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
SUV39H2	79723	broad.mit.edu	36	10	14978886	14978886	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:14978886G>T	uc001inh.1	+	c.33G>T	c.(31-33)TGG>TGT	p.W11C	SUV39H2_uc001ing.1_Missense_Mutation_p.W71C|SUV39H2_uc001ini.1_Missense_Mutation_p.W11C|SUV39H2_uc001inj.1_Missense_Mutation_p.W11C	NM_024670	NP_078946	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2	71	Chromo.				cell cycle|cell differentiation|chromatin assembly or disassembly|chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|chromosome, centromeric region|nucleus	chromatin binding|histone methyltransferase activity (H3-K9 specific)|protein binding|zinc ion binding			breast(2)|ovary(1)	3														0.097222	8.353967	31.744746	14	130	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14978886	14978886	15933	10	G	T	T	42	42	SUV39H2	T	3	3
PDZD3	79849	broad.mit.edu	36	11	118563210	118563210	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118563210A>T	uc001pvz.1	+	c.352A>T	c.(352-354)AGC>TGC	p.S118C	PDZD3_uc001pvy.1_Missense_Mutation_p.S118C|PDZD3_uc001pwa.1_5'UTR|PDZD3_uc001pwb.1_Missense_Mutation_p.S184C	NM_024791	NP_079067	Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	184	PDZ 1.				cGMP-mediated signaling|ion transport|negative regulation of cGMP biosynthetic process|receptor guanylyl cyclase signaling pathway|response to toxin|water transport	apical part of cell|brush border|cytosol|membrane fraction|subapical complex	guanylate cyclase inhibitor activity|ion channel inhibitor activity|protein C-terminus binding			breast(1)	1	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)												0.321429	25.766778	26.558939	9	19	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)	Missense_Mutation	SNP	118563210	118563210	12123	11	A	T	T	7	7	PDZD3	T	4	4
SYTL2	54843	broad.mit.edu	36	11	85123091	85123091	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:85123091C>T	uc001pbe.1	-	c.926G>A	c.(925-927)AGA>AAA	p.R309K	SYTL2_uc001pbf.2_Missense_Mutation_p.R309K	NM_032943	NP_116561	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2 isoform a	309					intracellular protein transport|vesicle docking involved in exocytosis	exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction	neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding|zinc ion binding			ovary(2)|large_intestine(1)	3		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)												0.432548	617.071325	618.925466	202	265	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)	Missense_Mutation	SNP	85123091	85123091	16004	11	C	T	T	32	32	SYTL2	T	2	2
PRIM1	5557	broad.mit.edu	36	12	55427008	55427008	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2514-01	TCGA-28-2514-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55427008T>C	uc001smd.1	-	c.337A>G	c.(337-339)ACA>GCA	p.T113A	PRIM1_uc001sme.1_Non-coding_Transcript|PRIM1_uc009zoz.1_Intron|PRIM1_uc001smf.1_Missense_Mutation_p.T113A	NM_000946	NP_000937	P49642	PRI1_HUMAN	DNA primase polypeptide 1	113					DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	DNA primase activity|metal ion binding				0														0.394366	91.381256	92.075625	28	43	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55427008	55427008	12933	12	T	C	C	58	58	PRIM1	C	4	4
TSFM	10102	broad.mit.edu	36	12	56476508	56476508	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2514-01	TCGA-28-2514-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:56476508T>C	uc001sqh.2	+	c.916T>C	c.(916-918)TCC>CCC	p.S306P	TSFM_uc001sqi.2_Missense_Mutation_p.S285P	NM_005726	NP_005717	P43897	EFTS_HUMAN	Ts translation elongation factor, mitochondrial	285						mitochondrion|nucleus	transcription elongation regulator activity|translation elongation factor activity				0	all_cancers(7;6.31e-80)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)													0.25	7.520099	8.201313	3	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56476508	56476508	17166	12	T	C	C	58	58	TSFM	C	4	4
IL26	55801	broad.mit.edu	36	12	66905754	66905754	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:66905754G>C	uc001stx.1	-	c.50C>G	c.(49-51)TCT>TGT	p.S17C		NM_018402	NP_060872	Q9NPH9	IL26_HUMAN	interleukin 26 precursor	17					cell-cell signaling|negative regulation of epithelial cell proliferation|positive regulation of cytokine secretion|positive regulation of ERK1 and ERK2 cascade|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of JAK-STAT cascade|positive regulation of protein kinase B signaling cascade|positive regulation of stress-activated MAPK cascade	cytosol|extracellular space|soluble fraction	cytokine activity				0														0.375	346.105011	349.946691	105	175	GG		KEEP	---	---	---	---	capture	Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000515)	Missense_Mutation	SNP	66905754	66905754	7980	12	G	C	C	33	33	IL26	C	3	3
