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
KCNK18	338567	broad.mit.edu	36	10	118959018	118959018	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:118959018G>A	uc001ldc.1	+	c.373G>A	c.(373-375)GTC>ATC	p.V125I		NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	125						integral to membrane|plasma membrane					0		Colorectal(252;0.19)												0.5625	311.160159	311.810725	108	84	GG		KEEP	---	---	---	---	capture		all cancers(201;0.0211)	Missense_Mutation	SNP	118959018	118959018	8370	10	G	A	A	40	40	KCNK18	A	1	1
KDELC2	143888	broad.mit.edu	36	11	107855402	107855402	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:107855402C>T	uc001pkj.2	-	c.1129G>A	c.(1129-1131)GTG>ATG	p.V377M	KDELC2_uc001pki.2_Missense_Mutation_p.V321M	NM_153705	NP_714916	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2	377						endoplasmic reticulum lumen				ovary(1)	1		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)												0.345679	80.51531	82.20017	28	53	CC		KEEP	---	---	---	---	capture		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)	Missense_Mutation	SNP	107855402	107855402	8424	11	C	T	T	19	19	KDELC2	T	1	1
OR4P4	81300	broad.mit.edu	36	11	55163327	55163327	+	Silent	SNP	G	T	T			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55163327G>T	uc001nhr.1	+	c.918G>T	c.(916-918)CTG>CTT	p.L306L		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	306	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.333333	53.478053	54.955064	20	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	55163327	55163327	11490	11	G	T	T	45	45	OR4P4	T	3	3
LRRC55	219527	broad.mit.edu	36	11	56706712	56706712	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56706712C>T	uc001njl.1	+	c.769C>T	c.(769-771)CGG>TGG	p.R257W		NM_001005210	NP_001005210	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	227	LRRCT.					integral to membrane					0														0.294964	107.021219	112.249528	41	98	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56706712	56706712	9386	11	C	T	T	23	23	LRRC55	T	1	1
LRP5	4041	broad.mit.edu	36	11	67962602	67962602	+	Silent	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:67962602G>A	uc001ont.1	+	c.4224G>A	c.(4222-4224)CAG>CAA	p.Q1408Q	LRP5_uc009ysg.1_Silent_p.Q818Q	NM_002335	NP_002326	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein	1408	Cytoplasmic (Potential).				adipose tissue development|bone marrow development|bone morphogenesis|canonical Wnt receptor signaling pathway|cholesterol homeostasis|endocytosis|glucose catabolic process|negative regulation of osteoblast differentiation|negative regulation of protein serine/threonine kinase activity|positive regulation of fat cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mesenchymal cell proliferation|positive regulation of mitosis|regulation of blood pressure|regulation of canonical Wnt receptor signaling pathway|retina morphogenesis in camera-type eye|retinal blood vessel morphogenesis|Wnt receptor signaling pathway involved in dorsal/ventral axis specification	endoplasmic reticulum|integral to membrane|plasma membrane|receptor complex	protein binding|receptor activity			lung(1)|pancreas(1)	2														0.22973	38.332896	43.292152	17	57	GG		KEEP	---	---	---	---	capture			Silent	SNP	67962602	67962602	9333	11	G	A	A	34	34	LRP5	A	2	2
ZNF215	7762	broad.mit.edu	36	11	6921017	6921017	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6921017G>A	uc001mey.1	+	c.611G>A	c.(610-612)CGT>CAT	p.R204H	ZNF215_uc001mez.1_Missense_Mutation_p.R204H	NM_013250	NP_037382	Q9UL58	ZN215_HUMAN	zinc finger protein 215	204	KRAB.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.296482	156.160156	163.524334	59	140	GG		KEEP	---	---	---	---	capture		Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)	Missense_Mutation	SNP	6921017	6921017	18362	11	G	A	A	40	40	ZNF215	A	1	1
