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
ARHGAP22	58504	broad.mit.edu	36	10	49337903	49337903	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:49337903G>A	uc001jgu.1	-	c.537C>T	c.(535-537)CAC>CAT	p.H179H	ARHGAP22_uc001jgt.1_Silent_p.H163H|ARHGAP22_uc001jgv.1_De_novo_Start_OutOfFrame|ARHGAP22_uc001jgs.1_Silent_p.H73H	NM_021226	NP_067049	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 2	163	Rho-GAP.				angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	GTPase activator activity			ovary(1)	1														0.548387	103.061056	103.189026	34	28	GG		KEEP	---	---	---	---	capture			Silent	SNP	49337903	49337903	883	10	G	A	A	40	40	ARHGAP22	A	1	1
TLL2	7093	broad.mit.edu	36	10	98146940	98146940	+	Silent	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98146940C>T	uc001kml.1	-	c.1377G>A	c.(1375-1377)GCG>GCA	p.A459A	TLL2_uc009xvf.1_Silent_p.A437A	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	459	CUB 1.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)												0.426471	82.860557	83.181416	29	39	CC		KEEP	---	---	---	---	capture		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)	Silent	SNP	98146940	98146940	16476	10	C	T	T	19	19	TLL2	T	1	1
OR4D10	390197	broad.mit.edu	36	11	59001539	59001539	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59001539C>T	uc001nnz.1	+	c.61C>T	c.(61-63)CGG>TGG	p.R21W		NM_001004705	NP_001004705	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D,	21	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.268293	112.622476	120.574105	44	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59001539	59001539	11461	11	C	T	T	31	31	OR4D10	T	1	1
OR52B2	255725	broad.mit.edu	36	11	6147925	6147925	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6147925C>T	uc001mch.1	-	c.208G>A	c.(208-210)GTC>ATC	p.V70I		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	70	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)				NSCLC(5;186 261 1778 7098 14207)								0.282178	147.003401	155.608326	57	145	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	6147925	6147925	11521	11	C	T	T	19	19	OR52B2	T	1	1
LTBR	4055	broad.mit.edu	36	12	6368232	6368232	+	Silent	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6368232C>T	uc001qny.1	+	c.781C>T	c.(781-783)CTG>TTG	p.L261L	LTBR_uc001qnz.1_Silent_p.L256L	NM_002342	NP_002333	P36941	TNR3_HUMAN	lymphotoxin beta receptor	261	Cytoplasmic (Potential).				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity				0										109				0.444444	181.384834	181.747076	60	75	CC		KEEP	---	---	---	---	capture			Silent	SNP	6368232	6368232	9453	12	C	T	T	28	28	LTBR	T	2	2
SLC17A8	246213	broad.mit.edu	36	12	99336031	99336031	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99336031G>A	uc001tho.1	+	c.1391G>A	c.(1390-1392)TGT>TAT	p.C464Y	SLC17A8_uc009ztx.1_Missense_Mutation_p.C414Y	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	464	Helical; (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3														0.359116	173.916098	177.082809	65	116	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99336031	99336031	14919	12	G	A	A	48	48	SLC17A8	A	2	2
SIAH3	283514	broad.mit.edu	36	13	45256035	45256035	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:45256035G>A	uc001vap.1	-	c.294C>T	c.(292-294)CAC>CAT	p.H98H		NM_198849	NP_942146	Q8IW03	SIAH3_HUMAN	seven in absentia homolog 3	98	SIAH-type; degenerate.|His-rich.				multicellular organismal development|ubiquitin-dependent protein catabolic process	nucleus	metal ion binding			ovary(1)	1														0.294118	60.186158	63.38582	25	60	GG		KEEP	---	---	---	---	capture			Silent	SNP	45256035	45256035	14796	13	G	A	A	40	40	SIAH3	A	1	1
DIO3	1735	broad.mit.edu	36	14	101098360	101098360	+	Silent	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:101098360C>T	uc001yki.2	+	c.696C>T	c.(694-696)TTC>TTT	p.F232F	DIO3-OS_uc001ykd.1_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	232	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|oxidation-reduction process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)	2		all_neural(303;0.185)												0.173077	32.527265	43.132252	18	86	CC		KEEP	---	---	---	---	capture			Silent	SNP	101098360	101098360	4705	14	C	T	T	31	31	DIO3	T	1	1
NRXN3	9369	broad.mit.edu	36	14	79397890	79397890	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:79397890G>A	uc001xun.1	+	c.3016G>A	c.(3016-3018)GCC>ACC	p.A1006T	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc001xup.2_Non-coding_Transcript|NRXN3_uc001xuq.2_Missense_Mutation_p.A582T|NRXN3_uc010asw.1_Missense_Mutation_p.A404T|NRXN3_uc001xur.2_Missense_Mutation_p.A377T	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1588	Helical; (Potential).				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)												0.181818	16.823522	22.052906	10	45	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)	Missense_Mutation	SNP	79397890	79397890	11072	14	G	A	A	38	38	NRXN3	A	1	1
