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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
FAM178A	55719	broad.mit.edu	37	10	102706855	102706855	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:102706855G>A	uc001krs.2	+	c.2994G>A	c.(2992-2994)TGG>TGA	p.W998*	FAM178A_uc001krt.3_Nonsense_Mutation_p.W998*	NM_001136123	NP_001129595	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 2	998											0														0.21875	48.824225	55.820982	21	75	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	102706855	102706855	5709	10	G	A	A	A	572	44	FAM178A	5	2
PNLIP	5406	broad.mit.edu	37	10	118310710	118310710	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118310710G>C	uc001lcm.2	+	c.425G>C	c.(424-426)GGA>GCA	p.G142A		NM_000936	NP_000927	P16233	LIPP_HUMAN	pancreatic lipase precursor	142					lipid catabolic process|retinoid metabolic process|steroid metabolic process	extracellular region	retinyl-palmitate esterase activity|triglyceride lipase activity			ovary(1)|central_nervous_system(1)	2				all cancers(201;0.0131)	Bentiromide(DB00522)|Orlistat(DB01083)									0.290323	28.362827	29.583706	9	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118310710	118310710	12575	10	G	C	C	C	533	41	PNLIP	3	3
SVIL	6840	broad.mit.edu	37	10	29777571	29777571	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:29777571C>T	uc001iut.1	-	c.4307G>A	c.(4306-4308)AGC>AAC	p.S1436N	SVIL_uc010qdw.1_Missense_Mutation_p.S350N|SVIL_uc001iuu.1_Missense_Mutation_p.S1010N|SVIL_uc009xlc.2_Missense_Mutation_p.S228N	NM_021738	NP_068506	O95425	SVIL_HUMAN	supervillin isoform 2	1436	Interaction with NEB.				cytoskeleton organization|skeletal muscle tissue development	cell junction|costamere|invadopodium|nucleus|podosome	actin filament binding			ovary(5)	5		Breast(68;0.103)												0.214286	6.516545	7.572594	3	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29777571	29777571	15941	10	C	T	T	T	364	28	SVIL	2	2
NDST2	8509	broad.mit.edu	37	10	75565704	75565704	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75565704C>T	uc001jvk.2	-	c.1517G>A	c.(1516-1518)CGG>CAG	p.R506Q	NDST2_uc010qks.1_Missense_Mutation_p.R132Q|NDST2_uc010qkt.1_Missense_Mutation_p.R383Q|NDST2_uc001jvl.1_5'Flank|NDST2_uc009xro.2_Missense_Mutation_p.R132Q|NDST2_uc010qku.1_Missense_Mutation_p.R381Q	NM_003635	NP_003626	P52849	NDST2_HUMAN	heparan glucosaminyl	506	Lumenal (Potential).|Heparan sulfate N-deacetylase 2.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1	Prostate(51;0.0112)													0.1625	26.227774	34.888506	13	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75565704	75565704	10655	10	C	T	T	T	299	23	NDST2	1	1
CCNJ	54619	broad.mit.edu	37	10	97810018	97810018	+	Silent	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:97810018G>A	uc010qoq.1	+	c.75G>A	c.(73-75)CTG>CTA	p.L25L	CCNJ_uc001klm.2_Silent_p.L25L|CCNJ_uc001kln.2_Silent_p.L25L	NM_001134375	NP_001127847	Q5T5M9	CCNJ_HUMAN	cyclin J isoform 1	25	Cyclin N-terminal.					nucleus				ovary(1)	1				Epithelial(162;6.1e-08)|all cancers(201;2.32e-06)										0.38	54.611254	55.24349	19	31	KEEP	---	---	---	---	capture		Silent	SNP	97810018	97810018	3055	10	G	A	A	A	574	45	CCNJ	2	2
GRIA4	2893	broad.mit.edu	37	11	105795326	105795326	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:105795326G>A	uc001pix.2	+	c.1678G>A	c.(1678-1680)GTG>ATG	p.V560M	GRIA4_uc001piw.2_Missense_Mutation_p.V560M	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	560	Helical; (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)									0.265306	30.752319	33.192352	13	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105795326	105795326	7048	11	G	A	A	A	520	40	GRIA4	1	1
USP47	55031	broad.mit.edu	37	11	11944424	11944424	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:11944424T>A	uc001mjs.2	+	c.1372T>A	c.(1372-1374)TCT>ACT	p.S458T	USP47_uc001mjq.1_Missense_Mutation_p.S478T|USP47_uc001mjr.2_Missense_Mutation_p.S390T	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	478					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of gene-specific transcription|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	specific transcriptional repressor activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)										0.333333	47.85824	49.112752	17	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11944424	11944424	17642	11	T	A	A	A	650	50	USP47	3	3
ETS1	2113	broad.mit.edu	37	11	128350260	128350260	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:128350260A>T	uc001qej.2	-	c.949T>A	c.(949-951)TCT>ACT	p.S317T	ETS1_uc010sbs.1_Missense_Mutation_p.S273T|ETS1_uc009zch.2_Missense_Mutation_p.S57T|ETS1_uc009zcg.2_Intron	NM_001143820	NP_001137292	P14921	ETS1_HUMAN	v-ets erythroblastosis virus E26 oncogene	273					cell motility|immune response|induction of apoptosis|negative regulation of cell cycle|negative regulation of cell cycle|negative regulation of cell proliferation|PML body organization|positive regulation of cellular component movement|positive regulation of erythrocyte differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|response to antibiotic|transcription from RNA polymerase II promoter	nucleus|nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding			lung(1)|central_nervous_system(1)|pleura(1)	3	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)										0.333333	65.030546	66.652914	22	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128350260	128350260	5468	11	A	T	T	T	156	12	ETS1	3	3
ANO5	203859	broad.mit.edu	37	11	22281166	22281166	+	Silent	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:22281166G>A	uc001mqi.2	+	c.1509G>A	c.(1507-1509)CAG>CAA	p.Q503Q	ANO5_uc001mqj.2_Silent_p.Q502Q	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	503	Extracellular (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.064516	-2.752909	9.469952	4	58	KEEP	---	---	---	---	capture		Silent	SNP	22281166	22281166	708	11	G	A	A	A	451	35	ANO5	2	2
MPPED2	744	broad.mit.edu	37	11	30516991	30516991	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:30516991G>C	uc001msr.2	-	c.388C>G	c.(388-390)CTT>GTT	p.L130V	MPPED2_uc001msq.3_Missense_Mutation_p.L130V|MPPED2_uc009yji.2_Missense_Mutation_p.L4V	NM_001584	NP_001575	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	130					nervous system development		hydrolase activity|metal ion binding			skin(1)	1										119				0.215909	42.371627	48.930666	19	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30516991	30516991	10134	11	G	C	C	C	455	35	MPPED2	3	3
UBQLNL	143630	broad.mit.edu	37	11	5537572	5537572	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5537572T>G	uc001maz.3	-	c.100A>C	c.(100-102)ATA>CTA	p.I34L	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	34	Ubiquitin-like.									large_intestine(2)	2		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)										0.220339	35.147979	39.392828	13	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5537572	5537572	17458	11	T	G	G	G	650	50	UBQLNL	4	4
OR4P4	81300	broad.mit.edu	37	11	55405947	55405947	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55405947G>T	uc010rij.1	+	c.114G>T	c.(112-114)ATG>ATT	p.M38I		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	38	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.186047	48.606226	60.555041	24	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55405947	55405947	11490	11	G	T	T	T	611	47	OR4P4	2	2
OR9G4	283189	broad.mit.edu	37	11	56510345	56510345	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56510345C>A	uc010rjo.1	-	c.943G>T	c.(943-945)GCC>TCC	p.A315S		NM_001005284	NP_001005284	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G,	315	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.319444	60.09695	62.184167	23	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56510345	56510345	11662	11	C	A	A	A	338	26	OR9G4	2	2
RIN1	9610	broad.mit.edu	37	11	66099816	66099816	+	Silent	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66099816A>T	uc001ohn.1	-	c.2283T>A	c.(2281-2283)GGT>GGA	p.G761G	RIN1_uc010roy.1_Silent_p.G392G|RIN1_uc009yrd.1_Silent_p.G454G|RIN1_uc010roz.1_Silent_p.G656G|RIN1_uc010rpa.1_Silent_p.G595G	NM_004292	NP_004283	Q13671	RIN1_HUMAN	ras inhibitor RIN1	761					endocytosis|signal transduction	cytoplasm|cytoskeleton|plasma membrane	GTPase activator activity|protein binding			lung(1)	1														0.298246	44.564716	46.631863	17	40	KEEP	---	---	---	---	capture		Silent	SNP	66099816	66099816	13848	11	A	T	T	T	119	10	RIN1	3	3
EPS8L2	64787	broad.mit.edu	37	11	722496	722496	+	Silent	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:722496C>A	uc010qwk.1	+	c.1203C>A	c.(1201-1203)GTC>GTA	p.V401V	EPS8L2_uc001lqt.2_Silent_p.V385V|EPS8L2_uc001lqu.2_Silent_p.V385V|EPS8L2_uc001lqv.2_Silent_p.V340V|EPS8L2_uc001lqw.2_5'UTR|EPS8L2_uc001lqx.2_5'UTR|EPS8L2_uc001lqy.2_5'Flank	NM_022772	NP_073609	Q9H6S3	ES8L2_HUMAN	epidermal growth factor receptor pathway	385						cytoplasm				pancreas(1)	1		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.428571	6.619463	6.651354	3	4	KEEP	---	---	---	---	capture		Silent	SNP	722496	722496	5389	11	C	A	A	A	379	30	EPS8L2	2	2
ATXN2	6311	broad.mit.edu	37	12	111923112	111923112	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:111923112C>T	uc001tsj.2	-	c.2961G>A	c.(2959-2961)ACG>ACA	p.T987T	ATXN2_uc001tsh.2_Silent_p.T722T|ATXN2_uc001tsi.2_Silent_p.T698T|ATXN2_uc001tsk.2_Intron|ATXN2_uc001tsg.2_Silent_p.T173T	NM_002973	NP_002964	Q99700	ATX2_HUMAN	ataxin 2	987	Pro-rich.				cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding			ovary(1)|breast(1)	2														0.121019	24.343931	46.422434	19	138	KEEP	---	---	---	---	capture		Silent	SNP	111923112	111923112	1231	12	C	T	T	T	340	27	ATXN2	1	1
SOX5	6660	broad.mit.edu	37	12	23728667	23728667	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:23728667T>A	uc001rfw.2	-	c.1270A>T	c.(1270-1272)AGT>TGT	p.S424C	SOX5_uc001rfx.2_Missense_Mutation_p.S411C|SOX5_uc001rfy.2_Intron|SOX5_uc001rfv.2_Missense_Mutation_p.S38C|SOX5_uc010siv.1_Missense_Mutation_p.S411C|SOX5_uc010siw.1_Non-coding_Transcript|SOX5_uc001rfz.1_Missense_Mutation_p.S376C	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	424					regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6														0.047059	-9.465151	9.107017	4	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23728667	23728667	15454	12	T	A	A	A	715	55	SOX5	3	3
GXYLT1	283464	broad.mit.edu	37	12	42491397	42491397	+	Silent	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:42491397C>A	uc001rms.3	-	c.1008G>T	c.(1006-1008)CCG>CCT	p.P336P	GXYLT1_uc001rmt.3_Silent_p.P305P	NM_173601	NP_775872	Q4G148	GXLT1_HUMAN	glycosyltransferase 8 domain containing 3	336	Lumenal (Potential).				O-glycan processing	integral to membrane	UDP-xylosyltransferase activity				0														0.372549	119.832	121.284202	38	64	KEEP	---	---	---	---	capture		Silent	SNP	42491397	42491397	7183	12	C	A	A	A	236	19	GXYLT1	1	1
ADAMTS20	80070	broad.mit.edu	37	12	43860531	43860531	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43860531C>A	uc010skx.1	-	c.1291G>T	c.(1291-1293)GCC>TCC	p.A431S		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	431	Peptidase M12B.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.290323	47.422744	49.866584	18	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43860531	43860531	267	12	C	A	A	A	338	26	ADAMTS20	2	2
ARID2	196528	broad.mit.edu	37	12	46254641	46254641	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:46254641C>G	uc001ros.1	+	c.4831C>G	c.(4831-4833)CAG>GAG	p.Q1611E	ARID2_uc001ror.2_Missense_Mutation_p.Q1611E|ARID2_uc009zkg.1_Missense_Mutation_p.Q1067E|ARID2_uc009zkh.1_Missense_Mutation_p.Q1238E|ARID2_uc001rou.1_Missense_Mutation_p.Q945E	NM_152641	NP_689854	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1611					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			ovary(6)|skin(1)	7	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)										0.425532	68.193027	68.420334	20	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46254641	46254641	930	12	C	G	G	G	377	29	ARID2	3	3
