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
SH2D4B	387694	broad.mit.edu	36	10	82353498	82353498	+	Missense_Mutation	SNP	C	T	T	rs61861597	unknown	TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:82353498C>T	uc001kck.1	+	c.827C>T	c.(826-828)CCG>CTG	p.P276L	SH2D4B_uc001kcl.1_Missense_Mutation_p.P227L|SH2D4B_uc001kcm.1_Missense_Mutation_p.P22L	NM_207372	NP_997255	Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	275											0			Colorectal(32;0.229)											0.95	64.690472	67.129619	19	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82353498	82353498	14727	10	C	T	T	23	23	SH2D4B	T	1	1
TRPM5	29850	broad.mit.edu	36	11	2385585	2385585	+	Silent	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:2385585G>A	uc009ydn.1	-	c.2922C>T	c.(2920-2922)AAC>AAT	p.N974N	TRPM5_uc001lwm.2_Silent_p.N972N	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,	972	Helical; (Potential).					integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)	3		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		NSCLC(1;49 61 17205 18850 43201)								0.272727	8.119877	8.632167	3	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	2385585	2385585	17140	11	G	A	A	44	44	TRPM5	A	2	2
KCNA4	3739	broad.mit.edu	36	11	29990185	29990185	+	Missense_Mutation	SNP	T	G	G			TCGA-12-3646-01	TCGA-12-3646-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:29990185T>G	uc001msk.1	-	c.617A>C	c.(616-618)GAA>GCA	p.E206A	KCNA4_uc009yjh.1_Missense_Mutation_p.E206A	NM_002233	NP_002224	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related	206						voltage-gated potassium channel complex	potassium ion binding|protein binding|voltage-gated potassium channel activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.486842	111.14968	111.16153	37	39	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29990185	29990185	8310	11	T	G	G	62	62	KCNA4	G	4	4
PRR5L	79899	broad.mit.edu	36	11	36440802	36440802	+	Silent	SNP	G	C	C			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:36440802G>C	uc001mwo.2	+	c.1047G>C	c.(1045-1047)CTG>CTC	p.L349L	PRR5L_uc001mwp.1_Silent_p.L349L|PRR5L_uc009ykk.1_Silent_p.L221L	NM_024841	NP_079117	Q6MZQ0	PRR5L_HUMAN	protor-2	349										ovary(1)	1														0.128205	9.189662	19.708799	10	68	GG		KEEP	---	---	---	---	capture			Silent	SNP	36440802	36440802	13051	11	G	C	C	47	47	PRR5L	C	3	3
OR5W2	390148	broad.mit.edu	36	11	55437811	55437811	+	Nonsense_Mutation	SNP	G	C	C			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55437811G>C	uc001nib.1	-	c.824C>G	c.(823-825)TCA>TGA	p.S275*		NM_001001960	NP_001001960	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W,	275	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1						Melanoma(48;171 1190 15239 43886 49348)								0.382353	84.035145	84.860121	26	42	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	55437811	55437811	11595	11	G	C	C	45	45	OR5W2	C	5	3
FOLR3	2352	broad.mit.edu	36	11	71527686	71527686	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:71527686C>T	uc001orx.1	+	c.200C>T	c.(199-201)ACG>ATG	p.T67M	FOLR3_uc001ory.1_Missense_Mutation_p.R110W	NM_000804	NP_000795	P41439	FOLR3_HUMAN	folate receptor 3 precursor	65					folic acid transport	extracellular region|extrinsic to membrane|membrane fraction	folic acid binding|receptor activity				0					Folic Acid(DB00158)									0.173077	15.641975	20.894103	9	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71527686	71527686	6225	11	C	T	T	19	19	FOLR3	T	1	1
LRRC32	2615	broad.mit.edu	36	11	76049058	76049058	+	Silent	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:76049058C>T	uc001oxq.2	-	c.1227G>A	c.(1225-1227)CTG>CTA	p.L409L	LRRC32_uc001oxr.2_Silent_p.L409L	NM_005512	NP_005503	Q14392	LRC32_HUMAN	leucine rich repeat containing 32 precursor	409	Extracellular (Potential).					integral to plasma membrane					0														0.611111	34.328061	34.522807	11	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	76049058	76049058	9362	11	C	T	T	21	21	LRRC32	T	2	2
CAPN5	726	broad.mit.edu	36	11	76503043	76503043	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:76503043C>T	uc009yup.1	+	c.734C>T	c.(733-735)GCC>GTC	p.A245V	CAPN5_uc001oxx.1_Missense_Mutation_p.A205V|CAPN5_uc009yuq.1_Missense_Mutation_p.A241V|CAPN5_uc001oxy.1_Missense_Mutation_p.A245V	NM_004055	NP_004046	O15484	CAN5_HUMAN	calpain 5	205	Calpain catalytic.				proteolysis|signal transduction	intracellular	calcium-dependent cysteine-type endopeptidase activity				0												OREG0021255	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.498433	499.436681	499.437219	159	160	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76503043	76503043	2747	11	C	T	T	26	26	CAPN5	T	2	2
GPRC5D	55507	broad.mit.edu	36	12	12994360	12994360	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:12994360G>T	uc001rbc.1	-	c.226C>A	c.(226-228)CTC>ATC	p.L76I		NM_018654	NP_061124	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, family C, group 5,	76	Helical; Name=2; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)										0.526786	190.730276	190.800385	59	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12994360	12994360	7003	12	G	T	T	36	36	GPRC5D	T	3	3
