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
PTEN	5728	broad.mit.edu	36	10	89701892	89701892	+	Missense_Mutation	SNP	A	G	G			TCGA-12-0828-01	TCGA-12-0828-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89701892A>G	uc001kfb.1	+	c.530A>G	c.(529-531)TAT>TGT	p.Y177C		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	177	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.Y177C(4)|p.V166fs*17(3)|p.G165fs*9(3)|p.Y27_N212>Y(2)|p.Y177fs*2(1)|p.Y177fs*1(1)|p.G165_*404del(1)|p.V175fs*3(1)|p.R172fs*5(1)|p.G165_K342del(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)				31		264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.742627	906.669183	926.569186	277	96	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89701892	89701892	13192	10	A	G	G	16	16	PTEN	G	4	4
OR10G9	219870	broad.mit.edu	36	11	123399611	123399611	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123399611C>T	uc001pzo.1	+	c.682C>T	c.(682-684)CAC>TAC	p.H228Y		NM_001001953	NP_001001953	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G,	228	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)										0.322751	159.294844	164.574992	61	128	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123399611	123399611	11310	11	C	T	T	21	21	OR10G9	T	2	2
OR5D14	219436	broad.mit.edu	36	11	55320106	55320106	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55320106C>T	uc001nhv.1	+	c.499C>T	c.(499-501)CGG>TGG	p.R167W		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	167	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)												0.387755	109.82539	110.907337	38	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55320106	55320106	11565	11	C	T	T	23	23	OR5D14	T	1	1
PRG3	10394	broad.mit.edu	36	11	56903593	56903593	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:56903593T>G	uc001njv.1	-	c.325A>C	c.(325-327)ACC>CCC	p.T109P		NM_006093	NP_006084	Q9Y2Y8	PRG3_HUMAN	proteoglycan 3	109	C-type lectin.				basophil activation|histamine biosynthetic process|immune response|leukotriene biosynthetic process|negative regulation of translation|neutrophil activation|positive regulation of interleukin-8 biosynthetic process|superoxide anion generation		sugar binding				0						Melanoma(154;1456 2519 19358 45229)								0.155172	8.45592	15.228873	9	49	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56903593	56903593	12923	11	T	G	G	50	50	PRG3	G	4	4
PLAC1L	219990	broad.mit.edu	36	11	59567635	59567635	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59567635G>A	uc001nol.1	+	c.182G>A	c.(181-183)CGG>CAG	p.R61Q		NM_173801	NP_776162	Q86WS3	PLACL_HUMAN	placenta-specific 1-like	61						extracellular region				ovary(2)	2														0.361111	76.539678	77.757823	26	46	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59567635	59567635	12439	11	G	A	A	39	39	PLAC1L	A	1	1
CEP57	9702	broad.mit.edu	36	11	95190659	95190659	+	Silent	SNP	T	C	C			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:95190659T>C	uc001pfp.1	+	c.565T>C	c.(565-567)TTG>CTG	p.L189L	CEP57_uc001pfo.1_Silent_p.L189L|CEP57_uc009ywn.1_Silent_p.L37L|CEP57_uc001pfq.1_Silent_p.L189L|CEP57_uc001pfr.1_Silent_p.L37L	NM_014679	NP_055494	Q86XR8	CEP57_HUMAN	translokin	189	Potential.|centrosome localization domain (CLD) (By similarity).				fibroblast growth factor receptor signaling pathway|G2/M transition of mitotic cell cycle|protein import into nucleus, translocation|spermatid development	centrosome|cytosol|Golgi apparatus|microtubule|nucleus	fibroblast growth factor binding|protein homodimerization activity			ovary(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												0.302632	66.399335	69.040423	23	53	TT		KEEP	---	---	---	---	capture			Silent	SNP	95190659	95190659	3389	11	T	C	C	52	52	CEP57	C	4	4
RPLP0	6175	broad.mit.edu	36	12	119119080	119119080	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:119119080G>C	uc001txp.1	-	c.833C>G	c.(832-834)GCT>GGT	p.A278G	GCN1L1_uc001txo.1_5'Flank|RPLP0_uc001txq.1_Missense_Mutation_p.A278G|RPLP0_uc001txr.1_Missense_Mutation_p.A216G	NM_053275	NP_444505	P05388	RLA0_HUMAN	ribosomal protein P0	278					endocrine pancreas development|interspecies interaction between organisms|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)													0.666667	6.65439	6.724931	2	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	119119080	119119080	14083	12	G	C	C	34	34	RPLP0	C	3	3
