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	i_TCGAscape_Amplification_Peaks	i_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_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
C10orf96	374355	broad.mit.edu	36	10	118074812	118074812	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118074812G>A	uc001lck.1	+	c.87G>A	c.(85-87)TCG>TCA	p.S29S		NM_198515	NP_940917	P0C7W6	CJ096_HUMAN	hypothetical protein LOC374355	29	Potential.									ovary(2)	2		Lung NSC(174;0.204)|all_lung(145;0.248)		all cancers(201;0.014)										0.6	58.953935	59.216234	18	12	GG		KEEP	---	---	---	---	capture			Silent	SNP	118074812	118074812	1664	10	G	A	A	39	39	C10orf96	A	1	1
FAM171A1	221061	broad.mit.edu	36	10	15296407	15296407	+	Nonsense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:15296407C>A	uc001iob.1	-	c.1186G>T	c.(1186-1188)GGA>TGA	p.G396*		NM_001010924	NP_001010924	Q5VUB5	F1711_HUMAN	hypothetical protein LOC221061	396	Cytoplasmic (Potential).					integral to membrane				ovary(2)|breast(1)	3														0.13	11.659712	24.949554	13	87	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	15296407	15296407	5695	10	C	A	A	21	21	FAM171A1	A	5	3
ATHL1	80162	broad.mit.edu	36	11	282060	282060	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:282060G>A	uc001lot.2	+	c.460G>A	c.(460-462)GGG>AGG	p.G154R	ATHL1_uc001lor.2_Missense_Mutation_p.G154R|ATHL1_uc001los.1_Missense_Mutation_p.G331R|ATHL1_uc001lou.2_5'Flank|ATHL1_uc001lov.2_5'Flank	NM_025092	NP_079368	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1	331					carbohydrate metabolic process		hydrolase activity, acting on glycosyl bonds			liver(1)|central_nervous_system(1)	2		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)										0.714286	17.377453	17.66568	5	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	282060	282060	1123	11	G	A	A	39	39	ATHL1	A	1	1
OR5D13	390142	broad.mit.edu	36	11	55297989	55297989	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1789-01	TCGA-19-1789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55297989A>G	uc001nhu.1	+	c.500A>G	c.(499-501)GAC>GGC	p.D167G		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		all_epithelial(135;0.196)												0.332278	319.588654	327.453302	105	211	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55297989	55297989	11564	11	A	G	G	10	10	OR5D13	G	4	4
OR5D13	390142	broad.mit.edu	36	11	55298069	55298069	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55298069C>T	uc001nhu.1	+	c.580C>T	c.(580-582)CCC>TCC	p.P194S		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	194	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		all_epithelial(135;0.196)												0.37037	314.528043	318.515551	100	170	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55298069	55298069	11564	11	C	T	T	22	22	OR5D13	T	2	2
PMCH	5367	broad.mit.edu	36	12	101115492	101115492	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:101115492G>A	uc001tjl.1	-	c.187C>T	c.(187-189)CTG>TTG	p.L63L		NM_002674	NP_002665	P20382	MCH_HUMAN	pro-melanin-concentrating hormone	63					cell differentiation|neuropeptide signaling pathway|spermatogenesis|synaptic transmission		melanin-concentrating hormone activity				0														0.460094	323.332015	323.626985	98	115	GG		KEEP	---	---	---	---	capture			Silent	SNP	101115492	101115492	12557	12	G	A	A	35	35	PMCH	A	2	2
CCDC62	84660	broad.mit.edu	36	12	121828139	121828139	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121828139G>A	uc001udc.1	+	c.185G>A	c.(184-186)CGG>CAG	p.R62Q	CCDC62_uc001udd.1_Missense_Mutation_p.R62Q|CCDC62_uc001ude.1_5'UTR	NM_201435	NP_958843	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62 isoform b	62	Potential.					cytoplasm|nucleus				ovary(2)|large_intestine(1)|pancreas(1)	4	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)										0.403587	294.911519	296.722181	90	133	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121828139	121828139	2956	12	G	A	A	39	39	CCDC62	A	1	1
SLC2A13	114134	broad.mit.edu	36	12	38444642	38444642	+	Missense_Mutation	SNP	T	G	G			TCGA-19-1789-01	TCGA-19-1789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:38444642T>G	uc001rmd.1	-	c.1550A>C	c.(1549-1551)TAT>TCT	p.Y517S	C12orf40_uc009zjv.1_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose	536	Cytoplasmic (Potential).					integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)												0.330827	145.262711	148.631862	44	89	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38444642	38444642	15039	12	T	G	G	49	49	SLC2A13	G	4	4
KRT7	3855	broad.mit.edu	36	12	50915332	50915332	+	Nonsense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50915332C>T	uc001saa.1	+	c.451C>T	c.(451-453)CAG>TAG	p.Q151*	KRT7_uc009zmf.1_Nonsense_Mutation_p.Q151*	NM_005556	NP_005547	P08729	K2C7_HUMAN	keratin 7	151	Rod.|Coil 1B.				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.105)										0.361446	83.527765	84.929665	30	53	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	50915332	50915332	8798	12	C	T	T	29	29	KRT7	T	5	2
LRP1	4035	broad.mit.edu	36	12	55878621	55878621	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55878621G>A	uc001snd.1	+	c.9577G>A	c.(9577-9579)GGC>AGC	p.G3193S		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3193	LDL-receptor class B 28.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.359551	88.781914	90.324397	32	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55878621	55878621	9324	12	G	A	A	47	47	LRP1	A	2	2
