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
SMC3	9126	broad.mit.edu	36	10	112340824	112340824	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:112340824A>G	uc001kze.1	+	c.1756A>G	c.(1756-1758)ACT>GCT	p.T586A		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	586	Flexible hinge.				cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)	2		Breast(234;0.0848)|Lung NSC(174;0.238)												0.77551	143.078176	146.498249	38	11	AA		KEEP	---	---	---	---	capture		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)	Missense_Mutation	SNP	112340824	112340824	15282	10	A	G	G	14	14	SMC3	G	4	4
ATE1	11101	broad.mit.edu	36	10	123677446	123677446	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:123677446G>A	uc001lfp.1	-	c.9C>T	c.(7-9)TTC>TTT	p.F3F	ATE1_uc001lfq.1_Silent_p.F3F|ATE1_uc001lfr.1_Intron|ATE1_uc009xzu.1_Intron	NM_007041	NP_008972	O95260	ATE1_HUMAN	arginyltransferase 1 isoform 2	3					protein arginylation	cytoplasm|nucleus	acyltransferase activity|arginyltransferase activity				0		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)												0.777778	23.929668	24.568332	7	2	GG		KEEP	---	---	---	---	capture			Silent	SNP	123677446	123677446	1097	10	G	A	A	33	33	ATE1	A	2	2
THNSL1	79896	broad.mit.edu	36	10	25353151	25353151	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:25353151G>A	uc001isi.2	+	c.993G>A	c.(991-993)AGG>AGA	p.R331R	ENKUR_uc001ish.1_Intron|THNSL1_uc009xkn.1_Silent_p.R331R	NM_024838	NP_079114	Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1	331					threonine biosynthetic process		ATP binding|pyridoxal phosphate binding|shikimate kinase activity|threonine synthase activity			pancreas(1)	1					L-Threonine(DB00156)|Pyridoxal Phosphate(DB00114)									0.676056	155.956414	157.944361	48	23	GG		KEEP	---	---	---	---	capture			Silent	SNP	25353151	25353151	16390	10	G	A	A	42	42	THNSL1	A	2	2
MMP8	4317	broad.mit.edu	36	11	102098539	102098539	+	Missense_Mutation	SNP	C	T	T	rs61747594	by-1000genomes	TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:102098539C>T	uc001phe.2	-	c.178G>A	c.(178-180)GTT>ATT	p.V60I		NM_002424	NP_002415	P22894	MMP8_HUMAN	matrix metalloproteinase 8 preproprotein	60					collagen catabolic process|proteolysis	extracellular space|proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase activity|zinc ion binding			ovary(3)|breast(1)	4	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)							p.V60I(MDAPCA2B-Tumor)|p.V60I(ALEXANDERCELLS-Tumor)|p.V60I(DAUDI-Tumor)|p.V60L(BCP1-Tumor)	426				0.320312	115.043008	118.707722	41	87	CC		KEEP	---	---	---	---	capture	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Missense_Mutation	SNP	102098539	102098539	10059	11	C	T	T	19	19	MMP8	T	1	1
HMBS	3145	broad.mit.edu	36	11	118468046	118468046	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118468046T>G	uc001puz.1	+	c.614T>G	c.(613-615)ATC>AGC	p.I205S	HMBS_uc009zao.1_Missense_Mutation_p.I150S|HMBS_uc001pvc.1_Missense_Mutation_p.I150S|HMBS_uc009zap.1_Missense_Mutation_p.I188S|HMBS_uc001pva.1_Missense_Mutation_p.I205S|HMBS_uc001pvb.1_Intron|HMBS_uc001pvd.1_Missense_Mutation_p.I188S|HMBS_uc001pve.1_Missense_Mutation_p.I188S|HMBS_uc001pvf.1_Missense_Mutation_p.I188S	NM_000190	NP_001019553	P08397	HEM3_HUMAN	hydroxymethylbilane synthase isoform 1	205					heme biosynthetic process|peptidyl-pyrromethane cofactor linkage	cytosol	hydroxymethylbilane synthase activity				0	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)												0.392857	74.741531	75.303236	22	34	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)	Missense_Mutation	SNP	118468046	118468046	7510	11	T	G	G	50	50	HMBS	G	4	4
RAG2	5897	broad.mit.edu	36	11	36571475	36571475	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:36571475C>A	uc001mwv.2	-	c.820G>T	c.(820-822)GTT>TTT	p.V274F	RAG2_uc009ykm.1_Missense_Mutation_p.V274F|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	274					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_lung(20;0.226)	all_hematologic(20;0.00756)												0.376812	153.859331	155.69991	52	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36571475	36571475	13465	11	C	A	A	17	17	RAG2	A	3	3
C11orf40	143501	broad.mit.edu	36	11	4549390	4549390	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4549390T>A	uc001lzc.1	-	c.493A>T	c.(493-495)ATA>TTA	p.I165L		NM_144663	NP_653264	Q8WZ69	CK040_HUMAN	hypothetical protein LOC143501	165										ovary(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)												0.347826	9.878715	10.399856	8	15	TT		KEEP	---	---	---	---	capture		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)	Missense_Mutation	SNP	4549390	4549390	1678	11	T	A	A	52	52	C11orf40	A	4	4
PPME1	51400	broad.mit.edu	36	11	73642200	73642200	+	Silent	SNP	T	C	C			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:73642200T>C	uc001ouw.1	+	c.1158T>C	c.(1156-1158)TGT>TGC	p.C386C	P4HA3_uc001ouy.2_Intron|PPME1_uc009yty.1_Silent_p.C270C|PPME1_uc001oux.1_Silent_p.C199C	NM_016147	NP_057231	Q9Y570	PPME1_HUMAN	protein phosphatase methylesterase 1	386					protein demethylation		protein C-terminal methylesterase activity|protein phosphatase 2A binding|protein phosphatase inhibitor activity|protein phosphatase type 2A regulator activity				0	Breast(11;3.29e-05)													0.38	63.01627	63.646737	19	31	TT		KEEP	---	---	---	---	capture			Silent	SNP	73642200	73642200	12782	11	T	C	C	60	60	PPME1	C	4	4
DAO	1610	broad.mit.edu	36	12	107812177	107812177	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107812177G>A	uc001tnr.2	+	c.517G>A	c.(517-519)GAA>AAA	p.E173K	DAO_uc001tnq.2_Missense_Mutation_p.E107K|DAO_uc009zvb.1_Non-coding_Transcript|DAO_uc001tns.2_Non-coding_Transcript	NM_001917	NP_001908	P14920	OXDA_HUMAN	D-amino-acid oxidase	173					glyoxylate metabolic process|oxidation-reduction process	peroxisomal matrix	binding|D-amino-acid oxidase activity			ovary(1)|skin(1)	2														0.351351	37.962708	38.684405	13	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107812177	107812177	4398	12	G	A	A	33	33	DAO	A	2	2