PTPRR	5801	broad.mit.edu	36	12	69425965	69425965	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:69425965C>T	uc001swi.1	-	c.907G>A	c.(907-909)GTG>ATG	p.V303M	PTPRR_uc001swh.1_Missense_Mutation_p.V58M|PTPRR_uc009zrs.1_Missense_Mutation_p.V97M	NM_002849	NP_002840	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	303	Cytoplasmic (Potential).				in utero embryonic development	cell surface|Golgi apparatus|integral to membrane|nucleus|perinuclear region of cytoplasm|plasma membrane	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)										0.389914	865.733165	874.306309	317	496	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69425965	69425965	13268	12	C	T	T	19	19	PTPRR	T	1	1
TNFSF13B	10673	broad.mit.edu	36	13	107720491	107720491	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:107720491C>A	uc001vqr.1	+	c.247C>A	c.(247-249)CTG>ATG	p.L83M	TNFSF13B_uc010agj.1_Missense_Mutation_p.L83M	NM_006573	NP_006564	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily,	83	Extracellular (Potential).				cell proliferation|immune response|signal transduction	extracellular space|integral to membrane|plasma membrane|soluble fraction	cytokine activity|tumor necrosis factor receptor binding				0	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)											0.571429	8.192634	8.222824	4	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107720491	107720491	16847	13	C	A	A	28	28	TNFSF13B	A	3	3
IRS2	8660	broad.mit.edu	36	13	109236017	109236017	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:109236017C>G	uc001vqv.1	-	c.385G>C	c.(385-387)GAG>CAG	p.E129Q		NM_003749	NP_003740	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	129	PH.				fibroblast growth factor receptor signaling pathway|glucose metabolic process|insulin receptor signaling pathway|lipid homeostasis|negative regulation of B cell apoptosis|negative regulation of kinase activity|negative regulation of plasma membrane long-chain fatty acid transport|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of B cell proliferation|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin secretion|response to glucose stimulus	cytosol|plasma membrane	insulin receptor binding|signal transducer activity			large_intestine(2)|upper_aerodigestive_tract(1)|kidney(1)|skin(1)	5	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			Melanoma(100;613 2409 40847)				156				0.26087	7.723989	8.929328	6	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	109236017	109236017	8145	13	C	G	G	31	31	IRS2	G	3	3
PCID2	55795	broad.mit.edu	36	13	112899457	112899457	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:112899457C>A	uc001vtc.1	-	c.302G>T	c.(301-303)AGA>ATA	p.R101I	PCID2_uc001vtd.1_Intron|PCID2_uc001vte.1_Intron|PCID2_uc001vtf.1_Intron|PCID2_uc001vtg.1_Non-coding_Transcript	NM_018386	NP_060856	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	76					negative regulation of apoptosis|negative regulation of cysteine-type endopeptidase activity|positive regulation of gene-specific transcription|positive regulation of mitotic cell cycle spindle assembly checkpoint|regulation of mRNA stability|spleen development		protein binding|transcription activator activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)											0.148148	101.571848	162.583031	76	437	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112899457	112899457	11999	13	C	A	A	32	32	PCID2	A	3	3
LRRK1	79705	broad.mit.edu	36	15	99341392	99341392	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:99341392C>T	uc002bwr.1	+	c.398C>T	c.(397-399)ACG>ATG	p.T133M	LRRK1_uc002bwq.1_Missense_Mutation_p.T133M	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	133	ANK 2.				protein phosphorylation|small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)							1100				0.220144	346.412028	396.476365	153	542	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99341392	99341392	9408	15	C	T	T	19	19	LRRK1	T	1	1
ZNF624	57547	broad.mit.edu	36	17	16466970	16466970	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:16466970T>G	uc010cpi.1	-	c.1955A>C	c.(1954-1956)AAA>ACA	p.K652T		NM_020787	NP_065838	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	652	C2H2-type 14.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		NSCLC(186;1023 2134 13330 38202 39800)								0.313725	178.111479	184.420648	64	140	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16466970	16466970	18643	17	T	G	G	64	64	ZNF624	G	4	4
