	NP_001123551	Q9HCE1	MOV10_HUMAN	Mov10, Moloney leukemia virus 10, homolog	188					mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding			ovary(4)	4	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)										0.108434	14.415534	27.023844	9	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113232258	113232258	10110	1	G	C	C	C	624	48	MOV10	3	3
SLC22A15	55356	broad.mit.edu	37	1	116577934	116577934	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:116577934G>A	uc001egb.3	+	c.1071G>A	c.(1069-1071)TTG>TTA	p.L357L		NM_018420	NP_060890	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	357	Helical; (Potential).				ion transport|transmembrane transport	integral to membrane	transporter activity			large_intestine(2)	2	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)						219				0.055556	-7.061307	7.905602	4	68	KEEP	---	---	---	---	capture		Silent	SNP	116577934	116577934	14942	1	G	A	A	A	581	45	SLC22A15	2	2
IGSF3	3321	broad.mit.edu	37	1	117131683	117131683	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117131683C>A	uc001egq.1	-	c.2133G>T	c.(2131-2133)CTG>CTT	p.L711L	IGSF3_uc001egr.1_Silent_p.L691L|IGSF3_uc001egs.1_Silent_p.L364L	NM_001542	NP_001533	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3 isoform 1	691	Ig-like C2-type 6.|Extracellular (Potential).					integral to membrane				ovary(2)	2	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)										0.072886	-13.902553	50.516283	25	318	KEEP	---	---	---	---	capture		Silent	SNP	117131683	117131683	7902	1	C	A	A	A	262	21	IGSF3	2	2
TTF2	8458	broad.mit.edu	37	1	117619347	117619347	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117619347C>T	uc001egy.2	+	c.1475C>T	c.(1474-1476)CCC>CTC	p.P492L	TTF2_uc001egx.1_Missense_Mutation_p.P492L	NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase	492					mRNA processing|regulation of transcription, DNA-dependent|RNA splicing	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|RNA polymerase II transcription termination factor activity|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)										0.087912	1.949301	17.564954	8	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117619347	117619347	17274	1	C	T	T	T	286	22	TTF2	2	2
NOTCH2	4853	broad.mit.edu	37	1	120468434	120468434	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120468434C>A	uc001eik.2	-	c.4006_splice	c.e25-1	p.G1336_splice		NM_024408	NP_077719			notch 2 preproprotein						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				0.125	5.795656	12.454924	6	42	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	120468434	120468434	10951	1	C	A	A	A	312	24	NOTCH2	5	2
NOTCH2	4853	broad.mit.edu	37	1	120510149	120510149	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120510149C>A	uc001eik.2	-	c.1360G>T	c.(1360-1362)GAG>TAG	p.E454*	NOTCH2_uc001eil.2_Nonsense_Mutation_p.E454*|NOTCH2_uc001eim.3_Nonsense_Mutation_p.E371*	NM_024408	NP_077719	Q04721	NOTC2_HUMAN	notch 2 preproprotein	454	Extracellular (Potential).|EGF-like 11; calcium-binding (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				0.123223	25.881946	55.244691	26	185	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	120510149	120510149	10951	1	C	A	A	A	377	29	NOTCH2	5	2
PRAMEF1	65121	broad.mit.edu	37	1	12854069	12854069	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:12854069G>A	uc001auj.1	+	c.293G>A	c.(292-294)TGG>TAG	p.W98*		NM_023013	NP_075389	O95521	PRAM1_HUMAN	PRAME family member 1	98											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)										0.09	4.910315	55.856046	27	273	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	12854069	12854069	12861	1	G	A	A	A	611	47	PRAMEF1	5	2
PDE4DIP	9659	broad.mit.edu	37	1	145015970	145015970	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145015970A>G	uc001elx.3	-	c.118T>C	c.(118-120)TCA>CCA	p.S40P	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elm.3_5'UTR|PDE4DIP_uc001eln.3_Missense_Mutation_p.S40P|PDE4DIP_uc001elo.2_Missense_Mutation_p.S111P|PDE4DIP_uc001emh.2_Missense_Mutation_p.S111P	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	Error:Variant_position_missing_in_Q5VU43_after_alignment					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(3)	3				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)						595				0.045673	-100.666901	83.236131	38	794	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145015970	145015970	12064	1	A	G	G	G	130	10	PDE4DIP	4	4
RPTN	126638	broad.mit.edu	37	1	152127623	152127623	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152127623G>T	uc001ezs.1	-	c.1952C>A	c.(1951-1953)CCT>CAT	p.P651H		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	651	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0														0.096875	15.974684	68.102981	31	289	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152127623	152127623	14144	1	G	T	T	T	455	35	RPTN	2	2
FLG	2312	broad.mit.edu	37	1	152278890	152278890	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152278890C>A	uc001ezu.1	-	c.8472G>T	c.(8470-8472)AGG>AGT	p.R2824S		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2824	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.060694	-28.95944	40.773317	21	325	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152278890	152278890	6160	1	C	A	A	A	233	18	FLG	2	2
FLG	2312	broad.mit.edu	37	1	152281932	152281932	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152281932C>T	uc001ezu.1	-	c.5430G>A	c.(5428-5430)CAG>CAA	p.Q1810Q		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1810	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.144231	109.608372	160.332122	60	356	KEEP	---	---	---	---	capture		Silent	SNP	152281932	152281932	6160	1	C	T	T	T	311	24	FLG	2	2
FLG2	388698	broad.mit.edu	37	1	152326246	152326246	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152326246G>A	uc001ezw.3	-	c.4016C>T	c.(4015-4017)ACA>ATA	p.T1339I		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1339							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.057432	-29.338483	31.488806	17	279	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152326246	152326246	6161	1	G	A	A	A	624	48	FLG2	2	2
LCE3D	84648	broad.mit.edu	37	1	152552269	152552269	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152552269G>T	uc001fab.2	-	c.144C>A	c.(142-144)TCC>TCA	p.S48S		NM_032563	NP_115952	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	48					keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)										0.087379	3.745821	21.355509	9	94	KEEP	---	---	---	---	capture		Silent	SNP	152552269	152552269	8995	1	G	T	T	T	496	39	LCE3D	1	1
LCE3A	353142	broad.mit.edu	37	1	152595480	152595480	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152595480G>T	uc010pdt.1	-	c.100C>A	c.(100-102)CCA>ACA	p.P34T		NM_178431	NP_848518	Q5TA76	LCE3A_HUMAN	late cornified envelope 3A	34					keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.11	9.2842	24.312253	11	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152595480	152595480	8992	1	G	T	T	T	559	43	LCE3A	2	2
KAZ	23254	broad.mit.edu	37	1	15438970	15438970	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:15438970G>C	uc001avm.3	+	c.2096G>C	c.(2095-2097)AGG>ACG	p.R699T	C1orf126_uc001avv.3_Non-coding_Transcript|C1orf126_uc009voh.2_Non-coding_Transcript|KAZ_uc001avs.3_Missense_Mutation_p.R146T	NM_201628	NP_963922	Q674X7	KAZRN_HUMAN	kazrin isoform E	699					keratinization	cornified envelope|cytoplasm|desmosome|nucleus					0														0.107143	2.503109	6.793596	3	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15438970	15438970	8292	1	G	C	C	C	455	35	KAZ	3	3
FLAD1	80308	broad.mit.edu	37	1	154956480	154956480	+	Missense_Mutation	SNP	G	A	A	rs1054257		TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154956480G>A	uc001fgf.1	+	c.310G>A	c.(310-312)GAA>AAA	p.E104K	FLAD1_uc001fgc.2_5'UTR|FLAD1_uc001fgd.1_Missense_Mutation_p.E104K|FLAD1_uc001fge.1_Missense_Mutation_p.E7K|FLAD1_uc001fgg.1_Missense_Mutation_p.E7K	NM_025207	NP_079483	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase isoform	104					FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cytosol	ATP binding|FMN adenylyltransferase activity			ovary(2)	2	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)											0.142857	7.014633	12.191101	6	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154956480	154956480	6158	1	G	A	A	A	585	45	FLAD1	2	2
PKLR	5313	broad.mit.edu	37	1	155269991	155269991	+	Missense_Mutation	SNP	G	T	T	rs8177962	byFrequency	TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155269991G>T	uc001fkb.3	-	c.181C>A	c.(181-183)CTG>ATG	p.L61M	RAG1AP1_uc010pey.1_Intron|PKLR_uc001fka.3_Missense_Mutation_p.L30M|PKLR_uc010pga.1_De_novo_Start_InFrame	NM_000298	NP_000289	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC isoform 1	61					endocrine pancreas development|energy reserve metabolic process|glycolysis|positive regulation of cellular metabolic process	cytosol	ATP binding|magnesium ion binding|potassium ion binding|pyruvate kinase activity			skin(3)|ovary(1)	4	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)									0.210526	8.495479	9.964563	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155269991	155269991	12401	1	G	T	T	T	438	34	PKLR	2	2
GON4L	54856	broad.mit.edu	37	1	155747565	155747565	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155747565C>A	uc001flz.2	-	c.1939G>T	c.(1939-1941)GTG>TTG	p.V647L	GON4L_uc001fly.1_Missense_Mutation_p.V647L|GON4L_uc009wrh.1_Missense_Mutation_p.V647L|GON4L_uc001fma.1_Missense_Mutation_p.V647L|GON4L_uc001fmb.3_5'Flank|GON4L_uc001fmc.2_Missense_Mutation_p.V647L|GON4L_uc001fmd.3_Missense_Mutation_p.V647L|GON4L_uc009wri.2_Missense_Mutation_p.V233L|GON4L_uc009wrj.1_Missense_Mutation_p.V162L|GON4L_uc001fme.2_Missense_Mutation_p.V475L	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	647					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.078431	-0.884413	17.645399	8	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155747565	155747565	6845	1	C	A	A	A	260	20	GON4L	2	2
NTRK1	4914	broad.mit.edu	37	1	156845991	156845991	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156845991G>A	uc001fqh.1	+	c.1621G>A	c.(1621-1623)GTG>ATG	p.V541M	NTRK1_uc001fqf.1_Missense_Mutation_p.V505M|NTRK1_uc009wsi.1_Missense_Mutation_p.V240M|NTRK1_uc001fqi.1_Missense_Mutation_p.V535M|NTRK1_uc009wsk.1_Missense_Mutation_p.V538M	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	541	Cytoplasmic (Potential).|Protein kinase.				activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|stomach(1)|central_nervous_system(1)	16	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)					290	TSP Lung(10;0.080)			0.145833	10.665641	16.396215	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156845991	156845991	11111	1	G	A	A	A	572	44	NTRK1	2	2
FCRL2	79368	broad.mit.edu	37	1	157737268	157737268	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157737268C>A	uc001fre.2	-	c.915G>T	c.(913-915)AGG>AGT	p.R305S	FCRL2_uc001frd.2_Missense_Mutation_p.R52S|FCRL2_uc010phz.1_Missense_Mutation_p.R305S|FCRL2_uc009wsp.2_Intron	NM_030764	NP_110391	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2 precursor	305	Ig-like C2-type 4.|Extracellular (Potential).				cell-cell signaling	integral to membrane|plasma membrane|soluble fraction	receptor activity|SH3/SH2 adaptor activity			ovary(1)|pancreas(1)	2	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)											0.075145	-4.557362	27.388417	13	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157737268	157737268	6032	1	C	A	A	A	233	18	FCRL2	2	2
OR10T2	128360	broad.mit.edu	37	1	158368632	158368632	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158368632T>C	uc010pih.1	-	c.625A>G	c.(625-627)ATG>GTG	p.M209V		NM_001004475	NP_001004475	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	all_hematologic(112;0.0378)													0.109375	9.389229	19.048788	7	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158368632	158368632	11325	1	T	C	C	C	637	49	OR10T2	4	4
CASQ1	844	broad.mit.edu	37	1	160160683	160160683	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160160683C>T	uc010pja.1	+	c.142C>T	c.(142-144)CGT>TGT	p.R48C		NM_001231	NP_001222	P31415	CASQ1_HUMAN	calsequestrin 1	42						mitochondrial matrix|sarcoplasmic reticulum lumen|smooth endoplasmic reticulum	calcium ion binding			central_nervous_system(1)	1	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.055556	-10.534182	15.607887	7	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160160683	160160683	2799	1	C	T	T	T	299	23	CASQ1	1	1
SPEN	23013	broad.mit.edu	37	1	16260605	16260605	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16260605C>G	uc001axk.1	+	c.7870C>G	c.(7870-7872)CGG>GGG	p.R2624G	SPEN_uc010obp.1_Missense_Mutation_p.R2583G	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	2624	RID.				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	14		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)						551				0.102941	30.907612	84.283634	35	305	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16260605	16260605	15550	1	C	G	G	G	295	23	SPEN	3	3
CLCNKA	1187	broad.mit.edu	37	1	16351353	16351353	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:16351353G>T	uc001axu.2	+	c.325G>T	c.(325-327)GGC>TGC	p.G109C	CLCNKA_uc001axt.2_Splice_Site_SNP|CLCNKA_uc001axv.2_Missense_Mutation_p.G109C|CLCNKA_uc010obw.1_Intron|CLCNKB_uc001axw.3_Intron	NM_004070	NP_004061	P51800	CLCKA_HUMAN	chloride channel Ka isoform 1	109					excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)									0.117647	4.475029	9.362093	4	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16351353	16351353	3605	1	G	T	T	T	455	35	CLCNKA	2	2
POU2F1	5451	broad.mit.edu	37	1	167334748	167334748	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167334748G>T	uc001gef.2	+	c.139G>T	c.(139-141)GTA>TTA	p.V47L	POU2F1_uc010plg.1_Non-coding_Transcript|POU2F1_uc001gec.2_Missense_Mutation_p.V35L|POU2F1_uc001ged.2_Missense_Mutation_p.V33L|POU2F1_uc001gee.2_Missense_Mutation_p.V35L|POU2F1_uc010plh.1_Missense_Mutation_p.V35L	NM_002697	NP_002688	P14859	PO2F1_HUMAN	POU class 2 homeobox 1	35					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			central_nervous_system(2)|breast(1)	3														0.059406	-8.639467	11.888392	6	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167334748	167334748	12701	1	G	T	T	T	624	48	POU2F1	2	2
RCSD1	92241	broad.mit.edu	37	1	167654682	167654682	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167654682A>T	uc001gem.2	+	c.133A>T	c.(133-135)AGG>TGG	p.R45W	RCSD1_uc010pli.1_Intron	NM_052862	NP_443094	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	45										ovary(2)|central_nervous_system(2)|skin(1)	5	all_hematologic(923;0.215)													0.06338	-10.426528	17.744493	9	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167654682	167654682	13654	1	A	T	T	T	36	3	RCSD1	3	3
F5	2153	broad.mit.edu	37	1	169511451	169511451	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169511451G>T	uc001ggg.1	-	c.2877C>A	c.(2875-2877)ATC>ATA	p.I959I		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	959	B.				cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)									0.102397	16.306433	88.983015	47	412	KEEP	---	---	---	---	capture		Silent	SNP	169511451	169511451	5542	1	G	T	T	T	525	41	F5	2	2
FMO2	2327	broad.mit.edu	37	1	171154916	171154916	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171154916G>T	uc001ghk.1	+	c.64G>T	c.(64-66)GTG>TTG	p.V22L	FMO2_uc010pmd.1_Intron	NM_001460	NP_001451	Q99518	FMO2_HUMAN	flavin containing monooxygenase 2	22					drug metabolic process|NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|host cell microsome|integral to membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.090909	18.932319	95.02322	41	410	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171154916	171154916	6197	1	G	T	T	T	624	48	FMO2	2	2
FMO1	2326	broad.mit.edu	37	1	171254341	171254341	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171254341G>T	uc009wvz.2	+	c.1257G>T	c.(1255-1257)TGG>TGT	p.W419C	FMO1_uc010pme.1_Missense_Mutation_p.W356C|FMO1_uc001ghl.2_Missense_Mutation_p.W419C|FMO1_uc001ghm.2_Missense_Mutation_p.W419C|FMO1_uc001ghn.2_Missense_Mutation_p.G395V	NM_002021	NP_002012	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	419					NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum lumen|integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.053571	-18.825479	16.476925	9	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171254341	171254341	6196	1	G	T	T	T	572	44	FMO1	2	2
C1orf9	51430	broad.mit.edu	37	1	172558024	172558024	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:172558024C>T	uc001giq.3	+	c.1783C>T	c.(1783-1785)CTT>TTT	p.L595F	C1orf9_uc010pmm.1_Missense_Mutation_p.L595F|C1orf9_uc009wwd.2_Missense_Mutation_p.L551F|C1orf9_uc010pmn.1_Missense_Mutation_p.L558F|C1orf9_uc010pmo.1_Non-coding_Transcript	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	595					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)		Colon(43;174 953 11768 38880 47057)								0.142857	25.423622	36.598708	13	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172558024	172558024	2143	1	C	T	T	T	312	24	C1orf9	2	2
TNN	63923	broad.mit.edu	37	1	175046689	175046689	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:175046689C>T	uc001gkl.1	+	c.135C>T	c.(133-135)ACC>ACT	p.T45T	TNN_uc010pmx.1_Silent_p.T45T	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	45					cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)						470				0.15	17.233728	24.281367	9	51	KEEP	---	---	---	---	capture		Silent	SNP	175046689	175046689	16864	1	C	T	T	T	301	24	TNN	2	2
PADI1	29943	broad.mit.edu	37	1	17555220	17555220	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17555220G>T	uc001bah.1	+	c.753G>T	c.(751-753)GTG>GTT	p.V251V		NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	251					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	Esophageal Squamous(80;414 1257 4580 27746 50832)								0.070423	-14.721116	39.372218	20	264	KEEP	---	---	---	---	capture		Silent	SNP	17555220	17555220	11793	1	G	T	T	T	600	47	PADI1	2	2
C1orf125	126859	broad.mit.edu	37	1	179364232	179364233	+	Splice_Site_DNP	DNP	GG	TT	TT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179364232_179364233GG>TT	uc001gmo.2	+	c.1005_splice	c.e11-1	p.R335_splice	C1orf125_uc009wxg.2_Splice_Site_DNP|C1orf125_uc001gmn.1_Splice_Site_DNP_p.R123_splice|C1orf125_uc010pnl.1_Splice_Site_DNP|C1orf125_uc001gmp.2_Splice_Site_DNP_p.R335_splice	NM_144696	NP_653297			hypothetical protein LOC126859 isoform 1												0														0.109091	28.242204	78.217429	36	294	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	179364232	179364233	2060	1	GG	TT	TT	TT	455	35	C1orf125	5	2
ZNF648	127665	broad.mit.edu	37	1	182026294	182026294	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:182026294G>T	uc001goz.2	-	c.852C>A	c.(850-852)TGC>TGA	p.C284*		NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	284	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						NSCLC(71;908 1374 5429 20458 35642)								0.157895	5.714421	7.833413	3	16	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	182026294	182026294	18658	1	G	T	T	T	490	38	ZNF648	5	1
TPR	7175	broad.mit.edu	37	1	186287681	186287681	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186287681G>C	uc001grv.2	-	c.6719C>G	c.(6718-6720)TCT>TGT	p.S2240C		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	2240					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)						1949				0.076336	-1.466018	22.661111	10	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186287681	186287681	16960	1	G	C	C	C	429	33	TPR	3	3
TPR	7175	broad.mit.edu	37	1	186315294	186315294	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186315294T>C	uc001grv.2	-	c.3069A>G	c.(3067-3069)AGA>AGG	p.R1023R		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	1023	Potential.				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)						1949				0.088235	12.597305	41.728522	15	155	KEEP	---	---	---	---	capture		Silent	SNP	186315294	186315294	16960	1	T	C	C	C	803	62	TPR	4	4
FAM5C	339479	broad.mit.edu	37	1	190203565	190203565	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190203565C>A	uc001gse.1	-	c.661G>T	c.(661-663)GAC>TAC	p.D221Y	FAM5C_uc010pot.1_Missense_Mutation_p.D119Y	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	221						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.046632	-27.25536	15.031201	9	184	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190203565	190203565	5817	1	C	A	A	A	377	29	FAM5C	2	2
FAM5C	339479	broad.mit.edu	37	1	190250818	190250819	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190250818_190250819GG>TT	uc001gse.1	-	c.298_299CC>AA	c.(298-300)CCT>AAT	p.P100N	FAM5C_uc010pot.1_Intron	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	100						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.168421	32.358136	42.236938	16	79	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	190250818	190250819	5817	1	GG	TT	TT	TT	455	35	FAM5C	2	2
UBR4	23352	broad.mit.edu	37	1	19486759	19486759	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19486759G>A	uc001bbi.2	-	c.5423C>T	c.(5422-5424)GCT>GTT	p.A1808V	UBR4_uc001bbm.1_Missense_Mutation_p.A1019V	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	1808					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)	23		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)										0.076923	-1.675163	10.237572	5	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19486759	19486759	17462	1	G	A	A	A	442	34	UBR4	2	2
CFHR3	10878	broad.mit.edu	37	1	196762554	196762554	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196762554T>G	uc001gtl.2	+	c.904T>G	c.(904-906)TGT>GGT	p.C302G	CFHR3_uc010poy.1_Missense_Mutation_p.C241G|CFHR1_uc001gtm.2_Intron	NM_021023	NP_066303	Q02985	FHR3_HUMAN	complement factor H-related 3 precursor	302	Sushi 5.					extracellular space					0														0.15	36.148058	50.299896	18	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196762554	196762554	3419	1	T	G	G	G	767	59	CFHR3	4	4
ASPM	259266	broad.mit.edu	37	1	197111989	197111989	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197111989T>C	uc001gtu.2	-	c.1393A>G	c.(1393-1395)ATA>GTA	p.I465V	ASPM_uc001gtv.2_Missense_Mutation_p.I465V|ASPM_uc001gtw.3_Intron	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	465					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.20442	103.10384	117.754074	37	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197111989	197111989	1075	1	T	C	C	C	637	49	ASPM	4	4
SYT2	127833	broad.mit.edu	37	1	202568477	202568477	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:202568477G>A	uc001gye.2	-	c.922C>T	c.(922-924)CCG>TCG	p.P308S	SYT2_uc010pqb.1_Missense_Mutation_p.P308S|SYT2_uc009xaf.2_Missense_Mutation_p.P138S	NM_001136504	NP_001129976	Q8N9I0	SYT2_HUMAN	synaptotagmin II	308	Phospholipid binding (By similarity).|C2 2.|Cytoplasmic (Potential).				neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)									0.184751	134.943331	166.727066	63	278	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	202568477	202568477	15995	1	G	A	A	A	559	43	SYT2	2	2
CR1L	1379	broad.mit.edu	37	1	207870881	207870881	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:207870881A>T	uc001hga.3	+	c.896A>T	c.(895-897)GAG>GTG	p.E299V	CR1L_uc001hfz.2_Non-coding_Transcript|CR1L_uc001hgb.1_Non-coding_Transcript	NM_175710	NP_783641	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	299	Sushi 5.					cytoplasm|extracellular region|membrane					0														0.087108	2.747223	52.310153	25	262	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207870881	207870881	3980	1	A	T	T	T	143	11	CR1L	3	3
USH2A	7399	broad.mit.edu	37	1	216172398	216172398	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216172398C>A	uc001hku.1	-	c.6488G>T	c.(6487-6489)TGG>TTG	p.W2163L		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2163	Extracellular (Potential).|Fibronectin type-III 8.				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.095238	12.896989	54.352196	24	228	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216172398	216172398	17598	1	C	A	A	A	273	21	USH2A	2	2
USH2A	7399	broad.mit.edu	37	1	216256812	216256812	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216256812G>T	uc001hku.1	-	c.5284C>A	c.(5284-5286)CCT>ACT	p.P1762T		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1762	Laminin G-like 2.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.053512	-31.917113	30.967629	16	283	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216256812	216256812	17598	1	G	T	T	T	572	44	USH2A	2	2
USH2A	7399	broad.mit.edu	37	1	216260106	216260106	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216260106G>A	uc001hku.1	-	c.4942C>T	c.(4942-4944)CTG>TTG	p.L1648L		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1648	Laminin G-like 1.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.054645	-16.606757	21.634595	10	173	KEEP	---	---	---	---	capture		Silent	SNP	216260106	216260106	17598	1	G	A	A	A	425	33	USH2A	2	2
USH2A	7399	broad.mit.edu	37	1	216371755	216371756	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216371755_216371756CC>AA	uc001hku.1	-	c.3982_3983GG>TT	c.(3982-3984)GGC>TTC	p.G1328F	USH2A_uc001hkv.2_Missense_Mutation_p.G1328F	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	1328	Fibronectin type-III 3.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.072072	-10.937624	31.021084	16	206	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	216371755	216371756	17598	1	CC	AA	AA	AA	338	26	USH2A	2	2
TAF1A	9015	broad.mit.edu	37	1	222734835	222734835	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222734835C>A	uc009xdz.1	-	c.1111G>T	c.(1111-1113)GAG>TAG	p.E371*	TAF1A_uc009xdy.1_Nonsense_Mutation_p.E62*|TAF1A_uc001hni.1_Nonsense_Mutation_p.E257*|TAF1A_uc001hnj.2_Nonsense_Mutation_p.E371*|TAF1A_uc001hnk.2_Nonsense_Mutation_p.E257*	NM_139352	NP_647603	Q15573	TAF1A_HUMAN	TBP-associated factor 1A isoform 2	371					regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter	RNA polymerase I transcription factor complex	DNA binding|general RNA polymerase II transcription factor activity|RNA polymerase I transcription factor activity				0				GBM - Glioblastoma multiforme(131;0.0186)										0.155844	38.49487	55.920512	24	130	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	222734835	222734835	16040	1	C	A	A	A	416	32	TAF1A	5	2
