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
MUC2	4583	broad.mit.edu	36	11	1082837	1082837	+	Silent	SNP	C	A	A			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1082837C>A	uc001lsx.1	+	c.11742C>A	c.(11740-11742)CCC>CCA	p.P3914P		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	3914						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.25	7.218977	7.900976	3	9	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Silent	SNP	1082837	1082837	10369	11	C	A	A	21	21	MUC2	A	3	3
MUC2	4583	broad.mit.edu	36	11	1083393	1083393	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1083393G>A	uc001lsx.1	+	c.12298G>A	c.(12298-12300)GGC>AGC	p.G4100S		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4100						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.147059	8.775496	12.825161	5	29	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1083393	1083393	10369	11	G	A	A	39	39	MUC2	A	1	1
USP28	57646	broad.mit.edu	36	11	113193696	113193696	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1832-01	TCGA-27-1832-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:113193696T>C	uc001poh.1	-	c.1357A>G	c.(1357-1359)AGT>GGT	p.S453G	USP28_uc001poi.1_Intron|USP28_uc001poj.2_Missense_Mutation_p.S453G|USP28_uc001pog.1_Missense_Mutation_p.S161G	NM_020886	NP_065937	Q96RU2	UBP28_HUMAN	ubiquitin specific protease 28	453					cell proliferation|DNA damage checkpoint|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA repair|protein deubiquitination|response to ionizing radiation|ubiquitin-dependent protein catabolic process	nucleolus|nucleoplasm	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			breast(2)|ovary(1)|large_intestine(1)|kidney(1)	5		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)				Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)								0.338624	196.137464	200.491688	64	125	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)	Missense_Mutation	SNP	113193696	113193696	17622	11	T	C	C	53	53	USP28	C	4	4
FOXRED1	55572	broad.mit.edu	36	11	125651501	125651501	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:125651501A>G	uc001qdi.1	+	c.974A>G	c.(973-975)TAT>TGT	p.Y325C	FOXRED1_uc001qdj.1_Missense_Mutation_p.Y114C|FOXRED1_uc001qdk.1_Missense_Mutation_p.Y114C	NM_017547	NP_060017	Q96CU9	FXRD1_HUMAN	FAD-dependent oxidoreductase domain containing	325					oxidation-reduction process	integral to membrane|mitochondrion	oxidoreductase activity|protein binding				0	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.224)												0.176471	16.060438	22.78146	12	56	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0729)	Missense_Mutation	SNP	125651501	125651501	6279	11	A	G	G	16	16	FOXRED1	G	4	4
DGKZ	8525	broad.mit.edu	36	11	46345004	46345004	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46345004A>C	uc001ncn.1	+	c.622A>C	c.(622-624)ACC>CCC	p.T208P	DGKZ_uc001nch.1_Intron|DGKZ_uc001nci.1_Intron|DGKZ_uc001ncj.1_Intron|DGKZ_uc001nck.1_Intron|DGKZ_uc001ncl.2_Intron|DGKZ_uc001ncm.2_Intron|DGKZ_uc009yky.1_Intron	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4	208					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3														0.375	6.72462	6.833503	3	5	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)	Missense_Mutation	SNP	46345004	46345004	4653	11	A	C	C	6	6	DGKZ	C	4	4
MS4A6A	64231	broad.mit.edu	36	11	59703934	59703934	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59703934G>A	uc001nos.2	-	c.312C>T	c.(310-312)ACC>ACT	p.T104T	MS4A6A_uc001noq.1_Silent_p.T76T|MS4A6A_uc001nor.1_Silent_p.T76T|MS4A6A_uc009ymv.1_Silent_p.T76T|MS4A6A_uc001not.1_Silent_p.T76T	NM_152852	NP_690591	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member	76	Extracellular (Potential).					integral to membrane	receptor activity				0														0.278351	70.771998	75.067654	27	70	GG		KEEP	---	---	---	---	capture			Silent	SNP	59703934	59703934	10257	11	G	A	A	43	43	MS4A6A	A	2	2
