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
TRUB1	142940	broad.mit.edu	36	10	116688102	116688102	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:116688102A>C	uc001lcd.1	+	c.100A>C	c.(100-102)ACC>CCC	p.T34P		NM_139169	NP_631908	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase homolog 1	34					pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding				0		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)												0.272727	7.422035	7.933029	3	8	AA		KEEP	---	---	---	---	capture		Epithelial(162;0.00879)|all cancers(201;0.0243)	Missense_Mutation	SNP	116688102	116688102	17153	10	A	C	C	10	10	TRUB1	C	4	4
C1QL3	389941	broad.mit.edu	36	10	16602992	16602992	+	Missense_Mutation	SNP	T	G	G			TCGA-27-2521-01	TCGA-27-2521-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:16602992T>G	uc001ioj.1	-	c.79A>C	c.(79-81)ACC>CCC	p.T27P		NM_001010908	NP_001010908	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	27						collagen				ovary(1)	1														0.428571	6.320841	6.352376	3	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16602992	16602992	2027	10	T	G	G	59	59	C1QL3	G	4	4
MPP7	143098	broad.mit.edu	36	10	28418645	28418645	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:28418645G>A	uc001iua.1	-	c.1084C>T	c.(1084-1086)CGA>TGA	p.R362*	MPP7_uc009xkz.1_Non-coding_Transcript|MPP7_uc001iub.1_Nonsense_Mutation_p.R362*|MPP7_uc009xla.1_Nonsense_Mutation_p.R362*	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN	palmitoylated membrane protein 7	362					establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity			ovary(1)	1														0.393064	386.14548	389.60085	136	210	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	28418645	28418645	10131	10	G	A	A	38	38	MPP7	A	5	1
APOA5	116519	broad.mit.edu	36	11	116166814	116166814	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:116166814G>A	uc001ppr.1	-	c.341C>T	c.(340-342)GCG>GTG	p.A114V	ZNF259_uc001ppp.1_5'Flank|ZNF259_uc009yzd.1_5'Flank|ZNF259_uc001ppq.1_5'Flank|APOA5_uc009yze.1_Missense_Mutation_p.A114V|APOA5_uc009yzf.1_Missense_Mutation_p.A114V|APOA5_uc009yzg.1_Missense_Mutation_p.A140V	NM_052968	NP_443200	Q6Q788	APOA5_HUMAN	apolipoprotein AV	114	Potential.				acylglycerol homeostasis|cholesterol homeostasis|lipid transport|lipoprotein metabolic process|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor-mediated endocytosis|positive regulation of triglyceride catabolic process|positive regulation of very-low-density lipoprotein particle remodeling|tissue regeneration|triglyceride catabolic process|triglyceride homeostasis	chylomicron|high-density lipoprotein particle|very-low-density lipoprotein particle	enzyme binding|heparin binding|lipoprotein lipase activator activity|low-density lipoprotein particle receptor binding|phosphatidylcholine binding				0	all_hematologic(175;0.0487)	all_cancers(61;3.31e-09)|all_epithelial(67;8.03e-06)|Breast(348;0.0126)|Melanoma(852;0.0153)|Acute lymphoblastic leukemia(157;0.0257)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0433)|all_neural(223;0.234)												0.614973	337.436143	339.659028	115	72	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;4.93e-06)|all cancers(92;0.000123)|OV - Ovarian serous cystadenocarcinoma(223;0.149)	Missense_Mutation	SNP	116166814	116166814	795	11	G	A	A	38	38	APOA5	A	1	1
CDC42BPG	55561	broad.mit.edu	36	11	64355655	64355655	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64355655G>C	uc001obs.2	-	c.3202C>G	c.(3202-3204)CTG>GTG	p.L1068V		NM_017525	NP_059995	Q6DT37	MRCKG_HUMAN	CDC42 binding protein kinase gamma (DMPK-like)	1068					actin cytoskeleton reorganization|intracellular signal transduction|protein phosphorylation	cell leading edge|centrosome	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			lung(3)|central_nervous_system(1)	4										665		OREG0004016	type=REGULATORY REGION|Gene=CDC42BPG|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.2	7.286935	8.963131	4	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64355655	64355655	3202	11	G	C	C	34	34	CDC42BPG	C	3	3
BRCA2	675	broad.mit.edu	36	13	31812389	31812389	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:31812389A>G	uc001uub.1	+	c.5897A>G	c.(5896-5898)CAT>CGT	p.H1966R		NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	1966					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding|transcription activator activity			ovary(19)|endometrium(8)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|lung(3)|pancreas(3)|cervix(1)|salivary_gland(1)|liver(1)|skin(1)|kidney(1)	57		Lung SC(185;0.0262)				Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)				677	TCGA Ovarian(8;0.087)			0.477733	375.936062	376.042478	118	129	AA		KEEP	---	---	---	---	capture		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)	Missense_Mutation	SNP	31812389	31812389	1530	13	A	G	G	8	8	BRCA2	G	4	4
