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
TDRD1	56165	broad.mit.edu	37	10	115973205	115973205	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115973205G>T	uc001lbg.1	+	c.1932G>T	c.(1930-1932)TTG>TTT	p.L644F	TDRD1_uc001lbf.2_Missense_Mutation_p.L578F|TDRD1_uc001lbh.1_Missense_Mutation_p.L635F|TDRD1_uc001lbi.1_Missense_Mutation_p.L635F|TDRD1_uc010qsc.1_Missense_Mutation_p.L248F|TDRD1_uc001lbj.2_Missense_Mutation_p.L353F	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	644					DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)										0.185567	36.988326	45.983144	18	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115973205	115973205	16256	10	G	T	T	T	607	47	TDRD1	2	2
PNLIPRP2	5408	broad.mit.edu	37	10	118386478	118386478	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118386478C>T	uc001lcq.2	+	c.437C>T	c.(436-438)GCG>GTG	p.A146V	PNLIPRP2_uc009xyu.1_Non-coding_Transcript|PNLIPRP2_uc009xyv.1_Non-coding_Transcript	NM_005396	NP_005387	P54317	LIPR2_HUMAN	pancreatic lipase-related protein 2	145					galactolipid catabolic process|lipid digestion|phospholipid catabolic process|triglyceride metabolic process	extracellular space	acylglycerol lipase activity|calcium ion binding|galactolipase activity|phospholipase activity|triglyceride lipase activity			large_intestine(1)	1				all cancers(201;0.015)										0.416667	14.184494	14.253856	5	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118386478	118386478	12577	10	C	T	T	T	351	27	PNLIPRP2	1	1
CUBN	8029	broad.mit.edu	37	10	16957945	16957945	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:16957945A>G	uc001ioo.2	-	c.7085T>C	c.(7084-7086)TTC>TCC	p.F2362S		NM_001081	NP_001072	O60494	CUBN_HUMAN	cubilin precursor	2362	CUB 17.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity			ovary(9)|breast(4)|pancreas(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)	18					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)					2704				0.150685	45.361245	62.424164	22	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16957945	16957945	4211	10	A	G	G	G	117	9	CUBN	4	4
SLC39A12	221074	broad.mit.edu	37	10	18331729	18331729	+	Silent	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:18331729C>G	uc001ipo.2	+	c.2043C>G	c.(2041-2043)CTC>CTG	p.L681L	SLC39A12_uc001ipn.2_Silent_p.L644L|SLC39A12_uc001ipp.2_Silent_p.L680L|SLC39A12_uc010qck.1_Silent_p.L547L	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	681	Poly-Leu.|Helical; (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2														0.140845	18.699444	27.539305	10	61	KEEP	---	---	---	---	capture		Silent	SNP	18331729	18331729	15112	10	C	G	G	G	405	32	SLC39A12	3	3
GPR158	57512	broad.mit.edu	37	10	25755589	25755589	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25755589G>A	uc001isj.2	+	c.1345G>A	c.(1345-1347)GCA>ACA	p.A449T		NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	449	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.179104	22.904929	29.362803	12	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25755589	25755589	6938	10	G	A	A	A	546	42	GPR158	2	2
GPR158	57512	broad.mit.edu	37	10	25887482	25887482	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:25887482T>A	uc001isj.2	+	c.2927T>A	c.(2926-2928)ATG>AAG	p.M976K	GPR158_uc001isk.2_Missense_Mutation_p.M351K	NM_020752	NP_065803	Q5T848	GP158_HUMAN	G protein-coupled receptor 158 precursor	976	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(4)|large_intestine(2)|pancreas(1)	7														0.111111	19.843218	44.057513	18	144	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25887482	25887482	6938	10	T	A	A	A	663	51	GPR158	3	3
DIP2C	22982	broad.mit.edu	37	10	327243	327243	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:327243C>A	uc001ifp.2	-	c.4315G>T	c.(4315-4317)GTG>TTG	p.V1439L		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1439						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)						1018				0.192308	11.265592	13.560006	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	327243	327243	4708	10	C	A	A	A	247	19	DIP2C	1	1
GJD4	219770	broad.mit.edu	37	10	35896733	35896733	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:35896733C>T	uc001iyy.1	+	c.292C>T	c.(292-294)CAC>TAC	p.H98Y		NM_153368	NP_699199	Q96KN9	CXD4_HUMAN	connexin40.1	98	Cytoplasmic (Potential).				cell communication	connexon complex|integral to membrane				large_intestine(2)|central_nervous_system(1)|pancreas(1)	4														0.16	11.764655	17.27963	8	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35896733	35896733	6687	10	C	T	T	T	325	25	GJD4	2	2
JMJD1C	221037	broad.mit.edu	37	10	64974357	64974357	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:64974357C>T	uc001jmn.2	-	c.1570G>A	c.(1570-1572)GAA>AAA	p.E524K	JMJD1C_uc001jml.2_Missense_Mutation_p.E305K|JMJD1C_uc001jmm.2_Missense_Mutation_p.E236K|JMJD1C_uc010qiq.1_Missense_Mutation_p.E342K|JMJD1C_uc009xpi.2_Missense_Mutation_p.E342K|JMJD1C_uc009xpj.1_Non-coding_Transcript|JMJD1C_uc001jmp.1_Missense_Mutation_p.E236K	NM_032776	NP_116165	Q15652	JHD2C_HUMAN	jumonji domain containing 1C isoform a	524					blood coagulation|oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding			ovary(4)|breast(1)	5	Prostate(12;0.0119)|all_hematologic(501;0.191)													0.114943	10.888455	23.599902	10	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64974357	64974357	8254	10	C	T	T	T	390	30	JMJD1C	2	2
HKDC1	80201	broad.mit.edu	37	10	70998835	70998835	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:70998835G>T	uc001jpf.3	+	c.533G>T	c.(532-534)CGA>CTA	p.R178L	HKDC1_uc010qje.1_Missense_Mutation_p.R41L	NM_025130	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	178					glycolysis	mitochondrion|nucleus	ATP binding|hexokinase activity			ovary(4)	4														0.4	23.294339	23.469582	8	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70998835	70998835	7484	10	G	T	T	T	481	37	HKDC1	1	1
ANXA7	310	broad.mit.edu	37	10	75139842	75139842	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75139842G>A	uc001jtz.2	-	c.1102C>T	c.(1102-1104)CTT>TTT	p.L368F	ANXA7_uc001jua.2_Missense_Mutation_p.L346F|ANXA7_uc001jub.2_Missense_Mutation_p.L306F|ANXA7_uc010qki.1_Missense_Mutation_p.L256F|ANXA7_uc009xre.2_Missense_Mutation_p.L275F|ANXA7_uc009xrf.1_Missense_Mutation_p.L288F	NM_004034	NP_004025	P20073	ANXA7_HUMAN	annexin VII isoform 2	368	Annexin 3.						calcium ion binding|calcium-dependent phospholipid binding|calcium-dependent protein binding			ovary(2)|central_nervous_system(1)	3	Prostate(51;0.0119)													0.233803	213.339469	236.364029	83	272	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75139842	75139842	731	10	G	A	A	A	455	35	ANXA7	2	2
ITIH2	3698	broad.mit.edu	37	10	7774362	7774362	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7774362C>A	uc001ijs.2	+	c.1709C>A	c.(1708-1710)TCG>TAG	p.S570*		NM_002216	NP_002207	P19823	ITIH2_HUMAN	inter-alpha globulin inhibitor H2 polypeptide	570					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)|pancreas(1)	2														0.069444	-5.959866	8.176502	5	67	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7774362	7774362	8208	10	C	A	A	A	403	31	ITIH2	5	1
ZMIZ1	57178	broad.mit.edu	37	10	81065350	81065350	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:81065350C>T	uc001kaf.2	+	c.2415C>T	c.(2413-2415)GCC>GCT	p.A805A	ZMIZ1_uc001kag.2_Silent_p.A681A|ZMIZ1_uc010qlq.1_5'Flank	NM_020338	NP_065071	Q9ULJ6	ZMIZ1_HUMAN	retinoic acid induced 17	805					transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding			ovary(2)|breast(1)	3	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)											0.230769	41.293699	46.492997	18	60	KEEP	---	---	---	---	capture		Silent	SNP	81065350	81065350	18287	10	C	T	T	T	262	21	ZMIZ1	2	2
CYP2C8	1558	broad.mit.edu	37	10	96802752	96802752	+	Silent	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:96802752A>T	uc001kkb.2	-	c.1044T>A	c.(1042-1044)ACT>ACA	p.T348T	CYP2C8_uc001kkc.2_Non-coding_Transcript|CYP2C8_uc010qoa.1_Silent_p.T278T|CYP2C8_uc010qob.1_Silent_p.T262T|CYP2C8_uc010qoc.1_Silent_p.T246T|CYP2C8_uc010qod.1_Silent_p.T262T	NM_000770	NP_000761	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C,	348					exogenous drug catabolic process|organic acid metabolic process|oxidative demethylation|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|caffeine oxidase activity|electron carrier activity|heme binding|oxygen binding				0		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Aminophenazone(DB01424)|Amiodarone(DB01118)|Amodiaquine(DB00613)|Benzphetamine(DB00865)|Carbamazepine(DB00564)|Cerivastatin(DB00439)|Diclofenac(DB00586)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lovastatin(DB00227)|Midazolam(DB00683)|Montelukast(DB00471)|Nicardipine(DB00622)|Paclitaxel(DB01229)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rifampin(DB01045)|Rosiglitazone(DB00412)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Tolbutamide(DB01124)|Torasemide(DB00214)|Tretinoin(DB00755)|Trimethoprim(DB00440)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zopiclone(DB01198)									0.164948	31.344182	41.675404	16	81	KEEP	---	---	---	---	capture		Silent	SNP	96802752	96802752	4332	10	A	T	T	T	80	7	CYP2C8	3	3
TLL2	7093	broad.mit.edu	37	10	98170137	98170137	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98170137G>T	uc001kml.1	-	c.1143C>A	c.(1141-1143)ATC>ATA	p.I381I	TLL2_uc009xvf.1_Silent_p.I359I	NM_012465	NP_036597	Q9Y6L7	TLL2_HUMAN	tolloid-like 2 precursor	381	CUB 1.				cell differentiation|multicellular organismal development|proteolysis	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)										0.416667	54.29332	54.583396	20	28	KEEP	---	---	---	---	capture		Silent	SNP	98170137	98170137	16476	10	G	T	T	T	421	33	TLL2	2	2
CNTN5	53942	broad.mit.edu	37	11	100061967	100061967	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:100061967G>T	uc001pga.2	+	c.1690G>T	c.(1690-1692)GCT>TCT	p.A564S	CNTN5_uc009ywv.1_Missense_Mutation_p.A564S|CNTN5_uc001pfz.2_Missense_Mutation_p.A564S|CNTN5_uc001pgb.2_Missense_Mutation_p.A490S|CNTN5_uc010ruk.1_5'UTR	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	564	Ig-like C2-type 5.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)						1117				0.163636	15.752752	21.655326	9	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100061967	100061967	3782	11	G	T	T	T	442	34	CNTN5	2	2
TRPC6	7225	broad.mit.edu	37	11	101359687	101359687	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:101359687C>T	uc001pgk.3	-	c.1274G>A	c.(1273-1275)TGG>TAG	p.W425*	TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Intron	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	425	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		Colon(166;1315 1927 11094 12848 34731)								0.156627	24.119067	33.460589	13	70	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	101359687	101359687	17134	11	C	T	T	T	273	21	TRPC6	5	2
GRIA4	2893	broad.mit.edu	37	11	105795480	105795480	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:105795480G>T	uc001pix.2	+	c.1832G>T	c.(1831-1833)TGT>TTT	p.C611F	GRIA4_uc001piw.2_Missense_Mutation_p.C611F	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	611	Cytoplasmic (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)									0.129032	12.955805	21.264773	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105795480	105795480	7048	11	G	T	T	T	624	48	GRIA4	2	2
ELMOD1	55531	broad.mit.edu	37	11	107518319	107518319	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:107518319C>A	uc010rvs.1	+	c.546C>A	c.(544-546)TAC>TAA	p.Y182*	ELMOD1_uc001pjm.2_Nonsense_Mutation_p.Y182*|ELMOD1_uc010rvt.1_Nonsense_Mutation_p.Y176*	NM_018712	NP_061182	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1 isoform 1	182	ELMO.				phagocytosis	cytoskeleton	GTPase activator activity				0		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)										0.208333	11.962231	13.852545	5	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	107518319	107518319	5260	11	C	A	A	A	220	17	ELMOD1	5	2
TMPRSS4	56649	broad.mit.edu	37	11	117984017	117984017	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117984017G>T	uc010rxo.1	+	c.777G>T	c.(775-777)CGG>CGT	p.R259R	TMPRSS4_uc010rxp.1_Silent_p.R254R|TMPRSS4_uc010rxq.1_Silent_p.R112R|TMPRSS4_uc010rxr.1_Silent_p.R234R|TMPRSS4_uc010rxs.1_Silent_p.R219R|TMPRSS4_uc009yzu.2_Non-coding_Transcript|TMPRSS4_uc010rxt.1_Silent_p.R234R	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	259	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)										0.172414	27.376976	36.195029	15	72	KEEP	---	---	---	---	capture		Silent	SNP	117984017	117984017	16790	11	G	T	T	T	548	43	TMPRSS4	2	2
SORL1	6653	broad.mit.edu	37	11	121360805	121360805	+	Silent	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:121360805C>G	uc001pxx.2	+	c.744C>G	c.(742-744)GTC>GTG	p.V248V		NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	248	Extracellular (Potential).				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|central_nervous_system(1)|pancreas(1)	13		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)						937				0.191489	22.746686	26.92632	9	38	KEEP	---	---	---	---	capture		Silent	SNP	121360805	121360805	15434	11	C	G	G	G	366	29	SORL1	3	3
BSX	390259	broad.mit.edu	37	11	122849973	122849973	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:122849973G>T	uc010rzs.1	-	c.455C>A	c.(454-456)ACG>AAG	p.T152K		NM_001098169	NP_001091639	Q3C1V8	BSH_HUMAN	brain specific homeobox	152	Homeobox.						transcription regulator activity				0		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0361)										0.171429	26.263803	33.401147	12	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122849973	122849973	1567	11	G	T	T	T	520	40	BSX	1	1
GRAMD1B	57476	broad.mit.edu	37	11	123471181	123471181	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123471181C>T	uc001pyw.2	+	c.567C>T	c.(565-567)TTC>TTT	p.F189F	GRAMD1B_uc001pyx.2_Silent_p.F182F|GRAMD1B_uc010rzw.1_Silent_p.F142F|GRAMD1B_uc010rzx.1_Silent_p.F142F|GRAMD1B_uc009zbe.1_Silent_p.F178F	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	182						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)						1503				0.166667	7.483762	10.013562	4	20	KEEP	---	---	---	---	capture		Silent	SNP	123471181	123471181	7024	11	C	T	T	T	415	32	GRAMD1B	2	2
OR10S1	219873	broad.mit.edu	37	11	123847658	123847658	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123847658G>C	uc001pzm.1	-	c.741C>G	c.(739-741)GGC>GGG	p.G247G		NM_001004474	NP_001004474	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S,	247	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)										0.135135	7.566241	12.326567	5	32	KEEP	---	---	---	---	capture		Silent	SNP	123847658	123847658	11324	11	G	C	C	C	535	42	OR10S1	3	3
OR10G4	390264	broad.mit.edu	37	11	123886982	123886982	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123886982G>T	uc010sac.1	+	c.701G>T	c.(700-702)CGC>CTC	p.R234L		NM_001004462	NP_001004462	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G,	234	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)										0.26087	57.485383	62.231205	24	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123886982	123886982	11307	11	G	T	T	T	494	38	OR10G4	1	1
CDON	50937	broad.mit.edu	37	11	125851151	125851151	+	Silent	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:125851151T>A	uc009zbw.2	-	c.3069A>T	c.(3067-3069)TCA>TCT	p.S1023S	CDON_uc001qdb.3_Silent_p.S400S|CDON_uc001qdc.3_Silent_p.S1023S	NM_016952	NP_058648	Q4KMG0	CDON_HUMAN	surface glycoprotein, Ig superfamily member	1023	Cytoplasmic (Potential).				cell adhesion|muscle cell differentiation|positive regulation of muscle cell differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)	4	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)										0.188889	37.320788	45.472796	17	73	KEEP	---	---	---	---	capture		Silent	SNP	125851151	125851151	3299	11	T	A	A	A	704	55	CDON	3	3
INSC	387755	broad.mit.edu	37	11	15247237	15247237	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:15247237G>T	uc001mly.2	+	c.1174G>T	c.(1174-1176)GCC>TCC	p.A392S	INSC_uc001mlz.2_Missense_Mutation_p.A345S|INSC_uc001mma.2_Missense_Mutation_p.A345S|INSC_uc010rcs.1_Missense_Mutation_p.A380S|INSC_uc001mmb.2_Missense_Mutation_p.A345S|INSC_uc001mmc.2_Missense_Mutation_p.A303S	NM_001031853	NP_001027024	Q1MX18	INSC_HUMAN	inscuteable isoform a	392					cell differentiation|nervous system development	cytoplasm	binding			ovary(2)|central_nervous_system(1)	3														0.096774	1.501819	6.55337	3	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15247237	15247237	8065	11	G	T	T	T	546	42	INSC	2	2
SOX6	55553	broad.mit.edu	37	11	16036488	16036488	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:16036488C>G	uc001mme.2	-	c.1771G>C	c.(1771-1773)GGA>CGA	p.G591R	SOX6_uc001mmd.2_Missense_Mutation_p.G554R|SOX6_uc001mmf.2_Missense_Mutation_p.G551R|SOX6_uc001mmg.2_Missense_Mutation_p.G578R	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	578					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.169231	17.279484	24.020138	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16036488	16036488	15455	11	C	G	G	G	286	22	SOX6	3	3
MRGPRX2	117194	broad.mit.edu	37	11	19077943	19077943	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:19077943G>T	uc001mph.2	-	c.7C>A	c.(7-9)CCA>ACA	p.P3T		NM_054030	NP_473371	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	3	Extracellular (Potential).				sensory perception of pain|sleep	integral to membrane|plasma membrane	G-protein coupled receptor activity|neuropeptide binding			ovary(1)	1						GBM(198;1966 2199 4849 37227 49954)								0.231771	194.703614	220.004153	89	295	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19077943	19077943	10160	11	G	T	T	T	533	41	MRGPRX2	2	2
NAV2	89797	broad.mit.edu	37	11	20101754	20101754	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20101754G>C	uc001mpr.3	+	c.5324G>C	c.(5323-5325)TGG>TCG	p.W1775S	NAV2_uc001mpp.2_Missense_Mutation_p.W1711S|NAV2_uc010rdm.1_Missense_Mutation_p.W1831S|NAV2_uc001mpt.2_Missense_Mutation_p.W824S|NAV2_uc009yhx.2_Missense_Mutation_p.W839S|NAV2_uc009yhy.1_Missense_Mutation_p.W737S|NAV2_uc009yhz.2_Missense_Mutation_p.W420S|NAV2_uc001mpu.2_Missense_Mutation_p.W213S	NM_182964	NP_892009	Q8IVL1	NAV2_HUMAN	neuron navigator 2 isoform 1	1831						nucleus	ATP binding|helicase activity			ovary(1)|pancreas(1)	2														0.188679	17.613394	22.427448	10	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20101754	20101754	10580	11	G	C	C	C	611	47	NAV2	3	3
NELL1	4745	broad.mit.edu	37	11	20907025	20907025	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:20907025A>C	uc009yid.2	+	c.626A>C	c.(625-627)AAC>ACC	p.N209T	NELL1_uc001mqe.2_Missense_Mutation_p.N181T|NELL1_uc001mqf.2_Missense_Mutation_p.N181T|NELL1_uc010rdo.1_Missense_Mutation_p.N124T|NELL1_uc010rdp.1_Intron	NM_006157	NP_006148	Q92832	NELL1_HUMAN	nel-like 1 isoform 1 precursor	181	TSP N-terminal.				cell adhesion|nervous system development	extracellular region	calcium ion binding|structural molecule activity			ovary(2)|large_intestine(1)	3														0.26087	33.879413	36.260355	12	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20907025	20907025	10732	11	A	C	C	C	26	2	NELL1	4	4
PAX6	5080	broad.mit.edu	37	11	31823443	31823443	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31823443T>C	uc001mtg.3	-	c.159A>G	c.(157-159)AAA>AAG	p.K53K	PAX6_uc001mtd.3_Intron|PAX6_uc001mte.3_Intron|PAX6_uc001mtf.3_Intron|PAX6_uc001mth.3_Intron|PAX6_uc009yjr.2_Intron	NM_001604	NP_001595	P26367	PAX6_HUMAN	paired box gene 6 isoform b	47	Paired.				central nervous system development|eye development|gene-specific transcription from RNA polymerase II promoter|negative regulation of neurogenesis|neuron fate commitment|organ morphogenesis|pancreatic A cell development|positive regulation of gene expression|regulation of transcription, DNA-dependent|response to wounding|visual perception	cytoplasm|nuclear chromatin	R-SMAD binding|RNA polymerase II core promoter sequence-specific DNA binding|sequence-specific DNA binding RNA polymerase II transcription factor activity|transcription activator activity|ubiquitin-protein ligase activity			ovary(2)|pancreas(1)	3	Lung SC(675;0.225)													0.125	5.207778	8.504869	3	21	KEEP	---	---	---	---	capture		Silent	SNP	31823443	31823443	11903	11	T	C	C	C	725	56	PAX6	4	4
ZNF195	7748	broad.mit.edu	37	11	3381315	3381315	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:3381315A>T	uc001lxt.2	-	c.923T>A	c.(922-924)GTC>GAC	p.V308D	ZNF195_uc001lxv.2_Missense_Mutation_p.V285D|ZNF195_uc001lxs.2_Missense_Mutation_p.V236D|ZNF195_uc010qxr.1_Missense_Mutation_p.V289D|ZNF195_uc009ydz.2_Missense_Mutation_p.V263D|ZNF195_uc001lxu.2_Missense_Mutation_p.V240D	NM_001130520	NP_001123992	O14628	ZN195_HUMAN	zinc finger protein 195 isoform 1	308					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)										0.349693	159.526052	162.775138	57	106	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3381315	3381315	18349	11	A	T	T	T	130	10	ZNF195	3	3
LRRC4C	57689	broad.mit.edu	37	11	40136113	40136113	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40136113C>A	uc001mxa.1	-	c.1730G>T	c.(1729-1731)GGA>GTA	p.G577V	LRRC4C_uc001mxc.1_Missense_Mutation_p.G573V|LRRC4C_uc001mxd.1_Missense_Mutation_p.G573V|LRRC4C_uc001mxb.1_Missense_Mutation_p.G573V	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	577					regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.160494	19.520717	28.42032	13	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40136113	40136113	9383	11	C	A	A	A	390	30	LRRC4C	2	2
OR51F1	256892	broad.mit.edu	37	11	4790884	4790885	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4790884_4790885CC>AA	uc010qyl.1	-	c.263_264GG>TT	c.(262-264)TGG>TTT	p.W88F		NM_001004752	NP_001004752	A6NLW9	A6NLW9_HUMAN	olfactory receptor, family 51, subfamily F,	88						integral to membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)										0.129032	6.579914	10.732593	4	27	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	4790884	4790885	11506	11	CC	AA	AA	AA	234	18	OR51F1	2	2
FOLH1	2346	broad.mit.edu	37	11	49175882	49175882	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:49175882C>G	uc001ngy.2	-	c.1786G>C	c.(1786-1788)GAT>CAT	p.D596H	FOLH1_uc001ngx.2_Missense_Mutation_p.D28H|FOLH1_uc001ngz.2_Missense_Mutation_p.D596H|FOLH1_uc009yly.2_Missense_Mutation_p.D581H|FOLH1_uc009ylz.2_Missense_Mutation_p.D581H|FOLH1_uc009yma.2_Missense_Mutation_p.D288H	NM_004476	NP_004467	Q04609	FOLH1_HUMAN	folate hydrolase 1 isoform 1	596	Extracellular (Probable).				proteolysis	cytoplasm|integral to plasma membrane|membrane fraction|nucleus	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity			large_intestine(1)	1					Capromab(DB00089)|L-Glutamic Acid(DB00142)									0.122807	11.783222	19.720767	7	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49175882	49175882	6221	11	C	G	G	G	377	29	FOLH1	3	3
OR51A7	119687	broad.mit.edu	37	11	4929496	4929496	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4929496G>A	uc010qyq.1	+	c.897G>A	c.(895-897)TGG>TGA	p.W299*		NM_001004749	NP_001004749	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A,	299	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.0625	-4.467302	11.468406	5	75	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	4929496	4929496	11498	11	G	A	A	A	559	43	OR51A7	5	2
OR51V1	283111	broad.mit.edu	37	11	5221342	5221342	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5221342C>A	uc010qyz.1	-	c.589G>T	c.(589-591)GCC>TCC	p.A197S		NM_001004760	NP_001004760	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V,	197	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.101266	4.752351	17.277692	8	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5221342	5221342	11517	11	C	A	A	A	364	28	OR51V1	2	2
SPRYD5	84767	broad.mit.edu	37	11	55658777	55658777	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55658777G>T	uc010rip.1	+	c.1028G>T	c.(1027-1029)TGG>TTG	p.W343L	SPRYD5_uc010riq.1_Missense_Mutation_p.W200L	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	343	B30.2/SPRY.					intracellular	zinc ion binding				0		all_epithelial(135;0.226)												0.187879	66.927962	81.97678	31	134	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55658777	55658777	15625	11	G	T	T	T	611	47	SPRYD5	2	2
TNKS1BP1	85456	broad.mit.edu	37	11	57077082	57077082	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57077082C>A	uc001njr.2	-	c.3103G>T	c.(3103-3105)GTG>TTG	p.V1035L	TNKS1BP1_uc001njs.2_Missense_Mutation_p.V1035L|TNKS1BP1_uc009ymd.1_Missense_Mutation_p.V486L	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	1035	Gly-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)												0.289855	55.794421	58.511982	20	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57077082	57077082	16861	11	C	A	A	A	247	19	TNKS1BP1	1	1
TNKS1BP1	85456	broad.mit.edu	37	11	57080341	57080341	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57080341G>C	uc001njr.2	-	c.1821C>G	c.(1819-1821)ACC>ACG	p.T607T	TNKS1BP1_uc001njs.2_Silent_p.T607T|TNKS1BP1_uc009ymd.1_Silent_p.T58T	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	607	Pro-rich.|Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)												0.333333	23.463763	24.129103	9	18	KEEP	---	---	---	---	capture		Silent	SNP	57080341	57080341	16861	11	G	C	C	C	600	47	TNKS1BP1	3	3
OR5B17	219965	broad.mit.edu	37	11	58126124	58126124	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58126124G>A	uc010rke.1	-	c.419C>T	c.(418-420)GCT>GTT	p.A140V		NM_001005489	NP_001005489	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B,	140	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(5;0.0027)	Breast(21;0.0778)												0.135417	18.604699	30.975004	13	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58126124	58126124	11559	11	G	A	A	A	442	34	OR5B17	2	2
OR5B2	390190	broad.mit.edu	37	11	58189978	58189978	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58189978C>A	uc010rkg.1	-	c.757G>T	c.(757-759)GTA>TTA	p.V253L		NM_001005566	NP_001005566	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B,	253	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Esophageal squamous(5;0.0027)	Breast(21;0.0778)												0.252747	55.194719	60.239093	23	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58189978	58189978	11560	11	C	A	A	A	260	20	OR5B2	2	2
OSBP	5007	broad.mit.edu	37	11	59344401	59344401	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59344401C>G	uc001noc.1	-	c.2158G>C	c.(2158-2160)GAC>CAC	p.D720H	OSBP_uc009ymr.1_Non-coding_Transcript	NM_002556	NP_002547	P22059	OSBP1_HUMAN	oxysterol binding protein	720					lipid transport	Golgi membrane	oxysterol binding			large_intestine(1)	1		all_epithelial(135;0.000236)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)										0.186147	104.589984	125.908861	43	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59344401	59344401	11684	11	C	G	G	G	377	29	OSBP	3	3
OR56B4	196335	broad.mit.edu	37	11	6129676	6129676	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6129676C>T	uc010qzx.1	+	c.668C>T	c.(667-669)TCC>TTC	p.S223F		NM_001005181	NP_001005181	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B,	223	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.363636	149.98639	152.315222	52	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6129676	6129676	11548	11	C	T	T	T	390	30	OR56B4	2	2
HPX	3263	broad.mit.edu	37	11	6458394	6458394	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6458394C>A	uc001mdg.2	-	c.717G>T	c.(715-717)AGG>AGT	p.R239S	HPX_uc001mdf.2_5'UTR|HPX_uc009yfc.2_Non-coding_Transcript	NM_000613	NP_000604	P02790	HEMO_HUMAN	hemopexin precursor	239					cellular iron ion homeostasis|interspecies interaction between organisms	extracellular space	heme transporter activity|metal ion binding|protein binding				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;5.46e-08)|BRCA - Breast invasive adenocarcinoma(625;0.19)										0.4	50.138478	50.532588	18	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6458394	6458394	7638	11	C	A	A	A	389	30	HPX	2	2