ANO2	57101	broad.mit.edu	36	12	5833541	5833541	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5833541G>A	uc001qnm.1	-	c.550C>T	c.(550-552)CGG>TGG	p.R184W		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	188	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.321875	303.814961	312.830673	103	217	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5833541	5833541	705	12	G	A	A	39	39	ANO2	A	1	1
LUM	4060	broad.mit.edu	36	12	90022102	90022102	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:90022102G>A	uc001tbm.1	-	c.988C>T	c.(988-990)CGT>TGT	p.R330C	LUM_uc001tbn.1_Non-coding_Transcript	NM_002345	NP_002336	P51884	LUM_HUMAN	lumican precursor	330					collagen fibril organization|visual perception	extracellular space|fibrillar collagen	collagen binding|extracellular matrix structural constituent			central_nervous_system(2)	2														0.348837	84.725296	86.458878	30	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	90022102	90022102	9461	12	G	A	A	40	40	LUM	A	1	1
PCDH9	5101	broad.mit.edu	36	13	66698100	66698100	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:66698100A>T	uc001vik.1	-	c.2474T>A	c.(2473-2475)GTG>GAG	p.V825E	PCDH9_uc001vil.1_Missense_Mutation_p.V825E|PCDH9_uc001vin.2_Missense_Mutation_p.V825E	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	825	Helical; (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)												0.394422	305.273197	307.720952	99	152	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.00819)	Missense_Mutation	SNP	66698100	66698100	11938	13	A	T	T	6	6	PCDH9	T	4	4
CDCA4	55038	broad.mit.edu	36	14	104548634	104548634	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104548634G>A	uc001yqa.1	-	c.678C>T	c.(676-678)TCC>TCT	p.S226S	CDCA4_uc001yqb.1_Silent_p.S226S|CDCA4_uc010axd.1_Silent_p.S226S	NM_145701	NP_663747	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	226						nucleus				ovary(1)	1		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)												0.35	39.038462	39.832262	14	26	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.142)	Silent	SNP	104548634	104548634	3217	14	G	A	A	39	39	CDCA4	A	1	1
OR4N5	390437	broad.mit.edu	36	14	19682098	19682098	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19682098C>T	uc001vwp.1	+	c.364C>T	c.(364-366)CGC>TGC	p.R122C		NM_001004724	NP_001004724	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N,	122	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)													0.411576	393.936746	396.061346	128	183	CC		KEEP	---	---	---	---	capture	Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)	Missense_Mutation	SNP	19682098	19682098	11489	14	C	T	T	23	23	OR4N5	T	1	1
EIF2AK4	440275	broad.mit.edu	36	15	38069780	38069780	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38069780G>A	uc001zkm.1	+	c.2541G>A	c.(2539-2541)CGG>CGA	p.R847R	EIF2AK4_uc010bbj.1_Silent_p.R548R|EIF2AK4_uc001zkn.1_5'Flank	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	847	Protein kinase 2.				protein phosphorylation|translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)								876				0.315315	198.966831	205.704325	70	152	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)	Silent	SNP	38069780	38069780	5188	15	G	A	A	43	43	EIF2AK4	A	2	2
NEDD4	4734	broad.mit.edu	36	15	53996126	53996126	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:53996126C>T	uc002adj.1	-	c.196G>A	c.(196-198)GTT>ATT	p.V66I	NEDD4_uc002adl.1_Intron|NEDD4_uc002adi.1_Missense_Mutation_p.V66I|NEDD4_uc010bfm.1_Missense_Mutation_p.V66I|NEDD4_uc002adk.1_Non-coding_Transcript	NM_198400	NP_006145	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally	66					development involved in symbiotic interaction|glucocorticoid receptor signaling pathway|negative regulation of sodium ion transport|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage|negative regulation of vascular endothelial growth factor receptor signaling pathway|neuron projection development|positive regulation of nucleocytoplasmic transport|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of protein catabolic process|progesterone receptor signaling pathway|protein K63-linked ubiquitination|protein targeting to lysosome|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|receptor internalization|regulation of dendrite morphogenesis|response to calcium ion|transmission of virus	apicolateral plasma membrane|cell cortex|chromatin|cytosol|perinuclear region of cytoplasm|ubiquitin ligase complex	beta-2 adrenergic receptor binding|phosphoserine binding|phosphothreonine binding|proline-rich region binding|protein domain specific binding|RNA polymerase binding|sodium channel inhibitor activity|ubiquitin binding|ubiquitin-protein ligase activity			ovary(1)|breast(1)|skin(1)	3														0.359833	245.381662	249.516566	86	153	CC		KEEP	---	---	---	---	capture		all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)	Missense_Mutation	SNP	53996126	53996126	10709	15	C	T	T	19	19	NEDD4	T	1	1
SCNN1G	6340	broad.mit.edu	36	16	23134032	23134032	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:23134032G>A	uc002dlm.1	+	c.1691G>A	c.(1690-1692)CGC>CAC	p.R564H		NM_001039	NP_001030	P51170	SCNNG_HUMAN	sodium channel, nonvoltage-gated 1, gamma	564	Cytoplasmic (By similarity).				excretion|sensory perception of taste	apical plasma membrane|integral to plasma membrane	ligand-gated sodium channel activity|WW domain binding			ovary(2)|large_intestine(1)|pancreas(1)	4					Amiloride(DB00594)|Triamterene(DB00384)									0.369863	152.724971	154.891601	54	92	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0366)	Missense_Mutation	SNP	23134032	23134032	14412	16	G	A	A	38	38	SCNN1G	A	1	1
PRSS27	83886	broad.mit.edu	36	16	2704246	2704246	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2704246A>C	uc002crf.1	-	c.329T>G	c.(328-330)GTG>GGG	p.V110G	PRSS27_uc002cre.1_Missense_Mutation_p.V74G|PRSS27_uc002crg.1_Missense_Mutation_p.V8G|PRSS27_uc010bst.1_Missense_Mutation_p.V8G	NM_031948	NP_114154	Q9BQR3	PRS27_HUMAN	marapsin	110	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1														0.24	7.151983	10.697868	12	38	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2704246	2704246	13071	16	A	C	C	6	6	PRSS27	C	4	4
