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
SVIL	6840	broad.mit.edu	36	10	29791337	29791337	+	Splice_Site_SNP	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:29791337C>T	uc001iut.1	-	c.6278_splice	c.e36-1	p.G2093_splice	LOC387647_uc001iuo.1_Intron|LOC387647_uc001iup.2_Intron|LOC387647_uc001iuq.1_Intron|SVIL_uc001iuu.1_Splice_Site_SNP_p.G1667_splice	NM_021738	NP_068506			supervillin isoform 2						cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)	5		Breast(68;0.103)												0.6	166.714684	167.413726	48	32	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	29791337	29791337	15941	10	C	T	T	24	24	SVIL	T	5	2
CDH23	64072	broad.mit.edu	36	10	73241509	73241509	+	Silent	SNP	C	G	G			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:73241509C>G	uc001jrx.2	+	c.9312C>G	c.(9310-9312)GGC>GGG	p.G3104G	CDH23_uc001jsg.2_Silent_p.G864G|CDH23_uc001jsh.2_Silent_p.G864G|CDH23_uc001jsi.2_Silent_p.G864G|CDH23_uc001jsj.2_5'Flank|CDH23_uc001jsk.2_5'Flank	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	3104	Cytoplasmic (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.272727	8.420259	8.93233	3	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	73241509	73241509	3237	10	C	G	G	28	28	CDH23	G	3	3
MUC5B	727897	broad.mit.edu	36	11	1207082	1207082	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1207082C>T	uc001ltb.2	+	c.1083C>T	c.(1081-1083)GAC>GAT	p.D361D	MUC5B_uc009yct.1_Silent_p.D361D	NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	361	TIL 1.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.333333	8.122148	8.34348	3	6	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	Silent	SNP	1207082	1207082	10373	11	C	T	T	19	19	MUC5B	T	1	1
PITPNM1	9600	broad.mit.edu	36	11	67022304	67022304	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67022304G>C	uc001olx.1	-	c.1550C>G	c.(1549-1551)GCC>GGC	p.A517G	PITPNM1_uc001olw.1_5'UTR|PITPNM1_uc001oly.1_Missense_Mutation_p.A517G|PITPNM1_uc001olz.1_Missense_Mutation_p.A517G	NM_004910	NP_004901	O00562	PITM1_HUMAN	phosphatidylinositol transfer protein,	517					brain development|lipid metabolic process|phototransduction|protein transport	cleavage furrow|endoplasmic reticulum membrane|Golgi cisterna membrane|lipid particle|membrane fraction|midbody	metal ion binding|phosphatidylinositol transporter activity			lung(2)|central_nervous_system(1)	3						GBM(28;144 709 4607 5525)								0.275862	8.303664	9.695004	8	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	67022304	67022304	12374	11	G	C	C	42	42	PITPNM1	C	3	3
LRRC32	2615	broad.mit.edu	36	11	76049956	76049956	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:76049956G>A	uc001oxq.2	-	c.329C>T	c.(328-330)GCG>GTG	p.A110V	LRRC32_uc001oxr.2_Missense_Mutation_p.A110V	NM_005512	NP_005503	Q14392	LRC32_HUMAN	leucine rich repeat containing 32 precursor	110	LRR 3.|Extracellular (Potential).					integral to plasma membrane					0														0.353659	75.959424	77.503575	29	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76049956	76049956	9362	11	G	A	A	38	38	LRRC32	A	1	1
ATF7IP	55729	broad.mit.edu	36	12	14541962	14541962	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:14541962G>A	uc001rbw.1	+	c.3501G>A	c.(3499-3501)AAG>AAA	p.K1167K	ATF7IP_uc001rbx.1_Silent_p.K1166K|ATF7IP_uc001rby.2_Silent_p.K1167K|ATF7IP_uc001rca.1_Silent_p.K1167K	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting	1167	Interaction with MBD1.|Fibronectin type-III.				DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5														0.381818	122.820767	124.169254	42	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	14541962	14541962	1106	12	G	A	A	36	36	ATF7IP	A	2	2
PDE3A	5139	broad.mit.edu	36	12	20660431	20660431	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:20660431C>T	uc001reh.1	+	c.1270C>T	c.(1270-1272)CGC>TGC	p.R424C		NM_000921	NP_000912	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	424					lipid metabolic process|platelet activation|signal transduction	cytosol|integral to membrane	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(3)	3	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277)									0.361538	126.59192	128.784119	47	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20660431	20660431	12058	12	C	T	T	27	27	PDE3A	T	1	1
SOAT2	8435	broad.mit.edu	36	12	51798944	51798944	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51798944G>A	uc001sbv.1	+	c.867G>A	c.(865-867)ACG>ACA	p.T289T	SOAT2_uc009zms.1_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2	289					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|intestinal cholesterol absorption|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1														0.376147	113.047029	114.514851	41	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	51798944	51798944	15411	12	G	A	A	38	38	SOAT2	A	1	1
GAPDH	2597	broad.mit.edu	36	12	6517359	6517359	+	Missense_Mutation	SNP	T	G	G			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6517359T>G	uc001qop.1	+	c.874T>G	c.(874-876)TCC>GCC	p.S292A	GAPDH_uc009zep.1_Missense_Mutation_p.S250A|GAPDH_uc001qoq.1_Missense_Mutation_p.S217A|GAPDH_uc001qor.1_Missense_Mutation_p.S251A|GAPDH_uc001qos.1_Missense_Mutation_p.S292A|GAPDH_uc001qot.1_Missense_Mutation_p.S292A|GAPDH_uc001qou.1_Missense_Mutation_p.S251A|GAPDH_uc001qov.1_Missense_Mutation_p.S250A|GAPDH_uc001qow.1_Missense_Mutation_p.S245A|GAPDH_uc001qox.1_Missense_Mutation_p.S118A	NM_002046	NP_002037	P04406	G3P_HUMAN	glyceraldehyde-3-phosphate dehydrogenase	292					gluconeogenesis|glycolysis|neuron apoptosis|oxidation-reduction process|peptidyl-cysteine S-trans-nitrosylation|protein stabilization	cytosol|membrane|nucleus|perinuclear region of cytoplasm	glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity|NAD binding|peptidyl-cysteine S-nitrosylase activity|protein binding				0					NADH(DB00157)							OREG0021628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.362069	123.130749	125.06729	42	74	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6517359	6517359	6500	12	T	G	G	54	54	GAPDH	G	4	4
