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
SVOP	55530	broad.mit.edu	36	12	107830596	107830596	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107830596G>C	uc001tnt.1	-	c.1491C>G	c.(1489-1491)TGC>TGG	p.C497W		NM_018711	NP_061181	Q8N4V2	SVOP_HUMAN	SV2 related protein	497	Helical; (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	ion transmembrane transporter activity				0														0.217391	8.179613	9.864357	5	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107830596	107830596	15943	12	G	C	C	34	34	SVOP	C	3	3
RNF34	80196	broad.mit.edu	36	12	120345608	120345608	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120345608A>C	uc001uam.1	+	c.965A>C	c.(964-966)GAC>GCC	p.D322A	RNF34_uc001uak.1_Missense_Mutation_p.D323A|RNF34_uc001ual.1_Missense_Mutation_p.D322A	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	322					apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)													0.3	6.921564	7.278781	3	7	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)	Missense_Mutation	SNP	120345608	120345608	13968	12	A	C	C	10	10	RNF34	C	4	4
BAZ2A	11176	broad.mit.edu	36	12	55281603	55281603	+	Silent	SNP	G	T	T			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55281603G>T	uc001slq.1	-	c.4071C>A	c.(4069-4071)TCC>TCA	p.S1357S	BAZ2A_uc001slo.1_Silent_p.S185S|BAZ2A_uc009zov.1_Silent_p.S327S|BAZ2A_uc009zow.1_Silent_p.S1325S|BAZ2A_uc001slp.1_Silent_p.S1355S	NM_013449	NP_038477	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1357	Pro-rich.				chromatin silencing at rDNA|DNA methylation|transcription, DNA-dependent	chromatin silencing complex|nucleolus|rDNA heterochromatin	DNA binding|histone acetyl-lysine binding|ligand-dependent nuclear receptor binding|RNA binding|transcription regulator activity|zinc ion binding				0														0.361111	13.869023	14.639847	13	23	GG		KEEP	---	---	---	---	capture			Silent	SNP	55281603	55281603	1352	12	G	T	T	47	47	BAZ2A	T	3	3
PPM1H	57460	broad.mit.edu	36	12	61481979	61481979	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:61481979C>T	uc001srk.2	-	c.640G>A	c.(640-642)GGA>AGA	p.G214R		NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)	214	PP2C-like.						phosphoprotein phosphatase activity			ovary(1)	1														0.425287	111.465694	111.887788	37	50	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)	Missense_Mutation	SNP	61481979	61481979	12776	12	C	T	T	23	23	PPM1H	T	1	1
CD163L1	283316	broad.mit.edu	36	12	7423081	7423081	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7423081C>T	uc001qsy.1	-	c.2131G>A	c.(2131-2133)GTG>ATG	p.V711M		NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	711	SRCR 7.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.276423	84.596779	90.13312	34	89	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7423081	7423081	3095	12	C	T	T	19	19	CD163L1	T	1	1
AK7	122481	broad.mit.edu	36	14	96022995	96022995	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:96022995G>A	uc001yfn.2	+	c.1982G>A	c.(1981-1983)CGA>CAA	p.R661Q		NM_152327	NP_689540	Q96M32	KAD7_HUMAN	adenylate kinase 7	661	Potential.|Glu-rich.				cell projection organization	cytosol	adenylate kinase activity|ATP binding|cytidylate kinase activity			ovary(1)	1		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)												0.384615	100.309451	101.369282	35	56	GG		KEEP	---	---	---	---	capture		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)	Missense_Mutation	SNP	96022995	96022995	447	14	G	A	A	37	37	AK7	A	1	1
RYR3	6263	broad.mit.edu	36	15	31732287	31732287	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31732287G>A	uc001zhi.1	+	c.4219G>A	c.(4219-4221)GTG>ATG	p.V1407M	RYR3_uc010bar.1_Missense_Mutation_p.V1407M	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1407	4 X approximate repeats.|B30.2/SPRY 3.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.353448	108.502786	110.715174	41	75	GG		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31732287	31732287	14250	15	G	A	A	40	40	RYR3	A	1	1