HERC2	8924	broad.mit.edu	36	15	26174893	26174893	+	Missense_Mutation	SNP	A	C	C			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:26174893A>C	uc001zbj.1	-	c.2683T>G	c.(2683-2685)TCC>GCC	p.S895A	HERC2_uc010ayw.1_Intron|HERC2_uc001zbl.1_Missense_Mutation_p.S590A	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	895					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(2)|central_nervous_system(1)	11		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)								1580				0.173913	6.485711	8.795541	4	19	AA		KEEP	---	---	---	---	capture		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)	Missense_Mutation	SNP	26174893	26174893	7341	15	A	C	C	10	10	HERC2	C	4	4
PAK6	56924	broad.mit.edu	36	15	38345613	38345613	+	Silent	SNP	C	G	G			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:38345613C>G	uc010bbl.1	+	c.483C>G	c.(481-483)CCC>CCG	p.P161P	PAK6_uc010bbm.1_Silent_p.P161P|PAK6_uc001zky.2_Silent_p.P161P|PAK6_uc010bbn.1_Silent_p.P161P|PAK6_uc001zlb.2_Silent_p.P161P	NM_001128628	NP_001122100	Q9NQU5	PAK6_HUMAN	p21-activated kinase 6	161	Linker.				protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(3)|large_intestine(1)|ovary(1)	5		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)							p.P161P(FADU-Tumor)	94				0.210526	8.503973	9.966478	4	15	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)	Silent	SNP	38345613	38345613	11820	15	C	G	G	23	23	PAK6	G	3	3
FBXO22	26263	broad.mit.edu	36	15	74012206	74012206	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:74012206A>G	uc002bbk.1	+	c.920A>G	c.(919-921)CAG>CGG	p.Q307R	FBXO22_uc002bbl.1_Missense_Mutation_p.Q203R|FBXO22OS_uc002bbm.1_Non-coding_Transcript	NM_147188	NP_671717	Q8NEZ5	FBX22_HUMAN	F-box only protein 22 isoform a	307					ubiquitin-dependent protein catabolic process		ubiquitin-protein ligase activity				0														0.534247	238.325699	238.47253	78	68	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74012206	74012206	5971	15	A	G	G	7	7	FBXO22	G	4	4
RRAD	6236	broad.mit.edu	36	16	65514924	65514925	+	Missense_Mutation	DNP	CA	AC	AC			TCGA-27-2521-01	TCGA-27-2521-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:65514924_65514925CA>AC	uc002eqn.2	-	c.644_645TG>GT	c.(643-645)GTG>GGT	p.V215G	RRAD_uc002eqo.2_Missense_Mutation_p.V215G	NM_001128850	NP_001122322	P55042	RAD_HUMAN	Ras-related associated with diabetes	215					small GTPase mediated signal transduction	plasma membrane	calmodulin binding|GTP binding|GTPase activity				0		Ovarian(137;0.192)												0.146067	21.120309	31.836434	13	76	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)	Missense_Mutation	DNP	65514924	65514925	14151	16	CA	AC	AC	21	21	RRAD	AC	3	3
MYO18A	399687	broad.mit.edu	36	17	24448968	24448968	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24448968C>T	uc002hdt.1	-	c.4066G>A	c.(4066-4068)GCG>ACG	p.A1356T	MYO18A_uc010csa.1_Missense_Mutation_p.A1356T|MYO18A_uc002hdu.1_Missense_Mutation_p.A1356T|MYO18A_uc002hds.1_Missense_Mutation_p.A898T	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	1356	Potential.				anti-apoptosis|DNA metabolic process	ER-Golgi intermediate compartment|myosin complex	ATP binding|DNA binding|DNA-dependent ATPase activity|identical protein binding|motor activity				0						Esophageal Squamous(182;472 2015 7001 15270 22562)								0.475248	286.975073	287.083417	96	106	CC		KEEP	---	---	---	---	capture	Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)		Missense_Mutation	SNP	24448968	24448968	10460	17	C	T	T	28	28	MYO18A	T	2	2
SUZ12	23512	broad.mit.edu	36	17	27344433	27344433	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:27344433G>A	uc002hgs.1	+	c.1261G>A	c.(1261-1263)GAA>AAA	p.E421K	SUZ12_uc002hgt.1_Missense_Mutation_p.E398K	NM_015355	NP_056170	Q15022	SUZ12_HUMAN	joined to JAZF1	421					negative regulation of cell differentiation|transcription, DNA-dependent	ESC/E(Z) complex	histone methyltransferase activity|methylated histone residue binding|zinc ion binding		JAZF1/SUZ12(131)	soft_tissue(98)|endometrium(33)	131		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)								249				0.449438	120.386362	120.584963	40	49	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27344433	27344433	15936	17	G	A	A	45	45	SUZ12	A	2	2
NMT1	4836	broad.mit.edu	36	17	40514547	40514547	+	Silent	SNP	T	C	C			TCGA-27-2521-01	TCGA-27-2521-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:40514547T>C	uc002ihz.1	+	c.141T>C	c.(139-141)AGT>AGC	p.S47S	NMT1_uc010dac.1_Intron|NMT1_uc002iia.1_Non-coding_Transcript	NM_021079	NP_066565	P30419	NMT1_HUMAN	N-myristoyltransferase 1	47					activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation	actin cytoskeleton|cell junction|cytosol	glycylpeptide N-tetradecanoyltransferase activity				0		Prostate(33;0.155)												0.212121	7.149878	12.725775	14	52	TT		KEEP	---	---	---	---	capture			Silent	SNP	40514547	40514547	10906	17	T	C	C	58	58	NMT1	C	4	4