CEP152	22995	broad.mit.edu	36	15	46863610	46863610	+	Splice_Site_SNP	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:46863610C>T	uc001zwz.1	-	c.1174_splice	c.e10-1	p.E392_splice	CEP152_uc001zwy.1_Splice_Site_SNP_p.E392_splice|CEP152_uc001zxa.1_Splice_Site_SNP_p.E299_splice	NM_014985	NP_055800			centrosomal protein 152kDa						G2/M transition of mitotic cell cycle	cytosol|microtubule organizing center				lung(2)	2		all_lung(180;0.0428)												0.391892	91.958123	92.715782	29	45	CC		KEEP	---	---	---	---	capture		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)	Splice_Site_SNP	SNP	46863610	46863610	3381	15	C	T	T	24	24	CEP152	T	5	2
FAM83G	644815	broad.mit.edu	36	17	18815733	18815733	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18815733G>A	uc002guw.1	-	c.2136C>T	c.(2134-2136)GAC>GAT	p.D712D	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002guv.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	712										ovary(1)	1														0.313433	108.790763	112.948691	42	92	GG		KEEP	---	---	---	---	capture			Silent	SNP	18815733	18815733	5865	17	G	A	A	40	40	FAM83G	A	1	1
GPR179	440435	broad.mit.edu	36	17	33740490	33740490	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:33740490G>T	uc002hpz.1	-	c.2488C>A	c.(2488-2490)CCC>ACC	p.P830T		NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN	GPR158-like 1	830	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(3)	3	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)												0.235294	8.629239	9.693082	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33740490	33740490	6949	17	G	T	T	44	44	GPR179	T	3	3
METRNL	284207	broad.mit.edu	36	17	78636197	78636197	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:78636197C>A	uc002kgh.1	+	c.265C>A	c.(265-267)CTC>ATC	p.L89I	METRNL_uc002kgi.1_Missense_Mutation_p.L7I	NM_001004431	NP_001004431	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation	89						extracellular region					0	Breast(20;0.000443)|all_neural(118;0.0779)													0.435897	187.466499	188.026416	68	88	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)		Missense_Mutation	SNP	78636197	78636197	9878	17	C	A	A	32	32	METRNL	A	3	3
METRNL	284207	broad.mit.edu	36	17	78636273	78636273	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:78636273C>T	uc002kgh.1	+	c.341C>T	c.(340-342)TCC>TTC	p.S114F	METRNL_uc002kgi.1_Missense_Mutation_p.S32F	NM_001004431	NP_001004431	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation	114						extracellular region					0	Breast(20;0.000443)|all_neural(118;0.0779)													0.412121	197.687967	198.794999	68	97	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)		Missense_Mutation	SNP	78636273	78636273	9878	17	C	T	T	30	30	METRNL	T	2	2
MAN2B1	4125	broad.mit.edu	36	19	12629940	12629940	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12629940C>G	uc002mub.2	-	c.1246G>C	c.(1246-1248)GAG>CAG	p.E416Q	MAN2B1_uc010dyv.1_Missense_Mutation_p.E415Q	NM_000528	NP_000519	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	416					protein deglycosylation	lysosome	alpha-mannosidase activity|zinc ion binding			ovary(4)|central_nervous_system(2)	6														0.284483	98.430043	103.264587	33	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12629940	12629940	9599	19	C	G	G	30	30	MAN2B1	G	3	3
IL12RB1	3594	broad.mit.edu	36	19	18032938	18032938	+	Silent	SNP	C	A	A			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18032938C>A	uc002nhx.1	-	c.1905G>T	c.(1903-1905)GGG>GGT	p.G635G	IL12RB1_uc002nhw.1_Silent_p.G595G	NM_005535	NP_005526	P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1 isoform 1	595	Cytoplasmic (Potential).				cellular response to interferon-gamma|interleukin-12-mediated signaling pathway|positive regulation of activated T cell proliferation|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response	interleukin-12 receptor complex|interleukin-23 receptor complex	cytokine receptor activity			pancreas(1)	1														0.166667	6.583763	9.113955	4	20	CC		KEEP	---	---	---	---	capture			Silent	SNP	18032938	18032938	7927	19	C	A	A	30	30	IL12RB1	A	3	3
MLL4	9757	broad.mit.edu	36	19	40904169	40904169	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40904169C>T	uc010eei.1	+	c.2080C>T	c.(2080-2082)CGG>TGG	p.R694W		NM_014727	NP_055542	Q9UMN6	MLL4_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 4	694	Pro-rich.				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)													0.323529	26.180848	27.138674	11	23	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0515)		Missense_Mutation	SNP	40904169	40904169	10013	19	C	T	T	31	31	MLL4	T	1	1