ZSCAN29	146050	broad.mit.edu	36	15	41445756	41445756	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41445756C>T	uc001zrk.1	-	c.1066G>A	c.(1066-1068)GAT>AAT	p.D356N	ZSCAN29_uc001zrj.1_Missense_Mutation_p.D236N|ZSCAN29_uc010bdf.1_Missense_Mutation_p.D355N|ZSCAN29_uc001zrl.1_Non-coding_Transcript|ZSCAN29_uc010bdg.1_Intron|ZSCAN29_uc001zrm.2_Missense_Mutation_p.D355N	NM_152455	NP_689668	Q8IWY8	ZSC29_HUMAN	zinc finger protein 690	356					regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)												0.416667	168.863278	169.737989	60	84	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;8.97e-07)	Missense_Mutation	SNP	41445756	41445756	18840	15	C	T	T	31	31	ZSCAN29	T	1	1
SLC28A2	9153	broad.mit.edu	36	15	43342651	43342651	+	Silent	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43342651G>A	uc001zva.1	+	c.363G>A	c.(361-363)TCG>TCA	p.S121S		NM_004212	NP_004203	O43868	S28A2_HUMAN	solute carrier family 28 (sodium-coupled	121	Helical; (Potential).				nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity			ovary(4)	4		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)				NSCLC(92;493 1501 26361 28917 47116)								0.366197	145.753125	147.99206	52	90	GG		KEEP	---	---	---	---	capture		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Silent	SNP	43342651	43342651	15029	15	G	A	A	40	40	SLC28A2	A	1	1
GRIN2A	2903	broad.mit.edu	36	16	10181380	10181380	+	Silent	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10181380G>A	uc002czp.1	-	c.390C>T	c.(388-390)GGC>GGT	p.G130G	GRIN2A_uc002czq.1_Silent_p.G130G|GRIN2A_uc002czr.2_Silent_p.G130G|GRIN2A_uc010buk.1_Silent_p.G130G	NM_000833	NP_000824	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	130	Extracellular (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.330097	92.350573	94.968186	34	69	GG		KEEP	---	---	---	---	capture			Silent	SNP	10181380	10181380	7058	16	G	A	A	38	38	GRIN2A	A	1	1
HS3ST3A1	9955	broad.mit.edu	36	17	13340813	13340813	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:13340813G>A	uc002gob.1	-	c.647C>T	c.(646-648)ACG>ATG	p.T216M		NM_006042	NP_006033	Q9Y663	HS3SA_HUMAN	heparan sulfate D-glucosaminyl	216	Substrate binding.|Lumenal (Potential).					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)												0.401786	124.329161	125.279713	45	67	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)	Missense_Mutation	SNP	13340813	13340813	7659	17	G	A	A	40	40	HS3ST3A1	A	1	1
MYO18A	399687	broad.mit.edu	36	17	24473333	24473333	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:24473333A>C	uc002hdt.1	-	c.1064T>G	c.(1063-1065)GTC>GGC	p.V355G	MYO18A_uc010csa.1_Missense_Mutation_p.V355G|MYO18A_uc002hdu.1_Missense_Mutation_p.V355G|MYO18A_uc002hds.1_5'UTR	NM_078471	NP_510880	Q92614	MY18A_HUMAN	myosin 18A isoform a	355					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)								0.235294	8.390283	9.480988	4	13	AA		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	24473333	24473333	10460	17	A	C	C	10	10	MYO18A	C	4	4
ABCA9	10350	broad.mit.edu	36	17	64528233	64528233	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:64528233C>T	uc002jhu.1	-	c.2491G>A	c.(2491-2493)GAA>AAA	p.E831K	ABCA9_uc010dez.1_Missense_Mutation_p.E831K	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9	831					transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|central_nervous_system(1)	5	Breast(10;1.47e-12)													0.37963	235.423654	238.158505	82	134	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64528233	64528233	40	17	C	T	T	31	31	ABCA9	T	1	1
LIPG	9388	broad.mit.edu	36	18	45355835	45355835	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:45355835C>T	uc002ldv.1	+	c.670C>T	c.(670-672)CGT>TGT	p.R224C	LIPG_uc002ldu.1_Missense_Mutation_p.R224C	NM_006033	NP_006024	Q9Y5X9	LIPE_HUMAN	endothelial lipase precursor	224					cholesterol homeostasis|high-density lipoprotein particle remodeling|phospholipid catabolic process|phospholipid homeostasis|positive regulation of cholesterol transport|positive regulation of high-density lipoprotein particle clearance|reverse cholesterol transport	extracellular space	heparin binding|lipoprotein lipase activity|phospholipase A1 activity|protein binding|triglyceride lipase activity			ovary(1)	1						Pancreas(126;280 1778 12814 26243 34948)								0.383838	104.13817	105.30444	38	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45355835	45355835	9150	18	C	T	T	27	27	LIPG	T	1	1
