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
AKR1C4	1109	broad.mit.edu	36	10	5228864	5228864	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:5228864G>A	uc001ihw.1	+	c.34G>A	c.(34-36)GAT>AAT	p.D12N		NM_001818	NP_001809	P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	12					androgen metabolic process|bile acid biosynthetic process|oxidation-reduction process	cytosol	aldo-keto reductase (NADP) activity|androsterone dehydrogenase (B-specific) activity|bile acid transmembrane transporter activity|chlordecone reductase activity|electron carrier activity			ovary(1)	1					NADH(DB00157)									0.116279	15.223771	33.927342	15	114	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5228864	5228864	475	10	G	A	A	45	45	AKR1C4	A	2	2
OPN4	94233	broad.mit.edu	36	10	88409035	88409035	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:88409035C>T	uc001kdp.1	+	c.663C>T	c.(661-663)AGC>AGT	p.S221S	OPN4_uc001kdq.1_Silent_p.S210S|OPN4_uc009xsx.1_5'Flank	NM_001030015	NP_001025186	Q9UHM6	OPN4_HUMAN	opsin 4 isoform 2	210	Extracellular (Potential).				phototransduction|protein-chromophore linkage|regulation of circadian rhythm|rhythmic process|visual perception	integral to membrane|plasma membrane	11-cis retinal binding|G-protein coupled photoreceptor activity			ovary(1)	1														0.65	114.431043	115.620104	39	21	CC		KEEP	---	---	---	---	capture			Silent	SNP	88409035	88409035	11288	10	C	T	T	27	27	OPN4	T	1	1
CYP2C9	1559	broad.mit.edu	36	10	96738625	96738625	+	Silent	SNP	C	T	T	rs2017319	by-cluster,by-frequency	TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:96738625C>T	uc001kka.2	+	c.1323C>T	c.(1321-1323)GCC>GCT	p.A441A	CYP2C9_uc009xut.1_Silent_p.A439A	NM_000771	NP_000762	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C,	441					exogenous drug catabolic process|monocarboxylic acid metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid metabolic process|urea metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	(S)-limonene 6-monooxygenase activity|(S)-limonene 7-monooxygenase activity|4-hydroxyacetophenone monooxygenase activity|caffeine oxidase activity|drug binding|electron carrier activity|heme binding|oxygen binding|steroid hydroxylase activity			ovary(2)	2		Colorectal(252;0.0902)			Acenocoumarol(DB01418)|Alosetron(DB00969)|Amiodarone(DB01118)|Antihemophilic Factor(DB00025)|Aprepitant(DB00673)|Bosentan(DB00559)|Carprofen(DB00821)|Carvedilol(DB01136)|Celecoxib(DB00482)|Clomipramine(DB01242)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Desogestrel(DB00304)|Diclofenac(DB00586)|Esomeprazole(DB00736)|Etodolac(DB00749)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Glibenclamide(DB01016)|Glimepiride(DB00222)|Glipizide(DB01067)|Guanfacine(DB01018)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Imipramine(DB00458)|Irbesartan(DB01029)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Losartan(DB00678)|Lumiracoxib(DB01283)|Marinol(DB00470)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mephenytoin(DB00532)|Metronidazole(DB00916)|Miconazole(DB01110)|Midazolam(DB00683)|Montelukast(DB00471)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Oxymorphone(DB01192)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pravastatin(DB00175)|Quinidine(DB00908)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Sertraline(DB01104)|Sildenafil(DB00203)|Sulfamethoxazole(DB01015)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tenoxicam(DB00469)|Terfenadine(DB00342)|Tolbutamide(DB01124)|Torasemide(DB00214)|Troleandomycin(DB01361)|Valdecoxib(DB00580)|Valsartan(DB00177)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)	Ovarian(54;1266 1406 16072 35076)								0.726619	349.029977	355.461811	101	38	CC		KEEP	---	---	---	---	capture		all cancers(201;6.93e-05)	Silent	SNP	96738625	96738625	4333	10	C	T	T	23	23	CYP2C9	T	1	1
HTR3A	3359	broad.mit.edu	36	11	113359106	113359106	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113359106C>T	uc001pon.1	+	c.429C>T	c.(427-429)GGC>GGT	p.G143G	HTR3A_uc001pom.1_Silent_p.G143G|HTR3A_uc009yyx.1_Non-coding_Transcript	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	143	Extracellular (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)			Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)									0.304348	159.048786	166.11841	63	144	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Silent	SNP	113359106	113359106	7744	11	C	T	T	27	27	HTR3A	T	1	1