WNT3A	89780	broad.mit.edu	37	1	228238526	228238526	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228238526T>A	uc001hrp.1	+	c.483T>A	c.(481-483)TTT>TTA	p.F161L	WNT3A_uc001hrq.1_Missense_Mutation_p.F161L	NM_033131	NP_149122	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family,	161					axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of heart induction by canonical Wnt receptor signaling pathway|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)												0.097561	2.480778	9.120081	4	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228238526	228238526	17963	1	T	A	A	A	816	63	WNT3A	3	3
WNT3A	89780	broad.mit.edu	37	1	228247907	228247907	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228247907C>A	uc001hrp.1	+	c.1060C>A	c.(1060-1062)CCC>ACC	p.P354T	WNT3A_uc001hrq.1_3'UTR	NM_033131	NP_149122	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family,	Error:Variant_position_missing_in_P56704_after_alignment					axis specification|cell proliferation in forebrain|cell-cell signaling|cellular response to retinoic acid|convergent extension|dermatome development|dorsal/ventral neural tube patterning|embryonic pattern specification|extracellular matrix organization|hemopoietic stem cell proliferation|hippocampus development|inner ear morphogenesis|mammary gland development|midbrain-hindbrain boundary development|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of heart induction by canonical Wnt receptor signaling pathway|notochord development|palate development|paraxial mesodermal cell fate commitment|positive regulation of catenin import into nucleus|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of receptor internalization|signalosome assembly|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuroblast division|Wnt receptor signaling pathway, calcium modulating pathway	cell surface|early endosome|extracellular space|late endosome|membrane raft|plasma membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|frizzled-2 binding|receptor agonist activity|signal transducer activity|transcription coactivator activity			ovary(1)	1		Prostate(94;0.0405)												0.2	8.785251	10.861254	5	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228247907	228247907	17963	1	C	A	A	A	378	30	WNT3A	2	2
RYR2	6262	broad.mit.edu	37	1	237756789	237756789	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237756789T>C	uc001hyl.1	+	c.4289T>C	c.(4288-4290)GTG>GCG	p.V1430A		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1430	Cytoplasmic (By similarity).|B30.2/SPRY 3.|4 X approximate repeats.				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)											0.166667	30.370525	39.85178	15	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237756789	237756789	14249	1	T	C	C	C	767	59	RYR2	4	4
OR1C1	26188	broad.mit.edu	37	1	247920993	247920993	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247920993G>T	uc010pza.1	-	c.716C>A	c.(715-717)TCC>TAC	p.S239Y		NM_012353	NP_036485	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C,	239	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)											0.115942	6.36726	16.377896	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247920993	247920993	11358	1	G	T	T	T	533	41	OR1C1	2	2
OR14C36	127066	broad.mit.edu	37	1	248512233	248512233	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248512233C>T	uc010pzl.1	+	c.157C>T	c.(157-159)CTT>TTT	p.L53F		NM_001001918	NP_001001918	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C,	53	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2														0.088235	11.441711	63.865424	27	279	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248512233	248512233	11352	1	C	T	T	T	312	24	OR14C36	2	2
AIM1L	55057	broad.mit.edu	37	1	26663815	26663815	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26663815C>A	uc001bmd.3	-	c.565G>T	c.(565-567)GGG>TGG	p.G189W	AIM1L_uc001bmf.3_Missense_Mutation_p.G80W	NM_001039775	NP_001034864	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	189	Beta/gamma crystallin 'Greek key' 4.						sugar binding			pancreas(1)	1		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)										0.062016	-11.807652	14.125577	8	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26663815	26663815	434	1	C	A	A	A	286	22	AIM1L	2	2
GMEB1	10691	broad.mit.edu	37	1	29037045	29037045	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:29037045C>T	uc001bra.2	+	c.912C>T	c.(910-912)CTC>CTT	p.L304L	GMEB1_uc001bqz.2_Silent_p.L294L|GMEB1_uc001brb.2_Silent_p.L294L	NM_006582	NP_006573	Q9Y692	GMEB1_HUMAN	glucocorticoid modulatory element binding	304					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|metal ion binding|transcription coactivator activity				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Breast(348;0.00502)|Renal(390;0.00555)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)										0.141844	30.923637	48.351145	20	121	KEEP	---	---	---	---	capture		Silent	SNP	29037045	29037045	6756	1	C	T	T	T	366	29	GMEB1	2	2
COL16A1	1307	broad.mit.edu	37	1	32154676	32154676	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32154676C>G	uc001btk.1	-	c.1631G>C	c.(1630-1632)GGC>GCC	p.G544A	COL16A1_uc001btj.1_Missense_Mutation_p.G373A|COL16A1_uc001btl.3_Missense_Mutation_p.G544A	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor	544	Triple-helical region 8 (COL8) with 1 imperfection.				cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		Colon(143;498 1786 21362 25193 36625)								0.076433	-1.868122	27.272689	12	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32154676	32154676	3811	1	C	G	G	G	338	26	COL16A1	3	3
KIAA0495	57212	broad.mit.edu	37	1	3662521	3662521	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3662521C>T	uc009vlm.2	-	c.247G>A	c.(247-249)GGC>AGC	p.G83S	KIAA0495_uc001akt.3_Non-coding_Transcript	NM_207306	NP_997189			hypothetical protein LOC57212 precursor												0	all_cancers(77;0.0338)|Ovarian(185;0.0634)|Lung NSC(156;0.172)|all_lung(157;0.182)	all_epithelial(116;1.83e-21)|all_lung(118;2e-08)|Lung NSC(185;7.5e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;1.27e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.204)										0.142857	8.960435	13.254602	5	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3662521	3662521	8487	1	C	T	T	T	299	23	KIAA0495	1	1
KIAA0467	23334	broad.mit.edu	37	1	43896034	43896034	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43896034C>T	uc001cjk.1	+	c.1757C>T	c.(1756-1758)TCA>TTA	p.S586L		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1485						peroxisome				breast(6)|ovary(4)|pancreas(1)	11	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)												0.054264	-12.972715	14.03569	7	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43896034	43896034	8485	1	C	T	T	T	377	29	KIAA0467	2	2
STIL	6491	broad.mit.edu	37	1	47765719	47765719	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:47765719C>A	uc001crd.1	-	c.559G>T	c.(559-561)GAC>TAC	p.D187Y	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Intron|STIL_uc010omo.1_Missense_Mutation_p.D187Y|STIL_uc001crc.1_Missense_Mutation_p.D187Y|STIL_uc001cre.1_Missense_Mutation_p.D187Y|STIL_uc001crg.1_Intron	NM_001048166	NP_001041631	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 1	187					cell proliferation|multicellular organismal development	cytosol					0		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)								992				0.091346	3.163864	38.18331	19	189	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47765719	47765719	15802	1	C	A	A	A	377	29	STIL	2	2
ECHDC2	55268	broad.mit.edu	37	1	53370711	53370711	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:53370711C>A	uc001cup.3	-	c.509G>T	c.(508-510)GGG>GTG	p.G170V	ECHDC2_uc001cun.2_Missense_Mutation_p.G93V|ECHDC2_uc001cuo.3_Missense_Mutation_p.G139V|ECHDC2_uc010onk.1_Missense_Mutation_p.G124V|ECHDC2_uc010onl.1_3'UTR|ECHDC2_uc010onm.1_3'UTR|ECHDC2_uc010onn.1_3'UTR	NM_018281	NP_060751	Q86YB7	ECHD2_HUMAN	enoyl Coenzyme A hydratase domain containing 2	170					fatty acid metabolic process	mitochondrion	lyase activity			central_nervous_system(1)	1														0.060606	-9.894682	10.057166	6	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53370711	53370711	5081	1	C	A	A	A	286	22	ECHDC2	2	2
PDE4B	5142	broad.mit.edu	37	1	66713328	66713328	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:66713328C>A	uc001dcn.2	+	c.467C>A	c.(466-468)CCA>CAA	p.P156Q	PDE4B_uc009war.2_Missense_Mutation_p.P64Q|PDE4B_uc001dco.2_Missense_Mutation_p.P156Q|PDE4B_uc001dcp.2_Missense_Mutation_p.P141Q	NM_001037341	NP_001032418	Q07343	PDE4B_HUMAN	phosphodiesterase 4B isoform 1	156					signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)									0.090323	4.421594	30.679914	14	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66713328	66713328	12061	1	C	A	A	A	273	21	PDE4B	2	2
LRRC7	57554	broad.mit.edu	37	1	70446128	70446128	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70446128T>A	uc001dep.2	+	c.664T>A	c.(664-666)TTA>ATA	p.L222I	LRRC7_uc009wbg.2_5'UTR	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	222	LRR 9.					centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13										783				0.075949	-11.947213	46.318227	24	292	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70446128	70446128	9396	1	T	A	A	A	777	60	LRRC7	3	3
UTS2	10911	broad.mit.edu	37	1	7910884	7910884	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:7910884G>T	uc001aoq.2	-	c.202C>A	c.(202-204)CTC>ATC	p.L68I	UTS2_uc001aor.2_Missense_Mutation_p.L68I|UTS2_uc001aos.2_Missense_Mutation_p.L83I	NM_006786	NP_006777	O95399	UTS2_HUMAN	urotensin 2 isoform b preproprotein	68					muscle contraction|regulation of blood pressure|synaptic transmission	extracellular space	hormone activity				0	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;1.38e-20)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.26e-71)|GBM - Glioblastoma multiforme(8;5.15e-36)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000386)|KIRC - Kidney renal clear cell carcinoma(229;0.000894)|STAD - Stomach adenocarcinoma(132;0.000951)|READ - Rectum adenocarcinoma(331;0.0642)										0.104651	6.206006	19.582961	9	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7910884	7910884	17669	1	G	T	T	T	429	33	UTS2	2	2
ELTD1	64123	broad.mit.edu	37	1	79383345	79383345	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:79383345T>C	uc001diq.3	-	c.1723A>G	c.(1723-1725)ATA>GTA	p.I575V		NM_022159	NP_071442	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain	575	Helical; Name=5; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(1)	1				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)										0.157895	14.729837	18.966171	6	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79383345	79383345	5276	1	T	C	C	C	637	49	ELTD1	4	4
WDR63	126820	broad.mit.edu	37	1	85561704	85561704	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:85561704G>C	uc001dkt.2	+	c.1263_splice	c.e11+1	p.Q421_splice	WDR63_uc009wcl.2_Splice_Site_SNP_p.Q382_splice	NM_145172	NP_660155			WD repeat domain 63											ovary(2)	2				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)										0.088372	16.37444	53.181653	19	196	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	85561704	85561704	17887	1	G	C	C	C	572	44	WDR63	5	3
CLCA2	9635	broad.mit.edu	37	1	86905963	86905963	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86905963G>T	uc001dlr.3	+	c.1336G>T	c.(1336-1338)GGT>TGT	p.G446C		NM_006536	NP_006527	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2 precursor	446	VWFA.|Extracellular (Potential).				cell adhesion	basal plasma membrane|cell junction|extracellular region|integral to plasma membrane	chloride channel activity			ovary(1)|breast(1)	2		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)								0.127329	51.946509	95.812876	41	281	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86905963	86905963	3594	1	G	T	T	T	559	43	CLCA2	2	2
HFM1	164045	broad.mit.edu	37	1	91816380	91816380	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:91816380A>G	uc001doa.3	-	c.2121T>C	c.(2119-2121)CAT>CAC	p.H707H	HFM1_uc009wdb.2_Intron|HFM1_uc010osu.1_Silent_p.H386H|HFM1_uc010osv.1_Silent_p.H391H	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	707	Helicase C-terminal.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)										0.085	8.408787	43.423605	17	183	KEEP	---	---	---	---	capture		Silent	SNP	91816380	91816380	7366	1	A	G	G	G	206	16	HFM1	4	4
LPPR4	9890	broad.mit.edu	37	1	99771695	99771695	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:99771695C>T	uc001dse.2	+	c.1421C>T	c.(1420-1422)CCC>CTC	p.P474L	LPPR4_uc010oue.1_Missense_Mutation_p.P416L	NM_014839	NP_055654	Q7Z2D5	LPPR4_HUMAN	plasticity related gene 1	474							phosphatidate phosphatase activity			ovary(3)	3		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)										0.086792	9.2777	55.051793	23	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99771695	99771695	9300	1	C	T	T	T	286	22	LPPR4	2	2
ZNF133	7692	broad.mit.edu	37	20	18296642	18296642	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:18296642G>T	uc010zrv.1	+	c.1156G>T	c.(1156-1158)GCC>TCC	p.A386S	ZNF133_uc010gcq.2_Missense_Mutation_p.A383S|ZNF133_uc010zrw.1_Missense_Mutation_p.A320S|ZNF133_uc010gcr.2_Missense_Mutation_p.A383S|ZNF133_uc010zrx.1_Missense_Mutation_p.A288S|ZNF133_uc002wql.3_Missense_Mutation_p.A382S|ZNF133_uc010gcs.2_Missense_Mutation_p.A382S|ZNF133_uc010zry.1_Missense_Mutation_p.A288S|ZNF133_uc002wqm.2_Missense_Mutation_p.A383S	NM_003434	NP_003425	P52736	ZN133_HUMAN	zinc finger protein 133	383	C2H2-type 7.				regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|pancreas(1)	2														0.261682	74.772845	80.258051	28	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18296642	18296642	18314	20	G	T	T	T	494	38	ZNF133	1	1
SLC24A3	57419	broad.mit.edu	37	20	19665861	19665861	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:19665861G>T	uc002wrl.2	+	c.1180G>T	c.(1180-1182)GGC>TGC	p.G394C		NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24	394	Cytoplasmic (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1														0.216981	49.304063	57.113258	23	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19665861	19665861	14964	20	G	T	T	T	559	43	SLC24A3	2	2
C20orf26	26074	broad.mit.edu	37	20	20144727	20144727	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20144727T>A	uc002wru.2	+	c.1060T>A	c.(1060-1062)TAT>AAT	p.Y354N	C20orf26_uc010gcw.1_Missense_Mutation_p.Y308N|C20orf26_uc010zse.1_Missense_Mutation_p.Y354N|C20orf26_uc010zsf.1_Missense_Mutation_p.Y354N	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	354										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)										0.207865	90.190715	104.251535	37	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20144727	20144727	2186	20	T	A	A	A	637	49	C20orf26	3	3
C20orf26	26074	broad.mit.edu	37	20	20269485	20269485	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20269485T>A	uc002wru.2	+	c.3029T>A	c.(3028-3030)ATG>AAG	p.M1010K	C20orf26_uc002wrw.2_Intron	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	1010										ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)										0.256757	50.992618	54.960666	19	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20269485	20269485	2186	20	T	A	A	A	663	51	C20orf26	3	3
SIGLEC1	6614	broad.mit.edu	37	20	3675457	3675457	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3675457C>A	uc002wja.2	-	c.2797G>T	c.(2797-2799)GAT>TAT	p.D933Y	SIGLEC1_uc002wjb.1_5'Flank|SIGLEC1_uc002wiz.3_Missense_Mutation_p.D933Y	NM_023068	NP_075556	Q9BZZ2	SN_HUMAN	sialoadhesin precursor	933	Ig-like C2-type 9.|Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|endocytosis|inflammatory response	extracellular region|integral to membrane|plasma membrane	sugar binding			pancreas(4)|ovary(2)|breast(1)|central_nervous_system(1)	8														0.230769	12.633686	14.36389	6	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3675457	3675457	14800	20	C	A	A	A	390	30	SIGLEC1	2	2
CENPB	1059	broad.mit.edu	37	20	3767008	3767008	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3767008C>A	uc002wjk.2	-	c.123G>T	c.(121-123)ACG>ACT	p.T41T	CDC25B_uc010zqk.1_5'Flank|CDC25B_uc010zql.1_5'Flank|CDC25B_uc010zqm.1_5'Flank	NM_001810	NP_001801	P07199	CENPB_HUMAN	centromere protein B	41	H-T-H motif.|HTH psq-type.					chromosome, centromeric region|nucleus	centromeric DNA binding|chromatin binding|satellite DNA binding				0														0.266667	22.494301	23.964581	8	22	KEEP	---	---	---	---	capture		Silent	SNP	3767008	3767008	3360	20	C	A	A	A	340	27	CENPB	1	1
L3MBTL	26013	broad.mit.edu	37	20	42159028	42159028	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42159028G>T	uc010zwh.1	+	c.1095G>T	c.(1093-1095)GAG>GAT	p.E365D	L3MBTL_uc002xkl.2_Missense_Mutation_p.E297D|L3MBTL_uc002xkm.2_Missense_Mutation_p.E297D|L3MBTL_uc010ggl.2_Missense_Mutation_p.E297D|L3MBTL_uc002xkn.1_Missense_Mutation_p.E56D|L3MBTL_uc002xko.2_5'Flank	NM_015478	NP_056293	Q9Y468	LMBL1_HUMAN	l(3)mbt-like isoform I	297	MBT 1.				chromatin modification|hemopoiesis|negative regulation of transcription, DNA-dependent|regulation of megakaryocyte differentiation|regulation of mitosis	chromatin|condensed chromosome|nucleoplasm	identical protein binding|methylated histone residue binding|nucleosomal histone binding|SAM domain binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding				0		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)											0.229008	50.57266	59.544382	30	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42159028	42159028	8914	20	G	T	T	T	425	33	L3MBTL	2	2
TOX2	84969	broad.mit.edu	37	20	42694687	42694687	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:42694687G>T	uc010ggo.2	+	c.1296G>T	c.(1294-1296)CTG>CTT	p.L432L	TOX2_uc002xle.3_Silent_p.L390L|TOX2_uc010ggp.2_Silent_p.L390L|TOX2_uc002xlf.3_Silent_p.L414L|TOX2_uc002xlg.2_Intron|TOX2_uc010zwk.1_Silent_p.L310L	NM_001098797	NP_001092267	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	414	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)											0.285714	24.963639	26.389347	10	25	KEEP	---	---	---	---	capture		Silent	SNP	42694687	42694687	16920	20	G	T	T	T	587	46	TOX2	2	2
KCNB1	3745	broad.mit.edu	37	20	47990102	47990102	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47990102G>T	uc002xur.1	-	c.1995C>A	c.(1993-1995)AAC>AAA	p.N665K	KCNB1_uc002xus.1_Missense_Mutation_p.N665K	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	665	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)	1			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)											0.252336	64.06848	70.034595	27	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47990102	47990102	8317	20	G	T	T	T	568	44	KCNB1	2	2
SLCO4A1	28231	broad.mit.edu	37	20	61296406	61296406	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61296406C>T	uc002ydb.1	+	c.1242C>T	c.(1240-1242)TTC>TTT	p.F414F	SLCO4A1_uc002ydc.1_Non-coding_Transcript|LOC100127888_uc002ydd.2_Non-coding_Transcript|SLCO4A1_uc002yde.1_5'Flank	NM_016354	NP_057438	Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family	414	Extracellular (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	thyroid hormone transmembrane transporter activity			ovary(1)	1	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)			Pancreas(168;741 2006 10379 40139 45334)				402				0.285714	30.28077	32.012717	12	30	KEEP	---	---	---	---	capture		Silent	SNP	61296406	61296406	15226	20	C	T	T	T	376	29	SLCO4A1	2	2
GMEB2	26205	broad.mit.edu	37	20	62250696	62250696	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62250696G>C	uc002yfp.1	-	c.55C>G	c.(55-57)CCG>GCG	p.P19A	GMEB2_uc002yfq.1_Missense_Mutation_p.P19A	NM_012384	NP_036516	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding	19					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleus	DNA binding|metal ion binding|RNA polymerase II transcription factor activity				0	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)											0.21875	17.90706	20.240052	7	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62250696	62250696	6757	20	G	C	C	C	533	41	GMEB2	3	3
PAK7	57144	broad.mit.edu	37	20	9520240	9520240	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:9520240G>T	uc002wnl.2	-	c.2029C>A	c.(2029-2031)CTA>ATA	p.L677I	PAK7_uc002wnk.2_Missense_Mutation_p.L677I|PAK7_uc002wnj.2_Missense_Mutation_p.L677I|PAK7_uc010gby.1_Missense_Mutation_p.L590I	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7	677	Protein kinase.				protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(7)|skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	15			COAD - Colon adenocarcinoma(9;0.194)							177				0.21374	191.888205	221.64118	84	309	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9520240	9520240	11821	20	G	T	T	T	451	35	PAK7	2	2
NRIP1	8204	broad.mit.edu	37	21	16337858	16337858	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:16337858C>A	uc002yjx.2	-	c.2656G>T	c.(2656-2658)GCC>TCC	p.A886S		NM_003489	NP_003480	P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	886					androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		androgen receptor binding|estrogen receptor binding|glucocorticoid receptor binding|transcription coactivator activity|transcription corepressor activity				0				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)										0.07967	-8.737645	56.88562	29	335	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16337858	16337858	11057	21	C	A	A	A	325	25	NRIP1	2	2
ADAMTS1	9510	broad.mit.edu	37	21	28212641	28212641	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:28212641C>A	uc002ymf.2	-	c.1619G>T	c.(1618-1620)TGT>TTT	p.C540F		NM_006988	NP_008919	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1	540	Disintegrin.				integrin-mediated signaling pathway|negative regulation of cell proliferation|proteolysis		heparin binding|zinc ion binding			lung(3)|large_intestine(2)|central_nervous_system(1)	6		Breast(209;0.000962)		Lung(58;0.215)										0.07	-3.600143	15.434806	7	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28212641	28212641	256	21	C	A	A	A	221	17	ADAMTS1	2	2
BACH1	571	broad.mit.edu	37	21	30699198	30699198	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:30699198G>T	uc002ynj.2	+	c.1053G>T	c.(1051-1053)TTG>TTT	p.L351F	BACH1_uc002ynk.2_Missense_Mutation_p.L351F|BACH1_uc002ynl.2_Non-coding_Transcript	NM_001186	NP_001177	O14867	BACH1_HUMAN	BTB and CNC homology 1 transcription factor	351					regulation of transcription, DNA-dependent	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|liver(1)	2														0.084592	1.64083	59.666309	28	303	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30699198	30699198	1304	21	G	T	T	T	620	48	BACH1	2	2
SON	6651	broad.mit.edu	37	21	34924172	34924172	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:34924172G>T	uc002yse.1	+	c.2635G>T	c.(2635-2637)GGC>TGC	p.G879C	SON_uc002ysb.1_Missense_Mutation_p.G879C|SON_uc002ysc.2_Missense_Mutation_p.G879C|SON_uc002ysd.2_Intron|SON_uc002ysf.1_Intron|SON_uc002ysg.2_5'Flank	NM_138927	NP_620305	P18583	SON_HUMAN	SON DNA-binding protein isoform F	879	17 X 10 AA tandem repeats of L-A-[ST]- [NSG]-[TS]-MDSQM.				anti-apoptosis	nuclear speck	DNA binding|double-stranded RNA binding			ovary(3)	3														0.116279	9.885523	22.364914	10	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34924172	34924172	15426	21	G	T	T	T	611	47	SON	2	2
SLC5A3	6526	broad.mit.edu	37	21	35468722	35468722	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:35468722A>T	uc002yto.2	+	c.1225A>T	c.(1225-1227)ATT>TTT	p.I409F	MRPS6_uc002ytp.2_Intron	NM_006933	NP_008864	P53794	SC5A3_HUMAN	solute carrier family 5 (inositol transporters),	409	Helical; (Potential).					integral to plasma membrane	myo-inositol:sodium symporter activity			ovary(2)	2														0.063636	-7.960619	13.838311	7	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35468722	35468722	15163	21	A	T	T	T	156	12	SLC5A3	3	3
PRAME	23532	broad.mit.edu	37	22	22892503	22892503	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22892503T>A	uc002zwf.2	-	c.598A>T	c.(598-600)AAG>TAG	p.K200*	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Nonsense_Mutation_p.K184*|PRAME_uc010gtr.2_Nonsense_Mutation_p.K200*|PRAME_uc002zwg.2_Nonsense_Mutation_p.K200*|PRAME_uc002zwh.2_Nonsense_Mutation_p.K200*|PRAME_uc002zwi.2_Nonsense_Mutation_p.K200*|PRAME_uc002zwj.2_Nonsense_Mutation_p.K200*|PRAME_uc002zwk.2_Nonsense_Mutation_p.K200*	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	200					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				0.121495	12.593232	27.634264	13	94	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	22892503	22892503	12860	22	T	A	A	A	806	62	PRAME	5	3
SEZ6L	23544	broad.mit.edu	37	22	26688944	26688944	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26688944G>T	uc003acb.2	+	c.667G>T	c.(667-669)GAG>TAG	p.E223*	SEZ6L_uc003acc.2_Nonsense_Mutation_p.E223*|SEZ6L_uc011akc.1_Nonsense_Mutation_p.E223*|SEZ6L_uc003acd.2_Nonsense_Mutation_p.E223*|SEZ6L_uc011akd.1_Nonsense_Mutation_p.E223*|SEZ6L_uc003ace.2_Nonsense_Mutation_p.E223*|SEZ6L_uc003acf.1_5'UTR|SEZ6L_uc010gvc.1_5'UTR	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	223	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.057034	-29.415452	24.672616	15	248	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	26688944	26688944	14632	22	G	T	T	T	533	41	SEZ6L	5	2
LIF	3976	broad.mit.edu	37	22	30639730	30639730	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:30639730C>A	uc003agz.2	-	c.519G>T	c.(517-519)TCG>TCT	p.S173S	LIF_uc011aks.1_3'UTR	NM_002309	NP_002300	P15018	LIF_HUMAN	leukemia inhibitory factor (cholinergic	173					immune response|leukemia inhibitory factor signaling pathway|negative regulation of hormone secretion|positive regulation of cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of macrophage differentiation|positive regulation of MAPKKK cascade|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis|positive regulation of peptidyl-serine phosphorylation of STAT protein|positive regulation of tyrosine phosphorylation of Stat1 protein|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of metanephric nephron tubule epithelial cell differentiation	extracellular space	cytokine activity|growth factor activity|leukemia inhibitory factor receptor binding				0			Epithelial(10;0.171)							26				0.14433	23.947831	35.711754	14	83	KEEP	---	---	---	---	capture		Silent	SNP	30639730	30639730	9105	22	C	A	A	A	288	23	LIF	1	1
