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
ABCC2	1244	broad.mit.edu	36	10	101594128	101594129	+	Missense_Mutation	DNP	GT	TC	TC			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101594128_101594129GT>TC	uc001kqf.2	+	c.3903_3904GT>TC	c.(3901-3906)CAGTTT>CATCTT	p.1301_1302QF>HL		NM_000392	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP),	1301_1302	Cytoplasmic (By similarity).|ABC transporter 2.					apical plasma membrane|integral to plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|organic anion transmembrane transporter activity			ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Norgestimate(DB00957)|Pravastatin(DB00175)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)									0.176471	6.925932	10.289554	6	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	101594128	101594129	54	10	GT	TC	TC	36	36	ABCC2	TC	3	3
DCPS	28960	broad.mit.edu	36	11	125679234	125679234	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125679234G>A	uc001qdp.1	+	c.49G>A	c.(49-51)GTG>ATG	p.V17M		NM_014026	NP_054745	Q96C86	DCPS_HUMAN	mRNA decapping enzyme	17					deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)										0.333333	7.593284	7.889853	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125679234	125679234	4472	11	G	A	A	40	40	DCPS	A	1	1
PHF21A	51317	broad.mit.edu	36	11	45912268	45912268	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:45912268G>A	uc001ncc.2	-	c.1870C>T	c.(1870-1872)CTC>TTC	p.L624F	PHF21A_uc001ncb.2_Missense_Mutation_p.L578F|PHF21A_uc009ykx.1_Missense_Mutation_p.L578F|PHF21A_uc001nca.1_3'UTR	NM_001101802	NP_001095272	Q96BD5	PF21A_HUMAN	BRAF35/HDAC2 complex isoform a	624	Required for transcriptional repression.				blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent	histone deacetylase complex	DNA binding|zinc ion binding			central_nervous_system(1)	1														0.235294	7.086865	8.181792	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45912268	45912268	12256	11	G	A	A	35	35	PHF21A	A	2	2
OR51E2	81285	broad.mit.edu	36	11	4659911	4659911	+	Silent	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4659911G>A	uc001lzk.1	-	c.607C>T	c.(607-609)CTG>TTG	p.L203L	OR51E2_uc009yel.1_Silent_p.L203L	NM_030774	NP_110401	Q9H255	O51E2_HUMAN	olfactory receptor, family 51, subfamily E,	203	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;3e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00476)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.142045	46.363226	68.101324	25	151	GG		KEEP	---	---	---	---	capture			Silent	SNP	4659911	4659911	11505	11	G	A	A	33	33	OR51E2	A	2	2
VWCE	220001	broad.mit.edu	36	11	60810374	60810374	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60810374G>A	uc001nra.1	-	c.529C>T	c.(529-531)CAC>TAC	p.H177Y	VWCE_uc001nrb.1_Non-coding_Transcript	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	177	EGF-like 2; calcium-binding (Potential).					extracellular region	calcium ion binding			ovary(1)	1														0.161765	11.100372	18.501406	11	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60810374	60810374	17816	11	G	A	A	47	47	VWCE	A	2	2
PTPN11	5781	broad.mit.edu	36	12	111399838	111399838	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111399838T>C	uc001ttx.1	+	c.854T>C	c.(853-855)TTT>TCT	p.F285S	PTPN11_uc001ttw.1_Missense_Mutation_p.F285S	NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	285	Tyrosine-protein phosphatase.		F -> L (in NS1).|F -> S (in NS1).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(372)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|ovary(1)|NS(1)|kidney(1)	388										372				0.12381	32.508441	61.621692	26	184	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111399838	111399838	13235	12	T	C	C	60	60	PTPN11	C	4	4
GPR81	27198	broad.mit.edu	36	12	121780540	121780540	+	Silent	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121780540G>A	uc001ucz.1	-	c.300C>T	c.(298-300)GCC>GCT	p.A100A	GPR81_uc001ucw.1_Non-coding_Transcript	NM_032554	NP_115943	Q9BXC0	GPR81_HUMAN	G protein-coupled receptor 81	100	Helical; Name=3; (Potential).				response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)|ovary(1)|pancreas(1)	4	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)										0.302326	72.417717	75.420573	26	60	GG		KEEP	---	---	---	---	capture			Silent	SNP	121780540	121780540	6986	12	G	A	A	39	39	GPR81	A	1	1
C14orf73	91828	broad.mit.edu	36	14	102642889	102642889	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:102642889C>T	uc001ymk.1	+	c.1481C>T	c.(1480-1482)TCC>TTC	p.S494F		NM_001077594	NP_001071062	Q17RC7	EX3L4_HUMAN	hypothetical protein LOC91828	494											0		Melanoma(154;0.155)	Epithelial(46;0.221)											0.8	26.704693	27.541601	8	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102642889	102642889	1829	14	C	T	T	30	30	C14orf73	T	2	2