NLRP12	91662	broad.mit.edu	36	19	59019006	59019006	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59019006G>A	uc002qcj.2	-	c.235C>T	c.(235-237)CGG>TGG	p.R79W	NLRP12_uc002qch.2_Missense_Mutation_p.R79W|NLRP12_uc002qci.2_Missense_Mutation_p.R79W|NLRP12_uc002qck.2_Non-coding_Transcript|NLRP12_uc010eqx.1_Missense_Mutation_p.R79W	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	79	DAPIN.				activation of caspase activity|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|lung(1)	5	Ovarian(34;0.19)													0.267267	219.353169	235.626185	89	244	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.026)	Missense_Mutation	SNP	59019006	59019006	10877	19	G	A	A	38	38	NLRP12	A	1	1
MUC16	94025	broad.mit.edu	36	19	8887244	8887244	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8887244G>A	uc002mkp.1	-	c.36742C>T	c.(36742-36744)CGT>TGT	p.R12248C		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	12250	SEA 2.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.260163	234.680811	253.868371	96	273	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8887244	8887244	10367	19	G	A	A	38	38	MUC16	A	1	1
MUC16	94025	broad.mit.edu	36	19	8946463	8946463	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8946463C>T	uc002mkp.1	-	c.6352G>A	c.(6352-6354)GCG>ACG	p.A2118T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	2118	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.213568	184.949837	215.122682	85	313	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8946463	8946463	10367	19	C	T	T	27	27	MUC16	T	1	1
EXOSC10	5394	broad.mit.edu	36	1	11074206	11074206	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11074206C>G	uc001asa.1	-	c.408G>C	c.(406-408)AAG>AAC	p.K136N	EXOSC10_uc001asb.1_Missense_Mutation_p.K136N|EXOSC10_uc009vmy.1_Missense_Mutation_p.K136N	NM_001001998	NP_001001998	Q01780	EXOSX_HUMAN	exosome component 10 isoform 1	136					CUT catabolic process|histone mRNA catabolic process|maturation of 5.8S rRNA|nuclear polyadenylation-dependent rRNA catabolic process|nuclear retention of unspliced pre-mRNA at the site of transcription|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasm|nuclear exosome (RNase complex)|nucleolus|transcriptionally active chromatin	3'-5' exonuclease activity|exoribonuclease activity|identical protein binding|nucleotide binding|protein serine/threonine kinase activity|RNA binding				0	Ovarian(185;0.249)	Lung NSC(185;1.74e-05)|all_lung(284;2.05e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)				Colon(179;105 1987 14326 27364 29542)								0.326531	92.265407	94.881786	32	66	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.18e-07)|COAD - Colon adenocarcinoma(227;8.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000315)|Kidney(185;0.000832)|KIRC - Kidney renal clear cell carcinoma(229;0.00269)|READ - Rectum adenocarcinoma(331;0.0526)|STAD - Stomach adenocarcinoma(313;0.202)	Missense_Mutation	SNP	11074206	11074206	5507	1	C	G	G	32	32	EXOSC10	G	3	3
UBIAD1	29914	broad.mit.edu	36	1	11256589	11256589	+	Silent	SNP	C	G	G			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11256589C>G	uc001asf.1	+	c.414C>G	c.(412-414)CTC>CTG	p.L138L		NM_013319	NP_037451	Q9Y5Z9	UBIA1_HUMAN	UbiA prenyltransferase domain containing 1	138	Helical; (Potential).				menaquinone biosynthetic process	endoplasmic reticulum membrane|integral to membrane|mitochondrion|nucleus	prenyltransferase activity				0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.012)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)												0.292683	105.550321	110.283968	36	87	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.52e-06)|COAD - Colon adenocarcinoma(227;0.000254)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0487)	Silent	SNP	11256589	11256589	17443	1	C	G	G	32	32	UBIAD1	G	3	3
TCHH	7062	broad.mit.edu	36	1	150347452	150347452	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150347452C>T	uc001ezp.2	-	c.4865G>A	c.(4864-4866)CGC>CAC	p.R1622H	TCHH_uc009wne.1_Missense_Mutation_p.R1622H	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	1622	23 X 26 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.342541	165.797236	169.760821	62	119	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150347452	150347452	16226	1	C	T	T	27	27	TCHH	T	1	1
SLAMF6	114836	broad.mit.edu	36	1	158723126	158723126	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158723126C>T	uc001fwe.1	-	c.994G>A	c.(994-996)GTG>ATG	p.V332M	SLAMF6_uc001fwd.1_Missense_Mutation_p.V331M	NM_052931	NP_443163	Q96DU3	SLAF6_HUMAN	activating NK receptor precursor	332						integral to membrane|plasma membrane	receptor activity			ovary(1)	1	all_cancers(52;1.05e-18)|all_hematologic(112;0.093)													0.29	76.33485	80.286708	29	71	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(70;0.0923)		Missense_Mutation	SNP	158723126	158723126	14863	1	C	T	T	19	19	SLAMF6	T	1	1