LRIG3	121227	broad.mit.edu	36	12	57560700	57560700	+	Silent	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:57560700C>A	uc001sqr.1	-	c.1731G>T	c.(1729-1731)GGG>GGT	p.G577G	LRIG3_uc009zqh.1_Silent_p.G517G	NM_153377	NP_700356	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like	577	Ig-like C2-type 1.					integral to membrane				ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;1.17e-18)											0.353741	140.426395	143.211242	52	95	CC		KEEP	---	---	---	---	capture			Silent	SNP	57560700	57560700	9319	12	C	A	A	30	30	LRIG3	A	3	3
RASA3	22821	broad.mit.edu	36	13	113802414	113802414	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:113802414G>A	uc001vui.1	-	c.869C>T	c.(868-870)ACG>ATG	p.T290M	RASA3_uc001vuj.1_De_novo_Start_InFrame	NM_007368	NP_031394	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	290					intracellular signal transduction|negative regulation of Ras protein signal transduction	cytoplasm|intrinsic to internal side of plasma membrane	calcium-release channel activity|metal ion binding|Ras GTPase activator activity			lung(1)|skin(1)	2	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)							4289				0.217391	10.962343	12.656611	5	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113802414	113802414	13522	13	G	A	A	40	40	RASA3	A	1	1
MMP14	4323	broad.mit.edu	36	14	22380563	22380563	+	Nonsense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22380563C>A	uc001whc.1	+	c.132C>A	c.(130-132)TAC>TAA	p.Y44*		NM_004995	NP_004986	P50281	MMP14_HUMAN	matrix metalloproteinase 14 preproprotein	44						extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)										0.333333	12.968051	13.460345	7	14	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	22380563	22380563	10043	14	C	A	A	18	18	MMP14	A	5	3
GREM1	26585	broad.mit.edu	36	15	30810339	30810339	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:30810339G>A	uc001zhe.1	+	c.156G>A	c.(154-156)CAG>CAA	p.Q52Q	GREM1_uc001zhd.1_Intron|GREM1_uc010baq.1_Silent_p.Q52Q	NM_013372	NP_037504	O60565	GREM1_HUMAN	gremlin-1 precursor	52					negative regulation of BMP signaling pathway|nervous system development|regulation of epithelial to mesenchymal transition	extracellular space	cytokine activity				0		all_lung(180;1.49e-09)		all cancers(64;2.97e-18)|Epithelial(43;3.15e-12)|GBM - Glioblastoma multiforme(186;2.32e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0107)										0.615385	24.601314	24.752873	8	5	GG		KEEP	---	---	---	---	capture			Silent	SNP	30810339	30810339	7039	15	G	A	A	34	34	GREM1	A	2	2
ZFYVE19	84936	broad.mit.edu	36	15	38887197	38887197	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38887197G>A	uc001zmt.1	+	c.118G>A	c.(118-120)GGG>AGG	p.G40R	DNAJC17_uc001zms.1_5'Flank|DNAJC17_uc010bbz.1_5'Flank|DNAJC17_uc010bca.1_5'Flank|DNAJC17_uc010bcb.1_5'Flank|ZFYVE19_uc001zmu.1_Missense_Mutation_p.G40R|ZFYVE19_uc001zmv.1_Intron|ZFYVE19_uc001zmw.1_5'Flank|ZFYVE19_uc001zmx.1_5'Flank|ZFYVE19_uc010bcc.1_5'Flank	NM_001077268	NP_001070736	Q96K21	ZFY19_HUMAN	zinc finger, FYVE domain containing 19	40							zinc ion binding				0		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)										0.266667	7.891926	8.63107	4	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38887197	38887197	18255	15	G	A	A	39	39	ZFYVE19	A	1	1
TMC5	79838	broad.mit.edu	36	16	19359040	19359040	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:19359040G>A	uc002dgc.2	+	c.179G>A	c.(178-180)AGA>AAA	p.R60K	TMC5_uc002dgb.2_Missense_Mutation_p.R60K	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	60	Extracellular (Potential).					integral to membrane					0														0.414226	312.682321	314.217669	99	140	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19359040	19359040	16518	16	G	A	A	33	33	TMC5	A	2	2
KIFC3	3801	broad.mit.edu	36	16	56361060	56361060	+	Missense_Mutation	SNP	A	C	C			TCGA-19-1789-01	TCGA-19-1789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56361060A>C	uc002emp.1	-	c.1166T>G	c.(1165-1167)GTG>GGG	p.V389G	KIFC3_uc002emm.1_Missense_Mutation_p.V250G|KIFC3_uc002emn.1_Non-coding_Transcript|KIFC3_uc002emo.2_Missense_Mutation_p.V250G|KIFC3_uc010cdf.1_Missense_Mutation_p.V250G|KIFC3_uc002emq.1_Missense_Mutation_p.V389G|KIFC3_uc002emr.1_Missense_Mutation_p.V166G	NM_005550	NP_005541	Q9BVG8	KIFC3_HUMAN	kinesin family member C3 isoform 1	389					epithelial cell-cell adhesion|microtubule-based movement|visual perception|zonula adherens maintenance	centrosome|cytoplasmic vesicle membrane|kinesin complex|microtubule|zonula adherens	ATP binding|microtubule motor activity			ovary(1)|central_nervous_system(1)	2		all_neural(199;0.224)												0.285714	6.979538	7.569164	4	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56361060	56361060	8625	16	A	C	C	6	6	KIFC3	C	4	4
KRT25	147183	broad.mit.edu	36	17	36160325	36160325	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36160325C>T	uc002hve.1	-	c.1008G>A	c.(1006-1008)GCG>GCA	p.A336A		NM_181534	NP_853512	Q7Z3Z0	K1C25_HUMAN	keratin 25	336	Rod.|Coil 2.					cytoplasm|intermediate filament	structural molecule activity			ovary(2)	2		Breast(137;0.00526)												0.509434	177.950946	177.959176	54	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	36160325	36160325	8777	17	C	T	T	27	27	KRT25	T	1	1