GNGT2	2793	broad.mit.edu	36	17	44639161	44639161	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2521-01	TCGA-27-2521-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:44639161T>C	uc002ioo.1	-	c.167A>G	c.(166-168)GAC>GGC	p.D56G		NM_031498	NP_113686	O14610	GBGT2_HUMAN	guanine nucleotide binding protein-gamma	56					G-protein coupled receptor protein signaling pathway|phototransduction|synaptic transmission	extracellular region|heterotrimeric G-protein complex	GTPase activity|signal transducer activity				0														0.105263	18.654197	48.113984	20	170	TT		KEEP	---	---	---	---	capture	Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)		Missense_Mutation	SNP	44639161	44639161	6803	17	T	C	C	58	58	GNGT2	C	4	4
WIPI1	55062	broad.mit.edu	36	17	63929544	63929544	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:63929544G>A	uc010dey.1	-	c.1306C>T	c.(1306-1308)CGT>TGT	p.R436C	WIPI1_uc002jhd.2_Non-coding_Transcript|WIPI1_uc002jhe.2_Non-coding_Transcript	NM_017983	NP_060453	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting	436					macroautophagy|vesicle targeting, trans-Golgi to endosome	autophagic vacuole membrane|clathrin-coated vesicle|cytosol|endosome membrane|PAS complex|pre-autophagosomal structure membrane|trans-Golgi network	androgen receptor binding|estrogen receptor binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding				0														0.45515	447.253985	447.779837	137	164	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63929544	63929544	17944	17	G	A	A	39	39	WIPI1	A	1	1
ACADVL	37	broad.mit.edu	36	17	7066009	7066009	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7066009G>A	uc002gev.1	+	c.637G>A	c.(637-639)GCT>ACT	p.A213T	DLG4_uc002get.2_5'Flank|ACADVL_uc002gew.1_Missense_Mutation_p.A191T|ACADVL_uc002gex.1_Missense_Mutation_p.A137T	NM_000018	NP_000009	P49748	ACADV_HUMAN	acyl-Coenzyme A dehydrogenase, very long chain	213	Catalytic.		A -> P (in ACADVLD).		energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA dehydrogenase|negative regulation of fatty acid biosynthetic process|negative regulation of fatty acid oxidation|regulation of cholesterol metabolic process|temperature homeostasis	mitochondrial inner membrane|mitochondrial nucleoid	long-chain-acyl-CoA dehydrogenase activity			ovary(2)	2														0.239583	53.580489	59.522238	23	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7066009	7066009	117	17	G	A	A	38	38	ACADVL	A	1	1
SLC39A3	29985	broad.mit.edu	36	19	2684097	2684097	+	Silent	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2684097G>A	uc002lwg.1	-	c.597C>T	c.(595-597)AGC>AGT	p.S199S		NM_144564	NP_653165	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter),	199	Helical; (Potential).					integral to membrane|plasma membrane	zinc ion transmembrane transporter activity				0		Hepatocellular(1079;0.137)												0.134831	13.201841	24.674894	12	77	GG		KEEP	---	---	---	---	capture		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)	Silent	SNP	2684097	2684097	15116	19	G	A	A	42	42	SLC39A3	A	2	2
PRAMEF2	65122	broad.mit.edu	36	1	12841544	12841544	+	Silent	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:12841544G>A	uc001aum.1	+	c.93G>A	c.(91-93)CTG>CTA	p.L31L		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	31											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)												0.164062	34.501331	48.218659	21	107	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	12841544	12841544	12872	1	G	A	A	46	46	PRAMEF2	A	2	2
NBPF14	25832	broad.mit.edu	36	1	146479155	146479155	+	Silent	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:146479155C>T	uc001eqq.1	-	c.1428G>A	c.(1426-1428)AAG>AAA	p.K476K	NBPF11_uc009wju.1_Intron|NBPF11_uc009wjs.1_Intron|NBPF11_uc009wjt.1_Intron|NBPF11_uc001eqf.1_Intron|NBPF11_uc001eqe.1_Intron|NBPF11_uc001eqg.1_Intron|NBPF11_uc009wjv.1_Intron|NBPF14_uc009wkc.1_Intron|NBPF14_uc009wkd.1_Intron|NBPF14_uc009wke.1_Intron|NBPF14_uc001eqt.1_Intron|NBPF14_uc001equ.1_Intron|NBPF14_uc001eqv.1_Silent_p.K143K|NBPF14_uc001eqw.1_Intron|NBPF14_uc001eqx.1_Non-coding_Transcript|NBPF14_uc001eqy.2_Silent_p.K143K|NBPF14_uc009wkb.1_Intron|NBPF14_uc001eqr.1_5'Flank|NBPF14_uc001eqs.1_Intron	NM_015383	NP_056198	Q5TI25	NBPFE_HUMAN	hypothetical protein LOC25832	476	NBPF 5.					cytoplasm				ovary(1)	1	all_hematologic(923;0.032)													0.181818	6.696888	8.706409	4	18	CC		KEEP	---	---	---	---	capture			Silent	SNP	146479155	146479155	10591	1	C	T	T	28	28	NBPF14	T	2	2