ERCC5	2073	broad.mit.edu	36	13	102318597	102318597	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:102318597C>T	uc001vpu.1	+	c.4029C>T	c.(4027-4029)CTC>CTT	p.L1343L	ERCC5_uc001vpw.1_Silent_p.L889L	NM_000123	NP_000114	P28715	ERCC5_HUMAN	XPG-complementing protein	889					negative regulation of apoptosis|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision, 3'-to lesion|response to UV-C|transcription-coupled nucleotide-excision repair|UV protection	nucleoplasm	bubble DNA binding|double-stranded DNA binding|endodeoxyribonuclease activity|metal ion binding|protein homodimerization activity|protein N-terminus binding|single-stranded DNA binding			ovary(4)|central_nervous_system(1)	5	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)									463				0.355072	140.131825	142.68782	49	89	CC		KEEP	---	---	---	---	capture			Silent	SNP	102318597	102318597	5409	13	C	T	T	30	30	ERCC5	T	2	2
MIPEP	4285	broad.mit.edu	36	13	23346985	23346985	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:23346985C>T	uc001uox.2	-	c.603G>A	c.(601-603)AAG>AAA	p.K201K		NM_005932	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	201					protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)												0.325	229.267033	235.789311	78	162	CC		KEEP	---	---	---	---	capture		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)	Silent	SNP	23346985	23346985	9982	13	C	T	T	24	24	MIPEP	T	2	2
DLK1	8788	broad.mit.edu	36	14	100270580	100270580	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:100270580C>T	uc001yhs.2	+	c.746C>T	c.(745-747)GCG>GTG	p.A249V	DLK1_uc001yhu.2_Intron	NM_003836	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog	249	Extracellular (Potential).				multicellular organismal development	extracellular space|integral to membrane|soluble fraction				ovary(2)	2		Melanoma(154;0.155)												0.4875	108.719109	108.729657	39	41	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100270580	100270580	4744	14	C	T	T	27	27	DLK1	T	1	1
SIN3A	25942	broad.mit.edu	36	15	73480143	73480143	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73480143C>T	uc002bai.1	-	c.1718G>A	c.(1717-1719)CGG>CAG	p.R573Q	SIN3A_uc002baj.1_Missense_Mutation_p.R573Q	NM_015477	NP_056292	Q96ST3	SIN3A_HUMAN	transcriptional co-repressor Sin3A	573	Interactions with SUDS3 and SAP130.|Interaction with NCOR1 (By similarity).				blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|Sin3 complex	protein binding			ovary(1)|lung(1)	2														0.344262	61.357447	62.663729	21	40	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73480143	73480143	14820	15	C	T	T	23	23	SIN3A	T	1	1
PKD1	5310	broad.mit.edu	36	16	2096266	2096266	+	Silent	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2096266G>A	uc002cos.1	-	c.7530C>T	c.(7528-7530)TAC>TAT	p.Y2510Y	PKD1_uc002cot.1_Silent_p.Y2510Y|PKD1_uc010bse.1_5'Flank	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	2510	Extracellular (Potential).|REJ.				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.489362	65.453256	65.456558	23	24	GG		KEEP	---	---	---	---	capture			Silent	SNP	2096266	2096266	12387	16	G	A	A	40	40	PKD1	A	1	1
QPRT	23475	broad.mit.edu	36	16	29616073	29616073	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2514-01	TCGA-28-2514-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:29616073T>G	uc002dto.1	+	c.734T>G	c.(733-735)GTG>GGG	p.V245G	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron	NM_014298	NP_055113	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	245					protein oligomerization|quinolinate catabolic process	cytosol	nicotinate-nucleotide diphosphorylase (carboxylating) activity|protein homodimerization activity				0					Niacin(DB00627)									0.232558	7.074007	10.297915	10	33	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29616073	29616073	13334	16	T	G	G	59	59	QPRT	G	4	4
CREBBP	1387	broad.mit.edu	36	16	3719063	3719063	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3719063C>T	uc002cvv.1	-	c.5986G>A	c.(5986-5988)GCC>ACC	p.A1996T	CREBBP_uc002cvw.1_Missense_Mutation_p.A1958T	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	1996					cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			ovary(6)|skin(2)|pancreas(1)|lung(1)	10		Ovarian(90;0.0266)								748				0.666667	18.652066	18.873206	6	3	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)	Missense_Mutation	SNP	3719063	3719063	4000	16	C	T	T	26	26	CREBBP	T	2	2
CNGB1	1258	broad.mit.edu	36	16	56475781	56475781	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56475781C>T	uc002emt.1	-	c.3544G>A	c.(3544-3546)GAC>AAC	p.D1182N	CNGB1_uc010cdh.1_Missense_Mutation_p.D1176N	NM_001297	NP_001288	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1 isoform	1182	Cytoplasmic (Potential).				sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)|pancreas(1)	4						Colon(156;1293 1853 16336 28962 38659)								0.447368	47.369999	47.46149	17	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56475781	56475781	3738	16	C	T	T	31	31	CNGB1	T	1	1