ACADVL	37	broad.mit.edu	36	17	7066874	7066874	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1789-01	TCGA-19-1789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7066874T>C	uc002gev.1	+	c.1043T>C	c.(1042-1044)CTG>CCG	p.L348P	ACADVL_uc002gew.1_Missense_Mutation_p.L326P|ACADVL_uc002gex.1_Missense_Mutation_p.L272P	NM_000018	NP_000009	P49748	ACADV_HUMAN	acyl-Coenzyme A dehydrogenase, very long chain	348	Catalytic.				energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial inner membrane|mitochondrial nucleoid	long-chain-acyl-CoA dehydrogenase activity			ovary(2)	2														0.366667	99.841715	101.251576	33	57	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7066874	7066874	117	17	T	C	C	55	55	ACADVL	C	4	4
EMILIN2	84034	broad.mit.edu	36	18	2881091	2881091	+	Silent	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:2881091C>A	uc002kln.1	+	c.966C>A	c.(964-966)ATC>ATA	p.I322I		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	322	Potential.				cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			ovary(1)	1				READ - Rectum adenocarcinoma(2;0.1)										0.436364	150.085881	150.473541	48	62	CC		KEEP	---	---	---	---	capture			Silent	SNP	2881091	2881091	5286	18	C	A	A	31	31	EMILIN2	A	3	3
ZNF780B	163131	broad.mit.edu	36	19	45233908	45233908	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45233908G>A	uc002omu.1	-	c.689C>T	c.(688-690)CCC>CTC	p.P230L	ZNF780B_uc002omv.1_Missense_Mutation_p.P85L	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	233	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)													0.320755	103.314489	106.338798	34	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45233908	45233908	18751	19	G	A	A	43	43	ZNF780B	A	2	2
PLAUR	5329	broad.mit.edu	36	19	48848258	48848258	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:48848258C>A	uc002oxf.1	-	c.713G>T	c.(712-714)CGA>CTA	p.R238L	PLAUR_uc002oxd.1_Missense_Mutation_p.R238L|PLAUR_uc002oxe.1_Missense_Mutation_p.R233L|PLAUR_uc002oxg.1_Missense_Mutation_p.R193L	NM_002659	NP_002650	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	238	UPAR/Ly6 3.				attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis	anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane	enzyme binding|U-plasminogen activator receptor activity			ovary(1)	1		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013)							OREG0025532	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.343478	430.63446	440.577457	158	302	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48848258	48848258	12449	19	C	A	A	31	31	PLAUR	A	3	3
SIGLEC8	27181	broad.mit.edu	36	19	56650539	56650539	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56650539G>A	uc002pwt.1	-	c.996C>T	c.(994-996)AAC>AAT	p.N332N	SIGLEC8_uc010eox.1_Silent_p.N239N|SIGLEC8_uc002pwu.2_Non-coding_Transcript	NM_014442	NP_055257	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	332	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion	integral to membrane	sugar binding|transmembrane receptor activity			ovary(2)|kidney(1)|central_nervous_system(1)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)										0.345455	157.320317	160.802183	57	108	GG		KEEP	---	---	---	---	capture			Silent	SNP	56650539	56650539	14809	19	G	A	A	40	40	SIGLEC8	A	1	1
NLRP12	91662	broad.mit.edu	36	19	59005862	59005862	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59005862C>T	uc002qcj.2	-	c.863G>A	c.(862-864)CGC>CAC	p.R288H	NLRP12_uc010eqw.1_5'Flank|NLRP12_uc002qch.2_Missense_Mutation_p.R288H|NLRP12_uc002qci.2_Missense_Mutation_p.R288H|NLRP12_uc002qck.2_Non-coding_Transcript|NLRP12_uc010eqx.1_Missense_Mutation_p.R288H	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	288	NACHT.				activation of caspase activity|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|lung(1)	5	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)										0.380952	70.38196	71.165844	24	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59005862	59005862	10877	19	C	T	T	27	27	NLRP12	T	1	1
NLRP4	147945	broad.mit.edu	36	19	61065273	61065273	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61065273C>T	uc002qmd.2	+	c.2122C>T	c.(2122-2124)CGT>TGT	p.R708C	NLRP4_uc002qme.1_Missense_Mutation_p.R708C|NLRP4_uc002qmf.1_Missense_Mutation_p.R633C|NLRP4_uc010etf.1_Missense_Mutation_p.R539C	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	708	LRR 2.						ATP binding	p.R708C(1)		ovary(5)|lung(3)|kidney(1)|pancreas(1)	10		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)										0.391129	297.62106	300.19457	97	151	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61065273	61065273	10882	19	C	T	T	31	31	NLRP4	T	1	1
VAV1	7409	broad.mit.edu	36	19	6779654	6779654	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6779654G>A	uc002mfu.1	+	c.1114G>A	c.(1114-1116)GAG>AAG	p.E372K	VAV1_uc010dva.1_Missense_Mutation_p.E372K|VAV1_uc002mfv.1_Missense_Mutation_p.E317K	NM_005428	NP_005419	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	372	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(3)|lung(2)|central_nervous_system(2)|kidney(2)|skin(1)	10										494				0.118421	11.824705	22.692392	9	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6779654	6779654	17696	19	G	A	A	37	37	VAV1	A	1	1