MCM5	4174	broad.mit.edu	37	22	35812721	35812721	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:35812721G>T	uc003anu.3	+	c.1504G>T	c.(1504-1506)GAC>TAC	p.D502Y	MCM5_uc010gwr.2_Missense_Mutation_p.D311Y|MCM5_uc003anv.3_Missense_Mutation_p.D459Y|MCM5_uc010gws.1_Non-coding_Transcript|MCM5_uc003anw.1_Missense_Mutation_p.D286Y	NM_006739	NP_006730	P33992	MCM5_HUMAN	minichromosome maintenance complex component 5	502	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	MCM complex	ATP binding|DNA binding|helicase activity|protein binding			ovary(1)	1														0.180556	17.917198	24.853489	13	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35812721	35812721	9779	22	G	T	T	T	533	41	MCM5	2	2
GRAP2	9402	broad.mit.edu	37	22	40365465	40365465	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40365465C>A	uc003ayh.1	+	c.741C>A	c.(739-741)GGC>GGA	p.G247G	GRAP2_uc003ayi.2_Non-coding_Transcript|GRAP2_uc011aom.1_Silent_p.G221G|GRAP2_uc011aon.1_Silent_p.G181G|GRAP2_uc010gya.1_Silent_p.G247G|GRAP2_uc011aoo.1_Silent_p.G175G|GRAP2_uc011aop.1_Silent_p.G207G|GRAP2_uc011aoq.1_Silent_p.G134G|GRAP2_uc003ayj.1_Silent_p.G247G	NM_004810	NP_004801	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	247					cell-cell signaling|Ras protein signal transduction|T cell costimulation|T cell receptor signaling pathway	cytosol	SH3/SH2 adaptor activity			central_nervous_system(1)	1														0.12766	15.246115	27.942909	12	82	KEEP	---	---	---	---	capture		Silent	SNP	40365465	40365465	7030	22	C	A	A	A	353	28	GRAP2	2	2
TNRC6B	23112	broad.mit.edu	37	22	40661743	40661743	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40661743A>G	uc011aor.1	+	c.1509A>G	c.(1507-1509)ACA>ACG	p.T503T	TNRC6B_uc003aym.2_Intron|TNRC6B_uc003ayn.3_Silent_p.T503T|TNRC6B_uc003ayo.2_Silent_p.T307T	NM_001162501	NP_001155973	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	503					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0										794				0.054348	-9.772646	9.464724	5	87	KEEP	---	---	---	---	capture		Silent	SNP	40661743	40661743	16882	22	A	G	G	G	93	8	TNRC6B	4	4
SBF1	6305	broad.mit.edu	37	22	50897899	50897899	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50897899C>A	uc003blh.2	-	c.3688G>T	c.(3688-3690)GGC>TGC	p.G1230C	SBF1_uc011arx.1_Missense_Mutation_p.G894C	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	1230	Myotubularin phosphatase.				protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)										0.176471	10.961198	14.291632	6	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50897899	50897899	14339	22	C	A	A	A	312	24	SBF1	2	2
IL18RAP	8807	broad.mit.edu	37	2	103061680	103061680	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:103061680G>C	uc002tbx.2	+	c.952G>C	c.(952-954)GAG>CAG	p.E318Q	IL18RAP_uc010fiz.2_Missense_Mutation_p.E176Q	NM_003853	NP_003844	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	318	Ig-like C2-type 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|inflammatory response|innate immune response	integral to membrane	transmembrane receptor activity			ovary(2)	2														0.065789	-3.875057	10.991341	5	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103061680	103061680	7949	2	G	C	C	C	585	45	IL18RAP	3	3
GREB1	9687	broad.mit.edu	37	2	11716594	11716594	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:11716594G>C	uc002rbk.1	+	c.570G>C	c.(568-570)AAG>AAC	p.K190N	GREB1_uc002rbl.2_Missense_Mutation_p.K190N|GREB1_uc002rbm.2_Missense_Mutation_p.K80N|GREB1_uc002rbn.1_Missense_Mutation_p.K190N	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	190						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		Ovarian(39;850 945 2785 23371 33093)								0.120968	25.7984	43.205425	15	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11716594	11716594	7037	2	G	C	C	C	464	36	GREB1	3	3
GLI2	2736	broad.mit.edu	37	2	121748105	121748105	+	Nonsense_Mutation	SNP	C	T	T	rs34298396		TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:121748105C>T	uc010flp.2	+	c.4615C>T	c.(4615-4617)CAG>TAG	p.Q1539*	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.3_Nonsense_Mutation_p.Q1211*|GLI2_uc002tmu.3_Nonsense_Mutation_p.Q1194*	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1539					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.097561	8.306536	28.258245	12	111	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	121748105	121748105	6706	2	C	T	T	T	273	21	GLI2	5	2
CCDC74A	90557	broad.mit.edu	37	2	132290296	132290296	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:132290296G>T	uc002tta.2	+	c.818G>T	c.(817-819)AGG>ATG	p.R273M	CCDC74A_uc002ttb.2_Missense_Mutation_p.R207M	NM_138770	NP_620125	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	273											0														0.121951	6.744904	12.484928	5	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132290296	132290296	2970	2	G	T	T	T	455	35	CCDC74A	2	2
LRP1B	53353	broad.mit.edu	37	2	141083400	141083400	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141083400C>A	uc002tvj.1	-	c.12271G>T	c.(12271-12273)GAG>TAG	p.E4091*		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4091	Extracellular (Potential).|LDL-receptor class B 36.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)			p.E4091*(NCIH727-Tumor)	2546	TSP Lung(27;0.18)			0.11236	18.476023	44.911482	20	158	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	141083400	141083400	9328	2	C	A	A	A	377	29	LRP1B	5	2
PLA2R1	22925	broad.mit.edu	37	2	160807954	160807954	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:160807954T>C	uc002ube.1	-	c.3437A>G	c.(3436-3438)AAA>AGA	p.K1146R	PLA2R1_uc010zcp.1_Missense_Mutation_p.K1146R|PLA2R1_uc002ubf.2_Missense_Mutation_p.K1146R	NM_007366	NP_031392	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1 isoform 1 precursor	1146	Extracellular (Potential).|C-type lectin 7.				endocytosis	extracellular space|integral to plasma membrane	receptor activity|sugar binding			ovary(1)	1														0.091575	23.385179	69.238918	25	248	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160807954	160807954	12436	2	T	C	C	C	832	64	PLA2R1	4	4
KCNH7	90134	broad.mit.edu	37	2	163253407	163253407	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:163253407C>A	uc002uch.1	-	c.2456G>T	c.(2455-2457)GGA>GTA	p.G819V		NM_033272	NP_150375	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H,	819	Cytoplasmic (Potential).|cNMP.				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity			ovary(3)	3					Ibutilide(DB00308)	GBM(196;1492 2208 17507 24132 45496)								0.207792	102.467837	120.745264	48	183	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	163253407	163253407	8342	2	C	A	A	A	390	30	KCNH7	2	2
CDCA7	83879	broad.mit.edu	37	2	174224139	174224139	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:174224139G>T	uc002uic.1	+	c.304G>T	c.(304-306)GAA>TAA	p.E102*	CDCA7_uc002uid.1_Intron|CDCA7_uc010zej.1_Nonsense_Mutation_p.E58*|CDCA7_uc010zek.1_Intron	NM_031942	NP_114148	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7 isoform 1	Error:Variant_position_missing_in_Q9BWT1_after_alignment					regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.116)											0.056075	-12.15325	10.217044	6	101	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	174224139	174224139	3219	2	G	T	T	T	481	37	CDCA7	5	1
HOXD10	3236	broad.mit.edu	37	2	176981615	176981615	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:176981615G>T	uc002ukj.2	+	c.54G>T	c.(52-54)TTG>TTT	p.L18F		NM_002148	NP_002139	P28358	HXD10_HUMAN	homeobox D10	18						nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)						294				0.064516	-9.408978	15.05821	8	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176981615	176981615	7611	2	G	T	T	T	581	45	HOXD10	2	2
SESTD1	91404	broad.mit.edu	37	2	180014052	180014052	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:180014052C>G	uc002uni.3	-	c.553G>C	c.(553-555)GAT>CAT	p.D185H		NM_178123	NP_835224	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	185					regulation of calcium ion transport via voltage-gated calcium channel activity		phosphatidic acid binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding|protein binding			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)											0.147059	11.862122	15.92198	5	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	180014052	180014052	14615	2	C	G	G	G	377	29	SESTD1	3	3
ITGA4	3676	broad.mit.edu	37	2	182390005	182390005	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:182390005C>G	uc002unu.2	+	c.2326C>G	c.(2326-2328)CTG>GTG	p.L776V	ITGA4_uc010frj.1_Missense_Mutation_p.L258V|ITGA4_uc002unv.2_Missense_Mutation_p.L21V	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	776	Extracellular (Potential).				B cell differentiation|blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)									0.054348	-6.705352	12.552888	5	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182390005	182390005	8182	2	C	G	G	G	363	28	ITGA4	3	3
ZNF804A	91752	broad.mit.edu	37	2	185801561	185801561	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185801561T>A	uc002uph.2	+	c.1438T>A	c.(1438-1440)TTA>ATA	p.L480I		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	480						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.047619	-44.851722	37.487106	18	360	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185801561	185801561	18768	2	T	A	A	A	725	56	ZNF804A	3	3
ITGAV	3685	broad.mit.edu	37	2	187533538	187533538	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:187533538A>T	uc002upq.2	+	c.2483A>T	c.(2482-2484)CAG>CTG	p.Q828L	ITGAV_uc010frs.2_Missense_Mutation_p.Q792L|ITGAV_uc010zfv.1_Missense_Mutation_p.Q782L	NM_002210	NP_002201	P06756	ITAV_HUMAN	integrin alpha-V isoform 1 precursor	828	Extracellular (Potential).				angiogenesis|axon guidance|blood coagulation|cell-matrix adhesion|entry of bacterium into host cell|entry of symbiont into host cell by promotion of host phagocytosis|entry of virus into host cell|ERK1 and ERK2 cascade|integrin-mediated signaling pathway|leukocyte migration|negative regulation of apoptosis|negative regulation of lipid storage|negative regulation of lipid transport|negative regulation of lipoprotein metabolic process|negative regulation of low-density lipoprotein particle receptor biosynthetic process|negative regulation of macrophage derived foam cell differentiation|positive regulation of cell adhesion|positive regulation of cell proliferation|regulation of apoptotic cell clearance	integrin complex	receptor activity|transforming growth factor beta binding			ovary(2)|kidney(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)		Melanoma(58;108 1995 6081)				606				0.125984	47.524907	82.208411	32	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187533538	187533538	8192	2	A	T	T	T	91	7	ITGAV	3	3
CDK15	65061	broad.mit.edu	37	2	202677286	202677286	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:202677286G>T	uc002uyt.2	+	c.448_splice	c.e4+1	p.A150_splice	CDK15_uc010ftm.2_Splice_Site_SNP_p.A15_splice|CDK15_uc002uys.2_Splice_Site_SNP_p.A99_splice|CDK15_uc010ftn.1_Splice_Site_SNP_p.A99_splice|CDK15_uc010fto.1_Splice_Site_SNP_p.A150_splice	NM_139158	NP_631897			PFTAIRE protein kinase 2						protein phosphorylation		ATP binding|cyclin-dependent protein kinase activity|metal ion binding|protein binding			breast(2)|ovary(1)|lung(1)|kidney(1)	5					Adenosine triphosphate(DB00171)					431				0.15748	43.31508	57.526801	20	107	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	202677286	202677286	3260	2	G	T	T	T	572	44	CDK15	5	2
CYP20A1	57404	broad.mit.edu	37	2	204154501	204154501	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:204154501G>T	uc010zif.1	+	c.1009G>T	c.(1009-1011)GTG>TTG	p.V337L	CYP20A1_uc002uzv.3_Missense_Mutation_p.V329L|CYP20A1_uc002uzx.3_Missense_Mutation_p.V227L|CYP20A1_uc002uzy.3_Missense_Mutation_p.V227L|CYP20A1_uc002uzw.3_Non-coding_Transcript|CYP20A1_uc010ftw.2_Missense_Mutation_p.V59L	NM_177538	NP_803882	Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A,	329					oxidation-reduction process	integral to membrane	electron carrier activity|heme binding|monooxygenase activity				0														0.044643	-15.022504	9.821325	5	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204154501	204154501	4317	2	G	T	T	T	624	48	CYP20A1	2	2
PTH2R	5746	broad.mit.edu	37	2	209358218	209358218	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:209358218T>A	uc010zjb.1	+	c.1520T>A	c.(1519-1521)GTC>GAC	p.V507D	PTH2R_uc002vdb.2_Missense_Mutation_p.V496D|PTH2R_uc010fuo.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor	496	Cytoplasmic (Potential).					integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)	1				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)										0.097744	5.178013	26.734911	13	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209358218	209358218	13215	2	T	A	A	A	754	58	PTH2R	3	3
APOB	338	broad.mit.edu	37	2	21234204	21234204	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21234204C>A	uc002red.2	-	c.5536G>T	c.(5536-5538)GCC>TCC	p.A1846S		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	1846					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)									0.151862	84.057424	124.641904	53	296	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21234204	21234204	796	2	C	A	A	A	325	25	APOB	2	2
APOB	338	broad.mit.edu	37	2	21242677	21242677	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:21242677G>T	uc002red.2	-	c.2917C>A	c.(2917-2919)CTG>ATG	p.L973M		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	973					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)									0.161572	65.335396	90.2833	37	192	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21242677	21242677	796	2	G	T	T	T	451	35	APOB	2	2
ABCA12	26154	broad.mit.edu	37	2	215818780	215818780	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:215818780G>T	uc002vew.2	-	c.6445C>A	c.(6445-6447)CAA>AAA	p.Q2149K	ABCA12_uc002vev.2_Missense_Mutation_p.Q1831K|ABCA12_uc010zjn.1_Missense_Mutation_p.Q1076K	NM_173076	NP_775099	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A, member 12	2149					cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity			ovary(6)|breast(1)|central_nervous_system(1)|pancreas(1)	9		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		Ovarian(66;664 1488 5121 34295)								0.046392	-22.898713	19.68416	9	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215818780	215818780	31	2	G	T	T	T	624	48	ABCA12	2	2
TNS1	7145	broad.mit.edu	37	2	218683451	218683451	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:218683451T>C	uc002vgt.2	-	c.3292A>G	c.(3292-3294)AGC>GGC	p.S1098G	TNS1_uc002vgr.2_Missense_Mutation_p.S1085G|TNS1_uc002vgs.2_Missense_Mutation_p.S1077G|TNS1_uc010zjv.1_Missense_Mutation_p.S1077G	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1098	Ser-rich.					cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)										0.084112	0.519416	19.330616	9	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	218683451	218683451	16884	2	T	C	C	C	702	54	TNS1	4	4
CXCR2	3579	broad.mit.edu	37	2	218999752	218999752	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:218999752C>G	uc002vgz.1	+	c.228C>G	c.(226-228)AGC>AGG	p.S76R	CXCR2_uc002vha.1_Missense_Mutation_p.S76R|CXCR2_uc002vhb.1_Missense_Mutation_p.S76R	NM_001557	NP_001548	P25025	CXCR2_HUMAN	interleukin 8 receptor beta	76	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|cellular defense response|dendritic cell chemotaxis|inflammatory response|neutrophil activation|neutrophil chemotaxis|positive regulation of cell proliferation	cell surface|integral to plasma membrane|mast cell granule	interleukin-8 receptor activity			lung(1)	1										62				0.044304	-19.665872	15.412668	7	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	218999752	218999752	4251	2	C	G	G	G	324	25	CXCR2	3	3
MFF	56947	broad.mit.edu	37	2	228212018	228212018	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228212018G>T	uc002vos.2	+	c.670G>T	c.(670-672)GCT>TCT	p.A224S	MFF_uc002vot.2_Missense_Mutation_p.A173S|MFF_uc002vou.2_Intron|MFF_uc002vov.2_Intron|MFF_uc002vow.2_Intron|MFF_uc002vox.2_Intron|MFF_uc002voy.2_Missense_Mutation_p.A224S|MFF_uc002voz.2_Intron|MFF_uc002vpa.2_Missense_Mutation_p.A12S	NM_020194	NP_064579	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	224	Cytoplasmic (Potential).					integral to membrane|mitochondrial outer membrane				large_intestine(1)	1														0.060606	-20.031701	26.686476	14	217	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228212018	228212018	9909	2	G	T	T	T	598	46	MFF	2	2
C2orf57	165100	broad.mit.edu	37	2	232457843	232457843	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:232457843G>T	uc002vrz.2	+	c.181G>T	c.(181-183)GCC>TCC	p.A61S		NM_152614	NP_689827	Q53QW1	CB057_HUMAN	hypothetical protein LOC165100	61										ovary(1)	1		Renal(207;0.025)|all_hematologic(139;0.0735)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;1.33e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)										0.188889	30.460952	38.588684	17	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232457843	232457843	2266	2	G	T	T	T	546	42	C2orf57	2	2
UGT1A9	54600	broad.mit.edu	37	2	234581303	234581303	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:234581303G>T	uc002vus.2	+	c.723G>T	c.(721-723)GAG>GAT	p.E241D	UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Intron|UGT1A10_uc002vur.2_Intron|UGT1A9_uc010zmw.1_Missense_Mutation_p.E241D	NM_021027	NP_066307	O60656	UD19_HUMAN	UDP glycosyltransferase 1 family, polypeptide A9	241					drug metabolic process|flavone metabolic process|negative regulation of fatty acid metabolic process|retinoic acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	enzyme binding|enzyme inhibitor activity|glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|retinoic acid binding			ovary(3)|breast(1)	4		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Entacapone(DB00494)|Etodolac(DB00749)|Indomethacin(DB00328)|Irinotecan(DB00762)|Mycophenolic acid(DB01024)|Oxyphenonium(DB00219)|Propofol(DB00818)|Sorafenib(DB00398)									0.044811	-116.386043	71.270878	38	810	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	234581303	234581303	17510	2	G	T	T	T	464	36	UGT1A9	2	2
ANKMY1	51281	broad.mit.edu	37	2	241448843	241448843	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241448843T>C	uc010fzd.1	-	c.2316A>G	c.(2314-2316)CTA>CTG	p.L772L	ANKMY1_uc002vyz.1_Silent_p.L683L|ANKMY1_uc002vza.1_Intron|ANKMY1_uc002vzb.1_Silent_p.L444L|ANKMY1_uc002vzc.1_Intron|ANKMY1_uc002vzd.1_Intron	NM_016552	NP_057636	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	683	ANK 5.						zinc ion binding			central_nervous_system(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)										0.153846	9.585887	12.561722	4	22	KEEP	---	---	---	---	capture		Silent	SNP	241448843	241448843	637	2	T	C	C	C	626	49	ANKMY1	4	4
DNMT3A	1788	broad.mit.edu	37	2	25469966	25469966	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:25469966T>C	uc002rgc.2	-	c.1076A>G	c.(1075-1077)TAC>TGC	p.Y359C	DNMT3A_uc002rgd.2_Missense_Mutation_p.Y359C|DNMT3A_uc010eyi.2_Non-coding_Transcript|DNMT3A_uc002rgb.2_Missense_Mutation_p.Y170C	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	359	Interaction with DNMT1 and DNMT3B.				regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|protein binding|zinc ion binding			haematopoietic_and_lymphoid_tissue(107)|ovary(3)	110	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.2	17.006128	19.935669	7	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25469966	25469966	4859	2	T	C	C	C	741	57	DNMT3A	4	4
XDH	7498	broad.mit.edu	37	2	31595228	31595228	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:31595228C>A	uc002rnv.1	-	c.1722G>T	c.(1720-1722)GTG>GTT	p.V574V		NM_000379	NP_000370	P47989	XDH_HUMAN	xanthine dehydrogenase	574					oxidation-reduction process|purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity			breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	5	Acute lymphoblastic leukemia(172;0.155)				Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)	Colon(66;682 1445 30109 40147)								0.173913	58.467247	76.974202	32	152	KEEP	---	---	---	---	capture		Silent	SNP	31595228	31595228	18007	2	C	A	A	A	262	21	XDH	2	2
MAP4K3	8491	broad.mit.edu	37	2	39515294	39515294	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:39515294G>A	uc002rro.2	-	c.1442C>T	c.(1441-1443)CCC>CTC	p.P481L	MAP4K3_uc002rrp.2_Missense_Mutation_p.P460L|MAP4K3_uc010yns.1_Missense_Mutation_p.P34L	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	481					JNK cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|pancreas(1)	7		all_hematologic(82;0.211)							p.P481L(HCC4006-Tumor)	525				0.178161	60.511811	77.500533	31	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39515294	39515294	9644	2	G	A	A	A	559	43	MAP4K3	2	2
SPTBN1	6711	broad.mit.edu	37	2	54852008	54852008	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:54852008A>C	uc002rxu.2	+	c.1250A>C	c.(1249-1251)CAG>CCG	p.Q417P	SPTBN1_uc002rxv.1_Missense_Mutation_p.Q417P|SPTBN1_uc002rxx.2_Missense_Mutation_p.Q404P	NM_003128	NP_003119	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1 isoform 1	417	Spectrin 2.				actin filament capping|axon guidance	cytosol|nucleolus|plasma membrane|sarcomere|spectrin	actin binding|calmodulin binding|protein binding|structural constituent of cytoskeleton			ovary(2)|breast(2)|central_nervous_system(2)	6			Lung(47;0.24)											0.2	39.606791	47.651667	19	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54852008	54852008	15633	2	A	C	C	C	91	7	SPTBN1	4	4
RSAD2	91543	broad.mit.edu	37	2	7018220	7018220	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:7018220T>G	uc002qyp.1	+	c.289T>G	c.(289-291)TCC>GCC	p.S97A		NM_080657	NP_542388	Q8WXG1	RSAD2_HUMAN	radical S-adenosyl methionine domain containing	97					defense response to virus	endoplasmic reticulum membrane|Golgi apparatus	catalytic activity|iron-sulfur cluster binding|metal ion binding				0	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)										0.145161	18.356326	25.846318	9	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7018220	7018220	14175	2	T	G	G	G	650	50	RSAD2	4	4
TIA1	7072	broad.mit.edu	37	2	70457967	70457967	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:70457967T>C	uc002sgj.3	-	c.143A>G	c.(142-144)TAT>TGT	p.Y48C	TIA1_uc002sgk.3_Missense_Mutation_p.Y48C|TIA1_uc002sgl.3_Non-coding_Transcript|TIA1_uc002sgm.3_Missense_Mutation_p.Y48C|TIA1_uc010yqt.1_Missense_Mutation_p.Y48C	NM_022173	NP_071505	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding	48	RRM 1.				apoptosis|induction of apoptosis|regulation of nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|poly(A) RNA binding|protein binding				0														0.06087	-4.155523	18.988505	7	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70457967	70457967	16415	2	T	C	C	C	637	49	TIA1	4	4
DYSF	8291	broad.mit.edu	37	2	71747970	71747970	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71747970C>T	uc010fen.2	+	c.1085C>T	c.(1084-1086)TCT>TTT	p.S362F	DYSF_uc010feg.2_Missense_Mutation_p.S361F|DYSF_uc010feh.2_Missense_Mutation_p.S330F|DYSF_uc002sig.3_Missense_Mutation_p.S330F|DYSF_uc010yqx.1_Non-coding_Transcript|DYSF_uc010fee.2_Missense_Mutation_p.S330F|DYSF_uc010fef.2_Missense_Mutation_p.S361F|DYSF_uc002sie.2_Missense_Mutation_p.S330F|DYSF_uc010fei.2_Missense_Mutation_p.S361F|DYSF_uc010fek.2_Missense_Mutation_p.S362F|DYSF_uc010fej.2_Missense_Mutation_p.S331F|DYSF_uc010fel.2_Missense_Mutation_p.S331F|DYSF_uc010feo.2_Missense_Mutation_p.S362F|DYSF_uc010fem.2_Missense_Mutation_p.S331F|DYSF_uc002sif.2_Missense_Mutation_p.S331F	NM_001130987	NP_001124459	O75923	DYSF_HUMAN	dysferlin isoform 1	330	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.053763	-7.8061	11.729373	5	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71747970	71747970	5045	2	C	T	T	T	416	32	DYSF	2	2
C2orf65	130951	broad.mit.edu	37	2	74867251	74867251	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:74867251A>G	uc002smy.2	-	c.152T>C	c.(151-153)CTA>CCA	p.L51P	C2orf65_uc010ysa.1_Missense_Mutation_p.L51P|C2orf65_uc002smz.2_Missense_Mutation_p.L51P	NM_138804	NP_620159	Q8TC57	CB065_HUMAN	hypothetical protein LOC130951	51					chromatin assembly|female gamete generation|RNA processing|spermatogenesis	integral to membrane				ovary(1)|pancreas(1)	2														0.191781	35.109454	41.585901	14	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74867251	74867251	2272	2	A	G	G	G	195	15	C2orf65	4	4
IMMT	10989	broad.mit.edu	37	2	86371860	86371860	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86371860C>T	uc002sqz.3	-	c.1808G>A	c.(1807-1809)TGT>TAT	p.C603Y	IMMT_uc002sqy.3_Missense_Mutation_p.C344Y|IMMT_uc002srb.3_Missense_Mutation_p.C592Y|IMMT_uc002sra.3_Missense_Mutation_p.C602Y|IMMT_uc010ytd.1_Missense_Mutation_p.C591Y|IMMT_uc010yte.1_Missense_Mutation_p.C556Y	NM_006839	NP_006830	Q16891	IMMT_HUMAN	inner membrane protein, mitochondrial isoform 1	603	Mitochondrial intermembrane (Potential).					integral to mitochondrial inner membrane	protein binding			skin(1)	1														0.168605	49.818522	67.671873	29	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86371860	86371860	8019	2	C	T	T	T	221	17	IMMT	2	2
ACTR1B	10120	broad.mit.edu	37	2	98274560	98274560	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98274560C>A	uc002syb.2	-	c.771G>T	c.(769-771)CGG>CGT	p.R257R		NM_005735	NP_005726	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B,	257						dynactin complex|microtubule organizing center	ATP binding|protein binding				0														0.1	1.818498	8.171577	4	36	KEEP	---	---	---	---	capture		Silent	SNP	98274560	98274560	211	2	C	A	A	A	275	22	ACTR1B	2	2
IMPG2	50939	broad.mit.edu	37	3	100949991	100949991	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:100949991T>A	uc003duq.1	-	c.3234_splice	c.e16-1	p.R1078_splice	IMPG2_uc011bhe.1_Splice_Site_SNP_p.R941_splice|IMPG2_uc010hpj.1_Intron	NM_016247	NP_057331			interphotoreceptor matrix proteoglycan 2						visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3														0.186567	56.524078	68.835676	25	109	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	100949991	100949991	8030	3	T	A	A	A	715	55	IMPG2	5	3
ATP2B2	491	broad.mit.edu	37	3	10392086	10392086	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10392086C>A	uc003bvt.2	-	c.2312G>T	c.(2311-2313)GGG>GTG	p.G771V	ATP2B2_uc003bvv.2_Missense_Mutation_p.G726V|ATP2B2_uc003bvw.2_Missense_Mutation_p.G726V|ATP2B2_uc010hdo.2_Missense_Mutation_p.G476V	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	771	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|central_nervous_system(1)	4						Ovarian(125;1619 1709 15675 19819 38835)								0.192308	9.458008	11.759807	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10392086	10392086	1159	3	C	A	A	A	286	22	ATP2B2	2	2