CCDC45	90799	broad.mit.edu	36	17	59949431	59949431	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2514-01	TCGA-28-2514-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59949431T>C	uc002jem.1	+	c.865T>C	c.(865-867)TCC>CCC	p.S289P	CCDC45_uc002jen.1_Non-coding_Transcript	NM_138363	NP_612372	Q96GE4	CCD45_HUMAN	coiled-coil domain containing 45	289							protein binding			ovary(1)	1	Breast(5;1.32e-14)													0.25	9.74202	11.822904	9	27	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(8;8.6e-12)		Missense_Mutation	SNP	59949431	59949431	2939	17	T	C	C	54	54	CCDC45	C	4	4
ONECUT2	9480	broad.mit.edu	36	18	53254356	53254356	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:53254356C>T	uc002lgo.1	+	c.410C>T	c.(409-411)TCG>TTG	p.S137L		NM_004852	NP_004843	O95948	ONEC2_HUMAN	one cut domain, family member 2	137					organ morphogenesis	nucleus	RNA polymerase II transcription factor activity|sequence-specific DNA binding			ovary(2)|central_nervous_system(1)	3		Colorectal(73;0.234)												0.625	30.352828	30.572469	10	6	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)	Missense_Mutation	SNP	53254356	53254356	11274	18	C	T	T	31	31	ONECUT2	T	1	1
LDLR	3949	broad.mit.edu	36	19	11082368	11082368	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11082368C>T	uc002mqk.2	+	c.981C>T	c.(979-981)CAC>CAT	p.H327H		NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	327	Extracellular (Potential).|EGF-like 1.		H -> Y (in FH).		cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)	2		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)			Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.290909	80.3618	84.666985	32	78	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Silent	SNP	11082368	11082368	9028	19	C	T	T	19	19	LDLR	T	1	1
CELF5	60680	broad.mit.edu	36	19	3244345	3244345	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3244345C>T	uc002lxm.1	+	c.1359C>T	c.(1357-1359)AGC>AGT	p.S453S	CELF5_uc002lxl.1_3'UTR|CELF5_uc010dtj.1_3'UTR|CELF5_uc002lxn.2_Non-coding_Transcript	NM_021938	NP_068757	Q8N6W0	CELF5_HUMAN	bruno-like 5, RNA binding protein	453	RRM 3.				mRNA processing	cytoplasm|nucleus	nucleotide binding|RNA binding			ovary(1)	1														0.305732	115.534777	120.826427	48	109	CC		KEEP	---	---	---	---	capture			Silent	SNP	3244345	3244345	3352	19	C	T	T	27	27	CELF5	T	1	1
FFAR2	2867	broad.mit.edu	36	19	40633357	40633357	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40633357C>T	uc002nzg.2	+	c.901C>T	c.(901-903)CGC>TGC	p.R301C	FFAR2_uc010eea.1_Missense_Mutation_p.R301C	NM_005306	NP_005297	O15552	FFAR2_HUMAN	free fatty acid receptor 2	301	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity|lipid binding			central_nervous_system(1)	1	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)					GBM(40;139 809 9833 23358 48736)				34				0.306818	214.209434	222.975962	81	183	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0724)		Missense_Mutation	SNP	40633357	40633357	6065	19	C	T	T	19	19	FFAR2	T	1	1
NLRP2	55655	broad.mit.edu	36	19	60186894	60186894	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60186894C>T	uc002qij.1	+	c.2016C>T	c.(2014-2016)GAC>GAT	p.D672D	NLRP2_uc010esm.1_Non-coding_Transcript|NLRP2_uc010esn.1_Silent_p.D648D|NLRP2_uc010eso.1_Silent_p.D669D|NLRP2_uc010esp.1_Silent_p.D650D	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	672					apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)	1														0.303738	167.292105	174.649801	65	149	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)	Silent	SNP	60186894	60186894	10880	19	C	T	T	19	19	NLRP2	T	1	1
PTPRH	5794	broad.mit.edu	36	19	60385214	60385214	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60385214C>T	uc002qjq.1	-	c.3180G>A	c.(3178-3180)CCG>CCA	p.P1060P	SYT5_uc002qjm.1_5'Flank|SYT5_uc002qjn.1_5'Flank|SYT5_uc002qjo.1_5'Flank|SYT5_uc002qjp.1_5'Flank|PTPRH_uc010esv.1_Silent_p.P882P	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1060	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)	3		Renal(1328;0.245)												0.27476	210.434295	224.726198	86	227	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)	Silent	SNP	60385214	60385214	13260	19	C	T	T	19	19	PTPRH	T	1	1