CCDC87	55231	broad.mit.edu	37	11	66358918	66358918	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66358918C>A	uc001oiq.3	-	c.1569G>T	c.(1567-1569)TGG>TGT	p.W523C	CCS_uc001oir.2_5'Flank	NM_018219	NP_060689	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	523										ovary(1)	1														0.117647	4.874928	9.76191	4	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66358918	66358918	2987	11	C	A	A	A	234	18	CCDC87	2	2
OR6A2	8590	broad.mit.edu	37	11	6816690	6816690	+	Missense_Mutation	SNP	C	G	G	rs111641381		TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6816690C>G	uc001mes.1	-	c.250G>C	c.(250-252)GCT>CCT	p.A84P		NM_003696	NP_003687	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A,	84	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|pancreas(1)	4		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)										0.293103	51.151949	53.374469	17	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6816690	6816690	11596	11	C	G	G	G	325	25	OR6A2	3	3
ODZ4	26011	broad.mit.edu	37	11	78413266	78413266	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:78413266G>C	uc001ozl.3	-	c.4392C>G	c.(4390-4392)CAC>CAG	p.H1464Q	ODZ4_uc009yvb.1_Missense_Mutation_p.H48Q	NM_001098816	NP_001092286	Q6N022	TEN4_HUMAN	odz, odd Oz/ten-m homolog 4	1464	Extracellular (Potential).				signal transduction	integral to membrane				ovary(2)|pancreas(2)	4														0.466667	62.91039	62.958315	21	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78413266	78413266	11242	11	G	C	C	C	516	40	ODZ4	3	3
FOLH1B	219595	broad.mit.edu	37	11	89405080	89405080	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:89405080C>A	uc001pda.2	+	c.207C>A	c.(205-207)CAC>CAA	p.H69Q		NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B	69		Zinc 2 (By similarity).			proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|central_nervous_system(1)	4														0.2	51.456873	61.085737	23	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89405080	89405080	6222	11	C	A	A	A	233	18	FOLH1B	2	2
FAT3	120114	broad.mit.edu	37	11	92257911	92257911	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:92257911A>G	uc001pdj.3	+	c.3404A>G	c.(3403-3405)TAC>TGC	p.Y1135C		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1135	Cadherin 10.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.265306	37.255588	39.692684	13	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	92257911	92257911	5927	11	A	G	G	G	182	14	FAT3	4	4
GPR83	10888	broad.mit.edu	37	11	94113409	94113409	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:94113409C>A	uc001pet.2	-	c.1178G>T	c.(1177-1179)AGG>ATG	p.R393M		NM_016540	NP_057624	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83 precursor	393	Cytoplasmic (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity			central_nervous_system(2)|ovary(1)	3		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.222222	26.467379	30.304843	12	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94113409	94113409	6988	11	C	A	A	A	312	24	GPR83	2	2
CNTN5	53942	broad.mit.edu	37	11	99827611	99827611	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:99827611G>T	uc001pga.2	+	c.747G>T	c.(745-747)CAG>CAT	p.Q249H	CNTN5_uc009ywv.1_Missense_Mutation_p.Q249H|CNTN5_uc001pfz.2_Missense_Mutation_p.Q249H|CNTN5_uc001pgb.2_Missense_Mutation_p.Q175H	NM_014361	NP_055176	O94779	CNTN5_HUMAN	contactin 5 isoform long	249	Ig-like C2-type 2.				cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)						1117				0.403226	74.462059	74.969903	25	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99827611	99827611	3782	11	G	T	T	T	451	35	CNTN5	2	2
CLEC9A	283420	broad.mit.edu	37	12	10205373	10205373	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10205373T>C	uc001qxa.2	+	c.87T>C	c.(85-87)TGT>TGC	p.C29C		NM_207345	NP_997228	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	29	Cytoplasmic (Potential).					integral to membrane	receptor activity|sugar binding			ovary(1)	1														0.377778	54.565085	55.154658	17	28	KEEP	---	---	---	---	capture		Silent	SNP	10205373	10205373	3660	12	T	C	C	C	777	60	CLEC9A	4	4
C12orf42	374470	broad.mit.edu	37	12	103696112	103696112	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:103696112G>T	uc001tjt.2	-	c.857C>A	c.(856-858)CCC>CAC	p.P286H	C12orf42_uc001tjs.2_Intron|C12orf42_uc009zuf.1_Missense_Mutation_p.P286H|C12orf42_uc001tju.2_Missense_Mutation_p.P191H	NM_198521	NP_940923	Q96LP6	CL042_HUMAN	hypothetical protein LOC374470	286										ovary(1)|central_nervous_system(1)	2														0.119048	4.853075	10.832431	5	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103696112	103696112	1732	12	G	T	T	T	559	43	C12orf42	2	2
POLR3B	55703	broad.mit.edu	37	12	106890557	106890557	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:106890557G>C	uc001tlp.2	+	c.2845G>C	c.(2845-2847)GGC>CGC	p.G949R	POLR3B_uc001tlq.2_Missense_Mutation_p.G891R	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	949					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2														0.098039	2.847299	11.087226	5	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106890557	106890557	12657	12	G	C	C	C	611	47	POLR3B	3	3
RFX4	5992	broad.mit.edu	37	12	107114577	107114577	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:107114577A>T	uc001tlt.2	+	c.1301A>T	c.(1300-1302)CAG>CTG	p.Q434L	RFX4_uc001tlr.2_Missense_Mutation_p.Q425L|RFX4_uc001tls.2_Missense_Mutation_p.Q434L|RFX4_uc001tlv.2_Missense_Mutation_p.Q331L	NM_213594	NP_998759	Q33E94	RFX4_HUMAN	regulatory factor X4 isoform c	425	Necessary for dimerization.				transcription, DNA-dependent	nucleus	DNA binding				0														0.244444	27.10215	29.781022	11	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107114577	107114577	13737	12	A	T	T	T	91	7	RFX4	3	3
NAA25	80018	broad.mit.edu	37	12	112481006	112481006	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112481006G>A	uc001ttm.2	-	c.2260C>T	c.(2260-2262)CTT>TTT	p.L754F	NAA25_uc001ttn.3_Non-coding_Transcript|NAA25_uc009zvz.1_Missense_Mutation_p.L726F|NAA25_uc009zwa.1_Missense_Mutation_p.L754F	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	754						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3														0.19697	32.536017	38.181752	13	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112481006	112481006	10516	12	G	A	A	A	455	35	NAA25	2	2
TBX3	6926	broad.mit.edu	37	12	115120979	115120979	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:115120979G>A	uc001tvt.1	-	c.27C>T	c.(25-27)GTC>GTT	p.V9V	TBX3_uc001tvu.1_Silent_p.V9V|TBX3_uc010syw.1_Silent_p.V9V	NM_016569	NP_057653	O15119	TBX3_HUMAN	T-box 3 protein isoform 2	9					anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	general transcriptional repressor activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding			ovary(2)	2	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)								OREG0022153	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.238806	36.220626	40.445753	16	51	KEEP	---	---	---	---	capture		Silent	SNP	115120979	115120979	16185	12	G	A	A	A	574	45	TBX3	2	2
PXN	5829	broad.mit.edu	37	12	120650328	120650328	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120650328T>C	uc001txt.2	-	c.1565A>G	c.(1564-1566)TAC>TGC	p.Y522C	PXN_uc001txu.2_Missense_Mutation_p.Y334C|PXN_uc001txv.2_Missense_Mutation_p.Y403C|PXN_uc001txx.2_Missense_Mutation_p.Y355C|PXN_uc001txy.2_Missense_Mutation_p.Y488C|PXN_uc001txz.2_Non-coding_Transcript	NM_001080855	NP_001074324	P49023	PAXI_HUMAN	paxillin isoform 1	522	LIM zinc-binding 3.				cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)									115				0.357143	14.782646	15.029161	5	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120650328	120650328	13310	12	T	C	C	C	741	57	PXN	4	4
KDM2B	84678	broad.mit.edu	37	12	121881939	121881939	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:121881939C>G	uc001uat.2	-	c.2327G>C	c.(2326-2328)CGC>CCC	p.R776P	KDM2B_uc001uaq.2_Missense_Mutation_p.R216P|KDM2B_uc010szy.1_Missense_Mutation_p.R216P|KDM2B_uc001uar.2_Missense_Mutation_p.R367P|KDM2B_uc001uas.2_Missense_Mutation_p.R745P|KDM2B_uc001uau.2_Intron|KDM2B_uc001uao.2_Missense_Mutation_p.R24P|KDM2B_uc010szx.1_Missense_Mutation_p.R24P|KDM2B_uc001uap.2_Non-coding_Transcript	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	776					oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)	1												OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.181818	16.977415	21.159814	8	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	121881939	121881939	8431	12	C	G	G	G	351	27	KDM2B	3	3
TCTN2	79867	broad.mit.edu	37	12	124184347	124184347	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:124184347C>T	uc001ufp.2	+	c.1602C>T	c.(1600-1602)CTC>CTT	p.L534L	TCTN2_uc009zya.2_Silent_p.L533L	NM_024809	NP_079085	Q96GX1	TECT2_HUMAN	tectonic family member 2 isoform 1	534	Extracellular (Potential).					integral to membrane				ovary(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)										0.125	6.049615	11.545428	5	35	KEEP	---	---	---	---	capture		Silent	SNP	124184347	124184347	16249	12	C	T	T	T	392	31	TCTN2	1	1
PLBD1	79887	broad.mit.edu	37	12	14706144	14706144	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:14706144C>A	uc001rcc.1	-	c.318G>T	c.(316-318)GAG>GAT	p.E106D		NM_024829	NP_079105	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	106					lipid catabolic process	extracellular region	hydrolase activity				0														0.416667	14.872991	14.945702	5	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14706144	14706144	12451	12	C	A	A	A	311	24	PLBD1	2	2
GUCY2C	2984	broad.mit.edu	37	12	14796519	14796519	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:14796519G>A	uc001rcd.2	-	c.1919C>T	c.(1918-1920)CCT>CTT	p.P640L		NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor	640	Cytoplasmic (Potential).|Protein kinase.				intracellular signal transduction|protein phosphorylation|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(1)	5										889				0.122222	14.758094	27.338654	11	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14796519	14796519	7176	12	G	A	A	A	455	35	GUCY2C	2	2
SLCO1B1	10599	broad.mit.edu	37	12	21392039	21392039	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:21392039C>A	uc001req.3	+	c.1992C>A	c.(1990-1992)GTC>GTA	p.V664V		NM_006446	NP_006437	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family,	664	Cytoplasmic (Potential).				bile acid metabolic process|sodium-independent organic anion transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	bile acid transmembrane transporter activity|sodium-independent organic anion transmembrane transporter activity|thyroid hormone transmembrane transporter activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5					Digoxin(DB00390)|Gemfibrozil(DB01241)|Pravastatin(DB00175)									0.234043	24.177182	27.24617	11	36	KEEP	---	---	---	---	capture		Silent	SNP	21392039	21392039	15220	12	C	A	A	A	366	29	SLCO1B1	2	2
KIAA0528	9847	broad.mit.edu	37	12	22635520	22635520	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:22635520C>A	uc010sit.1	-	c.1714G>T	c.(1714-1716)GTG>TTG	p.V572L	KIAA0528_uc010sir.1_Missense_Mutation_p.V385L|KIAA0528_uc010sis.1_Missense_Mutation_p.V570L|KIAA0528_uc001rfq.2_Missense_Mutation_p.V570L|KIAA0528_uc010siu.1_Missense_Mutation_p.V570L|KIAA0528_uc001rfr.2_Missense_Mutation_p.V561L|KIAA0528_uc009ziy.1_Missense_Mutation_p.V572L	NM_014802	NP_055617	Q86YS7	K0528_HUMAN	hypothetical protein LOC9847	570							protein binding			ovary(1)|large_intestine(1)|breast(1)|central_nervous_system(1)	4														0.145161	15.931596	23.442883	9	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22635520	22635520	8489	12	C	A	A	A	260	20	KIAA0528	2	2
PPFIBP1	8496	broad.mit.edu	37	12	27786365	27786365	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:27786365G>T	uc001ric.1	+	c.36G>T	c.(34-36)GCG>GCT	p.A12A	PPFIBP1_uc001rhy.1_Silent_p.A12A|PPFIBP1_uc001rhz.1_Silent_p.A12A|PPFIBP1_uc010sjr.1_Intron|PPFIBP1_uc001rib.1_Silent_p.A12A|PPFIBP1_uc001ria.2_Silent_p.A12A|PPFIBP1_uc001rid.1_Intron	NM_003622	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein binding protein 1	12					cell adhesion	plasma membrane	protein binding		PPFIBP1/ALK(3)	soft_tissue(3)|kidney(1)|skin(1)	5	Lung SC(9;0.0873)													0.091954	4.63753	19.222655	8	79	KEEP	---	---	---	---	capture		Silent	SNP	27786365	27786365	12743	12	G	T	T	T	509	40	PPFIBP1	1	1
DDX11	1663	broad.mit.edu	37	12	31254893	31254893	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:31254893G>T	uc001rjt.1	+	c.2179G>T	c.(2179-2181)GGC>TGC	p.G727C	DDX11_uc001rjr.1_Missense_Mutation_p.G727C|DDX11_uc001rjs.1_Intron|DDX11_uc001rju.1_Missense_Mutation_p.G399C|DDX11_uc001rjv.1_Missense_Mutation_p.G727C|DDX11_uc001rjw.1_Missense_Mutation_p.G701C|DDX11_uc009zjn.1_Non-coding_Transcript|DDX11_uc009zjo.1_5'Flank	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	727					G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding			breast(3)	3	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)										Multiple Myeloma(12;0.14)			0.230769	7.121948	7.982934	3	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31254893	31254893	4514	12	G	T	T	T	559	43	DDX11	2	2
C12orf35	55196	broad.mit.edu	37	12	32134160	32134160	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:32134160G>T	uc001rks.2	+	c.271G>T	c.(271-273)GAA>TAA	p.E91*		NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	91										ovary(1)	1	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)											0.210526	17.588453	20.527585	8	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	32134160	32134160	1726	12	G	T	T	T	429	33	C12orf35	5	2
ADAMTS20	80070	broad.mit.edu	37	12	43826126	43826126	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43826126G>T	uc010skx.1	-	c.3077C>A	c.(3076-3078)GCT>GAT	p.A1026D	ADAMTS20_uc001rno.1_Missense_Mutation_p.A180D|ADAMTS20_uc001rnp.1_Missense_Mutation_p.A180D	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	1026	TSP type-1 5.					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				0.114286	4.174984	9.308837	4	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43826126	43826126	267	12	G	T	T	T	442	34	ADAMTS20	2	2
RACGAP1	29127	broad.mit.edu	37	12	50390950	50390950	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:50390950C>T	uc001rvt.2	-	c.917G>A	c.(916-918)CGG>CAG	p.R306Q	RACGAP1_uc009zlm.1_Missense_Mutation_p.R306Q|RACGAP1_uc001rvs.2_Missense_Mutation_p.R306Q|RACGAP1_uc001rvu.2_Missense_Mutation_p.R306Q	NM_013277	NP_037409	Q9H0H5	RGAP1_HUMAN	Rac GTPase activating protein 1	306	Phorbol-ester/DAG-type.				blood coagulation|cytokinesis, actomyosin contractile ring assembly|cytokinesis, initiation of separation|embryo development|microtubule-based movement|neuroblast proliferation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction|spermatogenesis|sulfate transport	acrosomal vesicle|cytosol|microtubule|midbody|nucleus|spindle	alpha-tubulin binding|beta-tubulin binding|gamma-tubulin binding|GTPase activator activity|metal ion binding			kidney(1)	1														0.263158	41.205638	44.092954	15	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50390950	50390950	13436	12	C	T	T	T	299	23	RACGAP1	1	1
KCNA5	3741	broad.mit.edu	37	12	5154195	5154195	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:5154195C>T	uc001qni.2	+	c.882C>T	c.(880-882)CCC>CCT	p.P294P		NM_002234	NP_002225	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related	294						Golgi apparatus|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(2)|breast(2)	4														0.214286	6.619265	7.673277	3	11	KEEP	---	---	---	---	capture		Silent	SNP	5154195	5154195	8311	12	C	T	T	T	288	23	KCNA5	1	1
KRT5	3852	broad.mit.edu	37	12	52910607	52910607	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52910607T>A	uc001san.2	-	c.1253A>T	c.(1252-1254)GAG>GTG	p.E418V	KRT5_uc009zmh.2_Missense_Mutation_p.E418V	NM_000424	NP_000415	P13647	K2C5_HUMAN	keratin 5	418	Rod.|Coil 2.		E -> K (in K-EBS).		epidermis development|hemidesmosome assembly	cytosol|keratin filament	protein binding|structural constituent of cytoskeleton				0				BRCA - Breast invasive adenocarcinoma(357;0.189)										0.208333	40.480196	48.022045	20	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52910607	52910607	8794	12	T	A	A	A	702	54	KRT5	3	3
KRT71	112802	broad.mit.edu	37	12	52946657	52946657	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52946657A>G	uc001sao.2	-	c.205T>C	c.(205-207)TAT>CAT	p.Y69H		NM_033448	NP_258259	Q3SY84	K2C71_HUMAN	keratin 71	69	Head.|Gly-rich.						structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.194)										0.1	5.93214	15.497767	6	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52946657	52946657	8799	12	A	G	G	G	195	15	KRT71	4	4
KRT72	140807	broad.mit.edu	37	12	52992774	52992774	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52992774C>A	uc001sar.2	-	c.549G>T	c.(547-549)CTG>CTT	p.L183L	KRT72_uc001saq.2_Silent_p.L183L|KRT72_uc010sns.1_Silent_p.L183L|KRT72_uc010snt.1_5'UTR	NM_001146225	NP_001139697	Q14CN4	K2C72_HUMAN	keratin 72 isoform 1	183	Coil 1B.|Rod.					keratin filament	structural molecule activity			ovary(5)|pancreas(1)	6				BRCA - Breast invasive adenocarcinoma(357;0.195)										0.052023	-18.771936	17.948384	9	164	KEEP	---	---	---	---	capture		Silent	SNP	52992774	52992774	8800	12	C	A	A	A	314	25	KRT72	2	2
HOXC8	3224	broad.mit.edu	37	12	54403118	54403118	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54403118A>T	uc001ser.2	+	c.50A>T	c.(49-51)GAG>GTG	p.E17V		NM_022658	NP_073149	P31273	HXC8_HUMAN	homeobox C8	17						nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						GBM(197;701 2226 7002 18822 41696)								0.176166	59.527498	78.631941	34	159	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54403118	54403118	7608	12	A	T	T	T	143	11	HOXC8	3	3
PTPRB	5787	broad.mit.edu	37	12	70963527	70963527	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:70963527C>A	uc001swc.3	-	c.3562G>T	c.(3562-3564)GAG>TAG	p.E1188*	PTPRB_uc001swb.3_Nonsense_Mutation_p.E970*|PTPRB_uc010sto.1_Nonsense_Mutation_p.E970*|PTPRB_uc010stp.1_Nonsense_Mutation_p.E880*|PTPRB_uc001swa.3_Nonsense_Mutation_p.E1100*|PTPRB_uc001swd.3_Nonsense_Mutation_p.E1187*|PTPRB_uc009zrr.1_Nonsense_Mutation_p.E1067*	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	970	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)											0.246154	31.971507	35.787314	16	49	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	70963527	70963527	13253	12	C	A	A	A	390	30	PTPRB	5	2
PTPRB	5787	broad.mit.edu	37	12	71002929	71002929	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:71002929A>G	uc001swc.3	-	c.899T>C	c.(898-900)CTT>CCT	p.L300P	PTPRB_uc001swb.3_Missense_Mutation_p.L82P|PTPRB_uc010sto.1_Missense_Mutation_p.L82P|PTPRB_uc010stp.1_Missense_Mutation_p.L82P|PTPRB_uc001swa.3_Missense_Mutation_p.L300P|PTPRB_uc001swd.3_Missense_Mutation_p.L299P|PTPRB_uc009zrr.1_Missense_Mutation_p.L179P|PTPRB_uc001swe.2_Missense_Mutation_p.L300P	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	82	Fibronectin type-III 1.|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)											0.274194	51.749276	54.596019	17	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71002929	71002929	13253	12	A	G	G	G	39	3	PTPRB	4	4
TPH2	121278	broad.mit.edu	37	12	72372742	72372742	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:72372742C>T	uc009zrw.1	+	c.816C>T	c.(814-816)GGC>GGT	p.G272G	TPH2_uc001swy.2_Silent_p.G182G	NM_173353	NP_775489	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	272					aromatic amino acid family metabolic process|hormone biosynthetic process|oxidation-reduction process|serotonin biosynthetic process	cytosol	amino acid binding|iron ion binding|tryptophan 5-monooxygenase activity			ovary(2)|central_nervous_system(1)	3					L-Tryptophan(DB00150)									0.071429	-5.266131	21.236576	10	130	KEEP	---	---	---	---	capture		Silent	SNP	72372742	72372742	16946	12	C	T	T	T	353	28	TPH2	2	2
NAV3	89795	broad.mit.edu	37	12	78392159	78392159	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:78392159C>A	uc001syp.2	+	c.783C>A	c.(781-783)AGC>AGA	p.S261R	NAV3_uc001syo.2_Missense_Mutation_p.S261R	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN	neuron navigator 3	261						nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity			large_intestine(6)|ovary(5)|lung(2)|breast(1)|kidney(1)|pancreas(1)	16										1091				0.206897	13.034356	15.343508	6	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78392159	78392159	10581	12	C	A	A	A	324	25	NAV3	2	2
PAWR	5074	broad.mit.edu	37	12	79986434	79986434	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:79986434G>A	uc001syx.2	-	c.976C>T	c.(976-978)CAG>TAG	p.Q326*		NM_002583	NP_002574	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	326	Leucine-zipper.				actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity				0										121				0.2	11.933681	14.444891	6	24	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	79986434	79986434	11897	12	G	A	A	A	598	46	PAWR	5	2
SLC2A3	6515	broad.mit.edu	37	12	8085593	8085593	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:8085593G>T	uc001qtr.2	-	c.259C>A	c.(259-261)CGC>AGC	p.R87S	SLC2A3_uc001qts.2_Missense_Mutation_p.R87S	NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose	87	Cytoplasmic (Potential).				carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity	p.R87C(1)		ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		Colon(96;424 1461 14416 20933 23688)						OREG0021656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.142857	8.55399	12.853969	5	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8085593	8085593	15042	12	G	T	T	T	507	39	SLC2A3	1	1
PPFIA2	8499	broad.mit.edu	37	12	81839380	81839380	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:81839380C>A	uc001szo.1	-	c.525G>T	c.(523-525)AAG>AAT	p.K175N	PPFIA2_uc010sue.1_Missense_Mutation_p.K75N|PPFIA2_uc010sug.1_Non-coding_Transcript|PPFIA2_uc010suh.1_Non-coding_Transcript|PPFIA2_uc010sui.1_Non-coding_Transcript|PPFIA2_uc010suj.1_Non-coding_Transcript|PPFIA2_uc009zsi.1_Non-coding_Transcript	NM_003625	NP_003616	O75334	LIPA2_HUMAN	PTPRF interacting protein alpha 2	175	Glu-rich.				cell-matrix adhesion	cell surface|cytoplasm	protein binding			ovary(3)|lung(2)|pancreas(1)	6														0.166667	23.922472	32.14455	13	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81839380	81839380	12740	12	C	A	A	A	311	24	PPFIA2	2	2
TMTC3	160418	broad.mit.edu	37	12	88542250	88542250	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:88542250A>C	uc001tau.2	+	c.158A>C	c.(157-159)CAA>CCA	p.Q53P	TMTC3_uc009zsm.2_Non-coding_Transcript	NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat	53						integral to membrane	binding				0														0.304348	22.320528	23.103664	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88542250	88542250	16803	12	A	C	C	C	65	5	TMTC3	4	4
PZP	5858	broad.mit.edu	37	12	9311070	9311070	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:9311070C>A	uc001qvl.2	-	c.3240G>T	c.(3238-3240)CAG>CAT	p.Q1080H	PZP_uc009zgl.2_Missense_Mutation_p.Q866H	NM_002864	NP_002855			pregnancy-zone protein precursor											ovary(3)|large_intestine(1)	4						Melanoma(125;1402 1695 4685 34487 38571)								0.444444	173.473813	173.837972	60	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9311070	9311070	13327	12	C	A	A	A	415	32	PZP	2	2
ANKS1B	56899	broad.mit.edu	37	12	99837588	99837588	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:99837588C>A	uc001tge.1	-	c.1439_splice	c.e11-1	p.D480_splice	ANKS1B_uc001tgf.1_Splice_Site_SNP_p.D60_splice|ANKS1B_uc009ztt.1_Splice_Site_SNP_p.D446_splice	NM_152788	NP_690001			cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)										0.27	63.362186	68.149869	27	73	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	99837588	99837588	697	12	C	A	A	A	416	32	ANKS1B	5	2
FGF14	2259	broad.mit.edu	37	13	103053860	103053860	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:103053860G>A	uc001vpf.2	-	c.169C>T	c.(169-171)CTT>TTT	p.L57F		NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B	Error:Variant_position_missing_in_Q92915_after_alignment					cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			large_intestine(1)|ovary(1)	2	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.442857	94.409378	94.609236	31	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103053860	103053860	6080	13	G	A	A	A	429	33	FGF14	2	2
FGF14	2259	broad.mit.edu	37	13	103053862	103053862	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:103053862C>A	uc001vpf.2	-	c.167G>T	c.(166-168)TGT>TTT	p.C56F		NM_175929	NP_787125	Q92915	FGF14_HUMAN	fibroblast growth factor 14 isoform 1B	Error:Variant_position_missing_in_Q92915_after_alignment					cell death|cell-cell signaling|JNK cascade|nervous system development|signal transduction	nucleus	growth factor activity|heparin binding			large_intestine(1)|ovary(1)	2	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.444444	96.97349	97.168742	32	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103053862	103053862	6080	13	C	A	A	A	221	17	FGF14	2	2
COL4A2	1284	broad.mit.edu	37	13	111158940	111158940	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:111158940C>T	uc001vqx.2	+	c.4581C>T	c.(4579-4581)CAC>CAT	p.H1527H		NM_001846	NP_001837	P08572	CO4A2_HUMAN	alpha 2 type IV collagen preproprotein	1527	Collagen IV NC1.				angiogenesis|axon guidance|extracellular matrix organization|negative regulation of angiogenesis	collagen type IV	extracellular matrix structural constituent|protein binding			central_nervous_system(2)|ovary(1)	3	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)											0.272727	7.819885	8.332181	3	8	KEEP	---	---	---	---	capture		Silent	SNP	111158940	111158940	3828	13	C	T	T	T	220	17	COL4A2	2	2
SKA3	221150	broad.mit.edu	37	13	21742230	21742230	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:21742230C>T	uc001unt.2	-	c.640G>A	c.(640-642)GAG>AAG	p.E214K	SKA3_uc001unv.2_Missense_Mutation_p.E132K|SKA3_uc001unu.2_Missense_Mutation_p.E214K	NM_145061	NP_659498	Q8IX90	SKA3_HUMAN	SKA3	214					cell division|chromosome segregation|mitosis|regulation of microtubule polymerization or depolymerization	condensed chromosome outer kinetochore|cytoplasm|spindle microtubule	protein binding				0														0.2	18.175826	21.525005	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21742230	21742230	14849	13	C	T	T	T	377	29	SKA3	2	2
SACS	26278	broad.mit.edu	37	13	23909957	23909957	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:23909957C>A	uc001uon.2	-	c.8058G>T	c.(8056-8058)CTG>CTT	p.L2686L	SACS_uc001uoo.2_Silent_p.L2539L|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	2686					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)|skin(1)	11		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)						738				0.25	18.410854	20.001984	7	21	KEEP	---	---	---	---	capture		Silent	SNP	23909957	23909957	14284	13	C	A	A	A	262	21	SACS	2	2
FAM123A	219287	broad.mit.edu	37	13	25744599	25744599	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25744599C>G	uc001uqb.2	-	c.1159G>C	c.(1159-1161)GAC>CAC	p.D387H	FAM123A_uc001uqa.2_Missense_Mutation_p.D268H|FAM123A_uc001uqc.2_Missense_Mutation_p.D268H	NM_152704	NP_689917	Q8N7J2	F123A_HUMAN	hypothetical protein LOC219287 isoform 1	387										ovary(2)|large_intestine(1)|lung(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.365854	43.698875	44.353347	15	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25744599	25744599	5619	13	C	G	G	G	416	32	FAM123A	3	3
MTUS2	23281	broad.mit.edu	37	13	29599885	29599885	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:29599885G>C	uc001usl.3	+	c.1080G>C	c.(1078-1080)GGG>GGC	p.G360G		NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN	hypothetical protein LOC23281 isoform a	350						cytoplasm|microtubule	microtubule binding|protein homodimerization activity				0										344				0.5	82.742135	82.742135	30	30	KEEP	---	---	---	---	capture		Silent	SNP	29599885	29599885	10359	13	G	C	C	C	548	43	MTUS2	3	3