FLYWCH1	84256	broad.mit.edu	36	16	2923141	2923141	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2923141G>C	uc002csd.1	+	c.806G>C	c.(805-807)CGG>CCG	p.R269P	FLYWCH1_uc002csb.1_Missense_Mutation_p.R268P|FLYWCH1_uc002csc.1_Missense_Mutation_p.R268P|FLYWCH1_uc010bsv.1_5'UTR	NM_032296	NP_115672	Q4VC44	FWCH1_HUMAN	FLYWCH-type zinc finger 1 isoform a	269						nucleus	DNA binding|metal ion binding				0														0.25	6.645513	7.310202	3	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2923141	2923141	6189	16	G	C	C	39	39	FLYWCH1	C	3	3
CHD9	80205	broad.mit.edu	36	16	51847073	51847073	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:51847073A>G	uc002ehb.1	+	c.4090A>G	c.(4090-4092)ATT>GTT	p.I1364V	CHD9_uc002egy.1_Missense_Mutation_p.I1364V|CHD9_uc002ehc.1_Missense_Mutation_p.I1364V|CHD9_uc002ehf.1_Missense_Mutation_p.I478V	NM_025134	NP_079410	Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1364					cellular lipid metabolic process|chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|cytoplasm|nucleoplasm	ATP binding|chromatin binding|DNA binding|helicase activity|protein binding			lung(2)|central_nervous_system(1)|breast(1)|skin(1)|ovary(1)|kidney(1)	7		all_cancers(37;0.0212)								1157				0.36747	205.146259	207.703693	61	105	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51847073	51847073	3466	16	A	G	G	16	16	CHD9	G	4	4
CDH16	1014	broad.mit.edu	36	16	65504252	65504252	+	Silent	SNP	G	T	T			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65504252G>T	uc002eql.1	-	c.1098C>A	c.(1096-1098)CCC>CCA	p.P366P	CDH16_uc010cdy.1_Silent_p.P366P|CDH16_uc002eqm.1_Silent_p.P269P	NM_004062	NP_004053	O75309	CAD16_HUMAN	cadherin 16 precursor	366	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2		Ovarian(137;0.0563)												0.325581	78.329228	80.621253	28	58	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)	Silent	SNP	65504252	65504252	3230	16	G	T	T	39	39	CDH16	T	3	3
PLCG2	5336	broad.mit.edu	36	16	80525580	80525580	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:80525580G>A	uc002fgt.1	+	c.2785G>A	c.(2785-2787)GAG>AAG	p.E929K		NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	929					intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8										1880				0.333333	28.340026	29.078031	10	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	80525580	80525580	12462	16	G	A	A	37	37	PLCG2	A	1	1
RARA	5914	broad.mit.edu	36	17	35741165	35741165	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35741165T>C	uc002hum.1	+	c.169T>C	c.(169-171)TCC>CCC	p.S57P	RARA_uc002huk.1_Missense_Mutation_p.S57P|RARA_uc002hul.2_Missense_Mutation_p.S57P	NM_000964	NP_000955	P10276	RARA_HUMAN	retinoic acid receptor, alpha isoform 1	57	Modulating.				apoptotic cell clearance|cellular response to estrogen stimulus|cellular response to retinoic acid|estrogen receptor signaling pathway|negative regulation of gene-specific transcription|negative regulation of granulocyte differentiation|negative regulation of interferon-gamma production|negative regulation of tumor necrosis factor production|positive regulation of binding|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of gene-specific transcription|positive regulation of interleukin-13 production|positive regulation of interleukin-4 production|positive regulation of interleukin-5 production|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to estradiol stimulus	cell surface|cytoplasm|nucleoplasm	chromatin DNA binding|enzyme binding|protein domain specific binding|protein heterodimerization activity|receptor binding|retinoic acid binding|retinoic acid receptor activity|retinoic acid-responsive element binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription activator activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)|lung(1)	2		Breast(137;0.00328)			Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)					272				0.263158	9.408851	10.347253	5	14	TT		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(5;0.00143)		Missense_Mutation	SNP	35741165	35741165	13512	17	T	C	C	50	50	RARA	C	4	4
HEXIM2	124790	broad.mit.edu	36	17	40602645	40602645	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40602645C>T	uc010daf.1	+	c.613C>T	c.(613-615)CGA>TGA	p.R205*	HEXIM2_uc002iih.1_Nonsense_Mutation_p.R183*|HEXIM2_uc002iii.1_Nonsense_Mutation_p.R183*|HEXIM2_uc002iij.1_Nonsense_Mutation_p.R183*	NM_144608	NP_653209	Q96MH2	HEXI2_HUMAN	hexamthylene bis-acetamide inducible 2	183					negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding|transcription repressor activity				0														0.363636	33.59191	34.13137	12	21	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	40602645	40602645	7360	17	C	T	T	23	23	HEXIM2	T	5	1
TEX2	55852	broad.mit.edu	36	17	59626107	59626107	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59626107C>A	uc002jed.1	-	c.1725G>T	c.(1723-1725)GAG>GAT	p.E575D	TEX2_uc002jec.1_Missense_Mutation_p.E575D|TEX2_uc002jee.1_Missense_Mutation_p.E575D	NM_018469	NP_060939	Q8IWB9	TEX2_HUMAN	testis expressed sequence 2	575					signal transduction|sphingolipid metabolic process	integral to membrane				ovary(1)	1														0.370968	130.112567	131.92861	46	78	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)	Missense_Mutation	SNP	59626107	59626107	16308	17	C	A	A	24	24	TEX2	A	3	3
KDSR	2531	broad.mit.edu	36	18	59185315	59185315	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59185315G>C	uc010dpw.1	-	c.17C>G	c.(16-18)GCC>GGC	p.A6G		NM_002035	NP_002026	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase precursor	6					3-keto-sphinganine metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|extracellular space|integral to membrane	3-dehydrosphinganine reductase activity|binding				0									p.A6G(SNU719-Tumor)	107				0.444444	8.715872	8.736366	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59185315	59185315	8446	18	G	C	C	42	42	KDSR	C	3	3