TMEM132A	54972	broad.mit.edu	36	11	60460088	60460088	+	Silent	SNP	G	C	C			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:60460088G>C	uc001nqi.1	+	c.2208G>C	c.(2206-2208)GGG>GGC	p.G736G	TMEM132A_uc001nqj.1_Silent_p.G735G|TMEM132A_uc001nqm.1_5'UTR	NM_017870	NP_060340	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform a	735	Binds to HSPA5/GRP78 (By similarity).|Confers cellular localization similar to full-length form (By similarity).|Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane					0														0.190476	6.584654	8.470808	4	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	60460088	60460088	16576	11	G	C	C	42	42	TMEM132A	C	3	3
TRPV4	59341	broad.mit.edu	36	12	108721008	108721008	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:108721008G>A	uc001tpj.1	-	c.946C>T	c.(946-948)CGC>TGC	p.R316C	TRPV4_uc001tpg.1_Missense_Mutation_p.R282C|TRPV4_uc001tph.1_Missense_Mutation_p.R269C|TRPV4_uc001tpi.1_Missense_Mutation_p.R269C|TRPV4_uc001tpk.1_Missense_Mutation_p.R316C|TRPV4_uc001tpl.1_Missense_Mutation_p.R316C	NM_021625	NP_067638	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel,	316	Cytoplasmic (Potential).		R -> C (in CMT2C and SPSMA).		actin cytoskeleton reorganization|actin filament organization|calcium ion import|cell death|cell volume homeostasis|cell-cell junction assembly|cellular hypotonic response|cortical microtubule organization|elevation of cytosolic calcium ion concentration|microtubule polymerization|negative regulation of neuron projection development|osmosensory signaling pathway|positive regulation of microtubule depolymerization|response to mechanical stimulus	cortical actin cytoskeleton|filopodium|focal adhesion|growth cone|integral to membrane|lamellipodium|ruffle membrane	actin filament binding|alpha-tubulin binding|beta-tubulin binding|calcium channel activity|calmodulin binding|microtubule binding|protein binding|protein kinase C binding|SH2 domain binding			ovary(2)	2														0.302632	114.286426	119.576616	46	106	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108721008	108721008	17149	12	G	A	A	38	38	TRPV4	A	1	1
AACS	65985	broad.mit.edu	36	12	124165026	124165026	+	Silent	SNP	C	A	A			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:124165026C>A	uc001uhc.1	+	c.966C>A	c.(964-966)ACC>ACA	p.T322T	AACS_uc001uhd.1_Silent_p.T322T|AACS_uc009zyh.1_Non-coding_Transcript|AACS_uc009zyi.1_5'UTR	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	322					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.227848	41.70013	47.077935	18	61	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)	Silent	SNP	124165026	124165026	10	12	C	A	A	21	21	AACS	A	3	3
ING1	3621	broad.mit.edu	36	13	110166144	110166144	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:110166144A>G	uc001vri.1	+	c.353A>G	c.(352-354)GAG>GGG	p.E118G	ING1_uc001vrf.1_Intron|ING1_uc001vrg.1_Intron|ING1_uc001vrh.1_Intron	NM_005537	NP_005528	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1 isoform D	118					cell cycle|negative regulation of cell growth|negative regulation of cell proliferation	nucleus	zinc ion binding			ovary(1)	1	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)									145				0.3	7.151813	7.99852	6	14	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(86;0.188)		Missense_Mutation	SNP	110166144	110166144	8036	13	A	G	G	11	11	ING1	G	4	4
F10	2159	broad.mit.edu	36	13	112841676	112841676	+	Silent	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:112841676C>T	uc001vsx.1	+	c.261C>T	c.(259-261)GGC>GGT	p.G87G	F10_uc010agq.1_Non-coding_Transcript|F10_uc001vsy.1_Silent_p.G87G|F10_uc001vsz.1_Silent_p.G87G	NM_000504	NP_000495	P00742	FA10_HUMAN	coagulation factor X preproprotein	87	EGF-like 1; calcium-binding (Potential).				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of cell migration|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|intrinsic to external side of plasma membrane	calcium ion binding|phospholipid binding|protein binding|serine-type endopeptidase activity			pancreas(1)	1	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)			Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Heparin(DB01109)|Menadione(DB00170)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.177215	26.70002	34.456065	14	65	CC		KEEP	---	---	---	---	capture	all cancers(43;0.0805)|Epithelial(84;0.231)		Silent	SNP	112841676	112841676	5530	13	C	T	T	27	27	F10	T	1	1