PDS5B	23047	broad.mit.edu	37	13	33347329	33347329	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:33347329G>T	uc010abf.2	+	c.4175G>T	c.(4174-4176)CGT>CTT	p.R1392L	PDS5B_uc010abg.2_Intron	NM_015032	NP_055847	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog	1392					cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation	chromatin|nucleus	ATP binding|DNA binding|identical protein binding			ovary(2)|lung(1)|pancreas(1)	4		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)										0.515152	115.072129	115.08653	34	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33347329	33347329	12113	13	G	T	T	T	520	40	PDS5B	1	1
POSTN	10631	broad.mit.edu	37	13	38143443	38143443	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:38143443G>C	uc001uwo.3	-	c.2425C>G	c.(2425-2427)CAG>GAG	p.Q809E	POSTN_uc010tet.1_Missense_Mutation_p.Q310E|POSTN_uc001uwp.3_Missense_Mutation_p.Q752E|POSTN_uc001uwr.2_Intron|POSTN_uc001uwq.2_Intron|POSTN_uc010teu.1_Missense_Mutation_p.Q782E|POSTN_uc010tev.1_Missense_Mutation_p.Q722E|POSTN_uc010tew.1_Intron	NM_006475	NP_006466	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor isoform 1	809					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)										0.208333	13.661308	15.552014	5	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38143443	38143443	12688	13	G	C	C	C	585	45	POSTN	3	3
ENOX1	55068	broad.mit.edu	37	13	43798206	43798206	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:43798206G>A	uc001uza.3	-	c.1783C>T	c.(1783-1785)CAG>TAG	p.Q595*	ENOX1_uc001uzb.3_Nonsense_Mutation_p.Q595*|ENOX1_uc001uzc.3_Nonsense_Mutation_p.Q595*|ENOX1_uc001uyz.3_Nonsense_Mutation_p.Q204*	NM_001127615	NP_001121087	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	595					electron transport chain|rhythmic process|transport	extracellular space|plasma membrane	nucleic acid binding|nucleotide binding|oxidoreductase activity			pancreas(1)	1		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)										0.275862	19.08743	20.399411	8	21	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43798206	43798206	5319	13	G	A	A	A	598	46	ENOX1	5	2
C13orf18	80183	broad.mit.edu	37	13	46946391	46946391	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:46946391C>A	uc010acl.2	-	c.220G>T	c.(220-222)GGG>TGG	p.G74W	C13orf18_uc001vbf.3_Intron|C13orf18_uc001vbg.3_De_novo_Start_OutOfFrame|C13orf18_uc010tfz.1_Intron|C13orf18_uc010acm.2_Intron|C13orf18_uc010acn.2_Intron|C13orf18_uc001vbe.3_Missense_Mutation_p.G74W|C13orf18_uc001vbh.3_Missense_Mutation_p.G74W|C13orf18_uc001vbi.3_Intron|C13orf18_uc010aco.1_Missense_Mutation_p.G74W|C13orf18_uc010tga.1_Intron	NM_025113	NP_079389	Q9H714	CM018_HUMAN	hypothetical protein LOC80183	74											0		Lung NSC(96;2.31e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;2.19e-05)										0.444444	95.585975	95.780225	32	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46946391	46946391	1767	13	C	A	A	A	312	24	C13orf18	2	2
KLHL1	57626	broad.mit.edu	37	13	70456616	70456616	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:70456616C>A	uc001vip.2	-	c.1026G>T	c.(1024-1026)ATG>ATT	p.M342I	KLHL1_uc010thm.1_Missense_Mutation_p.M281I	NM_020866	NP_065917	Q9NR64	KLHL1_HUMAN	kelch-like 1 protein	342					actin cytoskeleton organization	cytoplasm|cytoskeleton	actin binding				0		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)										0.258065	20.600047	22.234922	8	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70456616	70456616	8677	13	C	A	A	A	273	21	KLHL1	2	2
DIO3	1735	broad.mit.edu	37	14	102028308	102028308	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:102028308C>T	uc010txq.1	+	c.397C>T	c.(397-399)CGC>TGC	p.R133C	DIO3OS_uc001ykd.1_5'Flank|MIR1247_hsa-mir-1247|MI0006382_5'Flank	NM_001362	NP_001353	P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	133	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|oxidation-reduction process	endosome membrane|integral to membrane|plasma membrane	thyroxine 5'-deiodinase activity|thyroxine 5-deiodinase activity			ovary(1)|central_nervous_system(1)	2		all_neural(303;0.185)												0.277778	27.840346	29.436258	10	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102028308	102028308	4705	14	C	T	T	T	299	23	DIO3	1	1
TRAF3	7187	broad.mit.edu	37	14	103369718	103369718	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:103369718G>A	uc001ymc.1	+	c.1087G>A	c.(1087-1089)GAG>AAG	p.E363K	TRAF3_uc001yme.1_Missense_Mutation_p.E338K|TRAF3_uc001ymd.1_Missense_Mutation_p.E363K|TRAF3_uc010txy.1_Missense_Mutation_p.E280K|TRAF3_uc001ymf.1_Missense_Mutation_p.E96K	NM_145725	NP_663777	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3 isoform 1	363					apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway	CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion	signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding				0		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)										0.217391	21.32323	24.713114	10	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103369718	103369718	16983	14	G	A	A	A	481	37	TRAF3	1	1
POTEG	404785	broad.mit.edu	37	14	19563492	19563492	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:19563492C>G	uc001vuz.1	+	c.1006C>G	c.(1006-1008)CTA>GTA	p.L336V	POTEG_uc001vva.1_Non-coding_Transcript|POTEG_uc010ahc.1_Non-coding_Transcript	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	336										ovary(1)	1														0.074236	0.184028	42.817485	17	212	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19563492	19563492	12696	14	C	G	G	G	415	32	POTEG	3	3
OR4K2	390431	broad.mit.edu	37	14	20344724	20344724	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20344724C>A	uc001vwh.1	+	c.298C>A	c.(298-300)CAG>AAG	p.Q100K		NM_001005501	NP_001005501	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K,	100	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.097561	14.158175	54.018888	24	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20344724	20344724	11482	14	C	A	A	A	273	21	OR4K2	2	2
OR4K5	79317	broad.mit.edu	37	14	20388794	20388794	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20388794C>A	uc010tkw.1	+	c.29C>A	c.(28-30)TCT>TAT	p.S10Y		NM_001005483	NP_001005483	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K,	10	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)										0.061538	-18.856526	20.30677	12	183	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20388794	20388794	11483	14	C	A	A	A	416	32	OR4K5	2	2
OR4K1	79544	broad.mit.edu	37	14	20404030	20404030	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:20404030A>G	uc001vwj.1	+	c.205A>G	c.(205-207)ATT>GTT	p.I69V		NM_001004063	NP_001004063	Q8NGD4	OR4K1_HUMAN	olfactory receptor, family 4, subfamily K,	69	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00124)										0.070833	-11.128502	34.540619	17	223	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20404030	20404030	11477	14	A	G	G	G	104	8	OR4K1	4	4
RNASE9	390443	broad.mit.edu	37	14	21024699	21024699	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21024699C>T	uc001vxq.3	-	c.545G>A	c.(544-546)CGT>CAT	p.R182H	RNASE9_uc010aho.2_Missense_Mutation_p.R177H|RNASE9_uc010ahp.2_Missense_Mutation_p.R182H|RNASE9_uc010ahq.2_Missense_Mutation_p.R182H|RNASE9_uc010ahr.2_Missense_Mutation_p.R182H|RNASE9_uc010ahs.2_Missense_Mutation_p.R177H|RNASE9_uc010aht.2_Missense_Mutation_p.R177H|RNASE9_uc010ahu.2_Missense_Mutation_p.R177H	NM_001110361	NP_001103831	P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)	177						extracellular region	nucleic acid binding|pancreatic ribonuclease activity			ovary(2)	2	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)										0.093023	2.472532	9.631663	4	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21024699	21024699	13887	14	C	T	T	T	247	19	RNASE9	1	1
CHD8	57680	broad.mit.edu	37	14	21868194	21868194	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:21868194C>T	uc001was.1	-	c.3926G>A	c.(3925-3927)AGG>AAG	p.R1309K	CHD8_uc001war.1_Missense_Mutation_p.R1205K|SNORD8_uc001wau.1_5'Flank	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1588					ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|chromatin assembly or disassembly|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	chromatin|MLL1 complex	ATP binding|beta-catenin binding|chromatin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding|transcription activator activity|transcription repressor activity			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)						886				0.132022	75.485008	122.312299	47	309	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21868194	21868194	3465	14	C	T	T	T	312	24	CHD8	2	2
PABPN1	8106	broad.mit.edu	37	14	23792260	23792260	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23792260C>T	uc001wjh.3	+	c.600C>T	c.(598-600)TCC>TCT	p.S200S	PABPN1_uc001wjj.2_Silent_p.S173S|PABPN1_uc001wjk.2_Silent_p.S173S	NM_004643	NP_004634	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1	173	Necessary for homooligomerization.|RRM.				modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)						17				0.042553	-13.383836	7.731481	4	90	KEEP	---	---	---	---	capture		Silent	SNP	23792260	23792260	11784	14	C	T	T	T	262	21	PABPN1	2	2
NFATC4	4776	broad.mit.edu	37	14	24846005	24846005	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24846005G>A	uc010tol.1	+	c.2751G>A	c.(2749-2751)CCG>CCA	p.P917P	NFATC4_uc010tok.1_Silent_p.P917P|NFATC4_uc010alr.2_Intron|NFATC4_uc010tom.1_Silent_p.P867P|NFATC4_uc010ton.1_Silent_p.P867P|NFATC4_uc010too.1_Intron|NFATC4_uc010alt.2_Silent_p.P886P|NFATC4_uc010top.1_Silent_p.P886P|NFATC4_uc010toq.1_Intron|NFATC4_uc001wpc.2_Silent_p.P854P|NFATC4_uc010tor.1_Intron|NFATC4_uc010tos.1_Silent_p.P784P|NFATC4_uc010tot.1_Silent_p.P842P|NFATC4_uc010tou.1_Silent_p.P784P|NFATC4_uc010tov.1_Intron|NFATC4_uc010tow.1_Intron|NFATC4_uc010alv.2_Silent_p.P842P|NFATC4_uc010tox.1_Silent_p.P784P|NFATC4_uc001wpd.2_Silent_p.P389P|NFATC4_uc010toy.1_Intron|NFATC4_uc010toz.1_Silent_p.P389P|NFATC4_uc010tpa.1_Silent_p.P142P|NFATC4_uc010tpb.1_Silent_p.P142P	NM_004554	NP_004545	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells,	854					cell differentiation|inflammatory response|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|intermediate filament cytoskeleton|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(1)|central_nervous_system(1)	2				GBM - Glioblastoma multiforme(265;0.018)										0.1875	13.832211	16.757568	6	26	KEEP	---	---	---	---	capture		Silent	SNP	24846005	24846005	10765	14	G	A	A	A	496	39	NFATC4	1	1
RALGAPA1	253959	broad.mit.edu	37	14	36192258	36192258	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:36192258C>A	uc001wtj.2	-	c.2079G>T	c.(2077-2079)CAG>CAT	p.Q693H	RALGAPA1_uc001wti.2_Missense_Mutation_p.Q693H|RALGAPA1_uc010tpv.1_Missense_Mutation_p.Q693H|RALGAPA1_uc010tpw.1_Missense_Mutation_p.Q693H|RALGAPA1_uc001wtk.1_Missense_Mutation_p.Q544H	NM_194301	NP_919277	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1	693					activation of Ral GTPase activity|signal transduction	cytosol|mitochondrion|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(3)|breast(1)	4														0.245283	31.349114	34.480981	13	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36192258	36192258	13473	14	C	A	A	A	415	32	RALGAPA1	2	2
MBIP	51562	broad.mit.edu	37	14	36785985	36785985	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:36785985T>C	uc001wtm.2	-	c.163A>G	c.(163-165)ATC>GTC	p.I55V	MBIP_uc001wto.2_Missense_Mutation_p.I55V|MBIP_uc010tpy.1_5'UTR|MBIP_uc001wtn.2_Missense_Mutation_p.I55V	NM_016586	NP_057670	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1 isoform 1	55					histone H3 acetylation|inactivation of MAPK activity involved in osmosensory signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytoplasm|nucleolus	identical protein binding|protein kinase inhibitor activity				0	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)						91				0.226667	40.633998	45.782496	17	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36785985	36785985	9737	14	T	C	C	C	676	52	MBIP	4	4
LRFN5	145581	broad.mit.edu	37	14	42356551	42356551	+	Silent	SNP	C	A	A	rs17854265		TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:42356551C>A	uc001wvm.2	+	c.723C>A	c.(721-723)CCC>CCA	p.P241P	LRFN5_uc010ana.2_Silent_p.P241P	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III	241	Extracellular (Potential).|LRRCT.					integral to membrane				ovary(5)|pancreas(2)|central_nervous_system(1)	8			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)										0.097826	5.11318	20.014018	9	83	KEEP	---	---	---	---	capture		Silent	SNP	42356551	42356551	9314	14	C	A	A	A	301	24	LRFN5	2	2
FAM179B	23116	broad.mit.edu	37	14	45481232	45481232	+	Silent	SNP	T	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45481232T>G	uc001wvw.2	+	c.3192T>G	c.(3190-3192)TCT>TCG	p.S1064S	FAM179B_uc001wvv.2_Silent_p.S1064S|FAM179B_uc010anc.2_Non-coding_Transcript	NM_015091	NP_055906	Q9Y4F4	F179B_HUMAN	hypothetical protein LOC23116	1064	Ser-rich.						binding				0														0.107143	6.40521	14.992491	6	50	KEEP	---	---	---	---	capture		Silent	SNP	45481232	45481232	5712	14	T	G	G	G	704	55	FAM179B	4	4
C14orf106	55320	broad.mit.edu	37	14	45696990	45696990	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:45696990G>A	uc001wwf.2	-	c.1622C>T	c.(1621-1623)TCA>TTA	p.S541L	C14orf106_uc010anh.2_Non-coding_Transcript	NM_018353	NP_060823	Q6P0N0	M18BP_HUMAN	chromosome 14 open reading frame 106	541					cell division|CenH3-containing nucleosome assembly at centromere|mitosis	chromosome, centromeric region|nucleoplasm	DNA binding				0						Ovarian(187;620 2054 7273 12043 20532)								0.264706	23.15972	24.861121	9	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	45696990	45696990	1786	14	G	A	A	A	585	45	C14orf106	2	2
SYT16	83851	broad.mit.edu	37	14	62541877	62541877	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:62541877G>T	uc001xfu.1	+	c.761G>T	c.(760-762)CGT>CTT	p.R254L	SYT16_uc010tsd.1_Missense_Mutation_p.R254L	NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	254										central_nervous_system(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)										0.085106	2.348845	18.742014	8	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62541877	62541877	15993	14	G	T	T	T	520	40	SYT16	1	1
KCNH5	27133	broad.mit.edu	37	14	63447944	63447944	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63447944T>A	uc001xfx.2	-	c.588A>T	c.(586-588)AAA>AAT	p.K196N	KCNH5_uc001xfy.2_Missense_Mutation_p.K196N|KCNH5_uc001xfz.1_Missense_Mutation_p.K138N|KCNH5_uc001xga.2_Missense_Mutation_p.K138N	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	196	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)										0.166667	32.312251	43.056938	17	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63447944	63447944	8340	14	T	A	A	A	777	60	KCNH5	3	3
SYNE2	23224	broad.mit.edu	37	14	64469443	64469443	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64469443C>T	uc001xgl.2	+	c.3792C>T	c.(3790-3792)ATC>ATT	p.I1264I	SYNE2_uc001xgm.2_Silent_p.I1264I	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1264	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.265823	53.236373	57.15305	21	58	KEEP	---	---	---	---	capture		Silent	SNP	64469443	64469443	15967	14	C	T	T	T	382	30	SYNE2	2	2
DPF3	8110	broad.mit.edu	37	14	73140967	73140967	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:73140967G>A	uc001xnc.2	-	c.852C>T	c.(850-852)TGC>TGT	p.C284C	DPF3_uc001xnd.1_Non-coding_Transcript|DPF3_uc001xnf.2_Non-coding_Transcript|DPF3_uc010ari.1_Silent_p.C284C|DPF3_uc010ttq.1_Silent_p.C294C	NM_012074	NP_036206	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	284	PHD-type 1.				chromatin modification|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nBAF complex	nucleic acid binding|zinc ion binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)										0.322581	27.340899	28.206451	10	21	KEEP	---	---	---	---	capture		Silent	SNP	73140967	73140967	4902	14	G	A	A	A	490	38	DPF3	1	1
GPR65	8477	broad.mit.edu	37	14	88477441	88477441	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:88477441C>A	uc001xvv.2	+	c.250C>A	c.(250-252)CCT>ACT	p.P84T		NM_003608	NP_003599	Q8IYL9	PSYR_HUMAN	G protein-coupled receptor 65	84	Extracellular (Potential).				actin cytoskeleton reorganization|activation of Rho GTPase activity|apoptosis|immune response|multicellular organismal development|positive regulation of cAMP biosynthetic process|positive regulation of stress fiber assembly|response to acidity	integral to plasma membrane	G-protein coupled receptor activity				0														0.322368	129.916705	134.17817	49	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88477441	88477441	6981	14	C	A	A	A	390	30	GPR65	2	2
GOLGA5	9950	broad.mit.edu	37	14	93299472	93299472	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:93299472C>T	uc001yaz.1	+	c.1725C>T	c.(1723-1725)ACC>ACT	p.T575T	GOLGA5_uc001yba.1_5'UTR	NM_005113	NP_005104	Q8TBA6	GOGA5_HUMAN	Golgi autoantigen, golgin subfamily a, 5	575	Cytoplasmic (Potential).|Potential.				Golgi organization|protein phosphorylation	cis-Golgi network|integral to membrane	ATP binding|protein homodimerization activity|protein tyrosine kinase activity|Rab GTPase binding			ovary(2)|lung(1)	3		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)						351				0.091503	6.738787	32.460568	14	139	KEEP	---	---	---	---	capture		Silent	SNP	93299472	93299472	6825	14	C	T	T	T	262	21	GOLGA5	2	2
KIAA1409	57578	broad.mit.edu	37	14	94156521	94156521	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94156521G>T	uc001ybv.1	+	c.6796G>T	c.(6796-6798)GGT>TGT	p.G2266C	KIAA1409_uc001ybs.1_Missense_Mutation_p.G2244C	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	2421						integral to membrane				ovary(10)|large_intestine(3)	13		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)						1186				0.159664	32.651321	45.785176	19	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94156521	94156521	8539	14	G	T	T	T	559	43	KIAA1409	2	2
DDX24	57062	broad.mit.edu	37	14	94517574	94517574	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94517574T>C	uc001ycj.2	-	c.2543A>G	c.(2542-2544)CAG>CGG	p.Q848R	DDX24_uc010twq.1_Missense_Mutation_p.Q805R|DDX24_uc010twr.1_Missense_Mutation_p.Q598R	NM_020414	NP_065147	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	848					RNA metabolic process	cytoplasm|nucleolus|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding			ovary(2)|kidney(1)|skin(1)	4		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)								OREG0022891	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.233333	37.71576	43.702799	21	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94517574	94517574	4522	14	T	C	C	C	715	55	DDX24	4	4
LRRK1	79705	broad.mit.edu	37	15	101552319	101552319	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:101552319A>G	uc002bwr.2	+	c.1388A>G	c.(1387-1389)AAA>AGA	p.K463R	LRRK1_uc010usb.1_Non-coding_Transcript|LRRK1_uc010usc.1_Non-coding_Transcript	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	463	LRR 8.				protein phosphorylation|small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)							1100				0.166667	38.912822	49.655073	17	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101552319	101552319	9408	15	A	G	G	G	13	1	LRRK1	4	4
MKRN3	7681	broad.mit.edu	37	15	23811059	23811059	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:23811059C>G	uc001ywh.3	+	c.130C>G	c.(130-132)CCA>GCA	p.P44A	MKRN3_uc001ywi.2_Missense_Mutation_p.P44A|MKRN3_uc010ayi.1_Missense_Mutation_p.P44A	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	44						ribonucleoprotein complex	ligase activity|nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(2)	4		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)						79				0.294118	14.377882	15.017183	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23811059	23811059	9998	15	C	G	G	G	390	30	MKRN3	3	3
C15orf2	23742	broad.mit.edu	37	15	24922540	24922540	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24922540C>A	uc001ywo.2	+	c.1526C>A	c.(1525-1527)CCT>CAT	p.P509H		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	509	Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)						443				0.196875	134.431193	161.834183	63	257	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24922540	24922540	1834	15	C	A	A	A	312	24	C15orf2	2	2
C15orf2	23742	broad.mit.edu	37	15	24923778	24923778	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24923778C>G	uc001ywo.2	+	c.2764C>G	c.(2764-2766)CCA>GCA	p.P922A		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	922					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)						443				0.116667	9.183122	17.85602	7	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24923778	24923778	1834	15	C	G	G	G	286	22	C15orf2	3	3
ZFP106	64397	broad.mit.edu	37	15	42742934	42742934	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42742934G>C	uc001zpw.2	-	c.1467C>G	c.(1465-1467)CCC>CCG	p.P489P	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Silent_p.P272P|ZFP106_uc001zpy.1_Silent_p.P512P	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	489						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)										0.347561	156.265855	159.610949	57	107	KEEP	---	---	---	---	capture		Silent	SNP	42742934	42742934	18225	15	G	C	C	C	444	35	ZFP106	3	3
ATP8B4	79895	broad.mit.edu	37	15	50303041	50303041	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:50303041C>A	uc001zxu.2	-	c.435_splice	c.e7+1	p.A145_splice	ATP8B4_uc010ber.2_Splice_Site_SNP_p.A18_splice|ATP8B4_uc010ufd.1_Splice_Site_SNP_p.A18_splice|ATP8B4_uc010ufe.1_Splice_Site_SNP	NM_024837	NP_079113			ATPase class I type 8B member 4						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|breast(2)|large_intestine(1)	5		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)										0.230769	7.017336	7.881788	3	10	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	50303041	50303041	1216	15	C	A	A	A	221	17	ATP8B4	5	2
TNFAIP8L3	388121	broad.mit.edu	37	15	51350531	51350531	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:51350531G>T	uc001zyy.2	-	c.426C>A	c.(424-426)AGC>AGA	p.S142R		NM_207381	NP_997264	Q5GJ75	TP8L3_HUMAN	tumor necrosis factor, alpha-induced protein	142											0				all cancers(107;0.000389)|GBM - Glioblastoma multiforme(94;0.00338)										0.487179	121.049084	121.060144	38	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51350531	51350531	16820	15	G	T	T	T	490	38	TNFAIP8L3	1	1
IGDCC3	9543	broad.mit.edu	37	15	65667452	65667452	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:65667452G>T	uc002aos.2	-	c.392C>A	c.(391-393)GCT>GAT	p.A131D		NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	131	Extracellular (Potential).|Ig-like C2-type 1.									ovary(3)	3														0.1	2.128124	6.900707	3	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65667452	65667452	7869	15	G	T	T	T	442	34	IGDCC3	2	2
FEM1B	10116	broad.mit.edu	37	15	68570886	68570886	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:68570886G>T	uc002arg.2	+	c.131G>T	c.(130-132)GGG>GTG	p.G44V		NM_015322	NP_056137	Q9UK73	FEM1B_HUMAN	fem-1 homolog b	44					apoptosis|induction of apoptosis|regulation of DNA damage checkpoint|regulation of ubiquitin-protein ligase activity	cytoplasm|nucleus	death receptor binding|ubiquitin-protein ligase activity				0														0.277778	24.337793	25.93564	10	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68570886	68570886	6047	15	G	T	T	T	559	43	FEM1B	2	2
STOML1	9399	broad.mit.edu	37	15	74284508	74284508	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:74284508C>A	uc002awe.2	-	c.57G>T	c.(55-57)CAG>CAT	p.Q19H	PML_uc002awm.2_5'Flank|PML_uc002awl.2_5'Flank|PML_uc002awj.1_5'Flank|PML_uc002awk.2_5'Flank|PML_uc002awn.2_5'Flank|PML_uc002awo.2_5'Flank|PML_uc002awp.2_5'Flank|PML_uc002awq.2_5'Flank|PML_uc002awr.2_5'Flank|PML_uc002aws.2_5'Flank|PML_uc002awt.2_5'Flank|PML_uc002awu.2_5'Flank|PML_uc002awv.2_5'Flank|PML_uc010ule.1_5'Flank|STOML1_uc002awf.2_Missense_Mutation_p.Q19H|STOML1_uc010bje.2_Missense_Mutation_p.Q19H|STOML1_uc010uld.1_5'UTR|STOML1_uc002awh.2_Missense_Mutation_p.Q19H|STOML1_uc002awg.2_Missense_Mutation_p.Q19H|STOML1_uc002awi.2_Intron	NM_004809	NP_004800	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	19						integral to membrane	sterol binding				0														0.157895	5.51281	7.63316	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74284508	74284508	15833	15	C	A	A	A	363	28	STOML1	2	2
ARNT2	9915	broad.mit.edu	37	15	80750269	80750269	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:80750269G>C	uc002bfr.2	+	c.147_splice	c.e3-1	p.G49_splice	ARNT2_uc002bfq.2_Splice_Site_SNP_p.G49_splice|ARNT2_uc010unm.1_Splice_Site_SNP_p.G38_splice|ARNT2_uc002bfs.2_Splice_Site_SNP_p.G38_splice	NM_014862	NP_055677			aryl hydrocarbon receptor nuclear translocator						central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)											0.166667	16.597904	21.022206	7	35	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	80750269	80750269	984	15	G	C	C	C	429	33	ARNT2	5	3
BNC1	646	broad.mit.edu	37	15	83933374	83933374	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83933374C>T	uc002bjt.1	-	c.629G>A	c.(628-630)AGC>AAC	p.S210N	BNC1_uc010uos.1_Missense_Mutation_p.S198N	NM_001717	NP_001708	Q01954	BNC1_HUMAN	basonuclin 1	210					epidermis development|positive regulation of cell proliferation|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3														0.211111	42.874874	49.822358	19	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83933374	83933374	1499	15	C	T	T	T	364	28	BNC1	2	2
AKAP13	11214	broad.mit.edu	37	15	86228000	86228000	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:86228000C>T	uc002blu.1	+	c.5197C>T	c.(5197-5199)CCA>TCA	p.P1733S	AKAP13_uc002blt.1_Missense_Mutation_p.P1711S|AKAP13_uc002blv.1_Missense_Mutation_p.P1729S|AKAP13_uc010bnf.1_Missense_Mutation_p.P351S|AKAP13_uc002blw.1_Missense_Mutation_p.P196S|AKAP13_uc002blx.1_5'UTR|AKAP13_uc010bne.1_Missense_Mutation_p.P382S	NM_006738	NP_006729	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 1	1729					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|ovary(1)|liver(1)	8						Melanoma(94;603 1453 3280 32295 32951)								0.290909	40.27513	42.431094	16	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86228000	86228000	452	15	C	T	T	T	338	26	AKAP13	2	2
ACAN	176	broad.mit.edu	37	15	89392931	89392931	+	Silent	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:89392931A>G	uc010upo.1	+	c.1995A>G	c.(1993-1995)CCA>CCG	p.P665P	ACAN_uc002bmx.2_Silent_p.P665P|ACAN_uc010upp.1_Silent_p.P665P|ACAN_uc002bna.2_Non-coding_Transcript	NM_013227	NP_037359			aggrecan isoform 2 precursor											ovary(2)|central_nervous_system(1)	3	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)											0.538462	21.52498	21.541662	7	6	KEEP	---	---	---	---	capture		Silent	SNP	89392931	89392931	118	15	A	G	G	G	67	6	ACAN	4	4
IGF1R	3480	broad.mit.edu	37	15	99500385	99500385	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:99500385G>T	uc002bul.2	+	c.3818G>T	c.(3817-3819)GGC>GTC	p.G1273V	IGF1R_uc010bon.2_Missense_Mutation_p.G1272V	NM_000875	NP_000866	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor precursor	1273	Protein kinase.|Cytoplasmic (Potential).				anti-apoptosis|immune response|insulin receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of DNA replication|protein autophosphorylation|protein tetramerization	integral to plasma membrane|microsome	ATP binding|identical protein binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor receptor activity|metal ion binding|phosphatidylinositol 3-kinase binding			lung(3)|kidney(3)|ovary(1)|central_nervous_system(1)	8	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Mecasermin(DB01277)					471				0.216216	16.458388	19.236465	8	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99500385	99500385	7872	15	G	T	T	T	546	42	IGF1R	2	2