MBIP	51562	broad.mit.edu	36	14	35859538	35859538	+	Missense_Mutation	SNP	G	C	C			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:35859538G>C	uc001wtm.1	-	c.8C>G	c.(7-9)GCT>GGT	p.A3G	MBIP_uc001wtn.1_Missense_Mutation_p.A3G|MBIP_uc001wto.1_Missense_Mutation_p.A3G	NM_016586	NP_057670	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1 isoform 1	3					histone H3 acetylation|inactivation of MAPK activity involved in osmosensory signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm|nucleolus	identical protein binding|protein kinase inhibitor activity				0	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)						91				0.178571	9.258984	11.981689	5	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35859538	35859538	9737	14	G	C	C	34	34	MBIP	C	3	3
PDIA3	2923	broad.mit.edu	36	15	41833372	41833372	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41833372G>A	uc001zsu.1	+	c.226G>A	c.(226-228)GGA>AGA	p.G76R	PDIA3_uc010bdp.1_Missense_Mutation_p.G56R	NM_005313	NP_005304	P30101	PDIA3_HUMAN	protein disulfide-isomerase A3 precursor	76	Thioredoxin 1.				cell redox homeostasis|glycerol ether metabolic process|post-translational protein modification|protein folding|protein import into nucleus|protein N-linked glycosylation via asparagine|protein retention in ER lumen|signal transduction	endoplasmic reticulum lumen|melanosome	cysteine-type endopeptidase activity|electron carrier activity|phospholipase C activity|protein binding|protein disulfide isomerase activity|protein disulfide oxidoreductase activity			ovary(1)	1		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)										0.166667	11.355821	14.516011	5	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41833372	41833372	12090	15	G	A	A	35	35	PDIA3	A	2	2
RFX7	64864	broad.mit.edu	36	15	54175156	54175156	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:54175156G>A	uc010bfn.1	-	c.2062C>T	c.(2062-2064)CAG>TAG	p.Q688*	RFX7_uc002adn.1_Nonsense_Mutation_p.Q502*	NM_022841	NP_073752	Q2KHR2	RFX7_HUMAN	regulatory factor X domain containing 2	591					regulation of transcription, DNA-dependent	nucleus	DNA binding				0														0.743243	350.957558	358.881294	110	38	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	54175156	54175156	13740	15	G	A	A	46	46	RFX7	A	5	2
ITGAM	3684	broad.mit.edu	36	16	31244347	31244347	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31244347G>A	uc002ebr.1	+	c.2534G>A	c.(2533-2535)CGC>CAC	p.R845H	ITGAM_uc002ebq.1_Missense_Mutation_p.R844H|ITGAM_uc010can.1_Missense_Mutation_p.R250H|ITGAM_uc002ebs.1_Missense_Mutation_p.R250H	NM_000632	NP_000623	P11215	ITAM_HUMAN	integrin alpha M precursor	844	Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	glycoprotein binding|receptor activity			kidney(1)	1														0.469325	457.573876	457.836974	153	173	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31244347	31244347	8191	16	G	A	A	38	38	ITGAM	A	1	1
ABCC11	85320	broad.mit.edu	36	16	46807681	46807681	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:46807681C>T	uc002eff.1	-	c.796G>A	c.(796-798)GGT>AGT	p.G266S	ABCC11_uc002efg.1_Missense_Mutation_p.G266S|ABCC11_uc002efh.1_Missense_Mutation_p.G266S	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	266	ABC transmembrane type-1 1.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|central_nervous_system(1)	4		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)												0.411232	673.231666	677.04507	227	325	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46807681	46807681	52	16	C	T	T	23	23	ABCC11	T	1	1
PKD1L2	114780	broad.mit.edu	36	16	79747996	79747996	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79747996G>A	uc002fgh.1	-	c.4094C>T	c.(4093-4095)GCG>GTG	p.A1365V	PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	1365	Helical; (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.355263	79.00924	80.409546	27	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79747996	79747996	12389	16	G	A	A	38	38	PKD1L2	A	1	1
PLCG2	5336	broad.mit.edu	36	16	80527289	80527289	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:80527289C>T	uc002fgt.1	+	c.2857C>T	c.(2857-2859)CGA>TGA	p.R953*		NM_002661	NP_002652	P16885	PLCG2_HUMAN	phospholipase C, gamma 2	953	PI-PLC Y-box.				intracellular signal transduction|phospholipid catabolic process|platelet activation	plasma membrane	phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity			large_intestine(4)|lung(2)|ovary(1)|skin(1)	8										1880				0.478261	106.2702	106.298611	33	36	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	80527289	80527289	12462	16	C	T	T	23	23	PLCG2	T	5	1
EIF4A3	9775	broad.mit.edu	36	17	75725883	75725883	+	Missense_Mutation	SNP	T	C	C			TCGA-12-3646-01	TCGA-12-3646-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75725883T>C	uc002jxs.1	-	c.880A>G	c.(880-882)ACG>GCG	p.T294A		NM_014740	NP_055555	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A,	294	Helicase C-terminal.				mRNA transport|negative regulation of translation|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|rRNA processing	catalytic step 2 spliceosome|cytoplasm|exon-exon junction complex|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|poly(A) RNA binding|protein binding			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)											0.4	8.777235	8.869693	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75725883	75725883	5217	17	T	C	C	58	58	EIF4A3	C	4	4
IMPA2	3613	broad.mit.edu	36	18	12018076	12018076	+	Silent	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:12018076C>A	uc002kqp.1	+	c.525C>A	c.(523-525)GGC>GGA	p.G175G	IMPA2_uc002kqo.1_5'UTR|IMPA2_uc002kqq.1_Silent_p.G55G	NM_014214	NP_055029	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	175					inositol phosphate dephosphorylation|signal transduction	cytoplasm	inositol-1(or 4)-monophosphatase activity|metal ion binding|protein homodimerization activity			skin(2)	2					Lithium(DB01356)									0.341176	83.445686	85.342167	29	56	CC		KEEP	---	---	---	---	capture			Silent	SNP	12018076	12018076	8024	18	C	A	A	26	26	IMPA2	A	3	3