GRAMD1A	57655	broad.mit.edu	36	19	40192711	40192711	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1747-01	TCGA-28-1747-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:40192711T>C	uc002nxj.1	+	c.320T>C	c.(319-321)ATT>ACT	p.I107T	GRAMD1A_uc002nxi.1_Missense_Mutation_p.I194T|GRAMD1A_uc002nxk.1_Missense_Mutation_p.I100T|GRAMD1A_uc002nxl.1_5'UTR	NM_020895	NP_065946	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A isoform 1	107	GRAM.					integral to membrane					0	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)													0.4	242.646371	244.224903	72	108	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(66;0.0849)		Missense_Mutation	SNP	40192711	40192711	7023	19	T	C	C	52	52	GRAMD1A	C	4	4
ZNF610	162963	broad.mit.edu	36	19	57560767	57560767	+	Silent	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:57560767G>A	uc002pyx.2	+	c.324G>A	c.(322-324)AGG>AGA	p.R108R	ZNF610_uc002pyy.2_Silent_p.R108R|ZNF610_uc002pyz.2_Silent_p.R65R|ZNF610_uc002pza.1_Silent_p.R108R	NM_173530	NP_775801	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	108					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.305556	205.895545	214.388998	77	175	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)	Silent	SNP	57560767	57560767	18631	19	G	A	A	41	41	ZNF610	A	2	2
PTPRH	5794	broad.mit.edu	36	19	60385074	60385074	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60385074C>T	uc002qjq.1	-	c.3208G>A	c.(3208-3210)GTA>ATA	p.V1070I	SYT5_uc002qjm.1_5'Flank|SYT5_uc002qjn.1_5'Flank|SYT5_uc002qjo.1_5'Flank|SYT5_uc002qjp.1_5'Flank|PTPRH_uc010esv.1_Missense_Mutation_p.V892I	NM_002842	NP_002833	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1070	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.				apoptosis	cytoplasm|integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(2)|large_intestine(1)	3		Renal(1328;0.245)												0.318841	173.394238	179.422823	66	141	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)	Missense_Mutation	SNP	60385074	60385074	13260	19	C	T	T	19	19	PTPRH	T	1	1
TUBB4	10382	broad.mit.edu	36	19	6446585	6446585	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6446585G>A	uc002mfg.1	-	c.925C>T	c.(925-927)CGC>TGC	p.R309C	TUBB4_uc002mff.1_Missense_Mutation_p.R237C	NM_006087	NP_006078	P04350	TBB4_HUMAN	tubulin, beta 4	309					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(2)	2		Hepatocellular(1079;0.00213)|Renal(1328;0.0183)												0.299213	97.59765	102.176224	38	89	GG		KEEP	---	---	---	---	capture		Lung(535;3.23e-05)|STAD - Stomach adenocarcinoma(1328;8.24e-05)|GBM - Glioblastoma multiforme(1328;0.00839)|READ - Rectum adenocarcinoma(264;0.155)	Missense_Mutation	SNP	6446585	6446585	17313	19	G	A	A	39	39	TUBB4	A	1	1
MUC16	94025	broad.mit.edu	36	19	8934488	8934488	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8934488G>T	uc002mkp.1	-	c.13958C>A	c.(13957-13959)ACA>AAA	p.T4653K		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4655	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.38125	188.038377	190.016844	61	99	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8934488	8934488	10367	19	G	T	T	48	48	MUC16	T	3	3
C19orf6	91304	broad.mit.edu	36	19	963523	963523	+	Silent	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:963523G>A	uc002lqr.1	-	c.657C>T	c.(655-657)TTC>TTT	p.F219F	C19orf6_uc002lqq.1_Non-coding_Transcript|C19orf6_uc002lqs.1_Silent_p.F219F	NM_001033026	NP_001028198	Q4ZIN3	MBRL_HUMAN	membralin isoform 1	219						cytoplasm|integral to membrane				pancreas(2)|breast(1)	3		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)												0.384615	6.556372	6.743818	5	8	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)|GBM - Glioblastoma multiforme(1328;0.0252)|STAD - Stomach adenocarcinoma(1328;0.18)	Silent	SNP	963523	963523	2005	19	G	A	A	41	41	C19orf6	A	2	2