MYH11	4629	broad.mit.edu	37	16	15917148	15917148	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:15917148C>T	uc002ddx.2	-	c.466G>A	c.(466-468)GCC>ACC	p.A156T	MYH11_uc002ddv.2_Missense_Mutation_p.A156T|MYH11_uc002ddw.2_Missense_Mutation_p.A156T|MYH11_uc002ddy.2_Missense_Mutation_p.A156T|MYH11_uc010bvg.2_5'UTR|MYH11_uc002deb.3_Missense_Mutation_p.A156T	NM_001040114	NP_001035203	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	156	Myosin head-like.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(4)|skin(2)|lung(1)	7										1257				0.294118	36.703517	38.639356	15	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15917148	15917148	10426	16	C	T	T	T	351	27	MYH11	1	1
CRAMP1L	57585	broad.mit.edu	37	16	1709950	1709950	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1709950A>T	uc010uvh.1	+	c.2299A>T	c.(2299-2301)ACG>TCG	p.T767S	CRAMP1L_uc002cmf.2_Non-coding_Transcript	NM_020825	NP_065876	Q96RY5	CRML_HUMAN	Crm, cramped-like	767						nucleus	DNA binding				0														0.136364	4.012844	6.827922	3	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1709950	1709950	3985	16	A	T	T	T	130	10	CRAMP1L	3	3
HAGH	3029	broad.mit.edu	37	16	1872326	1872326	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1872326T>G	uc002cna.2	-	c.289A>C	c.(289-291)ACA>CCA	p.T97P	HAGH_uc002cmz.2_Missense_Mutation_p.T49P|HAGH_uc010uvp.1_Missense_Mutation_p.T97P|HAGH_uc002cnb.1_Missense_Mutation_p.T49P|HAGH_uc010bry.1_Missense_Mutation_p.T97P	NM_005326	NP_005317	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase isoform 1	97					glutathione biosynthetic process	cytoplasm|mitochondrial matrix|mitochondrial matrix	hydroxyacylglutathione hydrolase activity|zinc ion binding			ovary(1)	1		Hepatocellular(780;0.00335)			Glutathione(DB00143)	Pancreas(55;1048 1176 25227 40124 41333)								0.230769	7.619927	8.482262	3	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1872326	1872326	7227	16	T	G	G	G	767	59	HAGH	4	4
LUC7L	55692	broad.mit.edu	37	16	242939	242939	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:242939G>A	uc002cgc.1	-	c.763C>T	c.(763-765)CGT>TGT	p.R255C	LUC7L_uc002cga.1_Missense_Mutation_p.R255C|LUC7L_uc002cgd.1_Non-coding_Transcript|LUC7L_uc002cge.1_Missense_Mutation_p.R255C|LUC7L_uc002cgb.1_Missense_Mutation_p.R169C	NM_201412	NP_958815	Q9NQ29	LUC7L_HUMAN	LUC7-like isoform b	255	Potential.|Arg/Ser-rich.						metal ion binding			central_nervous_system(1)	1		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)												0.27027	98.383379	105.401859	40	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	242939	242939	9458	16	G	A	A	A	494	38	LUC7L	1	1
KIAA0556	23247	broad.mit.edu	37	16	27751806	27751806	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:27751806C>G	uc002dow.2	+	c.2188C>G	c.(2188-2190)CCC>GCC	p.P730A		NM_015202	NP_056017	O60303	K0556_HUMAN	hypothetical protein LOC23247	730										ovary(4)|large_intestine(2)	6														0.189573	89.235225	108.333981	40	171	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27751806	27751806	8490	16	C	G	G	G	338	26	KIAA0556	3	3
ZSCAN10	84891	broad.mit.edu	37	16	3140535	3140535	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:3140535C>A	uc002ctv.1	-	c.735G>T	c.(733-735)CCG>CCT	p.P245P	ZSCAN10_uc002cty.1_5'UTR|ZSCAN10_uc002ctw.1_Silent_p.P163P|ZSCAN10_uc002ctx.1_Silent_p.P173P	NM_032805	NP_116194	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	245					regulation of transcription, DNA-dependent|viral reproduction	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity|zinc ion binding			ovary(1)	1														0.285714	21.0895	22.24275	8	20	KEEP	---	---	---	---	capture		Silent	SNP	3140535	3140535	18831	16	C	A	A	A	288	23	ZSCAN10	1	1
BBS2	583	broad.mit.edu	37	16	56531699	56531699	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56531699C>T	uc002ejd.2	-	c.1753G>A	c.(1753-1755)GAT>AAT	p.D585N		NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	585					adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														0.153846	29.140249	41.04873	16	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56531699	56531699	1359	16	C	T	T	T	390	30	BBS2	2	2
PSMD7	5713	broad.mit.edu	37	16	74336183	74336183	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:74336183T>A	uc002fcq.2	+	c.431T>A	c.(430-432)GTC>GAC	p.V144D	PSMD7_uc010vmr.1_Missense_Mutation_p.V67D	NM_002811	NP_002802	P51665	PSD7_HUMAN	proteasome 26S non-ATPase subunit 7	144				VH -> DQ (in Ref. 1; BAA08780).	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	proteasome regulatory particle	protein binding				0														0.180851	31.117266	40.121186	17	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74336183	74336183	13156	16	T	A	A	A	754	58	PSMD7	3	3
KIAA0513	9764	broad.mit.edu	37	16	85100771	85100771	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:85100771C>A	uc002fiu.2	+	c.94C>A	c.(94-96)CAG>AAG	p.Q32K	KIAA0513_uc002fis.3_Missense_Mutation_p.Q32K|KIAA0513_uc010voj.1_Missense_Mutation_p.Q32K|KIAA0513_uc002fit.2_Missense_Mutation_p.Q32K	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764	32						cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)										0.073171	-0.907316	6.772675	3	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85100771	85100771	8488	16	C	A	A	A	325	25	KIAA0513	2	2
GRIN2A	2903	broad.mit.edu	37	16	9857834	9857834	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:9857834C>G	uc002czo.3	-	c.3567G>C	c.(3565-3567)AAG>AAC	p.K1189N	GRIN2A_uc010uym.1_Missense_Mutation_p.K1189N|GRIN2A_uc010uyn.1_Missense_Mutation_p.K1032N|GRIN2A_uc002czr.3_Missense_Mutation_p.K1189N	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1189	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)					324				0.319885	326.776487	336.793389	111	236	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9857834	9857834	7058	16	C	G	G	G	363	28	GRIN2A	3	3
MYH2	4620	broad.mit.edu	37	17	10432292	10432292	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:10432292G>T	uc010coi.2	-	c.3459C>A	c.(3457-3459)AGC>AGA	p.S1153R	MYH2_uc002gmp.3_Missense_Mutation_p.S1153R|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1153	Potential.				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														0.109589	5.457923	16.479747	8	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10432292	10432292	10430	17	G	T	T	T	490	38	MYH2	1	1
ALKBH5	54890	broad.mit.edu	37	17	18111563	18111563	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:18111563G>C	uc010cpw.2	+	c.1038G>C	c.(1036-1038)GAG>GAC	p.E346D	ALKBH5_uc010cpx.2_Non-coding_Transcript	NM_017758	NP_060228	Q6P6C2	ALKB5_HUMAN	alkB, alkylation repair homolog 5	346					oxidation-reduction process	integral to membrane	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0	all_neural(463;0.228)					Ovarian(166;154 1953 40235 46283 46309)								0.258621	41.798197	44.85933	15	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18111563	18111563	533	17	G	C	C	C	425	33	ALKBH5	3	3
LGALS9	3965	broad.mit.edu	37	17	25974145	25974145	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:25974145G>A	uc002gzp.2	+	c.758_splice	c.e9+1	p.R253_splice	LGALS9_uc002gzq.2_Splice_Site_SNP_p.R221_splice|LGALS9_uc002gzr.2_Splice_Site_SNP_p.R164_splice|LGALS9_uc010waa.1_Splice_Site_SNP_p.R196_splice|LGALS9_uc002gzs.2_Splice_Site_SNP_p.R221_splice	NM_009587	NP_033665			galectin-9 isoform long						positive regulation of I-kappaB kinase/NF-kappaB cascade	cytoplasm|extracellular region	galactose binding|signal transducer activity				0	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)								0.25	16.711025	18.302298	7	21	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	25974145	25974145	9074	17	G	A	A	A	572	44	LGALS9	5	2
NF1	4763	broad.mit.edu	37	17	29657349	29657349	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29657349G>T	uc002hgg.2	+	c.5645G>T	c.(5644-5646)TGT>TTT	p.C1882F	NF1_uc002hgh.2_Missense_Mutation_p.C1861F|NF1_uc002hgi.1_Missense_Mutation_p.C894F|NF1_uc010cso.2_Missense_Mutation_p.C70F	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1882					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.C1882F(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.4375	42.444825	42.553849	14	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29657349	29657349	10756	17	G	T	T	T	624	48	NF1	2	2
NF1	4763	broad.mit.edu	37	17	29657351	29657351	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:29657351A>C	uc002hgg.2	+	c.5647A>C	c.(5647-5649)ACC>CCC	p.T1883P	NF1_uc002hgh.2_Missense_Mutation_p.T1862P|NF1_uc002hgi.1_Missense_Mutation_p.T895P|NF1_uc010cso.2_Missense_Mutation_p.T71P	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1883					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity			soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)						847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.4375	46.647502	46.756079	14	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29657351	29657351	10756	17	A	C	C	C	182	14	NF1	4	4
UTP6	55813	broad.mit.edu	37	17	30195071	30195071	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:30195071C>G	uc002hgr.2	-	c.1557G>C	c.(1555-1557)AAG>AAC	p.K519N	UTP6_uc002hgq.2_Missense_Mutation_p.K335N|UTP6_uc010cst.2_Missense_Mutation_p.K368N	NM_018428	NP_060898	Q9NYH9	UTP6_HUMAN	hepatocellular carcinoma-associated antigen 66	519	HAT 4.				rRNA processing	nucleolus	binding			ovary(1)	1		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)												0.083333	0.096514	6.449741	3	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30195071	30195071	17667	17	C	G	G	G	311	24	UTP6	3	3
UNC45B	146862	broad.mit.edu	37	17	33510569	33510569	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:33510569C>G	uc002hja.2	+	c.2503C>G	c.(2503-2505)CAC>GAC	p.H835D	UNC45B_uc002hjb.2_Missense_Mutation_p.H833D|UNC45B_uc002hjc.2_Missense_Mutation_p.H833D|UNC45B_uc010cto.2_Missense_Mutation_p.H754D	NM_173167	NP_775259	Q8IWX7	UN45B_HUMAN	cardiomyopathy associated 4 isoform 1	835					cell differentiation|muscle organ development		binding			ovary(3)|central_nervous_system(2)|breast(1)	6		Ovarian(249;0.17)												0.181818	13.933071	17.069192	6	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33510569	33510569	17547	17	C	G	G	G	221	17	UNC45B	3	3
TBC1D3G	654341	broad.mit.edu	37	17	34797757	34797757	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34797757G>A	uc002hmm.3	-	c.1379C>T	c.(1378-1380)ACG>ATG	p.T460M	TBC1D3C_uc002hll.1_Intron|TBC1D3G_uc010wcv.1_Intron|TBC1D3G_uc002hlm.2_Intron|TBC1D3C_uc002hme.3_Intron	NM_001040282	NP_001035372	Q6IPX1	TBC3C_HUMAN	TBC1 domain family, member 3G	460						intracellular	Rab GTPase activator activity				0		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)										0.142857	4.910855	7.492031	3	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34797757	34797757	16146	17	G	A	A	A	520	40	TBC1D3G	1	1
TADA2A	6871	broad.mit.edu	37	17	35802677	35802677	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:35802677C>T	uc002hnt.2	+	c.455C>T	c.(454-456)CCT>CTT	p.P152L	TADA2A_uc002hnu.1_Missense_Mutation_p.P152L|TADA2A_uc002hnv.2_Missense_Mutation_p.P152L|TADA2A_uc010wdd.1_Missense_Mutation_p.P152L|TADA2A_uc002hnw.2_Missense_Mutation_p.P51L|TADA2A_uc010cvb.2_Intron	NM_001488	NP_001479	O75478	TAD2A_HUMAN	transcriptional adaptor 2A isoform a	152					histone H3 acetylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|PCAF complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity|zinc ion binding			breast(3)	3														0.170732	14.297898	18.503722	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35802677	35802677	16031	17	C	T	T	T	312	24	TADA2A	2	2
KRT38	8687	broad.mit.edu	37	17	39597020	39597020	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:39597020C>T	uc002hwq.1	-	c.154G>A	c.(154-156)GCC>ACC	p.A52T		NM_006771	NP_006762	O76015	KRT38_HUMAN	keratin 38	52	Head.					intermediate filament	structural molecule activity				0		Breast(137;0.000496)												0.103448	1.801833	6.345099	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39597020	39597020	8790	17	C	T	T	T	325	25	KRT38	2	2
ADAM11	4185	broad.mit.edu	37	17	42854947	42854947	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:42854947C>T	uc002ihh.2	+	c.1879C>T	c.(1879-1881)CAG>TAG	p.Q627*	ADAM11_uc010wjd.1_Nonsense_Mutation_p.Q427*|ADAM11_uc002ihi.2_5'UTR	NM_002390	NP_002381	O75078	ADA11_HUMAN	ADAM metallopeptidase domain 11 preproprotein	627	Cys-rich.|Extracellular (Potential).				integrin-mediated signaling pathway|proteolysis	integral to membrane|plasma membrane	integrin binding|metalloendopeptidase activity|zinc ion binding			pancreas(1)	1		Prostate(33;0.0959)												0.178571	18.913819	24.362728	10	46	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	42854947	42854947	236	17	C	T	T	T	273	21	ADAM11	5	2
ABI3	51225	broad.mit.edu	37	17	47295250	47295250	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:47295250C>T	uc002iop.1	+	c.435C>T	c.(433-435)TGC>TGT	p.C145C	ABI3_uc002ioq.1_Silent_p.C139C	NM_016428	NP_057512	Q9P2A4	ABI3_HUMAN	NESH protein isoform 1	145					cellular component movement|regulation of cell migration	cytoplasm|lamellipodium	protein binding				0			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)											0.15	18.863191	28.166959	12	68	KEEP	---	---	---	---	capture		Silent	SNP	47295250	47295250	91	17	C	T	T	T	337	26	ABI3	2	2
EPX	8288	broad.mit.edu	37	17	56272420	56272420	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56272420C>T	uc002ivq.2	+	c.690C>T	c.(688-690)TTC>TTT	p.F230F		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase preproprotein	230					hydrogen peroxide catabolic process|oxidation-reduction process		heme binding|peroxidase activity|protein binding			ovary(2)	2														0.068493	-3.785541	10.275244	5	68	KEEP	---	---	---	---	capture		Silent	SNP	56272420	56272420	5393	17	C	T	T	T	376	29	EPX	2	2
EPX	8288	broad.mit.edu	37	17	56280504	56280504	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56280504C>A	uc002ivq.2	+	c.1771C>A	c.(1771-1773)CGG>AGG	p.R591R		NM_000502	NP_000493	P11678	PERE_HUMAN	eosinophil peroxidase preproprotein	591					hydrogen peroxide catabolic process|oxidation-reduction process		heme binding|peroxidase activity|protein binding			ovary(2)	2														0.066667	-6.712585	8.049326	5	70	KEEP	---	---	---	---	capture		Silent	SNP	56280504	56280504	5393	17	C	A	A	A	295	23	EPX	1	1
MED13	9969	broad.mit.edu	37	17	60040135	60040135	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60040135A>G	uc002izo.2	-	c.5042T>C	c.(5041-5043)ATC>ACC	p.I1681T		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1681					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			large_intestine(1)|ovary(1)	2														0.153846	12.232118	16.694309	6	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60040135	60040135	9819	17	A	G	G	G	156	12	MED13	4	4
MRC2	9902	broad.mit.edu	37	17	60742177	60742177	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:60742177G>T	uc002jad.2	+	c.387G>T	c.(385-387)CAG>CAT	p.Q129H	MRC2_uc002jac.2_Missense_Mutation_p.Q129H	NM_006039	NP_006030	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	129	Extracellular (Potential).|Ricin B-type lectin.				endocytosis	integral to membrane	receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.16	6.183359	8.937309	4	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60742177	60742177	10150	17	G	T	T	T	438	34	MRC2	2	2
KCNH6	81033	broad.mit.edu	37	17	61615561	61615561	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61615561G>T	uc002jay.2	+	c.1637G>T	c.(1636-1638)CGC>CTC	p.R546L	KCNH6_uc010wpl.1_Missense_Mutation_p.R423L|KCNH6_uc010wpm.1_Missense_Mutation_p.R546L|KCNH6_uc002jaz.1_Missense_Mutation_p.R493L	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	546	Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|signal transduction						0					Ibutilide(DB00308)									0.461538	18.749475	18.766122	6	7	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61615561	61615561	8341	17	G	T	T	T	494	38	KCNH6	1	1
GH2	2689	broad.mit.edu	37	17	61958133	61958133	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:61958133C>A	uc002jcl.1	-	c.455G>T	c.(454-456)TGG>TTG	p.W152L	GH2_uc002jcj.2_Intron|CSH2_uc002jck.2_Intron|GH2_uc002jcm.1_Intron|GH2_uc002jcn.1_Missense_Mutation_p.W137L|GH2_uc002jco.1_Missense_Mutation_p.W152L	NM_022557	NP_072051	P01242	SOM2_HUMAN	growth hormone 2 isoform 2	152						extracellular region	hormone activity			pancreas(1)	1														0.25	31.618895	34.805002	14	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61958133	61958133	6636	17	C	A	A	A	273	21	GH2	2	2
PRKAR1A	5573	broad.mit.edu	37	17	66518895	66518896	+	Splice_Site_DNP	DNP	AG	TT	TT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:66518895_66518896AG>TT	uc002jhg.2	+	c.178_splice	c.e3-1	p.E60_splice	PRKAR1A_uc002jhh.2_Splice_Site_DNP_p.E60_splice|PRKAR1A_uc002jhi.2_Splice_Site_DNP_p.E60_splice|PRKAR1A_uc002jhj.2_Splice_Site_DNP_p.E60_splice|PRKAR1A_uc002jhk.2_Splice_Site_DNP|PRKAR1A_uc002jhl.2_Splice_Site_DNP_p.E60_splice|PRKAR1A_uc002jhm.2_Splice_Site_DNP_p.E60_splice	NM_212471	NP_997636			cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding	p.?(1)		adrenal_gland(4)|thyroid(2)|soft_tissue(2)|lung(1)	9	Breast(10;1.64e-13)					Ovarian(167;637 1670 33025 39608 46699 51856)				165				0.291667	20.515697	21.448422	7	17	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	66518895	66518896	12946	17	AG	TT	TT	TT	91	7	PRKAR1A	5	3
GPS2	2874	broad.mit.edu	37	17	7216393	7216393	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7216393G>A	uc002gfv.1	-	c.855C>T	c.(853-855)CTC>CTT	p.L285L	GPS2_uc002gfw.1_Silent_p.L247L|GPS2_uc002gfx.1_Silent_p.L285L|NEURL4_uc002gfy.1_Non-coding_Transcript|GPS2_uc002gfz.1_Silent_p.L285L	NM_004489	NP_004480	Q13227	GPS2_HUMAN	G protein pathway suppressor 2	285					cell cycle|inactivation of MAPK activity|JNK cascade|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of JNK cascade	transcriptional repressor complex	GTPase inhibitor activity|protein binding|transcription corepressor activity			ovary(2)|pancreas(1)	3		Prostate(122;0.157)												0.477612	94.063243	94.094062	32	35	KEEP	---	---	---	---	capture		Silent	SNP	7216393	7216393	7009	17	G	A	A	A	522	41	GPS2	2	2
C17orf95	124512	broad.mit.edu	37	17	74729619	74729619	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74729619G>T	uc002jsr.2	+	c.424G>T	c.(424-426)GAA>TAA	p.E142*	C17orf95_uc002jsp.2_3'UTR|C17orf95_uc002jsq.2_Non-coding_Transcript|C17orf95_uc002jss.2_3'UTR|C17orf95_uc002jst.2_Nonsense_Mutation_p.E75*|C17orf95_uc002jsu.2_Non-coding_Transcript|MFSD11_uc002jsz.1_5'Flank|MFSD11_uc002jta.2_5'Flank	NM_001080510	NP_001073979	Q86XA0	MET23_HUMAN	hypothetical protein LOC124512	142						integral to membrane	methyltransferase activity				0														0.126316	15.029832	27.983914	12	83	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	74729619	74729619	1950	17	G	T	T	T	585	45	C17orf95	5	2
SEC14L1	6397	broad.mit.edu	37	17	75212642	75212642	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:75212642G>T	uc010dhc.2	+	c.2156G>T	c.(2155-2157)TGC>TTC	p.C719F	SEC14L1_uc002jto.2_3'UTR|SEC14L1_uc010wth.1_3'UTR|SEC14L1_uc002jtm.2_3'UTR|SEC14L1_uc010wti.1_3'UTR	NM_001039573	NP_001034662	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform b	Error:Variant_position_missing_in_Q92503_after_alignment					transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2														0.108108	11.015801	27.921789	12	99	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75212642	75212642	14467	17	G	T	T	T	598	46	SEC14L1	2	2
TP53	7157	broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	A	A	rs28934576		TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7577120C>A	uc002gim.2	-	c.818G>T	c.(817-819)CGT>CTT	p.R273L	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R273L|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R141L|TP53_uc010cng.1_Missense_Mutation_p.R141L|TP53_uc002gii.1_Missense_Mutation_p.R141L|TP53_uc010cnh.1_Missense_Mutation_p.R273L|TP53_uc010cni.1_Missense_Mutation_p.R273L|TP53_uc002gij.2_Missense_Mutation_p.R273L	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	273	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R273H(458)|p.R273L(83)|p.R273P(24)|p.0?(6)|p.?(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)	R273H(NCIH1793_LUNG)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PANC1_PANCREAS)|R273H(NCIH508_LARGE_INTESTINE)|R273H(NCIH1975_LUNG)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(NCIH2405_LUNG)|R273H(HEC59_ENDOMETRIUM)|R273H(NCIH1155_LUNG)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(EN_ENDOMETRIUM)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(MDAMB468_BREAST)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW620_LARGE_INTESTINE)|R273H(SUIT2_PANCREAS)|R273H(SW480_LARGE_INTESTINE)|R273H(SKMEL30_SKIN)|R273H(OC314_OVARY)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)	111	p.R273H(SW480-Tumor)|p.R273L(NCIH1876-Tumor)|p.R273H(SW620-Tumor)|p.R273H(MDAMB468-Tumor)|p.R273Y(SW1783-Tumor)|p.R273H(YD8-Tumor)|p.R273L(NCIH1838-Tumor)|p.R273H(HT29-Tumor)|p.R273H(MONOMAC6-Tumor)|p.R273L(SNU503-Tumor)|p.R273H(MOLT13-Tumor)|p.R273Y(PF382-Tumor)|p.R273L(NCIH1734-Tumor)|p.R273H(FTC133-Tumor)|p.R273H(SNU601-Tumor)|p.R273H(NCIH1975-Tumor)|p.R273H(NCIH1793-Tumor)|p.R273L(ECGI10-Tumor)|p.R273H(KP1NL-Tumor)|p.R273H(KP1N-Tumor)|p.R273L(NCIH1623-Tumor)|p.R273L(NCIH2009-Tumor)|p.R273H(NCIH508-Tumor)|p.R273H(MONOMAC1-Tumor)|p.R273H(HEC59-Tumor)|p.R273H(FTC238-Tumor)|p.R273H(OC316-Tumor)|p.R273Y(SNUC2A-Tumor)|p.R273H(SUDHL1-Tumor)|p.R273L(HCC38-Tumor)|p.R273H(NCIH2405-Tumor)|p.R273H(HEC6-Tumor)|p.R273H(EN-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.407407	33.118182	33.320635	11	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7577120	7577120	16923	17	C	A	A	A	247	19	TP53	1	1
DNAH2	146754	broad.mit.edu	37	17	7636533	7636533	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7636533T>C	uc002giu.1	+	c.528T>C	c.(526-528)GGT>GGC	p.G176G	DNAH2_uc002git.2_Silent_p.G176G|DNAH2_uc010vuk.1_Silent_p.G176G	NM_020877	NP_065928	Q9P225	DYH2_HUMAN	dynein heavy chain domain 3	176	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|central_nervous_system(1)	7		all_cancers(10;4.66e-07)|Prostate(122;0.081)												0.369565	39.957477	40.685152	17	29	KEEP	---	---	---	---	capture		Silent	SNP	7636533	7636533	4785	17	T	C	C	C	756	59	DNAH2	4	4
CHD3	1107	broad.mit.edu	37	17	7794055	7794055	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7794055A>C	uc002gjd.2	+	c.557A>C	c.(556-558)CAA>CCA	p.Q186P	CHD3_uc002gje.2_Missense_Mutation_p.Q127P|CHD3_uc002gjf.2_Missense_Mutation_p.Q127P|CHD3_uc002gjg.1_5'Flank	NM_001005271	NP_001005271	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	127					chromatin assembly or disassembly|chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	chromatin|microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|chromatin binding|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)												0.5	74.749347	74.749347	22	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7794055	7794055	3460	17	A	C	C	C	65	5	CHD3	4	4
ACTG1	71	broad.mit.edu	37	17	79478070	79478070	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:79478070G>T	uc002kaj.1	-	c.867C>A	c.(865-867)ATC>ATA	p.I289I	ACTG1_uc002kah.1_Silent_p.I167I|ACTG1_uc002kai.1_Silent_p.I246I|ACTG1_uc002kak.1_Silent_p.I289I|ACTG1_uc010wun.1_Silent_p.I289I|ACTG1_uc002kal.1_Silent_p.I289I|ACTG1_uc002kag.2_Non-coding_Transcript	NM_001614	NP_001605	P63261	ACTG_HUMAN	actin, gamma 1 propeptide	289					adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)	2	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)											0.333333	13.269302	13.63866	5	10	KEEP	---	---	---	---	capture		Silent	SNP	79478070	79478070	197	17	G	T	T	T	525	41	ACTG1	2	2
ZNF519	162655	broad.mit.edu	37	18	14105633	14105633	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:14105633G>C	uc002kst.1	-	c.906C>G	c.(904-906)AAC>AAG	p.N302K	ZNF519_uc002ksq.1_Intron|ZNF519_uc002ksr.1_Intron|ZNF519_uc010dlm.1_Intron	NM_145287	NP_660330	Q8TB69	ZN519_HUMAN	zinc finger protein 519	302	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.214286	44.889316	51.240363	18	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14105633	14105633	18558	18	G	C	C	C	620	48	ZNF519	3	3
TCEB3B	51224	broad.mit.edu	37	18	44561157	44561157	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:44561157A>G	uc002lcr.1	-	c.479T>C	c.(478-480)ATA>ACA	p.I160T	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_016427	NP_057511	Q8IYF1	ELOA2_HUMAN	elongin A2	160					transcription from RNA polymerase II promoter	integral to membrane|nucleus	DNA binding|transcription elongation regulator activity			ovary(2)|large_intestine(1)|pancreas(1)	4														0.090909	2.000283	9.393189	4	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44561157	44561157	16208	18	A	G	G	G	208	16	TCEB3B	4	4
WDR7	23335	broad.mit.edu	37	18	54694328	54694328	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:54694328G>T	uc002lgk.1	+	c.4363G>T	c.(4363-4365)GCG>TCG	p.A1455S	WDR7_uc002lgl.1_Missense_Mutation_p.A1422S	NM_015285	NP_056100	Q9Y4E6	WDR7_HUMAN	rabconnectin-3 beta isoform 1	1455										ovary(2)	2				Lung(128;0.0238)|Colorectal(16;0.0296)										0.255319	28.070166	30.632314	12	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54694328	54694328	17893	18	G	T	T	T	494	38	WDR7	1	1
SERPINB13	5275	broad.mit.edu	37	18	61256061	61256061	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61256061G>T	uc010xep.1	+	c.160G>T	c.(160-162)GAG>TAG	p.E54*	SERPINB13_uc002ljc.2_Nonsense_Mutation_p.E54*|SERPINB13_uc002ljd.2_5'UTR|SERPINB13_uc010xeq.1_5'UTR|SERPINB13_uc010xer.1_5'UTR	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN	serine (or cysteine) proteinase inhibitor, clade	54					regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity			ovary(1)	1														0.12	3.506173	7.048887	3	22	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	61256061	61256061	14588	18	G	T	T	T	533	41	SERPINB13	5	2
CDH7	1005	broad.mit.edu	37	18	63477063	63477063	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:63477063C>A	uc002ljz.2	+	c.334C>A	c.(334-336)CGT>AGT	p.R112S	CDH7_uc002lka.2_Missense_Mutation_p.R112S|CDH7_uc002lkb.2_Missense_Mutation_p.R112S	NM_033646	NP_387450	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2 preproprotein	112	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)	3		Esophageal squamous(42;0.129)												0.141026	16.786887	26.476297	11	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63477063	63477063	3244	18	C	A	A	A	403	31	CDH7	1	1
LAMA1	284217	broad.mit.edu	37	18	7016521	7016521	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:7016521G>A	uc002knm.2	-	c.2958C>T	c.(2956-2958)GGC>GGT	p.G986G	LAMA1_uc010wzj.1_Silent_p.G462G	NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	986	Laminin EGF-like 10.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.227273	34.989881	39.496396	15	51	KEEP	---	---	---	---	capture		Silent	SNP	7016521	7016521	8928	18	G	A	A	A	431	34	LAMA1	2	2
TXNDC2	84203	broad.mit.edu	37	18	9887622	9887622	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:9887622C>A	uc002koi.3	+	c.1146C>A	c.(1144-1146)ATC>ATA	p.I382I	TXNDC2_uc010wzq.1_Non-coding_Transcript|TXNDC2_uc002koh.3_Silent_p.I315I	NM_001098529	NP_001091999	Q86VQ3	TXND2_HUMAN	thioredoxin domain-containing 2 isoform 2	382	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.|18.				cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis	cytoplasm	electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity			ovary(1)|pancreas(1)	2														0.183432	58.614812	74.522437	31	138	KEEP	---	---	---	---	capture		Silent	SNP	9887622	9887622	17353	18	C	A	A	A	382	30	TXNDC2	2	2