EFNB2	1948	broad.mit.edu	36	13	105985290	105985290	+	Silent	SNP	C	A	A			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:105985290C>A	uc001vqi.1	-	c.24G>T	c.(22-24)GTG>GTT	p.V8V		NM_004093	NP_004084	P52799	EFNB2_HUMAN	ephrin B2	8					cell differentiation|cell-cell signaling|interspecies interaction between organisms|nervous system development	integral to plasma membrane	ephrin receptor binding			ovary(1)	1	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)													0.393258	107.604333	108.492603	35	54	CC		KEEP	---	---	---	---	capture			Silent	SNP	105985290	105985290	5144	13	C	A	A	17	17	EFNB2	A	3	3
CTSG	1511	broad.mit.edu	36	14	24113774	24113774	+	Missense_Mutation	SNP	G	T	T			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:24113774G>T	uc001wpq.1	-	c.286C>A	c.(286-288)CGC>AGC	p.R96S		NM_001911	NP_001902	P08311	CATG_HUMAN	cathepsin G preproprotein	96	Peptidase S1.				immune response|proteolysis	cell surface|extracellular space|plasma membrane|stored secretory granule	heparin binding|serine-type endopeptidase activity			ovary(2)	2														0.414365	221.491437	222.650417	75	106	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0269)	Missense_Mutation	SNP	24113774	24113774	4194	14	G	T	T	39	39	CTSG	T	3	3
LRFN5	145581	broad.mit.edu	36	14	41426551	41426551	+	Missense_Mutation	SNP	G	T	T			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:41426551G>T	uc001wvm.1	+	c.973G>T	c.(973-975)GGG>TGG	p.G325W	LRFN5_uc010ana.1_Missense_Mutation_p.G325W	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	325	Extracellular (Potential).|Ig-like.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8														0.388393	245.060398	247.509433	87	137	GG		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)	Missense_Mutation	SNP	41426551	41426551	9314	14	G	T	T	35	35	LRFN5	T	3	3
FOXN3	1112	broad.mit.edu	36	14	88716807	88716807	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:88716807G>A	uc001xxo.2	-	c.908C>T	c.(907-909)GCG>GTG	p.A303V	FOXN3_uc010atk.1_Missense_Mutation_p.A281V|FOXN3_uc001xxn.2_Missense_Mutation_p.A281V	NM_001085471	NP_001078940	O00409	FOXN3_HUMAN	checkpoint suppressor 1 isoform 1	303					DNA damage checkpoint|embryo development|G2 phase of mitotic cell cycle|negative regulation of gene-specific transcription from RNA polymerase II promoter|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein C-terminus binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|skin(1)	2														0.487805	57.895986	57.901312	20	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	88716807	88716807	6267	14	G	A	A	38	38	FOXN3	A	1	1
BAHD1	22893	broad.mit.edu	36	15	38545507	38545507	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38545507C>T	uc001zlu.2	+	c.2229C>T	c.(2227-2229)GAC>GAT	p.D743D	BAHD1_uc001zlt.2_Silent_p.D742D|BAHD1_uc010bbp.1_Silent_p.D739D|BAHD1_uc001zlv.2_Silent_p.D740D	NM_014952	NP_055767	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	743	BAH.				heterochromatin formation|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin silencing complex|chromosome	chromatin binding|DNA binding|protein binding				0		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)												0.46131	474.58946	475.027538	155	181	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)	Silent	SNP	38545507	38545507	1318	15	C	T	T	20	20	BAHD1	T	2	2
IL32	9235	broad.mit.edu	36	16	3059234	3059234	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3059234C>T	uc002cto.1	+	c.582C>T	c.(580-582)TTC>TTT	p.F194F	IL32_uc002ctk.1_Intron|IL32_uc010btb.1_Silent_p.F138F|IL32_uc002ctl.1_Silent_p.F148F|IL32_uc002ctm.1_Silent_p.F148F|IL32_uc002ctn.1_Silent_p.F148F|IL32_uc002cts.2_Silent_p.F148F|IL32_uc002ctp.1_Silent_p.F128F|IL32_uc002ctq.1_Silent_p.F194F|IL32_uc002ctr.1_Silent_p.F128F|IL32_uc002ctt.1_Silent_p.F148F|IL32_uc002ctu.1_Silent_p.F139F	NM_004221	NP_004212	P24001	IL32_HUMAN	interleukin 32 isoform B	194					cell adhesion|defense response|immune response	extracellular space	cytokine activity			pancreas(1)	1														0.353488	212.329597	216.401599	76	139	CC		KEEP	---	---	---	---	capture			Silent	SNP	3059234	3059234	7993	16	C	T	T	30	30	IL32	T	2	2
CHST5	23563	broad.mit.edu	36	16	74121526	74121526	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:74121526G>A	uc002fej.1	-	c.276C>T	c.(274-276)CCC>CCT	p.P92P	CHST5_uc002fei.1_Silent_p.P86P|CHST5_uc010cgw.1_Silent_p.P86P	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	86	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0														0.457143	99.295106	99.406618	32	38	GG		KEEP	---	---	---	---	capture			Silent	SNP	74121526	74121526	3541	16	G	A	A	39	39	CHST5	A	1	1
SUPT6H	6830	broad.mit.edu	36	17	24034961	24034961	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24034961G>A	uc002hby.1	+	c.2229G>A	c.(2227-2229)AAG>AAA	p.K743K	SUPT6H_uc010crt.1_Silent_p.K743K	NM_003170	NP_003161	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog	743					chromatin remodeling|regulation of transcription from RNA polymerase II promoter	nucleus	hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity|transcription elongation regulator activity			ovary(2)	2	Lung NSC(42;0.00431)													0.461538	55.945387	55.995714	18	21	GG		KEEP	---	---	---	---	capture			Silent	SNP	24034961	24034961	15920	17	G	A	A	35	35	SUPT6H	A	2	2