GORAB	92344	broad.mit.edu	36	1	168775195	168775195	+	Silent	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:168775195C>T	uc001gha.1	+	c.357C>T	c.(355-357)CCC>CCT	p.P119P	GORAB_uc009wvw.1_3'UTR|GORAB_uc001ggz.2_Silent_p.P119P|GORAB_uc001ghb.1_5'UTR|GORAB_uc009wvx.1_5'UTR|GORAB_uc001ghc.1_5'UTR	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	119						Golgi apparatus|nucleus					0														0.107843	21.194142	52.355624	22	182	CC		KEEP	---	---	---	---	capture			Silent	SNP	168775195	168775195	6847	1	C	T	T	23	23	GORAB	T	1	1
NEK7	140609	broad.mit.edu	36	1	196528705	196528705	+	Silent	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:196528705G>A	uc001gul.1	+	c.597G>A	c.(595-597)ACG>ACA	p.T199T	NEK7_uc001gum.1_Silent_p.T199T	NM_133494	NP_598001	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	199	Protein kinase.				protein phosphorylation	cytoplasm	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(1)|lung(1)	2									p.T199T(SNU1079-Tumor)|p.T199T(EN-Tumor)|p.T199T(TE10-Tumor)	180				0.410156	311.33212	313.135507	105	151	GG		KEEP	---	---	---	---	capture			Silent	SNP	196528705	196528705	10728	1	G	A	A	38	38	NEK7	A	1	1
MACF1	23499	broad.mit.edu	36	1	39525793	39525793	+	Missense_Mutation	SNP	A	T	T			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39525793A>T	uc009vvo.1	+	c.1772A>T	c.(1771-1773)GAA>GTA	p.E591V	MACF1_uc009vvp.1_Missense_Mutation_p.E591V|MACF1_uc001cda.1_Missense_Mutation_p.E499V	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	591	Spectrin 2.			VAISSSEDEGNLRFVYELLS -> GPSAPLKMKAISDLCMN YCL (in Ref. 1; BAA83821).	cell cycle arrest	cytoplasm|cytoskeleton	actin filament binding|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)	14	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.189103	113.125303	141.37233	59	253	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		Missense_Mutation	SNP	39525793	39525793	9521	1	A	T	T	9	9	MACF1	T	4	4
NPHP4	261734	broad.mit.edu	36	1	5891854	5891854	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:5891854G>C	uc001alq.1	-	c.1448C>G	c.(1447-1449)CCA>CGA	p.P483R	NPHP4_uc001als.1_Non-coding_Transcript|NPHP4_uc009vlt.1_Intron|NPHP4_uc001alt.1_Intron	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	483					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cilium|membrane|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)												0.375	9.023464	9.13303	3	5	GG		KEEP	---	---	---	---	capture		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)	Missense_Mutation	SNP	5891854	5891854	10985	1	G	C	C	47	47	NPHP4	C	3	3
HOOK1	51361	broad.mit.edu	36	1	60085409	60085409	+	Missense_Mutation	SNP	A	T	T			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:60085409A>T	uc009wad.1	+	c.893A>T	c.(892-894)GAA>GTA	p.E298V	HOOK1_uc001czo.1_Missense_Mutation_p.E298V|HOOK1_uc001czp.1_Non-coding_Transcript	NM_015888	NP_056972	Q9UJC3	HOOK1_HUMAN	hook homolog 1	298	Potential.|Sufficient for interaction with microtubules.				early endosome to late endosome transport|endosome organization|endosome to lysosome transport|lysosome organization|microtubule cytoskeleton organization|multicellular organismal development|protein transport	FHF complex|microtubule	identical protein binding			ovary(1)|breast(1)	2	all_cancers(7;0.000129)													0.437037	167.79905	168.266396	59	76	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60085409	60085409	7574	1	A	T	T	9	9	HOOK1	T	4	4
PDE4B	5142	broad.mit.edu	36	1	66604001	66604001	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:66604001C>T	uc001dcn.1	+	c.1348C>T	c.(1348-1350)CAT>TAT	p.H450Y	PDE4B_uc009war.1_Missense_Mutation_p.H358Y|PDE4B_uc001dco.1_Missense_Mutation_p.H450Y|PDE4B_uc001dcp.1_Missense_Mutation_p.H435Y|PDE4B_uc001dcq.1_Missense_Mutation_p.H278Y|PDE4B_uc009was.1_Missense_Mutation_p.H217Y	NM_001037341	NP_002591	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific isoform 1	450					signal transduction	cytosol|insoluble fraction|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding			ovary(2)|central_nervous_system(1)	3					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Cilostazol(DB01166)|Dyphylline(DB00651)|Enprofylline(DB00824)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Theophylline(DB00277)									0.366667	61.93223	62.87087	22	38	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66604001	66604001	12061	1	C	T	T	29	29	PDE4B	T	2	2