IPO5	3843	broad.mit.edu	36	13	97464353	97464353	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:97464353C>T	uc001vne.1	+	c.2263C>T	c.(2263-2265)CGT>TGT	p.R755C		NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5	737					interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)	2														0.11465	21.88603	44.819863	18	139	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97464353	97464353	8097	13	C	T	T	23	23	IPO5	T	1	1
SLC7A7	9056	broad.mit.edu	36	14	22314889	22314889	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:22314889C>T	uc001wgr.2	-	c.991G>A	c.(991-993)GCT>ACT	p.A331T	SLC7A7_uc001wgs.2_Missense_Mutation_p.A331T|SLC7A7_uc001wgt.2_Missense_Mutation_p.A331T|SLC7A7_uc001wgu.2_Missense_Mutation_p.A331T|SLC7A7_uc001wgv.2_Missense_Mutation_p.A331T	NM_003982	NP_003973	Q9UM01	YLAT1_HUMAN	solute carrier family 7 member 7	331					blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly	basolateral plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity			ovary(1)|breast(1)	2	all_cancers(95;8.44e-05)													0.391534	202.396025	204.346817	74	115	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00741)	Missense_Mutation	SNP	22314889	22314889	15200	14	C	T	T	25	25	SLC7A7	T	2	2
TPSD1	23430	broad.mit.edu	36	16	1246642	1246642	+	Silent	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1246642C>T	uc002clb.1	+	c.207C>T	c.(205-207)TCC>TCT	p.S69S	TPSD1_uc010brm.1_Silent_p.S7S	NM_012217	NP_036349	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	69	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0		Hepatocellular(780;0.00369)												0.23494	93.842626	104.510129	39	127	CC		KEEP	---	---	---	---	capture			Silent	SNP	1246642	1246642	16969	16	C	T	T	22	22	TPSD1	T	2	2
DNAH3	55567	broad.mit.edu	36	16	20882843	20882843	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:20882843G>A	uc002did.1	-	c.9864C>T	c.(9862-9864)GAC>GAT	p.D3288D	DNAH3_uc002dic.1_Silent_p.D723D	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3288					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(10)|large_intestine(2)|central_nervous_system(2)	14														0.262009	145.913871	157.645016	60	169	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.207)	Silent	SNP	20882843	20882843	4786	16	G	A	A	40	40	DNAH3	A	1	1
KIAA0556	23247	broad.mit.edu	36	16	27668690	27668690	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:27668690G>A	uc002dow.1	+	c.2908G>A	c.(2908-2910)GTC>ATC	p.V970I		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	970										ovary(4)|large_intestine(2)	6														0.337662	70.426781	72.221175	26	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27668690	27668690	8490	16	G	A	A	40	40	KIAA0556	A	1	1
TRIM72	493829	broad.mit.edu	36	16	31143135	31143135	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31143135C>T	uc002ebn.1	+	c.992C>T	c.(991-993)GCG>GTG	p.A331V		NM_001008274	NP_001008275	Q6ZMU5	TRI72_HUMAN	tripartite motif-containing 72	331	B30.2/SPRY.				exocytosis|muscle organ development|muscle system process|plasma membrane repair|protein homooligomerization	cytoplasmic vesicle membrane|sarcolemma	phosphatidylserine binding|zinc ion binding				0														0.361111	36.366097	36.976888	13	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31143135	31143135	17094	16	C	T	T	27	27	TRIM72	T	1	1
SMCR8	140775	broad.mit.edu	36	17	18160660	18160660	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18160660G>A	uc002gsy.2	+	c.832G>A	c.(832-834)GCC>ACC	p.A278T	TOP3A_uc002gsx.1_5'Flank|TOP3A_uc010cqa.1_5'Flank	NM_144775	NP_658988	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region,	278										central_nervous_system(1)	1														0.25	52.219125	57.212798	22	66	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18160660	18160660	15290	17	G	A	A	42	42	SMCR8	A	2	2
KRTAP4-3	85290	broad.mit.edu	36	17	36577810	36577810	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36577810G>A	uc010cxl.1	-	c.141C>T	c.(139-141)TCC>TCT	p.S47S		NM_033187	NP_149443	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	47	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].|3.					keratin filament					0		Breast(137;0.000496)												0.136364	7.422164	13.056046	6	38	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(17;0.000449)		Silent	SNP	36577810	36577810	8874	17	G	A	A	47	47	KRTAP4-3	A	2	2