CCDC151	115948	broad.mit.edu	36	19	11398542	11398542	+	Silent	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11398542G>A	uc002mrs.1	-	c.675C>T	c.(673-675)CAC>CAT	p.H225H	CCDC151_uc010dxz.1_Intron|CCDC151_uc002mrr.1_Silent_p.H160H	NM_145045	NP_659482	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	225	Potential.									ovary(1)	1														0.457143	45.793662	45.849867	16	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	11398542	11398542	2906	19	G	A	A	48	48	CCDC151	A	2	2
NPHS1	4868	broad.mit.edu	36	19	41009280	41009280	+	Silent	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:41009280G>A	uc002oby.2	-	c.3702C>T	c.(3700-3702)TTC>TTT	p.F1234F		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	1234	Binds to NPHS2.|Cytoplasmic (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.602941	132.581736	133.211305	41	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	41009280	41009280	10986	19	G	A	A	37	37	NPHS1	A	1	1
CASZ1	54897	broad.mit.edu	36	1	10643034	10643034	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10643034C>T	uc001aro.1	-	c.652G>A	c.(652-654)GCC>ACC	p.A218T	CASZ1_uc001arp.1_Missense_Mutation_p.A218T|CASZ1_uc001arq.1_Missense_Mutation_p.A77T|CASZ1_uc009vmx.1_Missense_Mutation_p.A242T	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	218					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding				0	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)										0.48	35.196544	35.205343	12	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10643034	10643034	2804	1	C	T	T	28	28	CASZ1	T	2	2
DCST1	149095	broad.mit.edu	36	1	153280844	153280844	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153280844G>A	uc001fgn.1	+	c.779G>A	c.(778-780)CGT>CAT	p.R260H		NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	260	Extracellular (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)											0.45098	139.440865	139.653511	46	56	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153280844	153280844	4473	1	G	A	A	40	40	DCST1	A	1	1
BAT2L2	23215	broad.mit.edu	36	1	169785956	169785956	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:169785956C>T	uc001ghs.1	+	c.5074C>T	c.(5074-5076)CGT>TGT	p.R1692C	BAT2L2_uc009wwa.1_Non-coding_Transcript	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1692	Potential.						protein C-terminus binding				0														0.1125	7.719102	19.58445	9	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169785956	169785956	1342	1	C	T	T	19	19	BAT2L2	T	1	1
LAMC2	3918	broad.mit.edu	36	1	181454198	181454198	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:181454198C>T	uc001gqa.2	+	c.455C>T	c.(454-456)GCG>GTG	p.A152V	LAMC2_uc001gpz.2_Missense_Mutation_p.A152V	NM_005562	NP_005553	Q13753	LAMC2_HUMAN	laminin, gamma 2 isoform a precursor	152	Laminin EGF-like 3.				cell adhesion|epidermis development|hemidesmosome assembly		heparin binding			ovary(1)	1														0.550459	182.793785	183.034518	60	49	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	181454198	181454198	8938	1	C	T	T	27	27	LAMC2	T	1	1
AHDC1	27245	broad.mit.edu	36	1	27746558	27746558	+	Silent	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:27746558C>A	uc009vsy.1	-	c.4656G>T	c.(4654-4656)CCG>CCT	p.P1552P	AHDC1_uc009vsz.1_Silent_p.P1552P|AHDC1_uc009vta.1_Silent_p.P1552P	NM_001029882	NP_001025053	Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1552							DNA binding			central_nervous_system(1)	1		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)										0.857143	40.30962	42.029598	12	2	CC		KEEP	---	---	---	---	capture			Silent	SNP	27746558	27746558	415	1	C	A	A	31	31	AHDC1	A	3	3
EYA3	2140	broad.mit.edu	36	1	28216331	28216331	+	Missense_Mutation	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:28216331C>A	uc001bpi.1	-	c.506G>T	c.(505-507)AGC>ATC	p.S169I	EYA3_uc001bpj.2_Missense_Mutation_p.S123I|EYA3_uc001bpk.1_Non-coding_Transcript	NM_001990	NP_001981	Q99504	EYA3_HUMAN	eyes absent 3	169					anatomical structure morphogenesis|double-strand break repair|histone dephosphorylation|multicellular organismal development|positive regulation of DNA repair|regulation of transcription, DNA-dependent|response to ionizing radiation|transcription, DNA-dependent|visual perception	cytoplasm	metal ion binding|protein binding|protein tyrosine phosphatase activity			ovary(2)	2		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)										0.11306	64.364402	140.187786	58	455	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28216331	28216331	5524	1	C	A	A	28	28	EYA3	A	3	3
ODF2L	57489	broad.mit.edu	36	1	86598800	86598800	+	Missense_Mutation	SNP	A	T	T			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:86598800A>T	uc001dln.1	-	c.1064T>A	c.(1063-1065)CTT>CAT	p.L355H	ODF2L_uc001dll.1_Missense_Mutation_p.L384H|ODF2L_uc001dlm.1_Missense_Mutation_p.L355H|ODF2L_uc001dlo.1_Missense_Mutation_p.L224H|ODF2L_uc001dlp.1_Missense_Mutation_p.L384H|ODF2L_uc001dlq.1_Missense_Mutation_p.L185H|ODF2L_uc009wcr.1_Missense_Mutation_p.L224H	NM_020729	NP_001007023	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like isoform	384	Potential.									ovary(1)	1				all cancers(265;0.0313)|Epithelial(280;0.0611)										0.483146	139.721915	139.743847	43	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86598800	86598800	11233	1	A	T	T	3	3	ODF2L	T	4	4