ZNF560	147741	broad.mit.edu	36	19	9439344	9439344	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9439344C>T	uc002mlp.1	-	c.1279G>A	c.(1279-1281)GCC>ACC	p.A427T	ZNF560_uc010dwr.1_Missense_Mutation_p.A321T	NM_152476	NP_689689	Q96MR9	ZN560_HUMAN	zinc finger protein 560	427					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|large_intestine(1)|liver(1)|pancreas(1)	4														0.179487	26.684861	34.256403	14	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9439344	9439344	18586	19	C	T	T	27	27	ZNF560	T	1	1
COL5A3	50509	broad.mit.edu	36	19	9950259	9950259	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9950259C>T	uc002mmq.1	-	c.3009G>A	c.(3007-3009)GTG>GTA	p.V1003V		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1003	Triple-helical region.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)	9			Epithelial(33;7.11e-05)											0.277108	121.272003	128.698993	46	120	CC		KEEP	---	---	---	---	capture			Silent	SNP	9950259	9950259	3836	19	C	T	T	21	21	COL5A3	T	2	2
HSD3B2	3284	broad.mit.edu	36	1	119763644	119763644	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:119763644G>A	uc001ehs.1	+	c.223G>A	c.(223-225)GTC>ATC	p.V75I	HSD3B2_uc001eht.1_Missense_Mutation_p.V75I|HSD3B2_uc001ehu.2_Missense_Mutation_p.V75I	NM_000198	NP_000189	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta-	75					androgen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process|oxidation-reduction process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity			ovary(2)	2	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	NADH(DB00157)|Trilostane(DB01108)									0.383721	282.267648	285.321184	99	159	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119763644	119763644	7686	1	G	A	A	40	40	HSD3B2	A	1	1
TNN	63923	broad.mit.edu	36	1	173359170	173359170	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:173359170C>T	uc001gkl.1	+	c.2662C>T	c.(2662-2664)CCC>TCC	p.P888S		NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N	888	Fibronectin type-III 8.				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				0.376106	253.323796	256.366542	85	141	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	173359170	173359170	16864	1	C	T	T	22	22	TNN	T	2	2
C1orf125	126859	broad.mit.edu	36	1	177718979	177718979	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:177718979C>T	uc001gmo.1	+	c.2091C>T	c.(2089-2091)CAC>CAT	p.H697H	C1orf125_uc009wxg.1_Non-coding_Transcript|C1orf125_uc001gmp.1_Silent_p.H697H	NM_144696	NP_653297	Q5T1B0	AXDN1_HUMAN	hypothetical protein LOC126859 isoform 1	697											0														0.444126	503.009991	503.953313	155	194	CC		KEEP	---	---	---	---	capture			Silent	SNP	177718979	177718979	2060	1	C	T	T	19	19	C1orf125	T	1	1
NINL	22981	broad.mit.edu	36	20	25407696	25407696	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:25407696C>T	uc002wux.1	-	c.2064G>A	c.(2062-2064)GAG>GAA	p.E688E	NINL_uc010gdn.1_Silent_p.E688E|NINL_uc010gdo.1_Silent_p.E471E	NM_025176	NP_079452	Q9Y2I6	NINL_HUMAN	ninein-like	688	Potential.				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.34375	33.018259	33.706911	11	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	25407696	25407696	10821	20	C	T	T	24	24	NINL	T	2	2
MANBAL	63905	broad.mit.edu	36	20	35363178	35363178	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1789-01	TCGA-19-1789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:35363178A>G	uc002xgu.1	+	c.98A>G	c.(97-99)CAG>CGG	p.Q33R	MANBAL_uc002xgv.1_Missense_Mutation_p.Q33R|MANBAL_uc002xgw.1_Non-coding_Transcript|MANBAL_uc010gfx.1_Non-coding_Transcript|MANBAL_uc010gfy.1_Non-coding_Transcript	NM_022077	NP_071360	Q9NQG1	MANBL_HUMAN	mannosidase, beta A, lysosomal-like	33	Helical; (Potential).					integral to membrane					0		Myeloproliferative disorder(115;0.00878)												0.191693	116.378901	144.240494	60	253	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35363178	35363178	9603	20	A	G	G	7	7	MANBAL	G	4	4
CHD6	84181	broad.mit.edu	36	20	39546631	39546631	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1789-01	TCGA-19-1789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:39546631T>C	uc002xka.1	-	c.2032A>G	c.(2032-2034)ATG>GTG	p.M678V		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	678					chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.311321	597.817499	617.979972	198	438	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39546631	39546631	3463	20	T	C	C	52	52	CHD6	C	4	4
PSMG1	8624	broad.mit.edu	36	21	39475609	39475609	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:39475609G>A	uc002yxi.1	-	c.200C>T	c.(199-201)CCG>CTG	p.P67L	PSMG1_uc002yxj.1_Missense_Mutation_p.P67L|PSMG1_uc010gob.1_Intron	NM_003720	NP_003711	O95456	PSMG1_HUMAN	Down syndrome critical region protein 2 isoform	67					proteasome assembly	endoplasmic reticulum	protein binding				0		Prostate(19;8.44e-08)												0.588235	36.653442	36.769059	10	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39475609	39475609	13164	21	G	A	A	39	39	PSMG1	A	1	1
TRPM2	7226	broad.mit.edu	36	21	44623319	44623319	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44623319C>T	uc010gpt.1	+	c.1026C>T	c.(1024-1026)AAC>AAT	p.N342N	TRPM2_uc002zet.1_Silent_p.N342N|TRPM2_uc002zeu.1_Silent_p.N342N|TRPM2_uc002zew.1_Silent_p.N342N|TRPM2_uc002zex.1_Silent_p.N128N	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	342	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.425532	55.196981	55.421877	20	27	CC		KEEP	---	---	---	---	capture			Silent	SNP	44623319	44623319	17137	21	C	T	T	19	19	TRPM2	T	1	1