SENP3	26168	broad.mit.edu	36	17	7414519	7414519	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7414519A>C	uc002ghm.1	+	c.1463A>C	c.(1462-1464)AAC>ACC	p.N488T	EIF4A1_uc002gho.1_5'UTR|EIF4A1_uc002ghr.1_5'Flank|EIF4A1_uc002ghq.1_5'Flank|EIF4A1_uc002ghp.1_5'Flank	NM_015670	NP_056485	Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific protease 3	488	Protease.				proteolysis	MLL1 complex|nucleolus	cysteine-type peptidase activity			ovary(1)|central_nervous_system(1)	2		Prostate(122;0.157)												0.212121	8.775482	11.352231	7	26	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7414519	7414519	14534	17	A	C	C	2	2	SENP3	C	4	4
ENPP7	339221	broad.mit.edu	36	17	75325586	75325586	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75325586G>A	uc002jxa.1	+	c.1178G>A	c.(1177-1179)CGG>CAG	p.R393Q		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	393					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3														0.219178	34.949442	40.267325	16	57	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)		Missense_Mutation	SNP	75325586	75325586	5328	17	G	A	A	39	39	ENPP7	A	1	1
DUS1L	64118	broad.mit.edu	36	17	77614090	77614090	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77614090C>T	uc002kdq.1	-	c.446G>A	c.(445-447)CGT>CAT	p.R149H	DUS1L_uc002kdp.1_Missense_Mutation_p.R18H|DUS1L_uc002kdr.1_Missense_Mutation_p.R149H|DUS1L_uc002kds.1_Non-coding_Transcript|DUS1L_uc002kdt.1_Non-coding_Transcript	NM_022156	NP_071439	Q6P1R4	DUS1L_HUMAN	PP3111 protein	149					oxidation-reduction process|tRNA processing		flavin adenine dinucleotide binding|tRNA dihydrouridine synthase activity				0	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)													0.255319	88.688434	96.310854	36	105	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)		Missense_Mutation	SNP	77614090	77614090	4990	17	C	T	T	19	19	DUS1L	T	1	1
DSEL	92126	broad.mit.edu	36	18	63332083	63332083	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1832-01	TCGA-27-1832-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr18:63332083T>C	uc002lke.1	-	c.773A>G	c.(772-774)AAT>AGT	p.N258S	DSEL_uc010dqm.1_Missense_Mutation_p.N258S	NM_032160	NP_115536	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	248						integral to membrane	isomerase activity|sulfotransferase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5		Esophageal squamous(42;0.129)												0.336406	235.114935	240.249169	73	144	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63332083	63332083	4959	18	T	C	C	52	52	DSEL	C	4	4
KLK15	55554	broad.mit.edu	36	19	56022797	56022797	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56022797G>A	uc002ptl.1	-	c.130C>T	c.(130-132)CGC>TGC	p.R44C	KLK15_uc002ptn.1_Missense_Mutation_p.R44C|KLK15_uc002ptm.1_Missense_Mutation_p.R44C|KLK15_uc002pto.1_Missense_Mutation_p.R43C|KLK15_uc010eod.1_Non-coding_Transcript	NM_017509	NP_059979	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15 isoform 4	44	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			lung(1)|breast(1)	2		all_neural(266;0.057)				Pancreas(140;10 2513 7143 9246)								0.208791	42.779989	49.921435	19	72	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)	Missense_Mutation	SNP	56022797	56022797	8717	19	G	A	A	40	40	KLK15	A	1	1
GNPAT	8443	broad.mit.edu	36	1	229478534	229478534	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:229478534A>C	uc001hup.2	+	c.1968A>C	c.(1966-1968)GAA>GAC	p.E656D		NM_014236	NP_055051	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	656					ether lipid biosynthetic process|fatty acid metabolic process|organ morphogenesis	peroxisomal matrix|peroxisomal membrane	glycerone-phosphate O-acyltransferase activity			ovary(3)|breast(1)	4	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)												0.190476	7.988953	9.869427	4	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	229478534	229478534	6810	1	A	C	C	2	2	GNPAT	C	4	4