ABTB2	25841	broad.mit.edu	36	11	34182751	34182751	+	Missense_Mutation	SNP	G	C	C			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:34182751G>C	uc001mvl.1	-	c.388C>G	c.(388-390)CGA>GGA	p.R130G		NM_145804	NP_665803	A8K6S9	A8K6S9_HUMAN	ankyrin repeat and BTB (POZ) domain containing	130							DNA binding			central_nervous_system(1)	1		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)												0.428571	8.69614	8.764682	6	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34182751	34182751	104	11	G	C	C	38	38	ABTB2	C	3	3
ULK1	8408	broad.mit.edu	36	12	130945582	130945582	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130945582C>T	uc001uje.1	+	c.83C>T	c.(82-84)GCG>GTG	p.A28V		NM_003565	NP_003556	O75385	ULK1_HUMAN	unc-51-like kinase 1	28	Protein kinase.|ATP (By similarity).				autophagy|protein localization|regulation of autophagy	autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	ATP binding|protein complex binding|protein serine/threonine kinase activity			ovary(1)|lung(1)|central_nervous_system(1)	3	all_neural(191;0.0982)|Medulloblastoma(191;0.163)									916				0.466667	21.124318	21.138738	7	8	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)	Missense_Mutation	SNP	130945582	130945582	17533	12	C	T	T	27	27	ULK1	T	1	1
CPNE8	144402	broad.mit.edu	36	12	37442218	37442218	+	Missense_Mutation	SNP	T	A	A			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:37442218T>A	uc001rls.1	-	c.643A>T	c.(643-645)ATC>TTC	p.I215F		NM_153634	NP_705898	Q86YQ8	CPNE8_HUMAN	copine VIII	215	C2 2.									pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)												0.371429	121.900681	123.424642	39	66	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37442218	37442218	3956	12	T	A	A	50	50	CPNE8	A	4	4
KIF21A	55605	broad.mit.edu	36	12	38012455	38012455	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:38012455C>A	uc001rly.1	-	c.2879G>T	c.(2878-2880)AGA>ATA	p.R960I	KIF21A_uc001rlv.1_5'UTR|KIF21A_uc001rlw.1_Missense_Mutation_p.R277I|KIF21A_uc001rlx.1_Missense_Mutation_p.R947I|KIF21A_uc001rlz.1_Missense_Mutation_p.R924I	NM_017641	NP_060111	Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	960	Potential.				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(4)|lung(1)|pancreas(1)	6		Lung NSC(34;0.179)|all_lung(34;0.213)												0.402332	388.458492	391.32559	138	205	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38012455	38012455	8599	12	C	A	A	32	32	KIF21A	A	3	3
GRIP1	23426	broad.mit.edu	36	12	65124733	65124733	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:65124733C>T	uc001stk.1	-	c.1429G>A	c.(1429-1431)GGA>AGA	p.G477R	GRIP1_uc001stj.1_Missense_Mutation_p.G259R|GRIP1_uc001stl.1_Missense_Mutation_p.G369R|GRIP1_uc001stm.1_Missense_Mutation_p.G477R	NM_021150	NP_066973	Q9Y3R0	GRIP1_HUMAN	glutamate receptor interacting protein 1	529	PDZ 4.				androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission	cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane	androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity			ovary(2)	2														0.435065	190.69145	191.25936	67	87	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)	Missense_Mutation	SNP	65124733	65124733	7066	12	C	T	T	21	21	GRIP1	T	2	2
KLHL1	57626	broad.mit.edu	36	13	69212592	69212592	+	Silent	SNP	T	C	C			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:69212592T>C	uc001vip.1	-	c.1737A>G	c.(1735-1737)CAA>CAG	p.Q579Q		NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	579	Kelch 3.				actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)												0.409524	132.631413	133.374108	43	62	TT		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)	Silent	SNP	69212592	69212592	8677	13	T	C	C	52	52	KLHL1	C	4	4