SLC44A3	126969	broad.mit.edu	36	1	95095502	95095502	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:95095502G>A	uc001dqv.2	+	c.1096G>A	c.(1096-1098)GGC>AGC	p.G366S	SLC44A3_uc001dqx.2_Missense_Mutation_p.G366S|SLC44A3_uc001dqw.2_Missense_Mutation_p.G318S|SLC44A3_uc009wds.1_Missense_Mutation_p.G269S	NM_001114106	NP_001107578	Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3 isoform 1	366						integral to membrane|plasma membrane	choline transmembrane transporter activity			kidney(1)	1		all_lung(203;0.000712)|Lung NSC(277;0.00316)			Choline(DB00122)									0.098592	8.273327	31.056584	14	128	GG		KEEP	---	---	---	---	capture		all cancers(265;0.039)|Epithelial(280;0.124)	Missense_Mutation	SNP	95095502	95095502	15134	1	G	A	A	39	39	SLC44A3	A	1	1
SPTLC3	55304	broad.mit.edu	36	20	13000999	13000999	+	Silent	SNP	C	G	G			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:13000999C>G	uc002wod.1	+	c.399C>G	c.(397-399)GCC>GCG	p.A133A		NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base	133					sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)									0.248538	207.234197	226.890422	85	257	CC		KEEP	---	---	---	---	capture			Silent	SNP	13000999	13000999	15639	20	C	G	G	22	22	SPTLC3	G	3	3
IDH1	3417	broad.mit.edu	36	2	208821357	208821357	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208821357C>T	uc002vcs.1	-	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.1_Missense_Mutation_p.R132H|IDH1_uc002vcu.1_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(1725)|p.R132?(210)|p.R132C(92)|p.R132L(48)|p.R132G(26)|p.R132S(11)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(1848)|haematopoietic_and_lymphoid_tissue(593)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2451						Pancreas(158;264 1958 3300 35450 36047)				134				0.33557	136.937205	140.485469	50	99	CC		KEEP	---	---	---	---	capture		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	Missense_Mutation	SNP	208821357	208821357	7794	2	C	T	T	19	19	IDH1	T	1	1
SCLY	51540	broad.mit.edu	36	2	238667293	238667293	+	Missense_Mutation	SNP	A	T	T			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:238667293A>T	uc010fyv.1	+	c.974A>T	c.(973-975)GAC>GTC	p.D325V	SCLY_uc002vxm.2_Missense_Mutation_p.D292V|SCLY_uc002vxn.2_3'UTR|SCLY_uc002vxp.2_5'Flank	NM_016510	NP_057594	Q96I15	SCLY_HUMAN	selenocysteine lyase	325					cellular amino acid metabolic process	cytosol	pyridoxal phosphate binding|selenocysteine lyase activity|transferase activity			ovary(2)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)				Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)								0.428571	42.364799	42.509431	15	20	AA		KEEP	---	---	---	---	capture		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)	Missense_Mutation	SNP	238667293	238667293	14389	2	A	T	T	10	10	SCLY	T	4	4
TET3	200424	broad.mit.edu	36	2	74181905	74181905	+	Silent	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74181905C>T	uc002skb.2	+	c.4077C>T	c.(4075-4077)CCC>CCT	p.P1359P		NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3	1359					oxidation-reduction process		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.464286	37.769643	37.800919	13	15	CC		KEEP	---	---	---	---	capture			Silent	SNP	74181905	74181905	16298	2	C	T	T	23	23	TET3	T	1	1
CLSTN2	64084	broad.mit.edu	36	3	141764388	141764388	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:141764388G>A	uc003etn.1	+	c.2258G>A	c.(2257-2259)CGC>CAC	p.R753H		NM_022131	NP_071414	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	753	Extracellular (Potential).				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding			large_intestine(2)|pancreas(1)|central_nervous_system(1)|skin(1)	5						GBM(45;858 913 3709 36904 37282)								0.181818	28.755485	37.12586	16	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141764388	141764388	3700	3	G	A	A	38	38	CLSTN2	A	1	1
LRRIQ4	344657	broad.mit.edu	36	3	171038068	171038068	+	Silent	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:171038068A>G	uc003fgb.1	+	c.1638A>G	c.(1636-1638)GGA>GGG	p.G546G		NM_001080460	NP_001073929	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	546											0														0.434783	34.949453	35.03417	10	13	AA		KEEP	---	---	---	---	capture			Silent	SNP	171038068	171038068	9407	3	A	G	G	9	9	LRRIQ4	G	4	4
STAB1	23166	broad.mit.edu	36	3	52511100	52511100	+	Missense_Mutation	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52511100G>A	uc003dej.1	+	c.370G>A	c.(370-372)GGG>AGG	p.G124R	STAB1_uc003dei.1_Missense_Mutation_p.G124R	NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	124	EGF-like 1.|Extracellular (Potential).				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|pancreas(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.421053	96.58962	97.002182	32	44	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)	Missense_Mutation	SNP	52511100	52511100	15755	3	G	A	A	39	39	STAB1	A	1	1