TNFSF14	8740	broad.mit.edu	36	19	6615993	6615993	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6615993G>A	uc002mfk.1	-	c.667C>T	c.(667-669)CGC>TGC	p.R223C	TNFSF14_uc002mfj.1_Missense_Mutation_p.R187C	NM_003807	NP_003798	O43557	TNF14_HUMAN	tumor necrosis factor ligand superfamily, member	223	Extracellular (Potential).				cellular response to mechanical stimulus|immune response|induction of apoptosis|release of cytoplasmic sequestered NF-kappaB|T cell homeostasis|T cell proliferation	cytoplasm|extracellular space|integral to membrane|plasma membrane	caspase inhibitor activity|cytokine activity|tumor necrosis factor receptor binding				0														0.3	219.060632	229.769367	90	210	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6615993	6615993	16848	19	G	A	A	40	40	TNFSF14	A	1	1
TNFSF14	8740	broad.mit.edu	36	19	6616273	6616273	+	Silent	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6616273G>A	uc002mfk.1	-	c.387C>T	c.(385-387)CAC>CAT	p.H129H	TNFSF14_uc002mfj.1_Silent_p.H93H	NM_003807	NP_003798	O43557	TNF14_HUMAN	tumor necrosis factor ligand superfamily, member	129	Extracellular (Potential).				cellular response to mechanical stimulus|immune response|induction of apoptosis|release of cytoplasmic sequestered NF-kappaB|T cell homeostasis|T cell proliferation	cytoplasm|extracellular space|integral to membrane|plasma membrane	caspase inhibitor activity|cytokine activity|tumor necrosis factor receptor binding				0														0.268657	43.418061	46.65636	18	49	GG		KEEP	---	---	---	---	capture			Silent	SNP	6616273	6616273	16848	19	G	A	A	40	40	TNFSF14	A	1	1
LRRC8E	80131	broad.mit.edu	36	19	7870176	7870176	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:7870176C>T	uc002mir.1	+	c.769C>T	c.(769-771)CGA>TGA	p.R257*		NM_025061	NP_079337	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member	257						integral to membrane				lung(1)|pancreas(1)	2														0.341463	121.142861	123.860394	42	81	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	7870176	7870176	9401	19	C	T	T	23	23	LRRC8E	T	5	1
PTPN22	26191	broad.mit.edu	36	1	114200752	114200752	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114200752G>A	uc001eds.1	-	c.421C>T	c.(421-423)CGC>TGC	p.R141C	PTPN22_uc009wgq.1_Missense_Mutation_p.R141C|PTPN22_uc001edt.1_Intron|PTPN22_uc009wgr.1_Missense_Mutation_p.R141C|PTPN22_uc009wgs.1_Intron|PTPN22_uc001edu.1_Missense_Mutation_p.R141C	NM_015967	NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type	141	Tyrosine-protein phosphatase.				negative regulation of T cell activation|negative regulation of T cell receptor signaling pathway|phosphoanandamide dephosphorylation|regulation of B cell receptor signaling pathway|regulation of innate immune response|regulation of natural killer cell proliferation|T cell differentiation	internal side of plasma membrane|nucleus|perinuclear region of cytoplasm	kinase binding|protein tyrosine phosphatase activity|SH3 domain binding			kidney(2)|lung(1)|skin(1)	4	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)								661				0.441667	150.553309	150.909793	53	67	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	Missense_Mutation	SNP	114200752	114200752	13244	1	G	A	A	38	38	PTPN22	A	1	1
PLCH2	9651	broad.mit.edu	36	1	2401258	2401258	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:2401258G>A	uc001aji.1	+	c.497G>A	c.(496-498)CGC>CAC	p.R166H	PLCH2_uc009vle.1_5'Flank|PLCH2_uc001ajj.1_5'Flank|PLCH2_uc001ajk.1_5'Flank	NM_014638	NP_055453	O75038	PLCH2_HUMAN	phospholipase C, eta 2	166					intracellular signal transduction|lipid catabolic process	cytoplasm|plasma membrane	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			central_nervous_system(3)|ovary(1)|skin(1)	5	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)												0.369863	67.064232	68.165219	27	46	GG		KEEP	---	---	---	---	capture		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)	Missense_Mutation	SNP	2401258	2401258	12464	1	G	A	A	38	38	PLCH2	A	1	1
FRRS1	391059	broad.mit.edu	36	1	99949087	99949087	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:99949087G>C	uc001dsh.1	-	c.1487C>G	c.(1486-1488)GCG>GGG	p.A496G		NM_001013660	NP_001013682	Q6ZNA5	FRRS1_HUMAN	stromal cell derived factor receptor 2 homolog	496	Helical; Name=5; (Potential).|Cytochrome b561.				electron transport chain|transport	integral to membrane	ferric-chelate reductase activity|metal ion binding				0		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)												0.28125	10.640203	12.127274	9	23	GG		KEEP	---	---	---	---	capture		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)	Missense_Mutation	SNP	99949087	99949087	6310	1	G	C	C	38	38	FRRS1	C	3	3
STAU1	6780	broad.mit.edu	36	20	47174417	47174417	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47174417C>T	uc002xud.1	-	c.724G>A	c.(724-726)GCC>ACC	p.A242T	STAU1_uc002xua.1_Missense_Mutation_p.A161T|STAU1_uc002xub.1_Missense_Mutation_p.A167T|STAU1_uc002xuc.1_Missense_Mutation_p.A161T|STAU1_uc002xue.1_Missense_Mutation_p.A161T|STAU1_uc002xuf.1_Missense_Mutation_p.A167T|STAU1_uc002xug.1_Missense_Mutation_p.A242T	NM_017453	NP_059348	O95793	STAU1_HUMAN	staufen isoform b	242	DRBM 2.					microtubule associated complex|rough endoplasmic reticulum|stress granule	double-stranded RNA binding	p.A242T(1)		ovary(4)|kidney(1)	5														0.436285	584.004204	585.636406	202	261	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)		Missense_Mutation	SNP	47174417	47174417	15792	20	C	T	T	27	27	STAU1	T	1	1