PPM1H	57460	broad.mit.edu	37	12	63195774	63195774	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:63195774C>A	uc001srk.3	-	c.578G>T	c.(577-579)GGG>GTG	p.G193V		NM_020700	NP_065751	Q9ULR3	PPM1H_HUMAN	protein phosphatase 1H (PP2C domain containing)	193	PP2C-like.						phosphoprotein phosphatase activity			ovary(1)	1			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)										0.333333	35.391373	36.39754	14	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63195774	63195774	12776	12	C	A	A	A	286	22	PPM1H	2	2
B4GALNT3	283358	broad.mit.edu	37	12	657408	657408	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:657408C>T	uc001qii.1	+	c.798C>T	c.(796-798)AAC>AAT	p.N266N	B4GALNT3_uc001qij.1_Silent_p.N168N	NM_173593	NP_775864	Q6L9W6	B4GN3_HUMAN	beta	266	Lumenal (Potential).					Golgi cisterna membrane|integral to membrane	N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity				0	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)											0.363636	21.793333	22.153451	8	14	KEEP	---	---	---	---	capture		Silent	SNP	657408	657408	1289	12	C	T	T	T	246	19	B4GALNT3	1	1
CPSF6	11052	broad.mit.edu	37	12	69652822	69652822	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:69652822C>G	uc001suu.3	+	c.1258C>G	c.(1258-1260)CCA>GCA	p.P420A	CPSF6_uc001sut.3_Missense_Mutation_p.P383A|CPSF6_uc010stk.1_Missense_Mutation_p.P14A	NM_007007	NP_008938	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6,	383	Pro-rich.				mRNA polyadenylation|protein tetramerization	mRNA cleavage factor complex|paraspeckles|ribonucleoprotein complex	mRNA binding|nucleotide binding|protein binding				0	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)											0.376147	129.103348	130.586318	41	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69652822	69652822	3968	12	C	G	G	G	390	30	CPSF6	3	3
PTPRB	5787	broad.mit.edu	37	12	70963486	70963486	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70963486C>T	uc001swc.3	-	c.3603G>A	c.(3601-3603)CTG>CTA	p.L1201L	PTPRB_uc001swb.3_Silent_p.L983L|PTPRB_uc010sto.1_Silent_p.L983L|PTPRB_uc010stp.1_Silent_p.L893L|PTPRB_uc001swa.3_Silent_p.L1113L|PTPRB_uc001swd.3_Silent_p.L1200L|PTPRB_uc009zrr.1_Silent_p.L1080L	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	983	Fibronectin type-III 11.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)											0.153846	22.286913	32.719689	14	77	KEEP	---	---	---	---	capture		Silent	SNP	70963486	70963486	13253	12	C	T	T	T	366	29	PTPRB	2	2
NAV3	89795	broad.mit.edu	37	12	78598805	78598805	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78598805C>T	uc001syp.2	+	c.6925C>T	c.(6925-6927)CCA>TCA	p.P2309S	NAV3_uc001syo.2_Missense_Mutation_p.P2287S|NAV3_uc010sub.1_Missense_Mutation_p.P1766S|NAV3_uc009zsf.2_Missense_Mutation_p.P1118S	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2309						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.381818	65.46207	66.135793	21	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78598805	78598805	10581	12	C	T	T	T	286	22	NAV3	2	2
PPP1R12A	4659	broad.mit.edu	37	12	80200036	80200036	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:80200036G>C	uc001syz.2	-	c.1733C>G	c.(1732-1734)TCT>TGT	p.S578C	PPP1R12A_uc010suc.1_Missense_Mutation_p.S491C|PPP1R12A_uc001sza.2_Intron|PPP1R12A_uc010sud.1_Missense_Mutation_p.S578C|PPP1R12A_uc001szb.2_Missense_Mutation_p.S578C|PPP1R12A_uc001szc.2_Missense_Mutation_p.S578C	NM_002480	NP_002471	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory (inhibitor)	578	Ser/Thr-rich.					contractile fiber	protein binding|signal transducer activity			ovary(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)	7														0.034335	-39.224224	15.920514	8	225	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80200036	80200036	12789	12	G	C	C	C	429	33	PPP1R12A	3	3
KLRG1	10219	broad.mit.edu	37	12	9162084	9162084	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:9162084C>G	uc001qvh.2	+	c.521C>G	c.(520-522)TCA>TGA	p.S174*	KLRG1_uc001qvg.2_Nonsense_Mutation_p.S174*	NM_005810	NP_005801	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G,	174	C-type lectin.|Extracellular (Potential).				cell surface receptor linked signaling pathway|cellular defense response|inflammatory response|regulation of immune response	integral to membrane	receptor activity|sugar binding			central_nervous_system(1)	1														0.163265	19.069021	24.347244	8	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9162084	9162084	8735	12	C	G	G	G	377	29	KLRG1	5	3
NALCN	259232	broad.mit.edu	37	13	101890210	101890210	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101890210C>A	uc001vox.1	-	c.1330G>T	c.(1330-1332)GGA>TGA	p.G444*	NALCN_uc001voy.2_Nonsense_Mutation_p.G159*|NALCN_uc001voz.2_Nonsense_Mutation_p.G444*|NALCN_uc001vpa.2_Nonsense_Mutation_p.G444*	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	444	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.41	124.252451	124.961147	41	59	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	101890210	101890210	10544	13	C	A	A	A	273	21	NALCN	5	2
F7	2155	broad.mit.edu	37	13	113772899	113772899	+	Silent	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:113772899G>C	uc001vsv.2	+	c.978G>C	c.(976-978)CGG>CGC	p.R326R	F7_uc001vsw.2_Silent_p.R304R|F7_uc010tjt.1_Silent_p.R257R	NM_000131	NP_000122	P08709	FA7_HUMAN	coagulation factor VII isoform a precursor	326	Peptidase S1.				anti-apoptosis|blood coagulation, extrinsic pathway|peptidyl-glutamic acid carboxylation|positive regulation of leukocyte chemotaxis|positive regulation of platelet-derived growth factor receptor signaling pathway|positive regulation of positive chemotaxis|positive regulation of protein kinase B signaling cascade|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|Golgi lumen|plasma membrane	calcium ion binding|glycoprotein binding|serine-type endopeptidase activity				0	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;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)									0.285714	6.347358	6.635612	2	5	KEEP	---	---	---	---	capture		Silent	SNP	113772899	113772899	5543	13	G	C	C	C	522	41	F7	3	3
TMCO3	55002	broad.mit.edu	37	13	114188487	114188487	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:114188487A>T	uc001vtu.3	+	c.1471A>T	c.(1471-1473)ATG>TTG	p.M491L	TMCO3_uc001vtt.3_Missense_Mutation_p.M491L	NM_017905	NP_060375	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	491						integral to membrane	solute:hydrogen antiporter activity				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)											0.123711	14.741086	28.170997	12	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114188487	114188487	16527	13	A	T	T	T	104	8	TMCO3	3	3
RNF17	56163	broad.mit.edu	37	13	25442836	25442836	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25442836C>T	uc001upr.2	+	c.4260C>T	c.(4258-4260)CAC>CAT	p.H1420H	RNF17_uc010aab.2_Non-coding_Transcript|RNF17_uc010tde.1_Silent_p.H1416H|RNF17_uc001ups.2_Silent_p.H1359H|RNF17_uc010aac.2_Silent_p.H612H|RNF17_uc010aad.2_Silent_p.H430H	NM_031277	NP_112567	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1420					multicellular organismal development	cytoplasm|nucleus	hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding			ovary(1)	1		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)										0.040404	-14.682617	7.839481	4	95	KEEP	---	---	---	---	capture		Silent	SNP	25442836	25442836	13938	13	C	T	T	T	246	19	RNF17	1	1
SHISA2	387914	broad.mit.edu	37	13	26620732	26620732	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:26620732C>T	uc001uqm.1	-	c.807G>A	c.(805-807)CTG>CTA	p.L269L		NM_001007538	NP_001007539	Q6UWI4	SHSA2_HUMAN	shisa homolog 2 precursor	269	Cytoplasmic (Potential).				multicellular organismal development	endoplasmic reticulum membrane|integral to membrane				ovary(1)|central_nervous_system(1)	2														0.18	16.354158	21.163577	9	41	KEEP	---	---	---	---	capture		Silent	SNP	26620732	26620732	14772	13	C	T	T	T	314	25	SHISA2	2	2
NBEA	26960	broad.mit.edu	37	13	35630161	35630161	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:35630161C>T	uc001uvb.2	+	c.987C>T	c.(985-987)AGC>AGT	p.S329S		NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	329						cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)										0.076923	-1.227441	8.289799	4	48	KEEP	---	---	---	---	capture		Silent	SNP	35630161	35630161	10583	13	C	T	T	T	324	25	NBEA	2	2
WBP4	11193	broad.mit.edu	37	13	41636806	41636806	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:41636806A>G	uc001uxt.2	+	c.29A>G	c.(28-30)AAG>AGG	p.K10R	WBP4_uc010tfd.1_Missense_Mutation_p.K10R	NM_007187	NP_009118	O75554	WBP4_HUMAN	WW domain-containing binding protein 4	10					nuclear mRNA cis splicing, via spliceosome	nuclear speck|spliceosomal complex	nucleic acid binding|proline-rich region binding|zinc ion binding			breast(2)|kidney(1)	3		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)						133				0.375	19.252082	19.469174	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41636806	41636806	17833	13	A	G	G	G	39	3	WBP4	4	4
RB1	5925	broad.mit.edu	37	13	48916812	48916812	+	Silent	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:48916812G>T	uc001vcb.2	+	c.342G>T	c.(340-342)TCG>TCT	p.S114S	RB1_uc010acs.1_Intron	NM_000321	NP_000312	P06400	RB_HUMAN	retinoblastoma 1	114					androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|transcription repressor activity|ubiquitin protein ligase binding	p.?(2)		lung(93)|eye(89)|central_nervous_system(47)|bone(22)|breast(20)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|soft_tissue(8)|prostate(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	355		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)			6	p.S114S(CCK81-Tumor)	568	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			0.408451	92.662841	93.182423	29	42	KEEP	---	---	---	---	capture		Silent	SNP	48916812	48916812	13559	13	G	T	T	T	509	40	RB1	1	1
PCDH17	27253	broad.mit.edu	37	13	58299398	58299398	+	Silent	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:58299398G>C	uc001vhq.1	+	c.3450G>C	c.(3448-3450)CGG>CGC	p.R1150R	PCDH17_uc010aec.1_Silent_p.R1149R|PCDH17_uc001vhr.1_Silent_p.R239R	NM_001040429	NP_001035519	O14917	PCD17_HUMAN	protocadherin 17 precursor	1150	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding			ovary(2)|pancreas(2)	4		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		Melanoma(72;952 1291 1619 12849 33676)								0.345238	144.323542	147.911229	58	110	KEEP	---	---	---	---	capture		Silent	SNP	58299398	58299398	11932	13	G	C	C	C	548	43	PCDH17	3	3
NIN	51199	broad.mit.edu	37	14	51239175	51239175	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:51239175C>A	uc001wyi.2	-	c.825G>T	c.(823-825)GAG>GAT	p.E275D	NIN_uc001wyj.2_Non-coding_Transcript|NIN_uc001wyk.2_Missense_Mutation_p.E275D|NIN_uc010tqp.1_Missense_Mutation_p.E281D|NIN_uc001wym.2_Missense_Mutation_p.E275D|NIN_uc001wyo.2_Missense_Mutation_p.E275D|NIN_uc001wyp.1_Missense_Mutation_p.E237D	NM_020921	NP_065972	Q8N4C6	NIN_HUMAN	ninein isoform 2	275					centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			ovary(1)|kidney(1)|central_nervous_system(1)|skin(1)	4	all_epithelial(31;0.00244)|Breast(41;0.127)									745				0.352941	83.021895	84.644048	30	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51239175	51239175	10818	14	C	A	A	A	415	32	NIN	2	2