CBLB	868	broad.mit.edu	37	3	105400431	105400431	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:105400431C>A	uc003dwc.2	-	c.2320G>T	c.(2320-2322)GAT>TAT	p.D774Y	CBLB_uc003dwa.2_Intron|CBLB_uc011bhi.1_Intron|CBLB_uc003dwd.1_Missense_Mutation_p.D774Y|CBLB_uc003dwe.1_3'UTR	NM_170662	NP_733762	Q13191	CBLB_HUMAN	Cas-Br-M (murine) ecotropic retroviral	774	Pro-rich.				cell surface receptor linked signaling pathway|NLS-bearing substrate import into nucleus	cytoplasm|nucleus	calcium ion binding|ligase activity|signal transducer activity|zinc ion binding			ovary(3)|lung(2)|skin(1)	6						GBM(93;588 1337 9788 29341 43499)								0.08	-0.835236	39.663676	18	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105400431	105400431	2820	3	C	A	A	A	377	29	CBLB	2	2
DZIP3	9666	broad.mit.edu	37	3	108327004	108327004	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108327004T>A	uc003dxd.2	+	c.101T>A	c.(100-102)CTG>CAG	p.L34Q	DZIP3_uc003dxf.1_Missense_Mutation_p.L34Q|DZIP3_uc011bhm.1_5'UTR|DZIP3_uc003dxe.1_Missense_Mutation_p.L34Q	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	34	Potential.				protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.064286	-5.923776	21.693285	9	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108327004	108327004	5051	3	T	A	A	A	715	55	DZIP3	3	3
PHLDB2	90102	broad.mit.edu	37	3	111688727	111688727	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:111688727G>A	uc010hqa.2	+	c.3506G>A	c.(3505-3507)CGG>CAG	p.R1169Q	PHLDB2_uc003dyc.2_Missense_Mutation_p.R1153Q|PHLDB2_uc003dyd.2_Missense_Mutation_p.R1126Q|PHLDB2_uc003dyg.2_Missense_Mutation_p.R1169Q|PHLDB2_uc003dyh.2_Missense_Mutation_p.R1126Q|PHLDB2_uc003dyi.2_Missense_Mutation_p.R660Q|PHLDB2_uc003dyj.2_Missense_Mutation_p.R224Q	NM_001134438	NP_001127910	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B,	1169	PH.					cytoplasm|intermediate filament cytoskeleton|plasma membrane				ovary(4)	4														0.110714	39.246261	81.100467	31	249	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111688727	111688727	12276	3	G	A	A	A	507	39	PHLDB2	1	1
WDR52	55779	broad.mit.edu	37	3	113120584	113120584	+	Silent	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113120584T>A	uc003eae.1	-	c.1173A>T	c.(1171-1173)ATA>ATT	p.I391I		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	391	WD 4.									central_nervous_system(1)	1														0.082803	1.625715	29.351467	13	144	KEEP	---	---	---	---	capture		Silent	SNP	113120584	113120584	17877	3	T	A	A	A	628	49	WDR52	3	3
ATG7	10533	broad.mit.edu	37	3	11348421	11348421	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:11348421G>T	uc003bwc.2	+	c.220G>T	c.(220-222)GCT>TCT	p.A74S	ATG7_uc003bwd.2_Missense_Mutation_p.A74S|ATG7_uc011aum.1_Missense_Mutation_p.A74S	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	74					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1														0.12987	51.108722	92.171131	40	268	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11348421	11348421	1120	3	G	T	T	T	598	46	ATG7	2	2
ZNF80	7634	broad.mit.edu	37	3	113955551	113955551	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113955551C>G	uc010hqo.2	-	c.371G>C	c.(370-372)CGC>CCC	p.R124P	ZNF80_uc003ebf.2_Non-coding_Transcript	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	124	C2H2-type 3; atypical.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				GBM(23;986 1114 21716)								0.2	26.795976	31.397994	11	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113955551	113955551	18766	3	C	G	G	G	351	27	ZNF80	3	3
COL6A6	131873	broad.mit.edu	37	3	130293296	130293296	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130293296G>T	uc010htl.2	+	c.3474G>T	c.(3472-3474)GTG>GTT	p.V1158V		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	1158	Nonhelical region.|VWFA 6.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.069307	-5.152608	14.206823	7	94	KEEP	---	---	---	---	capture		Silent	SNP	130293296	130293296	3841	3	G	T	T	T	587	46	COL6A6	2	2
DZIP1L	199221	broad.mit.edu	37	3	137813704	137813704	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:137813704C>A	uc003erq.2	-	c.708G>T	c.(706-708)CAG>CAT	p.Q236H	DZIP1L_uc003err.1_Missense_Mutation_p.Q236H	NM_173543	NP_775814	Q8IYY4	DZI1L_HUMAN	DAZ interacting protein 1-like	236	Potential.					intracellular	zinc ion binding			ovary(1)|pancreas(1)	2														0.08642	4.681066	32.69999	14	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137813704	137813704	5050	3	C	A	A	A	311	24	DZIP1L	2	2
CEP70	80321	broad.mit.edu	37	3	138289206	138289206	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:138289206T>C	uc003esl.2	-	c.419A>G	c.(418-420)CAA>CGA	p.Q140R	CEP70_uc011bmk.1_Missense_Mutation_p.Q120R|CEP70_uc011bml.1_Missense_Mutation_p.Q122R|CEP70_uc011bmm.1_Intron|CEP70_uc003esm.2_Missense_Mutation_p.Q140R|CEP70_uc003esn.2_Missense_Mutation_p.Q140R	NM_024491	NP_077817	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70 kDa	140	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center	protein binding				0														0.105528	22.832275	53.601961	21	178	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138289206	138289206	3392	3	T	C	C	C	819	63	CEP70	4	4
WNT7A	7476	broad.mit.edu	37	3	13916571	13916571	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:13916571G>T	uc003bye.1	-	c.171C>A	c.(169-171)GAC>GAA	p.D57E		NM_004625	NP_004616	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family,	57					activation of JUN kinase activity|anterior/posterior pattern formation|canonical Wnt receptor signaling pathway|cell proliferation in forebrain|cellular response to transforming growth factor beta stimulus|central nervous system vasculogenesis|cerebellar granule cell differentiation|dorsal/ventral pattern formation|embryonic axis specification|embryonic digit morphogenesis|embryonic forelimb morphogenesis|embryonic leg morphogenesis|lens fiber cell development|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neurogenesis|palate development|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of JNK cascade|positive regulation of synaptogenesis|regulation of axon diameter|satellite cell activation|satellite cell maintenance involved in skeletal muscle regeneration|sex differentiation|uterus development|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	cytokine activity|frizzled binding|receptor agonist activity|signal transducer activity			ovary(2)	2														0.139535	21.966129	32.73866	12	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13916571	13916571	17968	3	G	T	T	T	516	40	WNT7A	1	1
PLOD2	5352	broad.mit.edu	37	3	145828089	145828089	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:145828089C>G	uc003evr.1	-	c.485G>C	c.(484-486)CGC>CCC	p.R162P	PLOD2_uc011bnm.1_Missense_Mutation_p.R107P|PLOD2_uc003evs.1_Missense_Mutation_p.R162P	NM_182943	NP_891988	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase	162					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)									0.037594	-39.049455	22.378231	10	256	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145828089	145828089	12528	3	C	G	G	G	351	27	PLOD2	3	3
CPB1	1360	broad.mit.edu	37	3	148563381	148563381	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:148563381G>T	uc003ewl.2	+	c.949G>T	c.(949-951)GCT>TCT	p.A317S		NM_001871	NP_001862	P15086	CBPB1_HUMAN	pancreatic carboxypeptidase B1 preproprotein	317					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)											0.128049	28.855856	50.973836	21	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148563381	148563381	3934	3	G	T	T	T	598	46	CPB1	2	2
MED12L	116931	broad.mit.edu	37	3	151094924	151094924	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151094924A>G	uc003eyp.2	+	c.4169A>G	c.(4168-4170)GAT>GGT	p.D1390G	MED12L_uc011bnz.1_Missense_Mutation_p.D1250G|P2RY12_uc011boa.1_Intron|P2RY12_uc003eyx.1_Intron|MED12L_uc003eyy.1_Missense_Mutation_p.D553G	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	1390					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				0.224	76.8425	85.588075	28	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151094924	151094924	9818	3	A	G	G	G	156	12	MED12L	4	4
MBNL1	4154	broad.mit.edu	37	3	152132887	152132887	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:152132887C>T	uc003ezm.2	+	c.332C>T	c.(331-333)CCA>CTA	p.P111L	MBNL1_uc003ezh.2_Missense_Mutation_p.P111L|MBNL1_uc003ezi.2_Missense_Mutation_p.P111L|MBNL1_uc003ezj.2_Missense_Mutation_p.P54L|MBNL1_uc003ezl.2_Missense_Mutation_p.P111L|MBNL1_uc003ezp.2_Missense_Mutation_p.P111L|MBNL1_uc003ezn.2_Missense_Mutation_p.P111L|MBNL1_uc003ezo.2_Missense_Mutation_p.P111L|MBNL1_uc010hvp.2_Missense_Mutation_p.P19L	NM_207293	NP_997176	Q9NR56	MBNL1_HUMAN	muscleblind-like 1 isoform c	111					embryonic limb morphogenesis|in utero embryonic development|myoblast differentiation|nervous system development	nucleus|stress granule	double-stranded RNA binding|protein binding|zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)											0.107692	10.556644	30.405835	14	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152132887	152132887	9741	3	C	T	T	T	273	21	MBNL1	2	2
RAP2B	5912	broad.mit.edu	37	3	152880634	152880634	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:152880634C>T	uc003ezr.2	+	c.152C>T	c.(151-153)TCG>TTG	p.S51L		NM_002886	NP_002877	P61225	RAP2B_HUMAN	RAP2B, member of RAS oncogene family precursor	51					Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity			lung(2)	2			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)											0.133333	8.219364	14.091431	6	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152880634	152880634	13501	3	C	T	T	T	403	31	RAP2B	1	1
MME	4311	broad.mit.edu	37	3	154834521	154834521	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:154834521G>T	uc010hvr.1	+	c.508G>T	c.(508-510)GCA>TCA	p.A170S	MME_uc003fab.1_Missense_Mutation_p.A170S|MME_uc003fac.1_Missense_Mutation_p.A170S|MME_uc003fad.1_Missense_Mutation_p.A170S|MME_uc003fae.1_Missense_Mutation_p.A170S	NM_007289	NP_009220	P08473	NEP_HUMAN	membrane metallo-endopeptidase	170	Extracellular (Potential).				cell-cell signaling|proteolysis	integral to plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(2)|central_nervous_system(1)	3		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)									0.115578	25.807439	54.747519	23	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154834521	154834521	10035	3	G	T	T	T	442	34	MME	2	2
PLCH1	23007	broad.mit.edu	37	3	155211953	155211953	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:155211953A>G	uc011bok.1	-	c.2123T>C	c.(2122-2124)CTC>CCC	p.L708P	PLCH1_uc011boj.1_Missense_Mutation_p.L708P|PLCH1_uc011bol.1_Missense_Mutation_p.L690P	NM_001130960	NP_001124432	Q4KWH8	PLCH1_HUMAN	phospholipase C eta 1 isoform a	708	PI-PLC Y-box.				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)											0.086957	8.20427	28.022624	10	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155211953	155211953	12463	3	A	G	G	G	143	11	PLCH1	4	4
OTOL1	131149	broad.mit.edu	37	3	161217016	161217016	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:161217016C>T	uc011bpb.1	+	c.422C>T	c.(421-423)CCC>CTC	p.P141L		NM_001080440	NP_001073909	A6NHN0	OTOL1_HUMAN	otolin-1 precursor	141	Collagen-like 1.					collagen					0														0.135135	8.069401	12.826667	5	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161217016	161217016	11716	3	C	T	T	T	286	22	OTOL1	2	2
OTOL1	131149	broad.mit.edu	37	3	161221575	161221575	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:161221575G>T	uc011bpb.1	+	c.1279G>T	c.(1279-1281)GCC>TCC	p.A427S		NM_001080440	NP_001073909	A6NHN0	OTOL1_HUMAN	otolin-1 precursor	427	C1q.					collagen					0														0.126126	15.274507	30.431983	14	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161221575	161221575	11716	3	G	T	T	T	546	42	OTOL1	2	2
DAZL	1618	broad.mit.edu	37	3	16638346	16638346	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:16638346G>A	uc003cba.2	-	c.469C>T	c.(469-471)CCA>TCA	p.P157S	DAZL_uc003cbb.2_Missense_Mutation_p.P137S	NM_001351	NP_001342	Q92904	DAZL_HUMAN	deleted in azoospermia-like	137					germ cell development|multicellular organismal development|positive regulation of translational initiation|spermatogenesis	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding|translation activator activity				0														0.121795	21.14505	42.982263	19	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16638346	16638346	4417	3	G	A	A	A	572	44	DAZL	2	2
WDR49	151790	broad.mit.edu	37	3	167272528	167272528	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:167272528A>T	uc003fev.1	-	c.710T>A	c.(709-711)GTG>GAG	p.V237E	WDR49_uc003feu.1_Missense_Mutation_p.V62E|WDR49_uc011bpd.1_Missense_Mutation_p.V290E|WDR49_uc003few.1_Intron	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	237										large_intestine(1)|ovary(1)	2														0.068536	-10.02115	51.88673	22	299	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167272528	167272528	17875	3	A	T	T	T	78	6	WDR49	3	3
SAMD7	344658	broad.mit.edu	37	3	169644499	169644499	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:169644499T>A	uc003fgd.2	+	c.449T>A	c.(448-450)CTG>CAG	p.L150Q	SAMD7_uc003fge.2_Missense_Mutation_p.L150Q|SAMD7_uc011bpo.1_Missense_Mutation_p.L51Q	NM_182610	NP_872416	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	150										skin(1)	1	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)											0.065693	-5.622939	21.181842	9	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169644499	169644499	14304	3	T	A	A	A	715	55	SAMD7	3	3
NDUFB5	4711	broad.mit.edu	37	3	179336201	179336201	+	Splice_Site_SNP	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:179336201A>T	uc003fkc.2	+	c.343_splice	c.e5-2	p.H115_splice	NDUFB5_uc003fkd.2_Splice_Site_SNP|NDUFB5_uc003fke.2_Splice_Site_SNP_p.H63_splice	NM_002492	NP_002483			NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	integral to membrane|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)		NADH(DB00157)									0.169014	23.957764	31.319732	12	59	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	179336201	179336201	10683	3	A	T	T	T	195	15	NDUFB5	5	3
SATB1	6304	broad.mit.edu	37	3	18390976	18390976	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:18390976G>T	uc003cbi.2	-	c.2074C>A	c.(2074-2076)CAG>AAG	p.Q692K	SATB1_uc003cbh.2_Missense_Mutation_p.Q660K|SATB1_uc003cbj.2_Missense_Mutation_p.Q660K	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	660	Homeobox.				cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			ovary(1)|lung(1)|skin(1)	3														0.153465	48.159706	71.447038	31	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18390976	18390976	14334	3	G	T	T	T	611	47	SATB1	2	2
DGKG	1608	broad.mit.edu	37	3	186015948	186015948	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:186015948C>T	uc003fqa.2	-	c.215G>A	c.(214-216)AGC>AAC	p.S72N	DGKG_uc003fqb.2_Missense_Mutation_p.S72N|DGKG_uc003fqc.2_Missense_Mutation_p.S72N|DGKG_uc011brx.1_Missense_Mutation_p.S72N	NM_001346	NP_001337	P49619	DGKG_HUMAN	diacylglycerol kinase gamma isoform 1	72					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			breast(2)|central_nervous_system(1)|skin(1)	4	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)					546				0.076433	-4.036835	24.926041	12	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186015948	186015948	4648	3	C	T	T	T	364	28	DGKG	2	2
LEPREL1	55214	broad.mit.edu	37	3	189681780	189681780	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:189681780C>A	uc011bsk.1	-	c.2001G>T	c.(1999-2001)CTG>CTT	p.L667L	LEPREL1_uc003fsg.2_Silent_p.L486L	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a	667	Fe2OG dioxygenase.				negative regulation of cell proliferation|oxidation-reduction process	endoplasmic reticulum|Golgi apparatus	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-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)									0.088608	3.106291	30.247019	14	144	KEEP	---	---	---	---	capture		Silent	SNP	189681780	189681780	9054	3	C	A	A	A	210	17	LEPREL1	2	2
PYDC2	152138	broad.mit.edu	37	3	191179090	191179090	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:191179090G>T	uc011bso.1	+	c.139G>T	c.(139-141)GTA>TTA	p.V47L		NM_001083308	NP_001076777	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	47	DAPIN.					cytoplasm|nucleus					0														0.092025	4.815649	32.128463	15	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	191179090	191179090	13317	3	G	T	T	T	572	44	PYDC2	2	2
KCNH8	131096	broad.mit.edu	37	3	19384093	19384093	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:19384093A>T	uc003cbk.1	+	c.457A>T	c.(457-459)AGA>TGA	p.R153*	KCNH8_uc011awe.1_Nonsense_Mutation_p.R153*|KCNH8_uc010hex.1_De_novo_Start_InFrame	NM_144633	NP_653234	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H,	153	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	two-component sensor activity			ovary(1)	1						NSCLC(124;1625 1765 8018 24930 42026)								0.163462	32.214726	43.401169	17	87	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	19384093	19384093	8343	3	A	T	T	T	36	3	KCNH8	5	3
UBXN7	26043	broad.mit.edu	37	3	196088762	196088762	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:196088762C>T	uc003fwm.3	-	c.1261G>A	c.(1261-1263)GAT>AAT	p.D421N	UBXN7_uc003fwn.3_Missense_Mutation_p.D273N|UBXN7_uc010iae.2_Missense_Mutation_p.D259N	NM_015562	NP_056377	O94888	UBXN7_HUMAN	UBX domain containing 7	421	UBX.						protein binding			ovary(2)|pancreas(1)	3														0.111702	24.32983	52.348542	21	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196088762	196088762	17476	3	C	T	T	T	416	32	UBXN7	2	2
DCLK3	85443	broad.mit.edu	37	3	36779986	36779986	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36779986C>T	uc003cgi.2	-	c.165G>A	c.(163-165)GGG>GGA	p.G55G		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	55					protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8										128				0.171779	54.639637	71.214218	28	135	KEEP	---	---	---	---	capture		Silent	SNP	36779986	36779986	4464	3	C	T	T	T	275	22	DCLK3	2	2
DLEC1	9940	broad.mit.edu	37	3	38158563	38158563	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38158563C>A	uc003chp.1	+	c.4277C>A	c.(4276-4278)GCC>GAC	p.A1426D	DLEC1_uc003cho.1_Missense_Mutation_p.A1426D|DLEC1_uc010hgv.1_Missense_Mutation_p.A1429D|DLEC1_uc003chr.1_Missense_Mutation_p.A497D|DLEC1_uc010hgx.1_Non-coding_Transcript|DLEC1_uc003chs.1_5'UTR	NM_007337	NP_031363	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform	1426					negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|breast(1)|skin(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)										0.109091	20.417844	61.915757	30	245	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38158563	38158563	4732	3	C	A	A	A	338	26	DLEC1	2	2
ULK4	54986	broad.mit.edu	37	3	41746639	41746639	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:41746639C>A	uc003ckv.3	-	c.2691G>T	c.(2689-2691)CTG>CTT	p.L897L		NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	897					protein phosphorylation		ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)						538				0.098901	8.899278	38.211822	18	164	KEEP	---	---	---	---	capture		Silent	SNP	41746639	41746639	17536	3	C	A	A	A	366	29	ULK4	2	2
CCR3	1232	broad.mit.edu	37	3	46307221	46307221	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:46307221C>G	uc003cpl.1	+	c.671C>G	c.(670-672)ACA>AGA	p.T224R	CCR3_uc003cpg.1_Missense_Mutation_p.T191R|CCR3_uc003cpi.1_Missense_Mutation_p.T191R|CCR3_uc003cpj.1_Missense_Mutation_p.T191R|CCR3_uc003cpk.1_Missense_Mutation_p.T212R|CCR3_uc010hjb.1_Missense_Mutation_p.T209R	NM_178329	NP_847899	P51677	CCR3_HUMAN	CC chemokine receptor 3 isoform 1	191	Extracellular (Potential).				cell adhesion|cellular defense response|chemotaxis|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|inflammatory response|interspecies interaction between organisms|positive regulation of angiogenesis	integral to plasma membrane				ovary(2)|kidney(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)						19				0.091912	23.762434	69.382222	25	247	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46307221	46307221	3069	3	C	G	G	G	221	17	CCR3	3	3
COL7A1	1294	broad.mit.edu	37	3	48620455	48620455	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48620455C>A	uc003ctz.2	-	c.4509G>T	c.(4507-4509)GCG>GCT	p.A1503A		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1503	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(2)	9				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.133333	8.826861	14.692396	6	39	KEEP	---	---	---	---	capture		Silent	SNP	48620455	48620455	3842	3	C	A	A	A	288	23	COL7A1	1	1
TMEM89	440955	broad.mit.edu	37	3	48658432	48658432	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:48658432C>A	uc011bbo.1	-	c.323G>T	c.(322-324)GGA>GTA	p.G108V		NM_001008269	NP_001008270	A2RUT3	TMM89_HUMAN	transmembrane protein 89 precursor	108	Cytoplasmic (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)										0.121212	3.776393	8.418907	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48658432	48658432	16753	3	C	A	A	A	390	30	TMEM89	2	2
MST1R	4486	broad.mit.edu	37	3	49935063	49935063	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49935063C>A	uc003cxy.3	-	c.1936G>T	c.(1936-1938)GGC>TGC	p.G646C	MST1R_uc011bdd.1_Missense_Mutation_p.G646C|MST1R_uc011bdc.1_5'Flank	NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	646	IPT/TIG 1.|Extracellular (Potential).				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|protein phosphorylation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)						205				0.1875	6.015399	7.478767	3	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49935063	49935063	10284	3	C	A	A	A	286	22	MST1R	2	2
DNAH1	25981	broad.mit.edu	37	3	52360842	52360842	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52360842C>A	uc011bef.1	+	c.673C>A	c.(673-675)CAC>AAC	p.H225N	DNAH1_uc003ddt.1_Missense_Mutation_p.H225N	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	225	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.227273	12.463477	13.965285	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52360842	52360842	4779	3	C	A	A	A	273	21	DNAH1	2	2
EPHA3	2042	broad.mit.edu	37	3	89390951	89390951	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:89390951C>T	uc003dqy.2	+	c.1017C>T	c.(1015-1017)ACC>ACT	p.T339T	EPHA3_uc003dqx.1_Silent_p.T339T|EPHA3_uc010hon.1_Non-coding_Transcript	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor	339	Extracellular (Potential).|Fibronectin type-III 1.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding			lung(15)|ovary(7)|large_intestine(4)|central_nervous_system(2)|pancreas(1)	29	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)						416	TSP Lung(6;0.00050)			0.091667	6.136835	26.294823	11	109	KEEP	---	---	---	---	capture		Silent	SNP	89390951	89390951	5361	3	C	T	T	T	301	24	EPHA3	2	2
PROS1	5627	broad.mit.edu	37	3	93605211	93605211	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:93605211G>A	uc003drb.3	-	c.1292C>T	c.(1291-1293)CCT>CTT	p.P431L	PROS1_uc010hoo.2_Missense_Mutation_p.P300L|PROS1_uc003dqz.3_Missense_Mutation_p.P300L	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	431	Laminin G-like 1.				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)									0.145833	88.537876	129.07396	49	287	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93605211	93605211	13001	3	G	A	A	A	455	35	PROS1	2	2
ANK2	287	broad.mit.edu	37	4	114276798	114276798	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114276798G>T	uc003ibe.3	+	c.7024G>T	c.(7024-7026)GGA>TGA	p.G2342*	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Nonsense_Mutation_p.G2357*	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	2309					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)										0.104839	9.208722	28.443692	13	111	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	114276798	114276798	624	4	G	T	T	T	455	35	ANK2	5	2
NDST3	9348	broad.mit.edu	37	4	118975786	118975786	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:118975786C>A	uc003ibx.2	+	c.721C>A	c.(721-723)CCA>ACA	p.P241T	NDST3_uc011cgf.1_Missense_Mutation_p.P241T|NDST3_uc003ibw.2_Missense_Mutation_p.P241T	NM_004784	NP_004775	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan	241	Lumenal (Potential).|Heparan sulfate N-deacetylase 3.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			large_intestine(1)	1														0.062687	-23.688989	42.968186	21	314	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118975786	118975786	10656	4	C	A	A	A	286	22	NDST3	2	2
PRSS12	8492	broad.mit.edu	37	4	119259402	119259402	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:119259402A>T	uc003ica.1	-	c.570T>A	c.(568-570)GTT>GTA	p.V190V		NM_003619	NP_003610	P56730	NETR_HUMAN	neurotrypsin precursor	190	SRCR 1.					membrane	scavenger receptor activity				0														0.089552	0.900261	12.297238	6	61	KEEP	---	---	---	---	capture		Silent	SNP	119259402	119259402	13065	4	A	T	T	T	2	1	PRSS12	3	3
PRMT10	90826	broad.mit.edu	37	4	148605077	148605077	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:148605077C>A	uc003ilc.2	-	c.62G>T	c.(61-63)CGG>CTG	p.R21L	PRMT10_uc003ild.2_5'UTR	NM_138364	NP_612373	Q6P2P2	ANM10_HUMAN	protein arginine methyltransferase 10	21						cytoplasm	binding|protein methyltransferase activity			ovary(1)|central_nervous_system(1)	2														0.173913	8.091735	10.395589	4	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148605077	148605077	12979	4	C	A	A	A	299	23	PRMT10	1	1
CD38	952	broad.mit.edu	37	4	15842076	15842076	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:15842076G>T	uc011bxc.1	+	c.754G>T	c.(754-756)GAC>TAC	p.D252Y	CD38_uc003gol.1_Missense_Mutation_p.D252Y	NM_001775	NP_001766	P28907	CD38_HUMAN	CD38 antigen	252	Extracellular (Potential).				B cell receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of apoptosis|negative regulation of transcription, DNA-dependent|positive regulation of B cell proliferation|positive regulation of transcription, DNA-dependent|response to drug	integral to membrane|plasma membrane	binding|NAD+ nucleosidase activity|receptor activity|transcription activator activity|transcription repressor activity			ovary(2)	2														0.058394	-24.443742	31.590671	16	258	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15842076	15842076	3137	4	G	T	T	T	429	33	CD38	2	2
