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
SORCS1	114815	broad.mit.edu	36	10	108913733	108913733	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:108913733G>C	uc001kyl.1	-	c.542C>G	c.(541-543)TCT>TGT	p.S181C	SORCS1_uc001kym.1_Missense_Mutation_p.S181C|SORCS1_uc009xxs.1_Missense_Mutation_p.S181C|SORCS1_uc001kyn.1_Missense_Mutation_p.S181C|SORCS1_uc001kyo.2_Missense_Mutation_p.S181C	NM_001013031	NP_001013049	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform b	181	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)	1		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)												0.756757	95.313923	97.494967	28	9	GG		KEEP	---	---	---	---	capture		Epithelial(162;1.66e-05)|all cancers(201;0.000689)	Missense_Mutation	SNP	108913733	108913733	15430	10	G	C	C	33	33	SORCS1	C	3	3
SMC3	9126	broad.mit.edu	36	10	112334021	112334021	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:112334021G>T	uc001kze.1	+	c.1182G>T	c.(1180-1182)TGG>TGT	p.W394C		NM_005445	NP_005436	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	394	Potential.				cell division|DNA mediated transformation|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic spindle organization|negative regulation of DNA endoreduplication|signal transduction|sister chromatid cohesion	basement membrane|chromatin|chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nuclear matrix|nucleoplasm|spindle pole	ATP binding|dynein binding|microtubule motor activity|protein heterodimerization activity			ovary(1)|central_nervous_system(1)	2		Breast(234;0.0848)|Lung NSC(174;0.238)												0.658228	158.410633	160.154888	52	27	GG		KEEP	---	---	---	---	capture		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)	Missense_Mutation	SNP	112334021	112334021	15282	10	G	T	T	41	41	SMC3	T	3	3
DMBT1	1755	broad.mit.edu	36	10	124389752	124389752	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:124389752C>T	uc001lgk.1	+	c.6762C>T	c.(6760-6762)GAC>GAT	p.D2254D	DMBT1_uc001lgl.1_Silent_p.D2244D|DMBT1_uc001lgm.1_Silent_p.D1626D|DMBT1_uc009xzz.1_Silent_p.D2253D|DMBT1_uc009yab.1_Silent_p.D957D|DMBT1_uc009yac.1_Silent_p.D548D	NM_007329	NP_015568	Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1 isoform b	2254	ZP.				epithelial cell differentiation|induction of bacterial agglutination|innate immune response|interspecies interaction between organisms|protein transport|response to virus	extrinsic to membrane|phagocytic vesicle membrane|zymogen granule membrane	calcium-dependent protein binding|Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|pattern recognition receptor activity|scavenger receptor activity|zymogen binding			central_nervous_system(7)	7		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				Ovarian(182;93 2026 18125 22222 38972)								0.27027	74.502567	79.786463	30	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	124389752	124389752	4757	10	C	T	T	19	19	DMBT1	T	1	1
LRIT1	26103	broad.mit.edu	36	10	85982146	85982146	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:85982146G>A	uc001kcz.1	-	c.1389C>T	c.(1387-1389)TAC>TAT	p.Y463Y		NM_015613	NP_056428	Q9P2V4	LRIT1_HUMAN	retina specific protein PAL	463	Fibronectin type-III.|Lumenal (Potential).					integral to endoplasmic reticulum membrane					0														0.692308	56.556485	57.413269	18	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	85982146	85982146	9320	10	G	A	A	40	40	LRIT1	A	1	1
MUC5B	727897	broad.mit.edu	36	11	1224001	1224001	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1224001C>T	uc001ltb.2	+	c.9324C>T	c.(9322-9324)ACC>ACT	p.T3108T		NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	3105	7 X Cys-rich subdomain repeats.|Thr-rich.|17 X approximate tandem repeats, Ser/Thr- rich.			Missing (in Ref. 6; AAB61398).	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)												0.130435	12.223817	21.396982	9	60	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	Silent	SNP	1224001	1224001	10373	11	C	T	T	24	24	MUC5B	T	2	2
PAMR1	25891	broad.mit.edu	36	11	35410862	35410862	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:35410862G>A	uc001mwf.1	-	c.1832C>T	c.(1831-1833)TCC>TTC	p.S611F	PAMR1_uc001mwg.1_Missense_Mutation_p.S594F	NM_015430	NP_056245	Q6UXH9	PAMR1_HUMAN	regeneration associated muscle protease isoform	594	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(2)	2														0.531646	130.837389	130.90507	42	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35410862	35410862	11830	11	G	A	A	41	41	PAMR1	A	2	2
UNC93B1	81622	broad.mit.edu	36	11	67521787	67521787	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67521787C>T	uc001omw.1	-	c.840G>A	c.(838-840)CCG>CCA	p.P280P		NM_030930	NP_112192	Q9H1C4	UN93B_HUMAN	unc-93 homolog B1	280					innate immune response|intracellular protein transport|response to virus|toll-like receptor 3 signaling pathway|toll-like receptor 7 signaling pathway|toll-like receptor 9 signaling pathway	early phagosome|endoplasmic reticulum membrane|endosome|integral to membrane|lysosome					0														0.458333	31.822271	31.85852	11	13	CC		KEEP	---	---	---	---	capture			Silent	SNP	67521787	67521787	17556	11	C	T	T	27	27	UNC93B1	T	1	1
CNTN5	53942	broad.mit.edu	36	11	99631811	99631811	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:99631811C>A	uc001pga.1	+	c.2115C>A	c.(2113-2115)AAC>AAA	p.N705K	CNTN5_uc001pfz.2_Missense_Mutation_p.N705K|CNTN5_uc001pgb.1_Missense_Mutation_p.N631K	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	705	Fibronectin type-III 1.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)								1117				0.446809	120.257752	120.485145	42	52	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)	Missense_Mutation	SNP	99631811	99631811	3782	11	C	A	A	18	18	CNTN5	A	3	3
CUX2	23316	broad.mit.edu	36	12	110232628	110232628	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:110232628G>A	uc001tsa.1	+	c.1659G>A	c.(1657-1659)CTG>CTA	p.L553L		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	553	CUT 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|breast(1)	4														0.409091	74.908008	75.385684	27	39	GG		KEEP	---	---	---	---	capture			Silent	SNP	110232628	110232628	4225	12	G	A	A	47	47	CUX2	A	2	2
GPR133	283383	broad.mit.edu	36	12	130053775	130053775	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130053775C>T	uc001uit.2	+	c.1119C>T	c.(1117-1119)ACC>ACT	p.T373T		NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	373	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)													0.454545	185.221385	185.481635	65	78	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)	Silent	SNP	130053775	130053775	6917	12	C	T	T	23	23	GPR133	T	1	1
PTPRO	5800	broad.mit.edu	36	12	15546122	15546122	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:15546122C>T	uc001rcv.1	+	c.963C>T	c.(961-963)TAC>TAT	p.Y321Y	PTPRO_uc001rcu.1_Silent_p.Y321Y|PTPRO_uc001rcw.1_Silent_p.Y321Y	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	321	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|lung(1)	3		Hepatocellular(102;0.244)												0.277778	63.838218	67.836141	25	65	CC		KEEP	---	---	---	---	capture			Silent	SNP	15546122	15546122	13266	12	C	T	T	19	19	PTPRO	T	1	1
CACNA2D4	93589	broad.mit.edu	36	12	1862400	1862400	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:1862400G>A	uc001qjp.1	-	c.1379C>T	c.(1378-1380)GCG>GTG	p.A460V	CACNA2D4_uc009zds.1_Non-coding_Transcript|CACNA2D4_uc009zdt.1_Missense_Mutation_p.A348V	NM_172364	NP_758952	Q7Z3S7	CA2D4_HUMAN	voltage-gated calcium channel alpha(2)delta-4	460	VWFA.|Extracellular (Potential).				response to stimulus|visual perception	integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			ovary(1)	1	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)				Colon(2;101 179 21030 23310 28141)								0.62069	49.561568	49.940324	18	11	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)	Missense_Mutation	SNP	1862400	1862400	2667	12	G	A	A	38	38	CACNA2D4	A	1	1