OLFML1	283298	broad.mit.edu	36	11	7466120	7466120	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7466120C>T	uc001mfi.1	+	c.316C>T	c.(316-318)CGA>TGA	p.R106*	OLFML1_uc001mfh.1_Nonsense_Mutation_p.R106*	NM_198474	NP_940876	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	106	Potential.					extracellular region				ovary(2)	2														0.368421	80.188912	81.341781	28	48	CC		KEEP	---	---	---	---	capture		Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)	Nonsense_Mutation	SNP	7466120	7466120	11261	11	C	T	T	31	31	OLFML1	T	5	1
DIAPH3	81624	broad.mit.edu	36	13	59443256	59443257	+	Missense_Mutation	DNP	GA	AT	AT			TCGA-06-5414-01	TCGA-06-5414-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:59443256_59443257GA>AT	uc001vht.1	-	c.1689_1690TC>AT	c.(1687-1692)CCTCCC>CCATCC	p.P564S	DIAPH3_uc001vhu.1_Missense_Mutation_p.P301S|DIAPH3_uc001vhv.2_Missense_Mutation_p.P142S	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN	diaphanous homolog 3 isoform a	564	FH1.|Pro-rich.				actin cytoskeleton organization		actin binding|Rho GTPase binding			ovary(2)	2		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)												0.380952	22.69421	22.955529	8	13	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;2.77e-05)	Missense_Mutation	DNP	59443256	59443257	4699	13	GA	AT	AT	41	41	DIAPH3	AT	2	2
SLITRK1	114798	broad.mit.edu	36	13	83353311	83353311	+	Silent	SNP	C	A	A			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:83353311C>A	uc001vlk.1	-	c.333G>T	c.(331-333)CTG>CTT	p.L111L		NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein	111	Extracellular (Potential).|LRR 3.					integral to membrane				ovary(2)|central_nervous_system(1)	3	Medulloblastoma(90;0.18)	Breast(118;0.212)												0.238532	63.529665	70.312397	26	83	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.07)	Silent	SNP	83353311	83353311	15240	13	C	A	A	25	25	SLITRK1	A	3	3
SLC39A9	55334	broad.mit.edu	36	14	68989779	68989779	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:68989779G>A	uc001xle.1	+	c.472G>A	c.(472-474)GCT>ACT	p.A158T	SLC39A9_uc010aqx.1_Intron|SLC39A9_uc001xlf.2_Missense_Mutation_p.A158T|SLC39A9_uc001xlg.2_Non-coding_Transcript	NM_018375	NP_060845	Q9NUM3	S39A9_HUMAN	solute carrier family 39 (zinc transporter),	158	Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity				0														0.325203	121.879798	125.203038	40	83	GG		KEEP	---	---	---	---	capture		all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)	Missense_Mutation	SNP	68989779	68989779	15122	14	G	A	A	35	35	SLC39A9	A	2	2
KRT13	3860	broad.mit.edu	36	17	36913199	36913199	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36913199G>A	uc002hwu.1	-	c.601C>T	c.(601-603)CGC>TGC	p.R201C	KRT13_uc002hwv.1_Missense_Mutation_p.R201C|KRT13_uc002hww.1_Missense_Mutation_p.R94C|KRT13_uc010cxo.1_Missense_Mutation_p.R201C|KRT13_uc002hwx.1_Missense_Mutation_p.R189C	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a	201	Coil 1B.|Rod.				epidermis development	intermediate filament	structural molecule activity			ovary(2)|pancreas(1)	3		Breast(137;0.000286)												0.417391	136.274403	136.96064	48	67	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36913199	36913199	8765	17	G	A	A	38	38	KRT13	A	1	1
ATG4D	84971	broad.mit.edu	36	19	10518548	10518548	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10518548C>T	uc002mov.1	+	c.527C>T	c.(526-528)CCC>CTC	p.P176L	ATG4D_uc010dxh.1_Non-coding_Transcript|ATG4D_uc010dxi.1_Intron|ATG4D_uc010dxj.1_Intron	NM_032885	NP_116274	Q86TL0	ATG4D_HUMAN	APG4 autophagy 4 homolog D	176					autophagy|protein transport	cytoplasm	cysteine-type endopeptidase activity				0														0.214286	26.272005	30.492062	12	44	CC		KEEP	---	---	---	---	capture	Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)		Missense_Mutation	SNP	10518548	10518548	1118	19	C	T	T	22	22	ATG4D	T	2	2