GGTLC2	91227	broad.mit.edu	36	22	21318849	21318849	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:21318849G>T	uc010gts.1	+	c.34G>T	c.(34-36)GCC>TCC	p.A12S	GGTLC2_uc010gtt.1_Missense_Mutation_p.A12S	NM_199127	NP_954578	Q14390	GGTL2_HUMAN	gamma-glutamyltransferase-like 4 isoform 1	12					glutathione biosynthetic process		gamma-glutamyltransferase activity			ovary(1)	1	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.3e-31)|Acute lymphoblastic leukemia(6;5.54e-23)												0.210526	8.398079	9.864925	4	15	GG		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(21;0.145)	Missense_Mutation	SNP	21318849	21318849	6634	22	G	T	T	42	42	GGTLC2	T	3	3
SLC9A4	389015	broad.mit.edu	36	2	102462043	102462043	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:102462043C>T	uc002tbz.2	+	c.570C>T	c.(568-570)GAC>GAT	p.D190D		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	190	Extracellular (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			central_nervous_system(1)	1														0.461538	50.762368	50.810095	18	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	102462043	102462043	15213	2	C	T	T	19	19	SLC9A4	T	1	1
DPP10	57628	broad.mit.edu	36	2	116163926	116163926	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:116163926G>A	uc002tla.1	+	c.535G>A	c.(535-537)GTC>ATC	p.V179I	DPP10_uc002tlb.1_Missense_Mutation_p.V129I|DPP10_uc002tlc.1_Missense_Mutation_p.V175I|DPP10_uc002tle.1_Missense_Mutation_p.V129I|DPP10_uc002tlf.1_Missense_Mutation_p.V172I	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	179	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|breast(1)|skin(1)	9														0.393162	128.223157	129.392421	46	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116163926	116163926	4911	2	G	A	A	40	40	DPP10	A	1	1
ABCB11	8647	broad.mit.edu	36	2	169558501	169558501	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:169558501G>C	uc002ueo.1	-	c.749C>G	c.(748-750)CCT>CGT	p.P250R		NM_003742	NP_003733	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP),	250	Helical; (Potential).|ABC transmembrane type-1 1.				bile acid biosynthetic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism			ovary(2)|large_intestine(2)|breast(1)	5					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016)									0.428571	34.695415	34.819976	12	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169558501	169558501	43	2	G	C	C	35	35	ABCB11	C	3	3
DYSF	8291	broad.mit.edu	36	2	71654852	71654852	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71654852C>T	uc010fen.1	+	c.3245C>T	c.(3244-3246)GCG>GTG	p.A1082V	DYSF_uc002sie.1_Missense_Mutation_p.A1064V|DYSF_uc002sig.2_Missense_Mutation_p.A1050V|DYSF_uc010fee.1_Missense_Mutation_p.A1064V|DYSF_uc010fef.1_Missense_Mutation_p.A1081V|DYSF_uc010feg.1_Missense_Mutation_p.A1095V|DYSF_uc010feh.1_Missense_Mutation_p.A1050V|DYSF_uc010fei.1_Missense_Mutation_p.A1081V|DYSF_uc010fej.1_Missense_Mutation_p.A1051V|DYSF_uc002sif.1_Missense_Mutation_p.A1065V|DYSF_uc010fek.1_Missense_Mutation_p.A1082V|DYSF_uc010fel.1_Missense_Mutation_p.A1051V|DYSF_uc010fem.1_Missense_Mutation_p.A1065V|DYSF_uc010feo.1_Missense_Mutation_p.A1096V	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1064	Cytoplasmic (Potential).|Arg-rich.					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.413223	140.22848	141.023271	50	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71654852	71654852	5045	2	C	T	T	27	27	DYSF	T	1	1
TRAT1	50852	broad.mit.edu	36	3	110032311	110032311	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110032311C>T	uc003dxi.1	+	c.112C>T	c.(112-114)CGA>TGA	p.R38*	TRAT1_uc010hpx.1_Intron	NM_016388	NP_057472	Q6PIZ9	TRAT1_HUMAN	T-cell receptor interacting molecule	38	Cytoplasmic (Potential).				cellular defense response|negative regulation of receptor recycling|negative regulation of transport|positive regulation of calcium-mediated signaling|positive regulation of T cell receptor signaling pathway|T cell receptor signaling pathway	integral to plasma membrane|T cell receptor complex	phosphatidylinositol-4,5-bisphosphate 3-kinase activity|transmembrane receptor protein tyrosine kinase adaptor activity				0														0.33913	215.088632	220.346604	78	152	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	110032311	110032311	17010	3	C	T	T	19	19	TRAT1	T	5	1