KLHDC8A	55220	broad.mit.edu	36	1	203579230	203579230	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203579230G>A	uc001hcf.1	-	c.126C>T	c.(124-126)AAC>AAT	p.N42N	KLHDC8A_uc001hcg.1_Silent_p.N42N	NM_018203	NP_060673	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	42	Kelch 2.									ovary(1)	1	Breast(84;0.23)													0.257576	38.662229	42.166992	17	49	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(75;0.117)		Silent	SNP	203579230	203579230	8674	1	G	A	A	40	40	KLHDC8A	A	1	1
RAB3GAP2	25782	broad.mit.edu	36	1	218407572	218407572	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:218407572C>A	uc001hme.1	-	c.2875G>T	c.(2875-2877)GCT>TCT	p.A959S	RAB3GAP2_uc009xdv.1_Missense_Mutation_p.A959S|RAB3GAP2_uc001hmf.1_Non-coding_Transcript|RAB3GAP2_uc001hmg.1_Missense_Mutation_p.A539S|RAB3GAP2_uc001hmh.1_5'Flank	NM_012414	NP_036546	Q9H2M9	RBGPR_HUMAN	rab3 GTPase-activating protein, non-catalytic	959					intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity			central_nervous_system(1)	1														0.344444	429.166489	438.793608	155	295	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.0443)	Missense_Mutation	SNP	218407572	218407572	13395	1	C	A	A	26	26	RAB3GAP2	A	3	3
HHIPL2	79802	broad.mit.edu	36	1	220784125	220784125	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:220784125G>A	uc001hnh.1	-	c.351C>T	c.(349-351)TAC>TAT	p.Y117Y		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	117					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1														0.390977	294.626821	297.399481	104	162	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.0185)	Silent	SNP	220784125	220784125	7378	1	G	A	A	40	40	HHIPL2	A	1	1
NUP133	55746	broad.mit.edu	36	1	227673094	227673094	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:227673094G>A	uc001htn.1	-	c.1932C>T	c.(1930-1932)GCC>GCT	p.A644A		NM_018230	NP_060700	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	644					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA export from nucleus|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex	nucleocytoplasmic transporter activity|protein binding			breast(4)|ovary(1)	5	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)								578				0.310345	78.496074	81.281737	27	60	GG		KEEP	---	---	---	---	capture			Silent	SNP	227673094	227673094	11159	1	G	A	A	39	39	NUP133	A	1	1
TRIM62	55223	broad.mit.edu	36	1	33419369	33419369	+	Silent	SNP	G	C	C			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33419369G>C	uc001bxb.1	-	c.252C>G	c.(250-252)CTC>CTG	p.L84L		NM_018207	NP_060677	Q9BVG3	TRI62_HUMAN	tripartite motif-containing 62	84						intracellular	zinc ion binding				0		Myeloproliferative disorder(586;0.0393)												0.315789	18.843484	19.416752	6	13	GG		KEEP	---	---	---	---	capture			Silent	SNP	33419369	33419369	17083	1	G	C	C	45	45	TRIM62	C	3	3
SPEG	10290	broad.mit.edu	36	2	220061619	220061619	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:220061619G>A	uc010fwg.1	+	c.8014G>A	c.(8014-8016)GTG>ATG	p.V2672M		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	2672	Ig-like 9.				muscle organ development|negative regulation of cell proliferation|protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			ovary(4)|stomach(2)|central_nervous_system(1)	7		Renal(207;0.0183)								482				0.120879	9.718353	22.50442	11	80	GG		KEEP	---	---	---	---	capture		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)	Missense_Mutation	SNP	220061619	220061619	15548	2	G	A	A	40	40	SPEG	A	1	1
C2orf85	285093	broad.mit.edu	36	2	242462758	242462758	+	Silent	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:242462758C>T	uc010fzu.1	+	c.378C>T	c.(376-378)TAC>TAT	p.Y126Y		NM_173821	NP_776182	Q14D33	CB085_HUMAN	hypothetical protein LOC285093	126						integral to membrane				ovary(1)	1														0.363636	11.197683	11.377348	4	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	242462758	242462758	2292	2	C	T	T	19	19	C2orf85	T	1	1
DPPA4	55211	broad.mit.edu	36	3	110529528	110529528	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1829-01	TCGA-14-1829-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110529528T>G	uc003dxq.2	-	c.912A>C	c.(910-912)GAA>GAC	p.E304D		NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	304						nucleus	protein binding				0														0.234409	299.844701	329.847131	109	356	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110529528	110529528	4920	3	T	G	G	52	52	DPPA4	G	4	4