FOS	2353	broad.mit.edu	37	14	75747810	75747810	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75747810G>A	uc001xrn.2	+	c.826G>A	c.(826-828)GCA>ACA	p.A276T	FOS_uc010tva.1_Missense_Mutation_p.A240T|FOS_uc010asi.2_Missense_Mutation_p.A162T|FOS_uc001xro.2_Missense_Mutation_p.A128T	NM_005252	NP_005243	P01100	FOS_HUMAN	v-fos FBJ murine osteosarcoma viral oncogene	276					cellular response to reactive oxygen species|DNA methylation|inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|regulation of sequence-specific DNA binding transcription factor activity|SMAD protein signal transduction|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway		promoter binding|protein dimerization activity|R-SMAD binding|sequence-specific DNA binding transcription factor activity|specific RNA polymerase II transcription factor activity			lung(2)|ovary(1)	3		all_lung(585;0.0138)|all_epithelial(191;0.0263)|all_neural(303;0.112)		BRCA - Breast invasive adenocarcinoma(234;0.0117)						232				0.18	18.845478	23.659998	9	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75747810	75747810	6227	14	G	A	A	A	442	34	FOS	2	2
TTLL5	23093	broad.mit.edu	37	14	76135766	76135766	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:76135766C>T	uc010ask.1	+	c.82C>T	c.(82-84)CCA>TCA	p.P28S	TTLL5_uc001xrw.1_Missense_Mutation_p.P28S|TTLL5_uc001xrx.2_Missense_Mutation_p.P28S|TTLL5_uc001xrv.2_Missense_Mutation_p.P28S	NM_015072	NP_055887	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	28					protein modification process|transcription, DNA-dependent	cilium|microtubule basal body|nucleus	tubulin-tyrosine ligase activity			ovary(2)|central_nervous_system(1)	3				BRCA - Breast invasive adenocarcinoma(234;0.029)										0.306818	149.178028	155.037893	54	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76135766	76135766	17285	14	C	T	T	T	390	30	TTLL5	2	2
RIN3	79890	broad.mit.edu	37	14	93118141	93118141	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:93118141C>T	uc001yap.2	+	c.747C>T	c.(745-747)ACC>ACT	p.T249T	RIN3_uc010auk.2_5'UTR|RIN3_uc001yaq.2_Silent_p.T174T|RIN3_uc001yar.1_5'UTR|RIN3_uc001yas.1_5'UTR	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	249	Pro-rich.				endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding				0		all_cancers(154;0.0701)												0.106061	5.084947	15.254705	7	59	KEEP	---	---	---	---	capture		Silent	SNP	93118141	93118141	13850	14	C	T	T	T	288	23	RIN3	1	1
PAPOLA	10914	broad.mit.edu	37	14	97022723	97022723	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:97022723G>C	uc001yfq.2	+	c.1977G>C	c.(1975-1977)GAG>GAC	p.E659D	PAPOLA_uc001yfr.2_Missense_Mutation_p.E658D|PAPOLA_uc010twv.1_Missense_Mutation_p.E659D|PAPOLA_uc010avp.2_Missense_Mutation_p.E409D	NM_032632	NP_116021	P51003	PAPOA_HUMAN	poly(A) polymerase alpha	659	Nuclear localization signal 2 (By similarity).				mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|RNA binding				0		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		NSCLC(19;254 734 11908 35501 39234)								0.384946	593.218814	598.614814	179	286	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97022723	97022723	11846	14	G	C	C	C	425	33	PAPOLA	3	3
LINS1	55180	broad.mit.edu	37	15	101110081	101110081	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:101110081C>T	uc002bwe.2	-	c.1636G>A	c.(1636-1638)GAT>AAT	p.D546N	LINS1_uc002bwd.2_Missense_Mutation_p.D133N|LINS1_uc002bwf.2_Missense_Mutation_p.D546N|LINS1_uc002bwg.2_Missense_Mutation_p.D546N|LINS1_uc002bwh.2_Missense_Mutation_p.D546N	NM_001040614	NP_001035704	Q8NG48	LINES_HUMAN	lines homolog 1	546											0	Lung NSC(78;0.0018)|all_lung(78;0.00223)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.00095)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)											0.469388	70.119227	70.159362	23	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101110081	101110081	9145	15	C	T	T	T	377	29	LINS1	2	2
TRPM1	4308	broad.mit.edu	37	15	31318402	31318402	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31318402C>A	uc001zfm.2	-	c.3503G>T	c.(3502-3504)CGG>CTG	p.R1168L	TRPM1_uc010azy.2_Missense_Mutation_p.R1075L|TRPM1_uc001zfl.2_Non-coding_Transcript	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	1168	Cytoplasmic (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.238095	24.74757	27.376013	10	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31318402	31318402	17136	15	C	A	A	A	299	23	TRPM1	1	1
CAPN3	825	broad.mit.edu	37	15	42689048	42689048	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42689048A>T	uc001zpn.1	+	c.1166A>T	c.(1165-1167)CAC>CTC	p.H389L	CAPN3_uc001zpk.1_Missense_Mutation_p.H162L|CAPN3_uc001zpl.1_Missense_Mutation_p.H302L|CAPN3_uc010udf.1_Missense_Mutation_p.H302L|CAPN3_uc010udg.1_Missense_Mutation_p.H254L|CAPN3_uc001zpo.1_Missense_Mutation_p.H389L|CAPN3_uc001zpp.1_Missense_Mutation_p.H341L	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	389	Calpain catalytic.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)										0.346939	50.659885	51.673367	17	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42689048	42689048	2746	15	A	T	T	T	78	6	CAPN3	3	3
FOXB1	27023	broad.mit.edu	37	15	60297453	60297453	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:60297453C>G	uc002agj.1	+	c.291C>G	c.(289-291)TTC>TTG	p.F97L	FOXB1_uc010bgh.1_Intron	NM_012182	NP_036314	Q99853	FOXB1_HUMAN	forkhead box B1	97	Fork-head.				axon target recognition|cell migration in diencephalon|epithelial cell differentiation involved in mammary gland alveolus development|floor plate development|hypothalamus cell migration|inferior colliculus development|lactation|mammillothalamic axonal tract development|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of neuron apoptosis|regulation of sequence-specific DNA binding transcription factor activity|somitogenesis|telencephalon cell migration|visual learning	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(1)|central_nervous_system(1)	2														0.513514	63.031613	63.037846	19	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60297453	60297453	6234	15	C	G	G	G	402	31	FOXB1	3	3
TLN2	83660	broad.mit.edu	37	15	62949974	62949974	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:62949974G>C	uc002alb.3	+	c.665G>C	c.(664-666)CGG>CCG	p.R222P		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	222	FERM.				cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cell-cell junction|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(4)|breast(2)	6														0.043165	-18.620994	12.446695	6	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62949974	62949974	16478	15	G	C	C	C	507	39	TLN2	3	3
CA12	771	broad.mit.edu	37	15	63637803	63637803	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:63637803G>T	uc002amc.2	-	c.302C>A	c.(301-303)CCC>CAC	p.P101H	CA12_uc002amd.2_Missense_Mutation_p.P101H|CA12_uc002ame.2_Missense_Mutation_p.P41H	NM_001218	NP_001209	O43570	CAH12_HUMAN	carbonic anhydrase XII isoform 1 precursor	101	Extracellular (Potential).				one-carbon metabolic process	integral to membrane	carbonate dehydratase activity|zinc ion binding			ovary(1)	1					Acetazolamide(DB00819)									0.481481	39.07233	39.080441	13	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63637803	63637803	2629	15	G	T	T	T	559	43	CA12	2	2
ZNF263	10127	broad.mit.edu	37	16	3336081	3336081	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:3336081A>C	uc002cuq.2	+	c.701A>C	c.(700-702)CAG>CCG	p.Q234P	ZNF263_uc010uww.1_Intron|ZNF263_uc002cup.2_3'UTR	NM_005741	NP_005732	O14978	ZN263_HUMAN	zinc finger protein 263	234	KRAB.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.191011	36.721322	44.665222	17	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3336081	3336081	18395	16	A	C	C	C	91	7	ZNF263	4	4
CCDC135	84229	broad.mit.edu	37	16	57731941	57731941	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:57731941G>T	uc002emi.2	+	c.80G>T	c.(79-81)AGG>ATG	p.R27M	CCDC135_uc002emj.2_Missense_Mutation_p.R27M|CCDC135_uc002emk.2_Missense_Mutation_p.R27M	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	27	Potential.					cytoplasm				central_nervous_system(1)	1														0.285714	16.453067	17.311361	6	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57731941	57731941	2889	16	G	T	T	T	455	35	CCDC135	2	2
CDH5	1003	broad.mit.edu	37	16	66413319	66413319	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:66413319G>C	uc002eom.3	+	c.79G>C	c.(79-81)GGT>CGT	p.G27R	CDH5_uc002eon.1_Missense_Mutation_p.G27R	NM_001795	NP_001786	P33151	CADH5_HUMAN	cadherin 5, type 2 preproprotein	27					adherens junction organization|cell junction assembly|homophilic cell adhesion|regulation of establishment of cell polarity	integral to membrane|membrane fraction	beta-catenin binding|calcium ion binding|ion channel binding|receptor binding			ovary(2)|central_nervous_system(1)	3		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)										0.166667	8.522185	12.323366	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66413319	66413319	3242	16	G	C	C	C	455	35	CDH5	3	3
SPG7	6687	broad.mit.edu	37	16	89620342	89620342	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:89620342C>G	uc002fnj.2	+	c.2077C>G	c.(2077-2079)CAA>GAA	p.Q693E	SPG7_uc002fnl.2_Missense_Mutation_p.Q102E	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	693	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)										0.28	17.21363	18.302292	7	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89620342	89620342	15556	16	C	G	G	G	273	21	SPG7	3	3
MYH2	4620	broad.mit.edu	37	17	10450895	10450895	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10450895G>T	uc010coi.2	-	c.245C>A	c.(244-246)CCT>CAT	p.P82H	MYH2_uc002gmp.3_Missense_Mutation_p.P82H|MYH2_uc010coj.2_Missense_Mutation_p.P82H	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	82	Myosin head-like.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|lung(1)|kidney(1)	11														0.197368	103.00168	122.407473	45	183	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10450895	10450895	10430	17	G	T	T	T	455	35	MYH2	2	2
STAT3	6774	broad.mit.edu	37	17	40474456	40474456	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40474456A>G	uc002hzl.1	-	c.1945T>C	c.(1945-1947)TCA>CCA	p.S649P	STAT3_uc002hzk.1_Missense_Mutation_p.S649P|STAT3_uc002hzm.1_Missense_Mutation_p.S649P|STAT3_uc010wgh.1_Missense_Mutation_p.S551P|STAT3_uc002hzn.1_Missense_Mutation_p.S649P	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	649	SH2.				cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)						793				0.056075	-6.934153	15.227073	6	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40474456	40474456	15786	17	A	G	G	G	130	10	STAT3	4	4
SMARCA4	6597	broad.mit.edu	37	19	11169030	11169030	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:11169030G>C	uc010dxo.2	+	c.4620G>C	c.(4618-4620)AAG>AAC	p.K1540N	SMARCA4_uc002mqf.3_Missense_Mutation_p.K1508N|SMARCA4_uc010dxp.2_Missense_Mutation_p.K1508N|SMARCA4_uc010dxq.2_Missense_Mutation_p.K1475N|SMARCA4_uc010dxr.2_Missense_Mutation_p.K1474N|SMARCA4_uc002mqj.3_Missense_Mutation_p.K1478N|SMARCA4_uc010dxs.2_Missense_Mutation_p.K1477N|SMARCA4_uc002mqh.3_Missense_Mutation_p.K598N	NM_001128849	NP_001122321	P51532	SMCA4_HUMAN	SWI/SNF-related matrix-associated	1508	Bromo.				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of S phase of mitotic cell cycle|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription activator activity|transcription corepressor activity			lung(29)|ovary(7)|pancreas(7)|large_intestine(5)|prostate(3)|central_nervous_system(2)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|skin(1)|autonomic_ganglia(1)|kidney(1)	61		all_lung(6;0.0512)|Lung NSC(9;0.0568)								582				0.384615	17.272469	17.424051	5	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11169030	11169030	15268	19	G	C	C	C	425	33	SMARCA4	3	3