FBLN2	2199	broad.mit.edu	36	3	13645778	13645778	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:13645778G>A	uc003bya.1	+	c.2827G>A	c.(2827-2829)GGC>AGC	p.G943S	FBLN2_uc003byb.1_Missense_Mutation_p.G896S	NM_001004019	NP_001004019	P98095	FBLN2_HUMAN	fibulin 2 isoform a precursor	938	EGF-like 7; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(1)	1														0.307692	22.690033	23.547306	8	18	GG		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)		Missense_Mutation	SNP	13645778	13645778	5935	3	G	A	A	47	47	FBLN2	A	2	2
AGXT2L1	64850	broad.mit.edu	36	4	109887002	109887002	+	Splice_Site_SNP	SNP	A	G	G			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:109887002A>G	uc003hzc.1	-	c.1303_splice	c.e11+1	p.V435_splice	AGXT2L1_uc010imc.1_Splice_Site_SNP_p.V429_splice	NM_031279	NP_112569			alanine-glyoxylate aminotransferase 2-like 1						cellular amino acid metabolic process	mitochondrion	alanine-glyoxylate transaminase activity|pyridoxal phosphate binding			ovary(1)	1														0.297872	74.363662	77.796821	28	66	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000281)	Splice_Site_SNP	SNP	109887002	109887002	409	4	A	G	G	6	6	AGXT2L1	G	5	4
SYNPO2	171024	broad.mit.edu	36	4	120167465	120167465	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:120167465C>T	uc010inb.1	+	c.493C>T	c.(493-495)CAA>TAA	p.Q165*	SYNPO2_uc010ina.1_Nonsense_Mutation_p.Q165*|SYNPO2_uc003icm.2_Nonsense_Mutation_p.Q165*|SYNPO2_uc010inc.1_Nonsense_Mutation_p.Q93*	NM_133477	NP_597734	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform a	165						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2														0.288136	44.646159	47.024025	17	42	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	120167465	120167465	15978	4	C	T	T	21	21	SYNPO2	T	5	2
RBM47	54502	broad.mit.edu	36	4	40135238	40135238	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:40135238C>T	uc003gvc.2	-	c.430G>A	c.(430-432)GTG>ATG	p.V144M	RBM47_uc003gve.2_Non-coding_Transcript|RBM47_uc003gvd.2_Missense_Mutation_p.V144M|RBM47_uc003gvg.1_Missense_Mutation_p.V144M	NM_001098634	NP_001092104	A0AV96	RBM47_HUMAN	RNA binding motif protein 47 isoform a	144	RRM 1.					nucleus	nucleotide binding|RNA binding			breast(3)	3														0.230769	38.809257	43.995612	18	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40135238	40135238	13603	4	C	T	T	19	19	RBM47	T	1	1
LRRC66	339977	broad.mit.edu	36	4	52564270	52564270	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2514-01	TCGA-28-2514-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:52564270T>C	uc003gzi.1	-	c.542A>G	c.(541-543)AAT>AGT	p.N181S		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	181	LRR 4.					integral to membrane				ovary(1)|central_nervous_system(1)	2														0.460481	471.338537	471.732559	134	157	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52564270	52564270	9393	4	T	C	C	52	52	LRRC66	C	4	4
SULT1B1	27284	broad.mit.edu	36	4	70630907	70630907	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70630907G>A	uc003hen.1	-	c.679C>T	c.(679-681)CAC>TAC	p.H227Y		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	227	PAPS (By similarity).				3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.518868	165.819526	165.851957	55	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70630907	70630907	15896	4	G	A	A	45	45	SULT1B1	A	2	2
C4orf40	401137	broad.mit.edu	36	4	71056363	71056363	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71056363C>T	uc003hfa.2	+	c.55C>T	c.(55-57)CGG>TGG	p.R19W	C4orf40_uc003hfb.2_Missense_Mutation_p.R19W	NM_214711	NP_999876	Q6MZM9	CD040_HUMAN	hypothetical protein LOC401137	19						extracellular region					0														0.471698	76.471268	76.508184	25	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71056363	71056363	2364	4	C	T	T	19	19	C4orf40	T	1	1
AFM	173	broad.mit.edu	36	4	74584765	74584765	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74584765A>C	uc003hhb.1	+	c.1603A>C	c.(1603-1605)ATG>CTG	p.M535L		NM_001133	NP_001124	P43652	AFAM_HUMAN	afamin precursor	535	Albumin 3.				transport					ovary(2)	2	Breast(15;0.00102)													0.367647	84.461396	85.506958	25	43	AA		KEEP	---	---	---	---	capture	Epithelial(6;5.69e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|all cancers(17;0.000555)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Missense_Mutation	SNP	74584765	74584765	362	4	A	C	C	8	8	AFM	C	4	4
CAMK4	814	broad.mit.edu	36	5	110846404	110846404	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:110846404A>C	uc003kpf.1	+	c.851A>C	c.(850-852)GAT>GCT	p.D284A	CAMK4_uc010jbv.1_Missense_Mutation_p.D87A|CAMK4_uc003kpg.1_5'UTR	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	284	Protein kinase.				activation of phospholipase C activity|nerve growth factor receptor signaling pathway|protein phosphorylation|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)								687				0.415	277.681447	278.944141	83	117	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)	Missense_Mutation	SNP	110846404	110846404	2722	5	A	C	C	12	12	CAMK4	C	4	4