VSTM2L	128434	broad.mit.edu	36	20	35993477	35993477	+	Missense_Mutation	SNP	A	T	T			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:35993477A>T	uc002xhk.2	+	c.148A>T	c.(148-150)ATG>TTG	p.M50L		NM_080607	NP_542174	Q96N03	VTM2L_HUMAN	V-set and transmembrane domain containing 2	50	Ig-like.									ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.00878)												0.421648	834.869644	838.185099	261	358	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35993477	35993477	17799	20	A	T	T	8	8	VSTM2L	T	4	4
BCAS1	8537	broad.mit.edu	36	20	52025360	52025360	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:52025360G>A	uc002xws.2	-	c.1157C>T	c.(1156-1158)TCA>TTA	p.S386L	BCAS1_uc002xwt.2_Intron|BCAS1_uc010gil.1_Missense_Mutation_p.S386L|BCAS1_uc010gim.1_Intron	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	386						cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)											0.375	90.028721	91.126724	30	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52025360	52025360	1371	20	G	A	A	45	45	BCAS1	A	2	2
BIRC7	79444	broad.mit.edu	36	20	61339772	61339773	+	Missense_Mutation	DNP	GG	CC	CC			TCGA-12-3646-01	TCGA-12-3646-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:61339772_61339773GG>CC	uc002yej.1	+	c.422_423GG>CC	c.(421-423)TGG>TCC	p.W141S	BIRC7_uc002yei.1_Missense_Mutation_p.W141S|BIRC7_uc010gkc.1_Missense_Mutation_p.W141S	NM_139317	NP_647478	Q96CA5	BIRC7_HUMAN	livin inhibitor of apoptosis isoform alpha	141	BIR.				activation of JUN kinase activity|anti-apoptosis|DNA fragmentation involved in apoptotic nuclear change	cytoplasm|nucleus	enzyme binding|zinc ion binding			kidney(1)	1	all_cancers(38;2.72e-09)													0.6	9.025144	9.068736	3	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	61339772	61339773	1464	20	GG	CC	CC	47	47	BIRC7	CC	3	3
POTED	317754	broad.mit.edu	36	21	13909676	13909676	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:13909676G>A	uc002yjb.1	+	c.724G>A	c.(724-726)GCT>ACT	p.A242T		NM_174981	NP_778146	Q86YR6	POTED_HUMAN	pote protein	242	ANK 3.					plasma membrane				ovary(3)	3														0.486842	107.276588	107.287609	37	39	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13909676	13909676	12693	21	G	A	A	38	38	POTED	A	1	1
KRTAP19-5	337972	broad.mit.edu	36	21	30796114	30796114	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30796114G>A	uc002yoi.1	-	c.166C>T	c.(166-168)CGC>TGC	p.R56C		NM_181611	NP_853642	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	56						intermediate filament	protein binding				0														0.421488	313.122714	314.420344	102	140	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30796114	30796114	8847	21	G	A	A	39	39	KRTAP19-5	A	1	1
KRTAP10-12	386685	broad.mit.edu	36	21	44942164	44942164	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44942164G>A	uc002zfw.1	+	c.620G>A	c.(619-621)CGC>CAC	p.R207H	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198699	NP_941972	P60413	KR10C_HUMAN	keratin associated protein 10-12	207	19 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.5	253.211401	253.211401	87	87	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44942164	44942164	8823	21	G	A	A	38	38	KRTAP10-12	A	1	1
LCT	3938	broad.mit.edu	36	2	136278906	136278906	+	Silent	SNP	G	C	C			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:136278906G>C	uc002tuu.1	-	c.4365C>G	c.(4363-4365)CGC>CGG	p.R1455R		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1455	Extracellular (Potential).|4.|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|lung(1)|pancreas(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.169)										0.228571	59.663519	66.748559	24	81	GG		KEEP	---	---	---	---	capture			Silent	SNP	136278906	136278906	9017	2	G	C	C	46	46	LCT	C	3	3
PPIG	9360	broad.mit.edu	36	2	170173500	170173500	+	Silent	SNP	T	G	G			TCGA-12-3646-01	TCGA-12-3646-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:170173500T>G	uc002uez.1	+	c.363T>G	c.(361-363)GGT>GGG	p.G121G	PPIG_uc010fpx.1_Silent_p.G106G|PPIG_uc010fpy.1_Silent_p.G117G|PPIG_uc002ufa.2_Silent_p.G121G|PPIG_uc002ufb.1_Silent_p.G121G|PPIG_uc002ufc.1_Silent_p.G121G|PPIG_uc002ufd.1_Silent_p.G121G	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	121	PPIase cyclophilin-type.				protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)									0.424658	102.614818	102.975984	31	42	TT		KEEP	---	---	---	---	capture			Silent	SNP	170173500	170173500	12759	2	T	G	G	60	60	PPIG	G	4	4
TTC30A	92104	broad.mit.edu	36	2	178191667	178191667	+	Silent	SNP	A	C	C			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178191667A>C	uc002ulo.1	-	c.9T>G	c.(7-9)GGT>GGG	p.G3G		NM_152275	NP_689488	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	3					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)											0.235294	8.287546	9.381523	4	13	AA		KEEP	---	---	---	---	capture			Silent	SNP	178191667	178191667	17253	2	A	C	C	10	10	TTC30A	C	4	4