DCLRE1B	64858	broad.mit.edu	36	1	114255879	114255879	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:114255879G>A	uc001eeg.1	+	c.1142G>A	c.(1141-1143)TGG>TAG	p.W381*	DCLRE1B_uc001eeh.2_Nonsense_Mutation_p.W255*|DCLRE1B_uc001eei.1_Nonsense_Mutation_p.W255*	NM_022836	NP_073747	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B (PSO2 homolog, S.	381					cell cycle checkpoint|DNA repair|protection from non-homologous end joining at telomere|telomeric 3' overhang formation|telomeric loop formation	centrosome|chromosome, telomeric region|nucleus	5'-3' exonuclease activity|protein binding				0	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)												0.404762	246.155422	247.813226	85	125	GG		KEEP	---	---	---	---	capture		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)	Nonsense_Mutation	SNP	114255879	114255879	4466	1	G	A	A	47	47	DCLRE1B	A	5	2
PLA2G4A	5321	broad.mit.edu	36	1	185215142	185215142	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1747-01	TCGA-28-1747-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:185215142T>G	uc001gsc.1	+	c.2033T>G	c.(2032-2034)TTT>TGT	p.F678C		NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	678	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			breast(1)	1					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)									0.368132	230.399905	233.173022	67	115	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	185215142	185215142	12427	1	T	G	G	64	64	PLA2G4A	G	4	4
CLCA1	1179	broad.mit.edu	36	1	86727382	86727382	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:86727382A>G	uc001dlt.1	+	c.1298A>G	c.(1297-1299)CAC>CGC	p.H433R	CLCA1_uc001dls.1_Missense_Mutation_p.H372R	NM_001285	NP_001276	A8K7I4	CLCA1_HUMAN	chloride channel accessory 1 precursor	433	VWFA.				calcium ion transport	extracellular space|integral to plasma membrane	chloride channel activity			ovary(1)	1		Lung NSC(277;0.239)												0.325843	90.749015	93.141496	29	60	AA		KEEP	---	---	---	---	capture		all cancers(265;0.0249)|Epithelial(280;0.0476)	Missense_Mutation	SNP	86727382	86727382	3593	1	A	G	G	6	6	CLCA1	G	4	4
MOCS3	27304	broad.mit.edu	36	20	49009831	49009831	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:49009831G>C	uc002xvy.1	+	c.1045G>C	c.(1045-1047)GCA>CCA	p.A349P	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	349	Rhodanese.				enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			ovary(1)|skin(1)	2														0.336427	459.832435	469.990601	145	286	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49009831	49009831	10083	20	G	C	C	42	42	MOCS3	C	3	3
ANGPT4	51378	broad.mit.edu	36	20	801677	801677	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:801677G>A	uc002wei.1	-	c.1438C>T	c.(1438-1440)CGC>TGC	p.R480C		NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4	480	Fibrinogen C-terminal.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						Pancreas(181;481 2077 3259 31286 49856)								0.342105	116.097464	118.605312	39	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	801677	801677	615	20	G	A	A	39	39	ANGPT4	A	1	1
TRPM2	7226	broad.mit.edu	36	21	44623366	44623366	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44623366G>A	uc010gpt.1	+	c.1073G>A	c.(1072-1074)CGC>CAC	p.R358H	TRPM2_uc002zet.1_Missense_Mutation_p.R358H|TRPM2_uc002zeu.1_Missense_Mutation_p.R358H|TRPM2_uc002zew.1_Missense_Mutation_p.R358H|TRPM2_uc002zex.1_Missense_Mutation_p.R144H	NM_003307	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel,	358	Cytoplasmic (Potential).					integral to plasma membrane	ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.340206	82.743869	84.93373	33	64	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44623366	44623366	17137	21	G	A	A	38	38	TRPM2	A	1	1
NT5C1B	93034	broad.mit.edu	36	2	18629618	18629618	+	Silent	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:18629618C>T	uc010exr.1	-	c.372G>A	c.(370-372)TCG>TCA	p.S124S	NT5C1B_uc002rcy.1_Silent_p.S182S|NT5C1B_uc002rcz.1_Silent_p.S182S|NT5C1B_uc002rda.1_Silent_p.S122S|NT5C1B_uc010exs.1_Silent_p.S184S|NT5C1B_uc002rdb.1_5'UTR	NM_033253	NP_150278	Q96P26	5NT1B_HUMAN	5' nucleotidase, cytosolic IB isoform 2	182	Pro-rich.				purine base metabolic process|purine nucleotide catabolic process	cytosol	5'-nucleotidase activity|magnesium ion binding|nucleotide binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)	Ovarian(717;0.208)												0.428571	33.997869	34.121576	12	16	CC		KEEP	---	---	---	---	capture			Silent	SNP	18629618	18629618	11091	2	C	T	T	27	27	NT5C1B	T	1	1