DNAH5	1767	broad.mit.edu	36	5	13829771	13829771	+	Silent	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:13829771G>A	uc003jfd.2	-	c.9150C>T	c.(9148-9150)AGC>AGT	p.S3050S		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3050	AAA 4 (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)													0.417476	244.298267	245.525007	86	120	GG		KEEP	---	---	---	---	capture			Silent	SNP	13829771	13829771	4787	5	G	A	A	38	38	DNAH5	A	1	1
PCDHB7	56129	broad.mit.edu	36	5	140533473	140533473	+	Silent	SNP	G	T	T			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140533473G>T	uc003lit.1	+	c.873G>T	c.(871-873)ACG>ACT	p.T291T		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	291	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4														0.365385	233.248477	236.56161	76	132	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Silent	SNP	140533473	140533473	11967	5	G	T	T	40	40	PCDHB7	T	3	3
KIAA1244	57221	broad.mit.edu	36	6	138601376	138601376	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:138601376G>A	uc003qhu.2	+	c.458G>A	c.(457-459)CGT>CAT	p.R153H		NM_020340	NP_065073	Q5TH69	BIG3_HUMAN	brefeldin A-inhibited guanine	153					regulation of ARF protein signal transduction	cytoplasm|integral to membrane	ARF guanyl-nucleotide exchange factor activity			ovary(1)|skin(1)	2	Breast(32;0.135)													0.333333	186.197586	191.294187	69	138	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)	Missense_Mutation	SNP	138601376	138601376	8526	6	G	A	A	40	40	KIAA1244	A	1	1
RNASET2	8635	broad.mit.edu	36	6	167280217	167280217	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:167280217C>T	uc003qve.1	-	c.204G>A	c.(202-204)TGG>TGA	p.W68*	RNASET2_uc003qvf.1_5'UTR|RNASET2_uc003qvg.1_Silent_p.K5K|RNASET2_uc003qvh.1_Intron|RNASET2_uc003qvi.1_Intron	NM_003730	NP_003721	O00584	RNT2_HUMAN	ribonuclease T2 precursor	68					RNA catabolic process	extracellular region	ribonuclease T2 activity|RNA binding				0		Breast(66;1.53e-05)|Ovarian(120;0.0606)												0.277778	26.442352	28.037119	10	26	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)	Nonsense_Mutation	SNP	167280217	167280217	13895	6	C	T	T	26	26	RNASET2	T	5	2
CUL7	9820	broad.mit.edu	36	6	43121784	43121784	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43121784C>T	uc003otq.1	-	c.2684G>A	c.(2683-2685)AGT>AAT	p.S895N	CUL7_uc010jyg.1_Missense_Mutation_p.S174N|CUL7_uc010jyh.1_Intron|KLC4_uc003otr.1_Intron	NM_014780	NP_055595	Q14999	CUL7_HUMAN	cullin 7	895	DOC.				interspecies interaction between organisms|regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process|vasculogenesis	anaphase-promoting complex|mitochondrion	ubiquitin protein ligase binding			ovary(3)|kidney(1)	4														0.2	8.087894	9.762983	4	16	CC		KEEP	---	---	---	---	capture	all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)		Missense_Mutation	SNP	43121784	43121784	4220	6	C	T	T	20	20	CUL7	T	2	2
GRM8	2918	broad.mit.edu	36	7	126036753	126036753	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:126036753C>T	uc003vlr.2	-	c.1393G>A	c.(1393-1395)GGA>AGA	p.G465R	GRM8_uc003vls.2_Silent_p.T488T|GRM8_uc003vlt.2_Missense_Mutation_p.G465R|GRM8_uc010lkz.1_Non-coding_Transcript	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	465	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				ovary(5)|pancreas(1)	6		Prostate(267;0.186)			L-Glutamic Acid(DB00142)									0.497297	280.302196	280.303277	92	93	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	126036753	126036753	7082	7	C	T	T	23	23	GRM8	T	1	1
ABCA13	154664	broad.mit.edu	36	7	48413940	48413940	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:48413940C>T	uc003toq.1	+	c.11823C>T	c.(11821-11823)ACC>ACT	p.T3941T	ABCA13_uc010kys.1_Silent_p.T1070T|ABCA13_uc003tos.1_Silent_p.T822T|ABCA13_uc010kyt.1_Non-coding_Transcript	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3996	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.117647	10.2569	20.024568	8	60	CC		KEEP	---	---	---	---	capture			Silent	SNP	48413940	48413940	32	7	C	T	T	23	23	ABCA13	T	1	1
EIF4H	7458	broad.mit.edu	36	7	73239903	73239903	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:73239903G>T	uc003uad.1	+	c.86G>T	c.(85-87)GGT>GTT	p.G29V	EIF4H_uc010lbm.1_Missense_Mutation_p.G29V|EIF4H_uc003uae.1_Missense_Mutation_p.G29V|EIF4H_uc003uaf.1_Intron	NM_022170	NP_071496	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	29					interspecies interaction between organisms|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex|perinuclear region of cytoplasm	nucleotide binding|protein binding|translation initiation factor activity				0														0.2657	131.310131	141.601385	55	152	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73239903	73239903	5230	7	G	T	T	44	44	EIF4H	T	3	3