NWD1	284434	broad.mit.edu	36	19	16744984	16744984	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:16744984G>A	uc002net.2	+	c.2053G>A	c.(2053-2055)GCC>ACC	p.A685T	NWD1_uc002neu.2_Missense_Mutation_p.A820T|NWD1_uc002nev.2_Missense_Mutation_p.A614T	NM_001007525	NP_001007526	Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	820							ATP binding			ovary(2)|pancreas(2)	4														0.25	110.133948	120.81716	47	141	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16744984	16744984	11186	19	G	A	A	38	38	NWD1	A	1	1
MEGF8	1954	broad.mit.edu	36	19	47571667	47571667	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47571667G>A	uc002otl.2	+	c.7237G>A	c.(7237-7239)GTG>ATG	p.V2413M	MEGF8_uc002otm.2_Missense_Mutation_p.V2021M|MEGF8_uc002otn.2_Missense_Mutation_p.V74M	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2480	Extracellular (Potential).					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.529412	25.674688	25.687467	9	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47571667	47571667	9852	19	G	A	A	40	40	MEGF8	A	1	1
ZNF665	79788	broad.mit.edu	36	19	58360333	58360333	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:58360333C>T	uc010eqm.1	-	c.1222G>A	c.(1222-1224)GTC>ATC	p.V408I		NM_024733	NP_079009	Q9H7R5	ZN665_HUMAN	zinc finger protein 665	343	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.277487	140.100521	148.605532	53	138	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0196)	Missense_Mutation	SNP	58360333	58360333	18668	19	C	T	T	19	19	ZNF665	T	1	1
HCK	3055	broad.mit.edu	36	20	30138132	30138132	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:30138132G>A	uc002wxh.1	+	c.876G>A	c.(874-876)ATG>ATA	p.M292I	HCK_uc010gdy.1_Missense_Mutation_p.M271I|HCK_uc002wxi.1_Missense_Mutation_p.M270I	NM_002110	NP_002101	P08631	HCK_HUMAN	hemopoietic cell kinase isoform p61HCK	292	Protein kinase.				interspecies interaction between organisms|mesoderm development|protein phosphorylation|regulation of defense response to virus by virus|viral reproduction	caveola|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|central_nervous_system(2)|pancreas(1)	9										262				0.264151	32.721261	35.390356	14	39	GG		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Missense_Mutation	SNP	30138132	30138132	7276	20	G	A	A	45	45	HCK	A	2	2
PPARA	5465	broad.mit.edu	36	22	44973068	44973068	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44973068G>A	uc003bgw.1	+	c.124G>A	c.(124-126)GGC>AGC	p.G42S	PPARA_uc003bgx.1_Missense_Mutation_p.G42S|PPARA_uc010hab.1_Missense_Mutation_p.G42S|PPARA_uc003bgy.1_Non-coding_Transcript|PPARA_uc003bgz.1_Non-coding_Transcript|PPARA_uc003bha.2_Missense_Mutation_p.G42S|PPARA_uc003bhb.1_Missense_Mutation_p.G42S|PPARA_uc010hac.1_5'UTR	NM_005036	NP_005027	Q07869	PPARA_HUMAN	peroxisome proliferative activated receptor,	42					fatty acid metabolic process|fatty acid transport|negative regulation of appetite|negative regulation of cholesterol storage|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of glycolysis|negative regulation of macrophage derived foam cell differentiation|negative regulation of receptor biosynthetic process|negative regulation of sequestering of triglyceride|positive regulation of fatty acid beta-oxidation|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by positive regulation of transcription from an RNA polymerase II promoter|regulation