FZD7	8324	broad.mit.edu	36	2	202608252	202608252	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:202608252C>T	uc002uyw.1	+	c.637C>T	c.(637-639)CAG>TAG	p.Q213*		NM_003507	NP_003498	O75084	FZD7_HUMAN	frizzled 7	213	Extracellular (Potential).				axonogenesis|brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|mesenchymal to epithelial transition|negative regulation of cell-substrate adhesion|negative regulation of ectodermal cell fate specification|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of JNK cascade|positive regulation of phosphorylation|positive regulation of transcription, DNA-dependent|regulation of catenin import into nucleus|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development|Wnt receptor signaling pathway, calcium modulating pathway	apical part of cell|cytoplasm|integral to membrane|neuron projection membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			skin(2)|ovary(1)	3												OREG0015146	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.363636	9.695596	9.876092	4	7	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	202608252	202608252	6386	2	C	T	T	29	29	FZD7	T	5	2
IMPG2	50939	broad.mit.edu	36	3	102445578	102445578	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:102445578C>T	uc003duq.1	-	c.2287G>A	c.(2287-2289)GTT>ATT	p.V763I		NM_016247	NP_057331	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	763	Extracellular (Potential).				visual perception	integral to membrane|proteinaceous extracellular matrix	extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3														0.396396	796.784235	803.028931	264	402	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102445578	102445578	8030	3	C	T	T	18	18	IMPG2	T	2	2
GUCA1C	9626	broad.mit.edu	36	3	110155233	110155233	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110155233A>G	uc003dxj.1	-	c.67T>C	c.(67-69)TAC>CAC	p.Y23H	GUCA1C_uc003dxk.1_Missense_Mutation_p.Y23H	NM_005459	NP_005450	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	23	EF-hand 1.				signal transduction|visual perception		calcium ion binding|calcium sensitive guanylate cyclase activator activity				0						NSCLC(157;1360 1999 30631 40189 44208)								0.12	40.624534	72.445486	27	198	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110155233	110155233	7170	3	A	G	G	14	14	GUCA1C	G	4	4
DPPA2	151871	broad.mit.edu	36	3	110514161	110514161	+	Silent	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110514161G>A	uc003dxo.1	-	c.102C>T	c.(100-102)GAC>GAT	p.D34D	DPPA2_uc003dxp.1_Silent_p.D34D	NM_138815	NP_620170	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	34						nucleus	nucleic acid binding			ovary(2)	2														0.485876	274.048454	274.078811	86	91	GG		KEEP	---	---	---	---	capture			Silent	SNP	110514161	110514161	4918	3	G	A	A	40	40	DPPA2	A	1	1
NIPAL1	152519	broad.mit.edu	36	4	47732751	47732751	+	Silent	SNP	T	C	C			TCGA-12-3646-01	TCGA-12-3646-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:47732751T>C	uc003gxw.1	+	c.1038T>C	c.(1036-1038)ACT>ACC	p.T346T		NM_207330	NP_997213	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	346	Helical; (Potential).					integral to membrane					0														0.5	81.601948	81.601948	24	24	TT		KEEP	---	---	---	---	capture			Silent	SNP	47732751	47732751	10825	4	T	C	C	53	53	NIPAL1	C	4	4
GRID2	2895	broad.mit.edu	36	4	94912268	94912269	+	Nonsense_Mutation	DNP	CT	TA	TA			TCGA-12-3646-01	TCGA-12-3646-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94912268_94912269CT>TA	uc003hsz.2	+	c.2620_2621CT>TA	c.(2620-2622)CTG>TAG	p.L874*	GRID2_uc010iky.1_Nonsense_Mutation_p.L779*	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	874	Cytoplasmic (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|large_intestine(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)									0.567416	333.403562	334.112108	101	77	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	DNP	94912268	94912269	7050	4	CT	TA	TA	24	24	GRID2	TA	5	2
OR2Y1	134083	broad.mit.edu	36	5	180098826	180098826	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:180098826A>G	uc003mmf.1	-	c.839T>C	c.(838-840)ATT>ACT	p.I280T		NM_001001657	NP_001001657	Q8NGV0	OR2Y1_HUMAN	olfactory receptor, family 2, subfamily Y,	280	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(89;1.25e-05)|all_epithelial(37;4.36e-06)|Renal(175;0.000159)|Lung NSC(126;0.00317)|all_lung(126;0.0041)|Breast(19;0.114)	all_cancers(40;0.0834)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.484277	496.429482	496.497837	154	164	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	180098826	180098826	11441	5	A	G	G	4	4	OR2Y1	G	4	4
C7	730	broad.mit.edu	36	5	41017425	41017425	+	Missense_Mutation	SNP	C	G	G			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:41017425C>G	uc003jmh.1	+	c.2525C>G	c.(2524-2526)ACC>AGC	p.T842S		NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	842	Complement control factor I module 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)												0.464286	89.646711	89.70876	26	30	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41017425	41017425	2482	5	C	G	G	18	18	C7	G	3	3
SYNE1	23345	broad.mit.edu	36	6	152902826	152902826	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152902826G>A	uc010kiw.1	-	c.91C>T	c.(91-93)CGA>TGA	p.R31*	SYNE1_uc003qot.2_Nonsense_Mutation_p.R31*|SYNE1_uc003qou.2_Nonsense_Mutation_p.R31*|SYNE1_uc010kjb.1_Nonsense_Mutation_p.R31*|SYNE1_uc003qpa.1_Nonsense_Mutation_p.R31*	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	31	Actin-binding.|Cytoplasmic (Potential).|CH 1.				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.513514	181.571347	181.588803	57	54	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	152902826	152902826	15966	6	G	A	A	40	40	SYNE1	A	5	1