C14orf79	122616	broad.mit.edu	36	14	104528976	104528976	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104528976G>T	uc001ypy.1	+	c.673G>T	c.(673-675)GTT>TTT	p.V225F	C14orf79_uc001ypz.1_Non-coding_Transcript	NM_174891	NP_777551	Q96F83	CN079_HUMAN	hypothetical protein LOC122616	225											0		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)											0.461538	12.132522	12.150418	6	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	104528976	104528976	1830	14	G	T	T	48	48	C14orf79	T	3	3
CIITA	4261	broad.mit.edu	36	16	10908154	10908154	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10908154G>A	uc002daj.2	+	c.1307G>A	c.(1306-1308)CGG>CAG	p.R436Q	CIITA_uc002dag.2_Missense_Mutation_p.R435Q|CIITA_uc002dah.2_Missense_Mutation_p.R387Q|CIITA_uc010bup.1_Intron|CIITA_uc002dai.2_Missense_Mutation_p.R435Q|CIITA_uc002dak.2_Intron	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	435	NACHT.				interferon-gamma-mediated signaling pathway|negative regulation of collagen biosynthetic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of MHC class II biosynthetic process|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|promoter binding|protein C-terminus binding|protein complex binding|RNA polymerase II transcription factor activity|transcription activator activity|transcription coactivator activity|transcription repressor activity			central_nervous_system(1)	1										532				0.164706	22.896947	31.908985	14	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10908154	10908154	3562	16	G	A	A	39	39	CIITA	A	1	1
ABCC1	4363	broad.mit.edu	36	16	16123383	16123383	+	Silent	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:16123383C>T	uc010bvi.1	+	c.3441C>T	c.(3439-3441)AGC>AGT	p.S1147S	ABCC1_uc010bvj.1_Silent_p.S1088S|ABCC1_uc010bvk.1_Silent_p.S1091S|ABCC1_uc010bvl.1_Silent_p.S1147S|ABCC1_uc010bvm.1_Silent_p.S1032S|ABCC1_uc002del.2_Silent_p.S1041S	NM_004996	NP_004987	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C, member 1	1147	Cytoplasmic.|ABC transmembrane type-1 2.				hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug	Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)	4					Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138)									0.112903	6.428476	15.564446	7	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	16123383	16123383	50	16	C	T	T	26	26	ABCC1	T	2	2
SLC5A2	6524	broad.mit.edu	36	16	31407982	31407982	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31407982G>C	uc002ecf.2	+	c.1487G>C	c.(1486-1488)GGC>GCC	p.G496A	SLC5A2_uc010car.1_Non-coding_Transcript|C16orf58_uc002ecg.2_Non-coding_Transcript	NM_003041	NP_003032	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose	496	Extracellular (Potential).				carbohydrate metabolic process	integral to membrane	low-affinity glucose:sodium symporter activity			ovary(1)	1														0.75	6.923215	7.14775	3	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31407982	31407982	15162	16	G	C	C	42	42	SLC5A2	C	3	3
ADCY7	113	broad.mit.edu	36	16	48881980	48881980	+	Missense_Mutation	SNP	G	C	C			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:48881980G>C	uc002egd.1	+	c.283G>C	c.(283-285)GCC>CCC	p.A95P	ADCY7_uc002egb.1_Missense_Mutation_p.A95P|ADCY7_uc002egc.1_Missense_Mutation_p.A95P	NM_001114	NP_001105	P51828	ADCY7_HUMAN	adenylate cyclase 7	95	Helical; (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to ethanol|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of cAMP biosynthetic process|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding				0		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)	Bromocriptine(DB01200)									0.172414	6.563109	9.5021	5	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48881980	48881980	300	16	G	C	C	42	42	ADCY7	C	3	3
MMP15	4324	broad.mit.edu	36	16	56628900	56628900	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56628900C>A	uc002ena.1	+	c.186C>A	c.(184-186)TAC>TAA	p.Y62*		NM_002428	NP_002419	P51511	MMP15_HUMAN	matrix metalloproteinase 15 preproprotein	62					protein modification process|proteolysis	extracellular matrix|integral to plasma membrane	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			central_nervous_system(2)|breast(1)	3														0.5	8.686359	8.686359	4	4	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	56628900	56628900	10044	16	C	A	A	18	18	MMP15	A	5	3