DSG4	147409	broad.mit.edu	36	18	27222935	27222935	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:27222935C>T	uc002kwr.1	+	c.473C>T	c.(472-474)TCG>TTG	p.S158L	DSG4_uc002kwq.1_Missense_Mutation_p.S158L	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	desmoglein 4 isoform 2	158	Cadherin 2.|Extracellular (Potential).		Missing (in LAH1).		homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding			central_nervous_system(5)|ovary(3)	8														0.420635	304.829055	306.20741	106	146	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(10;0.00504)		Missense_Mutation	SNP	27222935	27222935	4963	18	C	T	T	31	31	DSG4	T	1	1
PCSK4	54760	broad.mit.edu	36	19	1434695	1434695	+	Missense_Mutation	SNP	T	G	G			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1434695T>G	uc002ltb.1	-	c.1345A>C	c.(1345-1347)ACC>CCC	p.T449P	PCSK4_uc002lsz.2_5'UTR|PCSK4_uc002lta.2_Missense_Mutation_p.T261P	NM_017573	NP_060043	Q6UW60	PCSK4_HUMAN	proprotein convertase subtilisin/kexin type 4	449					proteolysis	integral to membrane	serine-type endopeptidase activity				0		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)												0.333333	9.980739	10.455766	6	12	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1434695	1434695	12023	19	T	G	G	59	59	PCSK4	G	4	4
JAK3	3718	broad.mit.edu	36	19	17806947	17806947	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17806947C>T	uc002nhn.2	-	c.1992G>A	c.(1990-1992)CCG>CCA	p.P664P	JAK3_uc010ebh.1_Intron|JAK3_uc002nho.2_Silent_p.P664P	NM_000215	NP_000206	P52333	JAK3_HUMAN	Janus kinase 3	664	Protein kinase 1.				B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis	cytoskeleton|cytosol|endomembrane system|membrane	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			haematopoietic_and_lymphoid_tissue(36)|lung(3)|ovary(3)|stomach(2)|breast(2)	46								2		364				0.451327	132.377839	132.613482	51	62	CC		KEEP	---	---	---	---	capture			Silent	SNP	17806947	17806947	8243	19	C	T	T	27	27	JAK3	T	1	1
ZNF57	126295	broad.mit.edu	36	19	2869067	2869067	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5135-01	TCGA-26-5135-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2869067A>G	uc002lwr.1	+	c.1448A>G	c.(1447-1449)AAA>AGA	p.K483R		NM_173480	NP_775751	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	483	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						NSCLC(150;910 1964 4303 10464 26498)								0.442424	261.765441	262.240083	73	92	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	2869067	2869067	18596	19	A	G	G	1	1	ZNF57	G	4	4
SIPA1L3	23094	broad.mit.edu	36	19	43264169	43264169	+	Nonsense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43264169C>T	uc002ohk.1	+	c.124C>T	c.(124-126)CAG>TAG	p.Q42*		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	42					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2														0.319149	36.017646	37.379249	15	32	CC		KEEP	---	---	---	---	capture	Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)		Nonsense_Mutation	SNP	43264169	43264169	14826	19	C	T	T	21	21	SIPA1L3	T	5	2
CKM	1158	broad.mit.edu	36	19	50512984	50512984	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50512984C>T	uc002pbd.1	-	c.287G>A	c.(286-288)CGC>CAC	p.R96H		NM_001824	NP_001815	P06732	KCRM_HUMAN	muscle creatine kinase	96	Phosphagen kinase N-terminal.				creatine metabolic process	cytosol	ATP binding|creatine kinase activity				0		Ovarian(192;0.0336)|all_neural(266;0.112)			Creatine(DB00148)									0.406977	98.211982	98.860908	35	51	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Missense_Mutation	SNP	50512984	50512984	3584	19	C	T	T	27	27	CKM	T	1	1
MUC16	94025	broad.mit.edu	36	19	8923081	8923081	+	Silent	SNP	G	C	C			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8923081G>C	uc002mkp.1	-	c.25365C>G	c.(25363-25365)TCC>TCG	p.S8455S		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8457	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														0.346667	291.696481	297.92904	104	196	GG		KEEP	---	---	---	---	capture			Silent	SNP	8923081	8923081	10367	19	G	C	C	35	35	MUC16	C	3	3
KCNA10	3744	broad.mit.edu	36	1	110862862	110862862	+	Missense_Mutation	SNP	T	A	A			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:110862862T>A	uc001dzt.1	-	c.71A>T	c.(70-72)GAA>GTA	p.E24V		NM_005549	NP_005540	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related	24						voltage-gated potassium channel complex	intracellular cyclic nucleotide activated cation channel activity|voltage-gated potassium channel activity			ovary(3)|large_intestine(1)	4		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)												0.394366	75.481143	76.175539	28	43	TT		KEEP	---	---	---	---	capture		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Missense_Mutation	SNP	110862862	110862862	8307	1	T	A	A	62	62	KCNA10	A	4	4
TRIM33	51592	broad.mit.edu	36	1	114771423	114771423	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114771423C>T	uc001eew.1	-	c.1319G>A	c.(1318-1320)CGT>CAT	p.R440H	TRIM33_uc001eex.1_Missense_Mutation_p.R440H|TRIM33_uc009wgt.1_Missense_Mutation_p.R48H	NM_015906	NP_056990	Q9UPN9	TRI33_HUMAN	tripartite motif-containing 33 protein isoform	440					negative regulation of BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination|regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent	nucleus	co-SMAD binding|DNA binding|ligase activity|R-SMAD binding|zinc ion binding			central_nervous_system(3)|lung(2)|large_intestine(1)|breast(1)|skin(1)|ovary(1)	9	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)								377				0.393035	227.379587	229.393432	79	122	CC		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	114771423	114771423	17051	1	C	T	T	19	19	TRIM33	T	1	1