FGFBP2	83888	broad.mit.edu	37	4	15964725	15964725	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:15964725C>A	uc003gon.2	-	c.28G>T	c.(28-30)GTG>TTG	p.V10L		NM_031950	NP_114156	Q9BYJ0	FGFP2_HUMAN	killer-specific secretory protein of 37 kDa	10						extracellular space	growth factor binding				0														0.05814	-7.083989	10.507545	5	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15964725	15964725	6098	4	C	A	A	A	234	18	FGFBP2	2	2
ANXA10	11199	broad.mit.edu	37	4	169049310	169049310	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169049310G>T	uc003irm.2	+	c.94G>T	c.(94-96)GGA>TGA	p.G32*		NM_007193	NP_009124	Q9UJ72	ANX10_HUMAN	annexin A10	32	Annexin 1.						calcium ion binding|calcium-dependent phospholipid binding				0		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)										0.067164	-4.933846	21.069775	9	125	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	169049310	169049310	723	4	G	T	T	T	455	35	ANXA10	5	2
NEK1	4750	broad.mit.edu	37	4	170327885	170327885	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:170327885C>A	uc003isd.1	-	c.3236G>T	c.(3235-3237)TGT>TTT	p.C1079F	NEK1_uc003isb.1_Missense_Mutation_p.C1051F|NEK1_uc003isc.1_Missense_Mutation_p.C1007F|NEK1_uc003ise.1_Missense_Mutation_p.C1035F|NEK1_uc003isf.1_Missense_Mutation_p.C982F	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1051					cell division|cilium assembly|mitosis|protein phosphorylation	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)						366				0.075	-2.115307	12.714309	6	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170327885	170327885	10720	4	C	A	A	A	221	17	NEK1	2	2
WDR17	116966	broad.mit.edu	37	4	177069408	177069408	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:177069408G>T	uc003iuj.2	+	c.1891G>T	c.(1891-1893)GAC>TAC	p.D631Y	WDR17_uc003iuk.2_Missense_Mutation_p.D607Y|WDR17_uc003ium.3_Missense_Mutation_p.D607Y|WDR17_uc003iul.1_Intron|WDR17_uc003iun.2_5'Flank	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	631	WD 11.									ovary(2)|pancreas(1)	3		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)										0.088889	0.251685	38.66858	20	205	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	177069408	177069408	17850	4	G	T	T	T	533	41	WDR17	2	2
C4orf41	60684	broad.mit.edu	37	4	184614791	184614791	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:184614791C>A	uc003ivx.2	+	c.2287C>A	c.(2287-2289)CCT>ACT	p.P763T	C4orf41_uc003ivw.2_Missense_Mutation_p.P763T|C4orf41_uc010isc.2_Missense_Mutation_p.P107T|C4orf41_uc003ivy.2_Missense_Mutation_p.P369T	NM_021942	NP_068761	Q7Z392	CD041_HUMAN	hypothetical protein LOC60684 isoform a	763											0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;1.39e-26)|Epithelial(43;2.42e-22)|OV - Ovarian serous cystadenocarcinoma(60;6.85e-10)|GBM - Glioblastoma multiforme(59;6.71e-06)|Colorectal(24;9.67e-06)|STAD - Stomach adenocarcinoma(60;2.36e-05)|COAD - Colon adenocarcinoma(29;7.07e-05)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.171)										0.078431	-7.913609	38.762096	20	235	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	184614791	184614791	2365	4	C	A	A	A	286	22	C4orf41	2	2
FAT1	2195	broad.mit.edu	37	4	187540406	187540406	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187540406C>A	uc003izf.2	-	c.7334G>T	c.(7333-7335)GGG>GTG	p.G2445V		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2445	Extracellular (Potential).|Cadherin 22.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						Colon(197;1040 2055 4143 4984 49344)								0.100962	8.54678	41.59757	21	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	187540406	187540406	5925	4	C	A	A	A	286	22	FAT1	2	2
PPARGC1A	10891	broad.mit.edu	37	4	23886435	23886435	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:23886435G>A	uc003gqs.2	-	c.174C>T	c.(172-174)TGC>TGT	p.C58C	PPARGC1A_uc003gqt.2_Non-coding_Transcript|PPARGC1A_uc011bxp.1_5'Flank|PPARGC1A_uc010ier.1_Non-coding_Transcript|PPARGC1A_uc003gqu.3_Silent_p.C58C	NM_013261	NP_037393	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor	58					androgen receptor signaling pathway|brown fat cell differentiation|cellular glucose homeostasis|digestion|fatty acid oxidation|gluconeogenesis|mitochondrion organization|mRNA processing|neuron death|positive regulation of fatty acid oxidation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gluconeogenesis|positive regulation of histone acetylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein complex assembly|protein stabilization|response to muscle activity|response to starvation|RNA splicing|temperature homeostasis|transcription initiation from RNA polymerase II promoter	DNA-directed RNA polymerase II, core complex	androgen receptor binding|DNA binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|RNA binding|RNA polymerase II transcription mediator activity|transcription factor binding			ovary(2)|lung(2)|kidney(2)	6		Breast(46;0.0503)				Esophageal Squamous(29;694 744 13796 34866 44181)				410				0.091633	4.738019	46.915934	23	228	KEEP	---	---	---	---	capture		Silent	SNP	23886435	23886435	12730	4	G	A	A	A	594	46	PPARGC1A	2	2
PCDH7	5099	broad.mit.edu	37	4	31144176	31144176	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:31144176G>A	uc011bxx.1	+	c.3449G>A	c.(3448-3450)TGG>TAG	p.W1150*	PCDH7_uc011bxw.1_Nonsense_Mutation_p.W1103*	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	Error:Variant_position_missing_in_O60245_after_alignment					homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.086364	3.224858	41.338464	19	201	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31144176	31144176	11936	4	G	A	A	A	611	47	PCDH7	5	2
HGFAC	3083	broad.mit.edu	37	4	3444491	3444491	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:3444491A>T	uc010icw.2	+	c.150A>T	c.(148-150)ACA>ACT	p.T50T	HGFAC_uc003ghc.2_Silent_p.T50T	NM_001528	NP_001519	Q04756	HGFA_HUMAN	HGF activator preproprotein	50					proteolysis	extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(2)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)										0.103448	2.102469	6.645424	3	26	KEEP	---	---	---	---	capture		Silent	SNP	3444491	3444491	7370	4	A	T	T	T	80	7	HGFAC	3	3
TLR6	10333	broad.mit.edu	37	4	38830606	38830606	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:38830606C>A	uc003gtm.2	-	c.489G>T	c.(487-489)TTG>TTT	p.L163F	TLR6_uc010ifg.1_Missense_Mutation_p.L163F	NM_006068	NP_006059	Q9Y2C9	TLR6_HUMAN	toll-like receptor 6 precursor	163	Extracellular (Potential).|LRR 5.				activation of NF-kappaB-inducing kinase activity|cellular response to diacyl bacterial lipopeptide|defense response to bacterium|detection of diacyl bacterial lipopeptide|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-6 biosynthetic process|positive regulation of JUN kinase activity|T-helper 1 type immune response|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	integral to plasma membrane|phagocytic vesicle membrane	lipopeptide binding|transmembrane receptor activity			ovary(2)	2														0.079365	-0.650276	10.708012	5	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38830606	38830606	16485	4	C	A	A	A	324	25	TLR6	2	2
CHRNA9	55584	broad.mit.edu	37	4	40337915	40337915	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:40337915C>G	uc003gva.1	+	c.136C>G	c.(136-138)CTT>GTT	p.L46V		NM_017581	NP_060051	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9	46	Extracellular (Potential).				synaptic transmission	cell junction|postsynaptic membrane	calcium channel activity|receptor activity			breast(3)|central_nervous_system(1)	4					Nicotine(DB00184)	Esophageal Squamous(115;1297 1602 22235 25158 43327)								0.041322	-29.769351	24.987114	10	232	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40337915	40337915	3523	4	C	G	G	G	416	32	CHRNA9	3	3
APBB2	323	broad.mit.edu	37	4	40818215	40818215	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:40818215G>A	uc003gvn.2	-	c.2174C>T	c.(2173-2175)CCG>CTG	p.P725L	APBB2_uc010ifu.2_Missense_Mutation_p.P296L|APBB2_uc003gvm.2_Missense_Mutation_p.P702L|APBB2_uc003gvl.2_Missense_Mutation_p.P724L|APBB2_uc003gvk.2_Missense_Mutation_p.P176L	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	724	PID 2.				cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						Ovarian(3;20 75 16686 49997)								0.19375	147.10479	175.091159	62	258	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40818215	40818215	771	4	G	A	A	A	507	39	APBB2	1	1
ZBTB49	166793	broad.mit.edu	37	4	4304168	4304168	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:4304168G>T	uc003ghu.2	+	c.605G>T	c.(604-606)TGC>TTC	p.C202F	ZBTB49_uc003ghv.2_5'UTR|ZBTB49_uc010icy.2_Non-coding_Transcript|ZBTB49_uc010icz.2_5'UTR	NM_145291	NP_660334	Q6ZSB9	ZBT49_HUMAN	zinc finger protein 509	202					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.1	6.819564	30.813201	15	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4304168	4304168	18137	4	G	T	T	T	598	46	ZBTB49	2	2
SCFD2	152579	broad.mit.edu	37	4	54231838	54231838	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:54231838C>T	uc003gzu.2	-	c.271G>A	c.(271-273)GAC>AAC	p.D91N	SCFD2_uc010igm.2_Missense_Mutation_p.D91N	NM_152540	NP_689753	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	91					protein transport|vesicle docking involved in exocytosis					ovary(2)|pancreas(1)	3			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)											0.075	-0.046972	7.310408	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54231838	54231838	14371	4	C	T	T	T	390	30	SCFD2	2	2
ZNF595	152687	broad.mit.edu	37	4	60024	60024	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:60024T>C	uc003fzv.1	+	c.204T>C	c.(202-204)CAT>CAC	p.H68H	ZNF595_uc003fzu.1_Non-coding_Transcript|ZNF718_uc003fzt.3_Silent_p.H68H|ZNF595_uc010iay.1_Non-coding_Transcript|ZNF595_uc011bus.1_Intron|ZNF595_uc011but.1_Intron	NM_182524	NP_872330	Q7Z3I0	Q7Z3I0_HUMAN	zinc finger protein 595	68					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding				0		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)										0.064748	-8.714126	18.630054	9	130	KEEP	---	---	---	---	capture		Silent	SNP	60024	60024	18620	4	T	C	C	C	660	51	ZNF595	4	4
LPHN3	23284	broad.mit.edu	37	4	62542642	62542642	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62542642G>A	uc010ihh.2	+	c.368G>A	c.(367-369)TGT>TAT	p.C123Y	LPHN3_uc003hcq.3_Missense_Mutation_p.C123Y|LPHN3_uc010ihg.1_Missense_Mutation_p.C191Y	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	123	SUEL-type lectin.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.088949	8.245437	71.527608	33	338	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62542642	62542642	9290	4	G	A	A	A	624	48	LPHN3	2	2
LPHN3	23284	broad.mit.edu	37	4	62778449	62778449	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:62778449G>T	uc010ihh.2	+	c.1882G>T	c.(1882-1884)GAG>TAG	p.E628*	LPHN3_uc003hcq.3_Nonsense_Mutation_p.E628*|LPHN3_uc003hct.2_Intron|LPHN3_uc003hcs.1_Intron	NM_015236	NP_056051	Q9HAR2	LPHN3_HUMAN	latrophilin 3 precursor	623	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.144444	17.909848	28.869981	13	77	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	62778449	62778449	9290	4	G	T	T	T	429	33	LPHN3	5	2
STAP1	26228	broad.mit.edu	37	4	68449312	68449312	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68449312G>T	uc003hde.3	+	c.551G>T	c.(550-552)CGG>CTG	p.R184L	STAP1_uc003hdf.2_Missense_Mutation_p.R184L	NM_012108	NP_036240	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	184	SH2.				cellular membrane fusion|intracellular protein transport	cytoplasm					0														0.2	23.529708	27.708733	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68449312	68449312	15771	4	G	T	T	T	507	39	STAP1	1	1
UGT2A1	10941	broad.mit.edu	37	4	70504767	70504767	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70504767G>T	uc011caq.1	-	c.1195C>A	c.(1195-1197)CCA>ACA	p.P399T	UGT2A1_uc010ihu.2_Intron|UGT2A1_uc003hem.3_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Missense_Mutation_p.P190T	NM_001105677	NP_001099147	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	189	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.098592	2.191221	13.624495	7	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70504767	70504767	17511	4	G	T	T	T	572	44	UGT2A1	2	2
UGT2A1	10941	broad.mit.edu	37	4	70504773	70504773	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70504773G>T	uc011caq.1	-	c.1189C>A	c.(1189-1191)CCA>ACA	p.P397T	UGT2A1_uc010ihu.2_Intron|UGT2A1_uc003hem.3_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Missense_Mutation_p.P188T	NM_001105677	NP_001099147	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	187	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.123288	7.517517	17.668642	9	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70504773	70504773	17511	4	G	T	T	T	559	43	UGT2A1	2	2
MUC7	4589	broad.mit.edu	37	4	71346973	71346973	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71346973C>T	uc011cat.1	+	c.512C>T	c.(511-513)ACA>ATA	p.T171I	MUC7_uc011cau.1_Missense_Mutation_p.T171I|MUC7_uc003hfj.2_Missense_Mutation_p.T171I	NM_001145006	NP_001138478	Q8TAX7	MUC7_HUMAN	mucin 7, secreted precursor	171	1.|Thr-rich.					extracellular region	protein binding			ovary(2)|central_nervous_system(1)	3			Lung(101;0.211)											0.066667	-27.116019	34.463454	21	294	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71346973	71346973	10375	4	C	T	T	T	221	17	MUC7	2	2
ENAM	10117	broad.mit.edu	37	4	71510376	71510376	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71510376G>A	uc011caw.1	+	c.3233G>A	c.(3232-3234)AGG>AAG	p.R1078K		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin precursor	1078					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)											0.092369	16.973122	58.582975	23	226	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71510376	71510376	5305	4	G	A	A	A	455	35	ENAM	2	2
PTPN13	5783	broad.mit.edu	37	4	87730931	87730931	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:87730931G>A	uc003hpy.2	+	c.7108G>A	c.(7108-7110)GTG>ATG	p.V2370M	PTPN13_uc003hpz.2_Missense_Mutation_p.V2365M|PTPN13_uc003hqa.2_Missense_Mutation_p.V2346M|PTPN13_uc003hqb.2_Missense_Mutation_p.V2174M	NM_080685	NP_542416	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type	2365	Tyrosine-protein phosphatase.					cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)										0.125786	21.47765	43.188548	20	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87730931	87730931	13237	4	G	A	A	A	572	44	PTPN13	2	2
GRID2	2895	broad.mit.edu	37	4	94693482	94693482	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94693482A>T	uc011cdt.1	+	c.2857A>T	c.(2857-2859)ACT>TCT	p.T953S	GRID2_uc011cdu.1_Missense_Mutation_p.T858S	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	953	Cytoplasmic (Potential).|Interaction with AP4M1 (By similarity).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|large_intestine(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)									0.127273	24.468197	46.87354	21	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94693482	94693482	7050	4	A	T	T	T	78	6	GRID2	3	3
BMPR1B	658	broad.mit.edu	37	4	96075791	96075791	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:96075791C>A	uc003htm.3	+	c.1476C>A	c.(1474-1476)GCC>GCA	p.A492A	BMPR1B_uc010ilb.2_Silent_p.A492A|BMPR1B_uc003htn.3_Silent_p.A492A	NM_001203	NP_001194	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	492	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|protein phosphorylation	integral to plasma membrane|receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity			lung(2)|stomach(1)|skin(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)						166				0.1	7.475001	23.460298	10	90	KEEP	---	---	---	---	capture		Silent	SNP	96075791	96075791	1495	4	C	A	A	A	262	21	BMPR1B	2	2
DRD5	1816	broad.mit.edu	37	4	9784075	9784075	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:9784075C>A	uc003gmb.3	+	c.422C>A	c.(421-423)GCC>GAC	p.A141D		NM_000798	NP_000789	P21918	DRD5_HUMAN	dopamine receptor D5	141	Cytoplasmic (Potential).				activation of adenylate cyclase activity by dopamine receptor signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|cellular calcium ion homeostasis|negative regulation of NAD(P)H oxidase activity|reactive oxygen species metabolic process|synaptic transmission, dopaminergic	integral to plasma membrane					0					Apomorphine(DB00714)|Carphenazine(DB01038)|Fenoldopam(DB00800)|Zuclopenthixol(DB01624)									0.115385	2.921184	6.697338	3	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9784075	9784075	4944	4	C	A	A	A	338	26	DRD5	2	2
SEMA6A	57556	broad.mit.edu	37	5	115783221	115783221	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:115783221C>A	uc003krx.3	-	c.2232G>T	c.(2230-2232)ATG>ATT	p.M744I	SEMA6A_uc010jck.2_Missense_Mutation_p.M727I|SEMA6A_uc011cwe.1_Missense_Mutation_p.M106I|SEMA6A_uc003krv.3_Missense_Mutation_p.M154I|SEMA6A_uc003krw.3_Missense_Mutation_p.M204I|SEMA6A_uc010jcj.2_Missense_Mutation_p.M271I	NM_020796	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and	727	Cytoplasmic (Potential).				apoptosis|axon guidance|cell surface receptor linked signaling pathway|cytoskeleton organization|organ morphogenesis	axon|integral to membrane|plasma membrane	receptor activity			ovary(2)	2		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)										0.133523	68.152313	113.97338	47	305	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115783221	115783221	14525	5	C	A	A	A	325	25	SEMA6A	2	2
SRFBP1	153443	broad.mit.edu	37	5	121355925	121355925	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:121355925C>T	uc003kst.1	+	c.495C>T	c.(493-495)ATC>ATT	p.I165I		NM_152546	NP_689759	Q8NEF9	SRFB1_HUMAN	serum response factor binding protein 1	165					regulation of transcription, DNA-dependent|transcription, DNA-dependent	perinuclear region of cytoplasm					0		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)										0.1	8.641107	32.597534	15	135	KEEP	---	---	---	---	capture		Silent	SNP	121355925	121355925	15658	5	C	T	T	T	369	29	SRFBP1	2	2
ZNF608	57507	broad.mit.edu	37	5	123983235	123983235	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:123983235C>A	uc003ktq.1	-	c.2842G>T	c.(2842-2844)GAT>TAT	p.D948Y	ZNF608_uc003ktr.1_Intron|ZNF608_uc003kts.1_Missense_Mutation_p.D948Y|ZNF608_uc003ktt.1_Missense_Mutation_p.D948Y|ZNF608_uc003ktp.1_5'Flank	NM_020747	NP_065798	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	948	Ser-rich.					intracellular	zinc ion binding			skin(3)|ovary(2)|lung(1)	6		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)						447				0.138298	20.922826	32.804549	13	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123983235	123983235	18629	5	C	A	A	A	403	31	ZNF608	1	1
ADAMTS19	171019	broad.mit.edu	37	5	128864260	128864260	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128864260T>A	uc003kvb.1	+	c.1200T>A	c.(1198-1200)TTT>TTA	p.F400L	ADAMTS19_uc003kvc.1_Non-coding_Transcript	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	400	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)	8		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)						425				0.18232	63.770193	80.926042	33	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128864260	128864260	265	5	T	A	A	A	829	64	ADAMTS19	3	3
FAM53C	51307	broad.mit.edu	37	5	137681298	137681298	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137681298G>T	uc003lcv.2	+	c.921G>T	c.(919-921)CAG>CAT	p.Q307H	FAM53C_uc003lcw.2_Missense_Mutation_p.Q307H|FAM53C_uc011cyq.1_Non-coding_Transcript|FAM53C_uc011cyr.1_3'UTR	NM_001135647	NP_001129119	Q9NYF3	FA53C_HUMAN	hypothetical protein LOC51307	307										ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)											0.119403	10.260308	19.780542	8	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137681298	137681298	5803	5	G	T	T	T	451	35	FAM53C	2	2
PCDHA7	56141	broad.mit.edu	37	5	140215324	140215324	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140215324C>A	uc003lhq.2	+	c.1356C>A	c.(1354-1356)GCC>GCA	p.A452A	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc011dac.1_Silent_p.A452A	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	452	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			NSCLC(160;258 2013 5070 22440 28951)								0.128205	4.278205	9.512391	5	34	KEEP	---	---	---	---	capture		Silent	SNP	140215324	140215324	11949	5	C	A	A	A	275	22	PCDHA7	2	2
PCDHA11	56138	broad.mit.edu	37	5	140249939	140249939	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140249939G>A	uc003lia.2	+	c.1251G>A	c.(1249-1251)GTG>GTA	p.V417V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Silent_p.V417V	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	417	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.132075	16.28179	30.223284	14	92	KEEP	---	---	---	---	capture		Silent	SNP	140249939	140249939	11941	5	G	A	A	A	613	48	PCDHA11	2	2
PCDHGA1	56114	broad.mit.edu	37	5	140712208	140712208	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140712208C>A	uc003lji.1	+	c.1957C>A	c.(1957-1959)CCG>ACG	p.P653T	PCDHGA1_uc011dan.1_Missense_Mutation_p.P653T	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	653	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.173913	7.986153	10.294377	4	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140712208	140712208	11970	5	C	A	A	A	286	22	PCDHGA1	2	2
PCDHGB2	56103	broad.mit.edu	37	5	140740473	140740473	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140740473G>T	uc003ljs.1	+	c.771G>T	c.(769-771)CCG>CCT	p.P257P	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc011dar.1_Silent_p.P257P	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	257	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.236842	21.654373	24.060793	9	29	KEEP	---	---	---	---	capture		Silent	SNP	140740473	140740473	11983	5	G	T	T	T	496	39	PCDHGB2	1	1
SPINK7	84651	broad.mit.edu	37	5	147693701	147693701	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:147693701C>A	uc003lpd.2	+	c.126C>A	c.(124-126)GCC>GCA	p.A42A		NM_032566	NP_115955	P58062	ISK7_HUMAN	serine peptidase inhibitor, Kazal type 7	42	Kazal-like.					extracellular region	protein binding|serine-type endopeptidase inhibitor activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.201389	124.265586	148.164561	58	230	KEEP	---	---	---	---	capture		Silent	SNP	147693701	147693701	15576	5	C	A	A	A	262	21	SPINK7	2	2
LARP1	23367	broad.mit.edu	37	5	154183274	154183274	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:154183274T>A	uc003lvp.2	+	c.2408T>A	c.(2407-2409)GTG>GAG	p.V803E	LARP1_uc003lvo.2_Missense_Mutation_p.V726E|LARP1_uc010jie.1_Missense_Mutation_p.V598E	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	803							protein binding|RNA binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.084507	2.298521	14.735102	6	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154183274	154183274	8951	5	T	A	A	A	767	59	LARP1	3	3
ITK	3702	broad.mit.edu	37	5	156655369	156655369	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156655369T>A	uc003lwo.1	+	c.711T>A	c.(709-711)TAT>TAA	p.Y237*		NM_005546	NP_005537	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	237					cellular defense response|intracellular signal transduction|protein phosphorylation|T cell receptor signaling pathway	cytosol|plasma membrane	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(8)|lung(4)|skin(3)|stomach(1)|central_nervous_system(1)	17	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Esophageal Squamous(70;1378 1469 8785 19883)				330				0.241379	38.823028	42.360039	14	44	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	156655369	156655369	8213	5	T	A	A	A	660	51	ITK	5	3
PLEKHG4B	153478	broad.mit.edu	37	5	157021	157021	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:157021G>C	uc003jak.2	+	c.1414G>C	c.(1414-1416)GAC>CAC	p.D472H		NM_052909	NP_443141	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G	472					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			skin(1)	1			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)										0.210526	11.589966	13.062164	4	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157021	157021	12498	5	G	C	C	C	585	45	PLEKHG4B	3	3
DOCK2	1794	broad.mit.edu	37	5	169122864	169122864	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169122864C>A	uc003maf.2	+	c.901C>A	c.(901-903)CGG>AGG	p.R301R	DOCK2_uc011der.1_Non-coding_Transcript	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	301					actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.132479	51.234899	81.870212	31	203	KEEP	---	---	---	---	capture		Silent	SNP	169122864	169122864	4871	5	C	A	A	A	295	23	DOCK2	1	1
RASGEF1C	255426	broad.mit.edu	37	5	179555436	179555436	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:179555436C>A	uc003mlq.2	-	c.613G>T	c.(613-615)GCC>TCC	p.A205S	RASGEF1C_uc003mlr.2_Missense_Mutation_p.A205S|RASGEF1C_uc003mlp.3_Missense_Mutation_p.A54S	NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	205	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.2	15.499001	19.722646	10	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179555436	179555436	13532	5	C	A	A	A	338	26	RASGEF1C	2	2
CDH18	1016	broad.mit.edu	37	5	19747108	19747108	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19747108C>G	uc003jgc.2	-	c.466G>C	c.(466-468)GCT>CCT	p.A156P	CDH18_uc003jgd.2_Missense_Mutation_p.A156P|CDH18_uc011cnm.1_Missense_Mutation_p.A156P	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	156	Extracellular (Potential).|Cadherin 1.				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)													0.167939	49.53501	63.167783	22	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19747108	19747108	3232	5	C	G	G	G	351	27	CDH18	3	3
CDH12	1010	broad.mit.edu	37	5	21854832	21854832	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:21854832G>T	uc010iuc.2	-	c.594C>A	c.(592-594)GTC>GTA	p.V198V	CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Silent_p.V198V	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein	198	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2														0.118182	12.995906	28.768173	13	97	KEEP	---	---	---	---	capture		Silent	SNP	21854832	21854832	3227	5	G	T	T	T	470	37	CDH12	1	1