AOC3	8639	broad.mit.edu	36	17	38257128	38257128	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38257128C>G	uc002ibv.1	+	c.242C>G	c.(241-243)CCA>CGA	p.P81R		NM_003734	NP_003725	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3 precursor	81	Extracellular (Potential).				amine metabolic process|cell adhesion|inflammatory response|oxidation-reduction process	cell surface|integral to membrane|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|protein homodimerization activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			central_nervous_system(2)|ovary(1)	3		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	NSCLC(3;192 220 10664 11501 16477)								0.266667	7.297806	8.033585	4	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38257128	38257128	738	17	C	G	G	21	21	AOC3	G	3	3
ITGA3	3675	broad.mit.edu	36	17	45506878	45506878	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:45506878C>T	uc010dbm.1	+	c.1450C>T	c.(1450-1452)CTT>TTT	p.L484F	ITGA3_uc010dbl.1_Missense_Mutation_p.L484F	NM_005501	NP_005492	P26006	ITA3_HUMAN	integrin alpha 3 isoform b precursor	484	Extracellular (Potential).				blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|leukocyte migration	integrin complex	protein binding|receptor activity			ovary(2)|pancreas(1)	3														0.175676	25.331392	32.674905	13	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45506878	45506878	8181	17	C	T	T	20	20	ITGA3	T	2	2
SERPINB4	6318	broad.mit.edu	36	18	59456244	59456244	+	Missense_Mutation	SNP	T	G	G			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:59456244T>G	uc002ljf.1	-	c.862A>C	c.(862-864)AAA>CAA	p.K288Q	SERPINB4_uc002lje.1_Missense_Mutation_p.K267Q|SERPINB4_uc002ljg.1_Missense_Mutation_p.K288Q|SERPINB4_uc002ljh.1_Missense_Mutation_p.K288Q	NM_002974	NP_002965	P48594	SPB4_HUMAN	serine (or cysteine) proteinase inhibitor, clade	288					immune response|regulation of proteolysis	cytoplasm|extracellular region	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)|lung(1)	2										163				0.20398	185.838964	218.552333	82	320	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59456244	59456244	14591	18	T	G	G	63	63	SERPINB4	G	4	4
LAMA1	284217	broad.mit.edu	36	18	7023087	7023087	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1751-01	TCGA-28-1751-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:7023087A>T	uc002knm.1	-	c.2059T>A	c.(2059-2061)TCC>ACC	p.S687T		NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	687	Laminin IV type A 1.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.183673	10.431314	15.058747	9	40	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7023087	7023087	8928	18	A	T	T	10	10	LAMA1	T	4	4
SLC44A2	57153	broad.mit.edu	36	19	10606467	10606467	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:10606467C>T	uc002mpf.1	+	c.859C>T	c.(859-861)CGT>TGT	p.R287C	SLC44A2_uc002mpe.2_Missense_Mutation_p.R285C|SLC44A2_uc002mpg.1_Missense_Mutation_p.R7C|SLC44A2_uc002mph.1_5'Flank	NM_020428	NP_065161	Q8IWA5	CTL2_HUMAN	solute carrier family 44, member 2 isoform 1	287	Extracellular (Potential).				positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane|plasma membrane	choline transmembrane transporter activity|signal transducer activity			ovary(1)	1			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)									0.098592	8.966288	31.863473	14	128	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10606467	10606467	15133	19	C	T	T	27	27	SLC44A2	T	1	1
AP3D1	8943	broad.mit.edu	36	19	2069710	2069710	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2069710G>T	uc002lva.1	-	c.1603C>A	c.(1603-1605)CAG>AAG	p.Q535K	AP3D1_uc002luy.1_Missense_Mutation_p.Q444K|AP3D1_uc002luz.1_Missense_Mutation_p.Q535K	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	535	HEAT 10.				eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.4	7.690693	7.779956	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2069710	2069710	756	19	G	T	T	46	46	AP3D1	T	3	3
SIPA1L3	23094	broad.mit.edu	36	19	43301800	43301800	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:43301800G>A	uc002ohk.1	+	c.2306G>A	c.(2305-2307)CGA>CAA	p.R769Q		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	769	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)											0.673267	432.294414	437.770919	136	66	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43301800	43301800	14826	19	G	A	A	37	37	SIPA1L3	A	1	1
ZNF229	7772	broad.mit.edu	36	19	49624406	49624406	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49624406G>A	uc002oze.1	-	c.2390C>T	c.(2389-2391)ACG>ATG	p.T797M	ZNF229_uc010ejk.1_Missense_Mutation_p.T451M|ZNF229_uc010ejl.1_Missense_Mutation_p.T791M	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	797	C2H2-type 18.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Prostate(69;0.0352)												0.219178	43.368869	48.665795	16	57	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49624406	49624406	18373	19	G	A	A	40	40	ZNF229	A	1	1