SMG6	23293	broad.mit.edu	36	17	2142919	2142919	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:2142919G>A	uc002fub.1	-	c.2254C>T	c.(2254-2256)CGC>TGC	p.R752C		NM_017575	NP_060045	Q86US8	EST1A_HUMAN	Smg-6 homolog, nonsense mediated mRNA decay	752					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation|telomere maintenance	chromosome, telomeric region|cytoplasm|nucleolus|telomerase holoenzyme complex	endonuclease activity|metal ion binding|protein binding|telomeric DNA binding			central_nervous_system(2)|lung(1)|kidney(1)	4						Melanoma(59;28 1088 11621 25887 46638 50814)								0.192308	95.264611	115.941107	45	189	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2142919	2142919	15295	17	G	A	A	40	40	SMG6	A	1	1
KIAA1267	284058	broad.mit.edu	36	17	41464877	41464877	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:41464877G>A	uc002ikb.1	-	c.3130C>T	c.(3130-3132)CAC>TAC	p.H1044Y	KIAA1267_uc002ikc.1_Missense_Mutation_p.H1044Y|KIAA1267_uc002ikd.1_Missense_Mutation_p.H1044Y|KIAA1267_uc010dav.1_Missense_Mutation_p.H1043Y|KIAA1267_uc002ijz.1_Missense_Mutation_p.H375Y|KIAA1267_uc002ika.1_Missense_Mutation_p.H312Y	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	1044						MLL1 complex	protein binding				0		Melanoma(429;0.211)												0.333333	29.848421	30.814654	13	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41464877	41464877	8528	17	G	A	A	46	46	KIAA1267	A	2	2
SPAG9	9043	broad.mit.edu	36	17	46422080	46422080	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:46422080C>T	uc002itc.1	-	c.2770G>A	c.(2770-2772)GGA>AGA	p.G924R	SPAG9_uc002ita.1_Missense_Mutation_p.G259R|SPAG9_uc002itb.1_Missense_Mutation_p.G910R|SPAG9_uc002itd.1_Missense_Mutation_p.G914R|SPAG9_uc002ite.2_Missense_Mutation_p.G754R|SPAG9_uc002itf.2_Missense_Mutation_p.G745R	NM_003971	NP_003962	O60271	JIP4_HUMAN	sperm associated antigen 9 isoform 3	924					positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis	acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm				lung(1)	1			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)											0.413223	146.226307	147.021515	50	71	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46422080	46422080	15488	17	C	T	T	22	22	SPAG9	T	2	2
MTMR4	9110	broad.mit.edu	36	17	53939166	53939166	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:53939166C>T	uc002iwj.1	-	c.928G>A	c.(928-930)GAT>AAT	p.D310N		NM_004687	NP_004678	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	310	Myotubularin phosphatase.					cytoplasm|membrane	protein tyrosine phosphatase activity|zinc ion binding			skin(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.142857	11.463596	18.349863	8	48	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53939166	53939166	10339	17	C	T	T	30	30	MTMR4	T	2	2
NDUFV2	4729	broad.mit.edu	36	18	9124224	9124224	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9124224T>G	uc002knu.1	+	c.697T>G	c.(697-699)TCT>GCT	p.S233A	ANKRD12_uc002knv.2_5'Flank|ANKRD12_uc002knw.2_5'Flank	NM_021074	NP_066552	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2,	233					cardiac muscle tissue development|mitochondrial electron transport, NADH to ubiquinone|nervous system development|transport	mitochondrial respiratory chain complex I	2 iron, 2 sulfur cluster binding|electron carrier activity|metal ion binding|NAD binding|NADH dehydrogenase (ubiquinone) activity			ovary(1)	1					NADH(DB00157)									0.414861	368.470632	370.516857	134	189	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9124224	9124224	10699	18	T	G	G	54	54	NDUFV2	G	4	4
MAST1	22983	broad.mit.edu	36	19	12815345	12815345	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12815345C>T	uc002mvm.1	+	c.251C>T	c.(250-252)GCG>GTG	p.A84V	MAST1_uc002mvk.2_Missense_Mutation_p.A80V|MAST1_uc002mvl.1_Intron	NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	84					cytoskeleton organization|intracellular protein kinase cascade|protein phosphorylation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7										239				0.487805	218.149004	218.170906	80	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12815345	12815345	9708	19	C	T	T	27	27	MAST1	T	1	1
ZNF568	374900	broad.mit.edu	36	19	42132921	42132921	+	Silent	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:42132921C>T	uc002ofc.1	+	c.1026C>T	c.(1024-1026)TCC>TCT	p.S342S	ZNF568_uc002ofd.1_Silent_p.S266S|ZNF568_uc010efe.1_Silent_p.S266S|ZNF568_uc010eff.1_Intron|ZNF568_uc010efg.1_Intron	NM_198539	NP_940941	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	342	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)											0.401408	167.535975	168.745218	57	85	CC		KEEP	---	---	---	---	capture			Silent	SNP	42132921	42132921	18594	19	C	T	T	24	24	ZNF568	T	2	2