HCLS1	3059	broad.mit.edu	36	3	122838769	122838769	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122838769C>T	uc003eeh.2	-	c.479G>A	c.(478-480)CGG>CAG	p.R160Q		NM_005335	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	160	Cortactin 3.				erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|regulation of transcription, DNA-dependent|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0														0.430657	181.521039	182.091334	59	78	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0912)	Missense_Mutation	SNP	122838769	122838769	7277	3	C	T	T	23	23	HCLS1	T	1	1
SR140	23350	broad.mit.edu	36	3	144224549	144224549	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1829-01	TCGA-14-1829-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:144224549A>G	uc003evh.1	+	c.1183A>G	c.(1183-1185)AAT>GAT	p.N395D	SR140_uc003evi.1_5'UTR|SR140_uc003evj.1_Non-coding_Transcript|SR140_uc003evk.1_Missense_Mutation_p.N394D|SR140_uc003evl.1_5'Flank	NM_001080415	NP_001073884	O15042	SR140_HUMAN	U2-associated SR140 protein	395	Pro-rich.				RNA processing	nucleus	nucleotide binding|RNA binding				0						Colon(87;897 1320 15089 19747 35974)								0.333333	43.937723	44.970088	14	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144224549	144224549	15645	3	A	G	G	13	13	SR140	G	4	4
CACNA1D	776	broad.mit.edu	36	3	53814066	53814066	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1829-01	TCGA-14-1829-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53814066T>A	uc003dgu.2	+	c.5662T>A	c.(5662-5664)TAC>AAC	p.Y1888N	CACNA1D_uc003dgv.2_Missense_Mutation_p.Y1868N|CACNA1D_uc003dgy.2_Missense_Mutation_p.Y1844N|CACNA1D_uc003dgw.2_Missense_Mutation_p.Y1535N	NM_000720	NP_000711	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type,	1868	Cytoplasmic (Potential).				axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(6)|liver(1)	7					Verapamil(DB00661)									0.183333	7.868082	13.736094	11	49	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Missense_Mutation	SNP	53814066	53814066	2657	3	T	A	A	53	53	CACNA1D	A	4	4
NEK1	4750	broad.mit.edu	36	4	170583959	170583959	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1829-01	TCGA-14-1829-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:170583959A>C	uc003isd.1	-	c.2887T>G	c.(2887-2889)TCG>GCG	p.S963A	NEK1_uc003isb.1_Missense_Mutation_p.S935A|NEK1_uc003isc.1_Missense_Mutation_p.S891A|NEK1_uc003ise.1_Missense_Mutation_p.S919A|NEK1_uc003isf.1_Missense_Mutation_p.S866A	NM_012224	NP_036356	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	935					cell division|cilium assembly|mitosis|protein phosphorylation	nucleus|pericentriolar material	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(3)|ovary(2)|large_intestine(1)	6		Prostate(90;0.00601)|Renal(120;0.0183)								366				0.318182	10.458279	11.13919	7	15	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)	Missense_Mutation	SNP	170583959	170583959	10720	4	A	C	C	10	10	NEK1	C	4	4
SLIT2	9353	broad.mit.edu	36	4	20153231	20153231	+	Silent	SNP	T	C	C			TCGA-14-1829-01	TCGA-14-1829-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:20153231T>C	uc003gpr.1	+	c.2160T>C	c.(2158-2160)AGT>AGC	p.S720S	SLIT2_uc003gps.1_Silent_p.S712S	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2	720	LRRNT 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|initiation of Roundabout signal transduction|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|ovary(3)	7														0.341935	508.271376	518.542667	159	306	TT		KEEP	---	---	---	---	capture			Silent	SNP	20153231	20153231	15238	4	T	C	C	60	60	SLIT2	C	4	4
PKD2	5311	broad.mit.edu	36	4	89192182	89192182	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1829-01	TCGA-14-1829-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:89192182A>G	uc003hre.1	+	c.1564A>G	c.(1564-1566)ATA>GTA	p.I522V		NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	522	Helical; (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity				0		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)												0.115942	8.860296	18.877589	8	61	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)	Missense_Mutation	SNP	89192182	89192182	12391	4	A	G	G	16	16	PKD2	G	4	4
ETF1	2107	broad.mit.edu	36	5	137874787	137874787	+	Silent	SNP	T	C	C			TCGA-14-1829-01	TCGA-14-1829-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137874787T>C	uc003ldc.2	-	c.864A>G	c.(862-864)GGA>GGG	p.G288G	ETF1_uc003ldd.2_Silent_p.G255G|ETF1_uc010jex.1_Non-coding_Transcript	NM_004730	NP_004721	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	288					protein methylation|regulation of translational termination	cytoplasm	protein binding|ribosome binding|translation release factor activity, codon specific			ovary(2)	2														0.42953	214.772002	215.417862	64	85	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Silent	SNP	137874787	137874787	5461	5	T	C	C	58	58	ETF1	C	4	4