LZTR1	8216	broad.mit.edu	36	22	19673160	19673160	+	Missense_Mutation	SNP	A	G	G			TCGA-19-1789-01	TCGA-19-1789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:19673160A>G	uc002zto.1	+	c.592A>G	c.(592-594)AGG>GGG	p.R198G	LZTR1_uc002ztn.1_Missense_Mutation_p.R157G|LZTR1_uc010gsr.1_Missense_Mutation_p.R69G	NM_006767	NP_006758	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	198	Kelch 3.				anatomical structure morphogenesis		sequence-specific DNA binding transcription factor activity			ovary(2)|lung(2)	4	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)							1299				0.454545	45.822069	45.881109	15	18	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19673160	19673160	9514	22	A	G	G	7	7	LZTR1	G	4	4
ALMS1	7840	broad.mit.edu	36	2	73533196	73533196	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73533196C>A	uc002sje.1	+	c.6037C>A	c.(6037-6039)CCA>ACA	p.P2013T	ALMS1_uc002sjf.1_Missense_Mutation_p.P1969T|ALMS1_uc002sjg.2_Missense_Mutation_p.P1399T|ALMS1_uc002sjh.1_Missense_Mutation_p.P1399T	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	ALMS1	2011	34 X 47 AA approximate tandem repeat.				G2/M transition of mitotic cell cycle|visual perception	centrosome|cilium|cytosol|microtubule basal body|spindle pole				ovary(2)|breast(2)|lung(1)|pancreas(1)	6														0.459016	352.578671	352.934806	112	132	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73533196	73533196	538	2	C	A	A	30	30	ALMS1	A	3	3
CD8B	926	broad.mit.edu	36	2	86938942	86938942	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:86938942C>T	uc002ssa.1	-	c.152G>A	c.(151-153)CGC>CAC	p.R51H	RMND5A_uc002srs.2_Intron|CD8B_uc002srw.1_Missense_Mutation_p.R51H|CD8B_uc002srx.1_Missense_Mutation_p.R51H|CD8B_uc002sry.1_Missense_Mutation_p.R51H|CD8B_uc010fgt.1_Missense_Mutation_p.R51H|CD8B_uc002srz.1_Missense_Mutation_p.R51H	NM_172099	NP_742097	P10966	CD8B_HUMAN	CD8b antigen isoform 1 precursor	51	Ig-like V-type.|Extracellular (Potential).				immune response|regulation of defense response to virus by virus|regulation of immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway|viral reproduction	early endosome|extracellular region|integral to plasma membrane|T cell receptor complex	coreceptor activity|MHC class I protein binding				0														0.323741	125.9408	129.766841	45	94	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86938942	86938942	3173	2	C	T	T	27	27	CD8B	T	1	1
FNDC3B	64778	broad.mit.edu	36	3	173553451	173553451	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173553451G>A	uc010hwt.1	+	c.2679G>A	c.(2677-2679)CCG>CCA	p.P893P	FNDC3B_uc003fhy.1_Silent_p.P889P|FNDC3B_uc003fhz.2_Silent_p.P889P	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	893	Fibronectin type-III 7.					endoplasmic reticulum|integral to membrane				ovary(1)|breast(1)	2	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)										0.43913	308.637076	309.380099	101	129	GG		KEEP	---	---	---	---	capture			Silent	SNP	173553451	173553451	6212	3	G	A	A	40	40	FNDC3B	A	1	1
ZMAT3	64393	broad.mit.edu	36	3	180231458	180231458	+	Silent	SNP	G	C	C			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:180231458G>C	uc003fjg.1	-	c.294C>G	c.(292-294)CTC>CTG	p.L98L	ZMAT3_uc010hxa.1_Silent_p.L98L|ZMAT3_uc003fji.1_Silent_p.L98L	NM_022470	NP_071915	Q9HA38	ZMAT3_HUMAN	p53 target zinc finger protein isoform 1	98	Matrin-type 1.				apoptosis|protein transport|regulation of growth|response to DNA damage stimulus|transmembrane transport	nucleolus	RNA binding|zinc ion binding			ovary(2)	2	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)											0.40367	152.283201	153.166311	44	65	GG		KEEP	---	---	---	---	capture			Silent	SNP	180231458	180231458	18284	3	G	C	C	41	41	ZMAT3	C	3	3
FBXW12	285231	broad.mit.edu	36	3	48391858	48391858	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48391858G>A	uc003csr.1	+	c.297G>A	c.(295-297)ACG>ACA	p.T99T	FBXW12_uc010hjv.1_Silent_p.T80T|FBXW12_uc003css.1_Silent_p.T99T|FBXW12_uc010hjw.1_Silent_p.T20T	NM_207102	NP_996985	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	99	WD 1.										0				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.344262	61.456902	62.763413	21	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	48391858	48391858	6002	3	G	A	A	39	39	FBXW12	A	1	1
MAGI1	9223	broad.mit.edu	36	3	65431159	65431159	+	Silent	SNP	T	C	C			TCGA-19-1789-01	TCGA-19-1789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:65431159T>C	uc003dmn.1	-	c.798A>G	c.(796-798)ACA>ACG	p.T266T	MAGI1_uc003dmm.1_Silent_p.T266T|MAGI1_uc003dmo.1_Silent_p.T266T|MAGI1_uc003dmp.1_Silent_p.T266T|MAGI1_uc010hny.1_Silent_p.T151T|MAGI1_uc003dmr.2_Silent_p.T267T	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	266	Guanylate kinase-like.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			kidney(1)|pancreas(1)	2		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)										0.34058	278.653095	284.858944	94	182	TT		KEEP	---	---	---	---	capture			Silent	SNP	65431159	65431159	9573	3	T	C	C	55	55	MAGI1	C	4	4
TACR3	6870	broad.mit.edu	36	4	104860009	104860009	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:104860009C>T	uc003hxe.1	-	c.273G>A	c.(271-273)GCG>GCA	p.A91A		NM_001059	NP_001050	P29371	NK3R_HUMAN	tachykinin receptor 3	91	Helical; Name=1; (Potential).					integral to plasma membrane	tachykinin receptor activity			ovary(2)|skin(1)	3		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)										0.355505	459.031205	467.038821	155	281	CC		KEEP	---	---	---	---	capture			Silent	SNP	104860009	104860009	16028	4	C	T	T	19	19	TACR3	T	1	1