FPR2	2358	broad.mit.edu	36	19	56964161	56964161	+	Silent	SNP	C	A	A			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56964161C>A	uc002pxr.1	+	c.438C>A	c.(436-438)ATC>ATA	p.I146I	FPR2_uc002pxs.2_Silent_p.I146I|FPR2_uc010epf.1_Silent_p.I146I|FPR2_uc010epg.1_Silent_p.I146I	NM_001005738	NP_001453	P25090	FPR2_HUMAN	formyl peptide receptor-like 1	146	Helical; Name=4; (Potential).				cell adhesion|cellular component movement|chemotaxis|inflammatory response	integral to membrane|plasma membrane	N-formyl peptide receptor activity			ovary(1)	1														0.345238	169.713051	173.259545	58	110	CC		KEEP	---	---	---	---	capture			Silent	SNP	56964161	56964161	6285	19	C	A	A	31	31	FPR2	A	3	3
NLRP2	55655	broad.mit.edu	36	19	60186257	60186257	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60186257C>T	uc002qij.1	+	c.1379C>T	c.(1378-1380)GCG>GTG	p.A460V	NLRP2_uc010esm.1_Non-coding_Transcript|NLRP2_uc010esn.1_Missense_Mutation_p.A436V|NLRP2_uc010eso.1_Missense_Mutation_p.A457V|NLRP2_uc010esp.1_Missense_Mutation_p.A438V	NM_017852	NP_060322	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	460	NACHT.				apoptosis|positive regulation of caspase activity|positive regulation of interleukin-1 beta secretion	cytoplasm	ATP binding|Pyrin domain binding			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)										0.544118	107.549206	107.661962	37	31	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	60186257	60186257	10880	19	C	T	T	27	27	NLRP2	T	1	1
TCHH	7062	broad.mit.edu	36	1	150351760	150351760	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150351760C>T	uc001ezp.2	-	c.557G>A	c.(556-558)CGC>CAC	p.R186H	TCHH_uc009wne.1_Missense_Mutation_p.R186H	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	186					keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.345455	49.207821	50.367812	19	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150351760	150351760	16226	1	C	T	T	27	27	TCHH	T	1	1
SPTA1	6708	broad.mit.edu	36	1	156902777	156902777	+	Nonsense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156902777G>A	uc001fst.1	-	c.2173C>T	c.(2173-2175)CGA>TGA	p.R725*		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	725	Spectrin 8.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.368421	17.418538	17.708035	7	12	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	156902777	156902777	15630	1	G	A	A	37	37	SPTA1	A	5	1
NME7	29922	broad.mit.edu	36	1	167539030	167539030	+	Missense_Mutation	SNP	A	T	T			TCGA-12-0828-01	TCGA-12-0828-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167539030A>T	uc001gfu.1	-	c.417T>A	c.(415-417)GAT>GAA	p.D139E	NME7_uc001gft.1_Missense_Mutation_p.D103E|NME7_uc001gfv.1_Missense_Mutation_p.D139E	NM_013330	NP_932076	Q9Y5B8	NDK7_HUMAN	nucleoside-diphosphate kinase 7 isoform a	139					CTP biosynthetic process|GTP biosynthetic process|UTP biosynthetic process		ATP binding|metal ion binding|nucleoside diphosphate kinase activity			central_nervous_system(1)	1	all_hematologic(923;0.208)													0.343891	209.537939	214.292553	76	145	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	167539030	167539030	10899	1	A	T	T	12	12	NME7	T	4	4
TFB2M	64216	broad.mit.edu	36	1	244787328	244787328	+	Missense_Mutation	SNP	T	C	C			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:244787328T>C	uc001ibn.1	-	c.534A>G	c.(532-534)ATA>ATG	p.I178M		NM_022366	NP_071761	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	178					positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity			ovary(1)	1	all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376)		OV - Ovarian serous cystadenocarcinoma(106;0.00358)											0.4	119.585053	120.371196	36	54	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	244787328	244787328	16322	1	T	C	C	53	53	TFB2M	C	4	4
TMEM53	79639	broad.mit.edu	36	1	44892861	44892861	+	Missense_Mutation	SNP	G	T	T			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:44892861G>T	uc001cmc.1	-	c.791C>A	c.(790-792)ACA>AAA	p.T264K	TMEM53_uc001cmb.1_Intron|TMEM53_uc001cmd.1_Missense_Mutation_p.T191K|TMEM53_uc009vxh.1_Missense_Mutation_p.T147K	NM_024587	NP_078863	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	264						integral to membrane				ovary(2)	2	Acute lymphoblastic leukemia(166;0.155)													0.227273	6.739829	8.271857	5	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44892861	44892861	16718	1	G	T	T	48	48	TMEM53	T	3	3