NPHP4	261734	broad.mit.edu	36	1	5847882	5847882	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:5847882A>C	uc001alq.1	-	c.3683T>G	c.(3682-3684)GTC>GGC	p.V1228G	NPHP4_uc001alr.1_3'UTR	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	1228					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cilium|membrane|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)												0.461538	8.338084	8.364275	6	7	AA		KEEP	---	---	---	---	capture		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)	Missense_Mutation	SNP	5847882	5847882	10985	1	A	C	C	10	10	NPHP4	C	4	4
C22orf42	150297	broad.mit.edu	36	22	30876408	30876408	+	Silent	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:30876408C>T	uc003amd.1	-	c.552G>A	c.(550-552)TCG>TCA	p.S184S		NM_001010859	NP_001010859	Q6IC83	CV042_HUMAN	hypothetical protein LOC150297	184										ovary(1)	1														0.2657	149.858011	160.108427	55	152	CC		KEEP	---	---	---	---	capture			Silent	SNP	30876408	30876408	2231	22	C	T	T	23	23	C22orf42	T	1	1
TMPRSS6	164656	broad.mit.edu	36	22	35799536	35799536	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:35799536C>T	uc003aqt.1	-	c.1537G>A	c.(1537-1539)GAA>AAA	p.E513K	TMPRSS6_uc003aqs.1_Missense_Mutation_p.E522K	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	522	LDL-receptor class A 2.|Extracellular (Potential).				angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|plasma membrane	serine-type endopeptidase activity			breast(4)|ovary(1)	5														0.317881	126.850725	131.300973	48	103	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35799536	35799536	16792	22	C	T	T	31	31	TMPRSS6	T	1	1
COL5A2	1290	broad.mit.edu	36	2	189626429	189626429	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:189626429C>T	uc002uqk.1	-	c.2519G>A	c.(2518-2520)GGG>GAG	p.G840E	COL5A2_uc010frx.1_Missense_Mutation_p.G416E	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	840					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2														0.278481	60.441776	63.913337	22	57	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)		Missense_Mutation	SNP	189626429	189626429	3835	2	C	T	T	22	22	COL5A2	T	2	2
CPS1	1373	broad.mit.edu	36	2	211149364	211149364	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:211149364A>G	uc010fur.1	+	c.304A>G	c.(304-306)ATG>GTG	p.M102V	CPS1_uc002vee.2_Missense_Mutation_p.M96V	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	96	Anthranilate phosphoribosyltransferase homolog.				carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12														0.301158	240.158553	249.298936	78	181	AA		KEEP	---	---	---	---	capture		Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Missense_Mutation	SNP	211149364	211149364	3961	2	A	G	G	4	4	CPS1	G	4	4
NRXN1	9378	broad.mit.edu	36	2	50700701	50700701	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:50700701G>A	uc002rxe.2	-	c.1283C>T	c.(1282-1284)TCA>TTA	p.S428L	NRXN1_uc010fbq.1_Missense_Mutation_p.S115L|NRXN1_uc002rxb.2_Missense_Mutation_p.S100L|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_004801	NP_004792	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha1 precursor	226	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)												0.27907	29.482629	31.369867	12	31	GG		KEEP	---	---	---	---	capture	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)		Missense_Mutation	SNP	50700701	50700701	11070	2	G	A	A	45	45	NRXN1	A	2	2
EPHB1	2047	broad.mit.edu	36	3	136127375	136127375	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:136127375C>A	uc003eqt.1	+	c.86C>A	c.(85-87)ACT>AAT	p.T29N	EPHB1_uc010htz.1_Non-coding_Transcript	NM_004441	NP_004432	P54762	EPHB1_HUMAN	ephrin receptor EphB1 precursor	29	Extracellular (Potential).				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding			lung(7)|ovary(4)|stomach(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	18										376				0.230769	6.4309	7.286056	3	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	136127375	136127375	5367	3	C	A	A	20	20	EPHB1	A	3	3