PRSS16	10279	broad.mit.edu	36	6	27328591	27328591	+	Missense_Mutation	SNP	A	T	T			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27328591A>T	uc003nja.1	+	c.1034A>T	c.(1033-1035)AAG>ATG	p.K345M	PRSS16_uc003njb.1_Missense_Mutation_p.K88M|PRSS16_uc010jqq.1_Missense_Mutation_p.K122M|PRSS16_uc010jqr.1_Missense_Mutation_p.K96M|PRSS16_uc003njc.1_Non-coding_Transcript|PRSS16_uc003njd.1_Intron	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16	345					protein catabolic process|proteolysis	cytoplasmic membrane-bounded vesicle	serine-type peptidase activity			ovary(2)|central_nervous_system(2)	4						NSCLC(178;1118 2105 17078 23587 44429)								0.305085	98.254696	102.254676	36	82	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27328591	27328591	13066	6	A	T	T	3	3	PRSS16	T	4	4
DHX16	8449	broad.mit.edu	36	6	30748588	30748588	+	Missense_Mutation	SNP	G	T	T			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:30748588G>T	uc003nqz.1	-	c.10C>A	c.(10-12)CCG>ACG	p.P4T		NM_003587	NP_003578	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	4					mRNA processing|RNA splicing	nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(2)|kidney(2)	4														0.2	13.432589	15.944036	6	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30748588	30748588	4681	6	G	T	T	42	42	DHX16	T	3	3
TSGA13	114960	broad.mit.edu	36	7	130016349	130016349	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:130016349C>T	uc003vqi.1	-	c.149G>A	c.(148-150)CGG>CAG	p.R50Q	TSGA13_uc003vqj.1_Missense_Mutation_p.R50Q	NM_052933	NP_443165	Q96PP4	TSG13_HUMAN	testis specific, 13	50										ovary(2)	2	Melanoma(18;0.0435)													0.202381	82.363821	96.179816	34	134	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130016349	130016349	17170	7	C	T	T	23	23	TSGA13	T	1	1
GIMAP7	168537	broad.mit.edu	36	7	149848641	149848641	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149848641C>T	uc003whk.1	+	c.646C>T	c.(646-648)CGG>TGG	p.R216W	GIMAP7_uc010lpt.1_Missense_Mutation_p.R216W	NM_153236	NP_694968	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	216							GTP binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)										0.267782	166.706298	178.335719	64	175	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149848641	149848641	6652	7	C	T	T	19	19	GIMAP7	T	1	1
CALCR	799	broad.mit.edu	36	7	92903277	92903277	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:92903277C>T	uc003umv.1	-	c.1174G>A	c.(1174-1176)GTC>ATC	p.V392I	CALCR_uc003ums.1_Non-coding_Transcript|CALCR_uc003umt.1_Non-coding_Transcript|CALCR_uc003umu.1_Missense_Mutation_p.V358I|CALCR_uc003umw.2_Missense_Mutation_p.V358I	NM_001742	NP_001733	P30988	CALCR_HUMAN	calcitonin receptor	374	Helical; Name=6; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|elevation of cytosolic calcium ion concentration|positive regulation of adenylate cyclase activity|response to glucocorticoid stimulus	integral to plasma membrane	calcitonin binding|calcitonin binding|calcitonin receptor activity|calcitonin receptor activity|protein binding			ovary(3)|lung(1)|pancreas(1)	5	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Salmon Calcitonin(DB00017)									0.242187	77.361739	85.120692	31	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	92903277	92903277	2695	7	C	T	T	19	19	CALCR	T	1	1
ZNF655	79027	broad.mit.edu	36	7	99009120	99009120	+	Missense_Mutation	SNP	A	G	G			TCGA-12-3646-01	TCGA-12-3646-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99009120A>G	uc010lga.1	+	c.1558A>G	c.(1558-1560)ATT>GTT	p.I520V	ZNF655_uc003urh.1_Missense_Mutation_p.I485V|ZNF655_uc010lgc.1_Missense_Mutation_p.I520V|ZNF655_uc003urj.1_Missense_Mutation_p.I485V|ZNF655_uc003urk.1_Missense_Mutation_p.I322V|ZNF655_uc010lgd.1_Missense_Mutation_p.I322V	NM_001083956	NP_001077425	Q8N720	ZN655_HUMAN	zinc finger protein 655 isoform f	485					G1 phase|regulation of mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)													0.173469	67.402575	87.187238	34	162	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99009120	99009120	18663	7	A	G	G	8	8	ZNF655	G	4	4
FER1L6	654463	broad.mit.edu	36	8	125116711	125116711	+	Nonsense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:125116711C>T	uc003yqw.1	+	c.2299C>T	c.(2299-2301)CGA>TGA	p.R767*		NM_001039112	NP_001034201	Q2WGJ9	FR1L6_HUMAN	fer-1-like 6	767	Cytoplasmic (Potential).					integral to membrane				ovary(5)|central_nervous_system(1)|skin(1)	7	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)											0.442396	300.275068	300.901421	96	121	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	125116711	125116711	6052	8	C	T	T	19	19	FER1L6	T	5	1
GML	2765	broad.mit.edu	36	8	143925075	143925075	+	Silent	SNP	T	C	C			TCGA-12-3646-01	TCGA-12-3646-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143925075T>C	uc003yxg.1	+	c.444T>C	c.(442-444)TTT>TTC	p.F148F		NM_002066	NP_002057	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule	148					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|negative regulation of cell proliferation	anchored to membrane|extrinsic to membrane|plasma membrane				central_nervous_system(2)	2	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)													0.395833	117.629612	118.541231	38	58	TT		KEEP	---	---	---	---	capture			Silent	SNP	143925075	143925075	6761	8	T	C	C	63	63	GML	C	4	4
PRKDC	5591	broad.mit.edu	36	8	49028770	49028770	+	Silent	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:49028770G>A	uc003xqi.1	-	c.684C>T	c.(682-684)TCC>TCT	p.S228S	PRKDC_uc003xqj.1_Silent_p.S228S	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	228					cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				Esophageal Squamous(79;1091 1253 12329 31680 40677)				1566				0.136986	34.160955	52.874562	20	126	GG		KEEP	---	---	---	---	capture			Silent	SNP	49028770	49028770	12964	8	G	A	A	35	35	PRKDC	A	2	2