CLEC14A	161198	broad.mit.edu	36	14	37793583	37793583	+	Missense_Mutation	SNP	C	A	A			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:37793583C>A	uc001wum.1	-	c.1396G>T	c.(1396-1398)GTC>TTC	p.V466F		NM_175060	NP_778230	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	466	Cytoplasmic (Potential).					integral to membrane	sugar binding			ovary(3)	3	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)													0.686869	221.127734	224.201518	68	31	CC		KEEP	---	---	---	---	capture	Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)	Missense_Mutation	SNP	37793583	37793583	3636	14	C	A	A	20	20	CLEC14A	A	3	3
BLM	641	broad.mit.edu	36	15	89091634	89091634	+	Missense_Mutation	SNP	C	G	G			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:89091634C>G	uc002bpr.1	+	c.8C>G	c.(7-9)GCT>GGT	p.A3G	BLM_uc010bnx.1_Missense_Mutation_p.A3G	NM_000057	NP_000048	P54132	BLM_HUMAN	Bloom syndrome protein	3					double-strand break repair via homologous recombination|G2 phase of mitotic cell cycle|G2/M transition DNA damage checkpoint|negative regulation of cell division|positive regulation of transcription, DNA-dependent|protein oligomerization|regulation of cyclin-dependent protein kinase activity|replication fork processing|replication fork protection|response to X-ray	cytoplasm|lateral element|nuclear matrix|nucleolus|PML body	ATP binding|bubble DNA binding|DNA strand annealing activity|four-way junction helicase activity|G-quadruplex DNA binding|p53 binding			ovary(3)	3	Lung NSC(78;0.0875)|all_lung(78;0.109)								p.A3G(COLO205-Tumor)|p.A3G(DM3-Tumor)|p.A3G(T84-Tumor)|p.A3G(HCC2279-Tumor)|p.A3G(HEC6-Tumor)	462				0.25	6.96206	8.107904	5	15	CC		KEEP	---	---	---	---	capture	Lung(145;0.189)		Missense_Mutation	SNP	89091634	89091634	1470	15	C	G	G	28	28	BLM	G	3	3
SLCO3A1	28232	broad.mit.edu	36	15	90260511	90260511	+	Silent	SNP	G	C	C			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:90260511G>C	uc002bqx.1	+	c.465G>C	c.(463-465)TCG>TCC	p.S155S	SLCO3A1_uc002bqy.1_Silent_p.S155S|SLCO3A1_uc010boc.1_Non-coding_Transcript|SLCO3A1_uc002bqz.1_Silent_p.S97S	NM_013272	NP_037404	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family,	155	Extracellular (Potential).				sodium-independent organic anion transport	integral to membrane|plasma membrane	sodium-independent organic anion transmembrane transporter activity				0	Lung NSC(78;0.0158)|all_lung(78;0.0255)													0.6	9.425626	9.469276	3	2	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.0841)		Silent	SNP	90260511	90260511	15225	15	G	C	C	39	39	SLCO3A1	C	3	3
CDKN2D	1032	broad.mit.edu	36	19	10539076	10539076	+	Silent	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10539076G>A	uc002mpa.1	-	c.159C>T	c.(157-159)AGC>AGT	p.S53S	KRI1_uc002mox.1_5'Flank|KRI1_uc002moy.1_5'Flank|CDKN2D_uc002mpb.1_Silent_p.S53S	NM_001800	NP_524145	P55273	CDN2D_HUMAN	cyclin-dependent kinase inhibitor 2D	53	ANK 1.				anti-apoptosis|autophagic cell death|cell cycle arrest|DNA synthesis involved in DNA repair|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|negative regulation of caspase activity|negative regulation of cell growth|negative regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity|response to retinoic acid|response to UV|response to vitamin D	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|protein kinase binding				0										14				0.244792	109.228443	120.623038	47	145	GG		KEEP	---	---	---	---	capture	Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)		Silent	SNP	10539076	10539076	3295	19	G	A	A	46	46	CDKN2D	A	2	2
CCDC159	126075	broad.mit.edu	36	19	11325210	11325210	+	Missense_Mutation	SNP	C	G	G			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11325210C>G	uc002mrd.1	+	c.882C>G	c.(880-882)TGC>TGG	p.C294W	LPPR2_uc002mre.1_5'Flank|LPPR2_uc002mrf.1_5'Flank	NM_001080503	NP_001073972	P0C7I6	CC159_HUMAN	coiled-coil domain-containing-like	332										ovary(1)	1														0.428571	7.865718	7.941912	6	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11325210	11325210	2913	19	C	G	G	28	28	CCDC159	G	3	3
CYP4F11	57834	broad.mit.edu	36	19	15886181	15886181	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15886181C>T	uc002nbu.2	-	c.1331G>A	c.(1330-1332)CGT>CAT	p.R444H	CYP4F11_uc010eab.1_Silent_p.P422P|CYP4F11_uc002nbt.2_Missense_Mutation_p.R444H	NM_001128932	NP_001122404	Q9HBI6	CP4FB_HUMAN	cytochrome P450 family 4 subfamily F polypeptide	444					inflammatory response|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)	1														0.458515	319.65743	319.999243	105	124	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15886181	15886181	4351	19	C	T	T	19	19	CYP4F11	T	1	1