KIF9	64147	broad.mit.edu	36	3	47282243	47282243	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:47282243G>A	uc003cqx.1	-	c.897C>T	c.(895-897)CAC>CAT	p.H299H	KIF9_uc003cqy.1_Silent_p.H299H|KIF9_uc010hjp.1_Silent_p.H299H|KIF9_uc003cqz.1_Silent_p.H299H	NM_182902	NP_878905	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	299					blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0		Acute lymphoblastic leukemia(5;0.164)				Colon(44;962 1147 15977 24541)								0.187845	67.938513	84.469672	34	147	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)	Silent	SNP	47282243	47282243	8621	3	G	A	A	40	40	KIF9	A	1	1
NT5DC2	64943	broad.mit.edu	36	3	52534135	52534135	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:52534135G>C	uc003deo.1	-	c.1120C>G	c.(1120-1122)CGC>GGC	p.R374G	NT5DC2_uc003dem.1_Missense_Mutation_p.R244G|NT5DC2_uc003den.1_Missense_Mutation_p.R340G|NT5DC2_uc010hmi.1_Missense_Mutation_p.R315G|NT5DC2_uc010hmj.1_Missense_Mutation_p.R190G	NM_022908	NP_075059	Q9H857	NT5D2_HUMAN	5'-nucleotidase domain containing 2 isoform 2	374							hydrolase activity|metal ion binding				0														0.5	6.990249	6.990249	5	5	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;1.7e-05)|Kidney(197;0.00177)|KIRC - Kidney renal clear cell carcinoma(197;0.002)|OV - Ovarian serous cystadenocarcinoma(275;0.0476)	Missense_Mutation	SNP	52534135	52534135	11096	3	G	C	C	38	38	NT5DC2	C	3	3
WNT5A	7474	broad.mit.edu	36	3	55483519	55483519	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:55483519G>T	uc003dhn.1	-	c.570C>A	c.(568-570)TAC>TAA	p.Y190*	WNT5A_uc003dhm.1_Nonsense_Mutation_p.Y175*|WNT5A_uc010hmw.1_Nonsense_Mutation_p.Y175*|WNT5A_uc010hmx.1_Nonsense_Mutation_p.Y101*	NM_003392	NP_003383	P41221	WNT5A_HUMAN	wingless-type MMTV integration site family,	190					activation of JUN kinase activity|activation of protein kinase B activity|cartilage development|cellular protein localization|cellular response to calcium ion|cellular response to interferon-gamma|cellular response to lipopolysaccharide|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|cervix development|cochlea morphogenesis|convergent extension involved in organogenesis|dopaminergic neuron differentiation|dorsal/ventral axis specification|embryonic digit morphogenesis|embryonic skeletal system development|epithelial cell proliferation involved in mammary gland duct elongation|epithelial to mesenchymal transition|face development|genitalia development|heart looping|hemopoietic stem cell proliferation|keratinocyte differentiation|lateral sprouting involved in mammary gland duct morphogenesis|lens development in camera-type eye|male gonad development|mammary gland branching involved in thelarche|negative regulation of apoptosis|negative regulation of BMP signaling pathway|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of mesenchymal cell proliferation|neural tube closure|optic cup formation involved in camera-type eye development|palate development|positive regulation of angiogenesis|positive regulation of cartilage development|positive regulation of cGMP metabolic process|positive regulation of chemokine biosynthetic process|positive regulation of cytokine secretion involved in immune response|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of macrophage activation|positive regulation of macrophage cytokine production|positive regulation of mesenchymal cell proliferation|positive regulation of NF-kappaB transcription factor activity|positive regulation of ossification|positive regulation of protein catabolic process|positive regulation of protein kinase C signaling cascade|positive regulation of T cell chemotaxis|positive regulation of thymocyte apoptosis|positive regulation of type I interferon-mediated signaling pathway|primitive streak formation|regulation of branching involved in mammary gland duct morphogenesis|somitogenesis|tail morphogenesis|type B pancreatic cell development|urinary bladder development|uterus development|vagina development|Wnt receptor signaling pathway, calcium modulating pathway|wound healing	extracellular space|membrane fraction|plasma membrane|proteinaceous extracellular matrix	frizzled binding|frizzled-2 binding|promoter binding|receptor tyrosine kinase-like orphan receptor binding|specific transcriptional repressor activity|transcription activator activity				0														0.384615	13.77251	13.92399	5	8	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.00377)|Kidney(284;0.00408)|OV - Ovarian serous cystadenocarcinoma(275;0.204)	Nonsense_Mutation	SNP	55483519	55483519	17965	3	G	T	T	44	44	WNT5A	T	5	3