CEACAM19	56971	broad.mit.edu	36	19	49867958	49867958	+	Silent	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49867958C>T	uc002ozo.2	+	c.306C>T	c.(304-306)TTC>TTT	p.F102F	CEACAM19_uc002ozp.2_Silent_p.F102F	NM_020219	NP_064604	Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion	102	Extracellular (Potential).					integral to membrane					0	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)												0.614458	149.907569	150.85478	51	32	CC		KEEP	---	---	---	---	capture			Silent	SNP	49867958	49867958	3323	19	C	T	T	30	30	CEACAM19	T	2	2
NTRK1	4914	broad.mit.edu	36	1	155115638	155115639	+	Missense_Mutation	DNP	GC	CG	CG			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155115638_155115639GC>CG	uc001fqh.1	+	c.1906_1907GC>CG	c.(1906-1908)GCG>CGG	p.A636R	NTRK1_uc001fqf.1_Missense_Mutation_p.A600R|NTRK1_uc009wsi.1_Missense_Mutation_p.A335R|NTRK1_uc001fqi.1_Missense_Mutation_p.A630R|NTRK1_uc009wsk.1_Missense_Mutation_p.A633R	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	636	Cytoplasmic (Potential).|Protein kinase.				activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|stomach(1)|central_nervous_system(1)	16	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)					290	TSP Lung(10;0.080)			0.214286	6.810674	8.954611	6	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	155115638	155115639	11111	1	GC	CG	CG	46	46	NTRK1	CG	3	3
KLF17	128209	broad.mit.edu	36	1	44367881	44367881	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44367881G>A	uc001clp.1	+	c.351G>A	c.(349-351)ATG>ATA	p.M117I	KLF17_uc009vxf.1_Missense_Mutation_p.M80I	NM_173484	NP_775755	Q5JT82	KLF17_HUMAN	zinc finger protein 393	117					regulation of transcription from RNA polymerase II promoter	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.160156	79.089582	107.182105	41	215	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44367881	44367881	8657	1	G	A	A	48	48	KLF17	A	2	2
OSBPL9	114883	broad.mit.edu	36	1	51952311	51952311	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:51952311C>G	uc001csu.1	+	c.290C>G	c.(289-291)ACA>AGA	p.T97R	OSBPL9_uc001css.1_Missense_Mutation_p.T115R|OSBPL9_uc001csx.1_Non-coding_Transcript|OSBPL9_uc009vza.1_Missense_Mutation_p.T98R|OSBPL9_uc001cst.1_Missense_Mutation_p.T97R|OSBPL9_uc001csv.1_5'UTR|OSBPL9_uc001csw.1_Missense_Mutation_p.T97R	NM_148909	NP_683707	Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9 isoform f	97	PH.				lipid transport		lipid binding			central_nervous_system(1)	1														0.175	14.90025	18.886224	7	33	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51952311	51952311	11695	1	C	G	G	17	17	OSBPL9	G	3	3
PREX1	57580	broad.mit.edu	36	20	46682512	46682512	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:46682512T>A	uc002xtw.1	-	c.4340A>T	c.(4339-4341)CAC>CTC	p.H1447L	PREX1_uc002xtv.1_Missense_Mutation_p.H744L	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	1447					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)											0.210526	17.473451	21.897662	12	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46682512	46682512	12919	20	T	A	A	59	59	PREX1	A	4	4
MYT1	4661	broad.mit.edu	36	20	62309776	62309777	+	Missense_Mutation	DNP	CG	TC	TC			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62309776_62309777CG>TC	uc002yii.1	+	c.783_784CG>TC	c.(781-786)GACGAG>GATCAG	p.E262Q	MYT1_uc002yih.2_Intron|MYT1_uc002yij.1_5'UTR	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	262	Glu-rich.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GBM(59;481 1041 20555 21139 33705)			(HS688A.T-Tumor)	1819				0.333333	6.424728	6.644775	3	6	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	62309776	62309777	10501	20	CG	TC	TC	19	19	MYT1	TC	1	1
SLC37A1	54020	broad.mit.edu	36	21	42819006	42819006	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42819006C>G	uc002zbi.1	+	c.108C>G	c.(106-108)CAC>CAG	p.H36Q	SLC37A1_uc002zbj.1_Missense_Mutation_p.H36Q	NM_018964	NP_061837	P57057	GLPT_HUMAN	solute carrier family 37 member 1	36	Helical; (Potential).				carbohydrate transport|transmembrane transport	integral to membrane					0														0.186667	20.092571	27.017066	14	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42819006	42819006	15094	21	C	G	G	20	20	SLC37A1	G	3	3
ERBB4	2066	broad.mit.edu	36	2	212286539	212286539	+	Silent	SNP	T	C	C			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:212286539T>C	uc002veg.1	-	c.963A>G	c.(961-963)AAA>AAG	p.K321K	ERBB4_uc002veh.1_Silent_p.K321K|ERBB4_uc010fut.1_Silent_p.K321K	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	321	Cys-rich.|Extracellular (Potential).				cell proliferation|protein phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(12)|large_intestine(1)|breast(1)	14		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)						777	TSP Lung(8;0.080)			0.478632	187.893605	187.939913	56	61	TT		KEEP	---	---	---	---	capture			Silent	SNP	212286539	212286539	5402	2	T	C	C	64	64	ERBB4	C	4	4