PARS2	25973	broad.mit.edu	36	1	54996493	54996493	+	Silent	SNP	T	C	C			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:54996493T>C	uc001cxy.1	-	c.930A>G	c.(928-930)ACA>ACG	p.T310T	PARS2_uc009vzs.1_Silent_p.T310T	NM_152268	NP_689481	Q7L3T8	SYPM_HUMAN	prolyl-tRNA synthetase	310					prolyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|proline-tRNA ligase activity			ovary(2)	2					L-Proline(DB00172)									0.350755	787.932241	804.872698	302	559	TT		KEEP	---	---	---	---	capture			Silent	SNP	54996493	54996493	11884	1	T	C	C	51	51	PARS2	C	4	4
LRRC40	55631	broad.mit.edu	36	1	70384136	70384136	+	Missense_Mutation	SNP	C	G	G			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:70384136C>G	uc001der.1	-	c.1744G>C	c.(1744-1746)GCA>CCA	p.A582P		NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	582	LRR 20.									ovary(1)	1														0.166667	6.479834	9.018822	4	20	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70384136	70384136	9373	1	C	G	G	28	28	LRRC40	G	3	3
PDE9A	5152	broad.mit.edu	36	21	43054010	43054010	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr21:43054010T>G	uc002zbm.1	+	c.1009T>G	c.(1009-1011)TTC>GTC	p.F337V	PDE9A_uc002zbn.1_Missense_Mutation_p.F210V|PDE9A_uc002zbo.1_Missense_Mutation_p.F284V|PDE9A_uc002zbp.1_Missense_Mutation_p.F130V|PDE9A_uc002zbq.1_Missense_Mutation_p.F235V|PDE9A_uc002zbs.1_Missense_Mutation_p.F130V|PDE9A_uc002zbr.1_Missense_Mutation_p.F130V|PDE9A_uc002zbt.1_Missense_Mutation_p.F209V|PDE9A_uc002zbu.1_Missense_Mutation_p.F203V|PDE9A_uc002zbv.1_Missense_Mutation_p.F177V|PDE9A_uc002zbw.1_Missense_Mutation_p.F120V|PDE9A_uc002zbx.1_Missense_Mutation_p.F277V|PDE9A_uc002zby.1_Missense_Mutation_p.F120V|PDE9A_uc002zbz.1_Missense_Mutation_p.F229V|PDE9A_uc002zca.1_Missense_Mutation_p.F296V|PDE9A_uc002zcb.1_Missense_Mutation_p.F311V|PDE9A_uc002zcc.1_Missense_Mutation_p.F236V|PDE9A_uc002zcd.1_Missense_Mutation_p.F251V|PDE9A_uc002zce.1_Missense_Mutation_p.F270V|PDE9A_uc002zcf.1_Missense_Mutation_p.F130V|PDE9A_uc002zcg.1_Missense_Mutation_p.F130V|PDE9A_uc002zch.1_Missense_Mutation_p.F120V|PDE9A_uc010gpf.1_Missense_Mutation_p.F130V	NM_002606	NP_001001585	O76083	PDE9A_HUMAN	phosphodiesterase 9A isoform a	337	Catalytic (By similarity).				platelet activation|signal transduction	cytosol|endoplasmic reticulum|Golgi apparatus|perinuclear region of cytoplasm|ruffle membrane	3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding|protein binding				0														0.434524	968.280964	971.4466	365	475	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43054010	43054010	12076	21	T	G	G	60	60	PDE9A	G	4	4
GTPBP1	9567	broad.mit.edu	36	22	37452363	37452363	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:37452363G>A	uc003awg.1	+	c.1373G>A	c.(1372-1374)GGC>GAC	p.G458D		NM_004286	NP_004277	O00178	GTPB1_HUMAN	GTP binding protein 1	458					immune response|signal transduction		GTP binding|GTPase activity			ovary(1)	1	Melanoma(58;0.04)													0.385417	104.946255	106.05287	37	59	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37452363	37452363	7158	22	G	A	A	42	42	GTPBP1	A	2	2
DPP10	57628	broad.mit.edu	36	2	116163939	116163939	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:116163939C>T	uc002tla.1	+	c.548C>T	c.(547-549)GCG>GTG	p.A183V	DPP10_uc002tlb.1_Missense_Mutation_p.A133V|DPP10_uc002tlc.1_Missense_Mutation_p.A179V|DPP10_uc002tle.1_Missense_Mutation_p.A133V|DPP10_uc002tlf.1_Missense_Mutation_p.A176V	NM_020868	NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl peptidase 10 isoform long	183	Extracellular (Potential).				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity			ovary(5)|large_intestine(2)|breast(1)|skin(1)	9														0.196769	269.343757	327.664665	134	547	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116163939	116163939	4911	2	C	T	T	27	27	DPP10	T	1	1
SF3B1	23451	broad.mit.edu	36	2	197975943	197975943	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:197975943C>T	uc002uue.1	-	c.1781G>A	c.(1780-1782)CGA>CAA	p.R594Q		NM_012433	NP_036565	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1 isoform 1	594	HEAT 2.			R -> L (in Ref. 1; AAC97189).	nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding			pancreas(3)|ovary(1)|breast(1)|skin(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.246)											0.363636	12.39698	12.576969	4	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	197975943	197975943	14638	2	C	T	T	31	31	SF3B1	T	1	1