CALCRL	10203	broad.mit.edu	36	2	187932211	187932211	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:187932211A>T	uc002upv.2	-	c.815T>A	c.(814-816)ATT>AAT	p.I272N	CALCRL_uc010frt.1_Missense_Mutation_p.I272N	NM_005795	NP_005786	Q16602	CALRL_HUMAN	calcitonin receptor-like	272	Helical; Name=4; (Potential).					integral to plasma membrane				ovary(1)	1														0.3125	27.538256	28.539823	10	22	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)		Missense_Mutation	SNP	187932211	187932211	2696	2	A	T	T	4	4	CALCRL	T	4	4
BMPR2	659	broad.mit.edu	36	2	203105581	203105581	+	Missense_Mutation	SNP	A	G	G			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:203105581A>G	uc002uzf.2	+	c.1157A>G	c.(1156-1158)GAA>GGA	p.E386G	BMPR2_uc010ftr.1_Missense_Mutation_p.E386G	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II	386	Protein kinase.|Cytoplasmic (Potential).				anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|large_intestine(1)|stomach(1)|pancreas(1)	7										409				0.371429	178.268527	180.300236	52	88	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	203105581	203105581	1496	2	A	G	G	9	9	BMPR2	G	4	4
SCG2	7857	broad.mit.edu	36	2	224172003	224172003	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1747-01	TCGA-28-1747-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:224172003T>C	uc002vnm.1	-	c.242A>G	c.(241-243)TAC>TGC	p.Y81C	SCG2_uc010fwv.1_Missense_Mutation_p.Y81C	NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	81					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)												0.383966	308.151248	310.953524	91	146	TT		KEEP	---	---	---	---	capture		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)	Missense_Mutation	SNP	224172003	224172003	14372	2	T	C	C	57	57	SCG2	C	4	4
OR5K4	403278	broad.mit.edu	36	3	99555508	99555508	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:99555508G>A	uc003dsk.1	+	c.121G>A	c.(121-123)GGG>AGG	p.G41R		NM_001005517	NP_001005517	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K,	41	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.361111	605.723175	615.467783	208	368	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99555508	99555508	11579	3	G	A	A	43	43	OR5K4	A	2	2
ADAM29	11086	broad.mit.edu	36	4	176134183	176134183	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:176134183G>A	uc003iuc.1	+	c.932G>A	c.(931-933)CGT>CAT	p.R311H	ADAM29_uc003iud.1_Missense_Mutation_p.R311H|ADAM29_uc003iue.1_Missense_Mutation_p.R311H|ADAM29_uc010irr.1_Missense_Mutation_p.R311H	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	311	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)				Ovarian(140;1727 1835 21805 25838 41440)				106				0.398827	393.732771	396.784361	136	205	GG		KEEP	---	---	---	---	capture		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)	Missense_Mutation	SNP	176134183	176134183	248	4	G	A	A	40	40	ADAM29	A	1	1
PCDHA9	9752	broad.mit.edu	36	5	140210268	140210268	+	Silent	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140210268G>A	uc003lhu.1	+	c.2004G>A	c.(2002-2004)TCG>TCA	p.S668S	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhd.1_Intron|PCDHA3_uc003lhf.1_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA4_uc003lhi.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.1_Intron|PCDHA6_uc003lho.1_Intron|PCDHA6_uc003lhn.1_Intron|PCDHA7_uc003lhq.1_Intron|PCDHA8_uc003lhs.1_Intron|PCDHA9_uc003lht.1_Silent_p.S668S	NM_031857	NP_114063	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9 isoform 1 precursor	668	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			large_intestine(2)|ovary(2)	4						Melanoma(55;1800 1972 14909)								0.358696	83.529845	85.154938	33	59	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140210268	140210268	11951	5	G	A	A	38	38	PCDHA9	A	1	1