CTDSP1	58190	broad.mit.edu	36	2	218976257	218976257	+	Missense_Mutation	SNP	T	A	A			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:218976257T>A	uc002vhy.1	+	c.530T>A	c.(529-531)TTT>TAT	p.F177Y	CTDSP1_uc002vhx.1_Missense_Mutation_p.F176Y|CTDSP1_uc002vhz.1_Missense_Mutation_p.F36Y	NM_021198	NP_067021	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	177	FCP1 homology.				protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding			ovary(1)	1		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.428571	8.323929	8.355029	3	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	218976257	218976257	4162	2	T	A	A	64	64	CTDSP1	A	4	4
SLC16A14	151473	broad.mit.edu	36	2	230632106	230632106	+	Silent	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:230632106G>A	uc002vqd.1	-	c.207C>T	c.(205-207)CGC>CGT	p.R69R	FBXO36_uc010fxi.1_Intron|SLC16A14_uc002vqe.2_Silent_p.R69R|SLC16A14_uc002vqf.2_Silent_p.R69R	NM_152527	NP_689740	Q7RTX9	MOT14_HUMAN	solute carrier family 16 (monocarboxylic acid	69	Cytoplasmic (Potential).					integral to membrane|plasma membrane	symporter activity			ovary(4)|skin(1)	5		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)										0.198473	47.905418	58.995686	26	105	GG		KEEP	---	---	---	---	capture			Silent	SNP	230632106	230632106	14903	2	G	A	A	38	38	SLC16A14	A	1	1
DGKD	8527	broad.mit.edu	36	2	234025384	234025384	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234025384G>A	uc002vui.1	+	c.2203G>A	c.(2203-2205)GGC>AGC	p.G735S	DGKD_uc002vuj.1_Missense_Mutation_p.G691S|DGKD_uc010fyh.1_Missense_Mutation_p.G602S|DGKD_uc010fyi.1_Non-coding_Transcript	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	735					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)									0.11399	22.738694	51.087544	22	171	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	234025384	234025384	4646	2	G	A	A	47	47	DGKD	A	2	2
DNAJB8	165721	broad.mit.edu	36	3	129664537	129664537	+	Missense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:129664537G>A	uc003ekk.1	-	c.242C>T	c.(241-243)ACG>ATG	p.T81M	DNAJB8_uc010hst.1_Missense_Mutation_p.T81M	NM_153330	NP_699161	Q8NHS0	DNJB8_HUMAN	DnaJ homolog, subfamily B, member 8	81					protein folding		heat shock protein binding|unfolded protein binding				0				GBM - Glioblastoma multiforme(114;0.177)										0.333333	39.523612	40.684787	16	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129664537	129664537	4809	3	G	A	A	40	40	DNAJB8	A	1	1
PRKAR2A	5576	broad.mit.edu	36	3	48803063	48803063	+	Missense_Mutation	SNP	A	C	C			TCGA-28-1751-01	TCGA-28-1751-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48803063A>C	uc010hki.1	-	c.353T>G	c.(352-354)GTG>GGG	p.V118G	PRKAR2A_uc003cux.1_Missense_Mutation_p.V118G|PRKAR2A_uc003cuy.1_Missense_Mutation_p.V118G	NM_004157	NP_004148	P13861	KAP2_HUMAN	cAMP-dependent protein kinase, regulatory	118	Dimerization and phosphorylation.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|transmembrane transport|water transport	cytosol|membrane fraction	cAMP binding|cAMP-dependent protein kinase regulator activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)										0.263158	6.342754	7.423812	5	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48803063	48803063	12948	3	A	C	C	6	6	PRKAR2A	C	4	4
IQCF2	389123	broad.mit.edu	36	3	51872344	51872344	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51872344G>T	uc003dbt.1	+	c.413G>T	c.(412-414)TGC>TTC	p.C138F	IQCF1_uc003dbq.2_Intron|IQCF2_uc003dbu.1_Non-coding_Transcript	NM_203424	NP_982248	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	138											0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)										0.145833	7.502287	13.289909	7	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51872344	51872344	8109	3	G	T	T	46	46	IQCF2	T	3	3
NDST4	64579	broad.mit.edu	36	4	116111083	116111083	+	Silent	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:116111083G>A	uc003ibu.1	-	c.1173C>T	c.(1171-1173)AAC>AAT	p.N391N	NDST4_uc010imw.1_Non-coding_Transcript|NDST4_uc010imx.1_De_novo_Start_InFrame	NM_022569	NP_072091	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan	391	Lumenal (Potential).|Heparan sulfate N-deacetylase 4.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)										0.189189	14.599783	17.95118	7	30	GG		KEEP	---	---	---	---	capture			Silent	SNP	116111083	116111083	10657	4	G	A	A	40	40	NDST4	A	1	1