STK36	27148	broad.mit.edu	36	2	219249092	219249092	+	Silent	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219249092C>T	uc002viu.1	+	c.531C>T	c.(529-531)TAC>TAT	p.Y177Y	STK36_uc002viv.1_Silent_p.Y177Y	NM_015690	NP_056505	Q9NRP7	STK36_HUMAN	serine/threonine kinase 36	177	Protein kinase.				cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development|protein phosphorylation	aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus	ATP binding|magnesium ion binding|protein serine/threonine kinase activity|transcription factor binding			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)	8		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)						551				0.551804	1402.077627	1404.083389	474	385	CC		KEEP	---	---	---	---	capture			Silent	SNP	219249092	219249092	15822	2	C	T	T	19	19	STK36	T	1	1
COLEC11	78989	broad.mit.edu	36	2	3669381	3669381	+	Missense_Mutation	SNP	T	G	G			TCGA-12-0828-01	TCGA-12-0828-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:3669381T>G	uc002qya.1	+	c.614T>G	c.(613-615)ATC>AGC	p.I205S	COLEC11_uc002qxz.1_Missense_Mutation_p.I202S|COLEC11_uc002qyb.1_Missense_Mutation_p.I181S|COLEC11_uc002qyc.1_Missense_Mutation_p.I181S|COLEC11_uc010ewo.1_Missense_Mutation_p.I157S|COLEC11_uc010ewp.1_Missense_Mutation_p.I179S|COLEC11_uc010ewq.1_Missense_Mutation_p.I155S|COLEC11_uc010ewr.1_Missense_Mutation_p.I155S|COLEC11_uc010ews.1_Missense_Mutation_p.I131S	NM_024027	NP_076932	Q9BWP8	COL11_HUMAN	collectin sub-family member 11 isoform a	205	C-type lectin.					collagen	mannose binding				0	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)										0.208333	7.257686	9.154987	5	19	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3669381	3669381	3849	2	T	G	G	50	50	COLEC11	G	4	4
APBB2	323	broad.mit.edu	36	4	40710869	40710869	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:40710869C>T	uc003gvn.1	-	c.323G>A	c.(322-324)CGT>CAT	p.R108H	APBB2_uc003gvm.1_Missense_Mutation_p.R108H|APBB2_uc003gvl.1_Missense_Mutation_p.R91H	NM_173075	NP_775098	Q92870	APBB2_HUMAN	amyloid beta A4 precursor protein-binding,	108					cell cycle arrest|intracellular signal transduction|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|regulation of transcription, DNA-dependent	growth cone|lamellipodium|membrane|nucleus|synapse	beta-amyloid binding|transcription factor binding			ovary(2)|large_intestine(1)	3						Ovarian(3;20 75 16686 49997)								0.37234	96.197054	97.543626	35	59	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40710869	40710869	771	4	C	T	T	19	19	APBB2	T	1	1
AHRR	57491	broad.mit.edu	36	5	485995	485995	+	Missense_Mutation	SNP	G	C	C			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:485995G>C	uc003jav.1	+	c.1111G>C	c.(1111-1113)GCC>CCC	p.A371P	AHRR_uc003jaw.1_Missense_Mutation_p.A349P|AHRR_uc010isy.1_Missense_Mutation_p.A199P|AHRR_uc010isz.1_Missense_Mutation_p.A349P|AHRR_uc003jax.1_Missense_Mutation_p.A112P|AHRR_uc003jay.1_Missense_Mutation_p.A209P|AHRR_uc003jaz.1_5'UTR	NM_020731	NP_065782	A9YTQ3	AHRR_HUMAN	arylhydrocarbon receptor repressor	353					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			breast(2)	2			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)											0.159091	6.500768	11.388254	7	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	485995	485995	420	5	G	C	C	38	38	AHRR	C	3	3
LACE1	246269	broad.mit.edu	36	6	108751793	108751793	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:108751793G>A	uc003psj.1	+	c.211G>A	c.(211-213)GTT>ATT	p.V71I		NM_145315	NP_660358	Q8WV93	LACE1_HUMAN	lactation elevated 1	71							ATP binding			central_nervous_system(1)	1		all_cancers(87;1.5e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;6.79e-05)|Colorectal(196;0.0294)|all_lung(197;0.0486)|Lung SC(18;0.152)		BRCA - Breast invasive adenocarcinoma(108;0.00179)|Epithelial(106;0.0024)|all cancers(137;0.00379)|OV - Ovarian serous cystadenocarcinoma(136;0.0118)										0.309701	233.514312	242.168641	83	185	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108751793	108751793	8918	6	G	A	A	40	40	LACE1	A	1	1