MAST1	22983	broad.mit.edu	37	19	12958233	12958233	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:12958233C>T	uc002mvm.2	+	c.457C>T	c.(457-459)CCA>TCA	p.P153S	MAST1_uc002mvk.2_Missense_Mutation_p.P149S|MAST1_uc002mvl.2_Silent_p.P126P	NM_014975	NP_055790	Q9Y2H9	MAST1_HUMAN	microtubule associated serine/threonine kinase	153					cytoskeleton organization|intracellular protein kinase cascade|protein phosphorylation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|large_intestine(1)|skin(1)	7										239		OREG0025277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.380952	38.95357	39.487147	16	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	12958233	12958233	9708	19	C	T	T	T	286	22	MAST1	2	2
MRI1	84245	broad.mit.edu	37	19	13875414	13875414	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13875414G>T	uc002mxe.2	+	c.12G>T	c.(10-12)GAG>GAT	p.E4D	MRI1_uc002mxf.2_Missense_Mutation_p.E4D	NM_001031727	NP_001026897	Q9BV20	MTNA_HUMAN	translation initiation factor eIF-2B subunit	4					L-methionine salvage from methylthioadenosine	cell projection|cytoplasm|nucleus	identical protein binding|S-methyl-5-thioribose-1-phosphate isomerase activity				0														0.571429	12.300832	12.332004	4	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13875414	13875414	10163	19	G	T	T	T	451	35	MRI1	2	2
AKAP8	10270	broad.mit.edu	37	19	15484839	15484839	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15484839G>C	uc002nav.2	-	c.129C>G	c.(127-129)ACC>ACG	p.T43T	AKAP8_uc010dzy.2_5'Flank|AKAP8_uc010dzz.1_Non-coding_Transcript|AKAP8_uc010xog.1_Intron	NM_005858	NP_005849	O43823	AKAP8_HUMAN	A-kinase anchor protein 8	43					signal transduction	nuclear matrix				ovary(1)|breast(1)	2						GBM(190;1671 2163 3274 27186 30476)								0.541667	38.174772	38.210894	13	11	KEEP	---	---	---	---	capture		Silent	SNP	15484839	15484839	460	19	G	C	C	C	600	47	AKAP8	3	3
CALR3	125972	broad.mit.edu	37	19	16601253	16601253	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:16601253C>A	uc002ned.2	-	c.322G>T	c.(322-324)GGC>TGC	p.G108C	MED26_uc002nee.2_Intron	NM_145046	NP_659483	Q96L12	CALR3_HUMAN	calreticulin 3 precursor	108	N-domain.				protein folding	endoplasmic reticulum lumen	calcium ion binding|sugar binding|unfolded protein binding				0														0.157895	6.721318	10.977468	6	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16601253	16601253	2710	19	C	A	A	A	286	22	CALR3	2	2
ZNF99	7652	broad.mit.edu	37	19	22941185	22941185	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22941185C>A	uc010xrh.1	-	c.1253G>T	c.(1252-1254)TGC>TTC	p.C418F		NM_001080409	NP_001073878	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	418	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)												0.227273	36.888826	41.395452	15	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22941185	22941185	18808	19	C	A	A	A	325	25	ZNF99	2	2
ZNF536	9745	broad.mit.edu	37	19	30935733	30935733	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:30935733G>T	uc002nsu.1	+	c.1264G>T	c.(1264-1266)GCC>TCC	p.A422S	ZNF536_uc010edd.1_Missense_Mutation_p.A422S	NM_014717	NP_055532	O15090	ZN536_HUMAN	zinc finger protein 536	422					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(7)|large_intestine(2)	9	Esophageal squamous(110;0.0834)													0.614286	121.975035	122.813484	43	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30935733	30935733	18568	19	G	T	T	T	546	42	ZNF536	2	2
RHPN2	85415	broad.mit.edu	37	19	33493811	33493811	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:33493811G>A	uc002nuf.2	-	c.856C>T	c.(856-858)CAA>TAA	p.Q286*	RHPN2_uc010xro.1_Nonsense_Mutation_p.Q135*|RHPN2_uc002nue.2_Nonsense_Mutation_p.Q16*	NM_033103	NP_149094	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	286	BRO1.				signal transduction	perinuclear region of cytoplasm	protein binding			central_nervous_system(5)|ovary(1)	6	Esophageal squamous(110;0.137)									600				0.662162	154.693239	156.413632	49	25	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	33493811	33493811	13826	19	G	A	A	A	624	48	RHPN2	5	2
FFAR1	2864	broad.mit.edu	37	19	35842790	35842790	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:35842790G>T	uc002nzc.2	+	c.336G>T	c.(334-336)TTG>TTT	p.L112F		NM_005303	NP_005294	O14842	FFAR1_HUMAN	free fatty acid receptor 1	112	Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	integral to plasma membrane	G-protein coupled receptor activity|guanyl-nucleotide exchange factor activity|lipid binding			central_nervous_system(1)	1	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Icosapent(DB00159)									0.73913	108.759177	111.14972	34	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35842790	35842790	6064	19	G	T	T	T	607	47	FFAR1	2	2
HAUS5	23354	broad.mit.edu	37	19	36109850	36109850	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36109850G>T	uc002oam.1	+	c.1078G>T	c.(1078-1080)GAT>TAT	p.D360Y		NM_015302	NP_056117	O94927	HAUS5_HUMAN	HAUS augmin-like complex, subunit 5	360					cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle					0														0.705882	152.725207	155.313609	48	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36109850	36109850	7251	19	G	T	T	T	481	37	HAUS5	1	1
PSENEN	55851	broad.mit.edu	37	19	36237643	36237643	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36237643G>T	uc002obi.1	+	c.201G>T	c.(199-201)TGG>TGT	p.W67C	TMEM149_uc010eej.2_5'Flank|U2AF1L4_uc002obh.1_5'Flank|U2AF1L4_uc002obe.2_5'Flank|U2AF1L4_uc002obf.2_5'Flank|U2AF1L4_uc002obg.2_5'Flank|PSENEN_uc002obj.1_Missense_Mutation_p.W67C|PSENEN_uc002obk.1_Intron|LIN37_uc002obm.2_5'Flank	NM_172341	NP_758844	Q9NZ42	PEN2_HUMAN	presenilin enhancer 2	67	Helical; (Potential).				amyloid precursor protein catabolic process|apoptosis|induction of apoptosis by extracellular signals|membrane protein ectodomain proteolysis|membrane protein intracellular domain proteolysis|nerve growth factor receptor signaling pathway|Notch receptor processing|Notch signaling pathway|positive regulation of catalytic activity|protein processing	endoplasmic reticulum membrane|Golgi cisterna membrane|integral to plasma membrane	aspartic-type endopeptidase activity|protein binding			ovary(2)	2	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)							18				0.651376	227.255465	229.462786	71	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36237643	36237643	13105	19	G	T	T	T	559	43	PSENEN	2	2
NPHS1	4868	broad.mit.edu	37	19	36342405	36342405	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36342405C>A	uc002oby.2	-	c.228G>T	c.(226-228)AGG>AGT	p.R76S		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	76	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)	4	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)											0.139535	5.91075	11.338237	6	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36342405	36342405	10986	19	C	A	A	A	389	30	NPHS1	2	2
NFKBID	84807	broad.mit.edu	37	19	36387021	36387021	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:36387021G>T	uc002ocj.1	-	c.512C>A	c.(511-513)CCG>CAG	p.P171Q	NFKBID_uc002och.1_5'UTR|NFKBID_uc002oci.1_Missense_Mutation_p.P156Q	NM_139239	NP_640332	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene	156	ANK 4.				inflammatory response	nucleus					0														0.060241	-16.333689	17.337337	10	156	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36387021	36387021	10779	19	G	T	T	T	507	39	NFKBID	1	1
ZNF461	92283	broad.mit.edu	37	19	37149259	37149259	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:37149259C>A	uc002oem.2	-	c.78G>T	c.(76-78)GCG>GCT	p.A26A	ZNF461_uc002oen.2_Missense_Mutation_p.A8S|ZNF461_uc010xtj.1_Silent_p.A26A	NM_153257	NP_694989	Q8TAF7	ZN461_HUMAN	gonadotropin inducible transcription repressor	26	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)											0.155556	12.498875	17.595484	7	38	KEEP	---	---	---	---	capture		Silent	SNP	37149259	37149259	18518	19	C	A	A	A	340	27	ZNF461	1	1
ZNF284	342909	broad.mit.edu	37	19	44590210	44590210	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:44590210T>A	uc002oyg.1	+	c.579T>A	c.(577-579)CAT>CAA	p.H193Q	ZNF284_uc010ejd.2_Non-coding_Transcript	NM_001037813	NP_001032902	Q2VY69	ZN284_HUMAN	zinc finger protein 284	193	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)												0.355556	44.284432	45.112845	16	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44590210	44590210	18413	19	T	A	A	A	647	50	ZNF284	3	3
ZNF577	84765	broad.mit.edu	37	19	52381733	52381733	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52381733G>A	uc010yde.1	-	c.96C>T	c.(94-96)TTC>TTT	p.F32F	ZNF577_uc010ydd.1_Non-coding_Transcript|ZNF577_uc002pxx.3_Silent_p.F32F|ZNF577_uc002pxv.2_Silent_p.F25F|ZNF577_uc002pxw.2_Silent_p.F25F	NM_032679	NP_116068	Q9BSK1	ZN577_HUMAN	zinc finger protein 577 isoform a	32	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)										0.27619	67.223237	71.964863	29	76	KEEP	---	---	---	---	capture		Silent	SNP	52381733	52381733	18604	19	G	A	A	A	581	45	ZNF577	2	2
PRKCG	5582	broad.mit.edu	37	19	54403989	54403989	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54403989T>A	uc010yeg.1	+	c.1561T>A	c.(1561-1563)TAC>AAC	p.Y521N	PRKCG_uc002qcq.1_Missense_Mutation_p.Y521N|PRKCG_uc010yeh.1_Missense_Mutation_p.Y408N	NM_002739	NP_002730	P05129	KPCG_HUMAN	protein kinase C, gamma	521	Protein kinase.				activation of phospholipase C activity|cell death|intracellular signal transduction|negative regulation of protein catabolic process|negative regulation of protein ubiquitination|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of mismatch repair|protein phosphorylation|synaptic transmission	cytosol	ATP binding|protein kinase C activity|zinc ion binding	p.Y521N(1)		lung(4)|ovary(2)|pancreas(2)|large_intestine(1)	9	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)						505				0.446154	253.891096	254.383172	87	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54403989	54403989	12955	19	T	A	A	A	689	53	PRKCG	3	3
VSTM1	284415	broad.mit.edu	37	19	54561570	54561570	+	Silent	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54561570C>G	uc002qcw.3	-	c.345G>C	c.(343-345)CTG>CTC	p.L115L	VSTM1_uc010erb.2_Non-coding_Transcript|VSTM1_uc002qcx.3_Silent_p.L115L	NM_198481	NP_940883	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	115						integral to membrane					0	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)										0.365854	41.311805	41.961499	15	26	KEEP	---	---	---	---	capture		Silent	SNP	54561570	54561570	17796	19	C	G	G	G	262	21	VSTM1	3	3
TMC4	147798	broad.mit.edu	37	19	54664217	54664217	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:54664217C>G	uc010erf.2	-	c.2057G>C	c.(2056-2058)CGT>CCT	p.R686P	LENG1_uc002qdm.2_5'Flank|TMC4_uc002qdn.2_Missense_Mutation_p.R400P|TMC4_uc002qdo.2_Missense_Mutation_p.R680P	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1	686	Cytoplasmic (Potential).					integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)													0.078947	0.200185	7.0762	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54664217	54664217	16517	19	C	G	G	G	247	19	TMC4	3	3
NLRP5	126206	broad.mit.edu	37	19	56543981	56543981	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56543981C>A	uc002qmj.2	+	c.2281C>A	c.(2281-2283)CGG>AGG	p.R761R	NLRP5_uc002qmi.2_Silent_p.R742R	NM_153447	NP_703148	P59047	NALP5_HUMAN	NACHT, LRR and PYD containing protein 5	761						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)										0.214286	6.616815	7.672907	3	11	KEEP	---	---	---	---	capture		Silent	SNP	56543981	56543981	10883	19	C	A	A	A	347	27	NLRP5	1	1
EMR1	2015	broad.mit.edu	37	19	6921744	6921744	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6921744G>T	uc002mfw.2	+	c.1641G>T	c.(1639-1641)AGG>AGT	p.R547S	EMR1_uc010dvc.2_Missense_Mutation_p.R547S|EMR1_uc010dvb.2_Missense_Mutation_p.R495S|EMR1_uc010xji.1_Missense_Mutation_p.R406S|EMR1_uc010xjj.1_Missense_Mutation_p.R370S	NM_001974	NP_001965	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone	547	GPS.|Extracellular (Potential).|Ser/Thr-rich.				cell adhesion|neuropeptide signaling pathway	integral to plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(3)	3	all_hematologic(4;0.166)													0.428571	75.110453	75.391629	27	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6921744	6921744	5297	19	G	T	T	T	542	42	EMR1	2	2
RBP7	116362	broad.mit.edu	37	1	10068244	10068244	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:10068244G>A	uc001aqq.2	+	c.266G>A	c.(265-267)TGG>TAG	p.W89*	RBP7_uc009vms.2_Non-coding_Transcript	NM_052960	NP_443192	Q96R05	RET7_HUMAN	retinol binding protein 7, cellular	89						cytoplasm	retinal binding|retinol binding|transporter activity				0		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|BRCA - Breast invasive adenocarcinoma(304;0.000302)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00856)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)									0.142857	5.209895	7.791722	3	18	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10068244	10068244	13629	1	G	A	A	A	611	47	RBP7	5	2
VCAM1	7412	broad.mit.edu	37	1	101194690	101194690	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:101194690C>A	uc001dti.2	+	c.956C>A	c.(955-957)CCT>CAT	p.P319H	VCAM1_uc001dtj.2_Intron|VCAM1_uc010ouj.1_Missense_Mutation_p.P257H	NM_001078	NP_001069	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1 isoform a	319	Ig-like C2-type 4.|Extracellular (Potential).				B cell differentiation|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|leukocyte tethering or rolling|membrane to membrane docking|positive regulation of T cell proliferation|regulation of immune response	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex|apical part of cell|external side of plasma membrane|extracellular space|filopodium|integral to membrane|microvillus|podosome	cell adhesion molecule binding|integrin binding			central_nervous_system(1)	1		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)									0.175	27.909159	35.87398	14	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101194690	101194690	17702	1	C	A	A	A	312	24	VCAM1	2	2
VCAM1	7412	broad.mit.edu	37	1	101196963	101196963	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:101196963C>G	uc001dti.2	+	c.1414C>G	c.(1414-1416)CCT>GCT	p.P472A	VCAM1_uc001dtj.2_Missense_Mutation_p.P380A|VCAM1_uc010ouj.1_Missense_Mutation_p.P410A	NM_001078	NP_001069	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1 isoform a	472	Ig-like C2-type 5.|Extracellular (Potential).				B cell differentiation|heterophilic cell-cell adhesion|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|leukocyte tethering or rolling|membrane to membrane docking|positive regulation of T cell proliferation|regulation of immune response	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex|apical part of cell|external side of plasma membrane|extracellular space|filopodium|integral to membrane|microvillus|podosome	cell adhesion molecule binding|integrin binding			central_nervous_system(1)	1		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)									0.134831	12.82514	24.362632	12	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101196963	101196963	17702	1	C	G	G	G	286	22	VCAM1	3	3
COL11A1	1301	broad.mit.edu	37	1	103387096	103387097	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:103387096_103387097GG>AT	uc001dum.2	-	c.3721_3722CC>AT	c.(3721-3723)CCT>ATT	p.P1241I	COL11A1_uc001duk.2_Missense_Mutation_p.P425I|COL11A1_uc001dul.2_Missense_Mutation_p.P1229I|COL11A1_uc001dun.2_Missense_Mutation_p.P1190I|COL11A1_uc009weh.2_Missense_Mutation_p.P1113I	NM_080629	NP_542196	P12107	COBA1_HUMAN	alpha 1 type XI collagen isoform B	1229	Triple-helical region.				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging			ovary(6)|breast(3)|central_nervous_system(1)|pancreas(1)	11		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)										0.088235	1.498684	7.326188	3	31	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	103387096	103387097	3805	1	GG	AT	AT	AT	455	35	COL11A1	2	2
CSDE1	7812	broad.mit.edu	37	1	115262199	115262199	+	Splice_Site_SNP	SNP	C	T	T	rs112211707		TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:115262199C>T	uc001efi.2	-	c.2354_splice	c.e18+1	p.C785_splice	NRAS_uc009wgu.2_5'Flank|CSDE1_uc001efj.2_Non-coding_Transcript|CSDE1_uc001efk.2_Splice_Site_SNP_p.C739_splice|CSDE1_uc001efl.2_Splice_Site_SNP_p.C708_splice|CSDE1_uc001efm.2_Splice_Site_SNP_p.C754_splice|CSDE1_uc009wgv.2_Splice_Site_SNP_p.C739_splice|CSDE1_uc001efn.2_Splice_Site_SNP_p.C708_splice	NM_001007553	NP_001007554			upstream of NRAS isoform 1						male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding			ovary(1)	1	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.144144	23.023652	36.561321	16	95	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	115262199	115262199	4070	1	C	T	T	T	234	18	CSDE1	5	2
TTF2	8458	broad.mit.edu	37	1	117626662	117626662	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:117626662T>C	uc001egy.2	+	c.1926T>C	c.(1924-1926)CAT>CAC	p.H642H		NM_003594	NP_003585	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase	642	Helicase ATP-binding.				mRNA processing|regulation of transcription, DNA-dependent|RNA splicing	cytoplasm|spliceosomal complex|transcription elongation factor complex	ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|RNA polymerase II transcription termination factor activity|zinc ion binding			ovary(1)	1	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)										0.227273	46.252661	52.263571	20	68	KEEP	---	---	---	---	capture		Silent	SNP	117626662	117626662	17274	1	T	C	C	C	660	51	TTF2	4	4
ANKRD34A	284615	broad.mit.edu	37	1	145474737	145474737	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145474737G>T	uc001enq.1	+	c.1409G>T	c.(1408-1410)AGA>ATA	p.R470I	NBPF10_uc001emp.3_Intron|LIX1L_uc001enr.2_5'Flank	NM_001039888	NP_001034977	Q69YU3	AN34A_HUMAN	ankyrin repeat domain 34	470											0	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.341463	35.335907	36.247259	14	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145474737	145474737	669	1	G	T	T	T	429	33	ANKRD34A	2	2
FLG	2312	broad.mit.edu	37	1	152281636	152281636	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152281636C>T	uc001ezu.1	-	c.5726G>A	c.(5725-5727)AGG>AAG	p.R1909K		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	1909	Ser-rich.|Filaggrin 11.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.134969	35.539884	56.592391	22	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152281636	152281636	6160	1	C	T	T	T	312	24	FLG	2	2
GON4L	54856	broad.mit.edu	37	1	155727103	155727103	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155727103C>G	uc001flz.2	-	c.5265G>C	c.(5263-5265)CAG>CAC	p.Q1755H	GON4L_uc009wrg.1_Non-coding_Transcript|GON4L_uc001fly.1_Missense_Mutation_p.Q1755H|GON4L_uc009wrh.1_Missense_Mutation_p.Q1755H|GON4L_uc001fma.1_Missense_Mutation_p.Q1755H|GON4L_uc001fmb.3_Missense_Mutation_p.Q951H	NM_001037533	NP_001032622	Q3T8J9	GON4L_HUMAN	gon-4-like isoform a	1755	PAH 2.				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(3)	3	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)													0.111111	6.640672	13.369634	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155727103	155727103	6845	1	C	G	G	G	415	32	GON4L	3	3
SMG5	23381	broad.mit.edu	37	1	156244414	156244414	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156244414C>G	uc001foc.3	-	c.518G>C	c.(517-519)CGA>CCA	p.R173P		NM_015327	NP_056142	Q9UPR3	SMG5_HUMAN	SMG5 homolog nonsense mediated mRNA decay	173					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|nucleus	protein phosphatase 2A binding			ovary(2)|skin(2)|pancreas(1)	5	Hepatocellular(266;0.158)													0.264286	107.044473	114.054956	37	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156244414	156244414	15294	1	C	G	G	G	403	31	SMG5	3	3
TTC24	164118	broad.mit.edu	37	1	156555590	156555590	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156555590G>T	uc009wsc.1	+	c.702G>T	c.(700-702)GGG>GGT	p.G234G		NM_001105669	NP_001099139	A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	514							binding			pancreas(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.142857	17.935273	29.10677	13	78	KEEP	---	---	---	---	capture		Silent	SNP	156555590	156555590	17246	1	G	T	T	T	522	41	TTC24	2	2
PEAR1	375033	broad.mit.edu	37	1	156880522	156880522	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156880522C>T	uc001fqj.1	+	c.1938C>T	c.(1936-1938)CCC>CCT	p.P646P	PEAR1_uc001fqk.1_Silent_p.P271P	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	646	EGF-like 8.					integral to membrane				ovary(2)|central_nervous_system(1)	3	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)													0.133333	6.081492	9.994302	4	26	KEEP	---	---	---	---	capture		Silent	SNP	156880522	156880522	12133	1	C	T	T	T	288	23	PEAR1	1	1
OR10Z1	128368	broad.mit.edu	37	1	158576722	158576722	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158576722A>G	uc010pio.1	+	c.494A>G	c.(493-495)CAC>CGC	p.H165R		NM_001004478	NP_001004478	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)													0.16129	40.376692	57.310998	25	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158576722	158576722	11329	1	A	G	G	G	78	6	OR10Z1	4	4
SPTA1	6708	broad.mit.edu	37	1	158627308	158627308	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158627308C>A	uc001fst.1	-	c.2764G>T	c.(2764-2766)GTA>TTA	p.V922L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	922	Spectrin 10.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.141732	27.735548	43.523154	18	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158627308	158627308	15630	1	C	A	A	A	221	17	SPTA1	2	2
SPTA1	6708	broad.mit.edu	37	1	158639340	158639340	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158639340C>A	uc001fst.1	-	c.1691G>T	c.(1690-1692)CGG>CTG	p.R564L		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	564	Spectrin 6.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.318182	97.572413	100.760041	35	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158639340	158639340	15630	1	C	A	A	A	299	23	SPTA1	1	1
LY9	4063	broad.mit.edu	37	1	160786463	160786463	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160786463C>T	uc001fwu.2	+	c.1152C>T	c.(1150-1152)TCC>TCT	p.S384S	LY9_uc001fwv.2_Silent_p.S384S|LY9_uc001fww.2_Intron|LY9_uc001fwx.2_Intron|LY9_uc001fwy.1_Intron|LY9_uc001fwz.2_Silent_p.S36S	NM_002348	NP_002339	Q9HBG7	LY9_HUMAN	lymphocyte antigen 9 isoform a	384	Extracellular (Potential).|Ig-like C2-type 2.				cell adhesion|immunoglobulin mediated immune response	integral to membrane				ovary(1)	1	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)											0.175439	21.714504	27.376634	10	47	KEEP	---	---	---	---	capture		Silent	SNP	160786463	160786463	9478	1	C	T	T	T	288	23	LY9	1	1
GPA33	10223	broad.mit.edu	37	1	167032878	167032878	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167032878G>T	uc001gea.1	-	c.512C>A	c.(511-513)CCT>CAT	p.P171H		NM_005814	NP_005805	Q99795	GPA33_HUMAN	transmembrane glycoprotein A33 precursor	171	Ig-like C2-type.|Extracellular (Potential).					integral to plasma membrane	receptor activity				0														0.168421	30.76478	40.638488	16	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167032878	167032878	6860	1	G	T	T	T	455	35	GPA33	2	2
FMO2	2327	broad.mit.edu	37	1	171162565	171162565	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171162565C>T	uc001ghk.1	+	c.224C>T	c.(223-225)CCT>CTT	p.P75L	FMO2_uc010pmd.1_5'UTR	NM_001460	NP_001451	Q99518	FMO2_HUMAN	flavin containing monooxygenase 2	75					drug metabolic process|NADPH oxidation|organic acid metabolic process|toxin metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|host cell microsome|integral to membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding				0	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)													0.2	31.239111	36.67872	13	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	171162565	171162565	6197	1	C	T	T	T	312	24	FMO2	2	2
FMO4	2329	broad.mit.edu	37	1	171310612	171310612	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:171310612C>T	uc001gho.2	+	c.1311C>T	c.(1309-1311)ATC>ATT	p.I437I		NM_002022	NP_002013	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	437					oxidation-reduction process|xenobiotic metabolic process	integral to membrane|intrinsic to endoplasmic reticulum membrane|microsome	flavin adenine dinucleotide binding|flavin-containing monooxygenase activity|NADP binding			kidney(2)|skin(1)	3	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					Pancreas(24;816 862 7754 7993 32832)				211				0.168421	29.243559	39.135421	16	79	KEEP	---	---	---	---	capture		Silent	SNP	171310612	171310612	6199	1	C	T	T	T	395	31	FMO4	1	1
CROCC	9696	broad.mit.edu	37	1	17249187	17249187	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:17249187G>A	uc001azt.2	+	c.90G>A	c.(88-90)GAG>GAA	p.E30E	CROCC_uc009voy.1_Intron|CROCC_uc009voz.1_5'UTR	NM_014675	NP_055490	Q5TZA2	CROCC_HUMAN	ciliary rootlet coiled-coil	30					cell cycle|cell projection organization|centrosome organization|protein localization	actin cytoskeleton|centriole|ciliary rootlet|plasma membrane	kinesin binding|structural molecule activity			ovary(2)|breast(2)	4		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)										0.177419	22.094227	28.166358	11	51	KEEP	---	---	---	---	capture		Silent	SNP	17249187	17249187	4032	1	G	A	A	A	425	33	CROCC	2	2
TNN	63923	broad.mit.edu	37	1	175096171	175096171	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:175096171C>A	uc001gkl.1	+	c.2995C>A	c.(2995-2997)CAG>AAG	p.Q999K		NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	999	Fibronectin type-III 9.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)						470				0.146119	46.060585	72.434398	32	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175096171	175096171	16864	1	C	A	A	A	377	29	TNN	2	2
PAPPA2	60676	broad.mit.edu	37	1	176659552	176659552	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:176659552A>G	uc001gkz.2	+	c.2417A>G	c.(2416-2418)TAC>TGC	p.Y806C	PAPPA2_uc001gky.1_Missense_Mutation_p.Y806C|PAPPA2_uc009www.2_Non-coding_Transcript	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	806					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|lung(1)|breast(1)	14														0.12844	44.886562	74.175176	28	190	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176659552	176659552	11850	1	A	G	G	G	182	14	PAPPA2	4	4
ASTN1	460	broad.mit.edu	37	1	177030246	177030246	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:177030246C>A	uc001glc.2	-	c.439G>T	c.(439-441)GAG>TAG	p.E147*	ASTN1_uc001glb.1_Nonsense_Mutation_p.E147*|ASTN1_uc001gld.1_Nonsense_Mutation_p.E147*|ASTN1_uc009wwx.1_Nonsense_Mutation_p.E147*	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	147					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)	11										849				0.142857	47.693998	79.563428	37	222	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	177030246	177030246	1083	1	C	A	A	A	416	32	ASTN1	5	2
CACNA1E	777	broad.mit.edu	37	1	181549863	181549863	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181549863C>G	uc001gow.2	+	c.902C>G	c.(901-903)ACT>AGT	p.T301S	CACNA1E_uc009wxr.2_Missense_Mutation_p.T208S|CACNA1E_uc009wxs.2_Missense_Mutation_p.T208S	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	301	I.|Extracellular (Potential).				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.257426	73.306926	78.690308	26	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	181549863	181549863	2658	1	C	G	G	G	260	20	CACNA1E	3	3
GLT25D2	23127	broad.mit.edu	37	1	183942810	183942810	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:183942810C>A	uc001gqr.2	-	c.567G>T	c.(565-567)GTG>GTT	p.V189V	GLT25D2_uc010poj.1_Silent_p.V189V|GLT25D2_uc001gqs.2_Silent_p.V69V	NM_015101	NP_055916	Q8IYK4	GT252_HUMAN	glycosyltransferase 25 domain containing 2	189					lipopolysaccharide biosynthetic process	endoplasmic reticulum lumen	procollagen galactosyltransferase activity			ovary(1)|breast(1)	2						Esophageal Squamous(10;42 606 18489 38825)								0.094891	6.065249	28.649381	13	124	KEEP	---	---	---	---	capture		Silent	SNP	183942810	183942810	6735	1	C	A	A	A	262	21	GLT25D2	2	2