NCCRP1	342897	broad.mit.edu	36	19	44381722	44381722	+	Missense_Mutation	SNP	A	C	C			TCGA-32-2615-01	TCGA-32-2615-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44381722A>C	uc002okq.1	+	c.525A>C	c.(523-525)CAA>CAC	p.Q175H		NM_001001414	NP_001001414	Q6ZVX7	NCRP1_HUMAN	non-specific cytotoxic cell receptor protein 1	175	FBA.				protein catabolic process					ovary(1)	1						Melanoma(107;1207 1556 14956 29427 52130)								0.244444	9.121662	11.991938	11	34	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44381722	44381722	10612	19	A	C	C	2	2	NCCRP1	C	4	4
CRX	1406	broad.mit.edu	36	19	53034727	53034727	+	Silent	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:53034727G>A	uc002phq.2	+	c.591G>A	c.(589-591)CCG>CCA	p.P197P		NM_000554	NP_000545	O43186	CRX_HUMAN	cone-rod homeobox protein	197					organ morphogenesis|response to stimulus|visual perception		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.P197P(1)		breast(1)|central_nervous_system(1)	2		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)				Pancreas(57;461 1196 22201 40716 47188)								0.4375	188.828215	189.311056	63	81	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)	Silent	SNP	53034727	53034727	4041	19	G	A	A	39	39	CRX	A	1	1
C1orf161	126868	broad.mit.edu	36	1	116468419	116468419	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:116468419C>T	uc001egc.1	+	c.399C>T	c.(397-399)ATC>ATT	p.I133I		NM_152367	NP_689580	Q8N8X9	MB213_HUMAN	hypothetical protein LOC126868	133											0	Lung SC(450;0.184)	all_cancers(81;0.00142)|all_lung(203;0.000139)|all_epithelial(167;0.000401)|Lung NSC(69;0.000705)												0.546667	128.3807	128.523049	41	34	CC		KEEP	---	---	---	---	capture		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)	Silent	SNP	116468419	116468419	2076	1	C	T	T	31	31	C1orf161	T	1	1
LEFTY1	10637	broad.mit.edu	36	1	224141933	224141933	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:224141933T>C	uc001hpo.1	-	c.526A>G	c.(526-528)AAG>GAG	p.K176E	LEFTY1_uc009xej.1_3'UTR	NM_020997	NP_066277	O75610	LFTY1_HUMAN	left-right determination, factor B	176					cell growth|multicellular organismal development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity|transforming growth factor beta receptor binding				0	Breast(184;0.197)													0.266667	7.789903	8.530696	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	224141933	224141933	9039	1	T	C	C	62	62	LEFTY1	C	4	4
R3HDML	140902	broad.mit.edu	36	20	42412716	42412716	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:42412716G>A	uc002xls.1	+	c.632G>A	c.(631-633)GGC>GAC	p.G211D		NM_178491	NP_848586	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	211						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.028)												0.407407	97.3633	97.968782	33	48	GG		KEEP	---	---	---	---	capture	COAD - Colon adenocarcinoma(18;0.00189)		Missense_Mutation	SNP	42412716	42412716	13348	20	G	A	A	42	42	R3HDML	A	2	2
SMCR7L	54471	broad.mit.edu	36	22	38239698	38239698	+	Silent	SNP	C	G	G			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38239698C>G	uc003axw.2	+	c.816C>G	c.(814-816)GGC>GGG	p.G272G	SMCR7L_uc010gxz.1_Silent_p.G94G|SMCR7L_uc003axx.1_Silent_p.G272G|SMCR7L_uc003axy.1_Silent_p.G94G	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	272						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.304348	9.531556	10.374201	7	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	38239698	38239698	15289	22	C	G	G	28	28	SMCR7L	G	3	3
MPPED1	758	broad.mit.edu	36	22	42161069	42161069	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:42161069C>T	uc003bdw.1	+	c.396C>T	c.(394-396)AAC>AAT	p.N132N		NM_001044370	NP_001037835	O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	132							hydrolase activity				0		all_neural(38;0.0244)|Ovarian(80;0.0694)												0.62963	54.681536	55.080553	17	10	CC		KEEP	---	---	---	---	capture			Silent	SNP	42161069	42161069	10133	22	C	T	T	19	19	MPPED1	T	1	1