CRTC2	200186	broad.mit.edu	36	1	152194174	152194174	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152194174G>A	uc009woo.1	-	c.246C>T	c.(244-246)GCC>GCT	p.A82A	CRTC2_uc001fde.2_5'Flank|CRTC2_uc001fdf.2_5'Flank	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	82					interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding			ovary(2)	2	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)													0.303371	69.887649	72.961653	27	62	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.151)		Silent	SNP	152194174	152194174	4039	1	G	A	A	39	39	CRTC2	A	1	1
GON4L	54856	broad.mit.edu	36	1	154057908	154057908	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154057908G>A	uc001flz.2	-	c.944C>T	c.(943-945)ACG>ATG	p.T315M	GON4L_uc001fly.1_Missense_Mutation_p.T315M|GON4L_uc009wrh.1_Missense_Mutation_p.T315M|GON4L_uc001fma.1_Missense_Mutation_p.T315M|GON4L_uc001fmc.1_Missense_Mutation_p.T315M|GON4L_uc001fmd.2_Missense_Mutation_p.T315M|GON4L_uc009wri.1_De_novo_Start_OutOfFrame|GON4L_uc001fme.2_Missense_Mutation_p.T143M|GON4L_uc001fmf.2_Missense_Mutation_p.T9M	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	315					regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.342857	165.64451	169.463373	60	115	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154057908	154057908	6845	1	G	A	A	40	40	GON4L	A	1	1
SPTA1	6708	broad.mit.edu	36	1	156876336	156876336	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156876336C>T	uc001fst.1	-	c.4823G>A	c.(4822-4824)CGT>CAT	p.R1608H		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1608	Spectrin 16.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.403922	293.085352	295.139168	103	152	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156876336	156876336	15630	1	C	T	T	19	19	SPTA1	T	1	1
DUSP27	92235	broad.mit.edu	36	1	165330814	165330814	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165330814C>T	uc001geb.1	+	c.104C>T	c.(103-105)CCT>CTT	p.P35L		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	35					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.315789	7.365945	7.985518	6	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165330814	165330814	5009	1	C	T	T	24	24	DUSP27	T	2	2
DUSP27	92235	broad.mit.edu	36	1	165363020	165363020	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165363020G>A	uc001geb.1	+	c.2028G>A	c.(2026-2028)ACG>ACA	p.T676T		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	676					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.359375	63.00899	64.122514	23	41	GG		KEEP	---	---	---	---	capture			Silent	SNP	165363020	165363020	5009	1	G	A	A	40	40	DUSP27	A	1	1
OR2L13	284521	broad.mit.edu	36	1	246329662	246329662	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246329662G>A	uc001ids.1	+	c.362G>A	c.(361-363)CGT>CAT	p.R121H	OR2L13_uc009xha.1_Missense_Mutation_p.R121H	NM_175911	NP_787107	Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)								p.R121H(DND41-Tumor)	85				0.362694	375.442054	381.82345	140	246	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0132)		Missense_Mutation	SNP	246329662	246329662	11412	1	G	A	A	40	40	OR2L13	A	1	1
TMEM57	55219	broad.mit.edu	36	1	25630258	25630258	+	Splice_Site_SNP	SNP	T	G	G			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:25630258T>G	uc001bkk.1	+	c.80_splice	c.e1+2	p.S27_splice	TMEM57_uc009vru.1_Splice_Site_SNP_p.S27_splice|TMEM57_uc009vrv.1_Splice_Site_SNP_p.R27_splice|RHCE_uc001bkj.1_5'Flank|TMEM57_uc009vrt.1_Splice_Site_SNP	NM_018202	NP_060672			transmembrane protein 57							axon|integral to membrane|neuron projection terminus|nuclear membrane|synapse part					0		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)												0.266667	9.192323	9.930936	4	11	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)	Splice_Site_SNP	SNP	25630258	25630258	16723	1	T	G	G	59	59	TMEM57	G	5	4
HCRTR1	3061	broad.mit.edu	36	1	31857440	31857440	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:31857440G>A	uc009vtx.1	+	c.60G>A	c.(58-60)CCG>CCA	p.P20P	HCRTR1_uc001btb.1_Intron|HCRTR1_uc001btc.2_5'UTR|HCRTR1_uc001btd.1_Silent_p.P20P	NM_001525	NP_001516	O43613	OX1R_HUMAN	orexin receptor 1	20	Extracellular (Potential).				feeding behavior|neuropeptide signaling pathway|synaptic transmission	integral to plasma membrane				ovary(1)	1		Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.116)												0.371681	230.857447	234.119637	84	142	GG		KEEP	---	---	---	---	capture		STAD - Stomach adenocarcinoma(196;0.053)	Silent	SNP	31857440	31857440	7284	1	G	A	A	40	40	HCRTR1	A	1	1
MSH4	4438	broad.mit.edu	36	1	76042178	76042178	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:76042178G>A	uc001dhd.1	+	c.419G>A	c.(418-420)GGA>GAA	p.G140E		NM_002440	NP_002431	O15457	MSH4_HUMAN	mutS homolog 4	140					chiasma assembly|homologous chromosome segregation|meiotic mismatch repair|reciprocal meiotic recombination	mismatch repair complex|synaptonemal complex	ATP binding|damaged DNA binding|DNA-dependent ATPase activity|mismatched DNA binding			ovary(1)|lung(1)	2														0.432039	265.833026	266.664618	89	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76042178	76042178	10265	1	G	A	A	41	41	MSH4	A	2	2