IRX2	153572	broad.mit.edu	37	5	2748676	2748676	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:2748676G>A	uc003jda.2	-	c.1146C>T	c.(1144-1146)CTC>CTT	p.L382L	IRX2_uc003jdb.2_Silent_p.L382L	NM_001134222	NP_001127694	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	382					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			skin(1)	1				GBM - Glioblastoma multiforme(108;0.204)										0.244898	29.570456	32.480299	12	37	KEEP	---	---	---	---	capture		Silent	SNP	2748676	2748676	8148	5	G	A	A	A	418	33	IRX2	2	2
ADAMTS12	81792	broad.mit.edu	37	5	33549430	33549430	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33549430C>G	uc003jia.1	-	c.4184G>C	c.(4183-4185)CGG>CCG	p.R1395P	ADAMTS12_uc010iuq.1_Missense_Mutation_p.R1310P	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1395	TSP type-1 6.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.192661	73.311487	92.73343	42	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33549430	33549430	258	5	C	G	G	G	299	23	ADAMTS12	3	3
MGC42105	167359	broad.mit.edu	37	5	43245925	43245925	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43245925T>C	uc003jno.2	+	c.48T>C	c.(46-48)TAT>TAC	p.Y16Y		NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1	16					protein phosphorylation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9										94				0.142857	46.25216	78.257557	37	222	KEEP	---	---	---	---	capture		Silent	SNP	43245925	43245925	9942	5	T	C	C	C	660	51	MGC42105	4	4
HCN1	348980	broad.mit.edu	37	5	45262453	45262453	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:45262453G>A	uc003jok.2	-	c.2243C>T	c.(2242-2244)CCA>CTA	p.P748L		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	748	Gln-rich.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.166667	6.785041	9.314881	4	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45262453	45262453	7278	5	G	A	A	A	611	47	HCN1	2	2
ADAMTS16	170690	broad.mit.edu	37	5	5182390	5182390	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5182390G>T	uc003jdl.2	+	c.735G>T	c.(733-735)AAG>AAT	p.K245N	ADAMTS16_uc003jdk.1_Missense_Mutation_p.K245N|ADAMTS16_uc003jdj.1_Missense_Mutation_p.K245N	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	245					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.38806	72.415609	73.156895	26	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5182390	5182390	262	5	G	T	T	T	438	34	ADAMTS16	2	2
IQGAP2	10788	broad.mit.edu	37	5	75954410	75954410	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:75954410G>A	uc003kek.2	+	c.2447G>A	c.(2446-2448)AGG>AAG	p.R816K	IQGAP2_uc010izv.2_Missense_Mutation_p.R369K|IQGAP2_uc011csv.1_Missense_Mutation_p.R312K|IQGAP2_uc003kel.2_Missense_Mutation_p.R312K	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	816					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)										0.141975	42.6236	62.638794	23	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75954410	75954410	8118	5	G	A	A	A	455	35	IQGAP2	2	2
MSH3	4437	broad.mit.edu	37	5	80040324	80040324	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80040324G>T	uc003kgz.2	+	c.1654_splice	c.e12-1	p.T552_splice		NM_002439	NP_002430			mutS homolog 3						maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			ovary(1)	1		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		Melanoma(88;1010 1399 13793 26548 36275)				1101				0.125	5.744364	11.243335	5	35	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	80040324	80040324	10264	5	G	T	T	T	429	33	MSH3	5	2
RASGRF2	5924	broad.mit.edu	37	5	80409657	80409657	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80409657G>T	uc003kha.1	+	c.2388G>T	c.(2386-2388)GAG>GAT	p.E796D	RASGRF2_uc011ctn.1_Non-coding_Transcript	NM_006909	NP_008840	O14827	RGRF2_HUMAN	Ras protein-specific guanine	796					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|endoplasmic reticulum membrane|plasma membrane	protein binding|Rho guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|large_intestine(2)|central_nervous_system(1)|skin(1)	9		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)						847				0.131387	25.048581	43.149872	18	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80409657	80409657	13534	5	G	T	T	T	438	34	RASGRF2	2	2
XRCC4	7518	broad.mit.edu	37	5	82649012	82649012	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:82649012T>C	uc003kib.2	+	c.962T>C	c.(961-963)TTA>TCA	p.L321S	XRCC4_uc003kid.2_Missense_Mutation_p.L319S|XRCC4_uc003kic.2_Missense_Mutation_p.L319S|XRCC4_uc003kie.2_Missense_Mutation_p.L321S|XRCC4_uc003kig.2_Non-coding_Transcript	NM_022406	NP_071801	Q13426	XRCC4_HUMAN	X-ray repair cross complementing protein 4	321					DNA ligation involved in DNA repair|double-strand break repair via nonhomologous end joining|initiation of viral infection|positive regulation of ligase activity|provirus integration|response to X-ray	cytosol|DNA ligase IV complex|DNA-dependent protein kinase-DNA ligase 4 complex|nucleoplasm	DNA binding|protein C-terminus binding			skin(2)	2		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)										0.11811	78.547905	133.102563	45	336	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82649012	82649012	18038	5	T	C	C	C	793	61	XRCC4	4	4
AKD1	221264	broad.mit.edu	37	6	109962787	109962787	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:109962787T>C	uc003ptn.2	-	c.867A>G	c.(865-867)CTA>CTG	p.L289L	AKD1_uc003ptr.3_Silent_p.L289L	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	adenylate kinase domain containing 1 isoform 1	289					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			ovary(1)	1														0.057692	-6.221474	15.1062	6	98	KEEP	---	---	---	---	capture		Silent	SNP	109962787	109962787	463	6	T	C	C	C	782	61	AKD1	4	4
WASF1	8936	broad.mit.edu	37	6	110423279	110423279	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:110423279G>T	uc003ptv.1	-	c.1034C>A	c.(1033-1035)ACT>AAT	p.T345N	WASF1_uc003ptw.1_Missense_Mutation_p.T345N|WASF1_uc003ptx.1_Missense_Mutation_p.T345N|WASF1_uc003pty.1_Missense_Mutation_p.T345N	NM_003931	NP_003922	Q92558	WASF1_HUMAN	Wiskott-Aldrich syndrome protein family member	345					actin filament polymerization|cellular component movement	actin cytoskeleton	actin binding				0		all_cancers(87;1.18e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		OV - Ovarian serous cystadenocarcinoma(136;0.0364)|Epithelial(106;0.051)|all cancers(137;0.0687)										0.053004	-30.716995	29.009672	15	268	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110423279	110423279	17824	6	G	T	T	T	468	36	WASF1	2	2
AKAP7	9465	broad.mit.edu	37	6	131486289	131486289	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:131486289G>T	uc003qck.2	+	c.360G>T	c.(358-360)ATG>ATT	p.M120I	AKAP7_uc011ebz.1_Missense_Mutation_p.M98I|AKAP7_uc003qcl.1_Missense_Mutation_p.M1I	NM_016377	NP_057461	Q9P0M2	AKA7G_HUMAN	A-kinase anchor protein 7 isoform gamma	98					RNA metabolic process	cytosol	catalytic activity			ovary(2)	2	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)										0.095238	5.764156	23.036943	10	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131486289	131486289	459	6	G	T	T	T	611	47	AKAP7	2	2
PHACTR1	221692	broad.mit.edu	37	6	13206250	13206250	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:13206250G>T	uc010jpc.2	+	c.868G>T	c.(868-870)GGC>TGC	p.G290C	PHACTR1_uc011dir.1_Missense_Mutation_p.G359C|PHACTR1_uc003nag.1_Missense_Mutation_p.G290C|PHACTR1_uc003nah.1_Missense_Mutation_p.G290C	NM_030948	NP_112210	Q9C0D0	PHAR1_HUMAN	phosphatase and actin regulator 1	290						cell junction|cytoplasm|synapse	actin binding|protein phosphatase inhibitor activity				0	Breast(50;0.0427)|Ovarian(93;0.12)	all_hematologic(90;0.122)|Lung SC(78;0.195)	Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239)											0.125	4.417909	7.706632	3	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13206250	13206250	12232	6	G	T	T	T	507	39	PHACTR1	1	1
LPA	4018	broad.mit.edu	37	6	160999728	160999728	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160999728G>C	uc003qtl.2	-	c.4298C>G	c.(4297-4299)ACC>AGC	p.T1433S		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	3941	Kringle 35.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)									0.048193	-16.174883	19.800103	8	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160999728	160999728	9276	6	G	C	C	C	572	44	LPA	3	3
PLG	5340	broad.mit.edu	37	6	161132127	161132127	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161132127A>T	uc003qtm.3	+	c.311A>T	c.(310-312)AAG>ATG	p.K104M		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	104	Kringle 1.				extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.092784	4.601884	20.78618	9	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161132127	161132127	12512	6	A	T	T	T	39	3	PLG	3	3
PLG	5340	broad.mit.edu	37	6	161157957	161157957	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161157957C>A	uc003qtm.3	+	c.1720C>A	c.(1720-1722)CCG>ACG	p.P574T		NM_000301	NP_000292	P00747	PLMN_HUMAN	plasminogen	574					extracellular matrix disassembly|fibrinolysis|negative regulation of cell proliferation|negative regulation of cell-substrate adhesion|negative regulation of fibrinolysis|platelet activation|platelet degranulation|positive regulation of fibrinolysis|proteolysis|tissue remodeling	extracellular space|extrinsic to external side of plasma membrane|platelet alpha granule lumen	apolipoprotein binding|cell surface binding|serine-type endopeptidase activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Aminocaproic Acid(DB00513)|Streptokinase(DB00086)|Tranexamic Acid(DB00302)|Urokinase(DB00013)									0.073684	-3.536744	14.196096	7	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161157957	161157957	12512	6	C	A	A	A	338	26	PLG	2	2
PARK2	5071	broad.mit.edu	37	6	161969900	161969900	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161969900C>A	uc003qtx.3	-	c.1069G>T	c.(1069-1071)GGC>TGC	p.G357C	PARK2_uc003qtv.3_Intron|PARK2_uc010kkd.2_Missense_Mutation_p.G166C|PARK2_uc003qtw.3_Missense_Mutation_p.G166C|PARK2_uc003qty.3_Missense_Mutation_p.G329C|PARK2_uc003qtz.3_Missense_Mutation_p.G208C|PARK2_uc010kke.1_Missense_Mutation_p.G376C|PARK2_uc011egf.1_Missense_Mutation_p.G31C	NM_004562	NP_004553	O60260	PRKN2_HUMAN	parkin isoform 1	357	IBR-type.				aggresome assembly|central nervous system development|mitochondrion degradation|negative regulation of actin filament bundle assembly|negative regulation of cell death|negative regulation of protein phosphorylation|negative regulation of release of cytochrome c from mitochondria|neuron death|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein autoubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of reactive oxygen species metabolic process	aggresome|cytosol|endoplasmic reticulum|Golgi apparatus|mitochondrion|nucleus|perinuclear region of cytoplasm	chaperone binding|PDZ domain binding|protein kinase binding|ubiquitin-protein ligase activity|zinc ion binding				0		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)										0.063492	-15.096582	34.870133	16	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161969900	161969900	11866	6	C	A	A	A	273	21	PARK2	2	2
C6orf118	168090	broad.mit.edu	37	6	165715670	165715670	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165715670C>A	uc003qum.3	-	c.141G>T	c.(139-141)CGG>CGT	p.R47R	C6orf118_uc011egi.1_Non-coding_Transcript	NM_144980	NP_659417	Q5T5N4	CF118_HUMAN	hypothetical protein LOC168090	47											0		Breast(66;6.27e-05)|Ovarian(120;0.0228)|Prostate(117;0.0906)|all_neural(5;0.157)		OV - Ovarian serous cystadenocarcinoma(33;3.23e-18)|BRCA - Breast invasive adenocarcinoma(81;3.11e-06)|GBM - Glioblastoma multiforme(31;0.000313)										0.139344	22.98886	38.327867	17	105	KEEP	---	---	---	---	capture		Silent	SNP	165715670	165715670	2425	6	C	A	A	A	327	26	C6orf118	2	2
GPR31	2853	broad.mit.edu	37	6	167570484	167570484	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:167570484G>T	uc011egq.1	-	c.836C>A	c.(835-837)CCC>CAC	p.P279H		NM_005299	NP_005290	O00270	GPR31_HUMAN	G protein-coupled receptor 31	279	Helical; Name=7; (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)										0.097744	6.492222	28.047704	13	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167570484	167570484	6962	6	G	T	T	T	559	43	GPR31	2	2
ZNF165	7718	broad.mit.edu	37	6	28053456	28053456	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28053456A>T	uc003nkg.2	+	c.198A>T	c.(196-198)GCA>GCT	p.A66A	ZNF165_uc003nkh.2_Silent_p.A66A|ZNF165_uc003nki.3_Silent_p.A66A	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	66	SCAN box.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.123457	11.510374	22.734104	10	71	KEEP	---	---	---	---	capture		Silent	SNP	28053456	28053456	18331	6	A	T	T	T	67	6	ZNF165	3	3
RIPK1	8737	broad.mit.edu	37	6	3111188	3111188	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:3111188T>C	uc010jni.2	+	c.1728T>C	c.(1726-1728)TTT>TTC	p.F576F	RIPK1_uc003muv.3_Silent_p.F413F|RIPK1_uc003muw.3_Silent_p.F511F|RIPK1_uc011dhs.1_Silent_p.F530F|RIPK1_uc003mux.2_Silent_p.F576F	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine	576	Interaction with SQSTM1.				activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|regulation of oxygen and reactive oxygen species metabolic process|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|tumor necrosis factor-mediated signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)								138				0.104651	6.310196	19.683224	9	77	KEEP	---	---	---	---	capture		Silent	SNP	3111188	3111188	13857	6	T	C	C	C	816	63	RIPK1	4	4
STK19	8859	broad.mit.edu	37	6	31940267	31940267	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31940267G>A	uc003nyv.2	+	c.409G>A	c.(409-411)GAT>AAT	p.D137N	DOM3Z_uc003nyo.1_5'Flank|DOM3Z_uc003nyp.1_5'Flank|DOM3Z_uc003nyq.1_5'Flank|DOM3Z_uc003nyr.1_5'Flank|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'Flank|STK19_uc003nyt.2_Missense_Mutation_p.D94N|DOM3Z_uc003nyu.1_5'Flank|STK19_uc011dow.1_Missense_Mutation_p.D137N|STK19_uc011dox.1_Missense_Mutation_p.D94N|STK19_uc003nyw.2_Missense_Mutation_p.D137N|STK19_uc010jtn.1_Non-coding_Transcript	NM_032454	NP_115830	P49842	STK19_HUMAN	serine/threonine kinase 19 isoform 2	137					protein phosphorylation	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			skin(4)	4										192				0.181818	14.976424	19.160827	8	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31940267	31940267	15812	6	G	A	A	A	533	41	STK19	2	2
C6orf10	10665	broad.mit.edu	37	6	32260791	32260791	+	Silent	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32260791T>A	uc011dpy.1	-	c.1659A>T	c.(1657-1659)ACA>ACT	p.T553T	C6orf10_uc011dpx.1_Intron	NM_006781	NP_006772	Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	553	Lys-rich.					integral to membrane					0														0.097264	25.658214	79.116707	32	297	KEEP	---	---	---	---	capture		Silent	SNP	32260791	32260791	2418	6	T	A	A	A	704	55	C6orf10	3	3
ZBTB9	221504	broad.mit.edu	37	6	33423488	33423488	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33423488G>T	uc003oeq.2	+	c.611G>T	c.(610-612)GGA>GTA	p.G204V		NM_152735	NP_689948	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	204					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.225352	34.85983	39.782612	16	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33423488	33423488	18146	6	G	T	T	T	533	41	ZBTB9	2	2
SLC22A7	10864	broad.mit.edu	37	6	43267197	43267197	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43267197G>T	uc003out.2	+	c.469G>T	c.(469-471)GTG>TTG	p.V157L	SLC22A7_uc010jyl.1_Missense_Mutation_p.V155L|SLC22A7_uc003ous.2_Missense_Mutation_p.V155L	NM_153320	NP_696961	Q9Y694	S22A7_HUMAN	solute carrier family 22 member 7 isoform b	157	Helical; (Potential).					basolateral plasma membrane|integral to plasma membrane|membrane fraction	anion:anion antiporter activity|sodium-independent organic anion transmembrane transporter activity				0			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)											0.071429	-2.565333	10.669549	5	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43267197	43267197	14956	6	G	T	T	T	572	44	SLC22A7	2	2
CRISP2	7180	broad.mit.edu	37	6	49667532	49667532	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49667532C>G	uc003ozm.2	-	c.256G>C	c.(256-258)GAG>CAG	p.E86Q	CRISP2_uc003ozq.2_Missense_Mutation_p.E86Q|CRISP2_uc003ozl.2_Missense_Mutation_p.E86Q|CRISP2_uc003ozn.2_Missense_Mutation_p.E86Q|CRISP2_uc003ozr.2_Missense_Mutation_p.E86Q|CRISP2_uc003ozo.2_Missense_Mutation_p.E86Q|CRISP2_uc003ozp.2_Missense_Mutation_p.E86Q	NM_003296	NP_003287	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2 precursor	86						extracellular space					0	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)											0.126437	23.164628	35.008875	11	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49667532	49667532	4019	6	C	G	G	G	416	32	CRISP2	3	3
PKHD1	5314	broad.mit.edu	37	6	51889988	51889988	+	Silent	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:51889988T>A	uc003pah.1	-	c.4620A>T	c.(4618-4620)ACA>ACT	p.T1540T	PKHD1_uc003pai.2_Silent_p.T1540T	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1540	Extracellular (Potential).|IPT/TIG 10.				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			ovary(12)|large_intestine(5)|central_nervous_system(3)	20	Lung NSC(77;0.0605)									1537				0.081081	-0.81007	19.042188	9	102	KEEP	---	---	---	---	capture		Silent	SNP	51889988	51889988	12396	6	T	A	A	A	808	63	PKHD1	3	3
DST	667	broad.mit.edu	37	6	56458660	56458660	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56458660C>A	uc003pdf.2	-	c.6170G>T	c.(6169-6171)AGG>ATG	p.R2057M	DST_uc003pcz.3_Missense_Mutation_p.R1879M|DST_uc011dxj.1_Missense_Mutation_p.R1908M|DST_uc011dxk.1_Missense_Mutation_p.R1919M|DST_uc003pcy.3_Missense_Mutation_p.R1553M|DST_uc010kaa.1_Non-coding_Transcript	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	3965	Spectrin 2.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)							2498				0.103203	34.319944	122.534234	58	504	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56458660	56458660	4967	6	C	A	A	A	312	24	DST	2	2
EXOC2	55770	broad.mit.edu	37	6	564606	564606	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:564606C>T	uc003mtd.2	-	c.1606G>A	c.(1606-1608)GGC>AGC	p.G536S	EXOC2_uc003mte.2_Missense_Mutation_p.G536S|EXOC2_uc011dho.1_Missense_Mutation_p.G131S	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	536					exocytosis|protein transport					ovary(2)|breast(2)|pancreas(1)	5	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)										0.146893	48.829811	70.036172	26	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	564606	564606	5495	6	C	T	T	T	312	24	EXOC2	2	2
COL19A1	1310	broad.mit.edu	37	6	70847591	70847591	+	Silent	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70847591A>T	uc003pfc.1	+	c.1398A>T	c.(1396-1398)CTA>CTT	p.L466L	COL19A1_uc010kam.1_Silent_p.L362L	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	466	Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.096203	21.367588	85.955069	38	357	KEEP	---	---	---	---	capture		Silent	SNP	70847591	70847591	3814	6	A	T	T	T	171	14	COL19A1	3	3
GABRR1	2569	broad.mit.edu	37	6	89907909	89907909	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:89907909A>G	uc003pna.2	-	c.402T>C	c.(400-402)TCT>TCC	p.S134S	GABRR1_uc011dzv.1_Silent_p.S111S	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1	134	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)									0.080586	1.650244	99.943123	44	502	KEEP	---	---	---	---	capture		Silent	SNP	89907909	89907909	6427	6	A	G	G	G	28	3	GABRR1	4	4
ZAN	7455	broad.mit.edu	37	7	100344252	100344252	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100344252G>A	uc003uwj.2	+	c.858G>A	c.(856-858)CTG>CTA	p.L286L	ZAN_uc003uwk.2_Silent_p.L286L|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	286	MAM 2.|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)											0.077922	-2.40091	11.621213	6	71	KEEP	---	---	---	---	capture		Silent	SNP	100344252	100344252	18096	7	G	A	A	A	574	45	ZAN	2	2
ZAN	7455	broad.mit.edu	37	7	100388667	100388668	+	Nonsense_Mutation	DNP	CC	AT	AT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100388667_100388668CC>AT	uc003uwj.2	+	c.7461_7462CC>AT	c.(7459-7464)ACCCAG>ACATAG	p.Q2488*	ZAN_uc003uwk.2_Nonsense_Mutation_p.Q2488*|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript|ZAN_uc011kke.1_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	2488	VWFD 4.|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)											0.157895	10.049898	14.271697	6	32	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	100388667	100388668	18096	7	CC	AT	AT	AT	275	22	ZAN	5	2
SLC12A9	56996	broad.mit.edu	37	7	100451908	100451908	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100451908G>T	uc003uwp.2	+	c.89G>T	c.(88-90)GGA>GTA	p.G30V	SLC12A9_uc003uwo.1_Missense_Mutation_p.G30V|SLC12A9_uc003uwq.2_Missense_Mutation_p.G30V|SLC12A9_uc011kki.1_Intron|SLC12A9_uc003uwr.2_5'Flank|SLC12A9_uc003uws.2_5'Flank|SLC12A9_uc003uwt.2_5'Flank	NM_020246	NP_064631	Q9BXP2	S12A9_HUMAN	solute carrier family 12 (potassium/chloride	30	Cytoplasmic (Potential).					integral to membrane|plasma membrane	cation:chloride symporter activity				0	Lung NSC(181;0.041)|all_lung(186;0.0581)													0.26087	11.674657	12.844024	6	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100451908	100451908	14885	7	G	T	T	T	533	41	SLC12A9	2	2
MYL10	93408	broad.mit.edu	37	7	101266302	101266302	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:101266302G>T	uc003uyr.2	-	c.324C>A	c.(322-324)GAC>GAA	p.D108E		NM_138403	NP_612412	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	108	EF-hand 1.|1 (Potential).					mitochondrion	calcium ion binding			ovary(1)|breast(1)	2						Esophageal Squamous(24;575 709 17516 40384 51639)								0.25	11.183991	12.308365	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101266302	101266302	10439	7	G	T	T	T	464	36	MYL10	2	2
RELN	5649	broad.mit.edu	37	7	103252100	103252100	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103252100C>A	uc003vca.2	-	c.2853G>T	c.(2851-2853)GAG>GAT	p.E951D	RELN_uc010liz.2_Missense_Mutation_p.E951D	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	951	BNR 3.				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.067308	-4.848397	15.223561	7	97	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103252100	103252100	13689	7	C	A	A	A	259	20	RELN	2	2
RELN	5649	broad.mit.edu	37	7	103338523	103338523	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103338523C>T	uc003vca.2	-	c.920G>A	c.(919-921)AGC>AAC	p.S307N	RELN_uc010liz.2_Missense_Mutation_p.S307N	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	307					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		NSCLC(146;835 1944 15585 22231 52158)								0.126923	85.279237	155.914318	66	454	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103338523	103338523	13689	7	C	T	T	T	364	28	RELN	2	2
PIK3CG	5294	broad.mit.edu	37	7	106515241	106515241	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:106515241C>A	uc003vdv.3	+	c.2384C>A	c.(2383-2385)GCG>GAG	p.A795E	PIK3CG_uc003vdu.2_Missense_Mutation_p.A795E|PIK3CG_uc003vdw.2_Missense_Mutation_p.A795E	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	795					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.085714	2.899504	15.073643	6	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106515241	106515241	12340	7	C	A	A	A	351	27	PIK3CG	1	1
THSD7A	221981	broad.mit.edu	37	7	11486905	11486905	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:11486905A>G	uc003ssf.3	-	c.2752T>C	c.(2752-2754)TGC>CGC	p.C918R		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	918	TSP type-1 9.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)										0.28	58.044095	61.307308	21	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11486905	11486905	16407	7	A	G	G	G	104	8	THSD7A	4	4
THSD7A	221981	broad.mit.edu	37	7	11632988	11632988	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:11632988C>A	uc003ssf.3	-	c.1164G>T	c.(1162-1164)AGG>AGT	p.R388S		NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	388	TSP type-1 3.|Extracellular (Potential).					integral to membrane				ovary(3)	3				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)										0.337079	77.817671	79.909574	30	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11632988	11632988	16407	7	C	A	A	A	389	30	THSD7A	2	2
CTTNBP2	83992	broad.mit.edu	37	7	117431240	117431240	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117431240G>A	uc003vjf.2	-	c.2010C>T	c.(2008-2010)CCC>CCT	p.P670P		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	670										ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)										0.066667	-10.842583	32.940743	15	210	KEEP	---	---	---	---	capture		Silent	SNP	117431240	117431240	4204	7	G	A	A	A	496	39	CTTNBP2	1	1
PTPRZ1	5803	broad.mit.edu	37	7	121637945	121637945	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121637945C>A	uc003vjy.2	+	c.1125C>A	c.(1123-1125)CTC>CTA	p.L375L	PTPRZ1_uc003vjz.2_Silent_p.L375L	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	375	Extracellular (Potential).|Fibronectin type-III.				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.183673	17.14314	21.747285	9	40	KEEP	---	---	---	---	capture		Silent	SNP	121637945	121637945	13272	7	C	A	A	A	366	29	PTPRZ1	2	2
SPAM1	6677	broad.mit.edu	37	7	123593822	123593822	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123593822G>T	uc003vle.2	+	c.198G>T	c.(196-198)GAG>GAT	p.E66D	SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vld.2_Missense_Mutation_p.E66D|SPAM1_uc003vlf.3_Missense_Mutation_p.E66D|SPAM1_uc010lku.2_Missense_Mutation_p.E66D	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	66					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.152542	28.164087	41.812596	18	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123593822	123593822	15489	7	G	T	T	T	438	34	SPAM1	2	2
GRM8	2918	broad.mit.edu	37	7	126079199	126079199	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:126079199T>C	uc003vlr.2	-	c.2701A>G	c.(2701-2703)ATC>GTC	p.I901V	GRM8_uc003vls.2_Non-coding_Transcript|GRM8_uc011kof.1_Non-coding_Transcript|GRM8_uc003vlt.2_3'UTR|GRM8_uc010lkz.1_Non-coding_Transcript	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	901	Cytoplasmic (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				ovary(5)|pancreas(1)	6		Prostate(267;0.186)			L-Glutamic Acid(DB00142)									0.083333	13.524187	49.503187	17	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126079199	126079199	7082	7	T	C	C	C	637	49	GRM8	4	4