CEP135	9662	broad.mit.edu	36	4	56570683	56570683	+	Nonsense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:56570683C>T	uc003hbi.1	+	c.2362C>T	c.(2362-2364)CGA>TGA	p.R788*	CEP135_uc003hbj.1_Nonsense_Mutation_p.R494*	NM_025009	NP_079285	Q66GS9	CP135_HUMAN	centrosome protein 4	788	Potential.				centriole replication|centriole-centriole cohesion|G2/M transition of mitotic cell cycle	centriole|cytosol	protein C-terminus binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4	Glioma(25;0.08)|all_neural(26;0.101)													0.292929	75.231035	79.034614	29	70	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	56570683	56570683	3380	4	C	T	T	31	31	CEP135	T	5	1
WDFY3	23001	broad.mit.edu	36	4	85876439	85876439	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:85876439G>A	uc003hpd.1	-	c.6823C>T	c.(6823-6825)CGT>TGT	p.R2275C	WDFY3_uc003hpe.1_5'Flank	NM_014991	NP_055806	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3 isoform	2275						cytoplasmic part|extrinsic to membrane|nuclear envelope	1-phosphatidylinositol binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3		Hepatocellular(203;0.114)												0.232143	67.292079	74.651419	26	86	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;0.000808)	Missense_Mutation	SNP	85876439	85876439	17842	4	G	A	A	39	39	WDFY3	A	1	1
NKD2	85409	broad.mit.edu	36	5	1086498	1086498	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1086498G>A	uc003jbt.1	+	c.214G>A	c.(214-216)GCT>ACT	p.A72T	NKD2_uc010itf.1_Missense_Mutation_p.A72T	NM_033120	NP_149111	Q969F2	NKD2_HUMAN	naked cuticle homolog 2	72	Targeting to the basolateral cell membrane.				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)									126				0.388889	20.421046	20.615681	7	11	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)		Missense_Mutation	SNP	1086498	1086498	10843	5	G	A	A	38	38	NKD2	A	1	1
PCDHA1	56147	broad.mit.edu	36	5	140147391	140147391	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140147391G>A	uc003lhb.1	+	c.1332G>A	c.(1330-1332)GAG>GAA	p.E444E	PCDHA1_uc003lha.1_Silent_p.E444E|PCDHA1_uc003lgz.1_Silent_p.E444E	NM_018900	NP_061723	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1 isoform 1 precursor	444	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding				0														0.266187	192.50134	206.251463	74	204	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140147391	140147391	11939	5	G	A	A	35	35	PCDHA1	A	2	2
ATP6V0A4	50617	broad.mit.edu	36	7	138091056	138091056	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138091056G>T	uc003vuf.1	-	c.734C>A	c.(733-735)ACT>AAT	p.T245N	ATP6V0A4_uc003vug.1_Missense_Mutation_p.T245N|ATP6V0A4_uc003vuh.1_Missense_Mutation_p.T245N	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	245	Cytoplasmic (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1														0.146067	24.114407	34.832938	13	76	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138091056	138091056	1189	7	G	T	T	36	36	ATP6V0A4	T	3	3
ZNF467	168544	broad.mit.edu	36	7	149093980	149093980	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:149093980G>C	uc003wgd.1	-	c.544C>G	c.(544-546)CAC>GAC	p.H182D	ZNF467_uc003wgc.2_Intron	NM_207336	NP_997219	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	182	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.165)|Ovarian(565;0.177)													0.333333	7.22218	7.443496	3	6	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		Missense_Mutation	SNP	149093980	149093980	18520	7	G	C	C	46	46	ZNF467	C	3	3
RP9	6100	broad.mit.edu	36	7	33105520	33105520	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:33105520G>A	uc003tdm.1	-	c.237C>T	c.(235-237)CAC>CAT	p.H79H		NM_203288	NP_976033	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9	79	PIM1-binding (By similarity).				response to stimulus|RNA splicing|visual perception	nucleus	nucleic acid binding|protein binding|zinc ion binding				0														0.151976	80.80977	119.018274	50	279	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(11;0.0403)		Silent	SNP	33105520	33105520	14014	7	G	A	A	40	40	RP9	A	1	1