of glycolysis by positive regulation of transcription from an RNA polymerase II promoter|regulation of lipid transport by positive regulation of transcription from an RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	drug binding|ligand-regulated transcription factor activity|lipid binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription activator activity|ubiquitin conjugating enzyme binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)			Atorvastatin(DB01076)|Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Simvastatin(DB00641)					164				0.314286	160.168292	165.535286	55	120	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Missense_Mutation	SNP	44973068	44973068	12727	22	G	A	A	39	39	PPARA	A	1	1
MAPK8IP2	23542	broad.mit.edu	36	22	49390221	49390221	+	Missense_Mutation	SNP	A	G	G			TCGA-06-5414-01	TCGA-06-5414-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49390221A>G	uc003bmx.1	+	c.1628A>G	c.(1627-1629)GAG>GGG	p.E543G	MAPK8IP2_uc003bmy.1_Missense_Mutation_p.E516G	NM_012324	NP_036456	Q13387	JIP2_HUMAN	mitogen-activated protein kinase 8 interacting	543					behavioral fear response|dendrite morphogenesis|MAPKKK cascade|nonassociative learning|positive regulation of anti-apoptosis|regulation of excitatory postsynaptic membrane potential|regulation of JNK cascade|regulation of receptor activity|regulation of synaptic transmission, glutamatergic|signal complex assembly|social behavior	cytoplasm|postsynaptic density	beta-amyloid binding|kinesin binding|MAP-kinase scaffold activity|protein kinase activator activity|protein kinase binding			large_intestine(2)|central_nervous_system(1)	3		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)								297				0.428571	8.724279	8.755313	3	4	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(4;1.28e-70)|Epithelial(4;3.46e-65)|GBM - Glioblastoma multiforme(4;4.83e-06)|Lung(4;0.125)|BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49390221	49390221	9668	22	A	G	G	11	11	MAPK8IP2	G	4	4
CYTIP	9595	broad.mit.edu	36	2	158008710	158008710	+	Silent	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:158008710C>T	uc002tzj.1	-	c.69G>A	c.(67-69)GCG>GCA	p.A23A		NM_004288	NP_004279	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	23					regulation of cell adhesion	cell cortex|early endosome	protein binding			ovary(1)|kidney(1)	2														0.342105	141.651998	145.001089	52	100	CC		KEEP	---	---	---	---	capture			Silent	SNP	158008710	158008710	4372	2	C	T	T	19	19	CYTIP	T	1	1
SGOL2	151246	broad.mit.edu	36	2	201142814	201142814	+	Silent	SNP	A	G	G			TCGA-06-5414-01	TCGA-06-5414-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201142814A>G	uc002uvw.1	+	c.657A>G	c.(655-657)TTA>TTG	p.L219L	SGOL2_uc002uvv.2_Silent_p.L219L	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2	219					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)	2														0.363636	218.157233	221.034678	64	112	AA		KEEP	---	---	---	---	capture			Silent	SNP	201142814	201142814	14708	2	A	G	G	15	15	SGOL2	G	4	4
SPHKAP	80309	broad.mit.edu	36	2	228592461	228592461	+	Silent	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228592461G>A	uc002vpq.1	-	c.1353C>T	c.(1351-1353)GTC>GTT	p.V451V	SPHKAP_uc002vpp.1_Silent_p.V451V	NM_030623	NP_085126	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	451						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)												0.333333	127.774921	131.245156	47	94	GG		KEEP	---	---	---	---	capture		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)	Silent	SNP	228592461	228592461	15560	2	G	A	A	37	37	SPHKAP	A	1	1