GGTLC1	92086	broad.mit.edu	36	20	23915182	23915182	+	Missense_Mutation	SNP	A	G	G			TCGA-26-5135-01	TCGA-26-5135-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:23915182A>G	uc002wts.1	-	c.67T>C	c.(67-69)TCC>CCC	p.S23P	GGTLC1_uc002wtt.1_Missense_Mutation_p.S23P|GGTLC1_uc002wtu.1_Missense_Mutation_p.S23P	NM_178312	NP_842564	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	23							gamma-glutamyltransferase activity			ovary(1)	1														0.343511	151.342379	154.172874	45	86	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23915182	23915182	6633	20	A	G	G	11	11	GGTLC1	G	4	4
MATN4	8785	broad.mit.edu	36	20	43355866	43355866	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43355866C>T	uc002xnn.1	-	c.1701G>A	c.(1699-1701)ACG>ACA	p.T567T	MATN4_uc002xno.1_Silent_p.T526T|MATN4_uc002xnp.1_Silent_p.T485T	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	608	Potential.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)												0.355556	46.390367	47.216245	16	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	43355866	43355866	9720	20	C	T	T	23	23	MATN4	T	1	1
FAM65C	140876	broad.mit.edu	36	20	48665978	48665978	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:48665978G>A	uc002xvm.1	-	c.304C>T	c.(304-306)CGC>TGC	p.R102C	FAM65C_uc002xvn.1_Missense_Mutation_p.R102C	NM_080829	NP_543019	Q96MK2	FA65C_HUMAN	hypothetical protein LOC140876	102										ovary(2)	2														0.285714	19.788487	20.942344	8	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48665978	48665978	5824	20	G	A	A	40	40	FAM65C	A	1	1
OGFR	11054	broad.mit.edu	36	20	60915082	60915082	+	Missense_Mutation	SNP	G	C	C			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:60915082G>C	uc002ydj.1	+	c.1670G>C	c.(1669-1671)AGC>ACC	p.S557T	OGFR_uc002ydk.1_Missense_Mutation_p.S540T|OGFR_uc002ydl.1_Missense_Mutation_p.S505T	NM_007346	NP_031372	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	557	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].|3.				regulation of cell growth	cytoplasm|membrane|nucleus	opioid receptor activity				0	Breast(26;3.65e-08)													0.277778	12.165616	12.966631	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60915082	60915082	11248	20	G	C	C	34	34	OGFR	C	3	3
RRP7A	27341	broad.mit.edu	36	22	41241201	41241201	+	Silent	SNP	A	G	G	rs62239688	unknown	TCGA-26-5135-01	TCGA-26-5135-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41241201A>G	uc003bcp.1	-	c.429T>C	c.(427-429)TAT>TAC	p.Y143Y	RRP7A_uc003bcq.1_Silent_p.Y120Y	NM_015703	NP_056518	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A	120							nucleotide binding|RNA binding			central_nervous_system(1)	1														0.137255	8.490734	14.987423	7	44	AA		KEEP	---	---	---	---	capture			Silent	SNP	41241201	41241201	14169	22	A	G	G	8	8	RRP7A	G	4	4
C2orf70	339778	broad.mit.edu	36	2	26652387	26652387	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:26652387C>T	uc010eyn.1	+	c.188C>T	c.(187-189)CCC>CTC	p.P63L	C2orf70_uc002rhl.1_Missense_Mutation_p.P7L	NM_001105519	NP_001098989	A6NJV1	CB070_HUMAN	hypothetical protein LOC339778	63											0														0.37037	208.092917	210.886606	70	119	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26652387	26652387	2278	2	C	T	T	22	22	C2orf70	T	2	2
VAMP5	10791	broad.mit.edu	36	2	85672378	85672378	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:85672378G>A	uc002spu.1	+	c.23G>A	c.(22-24)CGG>CAG	p.R8Q		NM_006634	NP_006625	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	8	v-SNARE coiled-coil homology.|Cytoplasmic (Potential).				cell differentiation|vesicle-mediated transport	endomembrane system					0														0.333333	159.501434	163.77723	58	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	85672378	85672378	17681	2	G	A	A	39	39	VAMP5	A	1	1
ADCY5	111	broad.mit.edu	36	3	124529223	124529223	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:124529223C>T	uc003egh.1	-	c.1879G>A	c.(1879-1881)GAG>AAG	p.E627K	ADCY5_uc003egg.1_Missense_Mutation_p.E260K|ADCY5_uc003egi.1_Missense_Mutation_p.E186K	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	627	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4														0.390625	68.359798	69.030444	25	39	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0342)	Missense_Mutation	SNP	124529223	124529223	298	3	C	T	T	31	31	ADCY5	T	1	1
PSMD2	5708	broad.mit.edu	36	3	185504443	185504443	+	Silent	SNP	T	C	C			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:185504443T>C	uc003fnn.1	+	c.1338T>C	c.(1336-1338)CTT>CTC	p.L446L		NM_002808	NP_002799	Q13200	PSMD2_HUMAN	proteasome 26S non-ATPase subunit 2	446	PC 2.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|regulation of protein catabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	enzyme regulator activity|protein binding				0	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)				Bortezomib(DB00188)	Colon(24;313 636 6917 9932 15554)								0.398058	249.306778	251.17945	82	124	TT		KEEP	---	---	---	---	capture	Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Silent	SNP	185504443	185504443	13151	3	T	C	C	63	63	PSMD2	C	4	4
LRRC15	131578	broad.mit.edu	36	3	195561813	195561813	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:195561813G>A	uc003ftt.1	-	c.1255C>T	c.(1255-1257)CGG>TGG	p.R419W	LRRC15_uc003ftu.1_Missense_Mutation_p.R419W|LRRC15_uc010hzk.1_Missense_Mutation_p.R419W	NM_130830	NP_570843	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15 isoform b	419	Extracellular (Potential).					integral to membrane				ovary(3)	3	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)													0.431373	62.640778	62.850387	22	29	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)	Missense_Mutation	SNP	195561813	195561813	9344	3	G	A	A	38	38	LRRC15	A	1	1