STK32B	55351	broad.mit.edu	36	4	5499347	5499347	+	Silent	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:5499347G>A	uc003gih.1	+	c.609G>A	c.(607-609)TCG>TCA	p.S203S	STK32B_uc010ida.1_Silent_p.S156S	NM_018401	NP_060871	Q9NY57	ST32B_HUMAN	serine/threonine kinase 32B	203	Protein kinase.				protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity			breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	5										175				0.175	7.839164	11.812195	7	33	GG		KEEP	---	---	---	---	capture			Silent	SNP	5499347	5499347	15818	4	G	A	A	40	40	STK32B	A	1	1
WWC1	23286	broad.mit.edu	36	5	167768135	167768135	+	Missense_Mutation	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:167768135C>T	uc003lzu.1	+	c.766C>T	c.(766-768)CAC>TAC	p.H256Y	WWC1_uc003lzv.1_Missense_Mutation_p.H162Y|WWC1_uc003lzw.1_Missense_Mutation_p.H55Y	NM_015238	NP_056053	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	256					cell migration|positive regulation of MAPKKK cascade|regulation of hippo signaling cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perinuclear region of cytoplasm|ruffle membrane	protein binding|transcription coactivator activity			ovary(2)|breast(1)	3	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)										0.127451	16.309085	30.132458	13	89	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167768135	167768135	17985	5	C	T	T	29	29	WWC1	T	2	2
PDZD2	23037	broad.mit.edu	36	5	32110453	32110453	+	Missense_Mutation	SNP	A	T	T			TCGA-28-1751-01	TCGA-28-1751-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:32110453A>T	uc003jhl.1	+	c.3484A>T	c.(3484-3486)ACT>TCT	p.T1162S	PDZD2_uc003jhm.1_Missense_Mutation_p.T1162S	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1162					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|large_intestine(1)	7														0.275862	15.181087	16.498096	8	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32110453	32110453	12122	5	A	T	T	6	6	PDZD2	T	4	4
MAP1B	4131	broad.mit.edu	36	5	71526461	71526461	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71526461T>C	uc003kbw.2	+	c.1523T>C	c.(1522-1524)CTA>CCA	p.L508P	MAP1B_uc010iyw.1_Missense_Mutation_p.L525P|MAP1B_uc010iyx.1_Missense_Mutation_p.L382P|MAP1B_uc010iyy.1_Missense_Mutation_p.L382P	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	508						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		Melanoma(17;367 822 11631 31730 47712)								0.3	12.139838	12.856502	6	14	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71526461	71526461	9611	5	T	C	C	53	53	MAP1B	C	4	4
SYNE1	23345	broad.mit.edu	36	6	152694151	152694151	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:152694151C>G	uc010kiw.1	-	c.13362G>C	c.(13360-13362)GAG>GAC	p.E4454D	SYNE1_uc003qot.2_Missense_Mutation_p.E4383D|SYNE1_uc003qou.2_Missense_Mutation_p.E4454D|SYNE1_uc010kiz.1_Missense_Mutation_p.E209D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4454	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.134146	8.2906	18.942818	11	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152694151	152694151	15966	6	C	G	G	32	32	SYNE1	G	3	3
SYTL3	94120	broad.mit.edu	36	6	159006503	159006503	+	Missense_Mutation	SNP	C	G	G			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:159006503C>G	uc003qrp.1	+	c.199C>G	c.(199-201)CAG>GAG	p.Q67E	SYTL3_uc003qro.1_Missense_Mutation_p.Q67E|SYTL3_uc003qrq.1_Missense_Mutation_p.Q67E|SYTL3_uc003qrr.1_Missense_Mutation_p.Q67E|SYTL3_uc003qrs.1_Missense_Mutation_p.Q67E	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	67	RabBD.				intracellular protein transport	endomembrane system|membrane	Rab GTPase binding|zinc ion binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)										0.25	8.509044	9.40758	4	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	159006503	159006503	16005	6	C	G	G	21	21	SYTL3	G	3	3
SYTL3	94120	broad.mit.edu	36	6	159066627	159066627	+	Silent	SNP	C	T	T			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:159066627C>T	uc003qrp.1	+	c.825C>T	c.(823-825)CCC>CCT	p.P275P	SYTL3_uc003qro.1_Silent_p.P207P|SYTL3_uc003qrq.1_Silent_p.P207P|SYTL3_uc003qrr.1_Silent_p.P275P|SYTL3_uc003qrs.1_Silent_p.P207P	NM_001009991	NP_001009991	Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	275					intracellular protein transport	endomembrane system|membrane	Rab GTPase binding|zinc ion binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)										0.107943	63.522271	138.262214	53	438	CC		KEEP	---	---	---	---	capture			Silent	SNP	159066627	159066627	16005	6	C	T	T	21	21	SYTL3	T	2	2