ZNF254	9534	broad.mit.edu	37	19	24309364	24309364	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:24309364G>T	uc002nru.2	+	c.562G>T	c.(562-564)GTC>TTC	p.V188F	ZNF254_uc010xrk.1_Missense_Mutation_p.V103F	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	188					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)												0.24359	49.585121	54.259612	19	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24309364	24309364	18389	19	G	T	T	T	624	48	ZNF254	2	2
DMPK	1760	broad.mit.edu	37	19	46283080	46283080	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46283080C>T	uc002pdi.1	-	c.286G>A	c.(286-288)GAC>AAC	p.D96N	DMPK_uc010xxs.1_5'Flank|DMPK_uc002pdd.1_Missense_Mutation_p.D80N|DMPK_uc002pde.1_Missense_Mutation_p.D80N|DMPK_uc002pdf.1_Missense_Mutation_p.D70N|DMPK_uc002pdg.1_Missense_Mutation_p.D70N|DMPK_uc002pdh.1_Missense_Mutation_p.D70N|DMPK_uc010xxt.1_Missense_Mutation_p.D70N|DMPK_uc010xxu.1_Missense_Mutation_p.D80N	NM_001081563	NP_001075032	Q09013	DMPK_HUMAN	myotonic dystrophy protein kinase isoform 1	80					protein phosphorylation|regulation of heart contraction		ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)	3		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		Esophageal Squamous(35;307 869 9153 24033 28903)				152				0.103448	2.905202	7.44394	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46283080	46283080	4764	19	C	T	T	T	403	31	DMPK	1	1
DMWD	1762	broad.mit.edu	37	19	46287967	46287967	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46287967C>T	uc002pdj.1	-	c.1909G>A	c.(1909-1911)GAC>AAC	p.D637N	DMPK_uc002pdf.1_5'Flank|DMPK_uc002pdg.1_5'Flank|DMPK_uc002pdh.1_5'Flank|DMPK_uc002pdi.1_5'Flank|DMPK_uc010xxt.1_5'Flank|DMWD_uc002pdk.1_Intron|DMWD_uc010eko.1_Missense_Mutation_p.D322N	NM_004943	NP_004934	Q09019	DMWD_HUMAN	dystrophia myotonica-containing WD repeat motif	637	WD 5.				meiosis						0		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)										0.054795	-6.857422	8.379963	4	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46287967	46287967	4775	19	C	T	T	T	416	32	DMWD	2	2
DMWD	1762	broad.mit.edu	37	19	46289604	46289604	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46289604C>G	uc002pdj.1	-	c.1150G>C	c.(1150-1152)GAG>CAG	p.E384Q	DMWD_uc002pdk.1_Missense_Mutation_p.E384Q|DMWD_uc010eko.1_Missense_Mutation_p.E69Q	NM_004943	NP_004934	Q09019	DMWD_HUMAN	dystrophia myotonica-containing WD repeat motif	384					meiosis						0		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)										0.086957	2.164299	10.108137	4	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46289604	46289604	4775	19	C	G	G	G	416	32	DMWD	3	3
ZNF813	126017	broad.mit.edu	37	19	53994808	53994808	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53994808G>C	uc002qbu.2	+	c.1322G>C	c.(1321-1323)TGT>TCT	p.C441S	ZNF813_uc010eqq.1_Intron	NM_001004301	NP_001004301	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	441	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)										0.755556	124.972058	127.649006	34	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53994808	53994808	18773	19	G	C	C	C	624	48	ZNF813	3	3
NLRP5	126206	broad.mit.edu	37	19	56552450	56552450	+	Silent	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56552450G>A	uc002qmj.2	+	c.2949G>A	c.(2947-2949)CAG>CAA	p.Q983Q	NLRP5_uc002qmi.2_Silent_p.Q964Q	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	983	LRR 9.					mitochondrion|nucleolus	ATP binding			ovary(3)|skin(2)|kidney(1)	6		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)										0.046512	-26.326581	20.820289	10	205	KEEP	---	---	---	---	capture		Silent	SNP	56552450	56552450	10883	19	G	A	A	A	425	33	NLRP5	2	2
MUC16	94025	broad.mit.edu	37	19	9072492	9072492	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9072492G>T	uc002mkp.2	-	c.14954C>A	c.(14953-14955)TCA>TAA	p.S4985*		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	4987	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.402174	108.153706	108.924297	37	55	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	9072492	9072492	10367	19	G	T	T	T	585	45	MUC16	5	2
OR7E24	26648	broad.mit.edu	37	19	9361929	9361929	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9361929C>T	uc002mlb.1	+	c.210C>T	c.(208-210)GAC>GAT	p.D70D		NM_001079935	NP_001073404	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E,	70	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.078947	-0.104345	6.775644	3	35	KEEP	---	---	---	---	capture		Silent	SNP	9361929	9361929	11632	19	C	T	T	T	259	20	OR7E24	2	2
WDR3	10885	broad.mit.edu	37	1	118479447	118479447	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118479447A>T	uc010oxe.1	+	c.437A>T	c.(436-438)AAG>ATG	p.K146M	WDR3_uc001ehi.2_Intron|WDR3_uc001ehh.2_De_novo_Start_InFrame	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	146						nuclear membrane|nucleolus					0	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)										0.326531	128.639929	132.56883	48	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118479447	118479447	17858	1	A	T	T	T	39	3	WDR3	3	3
WDR3	10885	broad.mit.edu	37	1	118492649	118492649	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:118492649C>A	uc010oxe.1	+	c.1642C>A	c.(1642-1644)CTA>ATA	p.L548I	WDR3_uc001ehi.2_Intron	NM_006784	NP_006775	Q9UNX4	WDR3_HUMAN	WD repeat-containing protein 3	548	WD 10.					nuclear membrane|nucleolus					0	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)										0.075221	-1.814193	40.021887	17	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118492649	118492649	17858	1	C	A	A	A	259	20	WDR3	2	2
HMCN1	83872	broad.mit.edu	37	1	186050516	186050516	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186050516G>A	uc001grq.1	+	c.8777G>A	c.(8776-8778)CGA>CAA	p.R2926Q		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	2926	Ig-like C2-type 27.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.21659	110.42885	126.491127	47	170	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186050516	186050516	7511	1	G	A	A	A	481	37	HMCN1	1	1
CRB1	23418	broad.mit.edu	37	1	197404462	197404462	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197404462A>T	uc001gtz.2	+	c.3469A>T	c.(3469-3471)ATC>TTC	p.I1157F	CRB1_uc010poz.1_Missense_Mutation_p.I1133F|CRB1_uc010ppa.1_Non-coding_Transcript|CRB1_uc009wza.2_Missense_Mutation_p.I1045F|CRB1_uc010ppb.1_Intron|CRB1_uc010ppd.1_Missense_Mutation_p.I638F|CRB1_uc001gub.1_Missense_Mutation_p.I806F	NM_201253	NP_957705	P82279	CRUM1_HUMAN	crumbs homolog 1 precursor	1157	Extracellular (Potential).|EGF-like 15.				cell-cell signaling|establishment or maintenance of cell polarity|response to stimulus|visual perception	apical plasma membrane|extracellular region|integral to membrane	calcium ion binding|protein binding			ovary(5)|large_intestine(1)	6														0.421053	103.890064	104.302787	32	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197404462	197404462	3987	1	A	T	T	T	104	8	CRB1	3	3
CACNA1S	779	broad.mit.edu	37	1	201047024	201047024	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:201047024C>A	uc001gvv.2	-	c.1602G>T	c.(1600-1602)AGG>AGT	p.R534S		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	534	II.|Helical; Name=S4 of repeat II; (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.390244	43.187943	43.621368	16	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	201047024	201047024	2663	1	C	A	A	A	389	30	CACNA1S	2	2
RPS6KC1	26750	broad.mit.edu	37	1	213414788	213414788	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:213414788C>T	uc010ptr.1	+	c.1969C>T	c.(1969-1971)CAG>TAG	p.Q657*	RPS6KC1_uc001hkd.2_Nonsense_Mutation_p.Q645*|RPS6KC1_uc010pts.1_Nonsense_Mutation_p.Q445*|RPS6KC1_uc010ptt.1_Nonsense_Mutation_p.Q445*|RPS6KC1_uc010ptu.1_Nonsense_Mutation_p.Q476*|RPS6KC1_uc010ptv.1_Nonsense_Mutation_p.Q192*|RPS6KC1_uc001hke.2_Nonsense_Mutation_p.Q476*	NM_012424	NP_036556	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide	657					cell communication|protein phosphorylation|signal transduction	early endosome|membrane	ATP binding|phosphatidylinositol binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|breast(1)	8				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)						410				0.300752	106.046811	110.764294	40	93	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	213414788	213414788	14138	1	C	T	T	T	377	29	RPS6KC1	5	2
OR2L2	26246	broad.mit.edu	37	1	248201629	248201629	+	Silent	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248201629A>T	uc001idw.2	+	c.60A>T	c.(58-60)TCA>TCT	p.S20S	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	20	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)											0.378049	184.681008	186.830797	62	102	KEEP	---	---	---	---	capture		Silent	SNP	248201629	248201629	11413	1	A	T	T	T	54	5	OR2L2	3	3
OR14I1	401994	broad.mit.edu	37	1	248845530	248845530	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248845530C>A	uc001ieu.1	-	c.76G>T	c.(76-78)GCC>TCC	p.A26S		NM_001004734	NP_001004734	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I,	26	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.412281	145.311152	146.075147	47	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248845530	248845530	11353	1	C	A	A	A	351	27	OR14I1	1	1
STMN1	3925	broad.mit.edu	37	1	26227995	26227995	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26227995C>G	uc010oev.1	-	c.365G>C	c.(364-366)CGT>CCT	p.R122P	STMN1_uc001bkz.2_Missense_Mutation_p.R122P|STMN1_uc001bla.2_Missense_Mutation_p.R122P|STMN1_uc001blb.2_Missense_Mutation_p.R115P|STMN1_uc001blc.2_Missense_Mutation_p.R122P	NM_001145454	NP_001138926	P16949	STMN1_HUMAN	stathmin 1 isoform b	122	Potential.				cell differentiation|intracellular signal transduction|microtubule depolymerization|mitotic spindle organization|nervous system development|response to virus	cytoplasm|microtubule	signal transducer activity|tubulin binding				0		Colorectal(325;3.46e-05)|Lung NSC(340;0.000163)|all_lung(284;0.000234)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.013)|READ - Rectum adenocarcinoma(331;0.0649)										0.376344	114.913547	116.157366	35	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26227995	26227995	15828	1	C	G	G	G	247	19	STMN1	3	3
KIAA0467	23334	broad.mit.edu	37	1	43904467	43904467	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43904467G>T	uc001cjk.1	+	c.3909G>T	c.(3907-3909)AAG>AAT	p.K1303N		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	2202						peroxisome				breast(6)|ovary(4)|pancreas(1)	11	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)												0.043478	-16.111331	9.562819	5	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43904467	43904467	8485	1	G	T	T	T	438	34	KIAA0467	2	2
CHD5	26038	broad.mit.edu	37	1	6196606	6196606	+	Silent	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:6196606G>T	uc001amb.1	-	c.2667C>A	c.(2665-2667)CTC>CTA	p.L889L	CHD5_uc001ama.1_Non-coding_Transcript|CHD5_uc001amc.1_Non-coding_Transcript|CHD5_uc009vlx.1_Non-coding_Transcript	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	889	Helicase ATP-binding.				chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding			breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)						2304				0.1	0.063203	6.484479	4	36	KEEP	---	---	---	---	capture		Silent	SNP	6196606	6196606	3462	1	G	T	T	T	522	41	CHD5	2	2