TMEM59L	25789	broad.mit.edu	36	19	18592283	18592283	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18592283G>A	uc002njy.2	+	c.966G>A	c.(964-966)CCG>CCA	p.P322P		NM_012109	NP_036241	Q9UK28	TM59L_HUMAN	brain-specific membrane-anchored protein	322						Golgi membrane|integral to membrane|membrane fraction				ovary(2)	2														0.317919	147.586903	152.673199	55	118	GG		KEEP	---	---	---	---	capture			Silent	SNP	18592283	18592283	16725	19	G	A	A	40	40	TMEM59L	A	1	1
ZNF135	7694	broad.mit.edu	36	19	63270956	63270956	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63270956T>G	uc002qre.1	+	c.1292T>G	c.(1291-1293)ATT>AGT	p.I431S	ZNF135_uc002qrd.1_Intron|ZNF135_uc002qrf.1_Missense_Mutation_p.I389S|ZNF135_uc002qrg.2_Missense_Mutation_p.I401S	NM_003436	NP_003427	B4DHH9	B4DHH9_HUMAN	zinc finger protein 135	443					regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding			ovary(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)												0.247934	83.995423	90.986493	30	91	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)	Missense_Mutation	SNP	63270956	63270956	18316	19	T	G	G	52	52	ZNF135	G	4	4
MUC16	94025	broad.mit.edu	36	19	8946127	8946127	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8946127A>G	uc002mkp.1	-	c.6688T>C	c.(6688-6690)TCC>CCC	p.S2230P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2230	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														0.284404	96.59637	101.134349	31	78	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8946127	8946127	10367	19	A	G	G	10	10	MUC16	G	4	4
OR7G2	390882	broad.mit.edu	36	19	9074088	9074088	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9074088A>T	uc002mkr.1	-	c.895T>A	c.(895-897)TAT>AAT	p.Y299N		NM_001005193	NP_001005193	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G,	278	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						Esophageal Squamous(67;143 1448 28637 40648)								0.25	62.910566	69.313257	28	84	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9074088	9074088	11634	19	A	T	T	14	14	OR7G2	T	4	4
TNFRSF1B	7133	broad.mit.edu	36	1	12175619	12175619	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12175619A>C	uc001att.1	+	c.664A>C	c.(664-666)ACA>CCA	p.T222P	TNFRSF1B_uc001atu.1_Missense_Mutation_p.T27P|TNFRSF1B_uc009vnk.1_Non-coding_Transcript	NM_001066	NP_001057	P20333	TNR1B_HUMAN	tumor necrosis factor receptor 2 precursor	222	Extracellular (Potential).				apoptosis	extracellular region|integral to membrane|membrane raft|plasma membrane	tumor necrosis factor receptor activity	p.T222P(1)		liver(1)|central_nervous_system(1)	2	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)			Etanercept(DB00005)|Infliximab(DB00065)					222				0.468354	125.773258	125.841669	37	42	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Missense_Mutation	SNP	12175619	12175619	16835	1	A	C	C	6	6	TNFRSF1B	C	4	4
FLG2	388698	broad.mit.edu	36	1	150592963	150592963	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150592963C>T	uc001ezw.2	-	c.3923G>A	c.(3922-3924)CGC>CAC	p.R1308H		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	1308							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.421525	557.037708	559.429401	188	258	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150592963	150592963	6161	1	C	T	T	27	27	FLG2	T	1	1
ETV3L	440695	broad.mit.edu	36	1	155335191	155335191	+	Silent	SNP	G	T	T			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:155335191G>T	uc001fqq.1	-	c.417C>A	c.(415-417)TCC>TCA	p.S139S		NM_001004341	NP_001004341	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	139					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|central_nervous_system(1)	3	Hepatocellular(266;0.158)	Prostate(1639;0.184)												0.425532	144.8397	145.525434	60	81	GG		KEEP	---	---	---	---	capture			Silent	SNP	155335191	155335191	5473	1	G	T	T	43	43	ETV3L	T	3	3
PVRL4	81607	broad.mit.edu	36	1	159309698	159309698	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159309698C>T	uc001fxo.1	-	c.1249G>A	c.(1249-1251)GGG>AGG	p.G417R		NM_030916	NP_112178	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	417	Cytoplasmic (Potential).				adherens junction organization|cell adhesion|cell junction assembly	adherens junction|extracellular region|integral to membrane				ovary(2)	2	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)					NSCLC(76;1160 1387 14476 16172 29359)								0.309524	36.570382	37.922053	13	29	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.00165)		Missense_Mutation	SNP	159309698	159309698	13300	1	C	T	T	24	24	PVRL4	T	2	2
RGS1	5996	broad.mit.edu	36	1	190814110	190814110	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:190814110C>G	uc001gsi.1	+	c.416C>G	c.(415-417)GCA>GGA	p.A139G		NM_002922	NP_002913	Q08116	RGS1_HUMAN	regulator of G-protein signalling 1	139	RGS.				immune response|inhibition of adenylate cyclase activity by G-protein signaling pathway|negative regulation of signal transduction	cytoplasm|plasma membrane	calmodulin binding|GTPase activator activity|signal transducer activity				0		Breast(1374;0.188)												0.452381	261.884319	262.215934	76	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	190814110	190814110	13766	1	C	G	G	25	25	RGS1	G	3	3
THRAP3	9967	broad.mit.edu	36	1	36524934	36524934	+	Silent	SNP	T	C	C			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36524934T>C	uc001cae.2	+	c.516T>C	c.(514-516)TCT>TCC	p.S172S	THRAP3_uc001caf.2_Silent_p.S172S|THRAP3_uc001cag.1_Silent_p.S172S	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	172	Ser-rich.				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(5)|lung(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				Pancreas(129;785 1795 20938 23278 32581)				199				0.388614	537.106387	541.490592	157	247	TT		KEEP	---	---	---	---	capture			Silent	SNP	36524934	36524934	16402	1	T	C	C	53	53	THRAP3	C	4	4