MINA	84864	broad.mit.edu	36	3	99146800	99146800	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2521-01	TCGA-27-2521-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99146800T>C	uc003drz.1	-	c.1316A>G	c.(1315-1317)AAG>AGG	p.K439R	MINA_uc003dry.1_Missense_Mutation_p.K110R|MINA_uc003dsa.1_Missense_Mutation_p.K438R|MINA_uc003dsb.1_Missense_Mutation_p.K439R|MINA_uc003dsc.1_Missense_Mutation_p.K438R	NM_001042533	NP_694822	Q8IUF8	MINA_HUMAN	MYC induced nuclear antigen isoform a	439					ribosome biogenesis	cytoplasm|nucleolus				ovary(1)	1														0.106557	36.066364	73.560974	26	218	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99146800	99146800	9976	3	T	C	C	56	56	MINA	C	4	4
SOX30	11063	broad.mit.edu	36	5	156998232	156998232	+	Silent	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156998232G>A	uc003lxb.1	-	c.1464C>T	c.(1462-1464)AGC>AGT	p.S488S	SOX30_uc003lxc.1_Intron	NM_178424	NP_848511	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30 isoform a	488					regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|response to corticosteroid stimulus|transcription, DNA-dependent	nucleus|nucleus	sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity			ovary(1)|central_nervous_system(1)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)				Esophageal Squamous(31;525 799 19355 21125 41744)								0.736111	165.700103	169.332672	53	19	GG		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Silent	SNP	156998232	156998232	15452	5	G	A	A	38	38	SOX30	A	1	1
LAMA2	3908	broad.mit.edu	36	6	129705250	129705250	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:129705250G>T	uc003qbn.1	+	c.4381G>T	c.(4381-4383)GGA>TGA	p.G1461*	LAMA2_uc003qbo.1_Nonsense_Mutation_p.G1461*|LAMA2_uc010kfe.1_Nonsense_Mutation_p.G1461*	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	1461	Laminin EGF-like 15.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)	9														0.105023	17.070793	51.038528	23	196	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)	Nonsense_Mutation	SNP	129705250	129705250	8929	6	G	T	T	43	43	LAMA2	T	5	3
HIVEP2	3097	broad.mit.edu	36	6	143134960	143134960	+	Missense_Mutation	SNP	T	C	C			TCGA-27-2521-01	TCGA-27-2521-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:143134960T>C	uc003qjd.1	-	c.2609A>G	c.(2608-2610)CAG>CGG	p.Q870R		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	870					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4						Esophageal Squamous(107;843 1510 13293 16805 42198)								0.512605	192.272907	192.289276	61	58	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)	Missense_Mutation	SNP	143134960	143134960	7478	6	T	C	C	55	55	HIVEP2	C	4	4
GRM4	2914	broad.mit.edu	36	6	34111963	34111963	+	Silent	SNP	G	A	A			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:34111963G>A	uc003oir.2	-	c.1902C>T	c.(1900-1902)TTC>TTT	p.F634F	GRM4_uc010jvh.1_Silent_p.F634F|GRM4_uc010jvi.1_Silent_p.F326F|GRM4_uc010jvj.1_Silent_p.F518F|GRM4_uc003oio.1_Silent_p.F326F|GRM4_uc003oip.1_Non-coding_Transcript|GRM4_uc003oiq.1_Silent_p.F501F	NM_000841	NP_000832	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	634	Helical; Name=2; (Potential).				activation of MAPK activity|inhibition of adenylate cyclase activity by metabotropic glutamate receptor signaling pathway|neuroprotection|neurotransmitter secretion|positive regulation of MAPKKK cascade	cytoplasmic vesicle|integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(1)	1					L-Glutamic Acid(DB00142)									0.384615	71.767628	72.523258	25	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	34111963	34111963	7078	6	G	A	A	41	41	GRM4	A	2	2
FARS2	10667	broad.mit.edu	36	6	5558544	5558544	+	Silent	SNP	A	T	T			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:5558544A>T	uc010jnv.1	+	c.1209A>T	c.(1207-1209)GTA>GTT	p.V403V	FARS2_uc003mwr.2_Silent_p.V403V	NM_006567	NP_006558	O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2 precursor	403	FDX-ACB.				phenylalanyl-tRNA aminoacylation|tRNA processing	mitochondrial matrix|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)									0.093168	7.31233	34.107037	15	146	AA		KEEP	---	---	---	---	capture			Silent	SNP	5558544	5558544	5914	6	A	T	T	14	14	FARS2	T	4	4
ITGB8	3696	broad.mit.edu	36	7	20386821	20386821	+	Missense_Mutation	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:20386821A>G	uc003suu.1	+	c.643A>G	c.(643-645)AAT>GAT	p.N215D	ITGB8_uc003sut.2_Missense_Mutation_p.N215D	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor	215	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(2)	2										842				0.372881	186.39964	188.913571	66	111	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20386821	20386821	8205	7	A	G	G	5	5	ITGB8	G	4	4