FAM120B	84498	broad.mit.edu	36	6	170474269	170474269	+	Missense_Mutation	SNP	C	A	A			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:170474269C>A	uc003qxp.1	+	c.1912C>A	c.(1912-1914)CAA>AAA	p.Q638K	FAM120B_uc003qxo.1_Missense_Mutation_p.Q638K	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	638					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)										0.285068	163.329438	172.497755	63	158	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170474269	170474269	5614	6	C	A	A	29	29	FAM120B	A	3	3
HLA-DPA1	3113	broad.mit.edu	36	6	33144415	33144415	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:33144415C>T	uc003ocs.1	-	c.773G>A	c.(772-774)GGG>GAG	p.G258E	HLA-DPA1_uc010juk.1_Missense_Mutation_p.G258E	NM_033554	NP_291032	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP	258	Cytoplasmic (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0														0.119497	26.729726	49.306696	19	140	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33144415	33144415	7493	6	C	T	T	22	22	HLA-DPA1	T	2	2
COL9A1	1297	broad.mit.edu	36	6	70992409	70992409	+	Missense_Mutation	SNP	C	T	T			TCGA-12-0828-01	TCGA-12-0828-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:70992409C>T	uc003pfg.2	-	c.2528G>A	c.(2527-2529)CGT>CAT	p.R843H	COL9A1_uc003pfe.2_Missense_Mutation_p.R392H|COL9A1_uc003pff.2_Missense_Mutation_p.R600H	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	843	Triple-helical region (COL1).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	extracellular matrix structural constituent conferring tensile strength|metal ion binding			ovary(4)	4														0.266055	82.63289	88.017737	29	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70992409	70992409	3845	6	C	T	T	19	19	COL9A1	T	1	1
TECPR1	25851	broad.mit.edu	36	7	97704075	97704075	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:97704075G>A	uc003upg.1	-	c.1130C>T	c.(1129-1131)GCG>GTG	p.A377V	TECPR1_uc003uph.1_Missense_Mutation_p.A307V	NM_015395	NP_056210	Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	377						integral to membrane	protein binding			pancreas(1)	1														0.25	66.564971	72.917054	28	84	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97704075	97704075	16270	7	G	A	A	38	38	TECPR1	A	1	1
ZKSCAN1	7586	broad.mit.edu	36	7	99469382	99469382	+	Missense_Mutation	SNP	A	C	C			TCGA-12-0828-01	TCGA-12-0828-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99469382A>C	uc003usk.1	+	c.1318A>C	c.(1318-1320)AAG>CAG	p.K440Q	ZKSCAN1_uc003usl.1_Missense_Mutation_p.K404Q|ZKSCAN1_uc003usm.1_Missense_Mutation_p.K227Q	NM_003439	NP_003430	P17029	ZKSC1_HUMAN	zinc finger protein 36	440	C2H2-type 3.				regulation of transcription, DNA-dependent|viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)											0.357895	188.256595	191.630859	68	122	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99469382	99469382	18277	7	A	C	C	5	5	ZKSCAN1	C	4	4
FBXO25	26260	broad.mit.edu	36	8	403021	403021	+	Silent	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:403021G>A	uc003wox.1	+	c.858G>A	c.(856-858)TTG>TTA	p.L286L	FBXO25_uc003woy.1_Silent_p.L286L|FBXO25_uc003woz.1_Silent_p.L219L|FBXO25_uc003wpa.1_Silent_p.L69L	NM_183421	NP_904357	Q8TCJ0	FBX25_HUMAN	F-box only protein 25 isoform 1	286						nucleus|SCF ubiquitin ligase complex	actin binding|ubiquitin-protein ligase activity			lung(1)	1		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)										0.244726	249.790244	277.931056	116	358	GG		KEEP	---	---	---	---	capture			Silent	SNP	403021	403021	5973	8	G	A	A	45	45	FBXO25	A	2	2
CCIN	881	broad.mit.edu	36	9	36160726	36160726	+	Missense_Mutation	SNP	G	A	A			TCGA-12-0828-01	TCGA-12-0828-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:36160726G>A	uc003zzb.2	+	c.1227G>A	c.(1225-1227)ATG>ATA	p.M409I		NM_005893	NP_005884	Q13939	CALI_HUMAN	calicin	409	Kelch 3.				cell differentiation|multicellular organismal development|spermatogenesis	cytoskeletal calyx	structural constituent of cytoskeleton			ovary(1)	1			STAD - Stomach adenocarcinoma(86;0.228)											0.281818	158.152432	167.568448	62	158	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36160726	36160726	3003	9	G	A	A	45	45	CCIN	A	2	2
SPIN2A	54466	broad.mit.edu	36	X	57179010	57179010	+	Missense_Mutation	SNP	A	C	C			TCGA-12-0828-01	TCGA-12-0828-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:57179010A>C	uc004dvb.1	-	c.746T>G	c.(745-747)ATC>AGC	p.I249S	SPIN2A_uc010nkl.1_Missense_Mutation_p.I249S	NM_019003	NP_061876	Q99865	SPI2A_HUMAN	spindlin family, member 2	249					cell cycle|gamete generation						0														0.363636	22.171581	22.718525	12	21	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57179010	57179010	15565	23	A	C	C	12	12	SPIN2A	C	4	4