CHRM2	1129	broad.mit.edu	37	7	136700830	136700830	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136700830G>T	uc003vtf.1	+	c.1218G>T	c.(1216-1218)ATG>ATT	p.M406I	CHRM2_uc003vtg.1_Missense_Mutation_p.M406I|CHRM2_uc003vtj.1_Missense_Mutation_p.M406I|CHRM2_uc003vtk.1_Missense_Mutation_p.M406I|CHRM2_uc003vtl.1_Missense_Mutation_p.M406I|CHRM2_uc003vtm.1_Missense_Mutation_p.M406I|CHRM2_uc003vti.1_Missense_Mutation_p.M406I|CHRM2_uc003vto.1_Missense_Mutation_p.M406I|CHRM2_uc003vtn.1_Missense_Mutation_p.M406I	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	406	Helical; Name=6; (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)									0.054131	-34.834969	38.709223	19	332	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136700830	136700830	3511	7	G	T	T	T	611	47	CHRM2	2	2
PTN	5764	broad.mit.edu	37	7	136939605	136939605	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136939605C>T	uc003vtq.2	-	c.115_splice	c.e2+1	p.E39_splice	PTN_uc010lmx.2_Splice_Site_SNP_p.E39_splice|PTN_uc003vtr.1_Splice_Site_SNP_p.E39_splice	NM_002825	NP_002816			pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			pancreas(1)	1														0.082192	-0.001662	12.962061	6	67	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	136939605	136939605	13223	7	C	T	T	T	234	18	PTN	5	2
AKR1D1	6718	broad.mit.edu	37	7	137782631	137782631	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:137782631C>A	uc003vtz.2	+	c.398C>A	c.(397-399)CCT>CAT	p.P133H	AKR1D1_uc011kqb.1_Missense_Mutation_p.P133H|AKR1D1_uc011kqc.1_Non-coding_Transcript|AKR1D1_uc011kqd.1_Intron|AKR1D1_uc011kqe.1_Missense_Mutation_p.P133H|AKR1D1_uc011kqf.1_Missense_Mutation_p.P133H|AKR1D1_uc010lmy.1_Non-coding_Transcript	NM_005989	NP_005980	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	133			P -> R (in CBAS2).		androgen metabolic process|bile acid biosynthetic process|bile acid catabolic process|C21-steroid hormone metabolic process|cholesterol catabolic process|digestion|oxidation-reduction process	cytosol	aldo-keto reductase (NADP) activity|delta4-3-oxosteroid 5beta-reductase activity|steroid binding				0														0.092391	10.438039	41.204671	17	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137782631	137782631	476	7	C	A	A	A	312	24	AKR1D1	2	2
EPHB6	2051	broad.mit.edu	37	7	142563859	142563859	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142563859C>A	uc011kst.1	+	c.1247C>A	c.(1246-1248)CCT>CAT	p.P416H	EPHB6_uc011ksu.1_Missense_Mutation_p.P416H|EPHB6_uc003wbs.2_Missense_Mutation_p.P124H|EPHB6_uc003wbt.2_De_novo_Start_InFrame|EPHB6_uc003wbu.2_Missense_Mutation_p.P124H|EPHB6_uc003wbv.2_5'Flank	NM_004445	NP_004436	O15197	EPHB6_HUMAN	ephrin receptor EphB6 precursor	416	Extracellular (Potential).|Fibronectin type-III 1.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(5)|large_intestine(4)|central_nervous_system(3)|ovary(1)|pancreas(1)	14	Melanoma(164;0.059)									313				0.230769	7.017635	7.881683	3	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142563859	142563859	5371	7	C	A	A	A	312	24	EPHB6	2	2
TRPV5	56302	broad.mit.edu	37	7	142612069	142612069	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142612069G>T	uc003wby.1	-	c.1434C>A	c.(1432-1434)TTC>TTA	p.F478L		NM_019841	NP_062815	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel,	478	Cytoplasmic (Potential).				protein tetramerization	apical plasma membrane|integral to plasma membrane	calcium channel activity			ovary(3)|central_nervous_system(2)	5	Melanoma(164;0.059)													0.188976	45.90531	57.435162	24	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142612069	142612069	17150	7	G	T	T	T	581	45	TRPV5	2	2
FAM115A	9747	broad.mit.edu	37	7	143573604	143573604	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143573604C>G	uc003wdo.1	-	c.98G>C	c.(97-99)GGA>GCA	p.G33A	FAM115A_uc011ktu.1_Intron|FAM115A_uc003wdp.1_Missense_Mutation_p.G33A	NM_014719	NP_055534	Q9Y4C2	F115A_HUMAN	hypothetical protein LOC9747	33											0	Melanoma(164;0.0903)													0.089655	11.047517	35.614304	13	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143573604	143573604	5602	7	C	G	G	G	390	30	FAM115A	3	3
GIMAP8	155038	broad.mit.edu	37	7	150174229	150174229	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150174229G>T	uc003whj.2	+	c.1359G>T	c.(1357-1359)GCG>GCT	p.A453A		NM_175571	NP_783161	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	453						endoplasmic reticulum|Golgi apparatus|mitochondrion	GTP binding	p.A453A(1)		ovary(1)|breast(1)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)										0.059908	-16.745896	27.163513	13	204	KEEP	---	---	---	---	capture		Silent	SNP	150174229	150174229	6653	7	G	T	T	T	470	37	GIMAP8	1	1
TMEM176A	55365	broad.mit.edu	37	7	150498728	150498728	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150498728C>A	uc003whx.1	+	c.90C>A	c.(88-90)GCC>GCA	p.A30A	TMEM176B_uc003whu.3_5'Flank|TMEM176B_uc003whv.3_5'Flank|TMEM176B_uc003whw.3_5'Flank	NM_018487	NP_060957	Q96HP8	T176A_HUMAN	hepatocellular carcinoma-associated antigen 112	30						integral to membrane				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.097561	0.762067	7.435838	4	37	KEEP	---	---	---	---	capture		Silent	SNP	150498728	150498728	16626	7	C	A	A	A	262	21	TMEM176A	2	2
ATG9B	285973	broad.mit.edu	37	7	150720217	150720217	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:150720217G>C	uc011kvc.1	-	c.736C>G	c.(736-738)CCA>GCA	p.P246A	ATG9B_uc003wig.3_Non-coding_Transcript	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B	246	Lumenal (By similarity).				autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.098214	12.439893	30.530932	11	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	150720217	150720217	1122	7	G	C	C	C	572	44	ATG9B	3	3
DPP6	1804	broad.mit.edu	37	7	154645512	154645512	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:154645512G>T	uc003wlk.2	+	c.1689G>T	c.(1687-1689)ACG>ACT	p.T563T	DPP6_uc003wli.2_Silent_p.T499T|DPP6_uc003wlm.2_Silent_p.T501T|DPP6_uc011kvq.1_Silent_p.T456T	NM_130797	NP_570629	P42658	DPP6_HUMAN	dipeptidyl-peptidase 6 isoform 1	563	Extracellular (Potential).				cell death|proteolysis	integral to membrane	dipeptidyl-peptidase activity|serine-type peptidase activity			pancreas(3)|breast(1)	4	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			NSCLC(125;1384 1783 2490 7422 34254)								0.072993	-3.103246	22.539646	10	127	KEEP	---	---	---	---	capture		Silent	SNP	154645512	154645512	4914	7	G	T	T	T	496	39	DPP6	1	1
HDAC9	9734	broad.mit.edu	37	7	18914169	18914169	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:18914169C>G	uc003sui.2	+	c.2753C>G	c.(2752-2754)GCA>GGA	p.A918G	HDAC9_uc003sue.2_Missense_Mutation_p.A915G|HDAC9_uc003suh.2_Missense_Mutation_p.A915G|HDAC9_uc003suj.2_Missense_Mutation_p.A874G|HDAC9_uc003suk.2_Missense_Mutation_p.A163G	NM_178425	NP_848512	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 5	915	Histone deacetylase.				B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|specific transcriptional repressor activity|transcription corepressor activity|transcription repressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)									0.12	3.203955	6.752904	3	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18914169	18914169	7297	7	C	G	G	G	325	25	HDAC9	3	3
ITGB8	3696	broad.mit.edu	37	7	20444439	20444439	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20444439C>A	uc003suu.2	+	c.1876C>A	c.(1876-1878)CAC>AAC	p.H626N	ITGB8_uc011jyh.1_Missense_Mutation_p.H491N	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	626	IV.|Cysteine-rich tandem repeats.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(2)	2										842				0.224719	95.631044	108.008653	40	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20444439	20444439	8205	7	C	A	A	A	221	17	ITGB8	2	2
FKBP9	11328	broad.mit.edu	37	7	33014284	33014285	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:33014284_33014285GG>TT	uc011kal.1	+	c.436_437GG>TT	c.(436-438)GGG>TTG	p.G146L	AVL9_uc011kai.1_Intron|FKBP9_uc011kak.1_Intron|FKBP9_uc003tdh.2_Missense_Mutation_p.G93L|FKBP9_uc003tdg.2_Missense_Mutation_p.G93L|FKBP9_uc010kwm.2_5'UTR	NM_007270	NP_009201	O95302	FKBP9_HUMAN	FK506 binding protein 9 precursor	93	PPIase FKBP-type 1.				protein folding	endoplasmic reticulum|membrane	calcium ion binding|FK506 binding|peptidyl-prolyl cis-trans isomerase activity			central_nervous_system(13)|ovary(1)	14			GBM - Glioblastoma multiforme(11;0.0156)											0.041298	-55.404133	21.859262	14	325	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	33014284	33014285	6153	7	GG	TT	TT	TT	455	35	FKBP9	2	2
BBS9	27241	broad.mit.edu	37	7	33644806	33644806	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:33644806G>T	uc003tdn.1	+	c.2633_splice	c.e23-1	p.E878_splice	BBS9_uc003tdo.1_Splice_Site_SNP_p.E843_splice|BBS9_uc003tdp.1_Splice_Site_SNP_p.E873_splice|BBS9_uc003tdq.1_Splice_Site_SNP_p.E838_splice|BBS9_uc010kwn.1_Splice_Site_SNP|BBS9_uc003tdr.1_3'UTR|BBS9_uc003tds.1_Splice_Site_SNP_p.E301_splice|BBS9_uc003tdt.2_Intron	NM_198428	NP_940820			parathyroid hormone-responsive B1 isoform 2						fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding			ovary(3)|skin(1)	4			GBM - Glioblastoma multiforme(11;0.0894)											0.19403	131.350978	160.651389	65	270	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	33644806	33644806	1363	7	G	T	T	T	429	33	BBS9	5	2
AOAH	313	broad.mit.edu	37	7	36634038	36634038	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:36634038T>A	uc003tfh.3	-	c.847_splice	c.e12-1	p.N283_splice	AOAH_uc010kxf.2_Splice_Site_SNP_p.N283_splice|AOAH_uc011kba.1_Splice_Site_SNP_p.N251_splice	NM_001637	NP_001628			acyloxyacyl hydrolase precursor						inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity				0														0.100775	9.003521	29.510107	13	116	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	36634038	36634038	736	7	T	A	A	A	689	53	AOAH	5	3
POU6F2	11281	broad.mit.edu	37	7	39472830	39472830	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:39472830C>A	uc003thb.1	+	c.1181C>A	c.(1180-1182)CCC>CAC	p.P394H		NM_007252	NP_009183	P78424	PO6F2_HUMAN	POU class 6 homeobox 2 isoform 1	394	Gln-rich.				central nervous system development|ganglion mother cell fate determination|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter|visual perception	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1														0.122807	8.182779	16.124323	7	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39472830	39472830	12715	7	C	A	A	A	286	22	POU6F2	2	2
C7orf25	79020	broad.mit.edu	37	7	42949701	42949701	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:42949701A>T	uc003thx.3	-	c.973T>A	c.(973-975)TGC>AGC	p.C325S	C7orf25_uc003thw.2_Missense_Mutation_p.C267S|C7orf25_uc010kxq.2_Missense_Mutation_p.C267S|C7orf25_uc010kxr.2_Missense_Mutation_p.C325S	NM_001099858	NP_001093328	Q9BPX7	CG025_HUMAN	hypothetical protein LOC79020 a	267											0														0.090909	7.06903	31.191155	13	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42949701	42949701	2487	7	A	T	T	T	91	7	C7orf25	3	3
GCK	2645	broad.mit.edu	37	7	44187364	44187364	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44187364G>T	uc003tkk.1	-	c.751C>A	c.(751-753)CGC>AGC	p.R251S	GCK_uc003tkh.1_5'Flank|GCK_uc003tki.1_5'Flank|GCK_uc003tkj.1_Missense_Mutation_p.R249S|GCK_uc003tkl.2_Missense_Mutation_p.R250S	NM_033507	NP_277042	P35557	HXK4_HUMAN	glucokinase isoform 2	250					cellular response to insulin stimulus|cellular response to leptin stimulus|detection of glucose|endocrine pancreas development|glucose homeostasis|glucose transport|glycolysis|negative regulation of gluconeogenesis|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|regulation of glucose transport|regulation of glycolysis|transmembrane transport	cytosol|nucleoplasm	ATP binding|glucokinase activity|glucose binding|protein binding			lung(1)|skin(1)	2									p.R250C(NCIH1651-Tumor)|p.R250C(DV90-Tumor)	356				0.129032	6.186799	10.333852	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44187364	44187364	6559	7	G	T	T	T	507	39	GCK	1	1
RAMP3	10268	broad.mit.edu	37	7	45216911	45216911	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:45216911G>A	uc003tnb.2	+	c.62G>A	c.(61-63)GGG>GAG	p.G21E	RAMP3_uc003tnc.2_5'UTR	NM_005856	NP_005847	O60896	RAMP3_HUMAN	receptor activity modifying protein 3 precursor	21					intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway	integral to plasma membrane|lysosome	protein transporter activity				0					Pramlintide(DB01278)									0.285714	27.141384	28.580059	10	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45216911	45216911	13483	7	G	A	A	A	559	43	RAMP3	2	2
C7orf26	79034	broad.mit.edu	37	7	6631360	6631360	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:6631360G>C	uc003sqo.1	+	c.276G>C	c.(274-276)CAG>CAC	p.Q92H	C7orf26_uc003sqp.1_Missense_Mutation_p.Q73H|C7orf26_uc003sqq.1_5'UTR	NM_024067	NP_076972	Q96N11	CG026_HUMAN	hypothetical protein LOC79034	92										ovary(1)	1		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)										0.128655	41.969821	64.905086	22	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6631360	6631360	2488	7	G	C	C	C	425	33	C7orf26	3	3
BAZ1B	9031	broad.mit.edu	37	7	72883886	72883886	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:72883886C>A	uc003tyc.2	-	c.2827G>T	c.(2827-2829)GAC>TAC	p.D943Y		NM_032408	NP_115784	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	943					ATP-dependent chromatin remodeling|chromatin-mediated maintenance of transcription|DNA replication-dependent nucleosome disassembly|double-strand break repair|heart morphogenesis|transcription, DNA-dependent	WINAC complex	ATP binding|chromatin binding|histone acetyl-lysine binding|histone kinase activity|non-membrane spanning protein tyrosine kinase activity|protein complex scaffold|transcription regulator activity|vitamin D receptor activator activity|vitamin D receptor binding|zinc ion binding			ovary(4)|breast(1)	5		Lung NSC(55;0.0659)|all_lung(88;0.152)				Esophageal Squamous(112;1167 1561 21085 43672 48228)								0.145833	20.592395	32.168982	14	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72883886	72883886	1351	7	C	A	A	A	416	32	BAZ1B	2	2
GRM3	2913	broad.mit.edu	37	7	86416287	86416287	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:86416287G>T	uc003uid.2	+	c.1179G>T	c.(1177-1179)GTG>GTT	p.V393V	GRM3_uc010lef.2_Silent_p.V391V|GRM3_uc010leg.2_Silent_p.V265V|GRM3_uc010leh.2_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	393	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.061111	-18.056056	18.352777	11	169	KEEP	---	---	---	---	capture		Silent	SNP	86416287	86416287	7077	7	G	T	T	T	600	47	GRM3	2	2
GTPBP10	85865	broad.mit.edu	37	7	90014232	90014232	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:90014232A>C	uc003ukm.1	+	c.928A>C	c.(928-930)ATG>CTG	p.M310L	GTPBP10_uc003ukn.1_Missense_Mutation_p.M231L|GTPBP10_uc003uko.1_Missense_Mutation_p.M120L|CLDN12_uc003ukp.2_5'UTR|CLDN12_uc003ukq.2_5'UTR	NM_033107	NP_149098	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 isoform 2	310					ribosome biogenesis	chromosome|nucleolus	GTP binding|GTPase activity|magnesium ion binding				0														0.086022	4.153964	20.280514	8	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90014232	90014232	7159	7	A	C	C	C	104	8	GTPBP10	4	4
SAMD9	54809	broad.mit.edu	37	7	92735270	92735270	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:92735270C>A	uc003umf.2	-	c.141G>T	c.(139-141)AAG>AAT	p.K47N	SAMD9_uc003umg.2_Missense_Mutation_p.K47N	NM_017654	NP_060124	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	47	SAM.					cytoplasm				ovary(3)|breast(1)|central_nervous_system(1)	5	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)											0.0837	1.644095	41.620022	19	208	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92735270	92735270	14306	7	C	A	A	A	259	20	SAMD9	2	2
CALCR	799	broad.mit.edu	37	7	93065453	93065453	+	Silent	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:93065453G>A	uc003umv.1	-	c.1062C>T	c.(1060-1062)GTC>GTT	p.V354V	CALCR_uc011kia.1_Silent_p.V134V|CALCR_uc003ums.1_Non-coding_Transcript|CALCR_uc003umt.1_Non-coding_Transcript|CALCR_uc003umu.1_Silent_p.V320V|CALCR_uc003umw.2_Silent_p.V320V	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor isoform 2 precursor	336	Helical; Name=5; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(1)|pancreas(1)	5	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)									0.083916	1.994933	27.134543	12	131	KEEP	---	---	---	---	capture		Silent	SNP	93065453	93065453	2695	7	G	A	A	A	522	41	CALCR	2	2
CASD1	64921	broad.mit.edu	37	7	94166868	94166868	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:94166868A>G	uc003uni.3	+	c.928A>G	c.(928-930)ACT>GCT	p.T310A	CASD1_uc003unh.2_3'UTR|CASD1_uc003unj.3_Missense_Mutation_p.T310A	NM_022900	NP_075051	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1 precursor	310						integral to membrane				ovary(2)	2	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)											0.086643	16.34132	64.21383	24	253	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94166868	94166868	2783	7	A	G	G	G	182	14	CASD1	4	4
STAG3	10734	broad.mit.edu	37	7	99786548	99786548	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99786548T>C	uc003utx.1	+	c.624T>C	c.(622-624)TAT>TAC	p.Y208Y	STAG3_uc010lgs.1_5'UTR|STAG3_uc011kjk.1_Silent_p.Y150Y	NM_012447	NP_036579	Q9UJ98	STAG3_HUMAN	stromal antigen 3	208					chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(3)|skin(2)|lung(1)|kidney(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)									331				0.131222	45.132441	74.343575	29	192	KEEP	---	---	---	---	capture		Silent	SNP	99786548	99786548	15762	7	T	C	C	C	660	51	STAG3	4	4
RP1L1	94137	broad.mit.edu	37	8	10467521	10467521	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10467521C>T	uc003wtc.2	-	c.4087G>A	c.(4087-4089)GGA>AGA	p.G1363R		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	1363					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.126697	35.761786	65.804269	28	193	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10467521	10467521	14012	8	C	T	T	T	312	24	RP1L1	2	2
RIMS2	9699	broad.mit.edu	37	8	104898361	104898361	+	Silent	SNP	T	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:104898361T>C	uc003yls.2	+	c.868T>C	c.(868-870)TTG>CTG	p.L290L	RIMS2_uc003ylp.2_Silent_p.L512L|RIMS2_uc003ylw.2_Silent_p.L320L|RIMS2_uc003ylq.2_Silent_p.L320L|RIMS2_uc003ylr.2_Silent_p.L320L	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	543					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)							728				0.092511	17.68804	55.705463	21	206	KEEP	---	---	---	---	capture		Silent	SNP	104898361	104898361	13845	8	T	C	C	C	777	60	RIMS2	4	4
LRP12	29967	broad.mit.edu	37	8	105510247	105510247	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:105510247C>A	uc003yma.2	-	c.533G>T	c.(532-534)TGT>TTT	p.C178F	LRP12_uc003ymb.2_Missense_Mutation_p.C159F|LRP12_uc003ylz.2_5'Flank	NM_013437	NP_038465	Q9Y561	LRP12_HUMAN	low density lipoprotein-related protein 12	178	Extracellular (Potential).|LDL-receptor class A 1.				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding				0			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)											0.153374	46.36404	65.099162	25	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105510247	105510247	9327	8	C	A	A	A	221	17	LRP12	2	2
TRPS1	7227	broad.mit.edu	37	8	116617216	116617216	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:116617216C>A	uc003yny.2	-	c.980G>T	c.(979-981)GGA>GTA	p.G327V	TRPS1_uc011lhy.1_Missense_Mutation_p.G318V|TRPS1_uc010mcy.2_Missense_Mutation_p.G314V|TRPS1_uc003ynz.2_Missense_Mutation_p.G314V	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	314					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)							312				0.038251	-30.837831	11.364511	7	176	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116617216	116617216	17144	8	C	A	A	A	390	30	TRPS1	2	2
TRPS1	7227	broad.mit.edu	37	8	116631936	116631936	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:116631936G>C	uc003yny.2	-	c.389C>G	c.(388-390)GCT>GGT	p.A130G	TRPS1_uc011lhy.1_Missense_Mutation_p.A121G|TRPS1_uc010mcy.2_Missense_Mutation_p.A117G|TRPS1_uc003ynz.2_Missense_Mutation_p.A117G	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	117					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)							312				0.1	14.206539	38.192884	15	135	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116631936	116631936	17144	8	G	C	C	C	442	34	TRPS1	3	3
COL14A1	7373	broad.mit.edu	37	8	121309761	121309761	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:121309761G>C	uc003yox.2	+	c.4248G>C	c.(4246-4248)CAG>CAC	p.Q1416H	COL14A1_uc003yoz.2_Missense_Mutation_p.Q381H	NM_021110	NP_066933	Q05707	COEA1_HUMAN	collagen, type XIV, alpha 1 precursor	1416	Nonhelical region (NC4).|TSP N-terminal.				cell-cell adhesion|collagen fibril organization	collagen type XIV|extracellular space	collagen binding|extracellular matrix structural constituent|protein binding, bridging			ovary(4)|kidney(4)|skin(2)|pancreas(1)|central_nervous_system(1)	12	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)							1131				0.122449	18.927817	32.606463	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121309761	121309761	3809	8	G	C	C	C	425	33	COL14A1	3	3
TG	7038	broad.mit.edu	37	8	133953640	133953640	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133953640G>A	uc003ytw.2	+	c.5086G>A	c.(5086-5088)GGT>AGT	p.G1696S	TG_uc010mdw.2_Missense_Mutation_p.G455S|TG_uc011ljb.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1696	Type IIIA.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.082803	3.47521	86.843475	39	432	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133953640	133953640	16341	8	G	A	A	A	611	47	TG	2	2
ZFAT	57623	broad.mit.edu	37	8	135612705	135612705	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:135612705C>A	uc003yup.2	-	c.2449G>T	c.(2449-2451)GCA>TCA	p.A817S	ZFAT_uc003yun.2_Missense_Mutation_p.A805S|ZFAT_uc003yuo.2_Missense_Mutation_p.A805S|ZFAT_uc010meh.2_Missense_Mutation_p.A805S|ZFAT_uc010mei.2_Non-coding_Transcript|ZFAT_uc003yuq.2_Missense_Mutation_p.A805S|ZFAT_uc010mej.2_Missense_Mutation_p.A755S|ZFAT_uc003yur.2_Missense_Mutation_p.A805S|ZFATAS_uc003yus.1_Non-coding_Transcript	NM_020863	NP_065914	Q9P243	ZFAT_HUMAN	zinc finger protein 406 isoform ZFAT-1	817	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)											0.071429	-8.68496	28.308801	14	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135612705	135612705	18220	8	C	A	A	A	338	26	ZFAT	2	2
COL22A1	169044	broad.mit.edu	37	8	139707074	139707074	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139707074C>A	uc003yvd.2	-	c.2641G>T	c.(2641-2643)GAA>TAA	p.E881*	COL22A1_uc011ljo.1_Nonsense_Mutation_p.E181*	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	881	Pro-rich.|Gly-rich.|Collagen-like 7.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.109091	9.828895	34.842573	18	147	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	139707074	139707074	3819	8	C	A	A	A	390	30	COL22A1	5	2
DLGAP2	9228	broad.mit.edu	37	8	1497609	1497609	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:1497609G>T	uc003wpl.2	+	c.750G>T	c.(748-750)GCG>GCT	p.A250A	DLGAP2_uc003wpm.2_Silent_p.A250A	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	329					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)										0.094937	8.274	34.25178	15	143	KEEP	---	---	---	---	capture		Silent	SNP	1497609	1497609	4740	8	G	T	T	T	483	38	DLGAP2	1	1
CSGALNACT1	55790	broad.mit.edu	37	8	19276199	19276199	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:19276199G>T	uc011kyn.1	-	c.1195C>A	c.(1195-1197)CAT>AAT	p.H399N	CSGALNACT1_uc011kyo.1_Missense_Mutation_p.H399N|CSGALNACT1_uc003wzg.2_Non-coding_Transcript|CSGALNACT1_uc011kyp.1_Missense_Mutation_p.H398N	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	399	Lumenal (Potential).				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)										0.149425	21.514362	31.773013	13	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19276199	19276199	4079	8	G	T	T	T	611	47	CSGALNACT1	2	2
CSGALNACT1	55790	broad.mit.edu	37	8	19278006	19278006	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:19278006G>T	uc011kyn.1	-	c.977C>A	c.(976-978)ACC>AAC	p.T326N	CSGALNACT1_uc011kyo.1_Missense_Mutation_p.T326N|CSGALNACT1_uc003wzg.2_Non-coding_Transcript|CSGALNACT1_uc011kyp.1_Missense_Mutation_p.T325N	NM_001130518	NP_001123990	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	326	Lumenal (Potential).				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity			central_nervous_system(2)|ovary(1)	3				Colorectal(111;0.182)										0.115265	41.043243	87.869632	37	284	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19278006	19278006	4079	8	G	T	T	T	572	44	CSGALNACT1	2	2
KIF13B	23303	broad.mit.edu	37	8	28988082	28988082	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28988082C>A	uc003xhh.3	-	c.3043G>T	c.(3043-3045)GTC>TTC	p.V1015F		NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1015					microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)										0.117647	15.275705	32.375511	14	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28988082	28988082	8586	8	C	A	A	A	221	17	KIF13B	2	2
RBPMS	11030	broad.mit.edu	37	8	30332327	30332327	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:30332327G>T	uc011lba.1	+	c.99G>T	c.(97-99)CTG>CTT	p.L33L	RBPMS_uc003xic.1_Silent_p.L33L|RBPMS_uc003xid.1_Silent_p.L33L|RBPMS_uc003xie.1_Silent_p.L33L|RBPMS_uc003xif.1_5'Flank|RBPMS_uc003xib.2_Silent_p.L33L|RBPMS_uc010lvh.1_5'UTR	NM_006867	NP_006858	Q93062	RBPMS_HUMAN	RNA-binding protein with multiple splicing	33	RRM.				positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	cytoplasm|nucleus	nucleotide binding|poly(A) RNA binding|protein binding|transcription coactivator activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)										0.134615	78.368434	125.44952	49	315	KEEP	---	---	---	---	capture		Silent	SNP	30332327	30332327	13632	8	G	T	T	T	600	47	RBPMS	2	2
POTEA	340441	broad.mit.edu	37	8	43147866	43147866	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:43147866G>T	uc003xpz.1	+	c.239G>T	c.(238-240)AGA>ATA	p.R80I	POTEA_uc003xqa.1_Missense_Mutation_p.R80I	NM_001005365	NP_001005365	Q6S8J7	POTEA_HUMAN	POTE ankyrin domain family, member A isoform 2	80										ovary(1)	1														0.127273	6.139212	13.719431	7	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43147866	43147866	12690	8	G	T	T	T	429	33	POTEA	2	2