PCDHB6	56130	broad.mit.edu	36	5	140511170	140511170	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1829-01	TCGA-14-1829-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140511170T>C	uc003lir.1	+	c.1148T>C	c.(1147-1149)ATA>ACA	p.I383T		NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	383	Cadherin 4.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding				0														0.336283	240.943503	246.295814	76	150	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140511170	140511170	11966	5	T	C	C	49	49	PCDHB6	C	4	4
PCDHB7	56129	broad.mit.edu	36	5	140534474	140534474	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140534474G>A	uc003lit.1	+	c.1874G>A	c.(1873-1875)CGT>CAT	p.R625H		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	625	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4														0.373016	126.096664	127.87874	47	79	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140534474	140534474	11967	5	G	A	A	40	40	PCDHB7	A	1	1
GPR98	84059	broad.mit.edu	36	5	90091145	90091145	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:90091145G>T	uc003kju.1	+	c.12104G>T	c.(12103-12105)GGA>GTA	p.G4035V	GPR98_uc003kjt.1_Missense_Mutation_p.G1741V|GPR98_uc003kjv.2_Missense_Mutation_p.G1635V	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4035	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.369565	47.361115	48.049641	17	29	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Missense_Mutation	SNP	90091145	90091145	6997	5	G	T	T	41	41	GPR98	T	3	3
BCLAF1	9774	broad.mit.edu	36	6	136641320	136641320	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:136641320C>T	uc003qgx.1	-	c.392G>A	c.(391-393)CGG>CAG	p.R131Q	BCLAF1_uc003qgw.1_Missense_Mutation_p.R131Q|BCLAF1_uc003qgy.1_Missense_Mutation_p.R129Q	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	131					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|transcription repressor activity			ovary(1)	1	Colorectal(23;0.24)					Colon(142;1534 1789 5427 7063 28491)								0.109726	48.729097	109.168193	44	357	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)	Missense_Mutation	SNP	136641320	136641320	1404	6	C	T	T	23	23	BCLAF1	T	1	1
TRIM40	135644	broad.mit.edu	36	6	30222839	30222839	+	Silent	SNP	C	G	G			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30222839C>G	uc003npk.2	+	c.540C>G	c.(538-540)GGC>GGG	p.G180G	TRIM40_uc003npm.2_Silent_p.G151G	NM_138700	NP_619645	Q6P9F5	TRI40_HUMAN	tripartite motif-containing 40	180						intracellular	zinc ion binding			ovary(1)	1														0.193548	7.941905	10.670483	6	25	CC		KEEP	---	---	---	---	capture			Silent	SNP	30222839	30222839	17059	6	C	G	G	26	26	TRIM40	G	3	3
TREML1	340205	broad.mit.edu	36	6	41229782	41229782	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41229782G>A	uc003opw.1	-	c.68C>T	c.(67-69)CCT>CTT	p.P23L	TREML1_uc003opx.1_Missense_Mutation_p.P23L|TREML1_uc010jxk.1_Intron	NM_178174	NP_835468	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid	23	Ig-like V-type.|Extracellular (Potential).				calcium-mediated signaling|innate immune response|platelet activation	cell surface|integral to membrane|plasma membrane|platelet alpha granule	protein binding|receptor activity			breast(1)	1	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.241071	70.371868	77.220335	27	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41229782	41229782	17016	6	G	A	A	35	35	TREML1	A	2	2
GFRAL	389400	broad.mit.edu	36	6	55304553	55304553	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:55304553C>T	uc003pcm.1	+	c.104C>T	c.(103-105)GCA>GTA	p.A35V		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like	35	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)													0.3	47.124376	49.269986	18	42	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(124;0.23)		Missense_Mutation	SNP	55304553	55304553	6619	6	C	T	T	25	25	GFRAL	T	2	2
PIK3CG	5294	broad.mit.edu	36	7	106295362	106295362	+	Silent	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295362C>T	uc003vdv.2	+	c.120C>T	c.(118-120)ATC>ATT	p.I40I	PIK3CG_uc003vdu.1_Silent_p.I40I|PIK3CG_uc003vdw.1_Silent_p.I40I	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	40					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.172185	44.069381	59.404295	26	125	CC		KEEP	---	---	---	---	capture			Silent	SNP	106295362	106295362	12340	7	C	T	T	31	31	PIK3CG	T	1	1
C7orf66	154907	broad.mit.edu	36	7	108311362	108311362	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:108311362G>A	uc003vfo.1	-	c.286C>T	c.(286-288)CGG>TGG	p.R96W		NM_001024607	NP_001019778	A4D0T2	CG066_HUMAN	hypothetical protein LOC154907	96						integral to membrane				ovary(2)	2														0.268608	210.997368	225.925403	83	226	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108311362	108311362	2519	7	G	A	A	40	40	C7orf66	A	1	1