MLL2	8085	broad.mit.edu	36	12	47718483	47718483	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:47718483G>A	uc001rta.2	-	c.8923C>T	c.(8923-8925)CGC>TGC	p.R2975C		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	2975	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|promoter binding|protein binding|zinc ion binding			kidney(16)|lung(4)|skin(4)|ovary(3)|pancreas(2)	29														0.404762	148.827715	149.817494	51	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47718483	47718483	10011	12	G	A	A	39	39	MLL2	A	1	1
CRADD	8738	broad.mit.edu	36	12	92767903	92767903	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:92767903C>A	uc001tda.1	+	c.325C>A	c.(325-327)CAC>AAC	p.H109N		NM_003805	NP_003796	P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with	109					apoptosis|cellular response to mechanical stimulus|induction of apoptosis via death domain receptors|signal transduction	intracellular	death domain binding|protease binding|protein binding, bridging			ovary(1)	1														0.408163	117.795218	118.512299	40	58	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92767903	92767903	3984	12	C	A	A	25	25	CRADD	A	3	3
TPTE2	93492	broad.mit.edu	36	13	18937688	18937688	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:18937688G>A	uc001umd.1	-	c.529C>T	c.(529-531)CGA>TGA	p.R177*	TPTE2_uc001ume.1_Nonsense_Mutation_p.R100*|TPTE2_uc009zzl.1_Nonsense_Mutation_p.R66*|TPTE2_uc009zzm.1_5'UTR|TPTE2_uc009zzk.1_Non-coding_Transcript	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	177						endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)												0.354167	50.060509	50.960619	17	31	GG		KEEP	---	---	---	---	capture		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)	Nonsense_Mutation	SNP	18937688	18937688	16975	13	G	A	A	37	37	TPTE2	A	5	1
SPERT	220082	broad.mit.edu	36	13	45185388	45185388	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:45185388C>T	uc001van.1	+	c.227C>T	c.(226-228)GCC>GTC	p.A76V	SPERT_uc001vao.2_Missense_Mutation_p.A40V	NM_152719	NP_689932	Q8NA61	SPERT_HUMAN	spermatid associated	76						cytoplasmic membrane-bounded vesicle				central_nervous_system(1)|pancreas(1)	2		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)												0.164835	24.288648	33.980104	15	76	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)	Missense_Mutation	SNP	45185388	45185388	15551	13	C	T	T	26	26	SPERT	T	2	2
STRN3	29966	broad.mit.edu	36	14	30495160	30495160	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:30495160C>A	uc001wqu.2	-	c.322G>T	c.(322-324)GAG>TAG	p.E108*	STRN3_uc001wqv.2_Nonsense_Mutation_p.E108*	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	108	Potential.				negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)													0.378378	116.912957	118.357147	42	69	CC		KEEP	---	---	---	---	capture	LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)	Nonsense_Mutation	SNP	30495160	30495160	15850	14	C	A	A	32	32	STRN3	A	5	3
MAX	4149	broad.mit.edu	36	14	64613083	64613083	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:64613083G>A	uc001xif.1	-	c.347C>T	c.(346-348)CCC>CTC	p.P116L	MAX_uc001xic.1_Intron|MAX_uc001xie.1_3'UTR|MAX_uc010aql.1_Missense_Mutation_p.P30S|MAX_uc001xig.1_Missense_Mutation_p.P107L|MAX_uc001xih.1_Non-coding_Transcript	NM_002382	NP_002373	P61244	MAX_HUMAN	MAX protein isoform a	116					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|MLL1 complex	sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription regulator activity				0										99				0.332075	252.898131	259.52511	88	177	GG		KEEP	---	---	---	---	capture		all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)	Missense_Mutation	SNP	64613083	64613083	9723	14	G	A	A	43	43	MAX	A	2	2
OR4N4	283694	broad.mit.edu	36	15	19884381	19884381	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19884381G>A	uc001yuc.1	+	c.545G>A	c.(544-546)CGA>CAA	p.R182Q	LOC727924_uc001yub.1_Intron|OR4N4_uc001yue.2_Missense_Mutation_p.R182Q	NM_001005241	NP_001005241	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N,	182	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(4)	4		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)												0.28125	92.014834	97.54507	36	92	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)	Missense_Mutation	SNP	19884381	19884381	11488	15	G	A	A	37	37	OR4N4	A	1	1
HYDIN	54768	broad.mit.edu	36	16	69409966	69409966	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:69409966C>T	uc002ezr.1	-	c.14435G>A	c.(14434-14436)CGA>CAA	p.R4812Q	HYDIN_uc010cfy.1_Non-coding_Transcript	NM_032821	NP_116210	Q4G0P3	HYDIN_HUMAN	hydrocephalus inducing isoform a	4813										ovary(1)	1		Ovarian(137;0.0654)												0.195652	18.754029	22.722287	9	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69409966	69409966	7767	16	C	T	T	31	31	HYDIN	T	1	1
GLG1	2734	broad.mit.edu	36	16	73100300	73100300	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:73100300G>C	uc002fcx.1	-	c.496C>G	c.(496-498)CTA>GTA	p.L166V	GLG1_uc002fcy.2_Missense_Mutation_p.L166V|GLG1_uc002fcz.2_5'UTR	NM_012201	NP_036333	Q92896	GSLG1_HUMAN	golgi apparatus protein 1	166	Cys-rich GLG1 2.|Extracellular (Potential).					Golgi membrane|integral to membrane	receptor binding			ovary(1)|breast(1)	2										1034				0.340659	86.39121	88.436114	31	60	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73100300	73100300	6704	16	G	C	C	35	35	GLG1	C	3	3
CBFA2T3	863	broad.mit.edu	36	16	87473345	87473345	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:87473345C>T	uc002fmm.1	-	c.1496G>A	c.(1495-1497)CGG>CAG	p.R499Q	CBFA2T3_uc002fmk.1_5'UTR|CBFA2T3_uc002fml.1_Missense_Mutation_p.R413Q	NM_005187	NP_005178	O75081	MTG16_HUMAN	myeloid translocation gene on chromosome 16	499	Mediates interaction with PRKAR2A.|Potential.				cell proliferation|granulocyte differentiation|regulation of transcription, DNA-dependent	Golgi membrane|nucleolus|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(3)	3										305				0.327273	49.532949	50.987357	18	37	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(80;0.0275)	Missense_Mutation	SNP	87473345	87473345	2817	16	C	T	T	23	23	CBFA2T3	T	1	1
PEX12	5193	broad.mit.edu	36	17	30928419	30928419	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:30928419G>C	uc002hjp.1	-	c.431C>G	c.(430-432)TCT>TGT	p.S144C		NM_000286	NP_000277	O00623	PEX12_HUMAN	peroxisomal biogenesis factor 12	144	Cytoplasmic (Potential).				protein import into peroxisome matrix	integral to peroxisomal membrane	protein C-terminus binding|zinc ion binding				0														0.540284	391.814309	392.107905	114	97	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)	Missense_Mutation	SNP	30928419	30928419	12162	17	G	C	C	33	33	PEX12	C	3	3
P2RX5	5026	broad.mit.edu	36	17	3529667	3529667	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:3529667C>T	uc002fwh.1	-	c.1222G>A	c.(1222-1224)GGA>AGA	p.G408R	P2RX5_uc002fwd.1_Non-coding_Transcript|P2RX5_uc002fwi.1_Missense_Mutation_p.G409R|P2RX5_uc002fwj.1_Missense_Mutation_p.G384R|P2RX5_uc002fwk.1_Missense_Mutation_p.G408R|P2RX5_uc002fwl.1_Missense_Mutation_p.G385R	NM_002561	NP_002552	Q93086	P2RX5_HUMAN	purinergic receptor P2X5 isoform A	409	Cytoplasmic (Potential).				nervous system development|positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling	integral to plasma membrane	ATP binding|extracellular ATP-gated cation channel activity|purinergic nucleotide receptor activity				0														0.287671	56.148239	59.097964	21	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3529667	3529667	11756	17	C	T	T	23	23	P2RX5	T	1	1