KCNF1	3754	broad.mit.edu	36	2	10970107	10970107	+	Missense_Mutation	SNP	T	G	G			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:10970107T>G	uc002rax.1	+	c.104T>G	c.(103-105)GTG>GGG	p.V35G		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	35	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)													0.363636	6.45222	6.946572	8	14	TT		KEEP	---	---	---	---	capture		Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)	Missense_Mutation	SNP	10970107	10970107	8331	2	T	G	G	59	59	KCNF1	G	4	4
GLI2	2736	broad.mit.edu	36	2	121463541	121463541	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:121463541G>A	uc010flp.1	+	c.3581G>A	c.(3580-3582)AGC>AAC	p.S1194N	GLI2_uc002tmq.1_Intron|GLI2_uc002tmr.1_Intron|GLI2_uc002tmt.2_Missense_Mutation_p.S866N|GLI2_uc002tmu.2_Missense_Mutation_p.S849N	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	1194					axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(7)|central_nervous_system(1)	8	Renal(3;0.0496)	Prostate(154;0.0623)								376				0.166667	7.286784	9.814008	4	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121463541	121463541	6706	2	G	A	A	34	34	GLI2	A	2	2
THSD7B	80731	broad.mit.edu	36	2	137705204	137705204	+	Missense_Mutation	SNP	A	C	C			TCGA-32-2615-01	TCGA-32-2615-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:137705204A>C	uc002tva.1	+	c.1751A>C	c.(1750-1752)CAG>CCG	p.Q584P	THSD7B_uc002tvb.2_Missense_Mutation_p.Q474P	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7														0.432432	44.79071	44.938552	16	21	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.19)	Missense_Mutation	SNP	137705204	137705204	16408	2	A	C	C	7	7	THSD7B	C	4	4
TPO	7173	broad.mit.edu	36	2	1459953	1459953	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1459953C>T	uc002qwr.1	+	c.908C>T	c.(907-909)GCG>GTG	p.A303V	TPO_uc010ewj.1_Intron|TPO_uc002qwt.1_Intron|TPO_uc002qwu.1_Missense_Mutation_p.A303V|TPO_uc002qwv.1_Missense_Mutation_p.A303V|TPO_uc002qww.1_Missense_Mutation_p.A303V|TPO_uc002qwx.1_Missense_Mutation_p.A303V	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	303	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(6)|pancreas(6)|skin(3)|lung(1)|kidney(1)	17	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)			Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)					723				0.4	14.842712	14.974927	6	9	CC		KEEP	---	---	---	---	capture		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Missense_Mutation	SNP	1459953	1459953	16954	2	C	T	T	27	27	TPO	T	1	1
APOB	338	broad.mit.edu	36	2	21087211	21087211	+	Nonsense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21087211G>A	uc002red.1	-	c.6034C>T	c.(6034-6036)CGA>TGA	p.R2012*		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	2012					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.407216	232.482849	233.94349	79	115	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	21087211	21087211	796	2	G	A	A	40	40	APOB	A	5	1
DPPA4	55211	broad.mit.edu	36	3	110529530	110529530	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110529530C>T	uc003dxq.2	-	c.910G>A	c.(910-912)GAA>AAA	p.E304K		NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	304						nucleus	protein binding				0														0.298361	252.09561	263.186008	91	214	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110529530	110529530	4920	3	C	T	T	30	30	DPPA4	T	2	2
C3orf18	51161	broad.mit.edu	36	3	50578101	50578101	+	Missense_Mutation	SNP	A	C	C			TCGA-32-2615-01	TCGA-32-2615-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:50578101A>C	uc003dar.1	-	c.34T>G	c.(34-36)TTC>GTC	p.F12V	C3orf18_uc010hln.1_Intron|C3orf18_uc003das.1_Missense_Mutation_p.F12V|C3orf18_uc010hlo.1_Missense_Mutation_p.F12V|C3orf18_uc010hlp.1_Intron|C3orf18_uc003dat.1_Missense_Mutation_p.F12V	NM_016210	NP_057294	Q9UK00	CC018_HUMAN	hypothetical protein LOC51161	12						integral to membrane				pancreas(1)	1														0.285714	7.115376	8.079269	6	15	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)	Missense_Mutation	SNP	50578101	50578101	2304	3	A	C	C	2	2	C3orf18	C	4	4