SLC6A3	6531	broad.mit.edu	36	5	1462844	1462844	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1462844C>T	uc003jck.2	-	c.1390G>A	c.(1390-1392)GTC>ATC	p.V464I		NM_001044	NP_001035	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter	464	Helical; Name=9; (Potential).				cell death|neurotransmitter biosynthetic process	axon|cytoplasm|integral to plasma membrane|neuronal cell body				ovary(3)|breast(2)|pancreas(1)	6					Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)									0.327731	103.291451	106.419593	39	80	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Missense_Mutation	SNP	1462844	1462844	15182	5	C	T	T	19	19	SLC6A3	T	1	1
ZFYVE16	9765	broad.mit.edu	36	5	79804455	79804455	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79804455G>A	uc003kgr.2	+	c.4144G>A	c.(4144-4146)GTG>ATG	p.V1382M	ZFYVE16_uc003kgq.2_Missense_Mutation_p.V1382M|ZFYVE16_uc003kgs.2_Missense_Mutation_p.V1382M|ZFYVE16_uc003kgt.2_Missense_Mutation_p.V470M|ZFYVE16_uc003kgu.2_Missense_Mutation_p.V134M	NM_001105251	NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	1382					BMP signaling pathway|endosome transport|protein targeting to lysosome|regulation of endocytosis|vesicle organization	early endosome membrane	1-phosphatidylinositol binding|phosphatidylinositol-3,4,5-trisphosphate binding|protein binding|protein transporter activity|zinc ion binding				0		Lung NSC(167;0.00428)|all_lung(232;0.00455)|Ovarian(174;0.0261)				Melanoma(150;1452 1854 16018 17851 37292)								0.335937	120.582336	123.632014	43	85	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;1.6e-46)|Epithelial(54;2.02e-41)|all cancers(79;5.05e-36)	Missense_Mutation	SNP	79804455	79804455	18254	5	G	A	A	40	40	ZFYVE16	A	1	1
ACOT12	134526	broad.mit.edu	36	5	80679381	80679381	+	Silent	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:80679381C>T	uc003khl.2	-	c.621G>A	c.(619-621)GCG>GCA	p.A207A		NM_130767	NP_570123	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	207	Acyl coenzyme A hydrolase 2.				acyl-CoA metabolic process|fatty acid metabolic process	cytosol	acetyl-CoA hydrolase activity|carboxylesterase activity			ovary(1)|kidney(1)	2		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)												0.375221	593.579043	601.292608	212	353	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)	Silent	SNP	80679381	80679381	151	5	C	T	T	19	19	ACOT12	T	1	1
PCSK1	5122	broad.mit.edu	36	5	95761630	95761630	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:95761630G>A	uc003kls.1	-	c.1213C>T	c.(1213-1215)CGA>TGA	p.R405*	PCSK1_uc010jbi.1_Nonsense_Mutation_p.R95*	NM_000439	NP_000430	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	405	Catalytic.				cell-cell signaling|cellular nitrogen compound metabolic process|energy reserve metabolic process|hormone biosynthetic process|peptide biosynthetic process|peptide hormone processing|regulation of insulin secretion	extracellular space|stored secretory granule|transport vesicle	serine-type endopeptidase activity			ovary(2)	2		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)			Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)									0.306569	102.291051	106.867122	42	95	GG		KEEP	---	---	---	---	capture		all cancers(79;3.44e-16)	Nonsense_Mutation	SNP	95761630	95761630	12020	5	G	A	A	38	38	PCSK1	A	5	1
TCF21	6943	broad.mit.edu	36	6	134252291	134252291	+	Silent	SNP	C	T	T	rs61729591	unknown	TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:134252291C>T	uc003qei.2	+	c.63C>T	c.(61-63)GAC>GAT	p.D21D	TCF21_uc010kgf.1_Silent_p.D21D|TCF21_uc003qej.1_Silent_p.D21D	NM_198392	NP_938206	O43680	TCF21_HUMAN	transcription factor 21	21					branching involved in ureteric bud morphogenesis|mesoderm development|negative regulation of androgen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus	androgen receptor binding|E-box binding|protein dimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0	Colorectal(23;0.221)|Breast(56;0.247)									20				0.339506	152.419878	156.087792	55	107	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)	Silent	SNP	134252291	134252291	16217	6	C	T	T	19	19	TCF21	T	1	1