USP1	7398	broad.mit.edu	37	1	62908992	62908992	+	Splice_Site_SNP	SNP	T	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:62908992T>C	uc001daj.1	+	c.557_splice	c.e5+2	p.R186_splice	USP1_uc001dak.1_Splice_Site_SNP_p.R186_splice|USP1_uc001dal.1_Splice_Site_SNP_p.R186_splice	NM_001017415	NP_001017415			ubiquitin specific protease 1						DNA repair|monoubiquitinated protein deubiquitination|regulation of DNA repair|response to UV|ubiquitin-dependent protein catabolic process	nucleoplasm	cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1		all_neural(321;0.0281)		BRCA - Breast invasive adenocarcinoma(111;8.01e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00245)|OV - Ovarian serous cystadenocarcinoma(397;0.0535)		Ovarian(122;1846 2315 3982 19504)								0.125	5.610187	8.905064	3	21	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	62908992	62908992	17602	1	T	C	C	C	741	57	USP1	5	4
CACHD1	57685	broad.mit.edu	37	1	65099811	65099811	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:65099811G>A	uc001dbo.1	+	c.721G>A	c.(721-723)GAG>AAG	p.E241K	CACHD1_uc001dbp.1_5'UTR|CACHD1_uc001dbq.1_5'UTR	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	292	Extracellular (Potential).|VWFA.				calcium ion transport	integral to membrane				ovary(2)	2														0.293103	43.349368	45.573812	17	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65099811	65099811	2653	1	G	A	A	A	585	45	CACHD1	2	2
TGFBR3	7049	broad.mit.edu	37	1	92184900	92184900	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:92184900G>A	uc001doh.2	-	c.1535C>T	c.(1534-1536)TCA>TTA	p.S512L	TGFBR3_uc009wde.2_Missense_Mutation_p.S289L|TGFBR3_uc010osy.1_Missense_Mutation_p.S470L|TGFBR3_uc001doi.2_Missense_Mutation_p.S511L|TGFBR3_uc001doj.2_Missense_Mutation_p.S511L	NM_003243	NP_003234	Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	512	ZP.|Extracellular (Potential).				BMP signaling pathway|cardiac epithelial to mesenchymal transition|cardiac muscle cell proliferation|cell growth|cell migration|definitive erythrocyte differentiation|heart trabecula formation|immune response|intracellular protein kinase cascade|liver development|negative regulation of cellular component movement|negative regulation of epithelial cell proliferation|palate development|pathway-restricted SMAD protein phosphorylation|response to follicle-stimulating hormone stimulus|response to luteinizing hormone stimulus|response to prostaglandin E stimulus|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis	external side of plasma membrane|extracellular space|inhibin-betaglycan-ActRII complex|integral to plasma membrane|intracellular membrane-bounded organelle	coreceptor activity|heparin binding|PDZ domain binding|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type III|type II transforming growth factor beta receptor binding			ovary(3)	3		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)										0.534653	161.549493	161.654763	54	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92184900	92184900	16351	1	G	A	A	A	585	45	TGFBR3	2	2
SBF1	6305	broad.mit.edu	37	22	50903328	50903328	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:50903328C>A	uc003blh.2	-	c.1351G>T	c.(1351-1353)GCA>TCA	p.A451S	SBF1_uc011arx.1_Missense_Mutation_p.A115S|SBF1_uc003bli.2_Missense_Mutation_p.A452S	NM_002972	NP_002963	O95248	MTMR5_HUMAN	SET binding factor 1	451					protein dephosphorylation	integral to membrane|nucleus	protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)										0.078947	-0.205743	6.675595	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50903328	50903328	14339	22	C	A	A	A	338	26	SBF1	2	2
LRP2	4036	broad.mit.edu	37	2	170012818	170012818	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170012818C>G	uc002ues.2	-	c.12117G>C	c.(12115-12117)ATG>ATC	p.M4039I		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	4039	EGF-like 15; calcium-binding (Potential).|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	23				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)					2055				0.196262	53.012688	62.211879	21	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170012818	170012818	9329	2	C	G	G	G	377	29	LRP2	3	3
COL5A2	1290	broad.mit.edu	37	2	189914110	189914110	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:189914110G>T	uc002uqk.2	-	c.3110C>A	c.(3109-3111)CCA>CAA	p.P1037Q	COL5A2_uc010frx.2_Missense_Mutation_p.P613Q	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	1037					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)											0.451613	43.546019	43.609304	14	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	189914110	189914110	3835	2	G	T	T	T	611	47	COL5A2	2	2
SDPR	8436	broad.mit.edu	37	2	192701434	192701434	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:192701434C>T	uc002utb.2	-	c.493G>A	c.(493-495)GAG>AAG	p.E165K		NM_004657	NP_004648	O95810	SDPR_HUMAN	serum deprivation response protein	165						caveola|cytosol	phosphatidylserine binding|protein binding			ovary(1)|pancreas(1)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0647)		Phosphatidylserine(DB00144)									0.227273	23.227363	26.230995	10	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	192701434	192701434	14456	2	C	T	T	T	377	29	SDPR	2	2
FN1	2335	broad.mit.edu	37	2	216273069	216273069	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:216273069A>G	uc002vfa.2	-	c.2380T>C	c.(2380-2382)TCT>CCT	p.S794P	FN1_uc002vfb.2_Missense_Mutation_p.S794P|FN1_uc002vfc.2_Missense_Mutation_p.S794P|FN1_uc002vfd.2_Missense_Mutation_p.S794P|FN1_uc002vfe.2_Missense_Mutation_p.S794P|FN1_uc002vff.2_Missense_Mutation_p.S794P|FN1_uc002vfg.2_Missense_Mutation_p.S794P|FN1_uc002vfh.2_Missense_Mutation_p.S794P|FN1_uc002vfi.2_Missense_Mutation_p.S794P|FN1_uc002vfj.2_Missense_Mutation_p.S794P	NM_212482	NP_997647	P02751	FINC_HUMAN	fibronectin 1 isoform 1 preproprotein	794	Fibronectin type-III 2.				acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading	ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix	collagen binding|extracellular matrix structural constituent|heparin binding			central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1)	13		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1374				0.153226	37.963704	52.210441	19	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216273069	216273069	6204	2	A	G	G	G	156	12	FN1	4	4
SLC23A3	151295	broad.mit.edu	37	2	220034256	220034256	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:220034256A>C	uc010zkr.1	-	c.307T>G	c.(307-309)TGG>GGG	p.W103G	NHEJ1_uc002vjq.3_Intron|SLC23A3_uc010zks.1_Missense_Mutation_p.W103G|SLC23A3_uc010fwb.2_Missense_Mutation_p.W103G|SLC23A3_uc002vjs.1_5'Flank|SLC23A3_uc002vjt.1_5'Flank	NM_001144890	NP_001138362	Q6PIS1	S23A3_HUMAN	solute carrier family 23 (nucleobase	103	Helical; (Potential).				transmembrane transport	integral to membrane	protein binding|transporter activity				0		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)										0.188235	73.742454	89.304058	32	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220034256	220034256	14961	2	A	C	C	C	65	5	SLC23A3	4	4
ZPLD1	131368	broad.mit.edu	37	3	102187940	102187940	+	Silent	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:102187940C>A	uc003dvt.1	+	c.942C>A	c.(940-942)ACC>ACA	p.T314T	ZPLD1_uc003dvs.1_Silent_p.T298T|ZPLD1_uc011bhg.1_Silent_p.T298T	NM_175056	NP_778226	Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	298	ZP.|Extracellular (Potential).					integral to membrane				ovary(2)|central_nervous_system(1)	3														0.396825	150.710922	151.887551	50	76	KEEP	---	---	---	---	capture		Silent	SNP	102187940	102187940	18825	3	C	A	A	A	262	21	ZPLD1	2	2
MYLK	4638	broad.mit.edu	37	3	123345716	123345716	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123345716C>A	uc003ego.2	-	c.5187G>T	c.(5185-5187)AAG>AAT	p.K1729N	MYLK_uc010hrr.2_Missense_Mutation_p.K164N|MYLK_uc011bjv.1_Missense_Mutation_p.K529N|MYLK_uc011bjw.1_Missense_Mutation_p.K1729N|MYLK_uc003egp.2_Missense_Mutation_p.K1660N|MYLK_uc003egq.2_Missense_Mutation_p.K1678N|MYLK_uc003egr.2_Missense_Mutation_p.K1609N|MYLK_uc003egs.2_Missense_Mutation_p.K1553N	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1729	Calmodulin-binding.				aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)						766				0.372549	53.225232	53.947522	19	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123345716	123345716	10451	3	C	A	A	A	415	32	MYLK	2	2
NR2C2	7182	broad.mit.edu	37	3	15057759	15057759	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:15057759C>T	uc003bzi.2	+	c.431C>T	c.(430-432)TCC>TTC	p.S144F	NR2C2_uc003bzj.3_Missense_Mutation_p.S125F	NM_003298	NP_003289	P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	125	Nuclear receptor.|NR C4-type.				cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0														0.3	31.782278	33.213128	12	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15057759	15057759	11028	3	C	T	T	T	390	30	NR2C2	2	2
CCDC39	339829	broad.mit.edu	37	3	180378511	180378511	+	Silent	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:180378511G>T	uc010hxe.2	-	c.363C>A	c.(361-363)GGC>GGA	p.G121G	CCDC39_uc003fkn.2_Non-coding_Transcript	NM_181426	NP_852091	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	121	Potential.				axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium axoneme|cytoplasm|cytoskeleton				ovary(4)	4	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)											0.071429	-1.110493	6.839791	3	39	KEEP	---	---	---	---	capture		Silent	SNP	180378511	180378511	2933	3	G	T	T	T	587	46	CCDC39	2	2
ATP11B	23200	broad.mit.edu	37	3	182635879	182635879	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:182635879C>G	uc003flb.2	+	c.3521C>G	c.(3520-3522)TCA>TGA	p.S1174*	ATP11B_uc010hxg.2_Non-coding_Transcript	NM_014616	NP_055431	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	1174	Cytoplasmic (Potential).				aminophospholipid transport|ATP biosynthetic process	integral to membrane|nuclear inner membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)											0.0625	-2.552918	10.212003	4	60	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	182635879	182635879	1139	3	C	G	G	G	377	29	ATP11B	5	3
LAMP3	27074	broad.mit.edu	37	3	182871711	182871711	+	Missense_Mutation	SNP	G	C	C	rs115806403	by1000genomes	TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:182871711G>C	uc003flh.3	-	c.518C>G	c.(517-519)TCG>TGG	p.S173W		NM_014398	NP_055213	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	173	Lumenal (Potential).|Thr-rich.				cell proliferation	integral to membrane|lysosomal membrane				ovary(2)|central_nervous_system(1)	3	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)											0.39196	250.600724	252.635124	78	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	182871711	182871711	8942	3	G	C	C	C	481	37	LAMP3	3	3
STT3B	201595	broad.mit.edu	37	3	31656612	31656612	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:31656612A>G	uc011axe.1	+	c.893A>G	c.(892-894)TAC>TGC	p.Y298C	STT3B_uc010hft.1_Missense_Mutation_p.Y298C|STT3B_uc003cer.1_Missense_Mutation_p.Y298C|STT3B_uc003cet.2_Missense_Mutation_p.Y49C	NM_178862	NP_849193	Q8TCJ2	STT3B_HUMAN	source of immunodominant MHC-associated	298	Helical; (Potential).				protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex	dolichyl-diphosphooligosaccharide-protein glycotransferase activity|protein binding				0														0.452381	67.324853	67.407129	19	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31656612	31656612	15854	3	A	G	G	G	182	14	STT3B	4	4
BSN	8927	broad.mit.edu	37	3	49689543	49689543	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:49689543G>A	uc003cxe.3	+	c.2554G>A	c.(2554-2556)GCC>ACC	p.A852T		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	852					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	zinc ion binding			ovary(5)|central_nervous_system(1)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)										0.185185	10.160446	12.668484	5	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49689543	49689543	1561	3	G	A	A	A	494	38	BSN	1	1