ITIH3	3699	broad.mit.edu	36	3	52803947	52803947	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52803947C>T	uc003dfv.2	+	c.88C>T	c.(88-90)CTT>TTT	p.L30F		NM_002217	NP_002208	Q06033	ITIH3_HUMAN	inter-alpha (globulin) inhibitor H3	30	VIT.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|liver(1)	3														0.492857	219.762767	219.769139	69	71	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)	Missense_Mutation	SNP	52803947	52803947	8209	3	C	T	T	28	28	ITIH3	T	2	2
BOD1L	259282	broad.mit.edu	36	4	13214649	13214649	+	Silent	SNP	T	C	C			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:13214649T>C	uc003gmz.1	-	c.2973A>G	c.(2971-2973)AGA>AGG	p.R991R	BOD1L_uc010idr.1_Silent_p.R328R	NM_148894	NP_683692	Q8NFC6	BOD1L_HUMAN	hypothetical protein LOC259282	991	Lys-rich.						DNA binding			ovary(5)|breast(1)	6														0.450431	726.129257	727.121043	209	255	TT		KEEP	---	---	---	---	capture			Silent	SNP	13214649	13214649	1508	4	T	C	C	54	54	BOD1L	C	4	4
PET112L	5188	broad.mit.edu	36	4	152899511	152899511	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:152899511C>T	uc003iml.1	-	c.190G>A	c.(190-192)GCT>ACT	p.A64T	PET112L_uc003imm.2_Missense_Mutation_p.A64T	NM_004564	NP_004555	O75879	GATB_HUMAN	PET112-like	64						mitochondrion	ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding				0	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)			L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)									0.373984	136.319257	138.034444	46	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152899511	152899511	12155	4	C	T	T	26	26	PET112L	T	2	2
NUP54	53371	broad.mit.edu	36	4	77288500	77288500	+	Missense_Mutation	SNP	T	G	G			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77288500T>G	uc003hjs.1	-	c.52A>C	c.(52-54)ACC>CCC	p.T18P	NUP54_uc010ije.1_5'UTR|NUP54_uc003hjt.1_5'UTR	NM_017426	NP_059122	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	18	Gly-rich.|9 X 2 AA repeats of F-G.				carbohydrate metabolic process|glucose transport|mRNA transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleoplasm				ovary(1)|lung(1)	2														0.25	7.918709	8.601146	3	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77288500	77288500	11172	4	T	G	G	59	59	NUP54	G	4	4
EGR1	1958	broad.mit.edu	36	5	137831029	137831029	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:137831029C>T	uc003ldb.1	+	c.992C>T	c.(991-993)ACG>ATG	p.T331M		NM_001964	NP_001955	P18146	EGR1_HUMAN	early growth response 1	331					cellular response to heparin|cellular response to mycophenolic acid|glomerular mesangial cell proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of glomerular metanephric mesangial cell proliferation|regulation of protein sumoylation|type I interferon-mediated signaling pathway	cytoplasm|nucleus	protein binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity|zinc ion binding			ovary(1)	1														0.413978	220.943672	222.143993	77	109	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)		Missense_Mutation	SNP	137831029	137831029	5160	5	C	T	T	19	19	EGR1	T	1	1
PCDHA3	56145	broad.mit.edu	36	5	140161934	140161934	+	Missense_Mutation	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140161934C>T	uc003lhf.1	+	c.968C>T	c.(967-969)ACG>ATG	p.T323M	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhe.1_Missense_Mutation_p.T323M	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	323	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5														0.411111	221.817117	223.059229	74	106	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140161934	140161934	11945	5	C	T	T	19	19	PCDHA3	T	1	1
SH3RF2	153769	broad.mit.edu	36	5	145408924	145408924	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:145408924C>T	uc003lnt.1	+	c.1245C>T	c.(1243-1245)GAC>GAT	p.D415D	SH3RF2_uc003lnu.1_5'Flank	NM_152550	NP_689763	Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	415	SH3 3.						ligase activity|protein phosphatase 1 binding|zinc ion binding			ovary(1)	1												OREG0016895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.328125	110.199211	113.555822	42	86	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Silent	SNP	145408924	145408924	14751	5	C	T	T	19	19	SH3RF2	T	1	1