RAB11FIP5	26056	broad.mit.edu	36	2	73193000	73193000	+	Silent	SNP	G	C	C	rs34138742	unknown	TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:73193000G>C	uc002siu.2	-	c.414C>G	c.(412-414)GGC>GGG	p.G138G		NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	138					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0														0.25	6.822056	7.502051	3	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	73193000	73193000	13356	2	G	C	C	42	42	RAB11FIP5	C	3	3
DPPA4	55211	broad.mit.edu	36	3	110533442	110533442	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:110533442C>T	uc003dxq.2	-	c.305G>A	c.(304-306)TGG>TAG	p.W102*		NM_018189	NP_060659	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	102						nucleus	protein binding				0														0.401015	236.170041	237.862046	79	118	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	110533442	110533442	4920	3	C	T	T	21	21	DPPA4	T	5	2
FNDC3B	64778	broad.mit.edu	36	3	173578774	173578774	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173578774G>A	uc010hwt.1	+	c.3029G>A	c.(3028-3030)GGA>GAA	p.G1010E	FNDC3B_uc003fhy.1_Missense_Mutation_p.G1006E|FNDC3B_uc003fhz.2_Missense_Mutation_p.G1006E	NM_022763	NP_073600	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	1010	Fibronectin type-III 8.					endoplasmic reticulum|integral to membrane				ovary(1)|breast(1)	2	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)													0.370787	95.196743	96.484041	33	56	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)	Missense_Mutation	SNP	173578774	173578774	6212	3	G	A	A	41	41	FNDC3B	A	2	2
CPZ	8532	broad.mit.edu	36	4	8672143	8672143	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:8672143C>T	uc003glm.1	+	c.1858C>T	c.(1858-1860)CGG>TGG	p.R620W	CPZ_uc003gll.1_Non-coding_Transcript|CPZ_uc003glo.1_Missense_Mutation_p.R609W|CPZ_uc003gln.1_Missense_Mutation_p.R483W|CPZ_uc003glp.1_Non-coding_Transcript	NM_001014447	NP_001014448	Q66K79	CBPZ_HUMAN	carboxypeptidase Z isoform 1	620					proteolysis|Wnt receptor signaling pathway	proteinaceous extracellular matrix	metallocarboxypeptidase activity|zinc ion binding			ovary(2)|pancreas(1)	3														0.368421	60.664507	61.530076	21	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8672143	8672143	3978	4	C	T	T	23	23	CPZ	T	1	1
PCDHGB2	56103	broad.mit.edu	36	5	140721522	140721522	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140721522G>A	uc003ljs.1	+	c.1636G>A	c.(1636-1638)GTG>ATG	p.V546M	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGA5_uc003lju.1_5'Flank|PCDHGB2_uc003ljr.1_Missense_Mutation_p.V546M|PCDHGA5_uc003ljt.1_5'Flank	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	546	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.421053	93.897946	94.308231	32	44	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140721522	140721522	11983	5	G	A	A	40	40	PCDHGB2	A	1	1
GABRA6	2559	broad.mit.edu	36	5	161048654	161048654	+	Missense_Mutation	SNP	C	A	A			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161048654C>A	uc003lyu.2	+	c.347C>A	c.(346-348)ACC>AAC	p.T116N	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	116	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|large_intestine(1)|central_nervous_system(1)	9	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)			Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						TCGA Ovarian(5;0.080)			0.25	87.134908	95.314019	36	108	CC		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	161048654	161048654	6416	5	C	A	A	18	18	GABRA6	A	3	3
ADAMTS16	170690	broad.mit.edu	36	5	5199447	5199447	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5199447C>T	uc003jdl.1	+	c.380C>T	c.(379-381)ACG>ATG	p.T127M	ADAMTS16_uc003jdj.1_Missense_Mutation_p.T127M|ADAMTS16_uc003jdk.1_Missense_Mutation_p.T127M	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	127					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.386243	199.724376	201.869258	73	116	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5199447	5199447	262	5	C	T	T	19	19	ADAMTS16	T	1	1