PILRA	29992	broad.mit.edu	36	7	99834875	99834875	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99834875C>T	uc003uuo.1	+	c.733C>T	c.(733-735)CCA>TCA	p.P245S	PILRA_uc003uup.1_Missense_Mutation_p.P172S|PILRA_uc003uuq.1_Silent_p.S160S	NM_013439	NP_038467	Q9UKJ1	PILRA_HUMAN	paired immunoglobulin-like type 2 receptor alpha	245	Cytoplasmic (Potential).				interspecies interaction between organisms	extracellular region|integral to membrane|plasma membrane	protein binding|receptor activity				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.164384	21.559211	29.363417	12	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99834875	99834875	12349	7	C	T	T	26	26	PILRA	T	2	2
RAD21	5885	broad.mit.edu	36	8	117944664	117944664	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2514-01	TCGA-28-2514-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:117944664G>A	uc003yod.1	-	c.160C>T	c.(160-162)CGG>TGG	p.R54W		NM_006265	NP_006256	O60216	RAD21_HUMAN	RAD21 homolog	54					apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of gene-specific transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding			lung(1)|skin(1)	2	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)									357				0.424893	288.785544	289.93214	99	134	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117944664	117944664	13440	8	G	A	A	40	40	RAD21	A	1	1
PALM2-AKAP2	445815	broad.mit.edu	36	9	111725912	111725912	+	Silent	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111725912C>T	uc004bei.2	+	c.334C>T	c.(334-336)CTG>TTG	p.L112L	PALM2_uc004bef.1_Silent_p.L114L|PALM2_uc004beg.1_Silent_p.L114L|PALM2_uc004beh.2_Silent_p.L112L|PALM2-AKAP2_uc004bek.2_Silent_p.L112L|PALM2-AKAP2_uc004bej.2_Silent_p.L112L|PALM2-AKAP2_uc004bel.1_5'UTR	NM_001004065	NP_001004065	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 1	Error:Variant_position_missing_in_Q9Y2D5_after_alignment							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.456522	65.671799	65.747263	21	25	CC		KEEP	---	---	---	---	capture			Silent	SNP	111725912	111725912	11826	9	C	T	T	20	20	PALM2-AKAP2	T	2	2
ASTN2	23245	broad.mit.edu	36	9	118531142	118531142	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:118531142A>C	uc004bjs.1	-	c.2576T>G	c.(2575-2577)GTC>GGC	p.V859G	ASTN2_uc004bjr.1_Missense_Mutation_p.V855G|ASTN2_uc004bjt.1_Missense_Mutation_p.V808G	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	859	Extracellular (Potential).					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.307692	6.432155	6.901197	4	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118531142	118531142	1084	9	A	C	C	10	10	ASTN2	C	4	4
MEGF9	1955	broad.mit.edu	36	9	122424762	122424762	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2514-01	TCGA-28-2514-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:122424762A>G	uc004bkj.1	-	c.1007T>C	c.(1006-1008)TTG>TCG	p.L336S		NM_001080497	NP_001073966	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	299	Laminin EGF-like 2.|Extracellular (Potential).					integral to membrane	calcium ion binding|receptor activity				0														0.175	10.800387	14.791465	7	33	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122424762	122424762	9853	9	A	G	G	5	5	MEGF9	G	4	4
SERPINA7	6906	broad.mit.edu	36	X	105167390	105167390	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2514-01	TCGA-28-2514-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105167390C>T	uc004eme.1	-	c.316G>A	c.(316-318)GTA>ATA	p.V106I	SERPINA7_uc010npd.1_Missense_Mutation_p.V106I|SERPINA7_uc010npe.1_Missense_Mutation_p.V106I	NM_000354	NP_000345	P05543	THBG_HUMAN	serine (or cysteine) proteinase inhibitor, clade	106					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity				0					Levothyroxine(DB00451)|Liothyronine(DB00279)									0.845588	377.983047	393.494367	115	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105167390	105167390	14582	23	C	T	T	18	18	SERPINA7	T	2	2
MKI67	4288	broad.mit.edu	36	10	129791929	129791937	+	In_Frame_Del	DEL	CTCTTTGTG	-	-			TCGA-28-2514-01	TCGA-28-2514-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:129791929_129791937delCTCTTTGTG	uc001lke.1	-	c.8157_8165delCACAAAGAG	c.(8155-8166)AGCACAAAGAGG>AGG	p.STK2719del	MKI67_uc001lkf.1_In_Frame_Del_p.STK2359del|MKI67_uc009yav.1_In_Frame_Del_p.STK2294del|MKI67_uc009yaw.1_In_Frame_Del_p.STK1869del	NM_002417	NP_002408	P46013	KI67_HUMAN	antigen identified by monoclonal antibody Ki-67	2719_2721	16 X 122 AA approximate repeats.|15.				cell proliferation	nucleolus	ATP binding|protein C-terminus binding			ovary(4)|central_nervous_system(1)	5		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)												0.67			102	50				---	---	---	---	capture_indel			In_Frame_Del	DEL	129791929	129791937	9988	10	CTCTTTGTG	-	-	24	24	MKI67	-	5	5