PRSS16	10279	broad.mit.edu	36	6	27324966	27324966	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27324966G>A	uc003nja.1	+	c.446G>A	c.(445-447)CGC>CAC	p.R149H	PRSS16_uc003njb.1_Intron|PRSS16_uc010jqq.1_Missense_Mutation_p.R39H|PRSS16_uc010jqr.1_Missense_Mutation_p.R39H|PRSS16_uc003njc.1_Non-coding_Transcript|PRSS16_uc003njd.1_5'Flank	NM_005865	NP_005856	Q9NQE7	TSSP_HUMAN	protease, serine, 16	149					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)								0.24031	70.767536	78.70407	31	98	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27324966	27324966	13066	6	G	A	A	38	38	PRSS16	A	1	1
OR2J3	442186	broad.mit.edu	36	6	29188272	29188272	+	Missense_Mutation	SNP	T	C	C			TCGA-32-2615-01	TCGA-32-2615-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:29188272T>C	uc003nlz.1	+	c.626T>C	c.(625-627)TTT>TCT	p.F209S		NM_001005216	NP_001005216	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J,	209	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.343434	114.221532	116.364531	34	65	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29188272	29188272	11410	6	T	C	C	64	64	OR2J3	C	4	4
ZNF318	24149	broad.mit.edu	36	6	43433063	43433063	+	Nonsense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43433063G>A	uc003oux.1	-	c.967C>T	c.(967-969)CGA>TGA	p.R323*	ZNF318_uc003ouw.2_Non-coding_Transcript	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	323	Potential.				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(2)|breast(2)|central_nervous_system(1)	5														0.466019	146.681225	146.78541	48	55	GG		KEEP	---	---	---	---	capture	Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)		Nonsense_Mutation	SNP	43433063	43433063	18428	6	G	A	A	40	40	ZNF318	A	5	1
RHAG	6005	broad.mit.edu	36	6	49688206	49688206	+	Missense_Mutation	SNP	C	A	A	rs16879498	by-cluster,by-frequency,by-hapmap	TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:49688206C>A	uc003ozk.2	-	c.808G>T	c.(808-810)GTT>TTT	p.V270F	RHAG_uc010jzl.1_Missense_Mutation_p.V270F|RHAG_uc010jzm.1_Missense_Mutation_p.V270F	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	270	Helical; (Potential).				carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)	1	Lung NSC(77;0.0255)					Ovarian(176;476 2003 7720 43408 44749)								0.44	64.842667	64.999537	22	28	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49688206	49688206	13790	6	C	A	A	18	18	RHAG	A	3	3
TNPO3	23534	broad.mit.edu	36	7	128399798	128399798	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:128399798G>A	uc010lly.1	-	c.2450C>T	c.(2449-2451)TCT>TTT	p.S817F	TNPO3_uc003vol.1_Missense_Mutation_p.S783F|TNPO3_uc003vom.1_Missense_Mutation_p.S717F|TNPO3_uc010llz.1_Missense_Mutation_p.S719F|TNPO3_uc010llx.1_Missense_Mutation_p.S194F	NM_012470	NP_036602	Q9Y5L0	TNPO3_HUMAN	transportin 3	783					protein transport	cytoplasm|nucleus	protein binding|receptor activity			ovary(2)|skin(2)|lung(1)	5						Pancreas(147;583 2585 39696 52331)								0.101449	11.539498	33.413087	14	124	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128399798	128399798	16878	7	G	A	A	33	33	TNPO3	A	2	2
PARP12	64761	broad.mit.edu	36	7	139393245	139393245	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:139393245C>T	uc003vvl.1	-	c.894G>A	c.(892-894)CCG>CCA	p.P298P	PARP12_uc003vvk.1_Silent_p.P84P|PARP12_uc010lnf.1_Non-coding_Transcript	NM_022750	NP_073587	Q9H0J9	PAR12_HUMAN	zinc finger CCCH-type domain containing 1	298	WWE 1.					nucleus	NAD+ ADP-ribosyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)	3	Melanoma(164;0.0142)													0.506329	126.304107	126.306961	40	39	CC		KEEP	---	---	---	---	capture			Silent	SNP	139393245	139393245	11874	7	C	T	T	19	19	PARP12	T	1	1
NOBOX	135935	broad.mit.edu	36	7	143728260	143728260	+	Missense_Mutation	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143728260G>A	uc003wen.1	-	c.923C>T	c.(922-924)ACG>ATG	p.T308M		NM_001080413	NP_001073882			NOBOX oogenesis homeobox											ovary(1)	1	Melanoma(164;0.14)													0.353659	81.42894	82.98634	29	53	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143728260	143728260	10915	7	G	A	A	40	40	NOBOX	A	1	1