PFKFB4	5210	broad.mit.edu	36	3	48538042	48538042	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48538042C>T	uc003ctv.1	-	c.1052G>A	c.(1051-1053)CGG>CAG	p.R351Q	PFKFB4_uc003ctw.1_Missense_Mutation_p.R160Q|PFKFB4_uc003ctx.1_Missense_Mutation_p.R308Q|PFKFB4_uc010hkb.1_Missense_Mutation_p.R344Q|PFKFB4_uc010hkc.1_Intron	NM_004567	NP_004558	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,	351	Fructose-2,6-bisphosphatase.				fructose 2,6-bisphosphate metabolic process|glycolysis	cytosol	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity			breast(1)	1														0.37931	101.454338	102.566078	33	54	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)	Missense_Mutation	SNP	48538042	48538042	12185	3	C	T	T	23	23	PFKFB4	T	1	1
RXFP1	59350	broad.mit.edu	36	4	159757759	159757759	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:159757759G>A	uc003ipz.1	+	c.707G>A	c.(706-708)CGT>CAT	p.R236H	RXFP1_uc010iqj.1_Missense_Mutation_p.R65H|RXFP1_uc010iqk.1_Missense_Mutation_p.R104H|RXFP1_uc010iql.1_Missense_Mutation_p.R104H|RXFP1_uc010iqm.1_Missense_Mutation_p.R203H|RXFP1_uc010iqn.1_Missense_Mutation_p.R182H|RXFP1_uc010iqo.1_Missense_Mutation_p.R236H	NM_021634	NP_067647	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	236	Extracellular (Potential).|LRR 4.					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding				0	all_hematologic(180;0.24)	Renal(120;0.0854)												0.446602	266.262515	266.77532	92	114	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(41;0.0219)	Missense_Mutation	SNP	159757759	159757759	14239	4	G	A	A	40	40	RXFP1	A	1	1
ODZ3	55714	broad.mit.edu	36	4	183950536	183950536	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:183950536G>A	uc003ivd.1	+	c.5717G>A	c.(5716-5718)CGA>CAA	p.R1906Q		NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	1906	Extracellular (Potential).				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)												0.386555	127.095302	128.445662	46	73	GG		KEEP	---	---	---	---	capture		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)	Missense_Mutation	SNP	183950536	183950536	11241	4	G	A	A	37	37	ODZ3	A	1	1
ADD1	118	broad.mit.edu	36	4	2899933	2899933	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:2899933G>A	uc003gfq.1	+	c.2192G>A	c.(2191-2193)GGG>GAG	p.G731E	ADD1_uc003gfn.1_Non-coding_Transcript|ADD1_uc003gfo.1_3'UTR|ADD1_uc003gfp.1_3'UTR|ADD1_uc003gfr.1_Missense_Mutation_p.G700E|ADD1_uc003gfs.1_3'UTR	NM_014189	NP_054908	P35611	ADDA_HUMAN	adducin 1 (alpha) isoform b	700					actin filament bundle assembly|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|positive regulation of protein binding	cytosol|F-actin capping protein complex|nucleus|plasma membrane	actin filament binding|calmodulin binding|metal ion binding|protein heterodimerization activity|protein homodimerization activity|spectrin binding|transcription factor binding			ovary(1)	1						Esophageal Squamous(71;505 1201 20414 34538 37449)								0.410959	167.071073	168.077426	60	86	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (64;0.168)	Missense_Mutation	SNP	2899933	2899933	305	4	G	A	A	43	43	ADD1	A	2	2
SLC6A19	340024	broad.mit.edu	36	5	1269784	1269784	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1269784C>T	uc003jbw.2	+	c.999C>T	c.(997-999)TAC>TAT	p.Y333Y		NM_001003841	NP_001003841	Q695T7	S6A19_HUMAN	solute carrier family 6, member 19	333	Extracellular (Potential).				cellular nitrogen compound metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity				0	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)													0.444444	116.088543	116.330276	40	50	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Silent	SNP	1269784	1269784	15179	5	C	T	T	19	19	SLC6A19	T	1	1
SLIT3	6586	broad.mit.edu	36	5	168045299	168045299	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:168045299C>T	uc010jjg.1	-	c.3547G>A	c.(3547-3549)GTC>ATC	p.V1183I	SLIT3_uc003mab.1_Missense_Mutation_p.V1176I	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3	1176	Laminin G-like.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)	3	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)				Ovarian(29;311 847 10864 17279 24903)								0.402439	192.04885	193.403041	66	98	CC		KEEP	---	---	---	---	capture	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	168045299	168045299	15239	5	C	T	T	18	18	SLIT3	T	2	2
UGT3A1	133688	broad.mit.edu	36	5	35991660	35991660	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:35991660C>T	uc003jjv.1	-	c.1139G>A	c.(1138-1140)CGT>CAT	p.R380H	UGT3A1_uc003jjx.1_Missense_Mutation_p.R250H|UGT3A1_uc003jjw.1_Non-coding_Transcript	NM_152404	NP_689617	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide	380	Extracellular (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|central_nervous_system(1)	3	all_lung(31;0.000197)													0.378378	227.976067	230.845193	84	138	CC		KEEP	---	---	---	---	capture	Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)		Missense_Mutation	SNP	35991660	35991660	17521	5	C	T	T	19	19	UGT3A1	T	1	1
HCN1	348980	broad.mit.edu	36	5	45297893	45297893	+	Nonsense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45297893G>A	uc003jok.1	-	c.2560C>T	c.(2560-2562)CGA>TGA	p.R854*		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	854	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.413613	229.962248	231.211828	79	112	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45297893	45297893	7278	5	G	A	A	39	39	HCN1	A	5	1