KRT38	8687	broad.mit.edu	36	17	36847283	36847283	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36847283G>A	uc002hwq.1	-	c.1278C>T	c.(1276-1278)TGC>TGT	p.C426C		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	426	Tail.					intermediate filament	structural molecule activity				0		Breast(137;0.000496)												0.217391	10.870416	12.558739	5	18	GG		KEEP	---	---	---	---	capture			Silent	SNP	36847283	36847283	8790	17	G	A	A	38	38	KRT38	A	1	1
TP53	7157	broad.mit.edu	36	17	7519119	7519119	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7519119T>C	uc002gim.2	-	c.536A>G	c.(535-537)CAT>CGT	p.H179R	TP53_uc002gig.1_Missense_Mutation_p.H179R|TP53_uc002gih.1_Missense_Mutation_p.H179R|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.H47R|TP53_uc010cng.1_Missense_Mutation_p.H47R|TP53_uc002gii.1_Missense_Mutation_p.H47R|TP53_uc010cnh.1_Missense_Mutation_p.H179R|TP53_uc010cni.1_Missense_Mutation_p.H179R|TP53_uc002gij.2_Missense_Mutation_p.H179R|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.H86R|TP53_uc002gio.2_Missense_Mutation_p.H47R	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	179	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).	Zinc.	H -> Q (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> R (in sporadic cancers; somatic mutation).|HH -> QS (in a sporadic cancer; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> D (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.H179R(98)|p.H179L(31)|p.P177_C182delPHHERC(7)|p.0?(6)|p.C176_R181delCPHHER(3)|p.H179P(3)|p.R175_E180delRCPHHE(3)|p.P177fs*3(2)|p.V173fs*59(2)|p.R174fs*1(2)|p.H179fs*68(1)|p.C176fs*65(1)|p.P177_H179delPHH(1)|p.V173fs*23(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171_H179delEVVRRCPHH(1)|p.R174_E180>K(1)|p.P177_E180delPHHE(1)|p.E171fs*1(1)|p.R174fs*3(1)|p.E171fs*61(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.H179R(HS729-Tumor)|p.H179R(NCIH1568-Tumor)|p.H179R(YAPC-Tumor)|p.R174fs(THP1-Tumor)|p.H179R(KM12-Tumor)|p.H179R(KYSE450-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.357895	99.926437	101.614537	34	61	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7519119	7519119	16923	17	T	C	C	51	51	TP53	C	4	4
CCBE1	147372	broad.mit.edu	36	18	55257756	55257756	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:55257756T>G	uc002lib.1	-	c.950A>C	c.(949-951)AAG>ACG	p.K317T	CCBE1_uc010dpq.1_Missense_Mutation_p.K46T|CCBE1_uc002lia.1_Missense_Mutation_p.K170T	NM_133459	NP_597716	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	317	Collagen-like 2.				lymphangiogenesis|sprouting angiogenesis|venous blood vessel morphogenesis	collagen	calcium ion binding			ovary(1)	1		Colorectal(73;0.175)				NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)								0.357143	306.817915	312.373376	110	198	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55257756	55257756	2851	18	T	G	G	56	56	CCBE1	G	4	4
GCDH	2639	broad.mit.edu	36	19	12869135	12869135	+	Silent	SNP	A	T	T			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12869135A>T	uc002mvq.1	+	c.975A>T	c.(973-975)CCA>CCT	p.P325P	GCDH_uc002mvp.1_Silent_p.P325P	NM_000159	NP_000150	Q92947	GCDH_HUMAN	glutaryl-Coenzyme A dehydrogenase isoform a	325					lysine catabolic process|oxidation-reduction process	mitochondrial matrix	flavin adenine dinucleotide binding|glutaryl-CoA dehydrogenase activity|protein binding				0						GBM(123;875 1636 7726 16444 26754)								0.279412	51.501794	54.473723	19	49	AA		KEEP	---	---	---	---	capture			Silent	SNP	12869135	12869135	6553	19	A	T	T	6	6	GCDH	T	4	4
PDE4C	5143	broad.mit.edu	36	19	18188614	18188614	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18188614G>A	uc002nik.2	-	c.1422C>T	c.(1420-1422)TGC>TGT	p.C474C	PDE4C_uc002nil.2_Silent_p.C474C|PDE4C_uc002nif.2_Silent_p.C243C|PDE4C_uc002nig.2_Silent_p.C189C|PDE4C_uc002nih.2_Silent_p.C244C|PDE4C_uc010ebk.1_Silent_p.C368C|PDE4C_uc002nii.2_Silent_p.C442C|PDE4C_uc010ebl.1_Silent_p.C188C	NM_000923	NP_001092289	Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific isoform	474					signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Dyphylline(DB00651)									0.236994	90.48858	101.431	41	132	GG		KEEP	---	---	---	---	capture			Silent	SNP	18188614	18188614	12062	19	G	A	A	38	38	PDE4C	A	1	1
CILP2	148113	broad.mit.edu	36	19	19514191	19514191	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:19514191C>T	uc002nmw.2	+	c.618C>T	c.(616-618)AGC>AGT	p.S206S	CILP2_uc002nmv.2_Silent_p.S200S	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	200						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1														0.262295	40.07034	43.189883	16	45	CC		KEEP	---	---	---	---	capture			Silent	SNP	19514191	19514191	3564	19	C	T	T	26	26	CILP2	T	2	2
ZNF208	7757	broad.mit.edu	36	19	21946694	21946694	+	Silent	SNP	A	T	T			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:21946694A>T	uc002nqp.1	-	c.2598T>A	c.(2596-2598)ATT>ATA	p.I866I	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)	5		all_lung(12;0.0961)|Lung NSC(12;0.103)												0.264286	88.510631	95.634765	37	103	AA		KEEP	---	---	---	---	capture			Silent	SNP	21946694	21946694	18357	19	A	T	T	9	9	ZNF208	T	4	4
MLL4	9757	broad.mit.edu	36	19	40914680	40914680	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40914680C>T	uc010eei.1	+	c.5469C>T	c.(5467-5469)GAC>GAT	p.D1823D		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	1823					chromatin-mediated maintenance of transcription		DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			central_nervous_system(6)|breast(2)|ovary(1)|kidney(1)|skin(1)	11	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)													0.361702	45.65923	46.451554	17	30	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Silent	SNP	40914680	40914680	10013	19	C	T	T	17	17	MLL4	T	2	2
MEGF8	1954	broad.mit.edu	36	19	47564977	47564977	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47564977C>T	uc002otl.2	+	c.6423C>T	c.(6421-6423)ACC>ACT	p.T2141T	MEGF8_uc002otm.2_Silent_p.T1749T|MEGF8_uc002otn.2_5'Flank	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2208	Extracellular (Potential).|EGF-like 5.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.282609	69.576142	73.443121	26	66	CC		KEEP	---	---	---	---	capture			Silent	SNP	47564977	47564977	9852	19	C	T	T	23	23	MEGF8	T	1	1
ZNF813	126017	broad.mit.edu	36	19	58686144	58686144	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:58686144G>A	uc002qbu.2	+	c.846G>A	c.(844-846)CAG>CAA	p.Q282Q	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	282	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1														0.252747	120.557411	130.66456	46	136	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00619)	Silent	SNP	58686144	58686144	18773	19	G	A	A	33	33	ZNF813	A	2	2
PIAS3	10401	broad.mit.edu	36	1	144295919	144295919	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:144295919G>A	uc001eoc.1	+	c.1529G>A	c.(1528-1530)AGT>AAT	p.S510N	PIAS3_uc001eod.1_Missense_Mutation_p.S179N	NM_006099	NP_006090	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	510					positive regulation of protein sumoylation|protein sumoylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck	enzyme binding|nucleic acid binding|protein C-terminus binding|zinc ion binding				0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.310811	184.383828	191.466722	69	153	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144295919	144295919	12301	1	G	A	A	36	36	PIAS3	A	2	2