GPX5	2880	broad.mit.edu	36	6	28605306	28605306	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:28605306C>T	uc003nll.1	+	c.187C>T	c.(187-189)CAC>TAC	p.H63Y	GPX5_uc003nlm.1_Missense_Mutation_p.H63Y|GPX5_uc003nln.1_Non-coding_Transcript	NM_001509	NP_001500	O75715	GPX5_HUMAN	glutathione peroxidase 5 isoform 1 precursor	63					lipid metabolic process|oxidation-reduction process|response to oxidative stress	extracellular region	glutathione peroxidase activity				0					Glutathione(DB00143)									0.397849	202.592469	204.295658	74	112	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28605306	28605306	7019	6	C	T	T	25	25	GPX5	T	2	2
FAM50B	26240	broad.mit.edu	36	6	3795732	3795732	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:3795732G>A	uc003mvu.1	+	c.688G>A	c.(688-690)GCC>ACC	p.A230T	FAM50B_uc010jnp.1_Missense_Mutation_p.A230T	NM_012135	NP_036267	Q9Y247	FA50B_HUMAN	family with sequence similarity 50, member B	230						nucleus				pancreas(1)	1	Ovarian(93;0.0925)	all_hematologic(90;0.108)												0.295082	43.689407	45.946191	18	43	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3795732	3795732	5800	6	G	A	A	38	38	FAM50B	A	1	1
EGFR	1956	broad.mit.edu	36	7	55200537	55200537	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55200537G>T	uc003tqk.1	+	c.1793G>T	c.(1792-1794)GGA>GTA	p.G598V	EGFR_uc003tqi.1_Missense_Mutation_p.G598V|EGFR_uc003tqj.1_Missense_Mutation_p.G598V|EGFR_uc010kzg.1_Missense_Mutation_p.G553V|EGFR_uc003tqn.1_Non-coding_Transcript	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	598	Approximate.|Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	p.G598V(16)		lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.12228	111.578682	246.675456	118	847	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55200537	55200537	5156	7	G	T	T	41	41	EGFR	T	3	3
PCLO	27445	broad.mit.edu	36	7	82422971	82422971	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1747-01	TCGA-28-1747-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82422971G>A	uc003uhx.2	-	c.5234C>T	c.(5233-5235)CCG>CTG	p.P1745L	PCLO_uc003uhv.2_Missense_Mutation_p.P1745L	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	1676					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.261965	280.5221	300.812463	104	293	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82422971	82422971	12003	7	G	A	A	39	39	PCLO	A	1	1
TG	7038	broad.mit.edu	36	8	133994577	133994577	+	Silent	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:133994577C>T	uc003ytw.1	+	c.4263C>T	c.(4261-4263)ACC>ACT	p.T1421T	TG_uc010mdw.1_Silent_p.T180T	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin	1421					hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)								1778				0.417391	143.59426	144.275182	48	67	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)	Silent	SNP	133994577	133994577	16341	8	C	T	T	21	21	TG	T	2	2
BAI1	575	broad.mit.edu	36	8	143602646	143602646	+	Silent	SNP	A	C	C			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143602646A>C	uc003ywm.1	+	c.3291A>C	c.(3289-3291)GGA>GGC	p.G1097G		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1097	Helical; Name=5; (Potential).				axonogenesis|cell adhesion|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)									829				0.571429	10.698783	10.729772	4	3	AA		KEEP	---	---	---	---	capture			Silent	SNP	143602646	143602646	1319	8	A	C	C	10	10	BAI1	C	4	4
AKNA	80709	broad.mit.edu	36	9	116139192	116139192	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:116139192C>T	uc004biq.2	-	c.4283G>A	c.(4282-4284)CGC>CAC	p.R1428H	AKNA_uc004bin.2_Missense_Mutation_p.R675H|AKNA_uc004bio.2_Missense_Mutation_p.R888H|AKNA_uc004bip.2_Missense_Mutation_p.R1347H|AKNA_uc004bir.2_Missense_Mutation_p.R1428H|AKNA_uc004bis.2_Missense_Mutation_p.R1428H|AKNA_uc010mve.1_Missense_Mutation_p.R1309H	NM_030767	NP_110394	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1428					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(4)|central_nervous_system(2)	6														0.315789	14.040838	14.615648	6	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116139192	116139192	466	9	C	T	T	27	27	AKNA	T	1	1