C8A	731	broad.mit.edu	36	1	57155952	57155952	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:57155952G>A	uc001cyo.1	+	c.1730G>A	c.(1729-1731)CGG>CAG	p.R577Q		NM_000562	NP_000553	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	577	TSP type-1 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular space|membrane attack complex				ovary(1)|central_nervous_system(1)	2														0.328358	64.928818	66.67812	22	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57155952	57155952	2525	1	G	A	A	39	39	C8A	A	1	1
NPHP4	261734	broad.mit.edu	36	1	5891811	5891811	+	Silent	SNP	A	T	T			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:5891811A>T	uc001alq.1	-	c.1491T>A	c.(1489-1491)CCT>CCA	p.P497P	NPHP4_uc001als.1_Non-coding_Transcript|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	497					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cilium|membrane|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)												0.4	6.549204	6.592877	2	3	AA		KEEP	---	---	---	---	capture		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	5891811	5891811	10985	1	A	T	T	7	7	NPHP4	T	4	4
SYDE2	84144	broad.mit.edu	36	1	85421291	85421291	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:85421291C>T	uc009wcm.1	-	c.1622G>A	c.(1621-1623)CGA>CAA	p.R541Q	SYDE2_uc001dku.2_Missense_Mutation_p.R541Q	NM_032184	NP_115560	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2	541					activation of Rho GTPase activity|small GTPase mediated signal transduction	cytosol	Rho GTPase activator activity			ovary(1)|central_nervous_system(1)	2														0.419142	381.538759	383.274376	127	176	CC		KEEP	---	---	---	---	capture		all cancers(265;0.0126)|Epithelial(280;0.0336)	Missense_Mutation	SNP	85421291	85421291	15957	1	C	T	T	31	31	SYDE2	T	1	1
ABCG1	9619	broad.mit.edu	36	21	42581202	42581202	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42581202C>T	uc002zaq.1	+	c.1108C>T	c.(1108-1110)CGG>TGG	p.R370W	ABCG1_uc002zan.1_Missense_Mutation_p.R372W|ABCG1_uc002zam.1_Missense_Mutation_p.R348W|ABCG1_uc002zao.1_Missense_Mutation_p.R367W|ABCG1_uc002zap.1_Missense_Mutation_p.R370W|ABCG1_uc002zar.1_Missense_Mutation_p.R381W|ABCG1_uc010gpb.1_5'UTR	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1	370	Cytoplasmic (Potential).				amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|integral to plasma membrane|recycling endosome	ADP binding|ATP binding|cholesterol binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid binding|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)	2					Adenosine triphosphate(DB00171)									0.321739	212.982674	219.466464	74	156	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42581202	42581202	69	21	C	T	T	23	23	ABCG1	T	1	1
NEFH	4744	broad.mit.edu	36	22	28216168	28216168	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:28216168G>C	uc003afo.1	+	c.2539G>C	c.(2539-2541)GCC>CCC	p.A847P	NEFH_uc003afp.2_5'UTR	NM_021076	NP_066554	P12036	NFH_HUMAN	neurofilament, heavy polypeptide 200kDa	853	Tail.				cell death|nervous system development	neurofilament					0														0.263158	7.871736	8.842548	5	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28216168	28216168	10713	22	G	C	C	34	34	NEFH	C	3	3
SREBF2	6721	broad.mit.edu	36	22	40606777	40606777	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40606777C>T	uc003bbi.1	+	c.1873C>T	c.(1873-1875)CGC>TGC	p.R625C	LOC339674_uc003bba.1_Intron|SREBF2_uc003bbj.1_Non-coding_Transcript	NM_004599	NP_004590	Q12772	SRBP2_HUMAN	sterol regulatory element-binding transcription	625	Cytoplasmic (Potential).				cholesterol metabolic process	ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex	protein C-terminus binding			breast(2)|ovary(1)|central_nervous_system(1)	4														0.368932	109.0678	110.604697	38	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40606777	40606777	15656	22	C	T	T	23	23	SREBF2	T	1	1
TTC30B	150737	broad.mit.edu	36	2	178125729	178125729	+	Silent	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178125729G>C	uc002uln.1	-	c.9C>G	c.(7-9)GGC>GGG	p.G3G		NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	3					cell projection organization	cilium	binding				0														0.266667	7.351648	8.053586	4	11	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)		Silent	SNP	178125729	178125729	17254	2	G	C	C	42	42	TTC30B	C	3	3
TTC30A	92104	broad.mit.edu	36	2	178191667	178191667	+	Silent	SNP	A	C	C			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178191667A>C	uc002ulo.1	-	c.9T>G	c.(7-9)GGT>GGG	p.G3G		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	3					cell projection organization	cilium	binding				0														0.272727	6.419309	6.932216	3	8	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)		Silent	SNP	178191667	178191667	17253	2	A	C	C	10	10	TTC30A	C	4	4
TTN	7273	broad.mit.edu	36	2	179161071	179161071	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179161071C>A	uc002umr.1	-	c.55605G>T	c.(55603-55605)ATG>ATT	p.M18535I	TTN_uc002ums.1_Missense_Mutation_p.M12230I|TTN_uc010frc.1_Missense_Mutation_p.M12163I|TTN_uc010frd.1_Missense_Mutation_p.M12038I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	19462										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.391892	83.756077	84.514267	29	45	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179161071	179161071	17290	2	C	A	A	29	29	TTN	A	3	3
VWA3B	200403	broad.mit.edu	36	2	98294831	98294831	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:98294831G>C	uc002syo.1	+	c.3639G>C	c.(3637-3639)AAG>AAC	p.K1213N	VWA3B_uc002syn.1_Non-coding_Transcript|VWA3B_uc002syp.1_Missense_Mutation_p.K605N|VWA3B_uc002syq.1_Missense_Mutation_p.K489N|VWA3B_uc002syr.1_Missense_Mutation_p.K530N|VWA3B_uc002sys.2_Non-coding_Transcript	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1213										ovary(3)|large_intestine(2)	5														0.5	12.87225	12.87225	5	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	98294831	98294831	17810	2	G	C	C	34	34	VWA3B	C	3	3