FLG	2312	broad.mit.edu	36	1	150552824	150552824	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150552824G>T	uc001ezu.1	-	c.1162C>A	c.(1162-1164)CAC>AAC	p.H388N		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	388	Ser-rich.|Filaggrin 2.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.362369	584.420127	593.996408	208	366	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150552824	150552824	6160	1	G	T	T	47	47	FLG	T	3	3
FLG2	388698	broad.mit.edu	36	1	150589936	150589936	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150589936T>G	uc001ezw.2	-	c.6950A>C	c.(6949-6951)CAG>CCG	p.Q2317P		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	2317							calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.446602	421.529723	422.293262	138	171	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150589936	150589936	6161	1	T	G	G	55	55	FLG2	G	4	4
LCE3E	353145	broad.mit.edu	36	1	150805133	150805133	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150805133C>T	uc001faa.1	-	c.176G>A	c.(175-177)CGC>CAC	p.R59H	LCE3E_uc009wnh.1_Missense_Mutation_p.R59H	NM_178435	NP_848522	Q5T5B0	LCE3E_HUMAN	late cornified envelope 3E	59					keratinization					ovary(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.375	125.756593	127.514567	48	80	CC		KEEP	---	---	---	---	capture	Lung(1;0.000294)|LUAD - Lung adenocarcinoma(1;0.00527)|LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)	Missense_Mutation	SNP	150805133	150805133	8996	1	C	T	T	27	27	LCE3E	T	1	1
CD5L	922	broad.mit.edu	36	1	156072340	156072340	+	Silent	SNP	A	G	G			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156072340A>G	uc001frk.2	-	c.285T>C	c.(283-285)AGT>AGC	p.S95S		NM_005894	NP_005885	O43866	CD5L_HUMAN	CD5 molecule-like	95	SRCR 1.				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.087766	23.488364	88.103523	33	343	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.24)		Silent	SNP	156072340	156072340	3155	1	A	G	G	2	2	CD5L	G	4	4
ZNF124	7678	broad.mit.edu	36	1	245386813	245386813	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:245386813C>T	uc001ick.2	-	c.734G>A	c.(733-735)TGT>TAT	p.C245Y	ZNF124_uc001ici.2_Intron|ZNF124_uc001icj.1_Missense_Mutation_p.C183Y	NM_003431	NP_003422	Q15973	ZN124_HUMAN	zinc finger protein 124	245	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)													0.339394	147.730985	151.502519	56	109	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00739)		Missense_Mutation	SNP	245386813	245386813	18311	1	C	T	T	17	17	ZNF124	T	2	2
PGBD2	267002	broad.mit.edu	36	1	247179063	247179063	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:247179063T>A	uc001ifh.1	+	c.1657T>A	c.(1657-1659)TGG>AGG	p.W553R	PGBD2_uc001ifg.1_Missense_Mutation_p.W302R|PGBD2_uc009xhd.1_Missense_Mutation_p.W302R	NM_170725	NP_001017434	Q6P3X8	PGBD2_HUMAN	hypothetical protein LOC267002 isoform a	553										ovary(1)	1	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.012)												0.173077	54.432882	70.175242	27	129	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Missense_Mutation	SNP	247179063	247179063	12204	1	T	A	A	55	55	PGBD2	A	4	4
ARHGEF16	27237	broad.mit.edu	36	1	3379548	3379548	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3379548G>A	uc001akg.2	+	c.1069G>A	c.(1069-1071)GAG>AAG	p.E357K	ARHGEF16_uc001aki.1_Missense_Mutation_p.E69K|ARHGEF16_uc001akj.1_Missense_Mutation_p.E69K|ARHGEF16_uc009vli.1_Missense_Mutation_p.E61K	NM_014448	NP_055263	Q5VV41	ARHGG_HUMAN	Rho guanine exchange factor 16	357	DH.|Required for RHOG activation and mediates interaction with EPHA2.				activation of Cdc42 GTPase activity|activation of Rac GTPase activity|apoptosis|cell chemotaxis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|small GTPase mediated signal transduction	cytosol	PDZ domain binding|receptor tyrosine kinase binding|Rho GTPase binding|Rho guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)												0.369231	67.576015	68.555156	24	41	GG		KEEP	---	---	---	---	capture		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)	Missense_Mutation	SNP	3379548	3379548	913	1	G	A	A	37	37	ARHGEF16	A	1	1
HEYL	26508	broad.mit.edu	36	1	39864903	39864903	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39864903G>A	uc001cdp.1	-	c.850C>T	c.(850-852)CCT>TCT	p.P284S		NM_014571	NP_055386	Q9NQ87	HEYL_HUMAN	hairy/enhancer-of-split related with YRPW	284	Pro-rich.				nervous system development|Notch signaling pathway|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.5	11.1969	11.1969	4	4	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;1.1e-18)|Epithelial(16;2.77e-17)|all cancers(16;5.64e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Missense_Mutation	SNP	39864903	39864903	7363	1	G	A	A	43	43	HEYL	A	2	2
MAST2	23139	broad.mit.edu	36	1	46273216	46273216	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:46273216C>T	uc001cov.1	+	c.4288C>T	c.(4288-4290)CTT>TTT	p.L1430F	MAST2_uc001cow.1_Missense_Mutation_p.L1429F|MAST2_uc001cpa.2_Non-coding_Transcript	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	1430					protein phosphorylation|regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|breast(1)	9	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)									975				0.2	48.417788	57.22127	21	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46273216	46273216	9709	1	C	T	T	24	24	MAST2	T	2	2
SEL1L2	80343	broad.mit.edu	36	20	13847669	13847669	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:13847669T>A	uc010gcf.1	-	c.384A>T	c.(382-384)GAA>GAT	p.E128D	SEL1L2_uc002woq.2_De_novo_Start_InFrame|SEL1L2_uc002wor.1_Non-coding_Transcript	NM_025229	NP_079505	Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2	128	Extracellular (Potential).|Sel1-like 1.					integral to membrane	binding			ovary(1)	1														0.25	92.341804	101.212053	39	117	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13847669	13847669	14497	20	T	A	A	56	56	SEL1L2	A	4	4
CST1	1469	broad.mit.edu	36	20	23679299	23679299	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:23679299G>A	uc002wtp.1	-	c.205C>T	c.(205-207)CGG>TGG	p.R69W		NM_001898	NP_001889	P01037	CYTN_HUMAN	cystatin SN precursor	69						extracellular region	cysteine-type endopeptidase inhibitor activity			ovary(1)	1	Lung NSC(19;0.0676)|all_lung(19;0.148)													0.128205	18.744958	34.506731	15	102	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	23679299	23679299	4111	20	G	A	A	38	38	CST1	A	1	1
SPAG4	6676	broad.mit.edu	36	20	33670313	33670313	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33670313G>A	uc002xdb.1	+	c.772G>A	c.(772-774)GAC>AAC	p.D258N		NM_003116	NP_003107	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	258					spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity				0	Lung NSC(9;0.0053)|all_lung(11;0.00785)													0.225806	48.128194	54.550904	21	72	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.0127)		Missense_Mutation	SNP	33670313	33670313	15483	20	G	A	A	37	37	SPAG4	A	1	1
PROKR2	128674	broad.mit.edu	36	20	5230783	5230783	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:5230783C>T	uc002wlx.2	-	c.1058G>A	c.(1057-1059)CGT>CAT	p.R353H	PROKR2_uc010gbj.1_Missense_Mutation_p.R353H|PROKR2_uc010gbk.1_Missense_Mutation_p.R353H	NM_144773	NP_658986	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	353	Cytoplasmic (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5														0.305195	120.473364	125.683585	47	107	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5230783	5230783	12996	20	C	T	T	19	19	PROKR2	T	1	1