CPSF1	29894	broad.mit.edu	36	8	145595177	145595177	+	Silent	SNP	G	A	A			TCGA-32-2615-01	TCGA-32-2615-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145595177G>A	uc003zcj.1	-	c.1527C>T	c.(1525-1527)AAC>AAT	p.N509N		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	509					mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)					NSCLC(133;1088 1848 27708 34777 35269)								0.517241	43.924397	43.93188	15	14	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)		Silent	SNP	145595177	145595177	3962	8	G	A	A	40	40	CPSF1	A	1	1
XKR4	114786	broad.mit.edu	36	8	56432873	56432873	+	Silent	SNP	A	G	G			TCGA-32-2615-01	TCGA-32-2615-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:56432873A>G	uc003xsf.1	+	c.888A>G	c.(886-888)GTA>GTG	p.V296V		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	296						integral to membrane				pancreas(2)	2														0.153846	48.460797	64.838118	22	121	AA		KEEP	---	---	---	---	capture	Epithelial(17;0.000117)|all cancers(17;0.000836)		Silent	SNP	56432873	56432873	18014	8	A	G	G	16	16	XKR4	G	4	4
ASS1	445	broad.mit.edu	36	9	132332001	132332001	+	Silent	SNP	C	T	T			TCGA-32-2615-01	TCGA-32-2615-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:132332001C>T	uc010mza.1	+	c.717C>T	c.(715-717)TAC>TAT	p.Y239Y	ASS1_uc004bzm.1_Silent_p.Y163Y|ASS1_uc004bzn.1_Silent_p.Y163Y|ASS1_uc004bzo.1_Silent_p.Y144Y|ASS1_uc010mzb.1_Silent_p.Y201Y|ASS1_uc004bzp.1_Silent_p.Y163Y|ASS1_uc010mzc.1_Silent_p.Y163Y	NM_054012	NP_446464	P00966	ASSY_HUMAN	argininosuccinate synthetase 1	163					arginine biosynthetic process|urea cycle	cytosol	argininosuccinate synthase activity|ATP binding|protein binding			ovary(1)	1					Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)									0.393939	75.364235	76.004015	26	40	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Silent	SNP	132332001	132332001	1080	9	C	T	T	19	19	ASS1	T	1	1
CAMSAP1	157922	broad.mit.edu	36	9	137853786	137853786	+	Missense_Mutation	SNP	A	G	G			TCGA-32-2615-01	TCGA-32-2615-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:137853786A>G	uc004cgr.2	-	c.2542T>C	c.(2542-2544)TGC>CGC	p.C848R	CAMSAP1_uc004cgq.2_Missense_Mutation_p.C738R|CAMSAP1_uc010nbg.1_Missense_Mutation_p.C570R	NM_015447	NP_056262	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein	848						cytoplasm|microtubule				ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.2	6.883762	8.565874	4	16	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)	Missense_Mutation	SNP	137853786	137853786	2728	9	A	G	G	7	7	CAMSAP1	G	4	4
CTBS	1486	broad.mit.edu	36	1	84812613	84812621	+	In_Frame_Del	DEL	AGCAGCGCT	-	-			TCGA-32-2615-01	TCGA-32-2615-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:84812613_84812621delAGCAGCGCT	uc001dka.1	-	c.66_74delAGCGCTGCT	c.(64-75)CTAGCGCTGCTG>CTG	p.22_25LALL>L	CTBS_uc001dkb.1_5'UTR|CTBS_uc001dkc.1_5'UTR|CTBS_uc001dkd.1_5'UTR	NM_004388	NP_004379	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	22_25						lysosome	cation binding				0				all cancers(265;0.00727)|Epithelial(280;0.0192)|OV - Ovarian serous cystadenocarcinoma(397;0.166)										0.33			3	6				---	---	---	---	capture_indel			In_Frame_Del	DEL	84812613	84812621	4158	1	AGCAGCGCT	-	-	7	7	CTBS	-	5	5
IMPG1	3617	broad.mit.edu	36	6	76838888	76838889	+	Frame_Shift_Ins	INS	-	A	A			TCGA-32-2615-01	TCGA-32-2615-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:76838888_76838889insA	uc003pik.1	-	c.37_38insT	c.(37-39)TGGfs	p.W13fs		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	13					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				Pancreas(37;839 1141 2599 26037)								0.61			36	23				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	76838888	76838889	8029	6	-	A	A	21	21	IMPG1	A	5	5
ZNF282	8427	broad.mit.edu	36	7	148551872	148551873	+	Frame_Shift_Ins	INS	-	C	C			TCGA-32-2615-01	TCGA-32-2615-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148551872_148551873insC	uc003wfm.1	+	c.1216_1217insC	c.(1216-1218)GCCfs	p.A406fs	ZNF282_uc003wfo.2_Intron	NM_003575	NP_003566	Q9UDV7	ZN282_HUMAN	zinc finger protein 282	406					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription repressor activity|zinc ion binding				0	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)	Lung(243;0.145)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	148551872	148551873	18411	7	-	C	C	42	42	ZNF282	C	5	5