MRTO4	51154	broad.mit.edu	37	1	19584405	19584405	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19584405G>T	uc001bbs.2	+	c.420G>T	c.(418-420)GGG>GGT	p.G140G		NM_016183	NP_057267	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog	140					ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GBM(192;2418 3032 7540 48714)								0.114286	3.18708	8.312363	4	31	KEEP	---	---	---	---	capture		Silent	SNP	19584405	19584405	10245	1	G	T	T	T	535	42	MRTO4	2	2
PTPRC	5788	broad.mit.edu	37	1	198725066	198725066	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198725066C>A	uc001gur.1	+	c.3671C>A	c.(3670-3672)GCC>GAC	p.A1224D	PTPRC_uc001gus.1_Missense_Mutation_p.A1176D|PTPRC_uc001gut.1_Missense_Mutation_p.A1063D	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	1224	Tyrosine-protein phosphatase 2.|Cytoplasmic (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.100719	8.855643	31.003022	14	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	198725066	198725066	13254	1	C	A	A	A	338	26	PTPRC	2	2
LAMB3	3914	broad.mit.edu	37	1	209799187	209799187	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:209799187C>A	uc001hhg.2	-	c.1782G>T	c.(1780-1782)GAG>GAT	p.E594D	LAMB3_uc009xco.2_Missense_Mutation_p.E594D|LAMB3_uc001hhh.2_Missense_Mutation_p.E594D|LAMB3_uc010psl.1_Intron	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	594	Domain II.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|large_intestine(1)|ovary(1)	4				OV - Ovarian serous cystadenocarcinoma(81;0.0519)										0.565217	40.176309	40.261377	13	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209799187	209799187	8935	1	C	A	A	A	363	28	LAMB3	2	2
TRAF3IP3	80342	broad.mit.edu	37	1	209936199	209936199	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:209936199G>A	uc001hho.2	+	c.535G>A	c.(535-537)GCC>ACC	p.A179T	TRAF3IP3_uc001hhl.2_Missense_Mutation_p.A159T|TRAF3IP3_uc001hhm.1_Missense_Mutation_p.A179T|TRAF3IP3_uc001hhn.2_Missense_Mutation_p.A159T|TRAF3IP3_uc009xcr.2_Missense_Mutation_p.A179T	NM_025228	NP_079504	Q9Y228	T3JAM_HUMAN	TRAF3-interacting JNK-activating modulator	179	Cytoplasmic (Potential).					integral to membrane	protein binding			large_intestine(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.045)										0.107438	8.29493	26.793068	13	108	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209936199	209936199	16986	1	G	A	A	A	598	46	TRAF3IP3	2	2
IRF6	3664	broad.mit.edu	37	1	209968741	209968741	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:209968741C>A	uc001hhq.1	-	c.402G>T	c.(400-402)TGG>TGT	p.W134C	IRF6_uc010psm.1_Missense_Mutation_p.W39C|IRF6_uc009xct.1_Missense_Mutation_p.W134C	NM_006147	NP_006138	O14896	IRF6_HUMAN	interferon regulatory factor 6	134					cell cycle arrest|interferon-gamma-mediated signaling pathway|mammary gland epithelial cell differentiation|negative regulation of cell proliferation|positive regulation of transcription, DNA-dependent|type I interferon-mediated signaling pathway	cytoplasm|nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0351)										0.269565	75.657588	81.181064	31	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	209968741	209968741	8137	1	C	A	A	A	286	22	IRF6	2	2
SYT14	255928	broad.mit.edu	37	1	210194461	210194461	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:210194461G>T	uc001hhs.3	+	c.439G>T	c.(439-441)GCC>TCC	p.A147S	SYT14_uc001hht.3_Missense_Mutation_p.A102S|SYT14_uc001hhu.3_Non-coding_Transcript|SYT14_uc010psn.1_Missense_Mutation_p.A147S|SYT14_uc010pso.1_Missense_Mutation_p.A64S|SYT14_uc009xcv.2_Missense_Mutation_p.A102S	NM_001146261	NP_001139733	Q8NB59	SYT14_HUMAN	synaptotagmin XIV isoform 1	102	Cytoplasmic (Potential).					integral to membrane				ovary(1)|skin(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.085)										0.3125	77.213923	80.219217	30	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	210194461	210194461	15991	1	G	T	T	T	546	42	SYT14	2	2
USH2A	7399	broad.mit.edu	37	1	215972282	215972282	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215972282C>T	uc001hku.1	-	c.9925G>A	c.(9925-9927)GGA>AGA	p.G3309R		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	3309	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.119658	18.876552	35.477458	14	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215972282	215972282	17598	1	C	T	T	T	273	21	USH2A	2	2
MARK1	4139	broad.mit.edu	37	1	220771719	220771719	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220771719T>A	uc009xdw.2	+	c.356T>A	c.(355-357)ATA>AAA	p.I119K	MARK1_uc001hmn.3_Missense_Mutation_p.I119K|MARK1_uc010pun.1_Missense_Mutation_p.I119K|MARK1_uc001hmm.3_Missense_Mutation_p.I119K	NM_018650	NP_061120	Q9P0L2	MARK1_HUMAN	MAP/microtubule affinity-regulating kinase 1	119	Protein kinase.				intracellular protein kinase cascade|protein phosphorylation	cytoplasm|microtubule cytoskeleton	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(3)|central_nervous_system(2)|stomach(1)|lung(1)	7				GBM - Glioblastoma multiforme(131;0.0407)						258				0.461538	53.246982	53.296963	18	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220771719	220771719	9695	1	T	A	A	A	637	49	MARK1	3	3
MOSC2	54996	broad.mit.edu	37	1	220928449	220928449	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:220928449C>G	uc001hmq.2	+	c.433C>G	c.(433-435)CTC>GTC	p.L145V	MOSC2_uc001hmr.2_Missense_Mutation_p.L145V|MOSC2_uc009xdx.2_Missense_Mutation_p.L145V	NM_017898	NP_060368	Q969Z3	MOSC2_HUMAN	MOCO sulphurase C-terminal domain containing 2	145					oxidation-reduction process	mitochondrial outer membrane	molybdenum ion binding|oxidoreductase activity|pyridoxal phosphate binding				0				GBM - Glioblastoma multiforme(131;0.00499)|all cancers(67;0.204)										0.086957	1.496534	13.414654	6	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	220928449	220928449	10106	1	C	G	G	G	260	20	MOSC2	3	3
HHIPL2	79802	broad.mit.edu	37	1	222713539	222713539	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222713539C>A	uc001hnh.1	-	c.1263G>T	c.(1261-1263)ATG>ATT	p.M421I		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	421					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)										0.318182	73.362477	75.951865	28	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	222713539	222713539	7378	1	C	A	A	A	221	17	HHIPL2	2	2
HHIPL2	79802	broad.mit.edu	37	1	222717028	222717028	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:222717028C>T	uc001hnh.1	-	c.825G>A	c.(823-825)TTG>TTA	p.L275L		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	275					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)										0.206186	30.791105	38.693863	20	77	KEEP	---	---	---	---	capture		Silent	SNP	222717028	222717028	7378	1	C	T	T	T	272	21	HHIPL2	2	2
DNAH14	127602	broad.mit.edu	37	1	225152201	225152201	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:225152201A>G	uc001how.2	+	c.388A>G	c.(388-390)ATA>GTA	p.I130V	DNAH14_uc001hou.3_Missense_Mutation_p.I130V|DNAH14_uc001hot.3_Missense_Mutation_p.I130V|DNAH14_uc001hov.3_Missense_Mutation_p.I130V	NM_001373	NP_001364	Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy polypeptide 14 isoform	257					microtubule-based movement	cilium axoneme|cytoplasm|dynein complex|microtubule	ATP binding|microtubule motor activity			central_nervous_system(1)	1														0.153846	24.252387	33.185357	12	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	225152201	225152201	4783	1	A	G	G	G	156	12	DNAH14	4	4
ENAH	55740	broad.mit.edu	37	1	225688728	225688728	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:225688728T>A	uc001hpc.1	-	c.1646A>T	c.(1645-1647)CAG>CTG	p.Q549L	ENAH_uc001hpd.1_Missense_Mutation_p.Q528L|ENAH_uc001hpb.1_Missense_Mutation_p.Q168L	NM_001008493	NP_001008493	Q8N8S7	ENAH_HUMAN	enabled homolog isoform a	549	EVH2.				axon guidance|intracellular transport|T cell receptor signaling pathway	cytosol|filopodium|focal adhesion|lamellipodium|synapse	actin binding|SH3 domain binding|WW domain binding			ovary(1)	1	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.19)										0.322034	55.00411	56.663628	19	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	225688728	225688728	5304	1	T	A	A	A	715	55	ENAH	3	3
PRSS38	339501	broad.mit.edu	37	1	228003843	228003843	+	Silent	SNP	C	G	G	rs113353225	by1000genomes	TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228003843C>G	uc001hrh.2	+	c.201C>G	c.(199-201)CCC>CCG	p.P67P		NM_183062	NP_898885	A1L453	PRS38_HUMAN	marapsin 2 precursor	67	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)|pancreas(1)	2														0.5	47.624339	47.624339	15	15	KEEP	---	---	---	---	capture		Silent	SNP	228003843	228003843	13077	1	C	G	G	G	288	23	PRSS38	3	3
RYR2	6262	broad.mit.edu	37	1	237923091	237923091	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237923091C>T	uc001hyl.1	+	c.11341C>T	c.(11341-11343)CTC>TTC	p.L3781F	RYR2_uc010pya.1_Missense_Mutation_p.L196F	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3781					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.107784	20.83908	46.302128	18	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237923091	237923091	14249	1	C	T	T	T	312	24	RYR2	2	2
RYR2	6262	broad.mit.edu	37	1	237941969	237941969	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237941969C>T	uc001hyl.1	+	c.11779C>T	c.(11779-11781)CCT>TCT	p.P3927S	RYR2_uc010pya.1_Missense_Mutation_p.P342S	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	3927					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.212121	31.913115	36.970033	14	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237941969	237941969	14249	1	C	T	T	T	390	30	RYR2	2	2
ZP4	57829	broad.mit.edu	37	1	238048719	238048719	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238048719G>T	uc001hym.2	-	c.1132C>A	c.(1132-1134)CAG>AAG	p.Q378K	LOC100130331_uc010pyc.1_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4 preproprotein	378	ZP.|Extracellular (Potential).				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			ovary(1)	1	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			NSCLC(166;160 2029 11600 18754 19936)								0.15625	14.603816	21.831863	10	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	238048719	238048719	18822	1	G	T	T	T	585	45	ZP4	2	2
CHML	1122	broad.mit.edu	37	1	241798348	241798348	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:241798348G>C	uc001hzd.2	-	c.721C>G	c.(721-723)CAA>GAA	p.Q241E	OPN3_uc001hza.2_Intron|OPN3_uc001hzb.2_Intron|OPN3_uc001hzc.2_Intron	NM_001821	NP_001812	P26374	RAE2_HUMAN	choroideremia-like Rab escort protein 2	241					intracellular protein transport|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(4)	4	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)											0.078125	1.821298	13.466532	5	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	241798348	241798348	3485	1	G	C	C	C	585	45	CHML	3	3
ZNF695	57116	broad.mit.edu	37	1	247163267	247163267	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247163267C>A	uc009xgu.2	-	c.113G>T	c.(112-114)AGA>ATA	p.R38I	ZNF695_uc001ica.2_Non-coding_Transcript|ZNF695_uc001icb.1_Non-coding_Transcript|ZNF695_uc009xgt.1_Non-coding_Transcript|ZNF695_uc001ibx.2_Missense_Mutation_p.R38I|ZNF695_uc001iby.2_Non-coding_Transcript|ZNF695_uc001icc.2_Missense_Mutation_p.R38I	NM_020394	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein SBZF3	38	KRAB.				regulation of transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding				0	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)											0.113821	13.656768	31.754836	14	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247163267	247163267	18693	1	C	A	A	A	416	32	ZNF695	2	2
NLRP3	114548	broad.mit.edu	37	1	247587725	247587726	+	Missense_Mutation	DNP	GG	CT	CT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247587725_247587726GG>CT	uc001icr.2	+	c.980_981GG>CT	c.(979-981)CGG>CCT	p.R327P	NLRP3_uc001ics.2_Missense_Mutation_p.R327P|NLRP3_uc001icu.2_Missense_Mutation_p.R327P|NLRP3_uc001icw.2_Missense_Mutation_p.R327P|NLRP3_uc001icv.2_Missense_Mutation_p.R327P|NLRP3_uc010pyw.1_Missense_Mutation_p.R325P|NLRP3_uc001ict.1_Missense_Mutation_p.R325P	NM_001079821	NP_001073289	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3 isoform a	327	NACHT.				detection of biotic stimulus|induction of apoptosis|inflammatory response|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|positive regulation of interleukin-1 beta secretion|protein oligomerization|signal transduction	cytoplasm	ATP binding|peptidoglycan binding|protein binding			ovary(5)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	11	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)							412				0.24359	49.405661	54.066662	19	59	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	247587725	247587726	10881	1	GG	CT	CT	CT	507	39	NLRP3	3	3
OR2W5	441932	broad.mit.edu	37	1	247655361	247655361	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247655361G>T	uc001icz.1	+	c.932G>T	c.(931-933)GGC>GTC	p.G311V		NM_001004698	NP_001004698	A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W,	311					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)											0.203704	46.510528	55.297726	22	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247655361	247655361	11440	1	G	T	T	T	546	42	OR2W5	2	2
OR13G1	441933	broad.mit.edu	37	1	247835664	247835664	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247835664G>T	uc001idi.1	-	c.680C>A	c.(679-681)ACA>AAA	p.T227K		NM_001005487	NP_001005487	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G,	227	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)											0.163043	29.064094	38.99369	15	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247835664	247835664	11348	1	G	T	T	T	624	48	OR13G1	2	2
OR2M5	127059	broad.mit.edu	37	1	248308812	248308812	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248308812C>A	uc010pze.1	+	c.363C>A	c.(361-363)GAC>GAA	p.D121E		NM_001004690	NP_001004690	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M,	121	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|kidney(1)	3	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;0.0388)											0.147059	80.440886	121.119529	50	290	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248308812	248308812	11419	1	C	A	A	A	233	18	OR2M5	2	2
OR2M3	127062	broad.mit.edu	37	1	248366583	248366583	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248366583A>T	uc010pzg.1	+	c.214A>T	c.(214-216)ATG>TTG	p.M72L		NM_001004689	NP_001004689	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M,	72	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	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;0.0245)											0.241379	206.765608	226.195048	77	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248366583	248366583	11417	1	A	T	T	T	104	8	OR2M3	3	3
OR2T10	127069	broad.mit.edu	37	1	248756268	248756268	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248756268G>T	uc010pzn.1	-	c.802C>A	c.(802-804)CCT>ACT	p.P268T		NM_001004693	NP_001004693	Q8NGZ9	O2T10_HUMAN	olfactory receptor, family 2, subfamily T,	268	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.744186	95.707333	98.027921	32	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248756268	248756268	11423	1	G	T	T	T	533	41	OR2T10	2	2
PAQR7	164091	broad.mit.edu	37	1	26189367	26189367	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26189367T>G	uc001bkx.2	-	c.964A>C	c.(964-966)ACG>CCG	p.T322P		NM_178422	NP_848509	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	322	Helical; Name=7; (Potential).				cell differentiation|multicellular organismal development|oogenesis	integral to membrane|plasma membrane	receptor activity|steroid binding			breast(3)	3		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|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;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		Esophageal Squamous(111;1206 1556 18433 19151 38418)								0.342105	41.365678	42.201706	13	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26189367	26189367	11857	1	T	G	G	G	767	59	PAQR7	4	4
CCDC21	64793	broad.mit.edu	37	1	26582344	26582345	+	Nonsense_Mutation	DNP	GG	TT	TT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:26582344_26582345GG>TT	uc001bls.1	+	c.891_892GG>TT	c.(889-894)ATGGAG>ATTTAG	p.297_298ME>I*	CCDC21_uc001blr.2_Nonsense_Mutation_p.297_298ME>I*|CCDC21_uc010ofa.1_Nonsense_Mutation_p.246_247ME>I*	NM_022778	NP_073615	Q6P2H3	CCD21_HUMAN	coiled-coil domain containing 21	297_298											0		all_cancers(24;7e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.6e-26)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;9.48e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00917)|READ - Rectum adenocarcinoma(331;0.0649)										0.103448	6.033541	15.09065	6	52	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	26582344	26582345	2918	1	GG	TT	TT	TT	611	47	CCDC21	5	2
TSSK3	81629	broad.mit.edu	37	1	32829729	32829729	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:32829729T>C	uc001bvf.2	+	c.679T>C	c.(679-681)TCC>CCC	p.S227P		NM_052841	NP_443073	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	227	Protein kinase.				cell differentiation|multicellular organismal development|protein phosphorylation|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)								55				0.074074	-6.346881	18.984166	10	125	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32829729	32829729	17223	1	T	C	C	C	754	58	TSSK3	4	4
ZNF362	149076	broad.mit.edu	37	1	33760819	33760819	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:33760819C>T	uc001bxc.1	+	c.1059C>T	c.(1057-1059)TCC>TCT	p.S353S		NM_152493	NP_689706	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	353	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				Pancreas(162;1431 2676 35353 38425)						OREG0013342	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.186047	16.576935	20.548107	8	35	KEEP	---	---	---	---	capture		Silent	SNP	33760819	33760819	18460	1	C	T	T	T	288	23	ZNF362	1	1
C1orf94	84970	broad.mit.edu	37	1	34667708	34667708	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:34667708G>T	uc001bxt.2	+	c.1294G>T	c.(1294-1296)GAC>TAC	p.D432Y	C1orf94_uc001bxs.3_Missense_Mutation_p.D242Y	NM_001134734	NP_001128206	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform a	242							protein binding				0		Myeloproliferative disorder(586;0.0393)												0.172662	44.216026	58.286578	24	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34667708	34667708	2147	1	G	T	T	T	585	45	C1orf94	2	2
DFFB	1677	broad.mit.edu	37	1	3800259	3800259	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:3800259C>G	uc010nzn.1	+	c.1043C>G	c.(1042-1044)CCC>CGC	p.P348R	DFFB_uc001alc.2_Missense_Mutation_p.P324R|DFFB_uc001ale.2_Non-coding_Transcript|DFFB_uc009vlp.2_Non-coding_Transcript|DFFB_uc001alb.2_Non-coding_Transcript|DFFB_uc009vlq.2_Non-coding_Transcript|DFFB_uc009vlr.2_Missense_Mutation_p.P275R|DFFB_uc001ald.2_Missense_Mutation_p.P260R	NM_004402	NP_004393	O76075	DFFB_HUMAN	DNA fragmentation factor, 40 kD, beta	324					apoptotic chromosome condensation|DNA fragmentation involved in apoptotic nuclear change|intracellular signal transduction	cytosol|nucleoplasm	deoxyribonuclease activity|enzyme binding				0	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;2.05e-30)|all_epithelial(116;6.22e-21)|all_lung(118;2.65e-08)|Lung NSC(185;6.25e-06)|Breast(487;0.000659)|Renal(390;0.00121)|all_neural(13;0.0019)|Hepatocellular(190;0.00705)|Colorectal(325;0.0113)|all_hematologic(16;0.0194)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0548)|Medulloblastoma(700;0.211)		Epithelial(90;1.18e-39)|OV - Ovarian serous cystadenocarcinoma(86;7.28e-23)|GBM - Glioblastoma multiforme(42;2.95e-17)|Colorectal(212;1.23e-05)|COAD - Colon adenocarcinoma(227;5.94e-05)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00038)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)						1253				0.071429	-3.107164	12.784888	6	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3800259	3800259	4632	1	C	G	G	G	286	22	DFFB	3	3
GUCA2B	2981	broad.mit.edu	37	1	42620447	42620447	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:42620447C>G	uc001chc.1	+	c.187C>G	c.(187-189)CTG>GTG	p.L63V		NM_007102	NP_009033	Q16661	GUC2B_HUMAN	guanylate cyclase activator 2B precursor	63					excretion	extracellular region	calcium sensitive guanylate cyclase activator activity				0	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)												0.244444	19.894205	22.581609	11	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42620447	42620447	7172	1	C	G	G	G	311	24	GUCA2B	3	3
TIE1	7075	broad.mit.edu	37	1	43772922	43772922	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43772922C>T	uc001ciu.2	+	c.750C>T	c.(748-750)TTC>TTT	p.F250F	TIE1_uc010okd.1_Silent_p.F250F|TIE1_uc010oke.1_Silent_p.F205F|TIE1_uc009vwq.2_Intron|TIE1_uc010okf.1_5'UTR|TIE1_uc010okg.1_5'UTR|TIE1_uc010okc.1_Silent_p.F250F	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	250	Extracellular (Potential).|EGF-like 1.				mesoderm development|protein phosphorylation	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			stomach(1)|salivary_gland(1)|lung(1)|ovary(1)	4	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)								488				0.174603	20.285006	26.580974	11	52	KEEP	---	---	---	---	capture		Silent	SNP	43772922	43772922	16421	1	C	T	T	T	376	29	TIE1	2	2
YIPF1	54432	broad.mit.edu	37	1	54331985	54331985	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:54331985G>A	uc001cvu.2	-	c.719C>T	c.(718-720)TCT>TTT	p.S240F	YIPF1_uc001cvv.2_Non-coding_Transcript|YIPF1_uc001cvw.2_Non-coding_Transcript|YIPF1_uc001cvx.2_Non-coding_Transcript|YIPF1_uc001cvy.2_Non-coding_Transcript	NM_018982	NP_061855	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	240	Helical; (Potential).					integral to membrane|transport vesicle				large_intestine(1)|ovary(1)	2														0.25	46.216948	50.306441	18	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54331985	54331985	18060	1	G	A	A	A	429	33	YIPF1	2	2
C1orf175	374977	broad.mit.edu	37	1	55167807	55167807	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:55167807G>A	uc010ooe.1	+	c.3330G>A	c.(3328-3330)AAG>AAA	p.K1110K	C1orf175_uc001cxq.2_Non-coding_Transcript|C1orf175_uc001cxs.2_Non-coding_Transcript|C1orf175_uc010ood.1_Silent_p.K628K|C1orf175_uc010oof.1_Non-coding_Transcript|C1orf175_uc001cxr.1_Non-coding_Transcript|C1orf175_uc009vzq.1_Non-coding_Transcript|C1orf175_uc001cxt.1_Non-coding_Transcript|C1orf175_uc009vzr.1_Silent_p.K312K	NM_001039464	NP_001034553	Q68CQ1	HEAT8_HUMAN	hypothetical protein LOC374977	1110	HEAT 3.					integral to membrane	binding				0														0.151515	7.850677	11.693381	5	28	KEEP	---	---	---	---	capture		Silent	SNP	55167807	55167807	2083	1	G	A	A	A	451	35	C1orf175	2	2
DEPDC1	55635	broad.mit.edu	37	1	68960168	68960168	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:68960168C>A	uc001dem.3	-	c.259G>T	c.(259-261)GAT>TAT	p.D87Y	DEPDC1_uc001dek.3_Non-coding_Transcript|DEPDC1_uc001del.3_Missense_Mutation_p.D87Y	NM_001114120	NP_001107592	Q5TB30	DEP1A_HUMAN	DEP domain containing 1 isoform a	87	DEP.				intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	transcriptional repressor complex	GTPase activator activity|protein binding|transcription repressor activity				0				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)										0.193548	12.731294	15.44896	6	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68960168	68960168	4618	1	C	A	A	A	416	32	DEPDC1	2	2
TNNI3K	51086	broad.mit.edu	37	1	74901798	74901798	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:74901798G>T	uc001dge.1	+	c.2110G>T	c.(2110-2112)GTG>TTG	p.V704L	TNNI3K_uc001dgd.2_Missense_Mutation_p.V704L|TNNI3K_uc001dgf.1_Missense_Mutation_p.V603L	NM_001112808	NP_001106279	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform a	603	Protein kinase.				protein phosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10										765				0.125	13.324586	23.21592	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74901798	74901798	16870	1	G	T	T	T	624	48	TNNI3K	2	2
SLC2A7	155184	broad.mit.edu	37	1	9083086	9083086	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:9083086T>A	uc009vmo.1	-	c.202A>T	c.(202-204)ATG>TTG	p.M68L		NM_207420	NP_997303	Q6PXP3	GTR7_HUMAN	intestinal facilitative glucose transporter 7	68	Extracellular (Potential).					integral to membrane|plasma membrane	sugar transmembrane transporter activity				0	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)										0.111111	15.323851	31.46812	12	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9083086	9083086	15047	1	T	A	A	A	663	51	SLC2A7	3	3
CD93	22918	broad.mit.edu	37	20	23065248	23065248	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:23065248T>C	uc002wsv.2	-	c.1582A>G	c.(1582-1584)ACA>GCA	p.T528A		NM_012072	NP_036204	Q9NPY3	C1QR1_HUMAN	CD93 antigen precursor	528	Extracellular (Potential).				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	integral to membrane|plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding			large_intestine(2)	2	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)													0.25	28.013322	30.507021	11	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23065248	23065248	3175	20	T	C	C	C	767	59	CD93	4	4
TM9SF4	9777	broad.mit.edu	37	20	30738501	30738501	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:30738501C>G	uc002wxj.2	+	c.1164C>G	c.(1162-1164)TTC>TTG	p.F388L	TM9SF4_uc010zts.1_Missense_Mutation_p.F295L|TM9SF4_uc002wxk.2_Missense_Mutation_p.F371L|TM9SF4_uc010gdz.2_Missense_Mutation_p.F295L	NM_014742	NP_055557	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	388	Helical; (Potential).					integral to membrane				central_nervous_system(1)|pancreas(1)	2			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)											0.073171	0.090643	7.771425	3	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30738501	30738501	16510	20	C	G	G	G	376	29	TM9SF4	3	3
KIAA0406	9675	broad.mit.edu	37	20	36640451	36640451	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:36640451G>A	uc002xhl.2	-	c.1768C>T	c.(1768-1770)CCA>TCA	p.P590S	KIAA0406_uc002xhm.2_Missense_Mutation_p.P590S	NM_014657	NP_055472	O43156	TTI1_HUMAN	hypothetical protein LOC9675	590							binding				0		Myeloproliferative disorder(115;0.00874)												0.328571	61.996629	63.823032	23	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36640451	36640451	8480	20	G	A	A	A	559	43	KIAA0406	2	2
SMOX	54498	broad.mit.edu	37	20	4163480	4163480	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:4163480C>T	uc002wkp.2	+	c.1354C>T	c.(1354-1356)CTG>TTG	p.L452L	SMOX_uc002wkk.1_Silent_p.L399L|SMOX_uc002wkl.1_Silent_p.L399L|SMOX_uc002wkm.1_Silent_p.L452L|SMOX_uc002wkn.1_Intron|SMOX_uc010zqo.1_Silent_p.L376L|SMOX_uc002wko.1_Silent_p.L452L	NM_175839	NP_787033	Q9NWM0	SMOX_HUMAN	spermine oxidase isoform 1	452					oxidation-reduction process|polyamine biosynthetic process|xenobiotic metabolic process	cytosol|nucleus	polyamine oxidase activity			breast(1)	1					Spermine(DB00127)									0.15	8.728433	13.435731	6	34	KEEP	---	---	---	---	capture		Silent	SNP	4163480	4163480	15303	20	C	T	T	T	363	28	SMOX	2	2
HNF4A	3172	broad.mit.edu	37	20	43057040	43057040	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:43057040G>A	uc002xma.2	+	c.1195G>A	c.(1195-1197)GGA>AGA	p.G399R	HNF4A_uc002xlu.2_Missense_Mutation_p.G377R|HNF4A_uc002xlv.2_Missense_Mutation_p.G377R|HNF4A_uc002xlz.2_Missense_Mutation_p.G399R|HNF4A_uc010ggq.2_Missense_Mutation_p.G392R	NM_000457	NP_000448	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4 alpha isoform b	399					blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|positive regulation of gene-specific transcription from RNA polymerase II promoter|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process	cytoplasm	activating transcription factor binding|promoter binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|zinc ion binding			ovary(1)|lung(1)|skin(1)	3		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			Colon(79;2 1269 8820 14841 52347)								0.228571	20.781272	23.146663	8	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43057040	43057040	7545	20	G	A	A	A	559	43	HNF4A	2	2