RB1CC1	9821	broad.mit.edu	36	8	53733155	53733155	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:53733155C>T	uc003xre.2	-	c.1876G>A	c.(1876-1878)GAT>AAT	p.D626N	RB1CC1_uc003xrf.2_Missense_Mutation_p.D626N	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	626					autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|large_intestine(1)	9		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GBM(180;1701 2102 13475 42023 52570)								0.522989	291.328788	291.408967	91	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53733155	53733155	13560	8	C	T	T	30	30	RB1CC1	T	2	2
DBH	1621	broad.mit.edu	36	9	135491477	135491477	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135491477C>T	uc004cel.1	+	c.163C>T	c.(163-165)CCG>TCG	p.P55S		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta-hydroxylase precursor	55	Intragranular (Potential).				hormone biosynthetic process|oxidation-reduction process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)									0.315789	17.843255	18.416657	6	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	135491477	135491477	4421	9	C	T	T	22	22	DBH	T	2	2
LINGO2	158038	broad.mit.edu	36	9	27939327	27939327	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:27939327C>T	uc003zqu.1	-	c.1343G>A	c.(1342-1344)CGA>CAA	p.R448Q	LINGO2_uc010mjf.1_Missense_Mutation_p.R448Q|LINGO2_uc003zqv.1_Missense_Mutation_p.R448Q|LINGO2_uc010mjg.1_Missense_Mutation_p.R448Q	NM_152570	NP_689783	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	448	Ig-like C2-type.|Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)	2	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)										0.419643	139.502277	140.133892	47	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27939327	27939327	9142	9	C	T	T	31	31	LINGO2	T	1	1
GLDC	2731	broad.mit.edu	36	9	6544673	6544673	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:6544673C>T	uc003zkc.1	-	c.2311G>A	c.(2311-2313)GGA>AGA	p.G771R		NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	771					glycine catabolic process|oxidation-reduction process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)									0.466667	92.4966	92.554428	28	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6544673	6544673	6701	9	C	T	T	23	23	GLDC	T	1	1
TCEAL4	79921	broad.mit.edu	36	X	102728302	102728302	+	Missense_Mutation	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:102728302C>A	uc004ekl.1	+	c.43C>A	c.(43-45)CAA>AAA	p.Q15K	TCEAL4_uc004ekn.1_Missense_Mutation_p.Q15K|TCEAL4_uc004ekm.1_Missense_Mutation_p.Q15K|TCEAL4_uc004eko.1_Missense_Mutation_p.Q15K	NM_024863	NP_079139	Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	15	Glu-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0														0.324742	172.948975	178.241953	63	131	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102728302	102728302	16199	23	C	A	A	21	21	TCEAL4	A	3	3
MSL3	10943	broad.mit.edu	36	X	11700214	11700214	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:11700214G>A	uc004cuw.1	+	c.1300G>A	c.(1300-1302)GTG>ATG	p.V434M	MSL3_uc004cux.1_Missense_Mutation_p.V375M|MSL3_uc004cuy.1_Missense_Mutation_p.V268M	NM_078629	NP_006791	Q8N5Y2	MS3L1_HUMAN	male-specific lethal 3-like 1 isoform a	434					chromatin assembly or disassembly|histone H4-K16 acetylation|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|MSL complex	chromatin binding|DNA binding|methylated histone residue binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1														0.907216	295.065903	311.263316	88	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11700214	11700214	10272	23	G	A	A	48	48	MSL3	A	2	2
DOCK11	139818	broad.mit.edu	36	X	117703707	117703707	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117703707C>T	uc004eqp.2	+	c.6131C>T	c.(6130-6132)CCC>CTC	p.P2044L	DOCK11_uc004eqq.2_Missense_Mutation_p.P1823L	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	2044					blood coagulation	cytosol	GTP binding			ovary(3)	3														0.401709	290.705374	292.681425	94	140	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117703707	117703707	4870	23	C	T	T	22	22	DOCK11	T	2	2
ATP1B4	23439	broad.mit.edu	36	X	119384655	119384655	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:119384655G>A	uc004esr.1	+	c.311G>A	c.(310-312)CGA>CAA	p.R104Q	ATP1B4_uc004esq.1_Missense_Mutation_p.R104Q	NM_012069	NP_036201	Q9UN42	AT1B4_HUMAN	ATPase, (Na+)/K+ transporting, beta 4	104	Nuclear (Potential).				ATP biosynthetic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to plasma membrane|nuclear inner membrane	sodium:potassium-exchanging ATPase activity			ovary(1)|skin(1)	2														0.380645	174.885123	176.822813	59	96	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119384655	119384655	1154	23	G	A	A	37	37	ATP1B4	A	1	1
STAG2	10735	broad.mit.edu	36	X	122992582	122992582	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:122992582G>A	uc004eua.1	+	c.214G>A	c.(214-216)GGT>AGT	p.G72S	STAG2_uc004etz.2_Missense_Mutation_p.G72S|STAG2_uc004eub.1_Missense_Mutation_p.G72S|STAG2_uc004euc.1_Missense_Mutation_p.G72S|STAG2_uc004eud.1_Missense_Mutation_p.G72S|STAG2_uc004eue.1_Missense_Mutation_p.G72S	NM_001042749	NP_001036215	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform a	72					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5														0.360434	383.159684	389.492372	133	236	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122992582	122992582	15761	23	G	A	A	47	47	STAG2	A	2	2