STAR	6770	broad.mit.edu	36	8	38125001	38125001	+	Silent	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:38125001A>G	uc003xkv.1	-	c.180T>C	c.(178-180)GGT>GGC	p.G60G	STAR_uc010lwb.1_Silent_p.G60G|STAR_uc010lwc.1_Silent_p.G22G	NM_000349	NP_000340	P49675	STAR_HUMAN	steroidogenic acute regulatory protein isoform	60					C21-steroid hormone biosynthetic process	mitochondrial intermembrane space	cholesterol transporter activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.0151)|Lung NSC(58;0.0295)								134				0.425532	61.314041	61.55595	20	27	AA		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(644;0.188)	Silent	SNP	38125001	38125001	15773	8	A	G	G	2	2	STAR	G	4	4
GDF6	392255	broad.mit.edu	36	8	97226927	97226927	+	Missense_Mutation	SNP	G	C	C			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:97226927G>C	uc003yhp.1	-	c.408C>G	c.(406-408)GAC>GAG	p.D136E		NM_001001557	NP_001001557	Q6KF10	GDF6_HUMAN	growth differentiation factor 6 precursor	136					activin receptor signaling pathway|BMP signaling pathway|growth|pathway-restricted SMAD protein phosphorylation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription, DNA-dependent	extracellular space	cytokine activity|growth factor activity			ovary(1)|breast(1)|pancreas(1)	3	Breast(36;2.67e-05)													0.184211	18.304017	21.857048	7	31	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97226927	97226927	6585	8	G	C	C	40	40	GDF6	C	3	3
DEC1	50514	broad.mit.edu	36	9	117202512	117202512	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:117202512C>G	uc004bjk.1	+	c.67C>G	c.(67-69)CTT>GTT	p.L23V	DEC1_uc004bjl.1_Intron	NM_017418	NP_059114	Q9P2X7	DEC1_HUMAN	deleted in esophageal cancer 1	23					negative regulation of cell proliferation					ovary(1)	1														0.1	11.271236	27.255503	10	90	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117202512	117202512	4552	9	C	G	G	32	32	DEC1	G	3	3
ASTN2	23245	broad.mit.edu	36	9	118244596	118244596	+	Silent	SNP	G	T	T			TCGA-27-2521-01	TCGA-27-2521-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:118244596G>T	uc004bjs.1	-	c.3555C>A	c.(3553-3555)ACC>ACA	p.T1185T	ASTN2_uc004bjp.1_Silent_p.T278T|ASTN2_uc004bjq.1_Silent_p.T237T|ASTN2_uc004bjr.1_Silent_p.T1181T|ASTN2_uc004bjt.1_Silent_p.T1134T|ASTN2_uc004bjo.1_5'UTR	NM_198187	NP_937830	O75129	ASTN2_HUMAN	astrotactin 2 isoform c	1185	Extracellular (Potential).|Fibronectin type-III.					integral to membrane				ovary(3)|breast(1)|kidney(1)	5														0.639344	238.365287	240.449201	78	44	GG		KEEP	---	---	---	---	capture			Silent	SNP	118244596	118244596	1084	9	G	T	T	43	43	ASTN2	T	3	3
IFNW1	3467	broad.mit.edu	36	9	21131019	21131019	+	Missense_Mutation	SNP	C	G	G			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21131019C>G	uc003zol.1	-	c.551G>C	c.(550-552)AGA>ACA	p.R184T		NM_002177	NP_002168	P05000	IFNW1_HUMAN	interferon, omega 1	184					cell cycle arrest|defense response|response to virus	extracellular space	cytokine activity|cytokine receptor binding				0														0.578125	135.493091	135.836466	37	27	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(5;2.35e-185)|Lung(24;2.24e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)	Missense_Mutation	SNP	21131019	21131019	7853	9	C	G	G	32	32	IFNW1	G	3	3
IFNW1	3467	broad.mit.edu	36	9	21131108	21131108	+	Silent	SNP	C	G	G			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21131108C>G	uc003zol.1	-	c.462G>C	c.(460-462)CTG>CTC	p.L154L		NM_002177	NP_002168	P05000	IFNW1_HUMAN	interferon, omega 1	154					cell cycle arrest|defense response|response to virus	extracellular space	cytokine activity|cytokine receptor binding				0														0.672414	145.846359	147.375396	39	19	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(5;2.35e-185)|Lung(24;2.24e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)	Silent	SNP	21131108	21131108	7853	9	C	G	G	29	29	IFNW1	G	3	3
TMEM2	23670	broad.mit.edu	36	9	73514059	73514059	+	Missense_Mutation	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:73514059C>T	uc004aij.1	-	c.2921G>A	c.(2920-2922)CGC>CAC	p.R974H	TMEM2_uc010mos.1_Missense_Mutation_p.R911H	NM_013390	NP_037522	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2 isoform a	974						integral to membrane				ovary(2)	2		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)												0.635417	187.495204	189.045476	61	35	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)	Missense_Mutation	SNP	73514059	73514059	16656	9	C	T	T	27	27	TMEM2	T	1	1