EYA2	2139	broad.mit.edu	37	20	45717915	45717915	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:45717915G>A	uc002xsn.2	+	c.714G>A	c.(712-714)GCG>GCA	p.A238A	EYA2_uc002xsm.2_Silent_p.A233A|EYA2_uc010ghp.2_Silent_p.A233A|EYA2_uc002xso.2_Silent_p.A233A|EYA2_uc002xsp.2_Silent_p.A233A|EYA2_uc002xsq.2_Silent_p.A233A	NM_172113	NP_742111	O00167	EYA2_HUMAN	RecName: Full=Eyes absent homolog 2;          EC=3.1.3.48;	233					DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	magnesium ion binding|protein binding|protein tyrosine phosphatase activity			ovary(1)	1		Myeloproliferative disorder(115;0.0241)				Pancreas(120;56 1725 18501 25218 43520)								0.358209	66.875461	68.063811	24	43	KEEP	---	---	---	---	capture		Silent	SNP	45717915	45717915	5523	20	G	A	A	A	470	37	EYA2	1	1
ARFGEF2	10564	broad.mit.edu	37	20	47634062	47634062	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47634062A>T	uc002xtx.3	+	c.4484A>T	c.(4483-4485)GAG>GTG	p.E1495V	ARFGEF2_uc010zyf.1_Missense_Mutation_p.E788V	NM_006420	NP_006411	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine	1495					exocytosis|intracellular signal transduction|regulation of ARF protein signal transduction	cytosol|Golgi membrane	ARF guanyl-nucleotide exchange factor activity			breast(3)	3			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			Esophageal Squamous(176;1738 1974 26285 33069 35354)								0.328947	67.148168	69.120065	25	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47634062	47634062	864	20	A	T	T	T	143	11	ARFGEF2	3	3
ATP9A	10079	broad.mit.edu	37	20	50224125	50224125	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50224125T>A	uc002xwg.1	-	c.2746_splice	c.e26-1	p.G916_splice	ATP9A_uc010gih.1_Splice_Site_SNP_p.G780_splice|ATP9A_uc002xwf.1_Splice_Site_SNP_p.G88_splice	NM_006045	NP_006036			ATPase, class II, type 9A						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(4)	4														0.3125	14.37009	14.870332	5	11	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	50224125	50224125	1217	20	T	A	A	A	715	55	ATP9A	5	3
SALL4	57167	broad.mit.edu	37	20	50401195	50401195	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50401195T>C	uc002xwh.3	-	c.2771A>G	c.(2770-2772)AAT>AGT	p.N924S	SALL4_uc010gii.2_Missense_Mutation_p.N487S|SALL4_uc002xwi.3_Missense_Mutation_p.N147S	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	924					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.235294	21.884308	24.06188	8	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50401195	50401195	14293	20	T	C	C	C	676	52	SALL4	4	4
TSHZ2	128553	broad.mit.edu	37	20	51870769	51870769	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:51870769C>A	uc002xwo.2	+	c.772C>A	c.(772-774)CCC>ACC	p.P258T		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	258					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(23;0.1)											0.357143	97.896782	99.658751	35	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51870769	51870769	17175	20	C	A	A	A	338	26	TSHZ2	2	2
PRPF6	24148	broad.mit.edu	37	20	62616311	62616311	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62616311G>A	uc002yho.2	+	c.292G>A	c.(292-294)GAT>AAT	p.D98N	PRPF6_uc002yhp.2_Missense_Mutation_p.D98N	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	98					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)													0.145833	9.990223	15.78383	7	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62616311	62616311	13017	20	G	A	A	A	585	45	PRPF6	2	2
LIPI	149998	broad.mit.edu	37	21	15561448	15561448	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:15561448C>A	uc002yjm.2	-	c.402G>T	c.(400-402)TGG>TGT	p.W134C	LIPI_uc010gkw.1_Missense_Mutation_p.W67C	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	113					lipid catabolic process	extracellular region|extracellular space|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)										0.1875	10.528152	13.459352	6	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15561448	15561448	9152	21	C	A	A	A	390	30	LIPI	2	2
GRIK1	2897	broad.mit.edu	37	21	30949368	30949368	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:30949368G>T	uc011acs.1	-	c.2046C>A	c.(2044-2046)CCC>CCA	p.P682P	GRIK1_uc002ynn.2_Silent_p.P667P|GRIK1_uc011act.1_Silent_p.P543P|GRIK1_uc002yno.1_Silent_p.P682P	NM_000830	NP_000821	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	682	Extracellular (Potential).				central nervous system development|synaptic transmission	cell junction|postsynaptic membrane	kainate selective glutamate receptor activity			large_intestine(1)|ovary(1)	2					L-Glutamic Acid(DB00142)|Topiramate(DB00273)					608				0.438596	76.468986	76.65587	25	32	KEEP	---	---	---	---	capture		Silent	SNP	30949368	30949368	7052	21	G	T	T	T	600	47	GRIK1	2	2
KRTAP21-1	337977	broad.mit.edu	37	21	32127527	32127527	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32127527C>A	uc011adi.1	-	c.170G>T	c.(169-171)GGA>GTA	p.G57V		NM_181619	NP_853650	Q3LI58	KR211_HUMAN	keratin associated protein 21-1	57						intermediate filament				breast(1)	1														0.196203	59.924581	73.527314	31	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32127527	32127527	8857	21	C	A	A	A	390	30	KRTAP21-1	2	2
KRTAP11-1	337880	broad.mit.edu	37	21	32253685	32253685	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32253685C>T	uc002yov.2	-	c.159G>A	c.(157-159)CTG>CTA	p.L53L		NM_175858	NP_787054	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1	53						keratin filament	structural molecule activity			pancreas(1)	1														0.15625	24.987751	35.80085	15	81	KEEP	---	---	---	---	capture		Silent	SNP	32253685	32253685	8832	21	C	T	T	T	262	21	KRTAP11-1	2	2
TIAM1	7074	broad.mit.edu	37	21	32524991	32524991	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:32524991G>T	uc002yow.1	-	c.3329C>A	c.(3328-3330)CCT>CAT	p.P1110H	TIAM1_uc011adk.1_Missense_Mutation_p.P1110H|TIAM1_uc011adl.1_Missense_Mutation_p.P1050H	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1110	DH.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|lung(1)	5										780				0.308824	56.643496	58.861994	21	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32524991	32524991	16418	21	G	T	T	T	455	35	TIAM1	2	2
TTC3	7267	broad.mit.edu	37	21	38537944	38537944	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:38537944G>T	uc002yvz.2	+	c.3428G>T	c.(3427-3429)CGA>CTA	p.R1143L	TTC3_uc011aee.1_Missense_Mutation_p.R833L|TTC3_uc002ywa.2_Missense_Mutation_p.R1143L|TTC3_uc002ywb.2_Missense_Mutation_p.R1143L|TTC3_uc010gnf.2_Missense_Mutation_p.R908L|TTC3_uc002ywc.2_Missense_Mutation_p.R833L|TTC3_uc002ywd.1_Missense_Mutation_p.R207L	NM_001001894	NP_001001894	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1143					protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|breast(1)	3		Myeloproliferative disorder(46;0.0412)				Ovarian(38;194 1649 35661)								0.266667	87.196557	93.066071	32	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38537944	38537944	17252	21	G	T	T	T	481	37	TTC3	1	1
KRTAP10-9	386676	broad.mit.edu	37	21	46047096	46047096	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46047096C>A	uc002zfp.3	+	c.8C>A	c.(7-9)GCG>GAG	p.A3E	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198690	NP_941963	P60411	KR109_HUMAN	keratin associated protein 10-9	3						keratin filament					0														0.222222	39.190204	44.280509	16	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46047096	46047096	8831	21	C	A	A	A	351	27	KRTAP10-9	1	1
PRAME	23532	broad.mit.edu	37	22	22890528	22890528	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:22890528G>C	uc002zwf.2	-	c.1491C>G	c.(1489-1491)GAC>GAG	p.D497E	LOC96610_uc011aim.1_Intron|PRAME_uc011air.1_Missense_Mutation_p.D481E|PRAME_uc010gtr.2_Missense_Mutation_p.D497E|PRAME_uc002zwg.2_Missense_Mutation_p.D497E|PRAME_uc002zwh.2_Missense_Mutation_p.D497E|PRAME_uc002zwi.2_Missense_Mutation_p.D497E|PRAME_uc002zwj.2_Missense_Mutation_p.D497E|PRAME_uc002zwk.2_Missense_Mutation_p.D497E	NM_206956	NP_996839	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	497	Mediates interaction with RARA.				apoptosis|cell differentiation|negative regulation of apoptosis|negative regulation of cell differentiation|negative regulation of retinoic acid receptor signaling pathway|positive regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|plasma membrane	retinoic acid receptor binding|transcription repressor activity			central_nervous_system(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		Melanoma(73;1707 1838 15168 27201)				1184				0.336134	122.140761	124.929871	40	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22890528	22890528	12860	22	G	C	C	C	568	44	PRAME	3	3
MMP11	4320	broad.mit.edu	37	22	24123581	24123581	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:24123581A>G	uc002zxx.2	+	c.1060A>G	c.(1060-1062)ATT>GTT	p.I354V	MMP11_uc002zxy.2_Non-coding_Transcript|MMP11_uc002zxz.2_Non-coding_Transcript	NM_005940	NP_005931	P24347	MMP11_HUMAN	matrix metalloproteinase 11 preproprotein	354	Hemopexin-like 2.				collagen catabolic process|multicellular organismal development|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			large_intestine(1)	1		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)												0.4	6.449515	6.493082	2	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24123581	24123581	10040	22	A	G	G	G	104	8	MMP11	4	4
MYO18B	84700	broad.mit.edu	37	22	26388390	26388390	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26388390C>A	uc003abz.1	+	c.6218C>A	c.(6217-6219)TCC>TAC	p.S2073Y	MYO18B_uc003aca.1_Missense_Mutation_p.S1954Y|MYO18B_uc010guy.1_Missense_Mutation_p.S1955Y|MYO18B_uc010guz.1_Missense_Mutation_p.S1953Y|MYO18B_uc011aka.1_Missense_Mutation_p.S1227Y|MYO18B_uc011akb.1_Missense_Mutation_p.S1586Y|MYO18B_uc010gva.1_Missense_Mutation_p.S71Y	NM_032608	NP_115997	Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2073	Tail.|Potential.					nucleus|sarcomere|unconventional myosin complex	actin binding|ATP binding|motor activity			ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2)	12										968				0.514286	53.647937	53.654058	18	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26388390	26388390	10461	22	C	A	A	A	390	30	MYO18B	2	2
ASPHD2	57168	broad.mit.edu	37	22	26830423	26830423	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26830423C>G	uc003acg.2	+	c.842C>G	c.(841-843)ACG>AGG	p.T281R		NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	281	Lumenal (Potential).				oxidation-reduction process|peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1														0.276923	101.544551	107.370581	36	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26830423	26830423	1074	22	C	G	G	G	247	19	ASPHD2	3	3
EMID1	129080	broad.mit.edu	37	22	29654850	29654850	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:29654850C>A	uc003aeo.2	+	c.1255C>A	c.(1255-1257)CCC>ACC	p.P419T	EMID1_uc003aem.2_Missense_Mutation_p.P417T|EMID1_uc003aen.2_Missense_Mutation_p.P415T|EMID1_uc003aep.2_Missense_Mutation_p.P396T	NM_133455	NP_597712	Q96A84	EMID1_HUMAN	EMI domain containing 1	415						collagen					0														0.157895	4.813311	6.933823	3	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29654850	29654850	5283	22	C	A	A	A	286	22	EMID1	2	2
CSF2RB	1439	broad.mit.edu	37	22	37325814	37325814	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:37325814A>T	uc003aqc.3	+	c.683A>T	c.(682-684)AAG>ATG	p.K228M	CSF2RB_uc003aqa.3_Missense_Mutation_p.K228M	NM_000395	NP_000386	P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta	228	Fibronectin type-III 1.|Extracellular (Potential).				respiratory gaseous exchange	granulocyte macrophage colony-stimulating factor receptor complex	cytokine receptor activity			pancreas(1)	1					Sargramostim(DB00020)									0.333333	15.943365	16.386494	6	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37325814	37325814	4076	22	A	T	T	T	39	3	CSF2RB	3	3
SUN2	25777	broad.mit.edu	37	22	39134735	39134735	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:39134735A>T	uc011anz.1	-	c.1909T>A	c.(1909-1911)TGG>AGG	p.W637R	SUN2_uc011aoa.1_Missense_Mutation_p.W591R|SUN2_uc003awh.1_Missense_Mutation_p.W602R|SUN2_uc003awi.1_Missense_Mutation_p.W602R|SUN2_uc010gxq.1_Missense_Mutation_p.W623R|SUN2_uc010gxr.1_Missense_Mutation_p.W602R|SUN2_uc010gxs.1_Missense_Mutation_p.W602R	NM_015374	NP_056189	Q9UH99	SUN2_HUMAN	unc-84 homolog B	602	SUN.|Perinuclear space.				centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex	lamin binding|microtubule binding			large_intestine(1)	1														0.272727	15.842909	16.865523	6	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39134735	39134735	15912	22	A	T	T	T	91	7	SUN2	3	3
APOBEC3B	9582	broad.mit.edu	37	22	39380195	39380195	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:39380195C>T	uc003awo.1	+	c.133C>T	c.(133-135)CGC>TGC	p.R45C	APOBEC3A_uc011aoc.1_Intron|APOBEC3B_uc003awp.1_Missense_Mutation_p.R45C|APOBEC3B_uc003awq.1_Non-coding_Transcript|APOBEC3D_uc011aod.1_Intron|APOBEC3D_uc011aoe.1_Intron|APOBEC3D_uc011aof.1_Intron	NM_004900	NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic	45							hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)													0.238095	50.644029	55.848914	20	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39380195	39380195	801	22	C	T	T	T	299	23	APOBEC3B	1	1
TAB1	10454	broad.mit.edu	37	22	39813817	39813817	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:39813817G>A	uc003axr.2	+	c.741G>A	c.(739-741)GCG>GCA	p.A247A	TAB1_uc003axt.2_Silent_p.A171A|TAB1_uc011aok.1_Silent_p.A5A|TAB1_uc003axu.1_Silent_p.A171A	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7	171	PP2C-like.				activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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	cytosol|endosome membrane	catalytic activity|protein binding				0										336				0.36	53.237312	54.099541	18	32	KEEP	---	---	---	---	capture		Silent	SNP	39813817	39813817	16016	22	G	A	A	A	496	39	TAB1	1	1
PARVB	29780	broad.mit.edu	37	22	44527484	44527484	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:44527484G>C	uc003bem.2	+	c.593G>C	c.(592-594)TGG>TCG	p.W198S	PARVB_uc003ben.2_Missense_Mutation_p.W165S|PARVB_uc010gzn.2_Missense_Mutation_p.W113S|PARVB_uc003beo.2_Missense_Mutation_p.W128S	NM_001003828	NP_001003828	Q9HBI1	PARVB_HUMAN	parvin, beta isoform a	165	CH 1.				cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)												0.351351	29.655773	30.380302	13	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44527484	44527484	11886	22	G	C	C	C	611	47	PARVB	3	3
ACR	49	broad.mit.edu	37	22	51182598	51182598	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:51182598C>T	uc003bnh.3	+	c.675C>T	c.(673-675)TGC>TGT	p.C225C		NM_001097	NP_001088	P10323	ACRO_HUMAN	acrosin precursor	225	Peptidase S1.				acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)										0.425532	54.741801	54.956359	20	27	KEEP	---	---	---	---	capture		Silent	SNP	51182598	51182598	170	22	C	T	T	T	350	27	ACR	1	1
TGFBRAP1	9392	broad.mit.edu	37	2	105885840	105885840	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:105885840G>A	uc002tcq.2	-	c.2295C>T	c.(2293-2295)CTC>CTT	p.L765L	TGFBRAP1_uc010fjc.2_Silent_p.L534L|TGFBRAP1_uc002tcr.3_Silent_p.L765L	NM_004257	NP_004248	Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor	765					regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	cytoplasm|membrane	SMAD binding|small GTPase regulator activity|transforming growth factor beta receptor binding			central_nervous_system(1)|skin(1)	2						Esophageal Squamous(183;794 2019 9730 21801 48859)								0.276596	32.151599	34.265551	13	34	KEEP	---	---	---	---	capture		Silent	SNP	105885840	105885840	16352	2	G	A	A	A	522	41	TGFBRAP1	2	2
RANBP2	5903	broad.mit.edu	37	2	109383270	109383270	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:109383270C>T	uc002tem.3	+	c.6275C>T	c.(6274-6276)ACG>ATG	p.T2092M		NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2	2092	RanBD1 2.				carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(14)	soft_tissue(14)|pancreas(1)	15														0.419929	338.622476	340.18761	118	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109383270	109383270	13488	2	C	T	T	T	247	19	RANBP2	1	1
MERTK	10461	broad.mit.edu	37	2	112740432	112740432	+	Silent	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:112740432A>T	uc002thk.1	+	c.1158A>T	c.(1156-1158)GCA>GCT	p.A386A	MERTK_uc002thl.1_Silent_p.A210A	NM_006343	NP_006334	Q12866	MERTK_HUMAN	MER receptor tyrosine kinase precursor	386	Fibronectin type-III 2.|Extracellular (Potential).				cell surface receptor linked signaling pathway|cell-cell signaling|leukocyte migration|protein phosphorylation|visual perception	integral to plasma membrane|soluble fraction	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(4)|upper_aerodigestive_tract(1)|kidney(1)	6										602				0.097222	5.375719	17.071496	7	65	KEEP	---	---	---	---	capture		Silent	SNP	112740432	112740432	9868	2	A	T	T	T	67	6	MERTK	3	3
GREB1	9687	broad.mit.edu	37	2	11756808	11756808	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:11756808A>T	uc002rbk.1	+	c.3374A>T	c.(3373-3375)CAC>CTC	p.H1125L	GREB1_uc002rbp.1_Missense_Mutation_p.H123L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1125	Ser-rich.					integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		Ovarian(39;850 945 2785 23371 33093)								0.505882	134.617307	134.619812	43	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11756808	11756808	7037	2	A	T	T	T	78	6	GREB1	3	3
LRP1B	53353	broad.mit.edu	37	2	141607711	141607711	+	Silent	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141607711A>T	uc002tvj.1	-	c.4899T>A	c.(4897-4899)GCT>GCA	p.A1633A	LRP1B_uc010fnl.1_Silent_p.A815A	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1633	Extracellular (Potential).|LDL-receptor class B 14.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.126582	13.392227	24.143478	10	69	KEEP	---	---	---	---	capture		Silent	SNP	141607711	141607711	9328	2	A	T	T	T	28	3	LRP1B	3	3
TPO	7173	broad.mit.edu	37	2	1440084	1440084	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:1440084T>C	uc002qww.2	+	c.410T>C	c.(409-411)ATG>ACG	p.M137T	TPO_uc010ewj.2_Intron|TPO_uc010yin.1_Missense_Mutation_p.M137T|TPO_uc002qwu.2_Missense_Mutation_p.M137T|TPO_uc002qwr.2_Missense_Mutation_p.M137T|TPO_uc002qwx.2_Missense_Mutation_p.M137T|TPO_uc010yio.1_Missense_Mutation_p.M137T|TPO_uc010yip.1_Missense_Mutation_p.M137T	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	137	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity			ovary(6)|pancreas(6)|skin(3)|lung(1)|kidney(1)	17	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)					723				0.122807	6.381047	14.332938	7	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1440084	1440084	16954	2	T	C	C	C	663	51	TPO	4	4
KIF5C	3800	broad.mit.edu	37	2	149829990	149829990	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:149829990G>C	uc010zbu.1	+	c.1258G>C	c.(1258-1260)GAG>CAG	p.E420Q	KIF5C_uc002tws.1_Non-coding_Transcript	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C	420					microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.108)										0.42623	84.414223	84.708242	26	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149829990	149829990	8618	2	G	C	C	C	533	41	KIF5C	3	3
CYTIP	9595	broad.mit.edu	37	2	158275081	158275081	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:158275081C>A	uc002tzj.1	-	c.567G>T	c.(565-567)TGG>TGT	p.W189C	CYTIP_uc010zcl.1_Missense_Mutation_p.W83C	NM_004288	NP_004279	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	189					regulation of cell adhesion	cell cortex|early endosome	protein binding			ovary(1)|kidney(1)	2														0.142857	14.330469	22.076022	9	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158275081	158275081	4372	2	C	A	A	A	286	22	CYTIP	2	2
SCN3A	6328	broad.mit.edu	37	2	165947017	165947017	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165947017G>T	uc002ucx.2	-	c.5646C>A	c.(5644-5646)AAC>AAA	p.N1882K	SCN3A_uc010zcy.1_Missense_Mutation_p.N365K|SCN3A_uc002ucy.2_Missense_Mutation_p.N1833K|SCN3A_uc002ucz.2_Missense_Mutation_p.N1833K	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1882						voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.114754	7.580437	16.504634	7	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165947017	165947017	14400	2	G	T	T	T	568	44	SCN3A	2	2
TTC21B	79809	broad.mit.edu	37	2	166799852	166799852	+	Splice_Site_SNP	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:166799852C>G	uc002udk.2	-	c.430_splice	c.e5-1	p.G144_splice	TTC21B_uc002udl.2_Splice_Site_SNP_p.G144_splice	NM_024753	NP_079029			tetratricopeptide repeat domain 21B							cilium axoneme|cytoplasm|cytoskeleton	binding			ovary(2)|pancreas(2)|breast(1)	5														0.1	2.00055	6.798763	3	27	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	166799852	166799852	17242	2	C	G	G	G	312	24	TTC21B	5	3
XIRP2	129446	broad.mit.edu	37	2	168101434	168101434	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168101434C>A	uc002udx.2	+	c.3532C>A	c.(3532-3534)CAA>AAA	p.Q1178K	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.Q1003K|XIRP2_uc010fpq.2_Missense_Mutation_p.Q956K|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1003					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.146067	21.908487	32.643343	13	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168101434	168101434	18011	2	C	A	A	A	221	17	XIRP2	2	2
C2orf77	129881	broad.mit.edu	37	2	170531214	170531214	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:170531214C>G	uc002ufe.2	-	c.534G>C	c.(532-534)AAG>AAC	p.K178N		NM_001085447	NP_001078916	Q0VFZ6	CB077_HUMAN	hypothetical protein LOC129881	178											0														0.103448	3.102931	7.643626	3	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170531214	170531214	2284	2	C	G	G	G	415	32	C2orf77	3	3
TTN	7273	broad.mit.edu	37	2	179470391	179470391	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179470391G>A	uc010zfg.1	-	c.45927C>T	c.(45925-45927)TCC>TCT	p.S15309S	TTN_uc010zfh.1_Silent_p.S9004S|TTN_uc010zfi.1_Silent_p.S8937S|TTN_uc010zfj.1_Silent_p.S8812S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	3446										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.15625	29.114765	39.901258	15	81	KEEP	---	---	---	---	capture		Silent	SNP	179470391	179470391	17290	2	G	A	A	A	600	47	TTN	2	2
ZNF804A	91752	broad.mit.edu	37	2	185800734	185800734	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:185800734C>A	uc002uph.2	+	c.611C>A	c.(610-612)GCC>GAC	p.A204D		NM_194250	NP_919226	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	204						intracellular	zinc ion binding			ovary(6)|large_intestine(1)|pancreas(1)	8														0.369048	87.402532	88.668691	31	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185800734	185800734	18768	2	C	A	A	A	338	26	ZNF804A	2	2
PLCL1	5334	broad.mit.edu	37	2	198949933	198949933	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:198949933G>T	uc010fsp.2	+	c.1692G>T	c.(1690-1692)ATG>ATT	p.M564I	PLCL1_uc002uuv.3_Missense_Mutation_p.M485I	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	RecName: Full=Inactive phospholipase C-like protein 1;          Short=PLC-L1; AltName: Full=Phospholipase C-deleted in lung carcinoma; AltName: Full=Phospholipase C-related but catalytically inactive protein;          Short=PRIP;	564	Interaction with GABA A beta subunit (By similarity).				intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1					Quinacrine(DB01103)									0.239316	67.21036	74.502906	28	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	198949933	198949933	12465	2	G	T	T	T	624	48	PLCL1	2	2
ERBB4	2066	broad.mit.edu	37	2	212286761	212286761	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:212286761G>C	uc002veg.1	-	c.2935C>G	c.(2935-2937)CGA>GGA	p.R979G	ERBB4_uc002veh.1_Missense_Mutation_p.R979G|ERBB4_uc010zji.1_Missense_Mutation_p.R969G|ERBB4_uc010zjj.1_Missense_Mutation_p.R969G	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	979	Protein kinase.|Cytoplasmic (Potential).				cell proliferation|protein phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(12)|large_intestine(1)|breast(1)	14		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)						777	TSP Lung(8;0.080)			0.075	-0.057383	7.309629	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	212286761	212286761	5402	2	G	C	C	C	480	37	ERBB4	3	3
PAX3	5077	broad.mit.edu	37	2	223086091	223086091	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:223086091G>T	uc002vmt.1	-	c.808C>A	c.(808-810)CGC>AGC	p.R270S	PAX3_uc002vmy.1_Missense_Mutation_p.R269S|PAX3_uc002vmv.1_Missense_Mutation_p.R270S|PAX3_uc002vmw.1_Missense_Mutation_p.R270S|PAX3_uc002vmx.1_Missense_Mutation_p.R270S|PAX3_uc010fwo.2_Missense_Mutation_p.R270S	NM_181459	NP_852124	P23760	PAX3_HUMAN	paired box 3 isoform PAX3e	270	Homeobox.		R -> C (in WS1 and WS3).		apoptosis|organ morphogenesis|positive regulation of gene-specific transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)	765		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)						141				0.240602	77.632912	85.801355	32	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	223086091	223086091	11900	2	G	T	T	T	507	39	PAX3	1	1
SPHKAP	80309	broad.mit.edu	37	2	228886677	228886677	+	Silent	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228886677A>G	uc002vpq.2	-	c.447T>C	c.(445-447)CCT>CCC	p.P149P	SPHKAP_uc002vpp.2_Silent_p.P149P|SPHKAP_uc010zlx.1_Silent_p.P149P	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	149						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.166667	7.213319	9.109484	3	15	KEEP	---	---	---	---	capture		Silent	SNP	228886677	228886677	15560	2	A	G	G	G	28	3	SPHKAP	4	4
MYEOV2	150678	broad.mit.edu	37	2	241069409	241069409	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:241069409G>A	uc002vyu.1	-	c.300C>T	c.(298-300)TCC>TCT	p.S100S		NM_138336	NP_612209	Q8WXC6	MYOV2_HUMAN	hypothetical protein LOC150678 isoform 1	Error:Variant_position_missing_in_Q8WXC6_after_alignment											0		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)										0.2	9.389268	11.062777	4	16	KEEP	---	---	---	---	capture		Silent	SNP	241069409	241069409	10421	2	G	A	A	A	600	47	MYEOV2	2	2
FKBP1B	2281	broad.mit.edu	37	2	24276806	24276806	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:24276806G>C	uc002rer.2	+	c.72G>C	c.(70-72)GTG>GTC	p.V24V	FKBP1B_uc002res.2_Silent_p.V24V|FKBP1B_uc002ret.2_Non-coding_Transcript|FKBP1B_uc002reu.2_Non-coding_Transcript	NM_004116	NP_004107	P68106	FKB1B_HUMAN	FK506 binding protein 1B, 12.6 kDa isoform a	24	PPIase FKBP-type.				'de novo' protein folding|negative regulation of heart rate|negative regulation of protein phosphatase type 2B activity|protein maturation by protein folding|protein refolding|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|regulation of ryanodine-sensitive calcium-release channel activity|response to redox state	calcium channel complex|cytosol|sarcoplasmic reticulum membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity|receptor binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.460526	96.81577	96.918597	35	41	KEEP	---	---	---	---	capture		Silent	SNP	24276806	24276806	6145	2	G	C	C	C	600	47	FKBP1B	3	3
AGBL5	60509	broad.mit.edu	37	2	27282185	27282185	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27282185C>G	uc002rie.2	+	c.2002C>G	c.(2002-2004)CCT>GCT	p.P668A	AGBL5_uc002rid.2_Missense_Mutation_p.P668A|AGBL5_uc002rif.2_Non-coding_Transcript	NM_021831	NP_068603	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5 isoform 1	668					protein branching point deglutamylation|proteolysis	cytosol|nucleus	metallocarboxypeptidase activity|tubulin binding|zinc ion binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.109375	8.176664	17.847972	7	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27282185	27282185	381	2	C	G	G	G	390	30	AGBL5	3	3