JPH1	56704	broad.mit.edu	37	8	75156958	75156958	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:75156958C>A	uc003yae.2	-	c.1711G>T	c.(1711-1713)GAT>TAT	p.D571Y	JPH1_uc003yaf.2_Missense_Mutation_p.D571Y|JPH1_uc003yag.1_Missense_Mutation_p.D435Y	NM_020647	NP_065698	Q9HDC5	JPH1_HUMAN	junctophilin 1	571	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional membrane complex|junctional sarcoplasmic reticulum membrane|plasma membrane				ovary(1)	1	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)											0.091371	11.937975	45.04595	18	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75156958	75156958	8264	8	C	A	A	A	403	31	JPH1	1	1
ZFHX4	79776	broad.mit.edu	37	8	77690615	77690615	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77690615C>G	uc003yav.2	+	c.3187C>G	c.(3187-3189)CCA>GCA	p.P1063A	ZFHX4_uc003yau.1_Missense_Mutation_p.P1089A|ZFHX4_uc003yaw.1_Missense_Mutation_p.P1063A	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1063					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.11413	57.024062	111.096605	42	326	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77690615	77690615	18223	8	C	G	G	G	234	18	ZFHX4	3	3
PSKH2	85481	broad.mit.edu	37	8	87060802	87060802	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87060802C>A	uc011lfy.1	-	c.1047G>T	c.(1045-1047)CAG>CAT	p.Q349H		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	349					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3			STAD - Stomach adenocarcinoma(118;0.129)							100				0.044674	-41.88748	22.674946	13	278	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87060802	87060802	13118	8	C	A	A	A	415	32	PSKH2	2	2
SLC26A7	115111	broad.mit.edu	37	8	92307886	92307886	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:92307886G>T	uc003yez.2	+	c.432G>T	c.(430-432)AGG>AGT	p.R144S	SLC26A7_uc003yex.2_Missense_Mutation_p.R144S|SLC26A7_uc003yey.2_Non-coding_Transcript|SLC26A7_uc003yfa.2_Missense_Mutation_p.R144S	NM_134266	NP_599028	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform b	144	Extracellular (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)											0.114504	10.146551	29.342502	15	116	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92307886	92307886	15019	8	G	T	T	T	529	41	SLC26A7	2	2
RUNX1T1	862	broad.mit.edu	37	8	93026929	93026929	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:93026929G>A	uc011lgi.1	-	c.379C>T	c.(379-381)CCA>TCA	p.P127S	RUNX1T1_uc003yfc.1_Missense_Mutation_p.P89S|RUNX1T1_uc003yfd.2_Missense_Mutation_p.P116S|RUNX1T1_uc003yfe.1_Missense_Mutation_p.P79S|RUNX1T1_uc010mao.2_Missense_Mutation_p.P89S|RUNX1T1_uc003yfh.1_Missense_Mutation_p.P79S|RUNX1T1_uc003yfb.1_Missense_Mutation_p.P79S|RUNX1T1_uc003yff.1_Missense_Mutation_p.P79S|RUNX1T1_uc003yfg.1_Missense_Mutation_p.P79S	NM_175636	NP_783554	Q06455	MTG8_HUMAN	acute myelogenous leukemia 1 translocation 1	116					generation of precursor metabolites and energy|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)|central_nervous_system(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(11;0.0141)							213				0.155	57.834245	80.465786	31	169	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93026929	93026929	14227	8	G	A	A	A	559	43	RUNX1T1	2	2
RPL30	6156	broad.mit.edu	37	8	99054972	99054972	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:99054972C>A	uc003yif.2	-	c.199G>T	c.(199-201)GCT>TCT	p.A67S	RPL30_uc010mbk.1_Intron|SNORA72_uc003yig.1_5'Flank	NM_000989	NP_000980	P62888	RL30_HUMAN	ribosomal protein L30	67					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.192)											0.052632	-9.894076	10.186052	5	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99054972	99054972	14059	8	C	A	A	A	338	26	RPL30	2	2
TBC1D2	55357	broad.mit.edu	37	9	100983155	100983155	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:100983155C>A	uc011lvb.1	-	c.1334G>T	c.(1333-1335)AGG>ATG	p.R445M	TBC1D2_uc004ayq.2_Missense_Mutation_p.R445M|TBC1D2_uc004ayr.2_Missense_Mutation_p.R227M|TBC1D2_uc004ayo.3_Missense_Mutation_p.R445M	NM_018421	NP_060891	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	445						cell junction|cytoplasmic membrane-bounded vesicle|nucleus	Rab GTPase activator activity			ovary(3)	3		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)										0.1	2.971322	9.363611	4	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100983155	100983155	16130	9	C	A	A	A	312	24	TBC1D2	2	2
SVEP1	79987	broad.mit.edu	37	9	113139550	113139550	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113139550C>A	uc010mtz.2	-	c.10504_splice	c.e45+1	p.P3502_splice	SVEP1_uc010mty.2_Splice_Site_SNP_p.P1428_splice	NM_153366	NP_699197			polydom						cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.05102	-10.380868	10.518617	5	93	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	113139550	113139550	15940	9	C	A	A	A	247	19	SVEP1	5	1
SVEP1	79987	broad.mit.edu	37	9	113228273	113228273	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:113228273C>A	uc010mtz.2	-	c.3194G>T	c.(3193-3195)GGA>GTA	p.G1065V	SVEP1_uc010mua.1_Missense_Mutation_p.G1065V	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1065					cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.151515	8.052951	11.89184	5	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113228273	113228273	15940	9	C	A	A	A	390	30	SVEP1	2	2
C9orf84	158401	broad.mit.edu	37	9	114454436	114454436	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:114454436A>G	uc004bfr.2	-	c.3629T>C	c.(3628-3630)ATA>ACA	p.I1210T	C9orf84_uc011lwt.1_Non-coding_Transcript|C9orf84_uc004bfq.2_Missense_Mutation_p.I1171T|C9orf84_uc010mug.2_Missense_Mutation_p.I1121T	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	1210										ovary(2)	2														0.132231	29.821911	45.713639	16	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114454436	114454436	2616	9	A	G	G	G	208	16	C9orf84	4	4
ASTN2	23245	broad.mit.edu	37	9	119858334	119858334	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:119858334C>A	uc004bjs.1	-	c.1265G>T	c.(1264-1266)CGC>CTC	p.R422L	ASTN2_uc004bjr.1_Missense_Mutation_p.R422L|ASTN2_uc004bjt.1_Missense_Mutation_p.R371L	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	422	Cytoplasmic (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.119403	20.222278	39.262559	16	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119858334	119858334	1084	9	C	A	A	A	351	27	ASTN2	1	1
ASTN2	23245	broad.mit.edu	37	9	119976740	119976740	+	Silent	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:119976740C>A	uc004bjs.1	-	c.912G>T	c.(910-912)CGG>CGT	p.R304R	ASTN2_uc004bjr.1_Silent_p.R304R|ASTN2_uc004bjt.1_Silent_p.R304R	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	304	Cytoplasmic (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.147826	25.613922	39.303756	17	98	KEEP	---	---	---	---	capture		Silent	SNP	119976740	119976740	1084	9	C	A	A	A	275	22	ASTN2	2	2
ASTN2	23245	broad.mit.edu	37	9	119977022	119977022	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:119977022C>A	uc004bjs.1	-	c.631_splice	c.e3-1	p.G211_splice	ASTN2_uc004bjr.1_Splice_Site_SNP_p.G211_splice|ASTN2_uc004bjt.1_Splice_Site_SNP_p.G211_splice	NM_198187	NP_937830			astrotactin 2 isoform c							integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.134831	15.863443	27.351163	12	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	119977022	119977022	1084	9	C	A	A	A	312	24	ASTN2	5	2
PHYHD1	254295	broad.mit.edu	37	9	131689416	131689416	+	Missense_Mutation	SNP	G	T	T	rs17481121		TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:131689416G>T	uc004bwn.2	+	c.133G>T	c.(133-135)GTT>TTT	p.V45F	PHYHD1_uc004bwo.2_Missense_Mutation_p.V45F|PHYHD1_uc004bwm.2_Non-coding_Transcript|PHYHD1_uc004bwp.2_Missense_Mutation_p.V45F	NM_174933	NP_777593	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	45					oxidation-reduction process		metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0												OREG0019526	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.068493	-3.072719	10.975392	5	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131689416	131689416	12289	9	G	T	T	T	624	48	PHYHD1	2	2
GPR107	57720	broad.mit.edu	37	9	132854594	132854594	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:132854594A>T	uc004bze.2	+	c.797A>T	c.(796-798)TAC>TTC	p.Y266F	GPR107_uc004bzb.2_Missense_Mutation_p.Y77F|GPR107_uc004bzc.3_Non-coding_Transcript|GPR107_uc011mbx.1_Missense_Mutation_p.Y266F|GPR107_uc004bzd.2_Missense_Mutation_p.Y266F	NM_001136557	NP_001130029	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107 isoform 1	266	Helical; Name=1; (Potential).					integral to membrane					0		Ovarian(14;0.000531)												0.127168	29.930781	53.299126	22	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132854594	132854594	6897	9	A	T	T	T	182	14	GPR107	3	3
SETX	23064	broad.mit.edu	37	9	135140162	135140162	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135140162C>A	uc004cbk.2	-	c.7498G>T	c.(7498-7500)GCC>TCC	p.A2500S	SETX_uc004cbj.2_Missense_Mutation_p.A2148S|SETX_uc010mzt.2_Missense_Mutation_p.A2086S	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	2500					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA binding|DNA helicase activity			ovary(2)	2		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)										0.074468	-5.486185	29.461418	14	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135140162	135140162	14630	9	C	A	A	A	325	25	SETX	2	2
ADAMTSL1	92949	broad.mit.edu	37	9	18622356	18622356	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:18622356C>G	uc003zne.3	+	c.590C>G	c.(589-591)TCC>TGC	p.S197C	ADAMTSL1_uc003znb.2_Missense_Mutation_p.S197C|ADAMTSL1_uc003znc.3_Missense_Mutation_p.S197C	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	197						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|lung(1)	4				GBM - Glioblastoma multiforme(50;1.29e-17)										0.146067	24.752598	35.65281	13	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18622356	18622356	275	9	C	G	G	G	390	30	ADAMTSL1	3	3
CDKN2A	1029	broad.mit.edu	37	9	21971108	21971108	+	Missense_Mutation	SNP	C	T	T	rs11552822		TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:21971108C>T	uc003zpl.2	-	c.416G>A	c.(415-417)CGA>CAA	p.R139Q	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpj.2_3'UTR|CDKN2A_uc003zpk.2_Missense_Mutation_p.D84N|CDKN2A_uc010miu.2_Non-coding_Transcript	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4	Error:Variant_position_missing_in_P42771_after_alignment					cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(425)|p.D84Y(9)|p.D84N(3)|p.D84fs*63(2)|p.D84H(2)|p.H83fs*2(2)|p.E61_L94del(1)|p.V82_E88del(1)|p.V82_G89>G(1)|p.D84fs*0(1)|p.D84_F90del(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)			D84Y(LK2_LUNG)|D84Y(DU145_PROSTATE)	17	p.R139L(GSS-Tumor)|p.R139Q(LK2-Tumor)	76	TSP Lung(5;3.83e-07)			0.241379	17.147391	18.892187	7	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21971108	21971108	3290	9	C	T	T	T	403	31	CDKN2A	1	1
VLDLR	7436	broad.mit.edu	37	9	2652803	2652803	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:2652803G>T	uc003zhk.1	+	c.2440G>T	c.(2440-2442)GGT>TGT	p.G814C	VLDLR_uc003zhl.1_Missense_Mutation_p.G786C|VLDLR_uc003zhm.1_Non-coding_Transcript|VLDLR_uc003zhn.1_Missense_Mutation_p.G745C	NM_003383	NP_003374	P98155	VLDLR_HUMAN	very low density lipoprotein receptor isoform a	814	Helical; (Potential).				cholesterol metabolic process|endocytosis|lipid transport|memory|very-low-density lipoprotein particle clearance	coated pit|integral to membrane|membrane fraction|plasma membrane|very-low-density lipoprotein particle	apolipoprotein binding|calcium ion binding|low-density lipoprotein receptor activity|very-low-density lipoprotein particle receptor activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)										0.083333	1.233272	11.814751	5	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2652803	2652803	17741	9	G	T	T	T	455	35	VLDLR	2	2
DNAI1	27019	broad.mit.edu	37	9	34514443	34514443	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:34514443A>G	uc003zum.2	+	c.1621A>G	c.(1621-1623)ATG>GTG	p.M541V		NM_012144	NP_036276	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	541	WD 3.				cell projection organization	cilium axoneme|cytoplasm|dynein complex|microtubule	motor activity				0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)										0.099099	9.855739	27.679724	11	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34514443	34514443	4792	9	A	G	G	G	104	8	DNAI1	4	4
SEMA4D	10507	broad.mit.edu	37	9	92007407	92007407	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:92007407C>A	uc004aqo.1	-	c.553G>T	c.(553-555)GAA>TAA	p.E185*	SEMA4D_uc011ltm.1_Nonsense_Mutation_p.E185*|SEMA4D_uc011ltn.1_Non-coding_Transcript|SEMA4D_uc011lto.1_Non-coding_Transcript|SEMA4D_uc004aqp.1_Nonsense_Mutation_p.E183*	NM_006378	NP_006369	Q92854	SEM4D_HUMAN	semaphorin 4D isoform 1	185	Sema.|Extracellular (Potential).				anti-apoptosis|axon guidance|cell adhesion|immune response	integral to membrane|plasma membrane	receptor activity|receptor binding			ovary(1)|pancreas(1)	2														0.058824	-5.043812	8.80597	4	64	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	92007407	92007407	14520	9	C	A	A	A	377	29	SEMA4D	5	2
ROR2	4920	broad.mit.edu	37	9	94486259	94486259	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:94486259C>T	uc004arj.1	-	c.2517G>A	c.(2515-2517)CCG>CCA	p.P839P	ROR2_uc004ari.1_Intron	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	839	Cytoplasmic (Potential).|Pro-rich.				negative regulation of cell proliferation|positive regulation of cell migration|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(6)|central_nervous_system(5)|ovary(3)|large_intestine(2)	16									p.P839P(BFTC905-Tumor)	461				0.1	8.70286	24.661003	10	90	KEEP	---	---	---	---	capture		Silent	SNP	94486259	94486259	14006	9	C	T	T	T	288	23	ROR2	1	1
COL4A5	1287	broad.mit.edu	37	X	107930917	107930917	+	Silent	SNP	A	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107930917A>G	uc004enz.1	+	c.4521A>G	c.(4519-4521)CAA>CAG	p.Q1507Q	COL4A5_uc011mso.1_Silent_p.Q1504Q|COL4A5_uc011msp.1_Silent_p.Q183Q	NM_033380	NP_203699	P29400	CO4A5_HUMAN	type IV collagen alpha 5 isoform 2 precursor	1501	Collagen IV NC1.				axon guidance	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(3)|central_nervous_system(1)	4														0.15493	47.755946	63.912787	22	120	KEEP	---	---	---	---	capture		Silent	SNP	107930917	107930917	3832	23	A	G	G	G	37	3	COL4A5	4	4
TRPC5	7224	broad.mit.edu	37	X	111195283	111195283	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:111195283G>T	uc004epl.1	-	c.366C>A	c.(364-366)AGC>AGA	p.S122R	TRPC5_uc004epm.1_Missense_Mutation_p.S122R	NM_012471	NP_036603	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel,	122	ANK 3.|Cytoplasmic (Potential).				axon guidance	calcium channel complex|integral to plasma membrane	protein binding|store-operated calcium channel activity			urinary_tract(1)	1														0.33945	211.409022	216.364121	74	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111195283	111195283	17133	23	G	T	T	T	490	38	TRPC5	1	1
LHFPL1	340596	broad.mit.edu	37	X	111914413	111914413	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:111914413C>G	uc004epp.2	-	c.275G>C	c.(274-276)CGC>CCC	p.R92P	LHFPL1_uc004epq.2_Missense_Mutation_p.R69P|LHFPL1_uc010nqa.2_Intron|LHFPL1_uc010nqb.2_Missense_Mutation_p.R69P	NM_178175	NP_835469	Q86WI0	LHPL1_HUMAN	lipoma HMGIC fusion partner-like 1 precursor	69						integral to membrane					0														0.164557	44.99121	62.029918	26	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111914413	111914413	9090	23	C	G	G	G	351	27	LHFPL1	3	3
KIAA1210	57481	broad.mit.edu	37	X	118221794	118221794	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118221794C>A	uc004era.3	-	c.3399G>T	c.(3397-3399)CAG>CAT	p.Q1133H		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1133										ovary(4)|skin(1)	5														0.346939	140.254818	143.260983	51	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118221794	118221794	8522	23	C	A	A	A	363	28	KIAA1210	2	2
SEPT6	23157	broad.mit.edu	37	X	118771148	118771148	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118771148C>A	uc011mtw.1	-	c.888G>T	c.(886-888)GAG>GAT	p.E296D	SEPT6_uc010nqk.2_Intron|SEPT6_uc004ers.2_Missense_Mutation_p.E266D|SEPT6_uc004ert.2_Missense_Mutation_p.E266D|SEPT6_uc004eru.2_Missense_Mutation_p.E266D|SEPT6_uc004erv.2_Missense_Mutation_p.E266D|SEPT6_uc004erw.2_Missense_Mutation_p.E208D|SEPT6_uc011mtv.1_Missense_Mutation_p.E208D	NM_145800	NP_665799	Q14141	SEPT6_HUMAN	septin 6 isoform A	266					cell cycle|cytokinesis|interspecies interaction between organisms	cleavage furrow|condensed chromosome kinetochore|midbody|septin complex|spindle	GTP binding|protein binding			kidney(1)	1										265				0.262069	91.094206	98.516151	38	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118771148	118771148	14554	23	C	A	A	A	311	24	SEPT6	2	2
MAGEC1	9947	broad.mit.edu	37	X	140993918	140993919	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:140993918_140993919CC>AA	uc004fbt.2	+	c.728_729CC>AA	c.(727-729)TCC>TAA	p.S243*	MAGEC1_uc010nsl.1_Intron	NM_005462	NP_005453	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	243							protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)													0.127135	76.301436	147.811777	67	460	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	140993918	140993919	9561	23	CC	AA	AA	AA	390	30	MAGEC1	5	2
CTPS2	56474	broad.mit.edu	37	X	16711541	16711541	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:16711541C>A	uc004cxk.2	-	c.508G>T	c.(508-510)GCG>TCG	p.A170S	CTPS2_uc004cxl.2_Missense_Mutation_p.A170S|CTPS2_uc004cxm.2_Missense_Mutation_p.A170S	NM_001144002	NP_001137474	Q9NRF8	PYRG2_HUMAN	cytidine triphosphate synthase II	170					glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|pyrimidine nucleotide biosynthetic process	cytosol	ATP binding|CTP synthase activity			ovary(1)	1	Hepatocellular(33;0.0997)													0.18125	52.567625	67.8657	29	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16711541	16711541	4182	23	C	A	A	A	338	26	CTPS2	2	2
CNKSR2	22866	broad.mit.edu	37	X	21627541	21627541	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:21627541A>T	uc004czx.1	+	c.2498A>T	c.(2497-2499)CAA>CTA	p.Q833L	CNKSR2_uc004czw.2_Missense_Mutation_p.Q833L|CNKSR2_uc011mjn.1_Missense_Mutation_p.Q784L|CNKSR2_uc011mjo.1_Missense_Mutation_p.Q803L|CNKSR2_uc004czy.2_Missense_Mutation_p.Q425L	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	833					regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)	1														0.126582	13.926522	24.648453	10	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21627541	21627541	3745	23	A	T	T	T	65	5	CNKSR2	3	3
EIF2S3	1968	broad.mit.edu	37	X	24094891	24094891	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24094891G>T	uc004dbc.2	+	c.1408G>T	c.(1408-1410)GAT>TAT	p.D470Y		NM_001415	NP_001406	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2,	470						cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1														0.253521	43.812022	47.730683	18	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24094891	24094891	5200	23	G	T	T	T	429	33	EIF2S3	2	2
MXRA5	25878	broad.mit.edu	37	X	3240108	3240108	+	Silent	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:3240108C>G	uc004crg.3	-	c.3618G>C	c.(3616-3618)GTG>GTC	p.V1206V		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	1206						extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.287356	65.938823	69.467929	25	62	KEEP	---	---	---	---	capture		Silent	SNP	3240108	3240108	10397	23	C	G	G	G	262	21	MXRA5	3	3
FAM47A	158724	broad.mit.edu	37	X	34149563	34149563	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34149563G>T	uc004ddg.2	-	c.833C>A	c.(832-834)GCT>GAT	p.A278D		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	278										ovary(4)|central_nervous_system(1)	5														0.25641	23.128097	25.229348	10	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34149563	34149563	5790	23	G	T	T	T	442	34	FAM47A	2	2
FAM47B	170062	broad.mit.edu	37	X	34961677	34961677	+	Silent	SNP	C	G	G			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34961677C>G	uc004ddi.1	+	c.729C>G	c.(727-729)CGC>CGG	p.R243R		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	243	Pro-rich.									ovary(3)|breast(1)	4														0.117647	7.420493	14.743764	6	45	KEEP	---	---	---	---	capture		Silent	SNP	34961677	34961677	5791	23	C	G	G	G	340	27	FAM47B	3	3
CYBB	1536	broad.mit.edu	37	X	37668873	37668873	+	Silent	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37668873G>T	uc004ddr.2	+	c.1515G>T	c.(1513-1515)CTG>CTT	p.L505L	CYBB_uc011mkf.1_Silent_p.L473L|CYBB_uc011mkg.1_Silent_p.L238L	NM_000397	NP_000388	P04839	CY24B_HUMAN	cytochrome b-245 beta polypeptide	505	Cytoplasmic (Potential).		L -> R (in XCGD).		electron transport chain|inflammatory response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex	electron carrier activity|flavin adenine dinucleotide binding|heme binding|protein heterodimerization activity|superoxide-generating NADPH oxidase activity|voltage-gated ion channel activity			central_nervous_system(1)|skin(1)	2														0.2	10.659901	12.753433	5	20	KEEP	---	---	---	---	capture		Silent	SNP	37668873	37668873	4298	23	G	T	T	T	574	45	CYBB	2	2
MAGED2	10916	broad.mit.edu	37	X	54841708	54841708	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54841708G>T	uc004dtk.1	+	c.1414G>T	c.(1414-1416)GCA>TCA	p.A472S	MAGED2_uc004dtl.1_Missense_Mutation_p.A472S|MAGED2_uc004dtm.1_Missense_Mutation_p.A387S|MAGED2_uc010nkc.1_Intron|MAGED2_uc004dtn.1_Missense_Mutation_p.A472S|MAGED2_uc004dto.1_Missense_Mutation_p.A446S	NM_177433	NP_803182	Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	472	MAGE.									ovary(2)|breast(1)	3														0.128205	14.013438	24.505169	10	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54841708	54841708	9565	23	G	T	T	T	546	42	MAGED2	2	2
RPS6KA6	27330	broad.mit.edu	37	X	83374966	83374966	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:83374966T>A	uc004eej.1	-	c.716A>T	c.(715-717)TAT>TTT	p.Y239F	RPS6KA6_uc011mqt.1_Missense_Mutation_p.Y239F|RPS6KA6_uc011mqu.1_Missense_Mutation_p.Y136F|RPS6KA6_uc010nmo.1_Non-coding_Transcript	NM_014496	NP_055311	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase polypeptide 6	239	Protein kinase 1.				axon guidance|central nervous system development|intracellular protein kinase cascade|protein phosphorylation|synaptic transmission	cytosol|nucleoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(5)	5										287				0.108696	6.042841	13.019586	5	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83374966	83374966	14135	23	T	A	A	A	637	49	RPS6KA6	3	3
PCDH11X	27328	broad.mit.edu	37	X	91133196	91133196	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91133196C>A	uc004efk.1	+	c.1957C>A	c.(1957-1959)CGT>AGT	p.R653S	PCDH11X_uc004efl.1_Missense_Mutation_p.R653S|PCDH11X_uc004efo.1_Missense_Mutation_p.R653S|PCDH11X_uc010nmv.1_Missense_Mutation_p.R653S|PCDH11X_uc004efm.1_Missense_Mutation_p.R653S|PCDH11X_uc004efn.1_Missense_Mutation_p.R653S|PCDH11X_uc004efh.1_Missense_Mutation_p.R653S|PCDH11X_uc004efj.1_Missense_Mutation_p.R653S	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	653	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.3125	75.049979	77.551432	25	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91133196	91133196	11928	23	C	A	A	A	247	19	PCDH11X	1	1
KDM5D	8284	broad.mit.edu	37	Y	21894530	21894530	+	Silent	SNP	C	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:21894530C>T	uc011naz.1	-	c.1032G>A	c.(1030-1032)TTG>TTA	p.L344L	KDM5D_uc004fug.2_Silent_p.L344L|KDM5D_uc010nwy.2_Silent_p.L287L|KDM5D_uc011nba.1_Silent_p.L344L|KDM5D_uc004fuh.2_Silent_p.L299L	NM_001146705	NP_001140177	Q9BY66	KDM5D_HUMAN	jumonji, AT rich interactive domain 1D isoform	344	PHD-type 1.				chromatin modification|oxidation-reduction process|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			skin(1)	1					Vitamin C(DB00126)									0.243902	23.951067	26.387334	10	31	KEEP	---	---	---	---	capture		Silent	SNP	21894530	21894530	8442	24	C	T	T	T	220	17	KDM5D	2	2
PCDH11Y	83259	broad.mit.edu	37	Y	4968083	4968083	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:4968083A>T	uc004fqo.2	+	c.2464A>T	c.(2464-2466)ATT>TTT	p.I822F	PCDH11Y_uc010nwg.1_Missense_Mutation_p.I811F|PCDH11Y_uc004fql.1_Missense_Mutation_p.I811F|PCDH11Y_uc004fqm.1_Missense_Mutation_p.I811F|PCDH11Y_uc004fqn.1_Missense_Mutation_p.I822F|PCDH11Y_uc004fqp.1_Missense_Mutation_p.I593F	NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	822	Cadherin 7.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.144444	20.314304	31.27086	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4968083	4968083	11929	24	A	T	T	T	104	8	PCDH11Y	3	3
PCDH11Y	83259	broad.mit.edu	37	Y	5605402	5605402	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:5605402C>A	uc004fqo.2	+	c.3442C>A	c.(3442-3444)CCG>ACG	p.P1148T		NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	1148	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.152174	12.148557	17.432266	7	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5605402	5605402	11929	24	C	A	A	A	338	26	PCDH11Y	2	2
CPEB3	22849	broad.mit.edu	37	10	93999920	93999920	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:93999920_93999920delG	uc001khu.1	-	c.188_188delC	c.(187-189)CCGfs	p.P63fs	CPEB3_uc001khv.1_Frame_Shift_Del_p.P63fs|CPEB3_uc001khw.1_Frame_Shift_Del_p.P63fs|CPEB3_uc010qnn.1_Frame_Shift_Del_p.P63fs	NM_014912	NP_055727	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding	63	Pro-rich.						nucleotide binding|RNA binding				0		Colorectal(252;0.0869)												0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	93999920	93999920	3940	10	G	-	-	-	507	39	CPEB3	5	5
MUC20	200958	broad.mit.edu	37	3	195452664	195452664	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z062-01	TCGA-17-Z062-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:195452664_195452664delC	uc010hzo.2	+	c.677_677delC	c.(676-678)ACCfs	p.T226fs	MUC20_uc010hzp.2_Frame_Shift_Del_p.T191fs|MUC20_uc011bte.1_Non-coding_Transcript	NM_152673	NP_689886	Q8N307	MUC20_HUMAN	mucin 20 isoform L	397	12 X 20 AA approximate tandem repeats of S-S-E-S-S-A-S-S-D-S-P-H-P-V-I-T-P-S-R-A.|12; approximate.				protein homooligomerization	apical plasma membrane|basal plasma membrane|extracellular region|microvillus membrane					0	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)										0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	195452664	195452664	10370	3	C	-	-	-	222	18	MUC20	5	5