SRXN1	140809	broad.mit.edu	36	20	577466	577466	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:577466G>A	uc002wea.1	-	c.306C>T	c.(304-306)TAC>TAT	p.Y102Y	SRXN1_uc002web.1_Non-coding_Transcript	NM_080725	NP_542763	Q9BYN0	SRXN1_HUMAN	sulfiredoxin 1 homolog	102					oxidation-reduction process|response to oxidative stress	cytosol	antioxidant activity|ATP binding|DNA binding|sulfiredoxin activity			ovary(1)	1														0.547297	243.299135	243.591222	81	67	GG		KEEP	---	---	---	---	capture			Silent	SNP	577466	577466	15688	20	G	A	A	40	40	SRXN1	A	1	1
CBR3	874	broad.mit.edu	36	21	36429412	36429412	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:36429412G>T	uc002yve.1	+	c.52G>T	c.(52-54)GGC>TGC	p.G18C		NM_001236	NP_001227	O75828	CBR3_HUMAN	carbonyl reductase 3	18	NADP.				oxidation-reduction process	cytosol|nucleus	carbonyl reductase (NADPH) activity|NADPH binding				0														0.272727	7.820247	8.332429	3	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36429412	36429412	2828	21	G	T	T	39	39	CBR3	T	3	3
ERG	2078	broad.mit.edu	36	21	38717227	38717227	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:38717227G>A	uc010gnw.1	-	c.384C>T	c.(382-384)AAC>AAT	p.N128N	ERG_uc002ywz.1_Silent_p.N128N|ERG_uc010gnv.1_Silent_p.N29N|ERG_uc010gnx.1_Silent_p.N128N|ERG_uc002yxb.1_Silent_p.N128N|ERG_uc002yxc.2_Silent_p.N128N|ERG_uc002yxa.1_Silent_p.N121N	NM_182918	NP_891548	P11308	ERG_HUMAN	ets-related isoform 1	128	PNT.				cell proliferation|multicellular organismal development|protein phosphorylation|regulation of transcription, DNA-dependent	cytoplasm|nucleus|ribonucleoprotein complex	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity		TMPRSS2/ERG(2058)|FUS/ERG(163)|EWSR1/ERG(162)	prostate(2058)|bone(167)|haematopoietic_and_lymphoid_tissue(153)|soft_tissue(5)|lung(2)|ovary(1)	2386		Prostate(19;3.6e-06)				Esophageal Squamous(130;336 1700 3010 3083 40589)				177				0.333333	45.658142	46.912703	17	34	GG		KEEP	---	---	---	---	capture			Silent	SNP	38717227	38717227	5415	21	G	A	A	40	40	ERG	A	1	1
IL1F8	27177	broad.mit.edu	36	2	113496813	113496813	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:113496813C>T	uc002tiq.1	-	c.404G>A	c.(403-405)TGG>TAG	p.W135*		NM_014438	NP_055253	Q9NZH7	IL1F8_HUMAN	interleukin 1 family, member 8 isoform 1	135					immune response	extracellular space	cytokine activity|interleukin-1 receptor binding			ovary(1)	1														0.407895	90.007235	90.571516	31	45	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	113496813	113496813	7957	2	C	T	T	21	21	IL1F8	T	5	2
TTN	7273	broad.mit.edu	36	2	179262085	179262085	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179262085C>T	uc002umr.1	-	c.28303G>A	c.(28303-28305)GTC>ATC	p.V9435I	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.V6096I|TTN_uc010fre.1_Missense_Mutation_p.V546I	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10362										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.272727	61.868088	65.960886	24	64	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179262085	179262085	17290	2	C	T	T	19	19	TTN	T	1	1
CCDC108	255101	broad.mit.edu	36	2	219600686	219600686	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219600686C>T	uc002vjl.1	-	c.2141G>A	c.(2140-2142)CGC>CAC	p.R714H	CCDC108_uc010fwa.1_Missense_Mutation_p.R157H	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	714						integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)												0.363636	103.687495	105.478887	40	70	CC		KEEP	---	---	---	---	capture		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219600686	219600686	2863	2	C	T	T	27	27	CCDC108	T	1	1
COL6A3	1293	broad.mit.edu	36	2	237954570	237954570	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237954570C>T	uc002vwl.2	-	c.1624G>A	c.(1624-1626)GGC>AGC	p.G542S	COL6A3_uc002vwk.2_Missense_Mutation_p.G542S|COL6A3_uc002vwm.2_Missense_Mutation_p.G341S|COL6A3_uc002vwn.2_Missense_Mutation_p.G542S|COL6A3_uc002vwo.2_Missense_Mutation_p.G336S|COL6A3_uc002vwq.2_Missense_Mutation_p.G336S|COL6A3_uc002vwr.2_Missense_Mutation_p.G135S	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	542	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.443787	226.299043	226.764207	75	94	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Missense_Mutation	SNP	237954570	237954570	3839	2	C	T	T	23	23	COL6A3	T	1	1
PER2	8864	broad.mit.edu	36	2	238826537	238826537	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:238826537G>A	uc002vyc.1	-	c.2866C>T	c.(2866-2868)CCC>TCC	p.P956S		NM_022817	NP_073728	O15055	PER2_HUMAN	period 2	956	Pro-rich.				circadian rhythm|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			breast(1)	1		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)												0.315789	86.415174	89.282952	30	65	GG		KEEP	---	---	---	---	capture		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)	Missense_Mutation	SNP	238826537	238826537	12151	2	G	A	A	43	43	PER2	A	2	2
AQP12A	375318	broad.mit.edu	36	2	241280044	241280044	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241280044C>T	uc002vzu.1	+	c.41C>T	c.(40-42)ACC>ATC	p.T14I	AQP12A_uc002vzv.1_Intron	NM_198998	NP_945349	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	14	Helical; Name=1; (Potential).					integral to membrane	transporter activity				0		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)												0.302198	142.475012	148.823379	55	127	CC		KEEP	---	---	---	---	capture		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)	Missense_Mutation	SNP	241280044	241280044	835	2	C	T	T	18	18	AQP12A	T	2	2
NAALADL2	254827	broad.mit.edu	36	3	176434637	176434637	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:176434637C>G	uc003fit.1	+	c.768C>G	c.(766-768)AGC>AGG	p.S256R	NAALADL2_uc003fiu.1_Missense_Mutation_p.S249R|NAALADL2_uc010hwy.1_Missense_Mutation_p.S63R	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	256	Extracellular (Potential).				proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)												0.328467	137.940751	141.508479	45	92	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)	Missense_Mutation	SNP	176434637	176434637	10525	3	C	G	G	26	26	NAALADL2	G	3	3
YEATS2	55689	broad.mit.edu	36	3	184952700	184952700	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:184952700C>T	uc003fly.1	+	c.1115C>T	c.(1114-1116)TCA>TTA	p.S372L		NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	372					histone H3 acetylation|negative regulation of gene-specific transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	specific transcriptional repressor activity|TBP-class protein binding			ovary(2)|large_intestine(1)	3	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)													0.433735	303.13601	304.108503	108	141	CC		KEEP	---	---	---	---	capture	all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Missense_Mutation	SNP	184952700	184952700	18055	3	C	T	T	29	29	YEATS2	T	2	2
VPS8	23355	broad.mit.edu	36	3	186196949	186196949	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:186196949C>T	uc003fpb.1	+	c.3796C>T	c.(3796-3798)CGC>TGC	p.R1266C	VPS8_uc010hyd.1_Missense_Mutation_p.R1176C|VPS8_uc010hye.1_Missense_Mutation_p.R695C	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	1268	RING-type; atypical.						zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)													0.372881	124.470505	126.144914	44	74	CC		KEEP	---	---	---	---	capture	Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)		Missense_Mutation	SNP	186196949	186196949	17785	3	C	T	T	19	19	VPS8	T	1	1