ADAMTS16	170690	broad.mit.edu	36	5	5243212	5243212	+	Silent	SNP	T	C	C			TCGA-06-5414-01	TCGA-06-5414-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5243212T>C	uc003jdl.1	+	c.1176T>C	c.(1174-1176)TGT>TGC	p.C392C	ADAMTS16_uc003jdj.1_Silent_p.C392C|ADAMTS16_uc003jdk.1_Silent_p.C392C	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	392	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.321429	145.931957	149.893657	45	95	TT		KEEP	---	---	---	---	capture			Silent	SNP	5243212	5243212	262	5	T	C	C	60	60	ADAMTS16	C	4	4
VNN2	8875	broad.mit.edu	36	6	133120266	133120266	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:133120266G>A	uc003qdt.1	-	c.326C>T	c.(325-327)CCG>CTG	p.P109L	VNN2_uc003qds.1_5'UTR|VNN2_uc003qdu.1_5'UTR|VNN2_uc010kga.1_5'UTR|VNN2_uc010kgb.1_Missense_Mutation_p.P109L|VNN2_uc010kgc.1_Silent_p.S24S|VNN2_uc003qdv.1_Missense_Mutation_p.P56L	NM_004665	NP_004656	O95498	VNN2_HUMAN	vanin 2 isoform 1 precursor	109	CN hydrolase.				cellular component movement|pantothenate metabolic process	anchored to membrane|plasma membrane	pantetheine hydrolase activity				0														0.421053	175.270126	175.994771	56	77	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)	Missense_Mutation	SNP	133120266	133120266	17750	6	G	A	A	39	39	VNN2	A	1	1
TMEM63B	55362	broad.mit.edu	36	6	44215281	44215281	+	Silent	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:44215281C>T	uc003owr.1	+	c.507C>T	c.(505-507)TCC>TCT	p.S169S	TMEM63B_uc003owq.1_Silent_p.S169S|TMEM63B_uc010jyy.1_Silent_p.S72S|TMEM63B_uc003ows.1_Silent_p.S72S|TMEM63B_uc010jyz.1_5'Flank	NM_018426	NP_060896	Q5T3F8	TM63B_HUMAN	transmembrane protein 63B	169	Helical; (Potential).					integral to membrane	nucleotide binding|protein binding	p.S169S(1)		pancreas(2)|central_nervous_system(1)	3	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)													0.46875	139.771927	139.852963	45	51	CC		KEEP	---	---	---	---	capture	Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)		Silent	SNP	44215281	44215281	16730	6	C	T	T	23	23	TMEM63B	T	1	1
KEL	3792	broad.mit.edu	36	7	142368712	142368712	+	Splice_Site_SNP	SNP	T	C	C			TCGA-06-5414-01	TCGA-06-5414-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142368712T>C	uc003wcb.1	-	c.82_splice	c.e3-1	p.S28_splice		NM_000420	NP_000411			Kell blood group, metallo-endopeptidase						proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.2	7.887982	9.56305	4	16	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	142368712	142368712	8448	7	T	C	C	55	55	KEL	C	5	4
TUSC3	7991	broad.mit.edu	36	8	15564158	15564158	+	Silent	SNP	T	G	G			TCGA-06-5414-01	TCGA-06-5414-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:15564158T>G	uc003wwt.1	+	c.690T>G	c.(688-690)GGT>GGG	p.G230G	TUSC3_uc003wwr.1_Silent_p.G230G|TUSC3_uc003wws.1_Silent_p.G230G|TUSC3_uc003wwu.1_Silent_p.G230G|TUSC3_uc003wwv.1_Silent_p.G230G|TUSC3_uc003www.1_Silent_p.G230G|TUSC3_uc003wwx.1_Non-coding_Transcript|TUSC3_uc003wwy.1_Silent_p.G230G	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a	230	Helical; (Potential).				cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3														0.332192	310.685415	317.96532	97	195	TT		KEEP	---	---	---	---	capture		Colorectal(111;0.113)	Silent	SNP	15564158	15564158	17334	8	T	G	G	60	60	TUSC3	G	4	4