HCN1	348980	broad.mit.edu	36	5	45389053	45389053	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45389053C>T	uc003jok.1	-	c.1283G>A	c.(1282-1284)CGT>CAT	p.R428H		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	428	Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.348018	218.25179	222.881696	79	148	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45389053	45389053	7278	5	C	T	T	19	19	HCN1	T	1	1
PTCD2	79810	broad.mit.edu	36	5	71670294	71670294	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71670294C>T	uc003kcb.1	+	c.729C>T	c.(727-729)TTC>TTT	p.F243F	PTCD2_uc003kcc.1_Silent_p.F91F|PTCD2_uc003kcd.2_Non-coding_Transcript	NM_024754	NP_079030	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	243											0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)												0.372881	123.567515	125.243067	44	74	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)	Silent	SNP	71670294	71670294	13182	5	C	T	T	31	31	PTCD2	T	1	1
FCHO2	115548	broad.mit.edu	36	5	72406333	72406333	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:72406333C>T	uc003kcl.1	+	c.1588C>T	c.(1588-1590)CGG>TGG	p.R530W	FCHO2_uc010izb.1_De_novo_Start_OutOfFrame	NM_138782	NP_620137	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	530										ovary(1)	1		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)												0.407407	62.536773	62.94209	22	32	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)	Missense_Mutation	SNP	72406333	72406333	6025	5	C	T	T	19	19	FCHO2	T	1	1
TIAM2	26230	broad.mit.edu	36	6	155546157	155546157	+	Missense_Mutation	SNP	C	G	G			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155546157C>G	uc003qqb.1	+	c.2895C>G	c.(2893-2895)AGC>AGG	p.S965R	TIAM2_uc003qqd.1_Missense_Mutation_p.S965R|TIAM2_uc003qqe.1_Missense_Mutation_p.S965R|TIAM2_uc010kjj.1_Missense_Mutation_p.S498R|TIAM2_uc003qqf.1_Missense_Mutation_p.S341R|TIAM2_uc003qqg.1_Missense_Mutation_p.S277R	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	965	PDZ.				apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)												0.324324	153.857865	157.906881	48	100	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)	Missense_Mutation	SNP	155546157	155546157	16419	6	C	G	G	27	27	TIAM2	G	3	3
HLA-G	3135	broad.mit.edu	36	6	29905319	29905319	+	Silent	SNP	G	C	C			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29905319G>C	uc003nnw.2	+	c.765G>C	c.(763-765)GTG>GTC	p.V255V	HLA-G_uc003nny.2_Non-coding_Transcript|HLA-G_uc010jrn.1_Intron|HLA-G_uc003nnz.2_Silent_p.V163V	NM_002127	NP_002118	P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	255	Extracellular (Potential).|Ig-like C1-type.|Alpha-3.				antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4														0.340426	227.761137	233.034709	80	155	GG		KEEP	---	---	---	---	capture			Silent	SNP	29905319	29905319	7503	6	G	C	C	47	47	HLA-G	C	3	3
SKIV2L	6499	broad.mit.edu	36	6	32044682	32044682	+	Missense_Mutation	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32044682G>A	uc003nyn.1	+	c.3236G>A	c.(3235-3237)CGG>CAG	p.R1079Q	STK19_uc003nyt.1_5'Flank|STK19_uc010jtm.1_5'Flank|STK19_uc003nyv.1_5'Flank|STK19_uc003nyw.1_5'Flank	NM_006929	NP_008860	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like homolog	1079						nucleus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4														0.345324	120.256175	123.193052	48	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32044682	32044682	14854	6	G	A	A	39	39	SKIV2L	A	1	1
HMGCLL1	54511	broad.mit.edu	36	6	55468196	55468196	+	Missense_Mutation	SNP	T	C	C			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:55468196T>C	uc003pcn.1	-	c.865A>G	c.(865-867)AAT>GAT	p.N289D	HMGCLL1_uc003pco.1_Missense_Mutation_p.N259D|HMGCLL1_uc010jzx.1_Missense_Mutation_p.N160D	NM_019036	NP_061909	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-Coenzyme A	289							hydroxymethylglutaryl-CoA lyase activity|metal ion binding			ovary(1)|pancreas(1)	2	Lung NSC(77;0.0875)					Ovarian(35;840 893 7837 15538 42887)								0.258333	94.272965	100.619711	31	89	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.23)		Missense_Mutation	SNP	55468196	55468196	7521	6	T	C	C	64	64	HMGCLL1	C	4	4
PIK3CG	5294	broad.mit.edu	36	7	106295815	106295815	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295815C>T	uc003vdv.2	+	c.573C>T	c.(571-573)CGC>CGT	p.R191R	PIK3CG_uc003vdu.1_Silent_p.R191R|PIK3CG_uc003vdw.1_Silent_p.R191R	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	191					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21									p.R191R(NCIH2172-Tumor)	292				0.317881	112.546731	116.999455	48	103	CC		KEEP	---	---	---	---	capture			Silent	SNP	106295815	106295815	12340	7	C	T	T	27	27	PIK3CG	T	1	1
CTTNBP2	83992	broad.mit.edu	36	7	117155389	117155389	+	Missense_Mutation	SNP	C	A	A			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:117155389C>A	uc003vjf.1	-	c.4045G>T	c.(4045-4047)GTG>TTG	p.V1349L		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1349										ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)													0.303136	250.212888	260.142266	87	200	CC		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(290;0.133)	Missense_Mutation	SNP	117155389	117155389	4204	7	C	A	A	20	20	CTTNBP2	A	3	3