DMD	1756	broad.mit.edu	36	X	31110841	31110841	+	Silent	SNP	A	C	C			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:31110841A>C	uc004dda.1	-	c.9909T>G	c.(9907-9909)GCT>GCG	p.A3303A	DMD_uc004dcr.1_Silent_p.A843A|DMD_uc004dcs.1_Silent_p.A843A|DMD_uc004dct.1_Silent_p.A843A|DMD_uc004dcu.1_Silent_p.A843A|DMD_uc004dcv.1_Silent_p.A843A|DMD_uc004dcw.2_Silent_p.A1959A|DMD_uc004dcx.2_Silent_p.A1962A|DMD_uc004dcz.2_Silent_p.A3180A|DMD_uc004dcy.1_Silent_p.A3299A|DMD_uc004ddb.1_Silent_p.A3295A|DMD_uc004dcm.1_Silent_p.A235A|DMD_uc004dcn.1_Silent_p.A235A|DMD_uc004dco.1_Silent_p.A235A|DMD_uc004dcp.1_Silent_p.A235A|DMD_uc004dcq.1_Silent_p.A574A|DMD_uc010ngm.1_Silent_p.A235A	NM_004006	NP_004001	P11532	DMD_HUMAN	dystrophin Dp427m isoform	3303	Interaction with SYNM (By similarity).				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.190476	9.543759	13.360743	8	34	AA		KEEP	---	---	---	---	capture			Silent	SNP	31110841	31110841	4760	23	A	C	C	7	7	DMD	C	4	4
MAGEB16	139604	broad.mit.edu	36	X	35730720	35730720	+	Silent	SNP	A	G	G			TCGA-27-2521-01	TCGA-27-2521-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:35730720A>G	uc010ngt.1	+	c.486A>G	c.(484-486)CTA>CTG	p.L162L	MAGEB16_uc010ngu.1_Silent_p.L162L	NM_001099921	NP_001093391	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	162	MAGE.									lung(3)|ovary(2)|breast(1)	6										43				0.928571	305.056275	318.926493	78	6	AA		KEEP	---	---	---	---	capture			Silent	SNP	35730720	35730720	9555	23	A	G	G	15	15	MAGEB16	G	4	4
WDR13	64743	broad.mit.edu	36	X	48343709	48343709	+	Silent	SNP	C	T	T			TCGA-27-2521-01	TCGA-27-2521-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48343709C>T	uc004dkh.1	+	c.582C>T	c.(580-582)GAC>GAT	p.D194D	WDR13_uc010nif.1_Silent_p.D72D|WDR13_uc004dki.1_Silent_p.D102D|WDR13_uc004dkj.1_Silent_p.D194D|WDR13_uc004dkk.1_Silent_p.D102D|WDR13_uc004dkl.2_Silent_p.D102D	NM_017883	NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13 protein	194	WD 1.					cytoplasm|nucleus				ovary(2)	2														0.86	137.753115	144.008462	43	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	48343709	48343709	17848	23	C	T	T	19	19	WDR13	T	1	1
TP53	7157	broad.mit.edu	36	17	7517874	7517874	+	Frame_Shift_Del	DEL	A	-	-			TCGA-27-2521-01	TCGA-27-2521-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7517874_7517874delA	uc002gim.2	-	c.789_789delT	c.(787-789)AATfs	p.N263fs	TP53_uc002gig.1_Intron|TP53_uc002gih.1_Frame_Shift_Del_p.N263fs|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Frame_Shift_Del_p.N131fs|TP53_uc010cng.1_Frame_Shift_Del_p.N131fs|TP53_uc002gii.1_Frame_Shift_Del_p.N131fs|TP53_uc010cnh.1_Frame_Shift_Del_p.N263fs|TP53_uc010cni.1_Frame_Shift_Del_p.N263fs|TP53_uc002gij.2_Frame_Shift_Del_p.N263fs	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	263	|Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		GN -> PD (in a sporadic cancer; somatic mutation).|N -> S (in a sporadic cancer; somatic mutation).|N -> K (in a sporadic cancer; somatic mutation).|N -> D (in sporadic cancers; somatic mutation).|N -> H (in sporadic cancers; somatic mutation).|N -> I (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.0?(6)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262_S269delGNLLGRNS(2)|p.E258fs*71(1)|p.S261_L264>R(1)|p.N263K(1)|p.G262fs*2(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111		690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.95			52	3				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	7517874	7517874	16923	17	A	-	-	12	12	TP53	-	5	5
GRLF1	2909	broad.mit.edu	36	19	52195740	52195741	+	Frame_Shift_Ins	INS	-	C	C			TCGA-27-2521-01	TCGA-27-2521-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52195740_52195741insC	uc010ekv.1	+	c.4455_4456insC	c.(4453-4458)ATGCAGfs	p.M1485fs		NM_004491	NP_004482	Q9NRY4	GRLF1_HUMAN	glucocorticoid receptor DNA binding factor 1	1485_1486	Pro-rich.				axon guidance|negative regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|transcription, DNA-dependent	cytosol|nucleus	DNA binding|Rho GTPase activator activity|transcription corepressor activity|transcription repressor activity			central_nervous_system(1)	1		all_cancers(25;1.51e-09)|all_epithelial(76;1.87e-07)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|Ovarian(192;0.0129)|all_neural(266;0.026)|Breast(70;0.077)		all cancers(93;2.03e-05)|OV - Ovarian serous cystadenocarcinoma(262;2.57e-05)|Epithelial(262;0.00135)|GBM - Glioblastoma multiforme(486;0.0289)										0.36			4	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	52195740	52195741	7074	19	-	C	C	46	46	GRLF1	C	5	5
ZNF71	58491	broad.mit.edu	36	19	61824532	61824533	+	Frame_Shift_Ins	INS	-	G	G			TCGA-27-2521-01	TCGA-27-2521-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:61824532_61824533insG	uc002qnm.2	+	c.65_66insG	c.(64-66)ACGfs	p.T22fs	ZNF71_uc010eto.1_Frame_Shift_Ins_p.T22fs	NM_021216	NP_067039	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	22					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)										0.82			50	11				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	61824532	61824533	18710	19	-	G	G	19	19	ZNF71	G	5	5