CXXC4	80319	broad.mit.edu	36	4	105631414	105631414	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:105631414C>A	uc003hxg.1	-	c.488G>T	c.(487-489)GGA>GTA	p.G163V	CXXC4_uc010ilo.1_Intron	NM_025212	NP_079488	Q9H2H0	CXXC4_HUMAN	CXXC finger 4	163	Interaction with DVL1 (By similarity).|CXXC-type.				negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)										0.409836	145.217445	146.086096	50	72	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105631414	105631414	4258	4	C	A	A	30	30	CXXC4	A	3	3
SAP30	8819	broad.mit.edu	36	4	174531702	174531702	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:174531702G>C	uc003itd.1	+	c.479G>C	c.(478-480)AGA>ACA	p.R160T		NM_003864	NP_003855	O75446	SAP30_HUMAN	Sin3A-associated protein, 30kDa	160	Interaction with SIN3A (By similarity).				transcription, DNA-dependent	histone deacetylase complex	DNA binding|metal ion binding|protein binding|transcription corepressor activity			ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_neural(102;0.0837)|all_hematologic(60;0.107)		all cancers(43;1.15e-17)|Epithelial(43;4.33e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.62e-09)|STAD - Stomach adenocarcinoma(60;0.00278)|GBM - Glioblastoma multiforme(59;0.00659)|LUSC - Lung squamous cell carcinoma(193;0.0919)										0.370968	147.016058	148.830632	46	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	174531702	174531702	14314	4	G	C	C	33	33	SAP30	C	3	3
PCDH7	5099	broad.mit.edu	36	4	30333981	30333981	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:30333981C>T	uc010iez.1	+	c.1698C>T	c.(1696-1698)GAC>GAT	p.D566D	PCDH7_uc003gsj.1_Silent_p.D613D|PCDH7_uc003gsk.1_Silent_p.D613D	NM_032457	NP_115833	O60245	PCDH7_HUMAN	protocadherin 7 isoform c precursor	613	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4														0.37013	162.524649	164.810712	57	97	CC		KEEP	---	---	---	---	capture			Silent	SNP	30333981	30333981	11936	4	C	T	T	17	17	PCDH7	T	2	2
IRX1	79192	broad.mit.edu	36	5	3653793	3653793	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:3653793C>G	uc003jde.1	+	c.1383C>G	c.(1381-1383)GAC>GAG	p.D461E		NM_024337	NP_077313	P78414	IRX1_HUMAN	iroquois homeobox protein 1	461					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)|pancreas(1)	2														0.285714	12.594017	13.170953	4	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3653793	3653793	8147	5	C	G	G	17	17	IRX1	G	3	3
ESR1	2099	broad.mit.edu	36	6	152243510	152243510	+	Missense_Mutation	SNP	C	A	A			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152243510C>A	uc010kio.1	+	c.677C>A	c.(676-678)ACC>AAC	p.T226N	ESR1_uc003qom.2_Missense_Mutation_p.T224N|ESR1_uc010kin.1_Missense_Mutation_p.T224N|ESR1_uc010kip.1_Missense_Mutation_p.T224N|ESR1_uc003qon.2_Missense_Mutation_p.T224N|ESR1_uc003qoo.2_Missense_Mutation_p.T224N|ESR1_uc010kiq.1_5'UTR|ESR1_uc010kir.1_Intron|ESR1_uc010kis.1_Missense_Mutation_p.T5N	NM_001122742	NP_001116214	P03372	ESR1_HUMAN	estrogen receptor alpha isoform 4	224	NR C4-type.|Nuclear receptor.|Mediates interaction with DNTTIP2.				positive regulation of retinoic acid receptor signaling pathway|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	chromatin remodeling complex|cytoplasm|nucleoplasm	beta-catenin binding|enzyme binding|estrogen receptor activity|estrogen response element binding|nitric-oxide synthase regulator activity|sequence-specific DNA binding transcription factor activity|steroid binding|zinc ion binding			central_nervous_system(2)	2		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Chlorotrianisene(DB00269)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Dromostanolone(DB00858)|Drospirenone(DB01395)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Letrozole(DB01006)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)					249				0.363636	178.95734	181.655662	60	105	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152243510	152243510	5449	6	C	A	A	18	18	ESR1	A	3	3
HIST1H2AB	8335	broad.mit.edu	36	6	26141584	26141584	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:26141584C>T	uc003nft.1	-	c.192G>A	c.(190-192)CTG>CTA	p.L64L	HIST1H3B_uc003nfs.1_5'Flank	NM_003513	NP_066390	P04908	H2A1B_HUMAN	histone cluster 1, H2ab	64					nucleosome assembly	nucleosome|nucleus	DNA binding				0														0.451613	115.931876	116.121745	42	51	CC		KEEP	---	---	---	---	capture			Silent	SNP	26141584	26141584	7414	6	C	T	T	21	21	HIST1H2AB	T	2	2
PRSS16	10279	broad.mit.edu	36	6	27327612	27327612	+	Silent	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27327612C>T	uc003nja.1	+	c.822C>T	c.(820-822)CCC>CCT	p.P274P	PRSS16_uc003njb.1_Intron|PRSS16_uc010jqq.1_Intron|PRSS16_uc010jqr.1_Intron|PRSS16_uc003njc.1_Intron|PRSS16_uc003njd.1_Non-coding_Transcript	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16	274					protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)	4						NSCLC(178;1118 2105 17078 23587 44429)								0.383333	66.567806	67.262033	23	37	CC		KEEP	---	---	---	---	capture			Silent	SNP	27327612	27327612	13066	6	C	T	T	22	22	PRSS16	T	2	2