PLCD1	5333	broad.mit.edu	36	3	38025828	38025828	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38025828C>A	uc003chm.1	-	c.1608G>T	c.(1606-1608)CAG>CAT	p.Q536H	PLCD1_uc003chn.1_Missense_Mutation_p.Q515H	NM_006225	NP_006216	P51178	PLCD1_HUMAN	phospholipase C, delta 1 isoform 2	515	PI-PLC Y-box.				intracellular signal transduction|lipid catabolic process|phospholipid metabolic process	cytoplasm	calcium ion binding|GTPase activating protein binding|phosphatidylinositol phospholipase C activity|signal transducer activity			skin(1)	1														0.455285	161.293305	161.505836	56	67	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)	Missense_Mutation	SNP	38025828	38025828	12457	3	C	A	A	24	24	PLCD1	A	3	3
SCN10A	6336	broad.mit.edu	36	3	38758983	38758983	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38758983T>A	uc003ciq.1	-	c.1909A>T	c.(1909-1911)AGC>TGC	p.S637C		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	637					sensory perception	voltage-gated sodium channel complex				ovary(5)|large_intestine(1)|kidney(1)|skin(1)	8					Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)									0.334821	213.754391	219.163358	75	149	TT		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Missense_Mutation	SNP	38758983	38758983	14394	3	T	A	A	55	55	SCN10A	A	4	4
ITIH3	3699	broad.mit.edu	36	3	52817669	52817669	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52817669G>A	uc003dfv.2	+	c.2605G>A	c.(2605-2607)GTC>ATC	p.V869I		NM_002217	NP_002208	Q06033	ITIH3_HUMAN	inter-alpha (globulin) inhibitor H3	869					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|liver(1)	3														0.323944	60.700042	62.653615	23	48	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)	Missense_Mutation	SNP	52817669	52817669	8209	3	G	A	A	40	40	ITIH3	A	1	1
CXXC4	80319	broad.mit.edu	36	4	105631898	105631898	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:105631898G>A	uc003hxg.1	-	c.4C>T	c.(4-6)CAC>TAC	p.H2Y	CXXC4_uc010ilo.1_Intron	NM_025212	NP_079488	Q9H2H0	CXXC4_HUMAN	CXXC finger 4	2					negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis		DNA binding|PDZ domain binding|zinc ion binding			ovary(1)	1														0.371795	152.950869	155.186205	58	98	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;3.05e-08)	Missense_Mutation	SNP	105631898	105631898	4258	4	G	A	A	46	46	CXXC4	A	2	2
KLHL5	51088	broad.mit.edu	36	4	38793277	38793277	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:38793277G>A	uc003gtr.1	+	c.2143G>A	c.(2143-2145)GGG>AGG	p.G715R	KLHL5_uc003gtp.1_Missense_Mutation_p.G669R|KLHL5_uc003gtq.1_Missense_Mutation_p.G528R|KLHL5_uc003gts.1_Missense_Mutation_p.G715R|KLHL5_uc003gtt.1_Missense_Mutation_p.G654R|KLHL5_uc010ifk.1_Missense_Mutation_p.G223R	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN	kelch-like 5 isoform 1	715	Kelch 6.					cytoplasm|cytoskeleton	actin binding			ovary(1)	1														0.380952	97.303145	98.338437	32	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38793277	38793277	8706	4	G	A	A	43	43	KLHL5	A	2	2
IGJ	3512	broad.mit.edu	36	4	71746724	71746724	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71746724C>T	uc010ihz.1	-	c.185G>A	c.(184-186)CGT>CAT	p.R62H	IGJ_uc003hfn.2_Missense_Mutation_p.R46H	NM_144646	NP_653247	P01591	IGJ_HUMAN	immunoglobulin J chain	46					immune response	extracellular region	antigen binding				0														0.429487	195.22523	195.895232	67	89	CC		KEEP	---	---	---	---	capture	Lung(101;0.235)		Missense_Mutation	SNP	71746724	71746724	7893	4	C	T	T	19	19	IGJ	T	1	1
DGKQ	1609	broad.mit.edu	36	4	946607	946607	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:946607C>T	uc003gbw.1	-	c.1988G>A	c.(1987-1989)CGA>CAA	p.R663Q	DGKQ_uc010ibn.1_Missense_Mutation_p.R650Q	NM_001347	NP_001338	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta	663	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	activating transcription factor binding|ATP binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding			kidney(1)	1						Esophageal Squamous(17;537 645 4447 26373)								0.230769	7.418246	8.281749	3	10	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Missense_Mutation	SNP	946607	946607	4652	4	C	T	T	31	31	DGKQ	T	1	1
AP3S1	1176	broad.mit.edu	36	5	115266590	115266590	+	Splice_Site_SNP	SNP	T	C	C			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:115266590T>C	uc003krl.1	+	c.453_splice	c.e5+2	p.E151_splice	AP3S1_uc003krk.1_Splice_Site_SNP_p.E129_splice|AP3S1_uc003krm.1_Intron	NM_001284	NP_001275			adaptor-related protein complex 3, sigma 1						insulin receptor signaling pathway|intracellular protein transport|vesicle-mediated transport	AP-type membrane coat adaptor complex|cytoplasmic vesicle membrane|Golgi apparatus|transport vesicle	protein binding|protein transporter activity				0		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)												0.153846	6.685377	9.66343	4	22	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)	Splice_Site_SNP	SNP	115266590	115266590	759	5	T	C	C	57	57	AP3S1	C	5	4
PCDHA7	56141	broad.mit.edu	36	5	140195899	140195899	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140195899C>T	uc003lhq.1	+	c.1747C>T	c.(1747-1749)CGG>TGG	p.R583W	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhp.1_Missense_Mutation_p.R583W	NM_018910	NP_061733	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7 isoform 1 precursor	583	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)	1						NSCLC(160;258 2013 5070 22440 28951)								0.134228	21.610172	40.957149	20	129	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140195899	140195899	11949	5	C	T	T	27	27	PCDHA7	T	1	1
NMUR2	56923	broad.mit.edu	36	5	151764546	151764546	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:151764546G>A	uc003luv.2	-	c.322C>T	c.(322-324)CGC>TGC	p.R108C		NM_020167	NP_064552	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	108	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|arachidonic acid secretion|calcium ion transport|central nervous system development|elevation of cytosolic calcium ion concentration|regulation of smooth muscle contraction	integral to membrane|plasma membrane	GTP binding|intracellular calcium activated chloride channel activity|neuromedin U receptor activity			ovary(2)	2		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)												0.36129	150.77418	153.391202	56	99	GG		KEEP	---	---	---	---	capture	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)		Missense_Mutation	SNP	151764546	151764546	10910	5	G	A	A	38	38	NMUR2	A	1	1
TIMD4	91937	broad.mit.edu	36	5	156281701	156281701	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156281701C>T	uc003lwh.1	-	c.999G>A	c.(997-999)GCG>GCA	p.A333A	TIMD4_uc003lwg.1_Silent_p.A35A|TIMD4_uc010jii.1_Silent_p.A305A	NM_138379	NP_612388	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain	333	Helical; (Potential).					integral to membrane				ovary(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)												0.347826	41.260942	42.212337	16	30	CC		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Silent	SNP	156281701	156281701	16432	5	C	T	T	19	19	TIMD4	T	1	1
CDH18	1016	broad.mit.edu	36	5	19782973	19782973	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:19782973G>T	uc003jgc.1	-	c.358C>A	c.(358-360)CAG>AAG	p.Q120K	CDH18_uc003jgd.1_Missense_Mutation_p.Q120K|CDH18_uc010iua.1_Missense_Mutation_p.Q120K|CDH18_uc010itz.1_Missense_Mutation_p.Q120K	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	120	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.373418	169.353143	171.587485	59	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19782973	19782973	3232	5	G	T	T	46	46	CDH18	T	3	3
PRDM9	56979	broad.mit.edu	36	5	23559171	23559171	+	Silent	SNP	A	G	G			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:23559171A>G	uc003jgo.1	+	c.897A>G	c.(895-897)AGA>AGG	p.R299R		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	299	SET.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.367089	98.487359	99.700722	29	50	AA		KEEP	---	---	---	---	capture			Silent	SNP	23559171	23559171	12906	5	A	G	G	9	9	PRDM9	G	4	4