TLR9	54106	broad.mit.edu	37	3	52257315	52257315	+	Silent	SNP	A	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52257315A>C	uc003ddb.2	-	c.1308T>G	c.(1306-1308)CTT>CTG	p.L436L	TLR9_uc003dda.1_Silent_p.L339L	NM_017442	NP_059138	Q9NR96	TLR9_HUMAN	toll-like receptor 9 isoform A precursor	339	LRR 11.|Extracellular (Potential).				defense response to bacterium|fibroblast growth factor receptor signaling pathway|I-kappaB phosphorylation|inflammatory response|innate immune response|insulin receptor signaling pathway|maintenance of gastrointestinal epithelium|negative regulation of interleukin-6 production|negative regulation of interleukin-8 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of toll-like receptor signaling pathway|positive regulation of chemokine production|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of inflammatory response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-beta production|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-10 production|positive regulation of interleukin-12 production|positive regulation of interleukin-18 production|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of JNK cascade|positive regulation of JUN kinase activity|positive regulation of NF-kappaB import into nucleus|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of toll-like receptor signaling pathway|positive regulation of tumor necrosis factor production|response to molecule of bacterial origin	apical plasma membrane|basolateral plasma membrane|early phagosome|endoplasmic reticulum membrane|endosome membrane|extracellular region|integral to membrane|lysosome	interleukin-1 receptor binding|siRNA binding|transmembrane receptor activity			large_intestine(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)					82				0.054945	-6.592116	12.377734	5	86	KEEP	---	---	---	---	capture		Silent	SNP	52257315	52257315	16488	3	A	C	C	C	158	13	TLR9	4	4
COL8A1	1295	broad.mit.edu	37	3	99509625	99509625	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:99509625C>G	uc003dti.1	+	c.99C>G	c.(97-99)ATC>ATG	p.I33M	COL8A1_uc003dtg.1_Missense_Mutation_p.I33M|COL8A1_uc003dth.1_Missense_Mutation_p.I33M	NM_020351	NP_065084	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor	33	Nonhelical region (NC2).				angiogenesis|cell adhesion	basement membrane|collagen type VIII					0														0.177419	23.403557	29.47026	11	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99509625	99509625	3843	3	C	G	G	G	369	29	COL8A1	3	3
UGT2A1	10941	broad.mit.edu	37	4	70504819	70504819	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70504819C>A	uc011caq.1	-	c.1143G>T	c.(1141-1143)TTG>TTT	p.L381F	UGT2A1_uc010ihu.2_Intron|UGT2A1_uc003hem.3_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Missense_Mutation_p.L172F	NM_001105677	NP_001099147	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	171	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.461538	106.587753	106.688659	36	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70504819	70504819	17511	4	C	A	A	A	376	29	UGT2A1	2	2
C4orf40	401137	broad.mit.edu	37	4	71024571	71024571	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71024571C>A	uc003hfa.3	+	c.602C>A	c.(601-603)GCC>GAC	p.A201D	C4orf40_uc003hfb.3_Missense_Mutation_p.A201D	NM_214711	NP_999876	Q6MZM9	CD040_HUMAN	hypothetical protein LOC401137 precursor	201	Ala-rich.					extracellular region					0														0.169811	16.743249	22.210766	9	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71024571	71024571	2364	4	C	A	A	A	338	26	C4orf40	2	2
CNOT6L	246175	broad.mit.edu	37	4	78652605	78652605	+	Silent	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:78652605C>A	uc011ccd.1	-	c.960G>T	c.(958-960)GTG>GTT	p.V320V	CNOT6L_uc003hks.2_Silent_p.V320V|CNOT6L_uc003hkt.1_Silent_p.V163V	NM_144571	NP_653172	Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	320					nuclear-transcribed mRNA poly(A) tail shortening	cytosol	exonuclease activity|protein binding			large_intestine(1)	1														0.166667	16.137986	21.83039	9	45	KEEP	---	---	---	---	capture		Silent	SNP	78652605	78652605	3761	4	C	A	A	A	366	29	CNOT6L	2	2
ANTXR2	118429	broad.mit.edu	37	4	80993620	80993620	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:80993620C>A	uc003hlz.3	-	c.95G>T	c.(94-96)CGC>CTC	p.R32L	ANTXR2_uc003hly.3_Missense_Mutation_p.R32L|ANTXR2_uc003hlx.1_5'Flank|ANTXR2_uc010ijn.2_Missense_Mutation_p.R32L	NM_001145794	NP_001139266	P58335	ANTR2_HUMAN	anthrax toxin receptor 2 isoform 2	32						endoplasmic reticulum membrane|extracellular region|integral to membrane|plasma membrane	metal ion binding|protein binding|receptor activity			ovary(1)	1														0.333333	16.856769	17.293239	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80993620	80993620	720	4	C	A	A	A	351	27	ANTXR2	1	1
EIF4E	1977	broad.mit.edu	37	4	99809080	99809080	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:99809080G>C	uc011ceb.1	-	c.245C>G	c.(244-246)TCT>TGT	p.S82C	EIF4E_uc011cea.1_Missense_Mutation_p.S102C|EIF4E_uc003hue.2_Missense_Mutation_p.S82C|EIF4E_uc011cec.1_Missense_Mutation_p.S82C	NM_001130679	NP_001124151	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	82					G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)						88				0.136364	5.209285	8.026444	3	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99809080	99809080	5219	4	G	C	C	C	429	33	EIF4E	3	3
PCDHA4	56144	broad.mit.edu	37	5	140188367	140188367	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140188367A>T	uc003lhi.2	+	c.1595A>T	c.(1594-1596)CAG>CTG	p.Q532L	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Missense_Mutation_p.Q532L|PCDHA4_uc011daa.1_Missense_Mutation_p.Q532L	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	532	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.604651	87.660739	88.073916	26	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140188367	140188367	11946	5	A	T	T	T	91	7	PCDHA4	3	3
KIF4B	285643	broad.mit.edu	37	5	154393718	154393718	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:154393718G>A	uc010jih.1	+	c.299G>A	c.(298-300)GGT>GAT	p.G100D		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	100	Kinesin-motor.				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.119658	14.980325	31.584268	14	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154393718	154393718	8615	5	G	A	A	A	572	44	KIF4B	2	2
MYO10	4651	broad.mit.edu	37	5	16769271	16769271	+	Silent	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:16769271C>A	uc003jft.3	-	c.972G>T	c.(970-972)CGG>CGT	p.R324R	MYO10_uc010itx.2_5'Flank	NM_012334	NP_036466	Q9HD67	MYO10_HUMAN	myosin X	324	Myosin head-like.				axon guidance|signal transduction	myosin complex	actin binding|ATP binding|motor activity			ovary(2)|pancreas(1)	3														0.15	4.710911	7.061296	3	17	KEEP	---	---	---	---	capture		Silent	SNP	16769271	16769271	10457	5	C	A	A	A	275	22	MYO10	2	2
ATP6V0E1	8992	broad.mit.edu	37	5	172447277	172447277	+	Silent	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:172447277C>G	uc003mcd.1	+	c.189C>G	c.(187-189)CTC>CTG	p.L63L	SNORA74B_uc003mce.1_5'Flank	NM_003945	NP_003936	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0	63					ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)											0.592105	161.990401	162.553903	45	31	KEEP	---	---	---	---	capture		Silent	SNP	172447277	172447277	1194	5	C	G	G	G	405	32	ATP6V0E1	3	3
NSD1	64324	broad.mit.edu	37	5	176709559	176709559	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176709559T>A	uc003mfr.3	+	c.5986T>A	c.(5986-5988)TTC>ATC	p.F1996I	NSD1_uc003mft.3_Missense_Mutation_p.F1727I|NSD1_uc011dfx.1_Missense_Mutation_p.F1644I	NM_022455	NP_071900	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1996	S-adenosyl-L-methionine binding.|SET.				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	androgen receptor binding|chromatin binding|estrogen receptor binding|histone methyltransferase activity (H3-K36 specific)|histone methyltransferase activity (H4-K20 specific)|ligand-dependent nuclear receptor binding|retinoid X receptor binding|thyroid hormone receptor binding|transcription corepressor activity|zinc ion binding			ovary(2)|kidney(1)	3	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)						492				0.191781	58.815169	71.772666	28	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176709559	176709559	11074	5	T	A	A	A	832	64	NSD1	3	3
LMAN2	10960	broad.mit.edu	37	5	176778186	176778186	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176778186G>C	uc003mge.2	-	c.303C>G	c.(301-303)ATC>ATG	p.I101M	LMAN2_uc003mgd.2_Missense_Mutation_p.I101M	NM_006816	NP_006807	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2 precursor	101	Lumenal (Potential).|L-type lectin-like.				protein transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	sugar binding				0	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.217054	74.530085	84.053363	28	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176778186	176778186	9167	5	G	C	C	C	421	33	LMAN2	3	3
ADAMTS12	81792	broad.mit.edu	37	5	33684007	33684008	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33684007_33684008CC>AA	uc003jia.1	-	c.787_788GG>TT	c.(787-789)GGG>TTG	p.G263L	ADAMTS12_uc010iuq.1_Missense_Mutation_p.G263L	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	263	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|lung(1)|kidney(1)|skin(1)	7														0.384058	157.063048	158.680516	53	85	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	33684007	33684008	258	5	CC	AA	AA	AA	286	22	ADAMTS12	2	2
NLN	57486	broad.mit.edu	37	5	65077205	65077205	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:65077205C>G	uc003juf.2	+	c.779C>G	c.(778-780)ACC>AGC	p.T260S	NLN_uc003jue.2_Missense_Mutation_p.T260S|NLN_uc003jug.2_Missense_Mutation_p.T89S	NM_020726	NP_065777	Q9BYT8	NEUL_HUMAN	neurolysin precursor	260					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(1)	1		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)										0.553191	93.255556	93.371381	26	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65077205	65077205	10870	5	C	G	G	G	234	18	NLN	3	3
GPRC6A	222545	broad.mit.edu	37	6	117121855	117121856	+	Missense_Mutation	DNP	CT	AC	AC			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117121855_117121856CT>AC	uc003pxj.1	-	c.1439_1440AG>GT	c.(1438-1440)AAG>AGT	p.K480S	GPRC6A_uc003pxk.1_Missense_Mutation_p.K305S|GPRC6A_uc003pxl.1_Intron	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	480	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)										0.486486	159.639863	159.657648	54	57	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	117121855	117121856	7004	6	CT	AC	AC	AC	311	24	GPRC6A	2	2
RFX6	222546	broad.mit.edu	37	6	117216355	117216355	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:117216355C>A	uc003pxm.2	+	c.657C>A	c.(655-657)AGC>AGA	p.S219R		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	219					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	promoter binding|protein binding|transcription activator activity			ovary(1)|pancreas(1)	2														0.47619	32.248782	32.259149	10	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117216355	117216355	13739	6	C	A	A	A	324	25	RFX6	2	2
TRDN	10345	broad.mit.edu	37	6	123709670	123709670	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:123709670C>A	uc003pzj.1	-	c.1132G>T	c.(1132-1134)GAA>TAA	p.E378*	TRDN_uc003pzk.1_Nonsense_Mutation_p.E379*|TRDN_uc003pzl.1_Nonsense_Mutation_p.E379*|TRDN_uc010kem.1_5'UTR	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	378	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)										0.35	19.518347	19.915668	7	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123709670	123709670	17012	6	C	A	A	A	390	30	TRDN	5	2