OPN1LW	5956	broad.mit.edu	36	X	153075093	153075093	+	Missense_Mutation	SNP	C	T	T			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153075093C>T	uc004fjz.2	+	c.875C>T	c.(874-876)GCT>GTT	p.A292V		NM_020061	NP_064445	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	292	Helical; Name=6; (Potential).				phototransduction|protein-chromophore linkage|visual perception	integral to plasma membrane	G-protein coupled receptor activity|photoreceptor activity				0	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.59847	1020.626299	1025.035904	313	210	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153075093	153075093	11283	23	C	T	T	28	28	OPN1LW	T	2	2
BMX	660	broad.mit.edu	36	X	15484130	15484130	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:15484130G>A	uc004cww.1	+	c.1967G>A	c.(1966-1968)CGT>CAT	p.R656H	BMX_uc004cwx.2_Missense_Mutation_p.R656H|BMX_uc004cwy.2_Missense_Mutation_p.R656H	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	656	Protein kinase.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development|protein phosphorylation	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)									167				0.402381	521.144892	524.625821	169	251	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15484130	15484130	1498	23	G	A	A	40	40	BMX	A	1	1
MAGEB6	158809	broad.mit.edu	36	X	26123016	26123016	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:26123016G>A	uc004dbr.1	+	c.1132G>A	c.(1132-1134)GAC>AAC	p.D378N	MAGEB6_uc010ngc.1_Missense_Mutation_p.D158N|MAGEB6_uc010ngd.1_Missense_Mutation_p.D378N	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	378	MAGE.									ovary(3)	3														0.348548	243.55954	248.42325	84	157	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26123016	26123016	9560	23	G	A	A	37	37	MAGEB6	A	1	1
ARSF	416	broad.mit.edu	36	X	3031930	3031930	+	Silent	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:3031930C>A	uc004cre.1	+	c.1230C>A	c.(1228-1230)GTC>GTA	p.V410V	ARSF_uc004crf.1_Silent_p.V410V	NM_004042	NP_004033	P54793	ARSF_HUMAN	arylsulfatase F precursor	410						extracellular region	arylsulfatase activity|metal ion binding			ovary(2)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)												0.536913	261.908023	262.084662	80	69	CC		KEEP	---	---	---	---	capture			Silent	SNP	3031930	3031930	1009	23	C	A	A	31	31	ARSF	A	3	3
CXorf22	170063	broad.mit.edu	36	X	35895717	35895717	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:35895717G>A	uc004ddj.1	+	c.1661G>A	c.(1660-1662)CGC>CAC	p.R554H	CXorf22_uc010ngv.1_Non-coding_Transcript	NM_152632	NP_689845	Q6ZTR5	CX022_HUMAN	hypothetical protein LOC170063	554										large_intestine(1)|lung(1)|ovary(1)	3														0.520202	326.034642	326.105616	103	95	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35895717	35895717	4262	23	G	A	A	38	38	CXorf22	A	1	1
CFP	5199	broad.mit.edu	36	X	47371919	47371919	+	Missense_Mutation	SNP	G	A	A			TCGA-12-3646-01	TCGA-12-3646-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47371919G>A	uc004dig.2	-	c.469C>T	c.(469-471)CGG>TGG	p.R157W	CFP_uc004dih.1_Missense_Mutation_p.R157W|CFP_uc004dii.1_Missense_Mutation_p.R93W|CFP_uc010nhu.1_Missense_Mutation_p.R157W	NM_002621	NP_002612	P27918	PROP_HUMAN	complement factor properdin precursor	157	TSP type-1 2.				complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3														0.521739	36.900972	36.91049	12	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47371919	47371919	3426	23	G	A	A	39	39	CFP	A	1	1
NONO	4841	broad.mit.edu	36	X	70433174	70433174	+	Missense_Mutation	SNP	C	A	A			TCGA-12-3646-01	TCGA-12-3646-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70433174C>A	uc004dzn.1	+	c.685C>A	c.(685-687)CAG>AAG	p.Q229K	NONO_uc004dzo.1_Missense_Mutation_p.Q229K|NONO_uc004dzp.1_Missense_Mutation_p.Q229K|NONO_uc004dzq.1_Missense_Mutation_p.Q98K	NM_007363	NP_031389	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	229	RRM 2.|DBHS.				DNA recombination|DNA repair|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nuclear matrix|paraspeckles	DNA binding|identical protein binding|nucleotide binding|RNA binding		NONO/TFE3(2)	ovary(2)|kidney(2)	4	Renal(35;0.156)									130				0.36	27.194271	27.614417	9	16	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70433174	70433174	10937	23	C	A	A	21	21	NONO	A	3	3
MYO9B	4650	broad.mit.edu	36	19	17166946	17166946	+	Frame_Shift_Del	DEL	C	-	-			TCGA-12-3646-01	TCGA-12-3646-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:17166946_17166946delC	uc010eak.1	+	c.3710_3710delC	c.(3709-3711)ACGfs	p.T1237fs	MYO9B_uc002nfi.1_Frame_Shift_Del_p.T1237fs|MYO9B_uc002nfj.1_Frame_Shift_Del_p.T1237fs|MYO9B_uc002nfk.1_Frame_Shift_Del_p.T1237fs|MYO9B_uc002nfl.1_5'Flank	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	1237	Tail.				actin filament-based movement|Rho protein signal transduction	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1														0.62			8	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	17166946	17166946	10480	19	C	-	-	19	19	MYO9B	-	5	5
C19orf35	374872	broad.mit.edu	36	19	2231897	2231898	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-3646-01	TCGA-12-3646-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:2231897_2231898insG	uc002lvn.1	-	c.33_34insC	c.(31-36)CCCGAGfs	p.P11fs	SPPL2B_uc010dsw.1_Intron	NM_198532	NP_940934	Q6ZS72	CS035_HUMAN	hypothetical protein LOC374872	11_12										pancreas(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	2231897	2231898	1983	19	-	G	G	31	31	C19orf35	G	5	5