GATA1	2623	broad.mit.edu	36	X	48535703	48535703	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1747-01	TCGA-28-1747-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48535703A>C	uc004dkq.2	+	c.628A>C	c.(628-630)ACA>CCA	p.T210P		NM_002049	NP_002040	P15976	GATA1_HUMAN	GATA binding protein 1	210	Required for interaction with ZFPM1.|GATA-type 1.				blood coagulation|regulation of transcription from RNA polymerase II promoter	nuclear membrane|nucleolus|nucleoplasm	sequence-specific DNA binding transcription factor activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(213)|lung(2)	215						Pancreas(9;429 505 11287 29617)				37				0.16	6.486973	9.238067	4	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48535703	48535703	6517	23	A	C	C	2	2	GATA1	C	4	4
WDR45	11152	broad.mit.edu	36	X	48819979	48819979	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1747-01	TCGA-28-1747-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48819979T>G	uc004dmo.1	-	c.884A>C	c.(883-885)AAC>ACC	p.N295T	PRAF2_uc004dmh.1_5'Flank|PRAF2_uc004dmi.1_5'Flank|WDR45_uc004dmj.1_Missense_Mutation_p.N233T|WDR45_uc004dmk.1_Missense_Mutation_p.N272T|WDR45_uc004dml.1_Missense_Mutation_p.N273T|WDR45_uc004dmm.1_Missense_Mutation_p.N237T|WDR45_uc010nim.1_Intron|WDR45_uc004dmn.1_Missense_Mutation_p.N163T|WDR45_uc004dmp.1_Missense_Mutation_p.N273T	NM_007075	NP_009006	Q9Y484	WIPI4_HUMAN	WD repeat domain 45 isoform 1	272	WD 3.				autophagy|response to starvation	organelle membrane	phosphatidylinositol-3,5-bisphosphate binding			ovary(1)	1														0.333333	8.363971	8.675621	4	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48819979	48819979	17870	23	T	G	G	60	60	WDR45	G	4	4
NHSL2	340527	broad.mit.edu	36	X	71276268	71276268	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-1747-01	TCGA-28-1747-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:71276268C>A	uc010nli.1	+	c.1452C>A	c.(1450-1452)TAC>TAA	p.Y484*	NHSL2_uc004eak.1_Nonsense_Mutation_p.Y349*|NHSL2_uc010nlj.1_Nonsense_Mutation_p.Y349*	NM_001013627	NP_001013649			NHS-like 2												0	Renal(35;0.156)													0.2	7.151133	9.26957	5	20	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	71276268	71276268	10813	23	C	A	A	20	20	NHSL2	A	5	3
ALX4	60529	broad.mit.edu	36	11	44253677	44253677	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-1747-01	TCGA-28-1747-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:44253677_44253677delC	uc001myb.1	-	c.574_574delG	c.(574-576)GACfs	p.D192fs		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	192					hair follicle development		transcription regulator activity				0														0.36			88	155				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	44253677	44253677	561	11	C	-	-	30	30	ALX4	-	5	5
HEXIM1	10614	broad.mit.edu	36	17	40582436	40582436	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-1747-01	TCGA-28-1747-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40582436_40582436delC	uc002iig.1	+	c.96_96delC	c.(94-96)CGCfs	p.R32fs		NM_006460	NP_006451	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	32					negative regulation of cyclin-dependent protein kinase activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus	cyclin-dependent protein kinase inhibitor activity|protein binding|snRNA binding			ovary(1)	1												OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.35			77	144				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	40582436	40582436	7359	17	C	-	-	26	26	HEXIM1	-	5	5
GUCY1A3	2982	broad.mit.edu	36	4	156870986	156870989	+	Splice_Site_Del	DEL	ATGT	-	-			TCGA-28-1747-01	TCGA-28-1747-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:156870986_156870989delATGT	uc003iov.1	+	c.e11_splice_site			GUCY1A3_uc010iqd.1_3'UTR|GUCY1A3_uc003iow.1_3'UTR|GUCY1A3_uc003iox.1_3'UTR|GUCY1A3_uc003ioy.1_3'UTR|GUCY1A3_uc010iqe.1_3'UTR|GUCY1A3_uc003ioz.1_3'UTR|GUCY1A3_uc003ipa.1_Non-coding_Transcript|GUCY1A3_uc003ipb.1_3'UTR	NM_000856	NP_000847			guanylate cyclase 1, soluble, alpha 3 isoform A						blood circulation|intracellular signal transduction|nitric oxide mediated signal transduction|platelet activation	guanylate cyclase complex, soluble	GTP binding|guanylate cyclase activity|heme binding|receptor activity			central_nervous_system(2)|ovary(1)	3	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)										0.43			3	4				---	---	---	---	capture_indel			Splice_Site_Del	DEL	156870986	156870989	7174	4	ATGT	-	-	4	4	GUCY1A3	-	5	5