ABCC5	10057	broad.mit.edu	36	3	185147944	185147944	+	Silent	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:185147944C>T	uc003fmg.1	-	c.3276G>A	c.(3274-3276)ACG>ACA	p.T1092T	ABCC5_uc010hxl.1_Silent_p.T1049T|ABCC5_uc003fmf.1_Silent_p.T620T	NM_005688	NP_005679	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C, member 5	1092	ABC transmembrane type-1 2.					integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(2)|large_intestine(1)|central_nervous_system(1)	4	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)													0.295455	35.160203	36.805632	13	31	CC		KEEP	---	---	---	---	capture	Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Silent	SNP	185147944	185147944	57	3	C	T	T	19	19	ABCC5	T	1	1
CNTN4	152330	broad.mit.edu	36	3	3053881	3053881	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:3053881G>T	uc003bpc.1	+	c.1961G>T	c.(1960-1962)GGG>GTG	p.G654V	CNTN4_uc003bpb.1_Missense_Mutation_p.G325V|CNTN4_uc003bpd.1_Missense_Mutation_p.G654V|CNTN4_uc003bpe.1_Missense_Mutation_p.G326V|CNTN4_uc003bpf.1_Missense_Mutation_p.G325V|CNTN4_uc003bpg.1_5'Flank	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	654	Fibronectin type-III 1.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)												0.342007	250.106317	256.045008	92	177	GG		KEEP	---	---	---	---	capture		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)	Missense_Mutation	SNP	3053881	3053881	3781	3	G	T	T	43	43	CNTN4	T	3	3
FGB	2244	broad.mit.edu	36	4	155710377	155710377	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155710377C>T	uc003ioa.2	+	c.1220C>T	c.(1219-1221)ACG>ATG	p.T407M	FGB_uc003iob.2_Intron|FGB_uc010ipv.1_Missense_Mutation_p.T345M|FGB_uc010ipw.1_Intron|FGB_uc003ioc.2_Missense_Mutation_p.T188M	NM_005141	NP_005132	P02675	FIBB_HUMAN	fibrinogen, beta chain preproprotein	407	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen|soluble fraction	chaperone binding|eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)	2	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	NSCLC(106;1133 1613 21870 46110 52656)								0.357143	86.62884	88.137808	30	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155710377	155710377	6068	4	C	T	T	19	19	FGB	T	1	1
GRIA2	2891	broad.mit.edu	36	4	158453462	158453462	+	Silent	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:158453462C>T	uc003ipl.2	+	c.651C>T	c.(649-651)AAC>AAT	p.N217N	GRIA2_uc003ipm.2_Silent_p.N217N|GRIA2_uc003ipk.2_Silent_p.N170N|GRIA2_uc010iqh.1_Non-coding_Transcript	NM_000826	NP_001077089	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 1	217	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity	p.N217N(1)		central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)			L-Glutamic Acid(DB00142)									0.319018	148.647376	153.389359	52	111	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(41;0.0294)	Silent	SNP	158453462	158453462	7046	4	C	T	T	19	19	GRIA2	T	1	1
RAPGEF2	9693	broad.mit.edu	36	4	160470527	160470527	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:160470527T>G	uc003iqg.2	+	c.734T>G	c.(733-735)GTT>GGT	p.V245G		NM_014247	NP_055062	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2	245	cNMP.				cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction	integral to plasma membrane|intracellular	calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity			upper_aerodigestive_tract(1)|skin(1)	2	all_hematologic(180;0.24)									322				0.444444	174.990612	175.304391	52	65	TT		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(41;0.0817)	Missense_Mutation	SNP	160470527	160470527	13504	4	T	G	G	60	60	RAPGEF2	G	4	4
SORBS2	8470	broad.mit.edu	36	4	186782044	186782044	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:186782044G>A	uc003iyg.1	-	c.1863C>T	c.(1861-1863)CCC>CCT	p.P621P	SORBS2_uc003iya.1_Intron|SORBS2_uc003iyb.1_Intron|SORBS2_uc003iyc.1_Intron|SORBS2_uc003iyd.1_Intron|SORBS2_uc003iye.1_Intron|SORBS2_uc003iyf.1_Intron|SORBS2_uc003iyh.1_Intron|SORBS2_uc003iyi.1_Intron|SORBS2_uc003iyj.1_Intron|SORBS2_uc003iyk.1_Intron|SORBS2_uc003iyl.1_Silent_p.P507P|SORBS2_uc003iym.1_Silent_p.P607P|SORBS2_uc003iyn.1_Intron|SORBS2_uc003iyo.1_Intron	NM_021069	NP_066547	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2 isoform 2	507						actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc	cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(1)	1		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)				Esophageal Squamous(153;41 2433 9491 36028)								0.397436	179.613358	181.050252	62	94	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)	Silent	SNP	186782044	186782044	15428	4	G	A	A	47	47	SORBS2	A	2	2
ADRA2C	152	broad.mit.edu	36	4	3738379	3738379	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:3738379G>A	uc003ghm.1	+	c.248G>A	c.(247-249)CGC>CAC	p.R83H	ADRA2C_uc010icx.1_Missense_Mutation_p.R83H	NM_000683	NP_000674	P18825	ADA2C_HUMAN	alpha-2C-adrenergic receptor	83	Cytoplasmic (By similarity).				activation of MAPK activity by adrenergic receptor signaling pathway|activation of protein kinase B activity|blood coagulation|cell-cell signaling|energy reserve metabolic process|epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway|negative regulation of epinephrine secretion|negative regulation of norepinephrine secretion|positive regulation of neuron differentiation|regulation of insulin secretion	endosome|integral to plasma membrane	alpha-2A adrenergic receptor binding|alpha2-adrenergic receptor activity|epinephrine binding|protein heterodimerization activity|protein homodimerization activity				0					Bethanidine(DB00217)|Brimonidine(DB00484)|Debrisoquin(DB04840)|Fenoldopam(DB00800)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Lofexidine(DB04948)|Norepinephrine(DB00368)|Yohimbine(DB01392)	Esophageal Squamous(12;454 628 4517 14479)								0.3	16.043413	16.75749	6	14	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Missense_Mutation	SNP	3738379	3738379	340	4	G	A	A	38	38	ADRA2C	A	1	1