GCC1	79571	broad.mit.edu	36	7	127009832	127009832	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:127009832G>A	uc003vma.1	-	c.1800C>T	c.(1798-1800)GAC>GAT	p.D600D		NM_024523	NP_078799	Q96CN9	GCC1_HUMAN	Golgi coiled-coil protein 1	600	Potential.					Golgi membrane|plasma membrane	protein binding			ovary(2)	2														0.27027	123.566423	132.378574	50	135	GG		KEEP	---	---	---	---	capture			Silent	SNP	127009832	127009832	6551	7	G	A	A	36	36	GCC1	A	2	2
KEL	3792	broad.mit.edu	36	7	142353499	142353499	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142353499C>T	uc003wcb.1	-	c.1231G>A	c.(1231-1233)GTG>ATG	p.V411M		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	411	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.247059	49.634512	54.583645	21	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142353499	142353499	8448	7	C	T	T	19	19	KEL	T	1	1
TMEM195	392636	broad.mit.edu	36	7	15391692	15391692	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:15391692G>A	uc003stb.1	-	c.978C>T	c.(976-978)CCC>CCT	p.P326P		NM_001004320	NP_001004320	Q6ZNB7	ALKMO_HUMAN	transmembrane protein 195	326					ether lipid metabolic process|fatty acid biosynthetic process|membrane lipid metabolic process|oxidation-reduction process	endoplasmic reticulum membrane|integral to membrane	glyceryl-ether monooxygenase activity|iron ion binding				0														0.293878	212.707024	222.020682	72	173	GG		KEEP	---	---	---	---	capture			Silent	SNP	15391692	15391692	16652	7	G	A	A	35	35	TMEM195	A	2	2
ADAM7	8756	broad.mit.edu	36	8	24380301	24380301	+	Silent	SNP	G	A	A			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:24380301G>A	uc003xeb.1	+	c.489G>A	c.(487-489)CCG>CCA	p.P163P	ADAM7_uc003xea.1_Silent_p.P163P	NM_003817	NP_003808	Q9H2U9	ADAM7_HUMAN	a disintegrin and metalloproteinase domain 7	163	Extracellular (Potential).				proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			kidney(1)	1		Prostate(55;0.0181)												0.334711	219.898624	225.75024	81	161	GG		KEEP	---	---	---	---	capture		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)	Silent	SNP	24380301	24380301	252	8	G	A	A	40	40	ADAM7	A	1	1
SLCO5A1	81796	broad.mit.edu	36	8	70830294	70830294	+	Missense_Mutation	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:70830294C>T	uc003xyl.1	-	c.1177G>A	c.(1177-1179)GAT>AAT	p.D393N	SLCO5A1_uc010lzb.1_Missense_Mutation_p.D393N|SLCO5A1_uc003xyk.1_Missense_Mutation_p.D393N|SLCO5A1_uc010lzc.1_Missense_Mutation_p.D393N	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	393	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)													0.404412	161.598021	162.684319	55	81	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)		Missense_Mutation	SNP	70830294	70830294	15228	8	C	T	T	31	31	SLCO5A1	T	1	1
CEL	1056	broad.mit.edu	36	9	134936477	134936477	+	Silent	SNP	G	C	C			TCGA-26-5135-01	TCGA-26-5135-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134936477G>C	uc010naa.1	+	c.1776G>C	c.(1774-1776)GGG>GGC	p.G592G		NM_001807	NP_001798	P19835	CEL_HUMAN	carboxyl ester lipase precursor	589	3.|17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification|regulation of synaptic transmission|triglyceride metabolic process		acylglycerol lipase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			pancreas(1)	1														0.428571	10.424079	10.455211	3	4	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)	Silent	SNP	134936477	134936477	3342	9	G	C	C	43	43	CEL	C	3	3
RPL7A	6130	broad.mit.edu	36	9	135206977	135206977	+	Silent	SNP	C	T	T			TCGA-26-5135-01	TCGA-26-5135-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135206977C>T	uc004cde.1	+	c.477C>T	c.(475-477)CAC>CAT	p.H159H	MED22_uc004cdc.1_5'Flank|MED22_uc004cdd.1_5'Flank|RPL7A_uc004cdf.1_De_novo_Start_OutOfFrame|SNORD36A_uc010naj.1_5'Flank|SNORD36C_uc010nak.1_5'Flank	NM_000972	NP_000963	P62424	RL7A_HUMAN	ribosomal protein L7a	159					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|membrane fraction|polysomal ribosome	RNA binding|structural constituent of ribosome				0														0.355932	58.258842	59.337492	21	38	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)	Silent	SNP	135206977	135206977	14079	9	C	T	T	19	19	RPL7A	T	1	1
CDKN2A	1029	broad.mit.edu	36	9	21961137	21961137	+	Silent	SNP	T	G	G			TCGA-26-5135-01	TCGA-26-5135-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21961137T>G	uc003zpl.1	-	c.387A>C	c.(385-387)CGA>CGC	p.R129R	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpk.1_Missense_Mutation_p.D74A|CDKN2A_uc003zpj.1_3'UTR|CDKN2A_uc010miu.1_Non-coding_Transcript	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4	144			R -> C (in squamous cell carcinoma).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(425)|p.D74V(2)|p.L65fs*38(1)|p.V59fs*45(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.C72fs*71(1)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)						17		76	TSP Lung(5;3.83e-07)			0.25	6.318161	7.001169	3	9	TT		KEEP	---	---	---	---	capture		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	Silent	SNP	21961137	21961137	3290	9	T	G	G	58	58	CDKN2A	G	4	4
PMEPA1	56937	broad.mit.edu	36	20	55717999	55718001	+	In_Frame_Del	DEL	CGG	-	-			TCGA-26-5135-01	TCGA-26-5135-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:55717999_55718001delCGG	uc002xyq.1	-	c.44_46delCCG	c.(43-48)GCCGGG>GGG	p.A15del	PMEPA1_uc002xyr.1_Intron|PMEPA1_uc002xys.1_Intron|PMEPA1_uc002xyt.1_Intron	NM_020182	NP_954640	Q969W9	PMEPA_HUMAN	transmembrane prostate androgen-induced protein	15	Extracellular (Potential).				androgen receptor signaling pathway	integral to membrane|plasma membrane	WW domain binding			pancreas(1)	1														0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	55717999	55718001	12558	20	CGG	-	-	23	23	PMEPA1	-	5	5