TFAP2D	83741	broad.mit.edu	36	6	50804621	50804621	+	Missense_Mutation	SNP	T	C	C			TCGA-28-1751-01	TCGA-28-1751-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:50804621T>C	uc003paf.1	+	c.692T>C	c.(691-693)ATT>ACT	p.I231T		NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	231					regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)													0.137931	29.510285	47.905062	20	125	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50804621	50804621	16318	6	T	C	C	52	52	TFAP2D	C	4	4
RNF139	11236	broad.mit.edu	36	8	125556592	125556592	+	Missense_Mutation	SNP	G	T	T			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:125556592G>T	uc003yrc.1	+	c.61G>T	c.(61-63)GCG>TCG	p.A21S		NM_007218	NP_009149	Q8WU17	RN139_HUMAN	ring finger protein 139	21					regulation of protein ubiquitination	endoplasmic reticulum membrane|integral to membrane	ligase activity|protein binding|receptor activity|zinc ion binding			kidney(1)	1	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)											0.533333	20.094293	20.108389	8	7	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125556592	125556592	13919	8	G	T	T	42	42	RNF139	T	3	3
GPR64	10149	broad.mit.edu	36	X	18941833	18941833	+	Nonsense_Mutation	SNP	G	A	A			TCGA-28-1751-01	TCGA-28-1751-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:18941833G>A	uc004cyx.1	-	c.991C>T	c.(991-993)CAA>TAA	p.Q331*	GPR64_uc004cyw.1_Nonsense_Mutation_p.Q315*|GPR64_uc010nfj.1_Nonsense_Mutation_p.Q301*|GPR64_uc004cyy.1_Nonsense_Mutation_p.Q328*|GPR64_uc004cyz.1_Nonsense_Mutation_p.Q317*|GPR64_uc004czb.1_Nonsense_Mutation_p.Q331*|GPR64_uc004czc.1_Nonsense_Mutation_p.Q315*|GPR64_uc004czd.1_Nonsense_Mutation_p.Q307*|GPR64_uc004cze.1_Nonsense_Mutation_p.Q301*|GPR64_uc004czf.1_Nonsense_Mutation_p.Q293*|GPR64_uc004cza.1_Nonsense_Mutation_p.Q309*	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	331	Extracellular (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)													0.171053	27.058182	34.811335	13	63	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	18941833	18941833	6980	23	G	A	A	47	47	GPR64	A	5	2
TAF1	6872	broad.mit.edu	36	X	70591402	70591402	+	Missense_Mutation	SNP	C	A	A			TCGA-28-1751-01	TCGA-28-1751-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70591402C>A	uc004dzt.2	+	c.4968C>A	c.(4966-4968)GAC>GAA	p.D1656E	TAF1_uc004dzu.2_Missense_Mutation_p.D1635E|TAF1_uc010nle.1_Missense_Mutation_p.D60E|TAF1_uc010nlf.1_Missense_Mutation_p.D60E|TAF1_uc004dzx.2_Non-coding_Transcript|TAF1_uc004dzy.2_Non-coding_Transcript|TAF1_uc004dzw.1_Non-coding_Transcript|TAF1_uc004dzv.2_Missense_Mutation_p.D809E|TAF1_uc010nld.1_Non-coding_Transcript	NM_004606	NP_004597	P21675	TAF1_HUMAN	TBP-associated factor 1 isoform 1	1635	Asp/Glu-rich (acidic tail).|Protein kinase 2.				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|response to DNA damage stimulus|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	15	Renal(35;0.156)	all_lung(315;0.000321)								472				0.3	80.293893	83.879794	30	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70591402	70591402	16034	23	C	A	A	18	18	TAF1	A	3	3
MPP7	143098	broad.mit.edu	36	10	28567601	28567602	+	De_novo_Start_OutOfFrame	INS	-	T	T			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:28567601_28567602insT	uc001iua.1	-	c.-62_-61insA	c.(-64--59)CTGTGG>CTGATGG		MPP7_uc009xkz.1_Non-coding_Transcript|MPP7_uc001iub.1_De_novo_Start_OutOfFrame|MPP7_uc009xla.1_De_novo_Start_OutOfFrame	NM_173496	NP_775767			palmitoylated membrane protein 7						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														0.59			54	37				---	---	---	---	capture_indel			De_novo_Start_OutOfFrame	INS	28567601	28567602	10131	10	-	T	T	6	6	MPP7	T	5	5
KBTBD4	55709	broad.mit.edu	36	11	47553804	47553805	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:47553804_47553805insC	uc001nfw.1	-	c.687_688insG	c.(685-690)AACCCAfs	p.N229fs	NDUFS3_uc001nft.2_Intron|KBTBD4_uc001nfx.1_Frame_Shift_Ins_p.N204fs|KBTBD4_uc001nfy.1_Frame_Shift_Ins_p.N204fs|KBTBD4_uc001nfz.1_Frame_Shift_Ins_p.N220fs	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	204_205	BACK.									ovary(1)|central_nervous_system(1)	2														0.43			76	102				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	47553804	47553805	8300	11	-	C	C	43	43	KBTBD4	C	5	5
INCENP	3619	broad.mit.edu	36	11	61672555	61672561	+	Frame_Shift_Del	DEL	CTGCAGA	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:61672555_61672561delCTGCAGA	uc001nsw.1	+	c.2236_2242delCTGCAGA	c.(2236-2244)CTGCAGAAGfs	p.L746fs	INCENP_uc009ynw.1_Frame_Shift_Del_p.L750fs|INCENP_uc001nsx.1_Frame_Shift_Del_p.L742fs|INCENP_uc001nsy.1_Frame_Shift_Del_p.L160fs	NM_001040694	NP_001035784	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	746_748	Potential.				chromosome segregation|cytokinesis|mitotic prometaphase	centromeric heterochromatin|condensed chromosome kinetochore|cytosol|microtubule|spindle	protein binding			lung(1)	1														0.32			9	19				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	61672555	61672561	8034	11	CTGCAGA	-	-	28	28	INCENP	-	5	5