MED23	9439	broad.mit.edu	37	6	131943069	131943069	+	Silent	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:131943069A>T	uc003qcs.1	-	c.447T>A	c.(445-447)CCT>CCA	p.P149P	MED23_uc003qcq.2_Silent_p.P149P|MED23_uc003qct.1_Silent_p.P149P|MED23_uc011ecb.1_Non-coding_Transcript	NM_004830	NP_004821	Q9ULK4	MED23_HUMAN	mediator complex subunit 23 isoform a	149					regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	transcription factor complex	protein binding|transcription coactivator activity|transcription regulator activity			ovary(1)|kidney(1)	2	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608)										0.14433	23.982383	35.797269	14	83	KEEP	---	---	---	---	capture		Silent	SNP	131943069	131943069	9830	6	A	T	T	T	184	15	MED23	3	3
PDE10A	10846	broad.mit.edu	37	6	165792718	165792718	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:165792718C>A	uc003quo.2	-	c.1950G>T	c.(1948-1950)CAG>CAT	p.Q650H	PDE10A_uc011egj.1_Non-coding_Transcript|PDE10A_uc011egk.1_Missense_Mutation_p.Q570H|PDE10A_uc003qun.2_Missense_Mutation_p.Q640H	NM_001130690	NP_001124162	Q9Y233	PDE10_HUMAN	phosphodiesterase 10A isoform 1	640					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cAMP binding|cGMP binding|metal ion binding			ovary(3)	3		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Dipyridamole(DB00975)	Esophageal Squamous(22;308 615 5753 12038 40624)								0.164384	19.949281	27.762589	12	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165792718	165792718	12051	6	C	A	A	A	415	32	PDE10A	2	2
FRMD1	79981	broad.mit.edu	37	6	168461497	168461497	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:168461497G>T	uc003qwo.3	-	c.1286C>A	c.(1285-1287)CCG>CAG	p.P429Q	FRMD1_uc003qwm.3_Missense_Mutation_p.P223Q|FRMD1_uc011egs.1_Missense_Mutation_p.P200Q|FRMD1_uc011egt.1_Missense_Mutation_p.P364Q|FRMD1_uc003qwn.3_Missense_Mutation_p.P361Q	NM_024919	NP_079195	Q8N878	FRMD1_HUMAN	FERM domain containing 1 isoform 1	429						cytoskeleton	binding			ovary(1)	1		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)								0.375	8.723535	8.833058	3	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168461497	168461497	6299	6	G	T	T	T	507	39	FRMD1	1	1
RPS18	6222	broad.mit.edu	37	6	33243778	33243778	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33243778C>T	uc003odp.1	+	c.226C>T	c.(226-228)CAG>TAG	p.Q76*	RPS18_uc010jum.1_Non-coding_Transcript|RPS18_uc003odq.1_Non-coding_Transcript|B3GALT4_uc003odr.2_5'Flank	NM_022551	NP_072045	P62269	RS18_HUMAN	ribosomal protein S18	76					endocrine pancreas development|ribosome biogenesis|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	rRNA binding|structural constituent of ribosome				0														0.279412	51.793597	54.770771	19	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	33243778	33243778	14108	6	C	T	T	T	273	21	RPS18	5	2
UBR2	23304	broad.mit.edu	37	6	42627405	42627405	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42627405C>G	uc011dur.1	+	c.3254C>G	c.(3253-3255)TCA>TGA	p.S1085*	UBR2_uc011dus.1_Nonsense_Mutation_p.S730*|UBR2_uc003osh.2_Non-coding_Transcript	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1085						nucleus|plasma membrane	zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)											0.375	40.7072	41.258463	15	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	42627405	42627405	17460	6	C	G	G	G	377	29	UBR2	5	3
GNMT	27232	broad.mit.edu	37	6	42930898	42930898	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42930898C>T	uc003otd.2	+	c.540C>T	c.(538-540)TAC>TAT	p.Y180Y		NM_018960	NP_061833	Q14749	GNMT_HUMAN	glycine N-methyltransferase	180					protein homotetramerization|protein modification process|S-adenosylmethionine metabolic process		folic acid binding|glycine binding|glycine N-methyltransferase activity				0	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)									0.086957	0.069346	8.013674	4	42	KEEP	---	---	---	---	capture		Silent	SNP	42930898	42930898	6809	6	C	T	T	T	246	19	GNMT	1	1
TTBK1	84630	broad.mit.edu	37	6	43220499	43220499	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43220499G>A	uc003ouq.1	+	c.131G>A	c.(130-132)GGC>GAC	p.G44D		NM_032538	NP_115927	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	44	ATP (By similarity).|Protein kinase.				protein phosphorylation	cell junction|cytoplasm|nucleus	ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)							85				0.358209	59.9745	61.162813	24	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43220499	43220499	17230	6	G	A	A	A	546	42	TTBK1	2	2
SLC35B2	347734	broad.mit.edu	37	6	44224130	44224130	+	Silent	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:44224130G>A	uc003oxd.2	-	c.309C>T	c.(307-309)ACC>ACT	p.T103T	SLC35B2_uc011dvt.1_Intron|SLC35B2_uc011dvu.1_Intron	NM_178148	NP_835361	Q8TB61	S35B2_HUMAN	solute carrier family 35, member B2	103					positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi membrane|integral to membrane	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity|signal transducer activity			ovary(1)|central_nervous_system(1)	2	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)											0.089109	2.445829	19.62694	9	92	KEEP	---	---	---	---	capture		Silent	SNP	44224130	44224130	15073	6	G	A	A	A	600	47	SLC35B2	2	2
GPR111	222611	broad.mit.edu	37	6	47645579	47645579	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:47645579G>A	uc010jzj.1	+	c.277G>A	c.(277-279)GCT>ACT	p.A93T	GPR111_uc010jzk.1_Missense_Mutation_p.A25T|GPR111_uc003oyy.2_Non-coding_Transcript	NM_153839	NP_722581	Q8IZF7	GP111_HUMAN	G-protein coupled receptor 111	93	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			skin(1)	1														0.144444	21.640461	32.570927	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47645579	47645579	6902	6	G	A	A	A	546	42	GPR111	2	2
GFRAL	389400	broad.mit.edu	37	6	55223906	55223906	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:55223906C>A	uc003pcm.1	+	c.922C>A	c.(922-924)CAG>AAG	p.Q308K		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor	308	Extracellular (Potential).					integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)											0.257028	168.773278	182.106124	64	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55223906	55223906	6619	6	C	A	A	A	273	21	GFRAL	2	2
MUC17	140453	broad.mit.edu	37	7	100678546	100678546	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100678546A>G	uc003uxp.1	+	c.3849A>G	c.(3847-3849)ATA>ATG	p.I1283M	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1283	Extracellular (Potential).|Ser-rich.|19.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.256545	132.607003	142.951058	49	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100678546	100678546	10368	7	A	G	G	G	176	14	MUC17	4	4
MUC17	140453	broad.mit.edu	37	7	100681196	100681196	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100681196C>G	uc003uxp.1	+	c.6499C>G	c.(6499-6501)CCT>GCT	p.P2167A	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2167	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|34.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.394737	143.956989	145.060519	45	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100681196	100681196	10368	7	C	G	G	G	338	26	MUC17	3	3
NAMPT	10135	broad.mit.edu	37	7	105903950	105903950	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:105903950G>C	uc003vdq.2	-	c.857C>G	c.(856-858)GCG>GGG	p.A286G	NAMPT_uc003vdr.1_Missense_Mutation_p.A286G|NAMPT_uc011klu.1_Missense_Mutation_p.A199G	NM_005746	NP_005737	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	286					cell-cell signaling|NAD biosynthetic process|nicotinamide metabolic process|positive regulation of cell proliferation|positive regulation of nitric-oxide synthase biosynthetic process|signal transduction	cytosol	cytokine activity|nicotinamide phosphoribosyltransferase activity|nicotinate phosphoribosyltransferase activity|nicotinate-nucleotide diphosphorylase (carboxylating) activity			large_intestine(1)	1														0.210526	32.375242	36.78835	12	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105903950	105903950	10545	7	G	C	C	C	494	38	NAMPT	3	3
POT1	25913	broad.mit.edu	37	7	124503684	124503684	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:124503684T>C	uc003vlm.2	-	c.266A>G	c.(265-267)TAT>TGT	p.Y89C	POT1_uc011koe.1_Non-coding_Transcript|POT1_uc003vlk.2_Non-coding_Transcript|POT1_uc003vll.2_Non-coding_Transcript|POT1_uc003vlo.2_De_novo_Start_OutOfFrame|POT1_uc003vln.2_Non-coding_Transcript	NM_015450	NP_056265	Q9NUX5	POTE1_HUMAN	protection of telomeres 1 isoform 1	89					DNA duplex unwinding|negative regulation of telomere maintenance via telomerase|positive regulation of DNA strand elongation|positive regulation of helicase activity|positive regulation of telomerase activity|positive regulation of telomere maintenance via telomerase|telomere capping|telomere formation via telomerase|telomere maintenance via telomerase	nuclear telomere cap complex|nucleoplasm	DEAD/H-box RNA helicase binding|single-stranded telomeric DNA binding|telomerase inhibitor activity			central_nervous_system(1)	1						Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)								0.253968	92.846575	99.763844	32	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124503684	124503684	12689	7	T	C	C	C	637	49	POT1	4	4
TRIL	9865	broad.mit.edu	37	7	28997432	28997432	+	Silent	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:28997432G>A	uc003szt.2	-	c.231C>T	c.(229-231)TTC>TTT	p.F77F		NM_014817	NP_055632	Q7L0X0	TRIL_HUMAN	TLR4 interactor with leucine rich repeats	77	Extracellular (Potential).|LRR 1.				inflammatory response|innate immune response|regulation of cytokine production involved in immune response|toll-like receptor 4 signaling pathway	lipopolysaccharide receptor complex	lipopolysaccharide binding				0														0.166667	9.461914	12.617908	5	25	KEEP	---	---	---	---	capture		Silent	SNP	28997432	28997432	17029	7	G	A	A	A	477	37	TRIL	1	1
HECW1	23072	broad.mit.edu	37	7	43503272	43503272	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:43503272C>A	uc003tid.1	+	c.2665C>A	c.(2665-2667)CAG>AAG	p.Q889K	HECW1_uc011kbi.1_Missense_Mutation_p.Q855K	NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	889	Potential.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.302326	34.971039	36.464114	13	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43503272	43503272	7325	7	C	A	A	A	377	29	HECW1	2	2
PAPOLB	56903	broad.mit.edu	37	7	4901105	4901105	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:4901105C>T	uc003snk.2	-	c.337G>A	c.(337-339)GCA>ACA	p.A113T	RADIL_uc003sng.1_Intron|RADIL_uc011jwd.1_Intron|RADIL_uc003snj.1_Intron	NM_020144	NP_064529	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	112					mRNA processing|RNA polyadenylation	nucleus	ATP binding|polynucleotide adenylyltransferase activity|RNA binding			ovary(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)										0.08	-0.290689	8.663274	4	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4901105	4901105	11847	7	C	T	T	T	351	27	PAPOLB	1	1
EIF2AK1	27102	broad.mit.edu	37	7	6084286	6084286	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:6084286G>A	uc003spp.2	-	c.637C>T	c.(637-639)CGG>TGG	p.R213W	EIF2AK1_uc003spq.2_Missense_Mutation_p.R213W|EIF2AK1_uc011jwm.1_Missense_Mutation_p.R89W|EIF2AK1_uc003spr.1_Missense_Mutation_p.R5W	NM_014413	NP_055228	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha	213	Protein kinase.				negative regulation of hemoglobin biosynthetic process|negative regulation of translational initiation by iron|protein autophosphorylation|response to external stimulus|response to stress	cytoplasm	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|heme binding|protein homodimerization activity			upper_aerodigestive_tract(1)|stomach(1)|lung(1)|central_nervous_system(1)	4		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)						253				0.212121	15.711	18.236128	7	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6084286	6084286	5185	7	G	A	A	A	519	40	EIF2AK1	1	1