GPR37	2861	broad.mit.edu	36	7	124174561	124174561	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:124174561C>T	uc003vli.1	-	c.1096G>A	c.(1096-1098)GTA>ATA	p.V366I		NM_005302	NP_005293	O15354	GPR37_HUMAN	G protein-coupled receptor 37	366	Cytoplasmic (Potential).					endoplasmic reticulum membrane|integral to plasma membrane	G-protein coupled receptor activity			ovary(1)|central_nervous_system(1)	2														0.302326	136.64021	142.637539	52	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124174561	124174561	6966	7	C	T	T	19	19	GPR37	T	1	1
AKR1B10	57016	broad.mit.edu	36	7	133863211	133863211	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:133863211C>T	uc003vrr.1	+	c.8C>T	c.(7-9)ACG>ATG	p.T3M		NM_020299	NP_064695	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10	3					cellular aldehyde metabolic process|digestion|oxidation-reduction process|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding				0														0.275591	91.670342	97.428953	35	92	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	133863211	133863211	470	7	C	T	T	19	19	AKR1B10	T	1	1
URGCP	55665	broad.mit.edu	36	7	43883562	43883562	+	Silent	SNP	G	C	C			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43883562G>C	uc003tiw.1	-	c.2025C>G	c.(2023-2025)GTC>GTG	p.V675V	URGCP_uc003tiv.1_Silent_p.V600V|URGCP_uc003tix.1_Silent_p.V666V|URGCP_uc003tiy.1_Silent_p.V632V|URGCP_uc003tiz.1_Silent_p.V632V|URGCP_uc003tiu.1_Silent_p.V632V	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	675					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)	3														0.247934	85.738911	92.700856	30	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	43883562	43883562	17588	7	G	C	C	45	45	URGCP	C	3	3
URGCP	55665	broad.mit.edu	36	7	43883648	43883648	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43883648G>T	uc003tiw.1	-	c.1939C>A	c.(1939-1941)CCA>ACA	p.P647T	URGCP_uc003tiv.1_Missense_Mutation_p.P572T|URGCP_uc003tix.1_Missense_Mutation_p.P638T|URGCP_uc003tiy.1_Missense_Mutation_p.P604T|URGCP_uc003tiz.1_Missense_Mutation_p.P604T|URGCP_uc003tiu.1_Missense_Mutation_p.P604T	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	647					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)	3														0.337349	68.567526	70.51291	28	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43883648	43883648	17588	7	G	T	T	43	43	URGCP	T	3	3
URGCP	55665	broad.mit.edu	36	7	43884559	43884559	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43884559G>C	uc003tiw.1	-	c.1028C>G	c.(1027-1029)TCT>TGT	p.S343C	URGCP_uc003tiv.1_Missense_Mutation_p.S268C|URGCP_uc003tix.1_Missense_Mutation_p.S334C|URGCP_uc003tiy.1_Missense_Mutation_p.S300C|URGCP_uc003tiz.1_Missense_Mutation_p.S300C|URGCP_uc003tiu.1_Missense_Mutation_p.S300C	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	343					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)	3														0.224576	143.146111	159.598868	53	183	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43884559	43884559	17588	7	G	C	C	33	33	URGCP	C	3	3
URGCP	55665	broad.mit.edu	36	7	43885293	43885293	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43885293G>C	uc003tiw.1	-	c.294C>G	c.(292-294)ATC>ATG	p.I98M	URGCP_uc003tiv.1_Missense_Mutation_p.I23M|URGCP_uc003tix.1_Missense_Mutation_p.I89M|URGCP_uc003tiy.1_Missense_Mutation_p.I55M|URGCP_uc003tiz.1_Missense_Mutation_p.I55M|URGCP_uc003tiu.1_Missense_Mutation_p.I55M	NM_001077663	NP_001071131	Q8TCY9	URGCP_HUMAN	up-regulated gene 4 isoform 3	98					cell cycle	centrosome|nucleus	GTP binding			ovary(2)|liver(1)	3														0.21256	116.286289	132.090494	44	163	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43885293	43885293	17588	7	G	C	C	45	45	URGCP	C	3	3
USP42	84132	broad.mit.edu	36	7	6150254	6150254	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:6150254G>A	uc003sps.2	+	c.891G>A	c.(889-891)ATG>ATA	p.M297I	USP42_uc010kti.1_Missense_Mutation_p.M297I|USP42_uc010kth.1_Missense_Mutation_p.M230I	NM_032172	NP_115548	Q9H9J4	UBP42_HUMAN	ubiquitin specific protease 42	297					cell differentiation|protein deubiquitination|spermatogenesis|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(2)|pancreas(1)	3		Ovarian(82;0.0423)												0.245283	30.946707	34.080335	13	40	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)	Missense_Mutation	SNP	6150254	6150254	17637	7	G	A	A	47	47	USP42	A	2	2