ADAMTS12	81792	broad.mit.edu	36	5	33651691	33651691	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0743-01	TCGA-06-0743-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:33651691T>C	uc003jia.1	-	c.2387A>G	c.(2386-2388)CAG>CGG	p.Q796R	ADAMTS12_uc010iuq.1_Missense_Mutation_p.Q711R	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	796	Spacer 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.39521	209.01354	210.618502	66	101	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33651691	33651691	258	5	T	C	C	55	55	ADAMTS12	C	4	4
MAP3K1	4214	broad.mit.edu	36	5	56204266	56204266	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:56204266C>T	uc003jqw.2	+	c.1465C>T	c.(1465-1467)CCC>TCC	p.P489S		NM_005921	NP_005912	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase	489	RING-type.				cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding			ovary(1)|skin(1)	2		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)								201				0.121212	15.124473	29.052003	12	87	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)	Missense_Mutation	SNP	56204266	56204266	9626	5	C	T	T	30	30	MAP3K1	T	2	2
NAIP	4671	broad.mit.edu	36	5	70344085	70344085	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:70344085G>A	uc003kar.1	-	c.414C>T	c.(412-414)TAC>TAT	p.Y138Y	NAIP_uc003kat.1_Intron|NAIP_uc003kas.1_Intron	NM_004536	NP_004527	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein isoform	138					anti-apoptosis|apoptosis|negative regulation of caspase activity|nervous system development	basolateral plasma membrane|cytoplasm	caspase inhibitor activity|metal ion binding|nucleoside-triphosphatase activity|nucleotide binding	p.Y138Y(1)		central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)												0.227642	128.96838	145.720469	56	190	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)	Silent	SNP	70344085	70344085	10543	5	G	A	A	40	40	NAIP	A	1	1
FAM81B	153643	broad.mit.edu	36	5	94775527	94775527	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:94775527C>T	uc003kla.1	+	c.414C>T	c.(412-414)GAC>GAT	p.D138D	FAM81B_uc010jbe.1_5'UTR	NM_152548	NP_689761	Q96LP2	FA81B_HUMAN	hypothetical protein LOC153643	138										ovary(1)	1		all_cancers(142;1.1e-06)|all_epithelial(76;1.48e-09)|all_lung(232;0.000696)|Lung NSC(167;0.000947)|Ovarian(225;0.00473)												0.44697	170.504976	170.828416	59	73	CC		KEEP	---	---	---	---	capture		all cancers(79;1.04e-16)	Silent	SNP	94775527	94775527	5855	5	C	T	T	17	17	FAM81B	T	2	2
MYLIP	29116	broad.mit.edu	36	6	16251281	16251281	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:16251281A>C	uc003nbq.1	+	c.516A>C	c.(514-516)GAA>GAC	p.E172D	MYLIP_uc003nbr.1_5'UTR	NM_013262	NP_037394	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting	172	FERM.				cellular component movement|nervous system development	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|ubiquitin-protein ligase activity|zinc ion binding			pancreas(1)	1	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)												0.5	139.538796	139.538796	42	42	AA		KEEP	---	---	---	---	capture	Epithelial(50;0.241)		Missense_Mutation	SNP	16251281	16251281	10450	6	A	C	C	4	4	MYLIP	C	4	4
FKSG83	83954	broad.mit.edu	36	6	27401565	27401565	+	Silent	SNP	A	G	G			TCGA-06-0743-01	TCGA-06-0743-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27401565A>G	uc010jqt.1	+	c.525A>G	c.(523-525)AGA>AGG	p.R175R	FKSG83_uc010jqs.1_3'UTR	NM_032030	NP_114419	Q7LBC9	Q7LBC9_HUMAN	FKSG83	320						integral to membrane	pheromone receptor activity				0														0.681818	53.832422	54.478909	15	7	AA		KEEP	---	---	---	---	capture			Silent	SNP	27401565	27401565	6156	6	A	G	G	9	9	FKSG83	G	4	4
SLC22A7	10864	broad.mit.edu	36	6	43375416	43375416	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43375416G>A	uc003out.1	+	c.577G>A	c.(577-579)GTC>ATC	p.V193I	SLC22A7_uc010jyl.1_Missense_Mutation_p.V191I|SLC22A7_uc003ous.2_Missense_Mutation_p.V191I|SLC22A7_uc010jym.1_Missense_Mutation_p.V193I	NM_153320	NP_006663	Q9Y694	S22A7_HUMAN	solute carrier family 22 member 7 isoform b	193	Helical; (Potential).					basolateral plasma membrane|integral to plasma membrane|membrane fraction	anion:anion antiporter activity|sodium-independent organic anion transmembrane transporter activity				0														0.406699	241.03258	242.622416	85	124	GG		KEEP	---	---	---	---	capture	Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Missense_Mutation	SNP	43375416	43375416	14956	6	G	A	A	40	40	SLC22A7	A	1	1
MEP1A	4224	broad.mit.edu	36	6	46914802	46914802	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46914802C>T	uc010jzh.1	+	c.2211C>T	c.(2209-2211)ATC>ATT	p.I737I		NM_005588	NP_005579	Q16819	MEP1A_HUMAN	meprin A, alpha	737	Helical; (Potential).				digestion|proteolysis	extracellular space|integral to plasma membrane|soluble fraction	metalloendopeptidase activity|zinc ion binding			pancreas(2)|ovary(1)	3														0.45614	151.083583	151.274659	52	62	CC		KEEP	---	---	---	---	capture	Lung(136;0.192)		Silent	SNP	46914802	46914802	9864	6	C	T	T	31	31	MEP1A	T	1	1
C6orf221	154288	broad.mit.edu	36	6	74130011	74130011	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:74130011G>A	uc003pgt.2	+	c.361G>A	c.(361-363)GCC>ACC	p.A121T		NM_001017361	NP_001017361	Q587J8	ECAT1_HUMAN	hypothetical protein LOC154288	121											0														0.375	86.76517	87.966353	33	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74130011	74130011	2460	6	G	A	A	42	42	C6orf221	A	2	2
GIMAP6	474344	broad.mit.edu	36	7	149955871	149955871	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149955871C>T	uc003whn.1	-	c.748G>A	c.(748-750)GAA>AAA	p.E250K	GIMAP6_uc003whm.1_Missense_Mutation_p.E170K	NM_024711	NP_078987	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	250							GTP binding			ovary(1)	1														0.272152	226.710141	241.500253	86	230	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	149955871	149955871	6651	7	C	T	T	30	30	GIMAP6	T	2	2
ABP1	26	broad.mit.edu	36	7	150189094	150189094	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150189094C>T	uc003wia.1	+	c.2177C>T	c.(2176-2178)TCC>TTC	p.S726F	ABP1_uc003why.1_Missense_Mutation_p.S707F|ABP1_uc003whz.1_Missense_Mutation_p.S707F	NM_001091	NP_001082	P19801	ABP1_HUMAN	amiloride binding protein 1 precursor	707					amine metabolic process|oxidation-reduction process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding			ovary(2)|breast(2)	4	all_neural(206;0.219)				Amiloride(DB00594)|Spermine(DB00127)	Pancreas(195;1227 3054 24912 28503)								0.359649	117.144407	119.121066	41	73	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Missense_Mutation	SNP	150189094	150189094	99	7	C	T	T	30	30	ABP1	T	2	2
MACC1	346389	broad.mit.edu	36	7	20164746	20164746	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:20164746G>A	uc003sus.2	-	c.1763C>T	c.(1762-1764)GCT>GTT	p.A588V	MACC1_uc010kug.1_Missense_Mutation_p.A588V	NM_182762	NP_877439	Q6ZN28	MACC1_HUMAN	putative binding protein 7a5	588	SH3.				positive regulation of cell division|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	growth factor activity			ovary(2)	2														0.10687	36.750482	97.055141	42	351	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20164746	20164746	9520	7	G	A	A	34	34	MACC1	A	2	2
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>T	uc003tqk.1	+	c.866C>T	c.(865-867)GCC>GTC	p.A289V	EGFR_uc003tqh.1_Missense_Mutation_p.A289V|EGFR_uc003tqi.1_Missense_Mutation_p.A289V|EGFR_uc003tqj.1_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.257862	592.942935	643.655352	246	708	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55189316	55189316	5156	7	C	T	T	26	26	EGFR	T	2	2