SFTPC	6440	broad.mit.edu	36	8	22076128	22076128	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:22076128G>A	uc003xaw.2	+	c.286G>A	c.(286-288)GTC>ATC	p.V96I	SFTPC_uc003xax.2_Missense_Mutation_p.V47I|SFTPC_uc003xaz.2_Missense_Mutation_p.V47I|SFTPC_uc003xay.2_Missense_Mutation_p.V47I|BMP1_uc003xba.1_5'Flank|BMP1_uc003xbb.1_5'Flank|BMP1_uc003xbc.1_5'Flank|BMP1_uc003xbd.1_5'Flank|BMP1_uc003xbf.1_5'Flank|BMP1_uc003xbe.1_5'Flank|BMP1_uc003xbh.1_5'Flank|BMP1_uc003xbg.1_5'Flank	NM_003018	NP_003009	P11686	PSPC_HUMAN	surfactant, pulmonary-associated protein C	47					respiratory gaseous exchange	extracellular space					0														0.340659	167.745344	171.805037	62	120	GG		KEEP	---	---	---	---	capture		Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)	Missense_Mutation	SNP	22076128	22076128	14683	8	G	A	A	40	40	SFTPC	A	1	1
PHYHIP	9796	broad.mit.edu	36	8	22135212	22135212	+	Missense_Mutation	SNP	C	G	G			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:22135212C>G	uc003xbk.2	-	c.592G>C	c.(592-594)GAC>CAC	p.D198H	PHYHIP_uc003xbj.2_Missense_Mutation_p.D198H	NM_001099335	NP_055574	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	198											0														0.375	28.969093	29.298339	9	15	CC		KEEP	---	---	---	---	capture		Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)	Missense_Mutation	SNP	22135212	22135212	12290	8	C	G	G	30	30	PHYHIP	G	3	3
KCNB2	9312	broad.mit.edu	36	8	74010785	74010785	+	Missense_Mutation	SNP	C	T	T			TCGA-06-5414-01	TCGA-06-5414-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:74010785C>T	uc003xzb.1	+	c.641C>T	c.(640-642)ACG>ATG	p.T214M		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	214					regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			large_intestine(1)|ovary(1)|central_nervous_system(1)|pancreas(1)	4	Breast(64;0.137)													0.397321	248.918928	250.986849	89	135	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.105)		Missense_Mutation	SNP	74010785	74010785	8318	8	C	T	T	19	19	KCNB2	T	1	1
FLNA	2316	broad.mit.edu	36	X	153233186	153233186	+	Missense_Mutation	SNP	G	A	A			TCGA-06-5414-01	TCGA-06-5414-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:153233186G>A	uc004fkk.2	-	c.6980C>T	c.(6979-6981)TCT>TTT	p.S2327F	FLNA_uc004fki.2_Missense_Mutation_p.S370F|FLNA_uc010nuu.1_Missense_Mutation_p.S2319F	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	2327	Filamin 22.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)									518				0.285714	6.477648	7.067069	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153233186	153233186	6175	23	G	A	A	33	33	FLNA	A	2	2
USP2	9099	broad.mit.edu	36	11	118735056	118735056	+	Splice_Site_Del	DEL	T	-	-			TCGA-06-5414-01	TCGA-06-5414-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:118735056_118735056delT	uc001pwm.2	-	c.e6_splice_site			USP2_uc001pwn.2_Splice_Site_Del|USP2_uc001pwl.2_Splice_Site_Del	NM_004205	NP_004196			ubiquitin specific peptidase 2 isoform a						cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity			ovary(2)|urinary_tract(1)	3		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)										0.34			23	44				---	---	---	---	capture_indel			Splice_Site_Del	DEL	118735056	118735056	17614	11	T	-	-	55	55	USP2	-	5	5
SLC15A1	6564	broad.mit.edu	36	13	98134801	98134801	+	Splice_Site_Del	DEL	A	-	-			TCGA-06-5414-01	TCGA-06-5414-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:98134801_98134801delA	uc001vno.1	-	c.e25_splice_site				NM_005073	NP_005064			solute carrier family 15 (oligopeptide						digestion|protein transport	integral to plasma membrane|membrane fraction	peptide:hydrogen symporter activity			ovary(1)	1	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Cefadroxil(DB01140)|Ceftibuten(DB01415)|Cyclacillin(DB01000)									0.50			3	3				---	---	---	---	capture_indel			Splice_Site_Del	DEL	98134801	98134801	14893	13	A	-	-	5	5	SLC15A1	-	5	5