WBSCR17	64409	broad.mit.edu	37	7	70880904	70880904	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:70880904G>T	uc003tvy.2	+	c.619G>T	c.(619-621)GTC>TTC	p.V207F	WBSCR17_uc003tvz.2_5'UTR	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	207	Catalytic subdomain A.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)												0.242424	20.683419	22.679863	8	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70880904	70880904	17836	7	G	T	T	T	624	48	WBSCR17	2	2
HEATR2	54919	broad.mit.edu	37	7	803599	803599	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:803599G>A	uc010krz.1	+	c.1771G>A	c.(1771-1773)GTC>ATC	p.V591I	HEATR2_uc003siz.2_Missense_Mutation_p.V459I|HEATR2_uc003sja.2_Missense_Mutation_p.V49I	NM_017802	NP_060272	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	591							protein binding				0		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)										0.142857	5.012023	7.59217	3	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	803599	803599	7311	7	G	A	A	A	520	40	HEATR2	1	1
ABCB1	5243	broad.mit.edu	37	7	87179792	87179792	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:87179792C>A	uc003uiz.1	-	c.1216G>T	c.(1216-1218)GAA>TAA	p.E406*	ABCB1_uc011khc.1_Nonsense_Mutation_p.E342*	NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	406	ABC transporter 1.|Cytoplasmic (Potential).					apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)									0.25	41.210523	45.305444	18	54	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	87179792	87179792	41	7	C	A	A	A	416	32	ABCB1	5	2
ZNF623	9831	broad.mit.edu	37	8	144733483	144733483	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144733483C>T	uc003yzd.2	+	c.1441C>T	c.(1441-1443)CAT>TAT	p.H481Y	ZNF623_uc011lkp.1_Missense_Mutation_p.H441Y|ZNF623_uc003yzc.2_Missense_Mutation_p.H441Y	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	481	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)											0.481752	400.62081	400.702904	132	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144733483	144733483	18642	8	C	T	T	T	377	29	ZNF623	2	2
TMEM66	51669	broad.mit.edu	37	8	29927382	29927382	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:29927382G>A	uc003xhs.2	-	c.476C>T	c.(475-477)TCT>TTT	p.S159F	TMEM66_uc003xht.2_Missense_Mutation_p.S159F|TMEM66_uc003xhu.2_Missense_Mutation_p.S123F|TMEM66_uc003xhv.2_5'UTR	NM_016127	NP_057211	Q96BY9	TMM66_HUMAN	transmembrane protein 66 precursor	159						integral to membrane					0				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)										0.064516	-4.828426	13.510098	6	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29927382	29927382	16734	8	G	A	A	A	429	33	TMEM66	2	2
FNTA	2339	broad.mit.edu	37	8	42927367	42927367	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42927367C>T	uc003xps.2	+	c.550C>T	c.(550-552)CAG>TAG	p.Q184*	FNTA_uc003xpt.2_Nonsense_Mutation_p.Q93*|FNTA_uc003xpu.2_Nonsense_Mutation_p.Q117*|FNTA_uc003xpv.2_Non-coding_Transcript	NM_002027	NP_002018	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha isoform a	184	PFTA 3.				cellular component disassembly involved in apoptosis|positive regulation of deacetylase activity|positive regulation of tubulin deacetylation|protein farnesylation|protein geranylgeranylation|transforming growth factor beta receptor signaling pathway	cytosol|microtubule associated complex	alpha-tubulin binding|CAAX-protein geranylgeranyltransferase activity|microtubule binding|protein farnesyltransferase activity			ovary(1)	1	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)							148				0.08	-0.212234	13.287163	6	69	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	42927367	42927367	6219	8	C	T	T	T	377	29	FNTA	5	2
PXDNL	137902	broad.mit.edu	37	8	52321349	52321349	+	Silent	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:52321349C>T	uc003xqu.3	-	c.2835G>A	c.(2833-2835)GCG>GCA	p.A945A	PXDNL_uc003xqt.3_Non-coding_Transcript	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	945					hydrogen peroxide catabolic process|oxidation-reduction process	extracellular space	heme binding|peroxidase activity			ovary(1)|pancreas(1)	2		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)												0.4	11.899683	11.986567	4	6	KEEP	---	---	---	---	capture		Silent	SNP	52321349	52321349	13306	8	C	T	T	T	340	27	PXDNL	1	1
FAM82B	51115	broad.mit.edu	37	8	87487184	87487184	+	Splice_Site_SNP	SNP	T	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87487184T>G	uc003ydu.2	-	c.761_splice	c.e9-1	p.V254_splice	FAM82B_uc011lfz.1_Intron|FAM82B_uc011lga.1_Splice_Site_SNP_p.V224_splice	NM_016033	NP_057117			regulator of microtubule dynamics 1							microtubule|spindle pole	binding			ovary(1)	1														0.09375	3.500184	14.118994	6	58	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	87487184	87487184	5858	8	T	G	G	G	715	55	FAM82B	5	4
IFT74	80173	broad.mit.edu	37	9	27016972	27016972	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:27016972C>G	uc010mja.2	+	c.857C>G	c.(856-858)TCC>TGC	p.S286C	IFT74_uc010mjb.2_Missense_Mutation_p.S286C|IFT74_uc003zqf.3_Missense_Mutation_p.S286C|IFT74_uc003zqg.3_Missense_Mutation_p.S286C	NM_001099223	NP_001092693	Q96LB3	IFT74_HUMAN	coiled-coil domain containing 2 isoform a	286	Potential.					cytoplasmic membrane-bounded vesicle|intraflagellar transport particle B|microtubule-based flagellum					0		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)										0.08	-0.042402	8.96829	4	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27016972	27016972	7864	9	C	G	G	G	390	30	IFT74	3	3
C9orf79	286234	broad.mit.edu	37	9	90502913	90502913	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:90502913C>A	uc004app.3	+	c.3511C>A	c.(3511-3513)CTA>ATA	p.L1171I		NM_178828	NP_849150	Q6ZUB1	CI079_HUMAN	chromosome 9 open reading frame 79	1171						integral to membrane				ovary(3)	3														0.481481	37.871195	37.879361	13	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90502913	90502913	2613	9	C	A	A	A	311	24	C9orf79	2	2
LOC286238	286238	broad.mit.edu	37	9	91262362	91262362	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:91262362G>A	uc010mql.1	-	c.281C>T	c.(280-282)CCA>CTA	p.P94L		NM_001100111	NP_001093581			hypothetical protein LOC286238												0														0.617021	86.574804	87.136894	29	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91262362	91262362	9216	9	G	A	A	A	611	47	LOC286238	2	2
IL1RAPL2	26280	broad.mit.edu	37	X	105010959	105010959	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:105010959T>C	uc004elz.1	+	c.1366T>C	c.(1366-1368)TAC>CAC	p.Y456H		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	456	Cytoplasmic (Potential).|TIR.				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3														0.227273	13.465014	14.965626	5	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105010959	105010959	7963	23	T	C	C	C	637	49	IL1RAPL2	4	4
DCX	1641	broad.mit.edu	37	X	110644336	110644336	+	Missense_Mutation	SNP	C	T	T	rs56030372		TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:110644336C>T	uc011msv.1	-	c.830G>A	c.(829-831)CGT>CAT	p.R277H	DCX_uc004epd.2_Missense_Mutation_p.R277H|DCX_uc004epe.2_Missense_Mutation_p.R196H|DCX_uc004epf.2_Missense_Mutation_p.R196H|DCX_uc004epg.2_Missense_Mutation_p.R196H	NM_178152	NP_835365	O43602	DCX_HUMAN	doublecortin isoform b	277	Doublecortin 2.		R -> S (in epilepsy; resistant partial seizures; related to 'cryptogenic' epilepsy).		axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4														0.5	55.153021	55.153021	18	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110644336	110644336	4489	23	C	T	T	T	247	19	DCX	1	1
FRMPD4	9758	broad.mit.edu	37	X	12736345	12736345	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12736345C>T	uc004cuz.1	+	c.3400C>T	c.(3400-3402)CCT>TCT	p.P1134S	FRMPD4_uc011mij.1_Missense_Mutation_p.P1126S	NM_014728	NP_055543	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	1134					positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding			central_nervous_system(5)|ovary(3)|skin(2)|large_intestine(1)|lung(1)|pancreas(1)	13														0.568	220.128468	220.617989	71	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12736345	12736345	6309	23	C	T	T	T	390	30	FRMPD4	2	2
KDM5C	8242	broad.mit.edu	37	X	53231148	53231148	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53231148C>T	uc004drz.2	-	c.1754G>A	c.(1753-1755)CGC>CAC	p.R585H	KDM5C_uc011moc.1_Non-coding_Transcript|KDM5C_uc011mod.1_Missense_Mutation_p.R518H|KDM5C_uc004dsa.2_Missense_Mutation_p.R584H	NM_004187	NP_004178	P41229	KDM5C_HUMAN	jumonji, AT rich interactive domain 1C isoform	585	JmjC.				chromatin modification|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			kidney(9)|ovary(5)|salivary_gland(1)|autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|oesophagus(1)	18														0.075	-0.796214	6.607225	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53231148	53231148	8441	23	C	T	T	T	351	27	KDM5C	1	1
SHOX	6473	broad.mit.edu	37	X	591647	591647	+	Silent	SNP	G	C	C			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:591647G>C	uc004cph.1	+	c.15G>C	c.(13-15)ACG>ACC	p.T5T	SHOX_uc004cpi.2_Silent_p.T5T	NM_000451	NP_000442	O15266	SHOX_HUMAN	short stature homeobox isoform SHOXa	5					regulation of transcription, DNA-dependent|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity				0		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				Ovarian(95;18 1419 12424 14056 28266)								0.454545	17.020859	17.033165	5	6	KEEP	---	---	---	---	capture		Silent	SNP	591647	591647	14783	23	G	C	C	C	496	39	SHOX	3	3
MAGEE2	139599	broad.mit.edu	37	X	75003939	75003939	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:75003939A>T	uc004ecj.1	-	c.948T>A	c.(946-948)AAT>AAA	p.N316K		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	316	MAGE 2.									ovary(1)	1														0.56	48.853993	48.932564	14	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75003939	75003939	9569	23	A	T	T	T	102	8	MAGEE2	3	3
POSTN	10631	broad.mit.edu	37	13	38172778	38172778	+	Frame_Shift_Del	DEL	A	-	-			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:38172778_38172778delA	uc001uwo.3	-	c.86_86delT	c.(85-87)TTGfs	p.L29fs	POSTN_uc001uwp.3_Frame_Shift_Del_p.L29fs|POSTN_uc001uwr.2_Frame_Shift_Del_p.L29fs|POSTN_uc001uwq.2_Frame_Shift_Del_p.L29fs|POSTN_uc010teu.1_Frame_Shift_Del_p.L29fs|POSTN_uc010tev.1_Frame_Shift_Del_p.L29fs|POSTN_uc010tew.1_Frame_Shift_Del_p.L29fs|POSTN_uc010tex.1_Intron	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	29					cell adhesion|skeletal system development	proteinaceous extracellular matrix	heparin binding			ovary(2)	2		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)										0.32			28	59		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	38172778	38172778	12688	13	A	-	-	-	65	5	POSTN	5	5
SCN10A	6336	broad.mit.edu	37	3	38770107	38770107	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z000-01	TCGA-17-Z000-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38770107_38770107delC	uc003ciq.2	-	c.2566_2566delG	c.(2566-2568)GCCfs	p.A856fs		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	856	II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|large_intestine(1)|kidney(1)|skin(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)									0.36			32	56		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	38770107	38770107	14394	3	C	-	-	-	338	26	SCN10A	5	5