COL1A2	1278	broad.mit.edu	36	7	93894277	93894277	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93894277G>C	uc003ung.1	+	c.3127G>C	c.(3127-3129)GCT>CCT	p.A1043P		NM_000089	NP_000080	P08123	CO1A2_HUMAN	alpha 2 type I collagen	1043					axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging			central_nervous_system(3)|ovary(2)	5	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)				Collagenase(DB00048)									0.260274	55.891255	59.68929	19	54	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.0031)		Missense_Mutation	SNP	93894277	93894277	3816	7	G	C	C	46	46	COL1A2	C	3	3
NPTX2	4885	broad.mit.edu	36	7	98092198	98092198	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98092198G>A	uc003upl.1	+	c.672G>A	c.(670-672)GCG>GCA	p.A224A	NPTX2_uc010lfs.1_Non-coding_Transcript	NM_002523	NP_002514	P47972	NPTX2_HUMAN	neuronal pentraxin II	224					synaptic transmission	extracellular region	metal ion binding|sugar binding			central_nervous_system(2)	2	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)													0.25	336.777757	370.174645	147	441	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Silent	SNP	98092198	98092198	11008	7	G	A	A	40	40	NPTX2	A	1	1
TRRAP	8295	broad.mit.edu	36	7	98366277	98366277	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98366277G>T	uc003upp.1	+	c.3479G>T	c.(3478-3480)GGT>GTT	p.G1160V	TRRAP_uc003upq.1_Missense_Mutation_p.G1160V|TRRAP_uc003upr.1_Missense_Mutation_p.G852V	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	1160					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|stomach(2)|lung(1)|liver(1)	27	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)									1847				0.258503	185.311129	200.824628	76	218	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98366277	98366277	17152	7	G	T	T	44	44	TRRAP	T	3	3
VPS13B	157680	broad.mit.edu	36	8	100637899	100637899	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:100637899C>T	uc003yiv.1	+	c.4866C>T	c.(4864-4866)ATC>ATT	p.I1622I	VPS13B_uc003yiw.1_Silent_p.I1597I	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1622					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)					Colon(161;2205 2542 7338 31318)				1116				0.297872	37.93149	39.648188	14	33	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.00636)		Silent	SNP	100637899	100637899	17757	8	C	T	T	31	31	VPS13B	T	1	1
CSMD3	114788	broad.mit.edu	36	8	113771298	113771298	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:113771298C>T	uc003ynu.1	-	c.2130G>A	c.(2128-2130)TGG>TGA	p.W710*	CSMD3_uc003ynt.1_Nonsense_Mutation_p.W670*|CSMD3_uc003ynv.1_Nonsense_Mutation_p.W569*|CSMD3_uc003yns.1_5'UTR	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	710	Extracellular (Potential).|Sushi 3.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.45	105.48615	105.660863	36	44	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	113771298	113771298	4087	8	C	T	T	18	18	CSMD3	T	5	2
ZMAT4	79698	broad.mit.edu	36	8	40674018	40674018	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:40674018G>T	uc003xnr.1	-	c.252C>A	c.(250-252)TTC>TTA	p.F84L	ZMAT4_uc003xns.1_Missense_Mutation_p.F84L	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a	84	Matrin-type 2.					nucleus	DNA binding|zinc ion binding			central_nervous_system(1)|pancreas(1)	2	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)												0.405797	156.635866	157.715332	56	82	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(45;0.00722)		Missense_Mutation	SNP	40674018	40674018	18285	8	G	T	T	45	45	ZMAT4	T	3	3
C9orf84	158401	broad.mit.edu	36	9	113502076	113502076	+	Silent	SNP	G	A	A			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:113502076G>A	uc004bfr.1	-	c.2970C>T	c.(2968-2970)AAC>AAT	p.N990N	C9orf84_uc004bfq.1_Silent_p.N951N|C9orf84_uc010mug.1_Silent_p.N901N	NM_173521	NP_775792	Q5VXU9	CI084_HUMAN	hypothetical protein LOC158401 isoform 1	990										ovary(2)	2														0.377193	129.896111	131.405498	43	71	GG		KEEP	---	---	---	---	capture			Silent	SNP	113502076	113502076	2616	9	G	A	A	36	36	C9orf84	A	2	2
AGTR2	186	broad.mit.edu	36	X	115218549	115218549	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:115218549C>T	uc004eqh.2	+	c.988C>T	c.(988-990)CGC>TGC	p.R330C	AGTR2_uc010nqh.1_Missense_Mutation_p.R330C	NM_000686	NP_000677	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	330	Cytoplasmic (Potential).				behavior|blood vessel remodeling|brain development|G-protein signaling, coupled to cGMP nucleotide second messenger|intracellular protein kinase cascade|negative regulation of blood vessel endothelial cell migration|negative regulation of cell growth|negative regulation of heart rate|negative regulation of nerve growth factor receptor signaling pathway|nitric oxide mediated signal transduction|positive regulation of apoptosis|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of phosphoprotein phosphatase activity|positive regulation of vasodilation|regulation of systemic arterial blood pressure by circulatory renin-angiotensin	integral to plasma membrane	angiotensin type II receptor activity|receptor antagonist activity			ovary(2)|lung(1)	3														0.775194	332.161625	341.139072	100	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115218549	115218549	405	23	C	T	T	23	23	AGTR2	T	1	1
FLNA	2316	broad.mit.edu	36	X	153241639	153241639	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153241639C>T	uc004fkk.2	-	c.3718G>A	c.(3718-3720)GTG>ATG	p.V1240M	FLNA_uc010nuu.1_Missense_Mutation_p.V1240M	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1240	Filamin 10.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.26087	25.898148	28.275867	12	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153241639	153241639	6175	23	C	T	T	19	19	FLNA	T	1	1
FOXR2	139628	broad.mit.edu	36	X	55667187	55667187	+	Silent	SNP	C	T	T			TCGA-06-0743-01	TCGA-06-0743-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:55667187C>T	uc004duo.1	+	c.318C>T	c.(316-318)AAC>AAT	p.N106N		NM_198451	NP_940853	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	106					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|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|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			lung(2)|central_nervous_system(1)	3														0.978723	156.535965	158.314072	46	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	55667187	55667187	6278	23	C	T	T	17	17	FOXR2	T	2	2
PCDH11Y	83259	broad.mit.edu	36	Y	5665460	5665460	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0743-01	TCGA-06-0743-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrY:5665460G>T	uc004fqo.1	+	c.3500G>T	c.(3499-3501)AGC>ATC	p.S1167I		NM_032973	NP_116755	Q9BZA8	PC11Y_HUMAN	protocadherin 11 Y-linked isoform c	1167	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.714286	92.350622	94.075783	30	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5665460	5665460	11929	24	G	T	T	34	34	PCDH11Y	T	3	3
MUM1L1	139221	broad.mit.edu	36	X	105337273	105337273	+	Frame_Shift_Del	DEL	T	-	-			TCGA-06-0743-01	TCGA-06-0743-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:105337273_105337273delT	uc004emf.1	+	c.1192_1192delT	c.(1192-1194)TTTfs	p.F398fs	MUM1L1_uc004emg.1_Frame_Shift_Del_p.F398fs	NM_152423	NP_689636	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	398	PWWP.									ovary(2)|pancreas(1)|skin(1)	4														0.73			11	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	105337273	105337273	10380	23	T	-	-	60	60	MUM1L1	-	5	5