PRSS16	10279	broad.mit.edu	36	6	27327798	27327798	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27327798G>A	uc003nja.1	+	c.1008G>A	c.(1006-1008)CAG>CAA	p.Q336Q	PRSS16_uc003njb.1_Intron|PRSS16_uc010jqq.1_Intron|PRSS16_uc010jqr.1_Intron|PRSS16_uc003njc.1_Intron|PRSS16_uc003njd.1_Non-coding_Transcript	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16	336					protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)	4						NSCLC(178;1118 2105 17078 23587 44429)								0.470588	25.197183	25.210055	8	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	27327798	27327798	13066	6	G	A	A	35	35	PRSS16	A	2	2
EGFR	1956	broad.mit.edu	36	7	55191127	55191127	+	Missense_Mutation	SNP	C	T	T	rs67784074	unknown	TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55191127C>T	uc003tqk.1	+	c.1000C>T	c.(1000-1002)CGC>TGC	p.R334C	EGFR_uc003tqh.1_Missense_Mutation_p.R334C|EGFR_uc003tqi.1_Missense_Mutation_p.R334C|EGFR_uc003tqj.1_Missense_Mutation_p.R334C|EGFR_uc010kzg.1_Missense_Mutation_p.R289C	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	334	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.V30_R297>G(5)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.711409	997.895247	1016.063192	318	129	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55191127	55191127	5156	7	C	T	T	23	23	EGFR	T	1	1
ABCB4	5244	broad.mit.edu	36	7	86939907	86939907	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86939907G>A	uc003uiv.1	-	c.101C>T	c.(100-102)ACG>ATG	p.T34M	ABCB4_uc003uiw.1_Missense_Mutation_p.T34M|ABCB4_uc003uix.1_Missense_Mutation_p.T34M|ABCB4_uc003uiy.1_Missense_Mutation_p.T34M	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	34	Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.394737	47.019222	47.387001	15	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86939907	86939907	44	7	G	A	A	40	40	ABCB4	A	1	1
CSGALNACT1	55790	broad.mit.edu	36	8	19407240	19407240	+	Missense_Mutation	SNP	T	C	C			TCGA-19-1789-01	TCGA-19-1789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:19407240T>C	uc003wzd.2	-	c.386A>G	c.(385-387)GAC>GGC	p.D129G	CSGALNACT1_uc003wze.1_Missense_Mutation_p.D128G|CSGALNACT1_uc003wzf.1_Missense_Mutation_p.D127G|CSGALNACT1_uc003wzg.1_Non-coding_Transcript|CSGALNACT1_uc003wzh.1_Non-coding_Transcript	NM_018371	NP_060841	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate	129	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)										0.415966	317.870596	319.339857	99	139	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19407240	19407240	4079	8	T	C	C	58	58	CSGALNACT1	C	4	4
ST18	9705	broad.mit.edu	36	8	53236671	53236671	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:53236671C>T	uc003xqz.1	-	c.1411G>A	c.(1411-1413)GTG>ATG	p.V471M	ST18_uc003xra.1_Missense_Mutation_p.V471M|ST18_uc003xrb.1_Missense_Mutation_p.V471M	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	471						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)												0.322275	192.241775	198.151862	68	143	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53236671	53236671	15730	8	C	T	T	18	18	ST18	T	2	2
ROR2	4920	broad.mit.edu	36	9	93526533	93526533	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:93526533G>A	uc004arj.1	-	c.2064C>T	c.(2062-2064)TAC>TAT	p.Y688Y	ROR2_uc004ari.1_Silent_p.Y548Y	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	688	Cytoplasmic (Potential).|Protein kinase.				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										461				0.403361	142.37514	143.346799	48	71	GG		KEEP	---	---	---	---	capture			Silent	SNP	93526533	93526533	14006	9	G	A	A	40	40	ROR2	A	1	1
TIMM8A	1678	broad.mit.edu	36	X	100488198	100488198	+	Missense_Mutation	SNP	C	G	G			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:100488198C>G	uc004ehd.1	-	c.239G>C	c.(238-240)CGA>CCA	p.R80P		NM_004085	NP_004076	O60220	TIM8A_HUMAN	translocase of inner mitochondrial membrane 8	80					nervous system development|protein import into mitochondrial inner membrane|transmembrane transport	mitochondrial inner membrane|mitochondrial intermembrane space protein transporter complex	protein binding				0														0.484536	165.624296	165.644369	47	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100488198	100488198	16443	23	C	G	G	31	31	TIMM8A	G	3	3
MECP2	4204	broad.mit.edu	36	X	152949063	152949063	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152949063G>T	uc004fjw.2	-	c.1446C>A	c.(1444-1446)AAC>AAA	p.N482K	MECP2_uc004fjv.2_Missense_Mutation_p.N470K	NM_001110792	NP_001104262	P51608	MECP2_HUMAN	methyl CpG binding protein 2 isoform 2	470					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein domain specific binding|protein N-terminus binding|transcription corepressor activity|transcription repressor activity				0	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.278846	74.235255	78.808537	29	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152949063	152949063	9812	23	G	T	T	48	48	MECP2	T	3	3
CXorf23	256643	broad.mit.edu	36	X	19878873	19878873	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:19878873C>T	uc004czp.1	-	c.1664G>A	c.(1663-1665)CGA>CAA	p.R555Q	CXorf23_uc010nfn.1_Non-coding_Transcript|CXorf23_uc004czo.1_Missense_Mutation_p.R505Q	NM_198279	NP_938020	A2AJT9	CX023_HUMAN	hypothetical protein LOC256643	555						mitochondrion				lung(1)|skin(1)	2														0.324582	417.565147	429.001995	136	283	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19878873	19878873	4263	23	C	T	T	31	31	CXorf23	T	1	1