C10orf11	83938	broad.mit.edu	36	10	77488521	77488523	+	In_Frame_Del	DEL	GTC	-	-			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:77488521_77488523delGTC	uc001jxi.1	+	c.406_408delGTC	c.(406-408)GTCdel	p.V136del		NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	136											0	Prostate(51;0.0095)|all_epithelial(25;0.0221)													0.72			34	13				---	---	---	---	capture_indel			In_Frame_Del	DEL	77488521	77488523	1617	10	GTC	-	-	36	36	C10orf11	-	5	5
FAM83G	644815	broad.mit.edu	36	17	18822703	18822704	+	Frame_Shift_Ins	INS	-	G	G			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18822703_18822704insG	uc002guw.1	-	c.1000_1001insC	c.(1000-1002)CTGfs	p.L334fs	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002guv.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	334										ovary(1)	1														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	18822703	18822704	5865	17	-	G	G	7	7	FAM83G	G	5	5
AKAP8	10270	broad.mit.edu	36	19	15348791	15348805	+	In_Frame_Del	DEL	GGTGTTGGCAGGTCC	-	-			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15348791_15348805delGGTGTTGGCAGGTCC	uc002nav.1	-	c.40_54delGGACCTGCCAACACC	c.(40-54)GGACCTGCCAACACCdel	p.GPANT14del	AKAP8_uc010dzz.1_5'Flank	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	14_18					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						GBM(190;1671 2163 3274 27186 30476)								0.42			8	11				---	---	---	---	capture_indel			In_Frame_Del	DEL	15348791	15348805	460	19	GGTGTTGGCAGGTCC	-	-	43	43	AKAP8	-	5	5
MAP3K10	4294	broad.mit.edu	36	19	45390064	45390065	+	Frame_Shift_Ins	INS	-	A	A			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45390064_45390065insA	uc002ona.1	+	c.286_287insA	c.(286-288)CACfs	p.H96fs		NM_002446	NP_002437	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase	96					activation of JUN kinase activity|induction of apoptosis|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|protein homodimerization activity			ovary(2)|lung(2)|skin(1)|pancreas(1)	6										92				0.42			10	14				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	45390064	45390065	9627	19	-	A	A	21	21	MAP3K10	A	5	5
PADI2	11240	broad.mit.edu	36	1	17292694	17292695	+	In_Frame_Ins	INS	-	TGC	TGC			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17292694_17292695insTGC	uc001baf.1	-	c.483_484insGCA	c.(481-486)insGCA	p.161_162insA	PADI2_uc001bag.1_In_Frame_Ins_p.161_162insA	NM_007365	NP_031391	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	161_162					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity			ovary(3)|pancreas(1)|central_nervous_system(1)|skin(1)	6		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)									0.38			228	380				---	---	---	---	capture_indel			In_Frame_Ins	INS	17292694	17292695	11794	1	-	TGC	TGC	2	2	PADI2	TGC	5	5
OTOF	9381	broad.mit.edu	36	2	26549936	26549937	+	Frame_Shift_Ins	INS	-	CTTC	CTTC			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26549936_26549937insCTTC	uc002rhk.1	-	c.3411_3412insGAAG	c.(3409-3414)GTGCTGfs	p.V1137fs	OTOF_uc002rhh.1_Frame_Shift_Ins_p.V390fs|OTOF_uc002rhi.1_Frame_Shift_Ins_p.V447fs|OTOF_uc002rhj.1_Frame_Shift_Ins_p.V390fs	NM_194248	NP_919224	Q9HC10	OTOF_HUMAN	otoferlin isoform a	1137_1138	Cytoplasmic (Potential).		L -> P (in NSRAN).		cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding			ovary(3)|breast(2)|central_nervous_system(1)|pancreas(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GBM(102;732 1451 20652 24062 31372)								0.54			197	167				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	26549936	26549937	11715	2	-	CTTC	CTTC	34	34	OTOF	CTTC	5	5
LZTS1	11178	broad.mit.edu	36	8	20154683	20154687	+	Frame_Shift_Del	DEL	GCCGG	-	-			TCGA-12-0828-01	TCGA-12-0828-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:20154683_20154687delGCCGG	uc003wzr.1	-	c.1035_1039delCCGGC	c.(1033-1041)CTCCGGCAGfs	p.L345fs	LZTS1_uc010ltg.1_Frame_Shift_Del_p.L345fs	NM_021020	NP_066300	Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	345_347	Potential.				cell cycle|regulation of transcription, DNA-dependent|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	cell junction|dendritic spine|Golgi apparatus|nucleolus|nucleoplasm|postsynaptic density|postsynaptic membrane	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)										0.37			19	33				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	20154683	20154687	9515	8	GCCGG	-	-	46	46	LZTS1	-	5	5