UGT2B28	54490	broad.mit.edu	36	4	70182965	70182965	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70182965C>A	uc003hej.1	+	c.866C>A	c.(865-867)CCT>CAT	p.P289H	UGT2B28_uc010ihr.1_Missense_Mutation_p.P289H	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	289					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity				0					Flunitrazepam(DB01544)									0.377863	288.652484	292.085586	99	163	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70182965	70182965	17518	4	C	A	A	24	24	UGT2B28	A	3	3
DNAH5	1767	broad.mit.edu	36	5	13969467	13969467	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0126-01	TCGA-06-0126-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13969467A>G	uc003jfd.2	-	c.1187T>C	c.(1186-1188)CTG>CCG	p.L396P	DNAH5_uc003jfe.1_Non-coding_Transcript	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	396	Stem (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|breast(1)|central_nervous_system(1)|pancreas(1)	17	Lung NSC(4;0.00476)													0.393258	100.407747	101.294642	35	54	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13969467	13969467	4787	5	A	G	G	7	7	DNAH5	G	4	4
OR2Y1	134083	broad.mit.edu	36	5	180099424	180099424	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:180099424G>A	uc003mmf.1	-	c.241C>T	c.(241-243)CTC>TTC	p.L81F		NM_001001657	NP_001001657	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y,	81	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)												0.358025	84.747994	86.18778	29	52	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	180099424	180099424	11441	5	G	A	A	34	34	OR2Y1	A	2	2
HEATR7B2	133558	broad.mit.edu	36	5	41085273	41085273	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41085273G>T	uc003jmj.2	-	c.1367C>A	c.(1366-1368)ACT>AAT	p.T456N	HEATR7B2_uc003jmi.2_Missense_Mutation_p.T11N	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN	HEAT repeat family member 7B2	456							binding	p.T456N(1)		ovary(6)|central_nervous_system(2)	8														0.412698	78.737029	79.156789	26	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41085273	41085273	7318	5	G	T	T	36	36	HEATR7B2	T	3	3
SAMD5	389432	broad.mit.edu	36	6	147871912	147871912	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:147871912G>C	uc003qmc.1	+	c.155G>C	c.(154-156)CGC>CCC	p.R52P		NM_001030060	NP_001025231	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	52	SAM.										0		Ovarian(120;0.0907)												0.470588	9.303751	9.328838	8	9	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)	Missense_Mutation	SNP	147871912	147871912	14303	6	G	C	C	38	38	SAMD5	C	3	3
C6orf97	80129	broad.mit.edu	36	6	151956083	151956083	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:151956083C>T	uc003qol.1	+	c.1442C>T	c.(1441-1443)ACC>ATC	p.T481I		NM_025059	NP_079335	Q8IYT3	CF097_HUMAN	hypothetical protein LOC80129	481	Potential.										0		Ovarian(120;0.126)								349				0.318182	57.956154	59.893174	21	45	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(37;0.111)	OV - Ovarian serous cystadenocarcinoma(155;1.48e-10)	Missense_Mutation	SNP	151956083	151956083	2481	6	C	T	T	18	18	C6orf97	T	2	2
LGSN	51557	broad.mit.edu	36	6	64048630	64048630	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:64048630C>T	uc003peh.1	-	c.785G>A	c.(784-786)AGG>AAG	p.R262K	LGSN_uc003pei.1_Intron	NM_016571	NP_057655	Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase	262					glutamine biosynthetic process		glutamate-ammonia ligase activity			skin(1)	1					L-Glutamic Acid(DB00142)									0.350649	83.305224	84.818937	27	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64048630	64048630	9085	6	C	T	T	24	24	LGSN	T	2	2
SNRNP48	154007	broad.mit.edu	36	6	7547908	7547908	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:7547908G>T	uc003mxr.1	+	c.649G>T	c.(649-651)GAT>TAT	p.D217Y	SNRNP48_uc003mxs.1_Non-coding_Transcript|SNRNP48_uc003mxt.1_5'UTR	NM_152551	NP_689764	Q6IEG0	SNR48_HUMAN	U11/U12 snRNP 48K	217					mRNA processing|RNA splicing	cytoplasm|U12-type spliceosomal complex	metal ion binding				0														0.379747	83.12783	84.131086	30	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7547908	7547908	15357	6	G	T	T	33	33	SNRNP48	T	3	3
KLHL7	55975	broad.mit.edu	36	7	23129936	23129936	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:23129936G>A	uc003svs.2	+	c.136G>A	c.(136-138)GTG>ATG	p.V46M	KLHL7_uc003svp.2_Missense_Mutation_p.V24M|KLHL7_uc003svq.2_Missense_Mutation_p.V46M|KLHL7_uc003svr.2_Missense_Mutation_p.V24M|KLHL7_uc003svt.1_De_novo_Start_InFrame	NM_001031710	NP_001026880	Q8IXQ5	KLHL7_HUMAN	SBBI26 protein isoform 1	46	BTB.				response to stimulus|visual perception	Golgi apparatus|nucleolus|plasma membrane					0														0.321839	79.974258	82.424154	28	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23129936	23129936	8708	7	G	A	A	40	40	KLHL7	A	1	1
MRPL32	64983	broad.mit.edu	36	7	42943690	42943690	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:42943690C>T	uc003tia.1	+	c.557C>T	c.(556-558)ACC>ATC	p.T186I	MRPL32_uc003tib.1_Non-coding_Transcript|MRPL32_uc003tic.1_Missense_Mutation_p.T133I	NM_031903	NP_114109	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	186					translation	large ribosomal subunit|mitochondrial ribosome	structural constituent of ribosome				0														0.30137	59.82741	62.396398	22	51	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42943690	42943690	10188	7	C	T	T	18	18	MRPL32	T	2	2
WBSCR17	64409	broad.mit.edu	36	7	70524004	70524004	+	Silent	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70524004C>T	uc003tvy.1	+	c.939C>T	c.(937-939)GCC>GCT	p.A313A	WBSCR17_uc003tvz.1_Silent_p.A12A	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	313	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.322314	106.314218	109.690277	39	82	CC		KEEP	---	---	---	---	capture			Silent	SNP	70524004	70524004	17836	7	C	T	T	23	23	WBSCR17	T	1	1
GRM3	2913	broad.mit.edu	36	7	86306488	86306488	+	Silent	SNP	C	T	T			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86306488C>T	uc003uid.1	+	c.1722C>T	c.(1720-1722)GAC>GAT	p.D574D	GRM3_uc010lef.1_Intron|GRM3_uc010leg.1_Silent_p.D446D|GRM3_uc010leh.1_Silent_p.D166D	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	574	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)								0.349794	239.278045	244.080683	85	158	CC		KEEP	---	---	---	---	capture			Silent	SNP	86306488	86306488	7077	7	C	T	T	19	19	GRM3	T	1	1