SYVN1	84447	broad.mit.edu	36	11	64655575	64655587	+	Frame_Shift_Del	DEL	CTGGAGGTCCACG	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64655575_64655587delCTGGAGGTCCACG	uc001odb.1	-	c.588_600delCGTGGACCTCCAG	c.(586-600)TCCGTGGACCTCCAGfs	p.S196fs	SYVN1_uc001odc.1_Frame_Shift_Del_p.S196fs|SYVN1_uc009yqc.1_Frame_Shift_Del_p.S145fs	NM_172230	NP_757385	Q86TM6	SYVN1_HUMAN	synoviolin 1 isoform b	196_200	Lumenal (Potential).				ER-associated protein catabolic process|response to stress	endoplasmic reticulum membrane|integral to membrane|nucleus	acid-amino acid ligase activity|protein binding|zinc ion binding			ovary(1)	1														0.59			55	39				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	64655575	64655587	16008	11	CTGGAGGTCCACG	-	-	32	32	SYVN1	-	5	5
SH2B3	10019	broad.mit.edu	36	12	110370419	110370420	+	Frame_Shift_Ins	INS	-	T	T			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110370419_110370420insT	uc001tsf.1	+	c.1661_1662insT	c.(1660-1662)TCGfs	p.S554fs	SH2B3_uc001tse.1_Frame_Shift_Ins_p.S553fs	NM_005475	NP_005466	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	553					blood coagulation	cytosol	signal transducer activity			ovary(1)	1														0.47			21	24				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	110370419	110370420	14720	12	-	T	T	31	31	SH2B3	T	5	5
RAD52	5893	broad.mit.edu	36	12	906661	906663	+	In_Frame_Del	DEL	ATA	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:906661_906663delATA	uc001qis.1	-	c.376_378delTAT	c.(376-378)TATdel	p.Y126del	RAD52_uc001qit.1_5'UTR|RAD52_uc001qiu.1_In_Frame_Del_p.Y126del|RAD52_uc001qiv.1_Non-coding_Transcript|RAD52_uc001qiw.1_Intron|RAD52_uc001qix.1_In_Frame_Del_p.Y126del	NM_134424	NP_602296	P43351	RAD52_HUMAN	RAD52 homolog	126					DNA recombinase assembly|mitotic recombination|reciprocal meiotic recombination	nucleoplasm	DNA binding|protein binding			central_nervous_system(1)	1	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)											0.59			366	250				---	---	---	---	capture_indel			In_Frame_Del	DEL	906661	906663	13451	12	ATA	-	-	8	8	RAD52	-	5	5
CHGA	1113	broad.mit.edu	36	14	92467706	92467709	+	Frame_Shift_Del	DEL	GGCT	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:92467706_92467709delGGCT	uc001ybc.2	+	c.714_717delGGCT	c.(712-717)GAGGCTfs	p.E238fs	CHGA_uc010aum.1_Non-coding_Transcript|CHGA_uc001ybd.2_Intron	NM_001275	NP_001266	P10645	CMGA_HUMAN	chromogranin A precursor	238_239					regulation of blood pressure	extracellular space					0		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)								0.48			13	14				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	92467706	92467709	3472	14	GGCT	-	-	35	35	CHGA	-	5	5
VPS33B	26276	broad.mit.edu	36	15	89343966	89343968	+	In_Frame_Del	DEL	CAA	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89343966_89343968delCAA	uc002bqp.1	-	c.1717_1719delTTG	c.(1717-1719)TTGdel	p.L573del	VPS33B_uc002bqq.1_In_Frame_Del_p.L482del	NM_018668	NP_061138	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33B (yeast homolog))	573					cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis	late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule	protein binding			ovary(1)	1	Lung NSC(78;0.0987)|all_lung(78;0.175)													0.38			30	48				---	---	---	---	capture_indel			In_Frame_Del	DEL	89343966	89343968	17769	15	CAA	-	-	21	21	VPS33B	-	5	5
ATP13A2	23400	broad.mit.edu	36	1	17188983	17188984	+	Frame_Shift_Del	DEL	TG	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17188983_17188984delTG	uc001baa.1	-	c.2514_2515delCA	c.(2512-2517)CCCAAGfs	p.P838fs	ATP13A2_uc001azz.1_5'UTR|ATP13A2_uc001bab.1_Frame_Shift_Del_p.P833fs|ATP13A2_uc001bac.1_Intron	NM_022089	NP_071372	Q9NQ11	AT132_HUMAN	ATPase type 13A2 isoform 1	838_839	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)										0.64			9	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	17188983	17188984	1143	1	TG	-	-	63	63	ATP13A2	-	5	5
PTCD1	26024	broad.mit.edu	36	7	98870709	98870714	+	In_Frame_Del	DEL	CCACCT	-	-			TCGA-28-1751-01	TCGA-28-1751-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:98870709_98870714delCCACCT	uc003uqh.1	-	c.88_93delAGGTGG	c.(88-93)AGGTGGdel	p.RW30del	PDAP1_uc010lfv.1_Intron	NM_015545	NP_056360	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	30_31										ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)											0.32			30	64				---	---	---	---	capture_indel			In_Frame_Del	DEL	98870709	98870714	13181	7	CCACCT	-	-	22	22	PTCD1	-	5	5