CCDC146	57639	broad.mit.edu	36	7	76634915	76634915	+	De_novo_Start_OutOfFrame	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:76634915G>A	uc003uga.1	+	c.-6G>A	c.(-8--4)TCGTG>TCATG		CCDC146_uc003ufz.1_De_novo_Start_OutOfFrame	NM_020879	NP_065930			coiled-coil domain containing 146											ovary(1)|central_nervous_system(1)	2		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)												0.135135	8.08059	12.828358	5	32	GG		KEEP	---	---	---	---	capture			De_novo_Start_OutOfFrame	SNP	76634915	76634915	2900	7	G	A	A	40	40	CCDC146	A	5	1
CROT	54677	broad.mit.edu	36	7	86836665	86836665	+	Silent	SNP	G	T	T			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86836665G>T	uc003uiu.1	+	c.669G>T	c.(667-669)CTG>CTT	p.L223L	CROT_uc003uit.1_Silent_p.L195L	NM_021151	NP_066974	Q9UKG9	OCTC_HUMAN	peroxisomal carnitine O-octanoyltransferase	195					fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity			ovary(2)|lung(1)	3	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)									0.206897	166.592566	194.310321	72	276	GG		KEEP	---	---	---	---	capture			Silent	SNP	86836665	86836665	4033	7	G	T	T	48	48	CROT	T	3	3
RRS1	23212	broad.mit.edu	36	8	67504344	67504344	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:67504344C>G	uc003xwa.1	+	c.424C>G	c.(424-426)CGG>GGG	p.R142G	ADHFE1_uc003xwb.2_5'Flank|ADHFE1_uc003xwd.2_5'Flank|ADHFE1_uc003xwe.2_5'Flank|ADHFE1_uc003xwc.2_5'Flank|ADHFE1_uc003xwf.2_5'Flank	NM_015169	NP_055984	Q15050	RRS1_HUMAN	homolog of yeast ribosome biogenesis regulatory	142					mitotic metaphase plate congression|ribosome biogenesis	condensed nuclear chromosome|nucleolus					0		Lung NSC(129;0.197)												0.368421	9.381851	9.721972	7	12	CC		KEEP	---	---	---	---	capture	Epithelial(68;0.0391)|all cancers(69;0.0898)|BRCA - Breast invasive adenocarcinoma(89;0.111)|OV - Ovarian serous cystadenocarcinoma(28;0.226)		Missense_Mutation	SNP	67504344	67504344	14172	8	C	G	G	27	27	RRS1	G	3	3
GPR107	57720	broad.mit.edu	36	9	131888553	131888553	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1832-01	TCGA-27-1832-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:131888553A>G	uc004bze.1	+	c.598A>G	c.(598-600)AAT>GAT	p.N200D	GPR107_uc004bzb.1_Missense_Mutation_p.N11D|GPR107_uc004bzc.2_Non-coding_Transcript|GPR107_uc004bzd.1_Missense_Mutation_p.N200D	NM_020960	NP_066011	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107 isoform 3	200						integral to membrane					0		Ovarian(14;0.000531)												0.252941	128.152926	137.566982	43	127	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131888553	131888553	6897	9	A	G	G	13	13	GPR107	G	4	4
CDR1	1038	broad.mit.edu	36	X	139693570	139693570	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1832-01	TCGA-27-1832-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:139693570C>T	uc004fbg.1	-	c.628G>A	c.(628-630)GGA>AGA	p.G210R		NM_004065	NP_004056	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1,	210											0	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)												0.190265	93.822662	114.079359	43	183	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139693570	139693570	3300	23	C	T	T	23	23	CDR1	T	1	1
PHF16	9767	broad.mit.edu	36	X	46803237	46803237	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46803237G>C	uc004dgx.1	+	c.2286G>C	c.(2284-2286)CAG>CAC	p.Q762H	PHF16_uc004dgy.1_Missense_Mutation_p.Q762H	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	762					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.235955	51.329935	57.003639	21	68	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46803237	46803237	12250	23	G	C	C	35	35	PHF16	C	3	3
SHROOM2	357	broad.mit.edu	36	X	9823658	9823658	+	Silent	SNP	G	A	A			TCGA-27-1832-01	TCGA-27-1832-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:9823658G>A	uc004csu.1	+	c.1710G>A	c.(1708-1710)ACG>ACA	p.T570T		NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	570					apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	6		Hepatocellular(5;0.000888)												0.272727	6.754025	7.24548	3	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	9823658	9823658	14789	23	G	A	A	40	40	SHROOM2	A	1	1