TRIM4	89122	broad.mit.edu	36	7	99354592	99354592	+	Silent	SNP	G	A	A			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99354592G>A	uc003usd.1	-	c.369C>T	c.(367-369)ATC>ATT	p.I123I	TRIM4_uc003use.1_Silent_p.I123I|TRIM4_uc003usf.1_Silent_p.I123I	NM_033017	NP_148977	Q9C037	TRIM4_HUMAN	tripartite motif protein TRIM4 isoform alpha	123	B box-type.				protein trimerization	cytoplasm|plasma membrane	zinc ion binding			ovary(1)|kidney(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)												0.3	13.132419	13.853771	6	14	GG		KEEP	---	---	---	---	capture			Silent	SNP	99354592	99354592	17058	7	G	A	A	37	37	TRIM4	A	1	1
TAF2	6873	broad.mit.edu	36	8	120900773	120900773	+	Nonsense_Mutation	SNP	G	C	C			TCGA-14-1829-01	TCGA-14-1829-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:120900773G>C	uc003you.1	-	c.293C>G	c.(292-294)TCA>TGA	p.S98*		NM_003184	NP_003175	Q6P1X5	TAF2_HUMAN	TBP-associated factor 2	98					G2/M transition of mitotic cell cycle|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor TFIID complex|transcription factor TFTC complex	metallopeptidase activity|promoter binding|protein binding|zinc ion binding			large_intestine(2)|ovary(2)|kidney(1)	5	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)													0.100977	35.510789	84.273483	31	276	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.00185)		Nonsense_Mutation	SNP	120900773	120900773	16045	8	G	C	C	45	45	TAF2	C	5	3
EBF2	64641	broad.mit.edu	36	8	25774629	25774629	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25774629C>A	uc003xes.1	-	c.1195G>T	c.(1195-1197)GCT>TCT	p.A399S	PPP2R2A_uc003xek.1_Intron|EBF2_uc010lug.1_Non-coding_Transcript	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	399					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|transcription regulator activity			ovary(3)	3		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)				Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)								0.375	192.001101	194.417407	66	110	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)	Missense_Mutation	SNP	25774629	25774629	5067	8	C	A	A	25	25	EBF2	A	3	3
LY96	23643	broad.mit.edu	36	8	75084858	75084858	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1829-01	TCGA-14-1829-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:75084858A>G	uc003yad.1	+	c.271A>G	c.(271-273)AAA>GAA	p.K91E		NM_015364	NP_056179	Q9Y6Y9	LY96_HUMAN	MD-2 protein	91					cellular defense response|detection of lipopolysaccharide|I-kappaB kinase/NF-kappaB cascade|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent 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	extracellular space|lipopolysaccharide receptor complex|plasma membrane	coreceptor activity|lipopolysaccharide receptor activity|protein binding				0	Breast(64;0.0311)					GBM(131;1357 1748 34893 50149 52212)								0.336134	115.324941	118.122497	40	79	AA		KEEP	---	---	---	---	capture	Epithelial(68;0.0208)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0619)		Missense_Mutation	SNP	75084858	75084858	9479	8	A	G	G	5	5	LY96	G	4	4
C9orf131	138724	broad.mit.edu	36	9	35035372	35035372	+	Missense_Mutation	SNP	C	G	G	rs3739871	by-cluster,by-frequency,by-hapmap	TCGA-14-1829-01	TCGA-14-1829-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35035372C>G	uc003zvw.1	+	c.2746C>G	c.(2746-2748)CCA>GCA	p.P916A	C9orf131_uc003zvu.1_Missense_Mutation_p.P868A|C9orf131_uc003zvv.1_Missense_Mutation_p.P843A|C9orf131_uc003zvx.1_Missense_Mutation_p.P881A	NM_203299	NP_976044	Q5VYM1	CI131_HUMAN	hypothetical protein LOC138724 isoform A	916											0	all_epithelial(49;0.22)													0.33913	367.14986	375.005552	117	228	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)		Missense_Mutation	SNP	35035372	35035372	2570	9	C	G	G	30	30	C9orf131	G	3	3
LHFPL3	375612	broad.mit.edu	36	7	103756472	103756473	+	In_Frame_Ins	INS	-	GCC	GCC			TCGA-14-1829-01	TCGA-14-1829-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:103756472_103756473insGCC	uc003vce.1	+	c.9_10insGCC	c.(7-12)insGCC	p.14_15insA	LHFPL3_uc003vcf.1_In_Frame_Ins_p.14_15insA	NM_199000	NP_945351	Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	Error:Variant_position_missing_in_Q86UP9_after_alignment_1						integral to membrane					0														0.31			4	9				---	---	---	---	capture_indel			In_Frame_Ins	INS	103756472	103756473	9092	7	-	GCC	GCC	11	11	LHFPL3	GCC	5	5
GPSM1	26086	broad.mit.edu	36	9	138363984	138363985	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-1829-01	TCGA-14-1829-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138363984_138363985insC	uc004chd.1	+	c.1334_1335insC	c.(1333-1335)GGCfs	p.G445fs		NM_015597	NP_056412	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1 (AGS3-like, C.	468	Mediates association with membranes (By similarity).|Interaction with STK11 (By similarity).				cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity				0		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	138363984	138363985	7010	9	-	C	C	42	42	GPSM1	C	5	5