YY2	404281	broad.mit.edu	36	X	21784788	21784788	+	Missense_Mutation	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:21784788G>A	uc010nfq.1	+	c.919G>A	c.(919-921)GGC>AGC	p.G307S	MBTPS2_uc004dab.1_Intron|MBTPS2_uc004dac.1_Intron|MBTPS2_uc010nfr.1_Intron|YY2_uc004dad.1_Missense_Mutation_p.G89S	NM_206923	NP_996806	O15391	TYY2_HUMAN	YY2 transcription factor	89	Mediates transcriptional activation.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	DNA binding|zinc ion binding			breast(1)|skin(1)	2														0.421245	364.396878	365.868803	115	158	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21784788	21784788	18092	23	G	A	A	43	43	YY2	A	2	2
MXRA5	25878	broad.mit.edu	36	X	3238737	3238737	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3238737G>C	uc004crg.2	-	c.7507C>G	c.(7507-7509)CTG>GTG	p.L2503V		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican	2503	Ig-like C2-type 9.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)	7		all_lung(23;0.00031)|Lung NSC(23;0.000946)												0.5	17.875532	17.875532	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3238737	3238737	10397	23	G	C	C	35	35	MXRA5	C	3	3
USP11	8237	broad.mit.edu	36	X	46986436	46986436	+	Missense_Mutation	SNP	G	T	T			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46986436G>T	uc004dhp.1	+	c.1320G>T	c.(1318-1320)CAG>CAT	p.Q440H	USP11_uc004dhq.1_Missense_Mutation_p.Q167H	NM_004651	NP_004642	P51784	UBP11_HUMAN	ubiquitin specific protease 11	440					protein deubiquitination|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)|central_nervous_system(1)	2														0.398496	161.129382	162.332881	53	80	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46986436	46986436	17604	23	G	T	T	35	35	USP11	T	3	3
NONO	4841	broad.mit.edu	36	X	70434472	70434472	+	Missense_Mutation	SNP	C	T	T			TCGA-19-1789-01	TCGA-19-1789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70434472C>T	uc004dzn.1	+	c.1090C>T	c.(1090-1092)CGG>TGG	p.R364W	NONO_uc004dzo.1_Missense_Mutation_p.R364W|NONO_uc004dzp.1_Missense_Mutation_p.R364W|NONO_uc004dzq.1_Missense_Mutation_p.R233W	NM_007363	NP_031389	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	364	Potential.|DBHS.				DNA recombination|DNA repair|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|identical protein binding|nucleotide binding|RNA binding		NONO/TFE3(2)	ovary(2)|kidney(2)	4	Renal(35;0.156)									130				0.451613	217.646595	217.959431	70	85	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70434472	70434472	10937	23	C	T	T	27	27	NONO	T	1	1
HDAC8	55869	broad.mit.edu	36	X	71627571	71627571	+	Silent	SNP	G	A	A			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:71627571G>A	uc004eau.1	-	c.561C>T	c.(559-561)GAC>GAT	p.D187D	HDAC8_uc010nlk.1_Silent_p.D58D|HDAC8_uc004eav.2_Silent_p.D187D|HDAC8_uc004eaw.2_Non-coding_Transcript	NM_018486	NP_060956	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	187	Histone deacetylase.				chromatin assembly or disassembly|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|nuclear chromosome	histone deacetylase activity (H3-K16 specific)|metal ion 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)|transcription factor binding				0	Renal(35;0.156)				Vorinostat(DB02546)					97				0.383436	398.201874	402.084598	125	201	GG		KEEP	---	---	---	---	capture			Silent	SNP	71627571	71627571	7296	23	G	A	A	40	40	HDAC8	A	1	1
LPAR4	2846	broad.mit.edu	36	X	77897606	77897606	+	Missense_Mutation	SNP	G	C	C			TCGA-19-1789-01	TCGA-19-1789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:77897606G>C	uc010nme.1	+	c.584G>C	c.(583-585)CGT>CCT	p.R195P	LPAR4_uc004edd.1_Missense_Mutation_p.R195P	NM_005296	NP_005287	Q99677	LPAR4_HUMAN	lysophosphatidic acid receptor 4	195	Extracellular (Potential).					integral to plasma membrane	lipid binding|purinergic nucleotide receptor activity, G-protein coupled	p.R195H(1)		ovary(3)	3														0.362385	250.359827	253.994864	79	139	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77897606	77897606	9280	23	G	C	C	40	40	LPAR4	C	3	3
LRRC16B	90668	broad.mit.edu	36	14	23599041	23599042	+	Frame_Shift_Del	DEL	TC	-	-			TCGA-19-1789-01	TCGA-19-1789-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23599041_23599042delTC	uc001wlj.2	+	c.1891_1892delTC	c.(1891-1893)TCCfs	p.S631fs	LRRC16B_uc001wlk.2_5'Flank	NM_138360	NP_612369	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	631										ovary(2)|breast(2)|pancreas(1)	5				GBM - Glioblastoma multiforme(265;0.019)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	23599041	23599042	9346	14	TC	-	-	58	58	LRRC16B	-	5	5
NFYC	4802	broad.mit.edu	36	1	41008768	41008769	+	Frame_Shift_Ins	INS	-	C	C			TCGA-19-1789-01	TCGA-19-1789-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:41008768_41008769insC	uc001cge.2	+	c.1058_1059insC	c.(1057-1059)CACfs	p.H353fs	NFYC_uc001cfz.2_Intron|NFYC_uc009vwd.1_Intron|NFYC_uc001cfx.2_Intron|NFYC_uc001cfy.2_Intron|NFYC_uc001cgb.2_Frame_Shift_Ins_p.H334fs|NFYC_uc001cgd.2_Intron	NM_014223	NP_055038	Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma isoform 2	353					protein folding|regulation of transcription from RNA polymerase II promoter	CCAAT-binding factor complex	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			breast(2)|kidney(1)	3	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.72e-17)											0.43			3	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	41008768	41008769	10791	1	-	C	C	6	6	NFYC	C	5	5