COL1A2	1278	broad.mit.edu	36	7	93892889	93892889	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93892889G>A	uc003ung.1	+	c.2813G>A	c.(2812-2814)CGC>CAC	p.R938H		NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen	938					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging	p.R938H(1)		central_nervous_system(3)|ovary(2)	5	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)				Collagenase(DB00048)									0.235714	80.50442	89.44576	33	107	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	93892889	93892889	3816	7	G	A	A	38	38	COL1A2	A	1	1
TGFBR1	7046	broad.mit.edu	36	9	100948676	100948676	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:100948676G>A	uc004azc.1	+	c.1219G>A	c.(1219-1221)GTA>ATA	p.V407I	TGFBR1_uc004azd.1_Missense_Mutation_p.V330I	NM_004612	NP_004603	P36897	TGFR1_HUMAN	transforming growth factor, beta receptor I	407	Protein kinase.|Cytoplasmic (Potential).				activation of MAPKK activity|anterior/posterior pattern formation|artery morphogenesis|collagen fibril organization|embryonic cranial skeleton morphogenesis|germ cell migration|heart development|kidney development|neuron fate commitment|palate development|parathyroid gland development|pathway-restricted SMAD protein phosphorylation|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|pharyngeal system development|positive regulation of cell growth|positive regulation of cell proliferation|positive regulation of cellular component movement|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of SMAD protein import into nucleus|positive regulation of survival gene product expression|positive regulation of transcription, DNA-dependent|response to cholesterol|thymus development|transforming growth factor beta receptor signaling pathway	transforming growth factor beta receptor complex	ATP binding|I-SMAD binding|metal ion binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type I|type II transforming growth factor beta receptor binding			lung(2)|ovary(1)	3		Acute lymphoblastic leukemia(62;0.0559)								168				0.410256	491.620952	494.366982	160	230	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100948676	100948676	16349	9	G	A	A	36	36	TGFBR1	A	2	2
ORM2	5005	broad.mit.edu	36	9	116132571	116132571	+	Silent	SNP	C	A	A			TCGA-06-0126-01	TCGA-06-0126-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116132571C>A	uc004bil.1	+	c.151C>A	c.(151-153)CGA>AGA	p.R51R		NM_000608	NP_000599	P19652	A1AG2_HUMAN	orosomucoid 2	51					acute-phase response|regulation of immune system process	extracellular space	binding				0		Myeloproliferative disorder(63;0.163)				NSCLC(65;867 1308 1814 2391 12508)								0.555556	64.702871	64.799459	20	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	116132571	116132571	11679	9	C	A	A	31	31	ORM2	A	3	3
TEK	7010	broad.mit.edu	36	9	27148007	27148007	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0126-01	TCGA-06-0126-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:27148007T>A	uc003zqi.2	+	c.231T>A	c.(229-231)GAT>GAA	p.D77E	TEK_uc010mjc.1_Intron|TEK_uc003zqj.1_Missense_Mutation_p.D54E	NM_000459	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial precursor	77	Extracellular (Potential).|Ig-like C2-type 1.				angiogenesis|blood coagulation|cell-cell signaling|leukocyte migration|positive regulation of ERK1 and ERK2 cascade|positive regulation of protein kinase B signaling cascade|protein oligomerization|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	apical plasma membrane|basolateral plasma membrane|cell surface|integral to plasma membrane|membrane raft|microvillus	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	p.D77E(1)		ovary(3)|central_nervous_system(3)|breast(3)|lung(2)|kidney(1)	12		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)								493				0.414894	123.316216	123.90814	39	55	TT		KEEP	---	---	---	---	capture		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Missense_Mutation	SNP	27148007	27148007	16278	9	T	A	A	51	51	TEK	A	4	4
CDK20	23552	broad.mit.edu	36	9	89775531	89775531	+	Silent	SNP	G	A	A			TCGA-06-0126-01	TCGA-06-0126-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:89775531G>A	uc004apr.1	-	c.480C>T	c.(478-480)TAC>TAT	p.Y160Y	CDK20_uc004aps.1_Silent_p.Y160Y|CDK20_uc004apt.1_Silent_p.Y173Y|CDK20_uc004apu.1_Silent_p.Y160Y	NM_001039803	NP_001034892	Q8IZL9	CDK20_HUMAN	cell cycle related kinase isoform 3	160	Protein kinase.				cell division|multicellular organismal development|protein phosphorylation	cilium|mitochondrion|nucleus	ATP binding|cyclin-dependent protein kinase activity				0										143				0.375	54.153839	54.924463	21	35	GG		KEEP	---	---	---	---	capture			Silent	SNP	89775531	89775531	3266	9	G	A	A	48	48	CDK20	A	2	2
RYR3	6263	broad.mit.edu	36	15	31917293	31917294	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-0126-01	TCGA-06-0126-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31917293_31917294insA	uc001zhi.1	+	c.11820_11821insA	c.(11818-11823)TCCAAAfs	p.S3940fs	RYR3_uc010bar.1_Frame_Shift_Ins_p.S3935fs	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3940_3941	EF-hand.				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)										0.32			26	56				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	31917293	31917294	14250	15	-	A	A	21	21	RYR3	A	5	5
C8orf76	84933	broad.mit.edu	36	8	124312922	124312924	+	In_Frame_Del	DEL	AAG	-	-			TCGA-06-0126-01	TCGA-06-0126-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124312922_124312924delAAG	uc003yqc.1	-	c.612_614delCTT	c.(610-615)TTCTTT>TTT	p.204_205FF>F	C8orf76_uc003yqd.2_In_Frame_Del_p.172_173FF>F	NM_032847	NP_116236	Q96K31	CH076_HUMAN	hypothetical protein LOC84933	204_205							binding			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)											0.43			88	116				---	---	---	---	capture_indel			In_Frame_Del	DEL	124312922	124312924	2549	8	AAG	-	-	1	1	C8orf76	-	5	5