PLB1	151056	broad.mit.edu	37	2	28828816	28828816	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:28828816G>T	uc002rmb.1	+	c.3057_splice	c.e42+1	p.M1019_splice	PLB1_uc010ezj.1_Splice_Site_SNP_p.M1008_splice|PLB1_uc002rme.1_Intron|PLB1_uc002rmf.1_Splice_Site_SNP	NM_153021	NP_694566			phospholipase B1 precursor						lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|breast(1)	7	Acute lymphoblastic leukemia(172;0.155)													0.504587	176.229112	176.231302	55	54	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	28828816	28828816	12450	2	G	T	T	T	572	44	PLB1	5	2
LTBP1	4052	broad.mit.edu	37	2	33359884	33359884	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33359884A>T	uc002ros.2	+	c.1058A>T	c.(1057-1059)AAG>ATG	p.K353M	LTBP1_uc002rot.2_Missense_Mutation_p.K27M|LTBP1_uc002rou.2_Missense_Mutation_p.K27M|LTBP1_uc002rov.2_Missense_Mutation_p.K27M|LTBP1_uc010ymz.1_Missense_Mutation_p.K27M|LTBP1_uc010yna.1_Missense_Mutation_p.K27M	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	353					negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)												0.442105	121.12991	121.408304	42	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33359884	33359884	9449	2	A	T	T	T	39	3	LTBP1	3	3
TTC15	51112	broad.mit.edu	37	2	3405623	3405623	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:3405623G>T	uc002qxm.1	+	c.1123G>T	c.(1123-1125)GAC>TAC	p.D375Y	TTC15_uc002qxn.1_Missense_Mutation_p.D375Y|TTC15_uc010ewm.1_Missense_Mutation_p.D375Y	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	tetratricopeptide repeat domain 15	375							binding			ovary(2)|breast(1)|pancreas(1)	4	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)										0.329897	92.073587	94.557999	32	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3405623	3405623	17236	2	G	T	T	T	481	37	TTC15	1	1
SLC8A1	6546	broad.mit.edu	37	2	40656449	40656449	+	Silent	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:40656449T>A	uc002rrx.2	-	c.972A>T	c.(970-972)CGA>CGT	p.R324R	SLC8A1_uc002rry.2_Silent_p.R324R|SLC8A1_uc002rrz.2_Silent_p.R324R|SLC8A1_uc002rsa.2_Silent_p.R324R|SLC8A1_uc002rsd.3_Silent_p.R324R|SLC8A1_uc002rsb.1_Silent_p.R324R|SLC8A1_uc010fan.1_Silent_p.R324R|SLC8A1_uc002rsc.1_Silent_p.R324R	NM_021097	NP_066920	P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium	324	Cytoplasmic (Potential).				cell communication|muscle contraction|platelet activation	integral to plasma membrane	calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding			ovary(1)|kidney(1)|central_nervous_system(1)	3					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)									0.052632	-10.504519	9.587596	5	90	KEEP	---	---	---	---	capture		Silent	SNP	40656449	40656449	15203	2	T	A	A	A	691	54	SLC8A1	3	3
NRXN1	9378	broad.mit.edu	37	2	50699546	50699546	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:50699546G>T	uc010fbq.2	-	c.3254C>A	c.(3253-3255)GCC>GAC	p.A1085D	NRXN1_uc002rxb.3_Missense_Mutation_p.A717D|NRXN1_uc002rxe.3_Missense_Mutation_p.A1045D|NRXN1_uc002rxc.1_Non-coding_Transcript	NM_001135659	NP_001129131	P58400	NRX1B_HUMAN	neurexin 1 isoform alpha2 precursor	224	Extracellular (Potential).|Laminin G-like.				neuron cell-cell adhesion|neuronal signal transduction	cell surface|endocytic vesicle|integral to membrane|presynaptic membrane	cell adhesion molecule binding|receptor binding			ovary(2)	2		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)											0.208333	21.420285	25.205016	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50699546	50699546	11070	2	G	T	T	T	546	42	NRXN1	2	2
EHBP1	23301	broad.mit.edu	37	2	63272278	63272278	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:63272278G>T	uc002sby.2	+	c.3568G>T	c.(3568-3570)GAT>TAT	p.D1190Y	EHBP1_uc010fcp.2_Missense_Mutation_p.D1119Y|EHBP1_uc002sbz.2_Missense_Mutation_p.D1119Y|EHBP1_uc002scb.2_Missense_Mutation_p.D1155Y|LOC100132215_uc002scc.3_Non-coding_Transcript	NM_015252	NP_056067	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1 isoform 1	1190	Potential.					cytoplasm|membrane				ovary(1)|breast(1)	2	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)							379				0.555556	15.177478	15.202151	5	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	63272278	63272278	5164	2	G	T	T	T	481	37	EHBP1	1	1
KDM3A	55818	broad.mit.edu	37	2	86707321	86707321	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86707321G>T	uc002sri.3	+	c.2348G>T	c.(2347-2349)GGT>GTT	p.G783V	KDM3A_uc010ytj.1_Missense_Mutation_p.G783V|KDM3A_uc010ytk.1_Missense_Mutation_p.G731V	NM_018433	NP_060903	Q9Y4C1	KDM3A_HUMAN	jumonji domain containing 1A	783					androgen receptor signaling pathway|cell differentiation|formaldehyde biosynthetic process|histone H3-K9 demethylation|hormone-mediated signaling pathway|oxidation-reduction process|positive regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleus	androgen receptor binding|iron ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen			breast(2)|ovary(1)|central_nervous_system(1)	4						NSCLC(96;1150 1523 6936 46253 49736)								0.294118	67.941627	71.165989	25	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86707321	86707321	8432	2	G	T	T	T	572	44	KDM3A	2	2
EIF2AK3	9451	broad.mit.edu	37	2	88889990	88889990	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:88889990C>A	uc002stc.3	-	c.1136G>T	c.(1135-1137)AGA>ATA	p.R379I		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	379	Lumenal (Potential).				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3						GBM(138;671 1851 16235 39058 45249)				242				0.123077	9.751479	18.790807	8	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88889990	88889990	5187	2	C	A	A	A	416	32	EIF2AK3	2	2
EIF5B	9669	broad.mit.edu	37	2	99988158	99988158	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:99988158G>T	uc002tab.2	+	c.1517G>T	c.(1516-1518)TGG>TTG	p.W506L		NM_015904	NP_056988	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	506					regulation of translational initiation	cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			ovary(1)|pancreas(1)	2						Colon(162;2388 2567 2705 3444)								0.078125	-1.278305	10.371047	5	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99988158	99988158	5235	2	G	T	T	T	611	47	EIF5B	2	2
DZIP3	9666	broad.mit.edu	37	3	108406848	108406848	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108406848A>G	uc003dxd.2	+	c.3175A>G	c.(3175-3177)AAA>GAA	p.K1059E	DZIP3_uc003dxf.1_Missense_Mutation_p.K1059E|DZIP3_uc011bhm.1_Missense_Mutation_p.K510E	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	1059					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.232558	27.429225	30.244267	10	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108406848	108406848	5051	3	A	G	G	G	117	9	DZIP3	4	4
ADCY5	111	broad.mit.edu	37	3	123003542	123003542	+	Nonsense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123003542G>C	uc003egh.1	-	c.3699C>G	c.(3697-3699)TAC>TAG	p.Y1233*	ADCY5_uc003egg.1_Nonsense_Mutation_p.Y891*	NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	1233	Cytoplasmic (Potential).				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)										0.193878	43.892479	52.457521	19	79	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123003542	123003542	298	3	G	C	C	C	568	44	ADCY5	5	3
KALRN	8997	broad.mit.edu	37	3	124044878	124044878	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:124044878G>A	uc003ehg.2	+	c.1138G>A	c.(1138-1140)GAG>AAG	p.E380K	KALRN_uc010hrv.1_Missense_Mutation_p.E380K|KALRN_uc003ehf.1_Missense_Mutation_p.E380K|KALRN_uc011bjy.1_Missense_Mutation_p.E380K	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	380	Spectrin 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5										1865				0.152174	9.927199	15.231009	7	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124044878	124044878	8279	3	G	A	A	A	585	45	KALRN	2	2
TSEN2	80746	broad.mit.edu	37	3	12571270	12571270	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:12571270C>T	uc003bxc.2	+	c.1146C>T	c.(1144-1146)GTC>GTT	p.V382V	TSEN2_uc003bwz.2_Silent_p.V323V|TSEN2_uc003bxa.2_Silent_p.V356V|TSEN2_uc011auq.1_Silent_p.V356V|TSEN2_uc003bxb.2_Silent_p.V382V|TSEN2_uc011aur.1_Silent_p.V291V	NM_025265	NP_079541	Q8NCE0	SEN2_HUMAN	tRNA-intron nuclease 2 isoform 1	382					mRNA processing|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|nucleolus|tRNA-intron endonuclease complex	nucleic acid binding|tRNA-intron endonuclease activity			central_nervous_system(1)	1														0.216216	18.680293	21.429073	8	29	KEEP	---	---	---	---	capture		Silent	SNP	12571270	12571270	17163	3	C	T	T	T	366	29	TSEN2	2	2
COL6A6	131873	broad.mit.edu	37	3	130285743	130285743	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130285743T>A	uc010htl.2	+	c.1480T>A	c.(1480-1482)TCC>ACC	p.S494T		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	494	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.201923	42.412957	51.003562	21	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130285743	130285743	3841	3	T	A	A	A	702	54	COL6A6	3	3
FAIM	55179	broad.mit.edu	37	3	138351858	138351858	+	Silent	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:138351858G>C	uc003esp.2	+	c.579G>C	c.(577-579)CGG>CGC	p.R193R	FAIM_uc003esq.2_Silent_p.R181R|FAIM_uc003esr.2_Silent_p.R159R|FAIM_uc003ess.2_Silent_p.R159R	NM_001033030	NP_001028202	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule isoform a	159					apoptosis	cytoplasm					0														0.142857	10.353456	14.652866	5	30	KEEP	---	---	---	---	capture		Silent	SNP	138351858	138351858	5572	3	G	C	C	C	522	41	FAIM	3	3
XRN1	54464	broad.mit.edu	37	3	142123763	142123763	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:142123763T>C	uc003eus.2	-	c.1869A>G	c.(1867-1869)GAA>GAG	p.E623E	XRN1_uc010huu.2_Silent_p.E89E|XRN1_uc003eut.2_Silent_p.E623E|XRN1_uc003euu.2_Silent_p.E623E|XRN1_uc003euv.1_Silent_p.E484E	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a	623					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3														0.266667	11.993846	12.731034	4	11	KEEP	---	---	---	---	capture		Silent	SNP	142123763	142123763	18042	3	T	C	C	C	777	60	XRN1	4	4
C3orf20	84077	broad.mit.edu	37	3	14756870	14756870	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:14756870G>A	uc003byy.2	+	c.1388G>A	c.(1387-1389)TGG>TAG	p.W463*	C3orf20_uc003byz.2_Nonsense_Mutation_p.W341*|C3orf20_uc003bza.2_Nonsense_Mutation_p.W341*|C3orf20_uc003bzb.1_5'UTR	NM_032137	NP_115513	Q8ND61	CC020_HUMAN	hypothetical protein LOC84077	463						cytoplasm|integral to membrane				ovary(3)	3														0.125	4.107627	7.405382	3	21	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	14756870	14756870	2306	3	G	A	A	A	611	47	C3orf20	5	2
WWTR1	25937	broad.mit.edu	37	3	149374755	149374755	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:149374755G>A	uc003exe.2	-	c.339C>T	c.(337-339)CTC>CTT	p.L113L	WWTR1_uc003exf.2_Silent_p.L113L|WWTR1_uc011bns.1_Silent_p.L113L|WWTR1_uc003exh.2_Silent_p.L113L	NM_015472	NP_056287	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	113					hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent	cytoplasm	transcription coactivator activity			breast(3)	3			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)											0.5	12.699871	12.699871	4	4	KEEP	---	---	---	---	capture		Silent	SNP	149374755	149374755	17991	3	G	A	A	A	522	41	WWTR1	2	2
P2RY12	64805	broad.mit.edu	37	3	151056493	151056493	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151056493C>A	uc003eyw.1	-	c.141G>T	c.(139-141)ATG>ATT	p.M47I	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron|P2RY12_uc011boa.1_Missense_Mutation_p.M47I|P2RY12_uc003eyx.1_Missense_Mutation_p.M47I	NM_176876	NP_795345	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y12	47	Cytoplasmic (Potential).				platelet activation	integral to membrane|plasma membrane	guanyl-nucleotide exchange factor activity				0			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Ticlopidine(DB00208)|Treprostinil(DB00374)									0.093023	1.365567	8.532773	4	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151056493	151056493	11762	3	C	A	A	A	377	29	P2RY12	2	2
PLCH1	23007	broad.mit.edu	37	3	155241685	155241685	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:155241685C>A	uc011bok.1	-	c.1434_splice	c.e10+1	p.Y478_splice	PLCH1_uc011boj.1_Splice_Site_SNP_p.Y478_splice|PLCH1_uc011bol.1_Splice_Site_SNP_p.Y460_splice	NM_001130960	NP_001124432			phospholipase C eta 1 isoform a						lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)											0.189474	39.595781	48.163594	18	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	155241685	155241685	12463	3	C	A	A	A	221	17	PLCH1	5	2
HACL1	26061	broad.mit.edu	37	3	15621483	15621483	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:15621483G>T	uc003caf.2	-	c.737C>A	c.(736-738)CCC>CAC	p.P246H	HACL1_uc011avr.1_Non-coding_Transcript|HACL1_uc011avs.1_Missense_Mutation_p.P219H|HACL1_uc011avt.1_Missense_Mutation_p.P220H|HACL1_uc003cag.2_5'UTR|HACL1_uc011avu.1_Missense_Mutation_p.P164H|HACL1_uc010hep.2_Intron	NM_012260	NP_036392	Q9UJ83	HACL1_HUMAN	2-hydroxyphytanoyl-CoA lyase	246					fatty acid alpha-oxidation	peroxisomal matrix	carbon-carbon lyase activity|identical protein binding|magnesium ion binding|thiamine pyrophosphate binding				0														0.127907	13.663873	25.275052	11	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15621483	15621483	7223	3	G	T	T	T	559	43	HACL1	2	2
SI	6476	broad.mit.edu	37	3	164704960	164704960	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164704960C>T	uc003fei.2	-	c.5163G>A	c.(5161-5163)CAG>CAA	p.Q1721Q		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	1721	Sucrase.|Lumenal.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.15493	22.577821	30.655269	11	60	KEEP	---	---	---	---	capture		Silent	SNP	164704960	164704960	14792	3	C	T	T	T	311	24	SI	2	2
SI	6476	broad.mit.edu	37	3	164748519	164748519	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164748519C>A	uc003fei.2	-	c.2873G>T	c.(2872-2874)CGT>CTT	p.R958L		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	958	Lumenal.|P-type 2.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.186813	38.723891	47.083007	17	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	164748519	164748519	14792	3	C	A	A	A	247	19	SI	1	1
BCHE	590	broad.mit.edu	37	3	165503989	165503989	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:165503989C>A	uc003fem.3	-	c.1628G>T	c.(1627-1629)CGT>CTT	p.R543L	BCHE_uc003fen.3_Non-coding_Transcript	NM_000055	NP_000046	P06276	CHLE_HUMAN	butyrylcholinesterase precursor	543			R -> C (in BChE deficiency).		acetylcholine catabolic process|choline metabolic process|cocaine metabolic process|synaptic transmission, cholinergic	endoplasmic reticulum lumen|extracellular space|membrane	acetylcholinesterase activity|beta-amyloid binding|cholinesterase activity|enzyme binding			ovary(3)|pancreas(1)	4					Ambenonium(DB01122)|Atropine(DB00572)|Bambuterol(DB01408)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinnarizine(DB00568)|Demecarium bromide(DB00944)|Dibucaine(DB00527)|Donepezil(DB00843)|Echothiophate Iodide(DB01057)|Edrophonium(DB01010)|Ethopropazine(DB00392)|Etomidate(DB00292)|Galantamine(DB00674)|Hexafluronium bromide(DB00941)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Mivacurium(DB01226)|Neostigmine(DB01400)|Pancuronium(DB01337)|Pralidoxime(DB00733)|Procainamide(DB01035)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Terbutaline(DB00871)|Trimethaphan(DB01116)									0.15	11.928152	16.621504	6	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	165503989	165503989	1379	3	C	A	A	A	247	19	BCHE	1	1
NCEH1	57552	broad.mit.edu	37	3	172351586	172351586	+	Silent	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:172351586A>T	uc011bpx.1	-	c.1026T>A	c.(1024-1026)CCT>CCA	p.P342P	NCEH1_uc003fig.2_Silent_p.P334P|NCEH1_uc011bpw.1_Silent_p.P169P|NCEH1_uc011bpy.1_Silent_p.P169P	NM_001146276	NP_001139748	Q6PIU2	NCEH1_HUMAN	arylacetamide deacetylase-like 1 isoform a	302	Lumenal (Potential).				lipid catabolic process	endoplasmic reticulum|integral to membrane|microsome	carboxylesterase activity				0														0.170732	28.510333	36.909278	14	68	KEEP	---	---	---	---	capture		Silent	SNP	172351586	172351586	10614	3	A	T	T	T	80	7	NCEH1	3	3
SPATA16	83893	broad.mit.edu	37	3	172834930	172834930	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:172834930G>T	uc003fin.3	-	c.592C>A	c.(592-594)CAG>AAG	p.Q198K		NM_031955	NP_114161	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	198					cell differentiation|multicellular organismal development|spermatogenesis	Golgi apparatus	binding			ovary(2)	2	Ovarian(172;0.00319)|Breast(254;0.197)		LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14)											0.304348	78.063278	81.206634	28	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172834930	172834930	15509	3	G	T	T	T	624	48	SPATA16	2	2
ETV5	2119	broad.mit.edu	37	3	185783743	185783743	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185783743G>C	uc003fpy.2	-	c.895C>G	c.(895-897)CCG>GCG	p.P299A	ETV5_uc003fpz.2_Missense_Mutation_p.P257A	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	257					cellular response to oxidative stress|regulation of transcription, DNA-dependent	nucleus	promoter binding|sequence-specific DNA binding transcription factor activity			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)							170				0.135593	10.562946	18.153756	8	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185783743	185783743	5475	3	G	C	C	C	559	43	ETV5	3	3
RNF168	165918	broad.mit.edu	37	3	196198808	196198808	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:196198808C>T	uc003fwq.2	-	c.1598G>A	c.(1597-1599)AGA>AAA	p.R533K	RNF168_uc010iah.2_Missense_Mutation_p.R366K	NM_152617	NP_689830	Q8IYW5	RN168_HUMAN	ring finger protein 168	533					double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation	nucleus|ubiquitin ligase complex	chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding				0	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)										0.338983	116.259064	118.966279	40	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196198808	196198808	13936	3	C	T	T	T	416	32	RNF168	2	2
ZNF385D	79750	broad.mit.edu	37	3	21467010	21467010	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:21467010C>G	uc003cce.2	-	c.826G>C	c.(826-828)GTC>CTC	p.V276L		NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	276	Matrin-type 3.					nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(1)	3														0.111111	9.782668	19.197912	7	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21467010	21467010	18470	3	C	G	G	G	247	19	ZNF385D	3	3
ZNF385D	79750	broad.mit.edu	37	3	21552355	21552355	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:21552355G>T	uc003cce.2	-	c.437C>A	c.(436-438)ACA>AAA	p.T146K	ZNF385D_uc010hfb.1_Non-coding_Transcript	NM_024697	NP_078973	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	146	Thr-rich.					nucleus	nucleic acid binding|zinc ion binding			large_intestine(2)|ovary(1)	3														0.170213	30.434518	40.115828	16	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21552355	21552355	18470	3	G	T	T	T	624	48	ZNF385D	2	2
UBP1	7342	broad.mit.edu	37	3	33438574	33438574	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:33438574C>A	uc003cfq.3	-	c.1234G>T	c.(1234-1236)GCC>TCC	p.A412S	FBXL2_uc011axq.1_Intron|FBXL2_uc011axr.1_Intron|UBP1_uc003cfr.3_Missense_Mutation_p.A376S|UBP1_uc010hga.2_Missense_Mutation_p.A412S	NM_014517	NP_055332	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a) isoform a	412					negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|viral genome replication	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription corepressor activity			kidney(2)	2														0.166667	10.825381	14.62002	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33438574	33438574	17453	3	C	A	A	A	364	28	UBP1	2	2
CHL1	10752	broad.mit.edu	37	3	424303	424304	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:424303_424304GG>TT	uc003bot.2	+	c.2125_2126GG>TT	c.(2125-2127)GGG>TTG	p.G709L	CHL1_uc003bou.2_Missense_Mutation_p.G693L|CHL1_uc003bow.1_Missense_Mutation_p.G693L|CHL1_uc011asi.1_Missense_Mutation_p.G709L	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	693	Fibronectin type-III 1.|Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)						659				0.153846	11.961967	17.926381	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	424303	424304	3483	3	GG	TT	TT	TT	455	35	CHL1	2	2
C3orf39	84892	broad.mit.edu	37	3	43121364	43121364	+	Silent	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:43121364C>G	uc003cmq.1	-	c.1560G>C	c.(1558-1560)GTG>GTC	p.V520V	C3orf39_uc003cmr.1_Silent_p.V520V	NM_032806	NP_116195	Q8NAT1	AGO61_HUMAN	glycosyltransferase precursor	520						extracellular region	transferase activity, transferring glycosyl groups			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0571)|Kidney(284;0.0718)										0.090909	1.898646	7.467	3	30	KEEP	---	---	---	---	capture		Silent	SNP	43121364	43121364	2322	3	C	G	G	G	366	29	C3orf39	3	3
KIF9	64147	broad.mit.edu	37	3	47278048	47278048	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47278048C>A	uc010hjp.2	-	c.1986G>T	c.(1984-1986)AAG>AAT	p.K662N	KIF9_uc003cqx.2_Missense_Mutation_p.K662N|KIF9_uc003cqy.2_Missense_Mutation_p.K597N|KIF9_uc011bat.1_Non-coding_Transcript	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	662	Potential.				blood coagulation|microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		Colon(44;962 1147 15977 24541)								0.130435	3.607487	6.66533	3	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47278048	47278048	8621	3	C	A	A	A	363	28	KIF9	2	2
ARL6IP5	10550	broad.mit.edu	37	3	69153634	69153634	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:69153634G>A	uc003dnr.2	+	c.414G>A	c.(412-414)TCG>TCA	p.S138S		NM_006407	NP_006398	O75915	PRAF3_HUMAN	ADP-ribosylation-like factor 6 interacting	138	Cytoplasmic (By similarity).|Targeting to endoplasmic reticulum membrane (By similarity).				L-glutamate transport	endoplasmic reticulum membrane|integral to membrane				ovary(1)	1		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)										0.122222	13.564932	26.14086	11	79	KEEP	---	---	---	---	capture		Silent	SNP	69153634	69153634	962	3	G	A	A	A	509	40	ARL6IP5	1	1
SHQ1	55164	broad.mit.edu	37	3	72893552	72893552	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:72893552C>A	uc003dpf.2	-	c.166G>T	c.(166-168)GTA>TTA	p.V56L	SHQ1_uc010hod.2_5'UTR	NM_018130	NP_060600	Q6PI26	SHQ1_HUMAN	SHQ1 homolog	56	CS.				ribonucleoprotein complex assembly	cytosol|nucleoplasm	protein binding			ovary(2)|large_intestine(1)	3		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)										0.076923	-0.107487	7.039792	3	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72893552	72893552	14787	3	C	A	A	A	221	17	SHQ1	2	2
ROBO1	6091	broad.mit.edu	37	3	79174643	79174643	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:79174643G>T	uc003dqe.2	-	c.135C>A	c.(133-135)CCC>CCA	p.P45P		NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	45	Extracellular (Potential).				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)						693				0.326531	42.564087	43.882258	16	33	KEEP	---	---	---	---	capture		Silent	SNP	79174643	79174643	13992	3	G	T	T	T	600	47	ROBO1	2	2
CAV3	859	broad.mit.edu	37	3	8787262	8787262	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:8787262C>A	uc003bra.2	+	c.165C>A	c.(163-165)GAC>GAA	p.D55E	C3orf32_uc003bqz.2_5'Flank|CAV3_uc003brb.2_Missense_Mutation_p.D55E	NM_001234	NP_001225	P56539	CAV3_HUMAN	caveolin 3	55	Cytoplasmic (Potential).				cell growth|elevation of cytosolic calcium ion concentration|muscle organ development|negative regulation of cardiac muscle hypertrophy|negative regulation of cell size|negative regulation of MAP kinase activity|negative regulation of sarcomere organization|positive regulation of microtubule polymerization|regulation of skeletal muscle contraction|regulation of ventricular cardiomyocyte membrane repolarization|T-tubule organization	caveola|dystrophin-associated glycoprotein complex|Golgi membrane|neuromuscular junction|T-tubule	protein C-terminus binding|protein complex binding|protein complex scaffold|sodium channel regulator activity				0														0.179487	15.50619	19.2711	7	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8787262	8787262	2814	3	C	A	A	A	246	19	CAV3	1	1
ZNF654	55279	broad.mit.edu	37	3	88188515	88188515	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:88188515C>T	uc003dqv.2	+	c.55C>T	c.(55-57)CAT>TAT	p.H19Y	CGGBP1_uc003dqu.2_Intron	NM_018293	NP_060763	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	19					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)										0.183673	17.444339	22.047409	9	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88188515	88188515	18662	3	C	T	T	T	377	29	ZNF654	2	2
ANK2	287	broad.mit.edu	37	4	114253221	114253221	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114253221C>G	uc003ibe.3	+	c.3219C>G	c.(3217-3219)TTC>TTG	p.F1073L	ANK2_uc003ibd.3_Missense_Mutation_p.F1064L|ANK2_uc003ibf.3_Missense_Mutation_p.F1073L|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibc.2_Missense_Mutation_p.F1049L|ANK2_uc011cgb.1_Missense_Mutation_p.F1088L	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	1040	ZU5.|Interaction with SPTBN1.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.11236	12.28775	25.493817	10	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114253221	114253221	624	4	C	G	G	G	389	30	ANK2	3	3
ANK2	287	broad.mit.edu	37	4	114276239	114276239	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:114276239G>A	uc003ibe.3	+	c.6465G>A	c.(6463-6465)CTG>CTA	p.L2155L	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_5'Flank|ANK2_uc011cgb.1_Silent_p.L2170L	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	2122					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.148515	24.953484	36.93312	15	86	KEEP	---	---	---	---	capture		Silent	SNP	114276239	114276239	624	4	G	A	A	A	574	45	ANK2	2	2
QRFPR	84109	broad.mit.edu	37	4	122254118	122254118	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122254118G>T	uc010inj.1	-	c.655C>A	c.(655-657)CTT>ATT	p.L219I	QRFPR_uc010ink.1_Non-coding_Transcript|QRFPR_uc003ids.2_Missense_Mutation_p.L219I	NM_198179	NP_937822	Q96P65	QRFPR_HUMAN	G protein-coupled receptor 103	219	Helical; Name=5; (Potential).					integral to membrane|plasma membrane	neuropeptide Y receptor activity				0														0.285714	77.614096	81.936604	30	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122254118	122254118	13336	4	G	T	T	T	455	35	QRFPR	2	2
FAT4	79633	broad.mit.edu	37	4	126239846	126239846	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126239846G>T	uc003ifj.3	+	c.2280G>T	c.(2278-2280)CAG>CAT	p.Q760H		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	760	Cadherin 7.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.140845	15.200715	24.041304	10	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126239846	126239846	5928	4	G	T	T	T	464	36	FAT4	2	2
PCDH10	57575	broad.mit.edu	37	4	134084246	134084246	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:134084246G>T	uc003iha.2	+	c.2912G>T	c.(2911-2913)AGC>ATC	p.S971I		NM_032961	NP_116586	Q9P2E7	PCD10_HUMAN	protocadherin 10 isoform 1 precursor	971	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1				LUSC - Lung squamous cell carcinoma(193;0.227)										0.090909	2.895538	19.603462	9	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134084246	134084246	11927	4	G	T	T	T	442	34	PCDH10	2	2
CRIPAK	285464	broad.mit.edu	37	4	1389402	1389402	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:1389402C>T	uc003gdf.2	+	c.1103C>T	c.(1102-1104)GCC>GTC	p.A368V		NM_175918	NP_787114	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	368	Interaction with PAK1.				ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0106)											0.108108	2.774943	8.409258	4	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1389402	1389402	4016	4	C	T	T	T	338	26	CRIPAK	2	2
LRBA	987	broad.mit.edu	37	4	151749751	151749751	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:151749751G>A	uc010ipj.2	-	c.4752C>T	c.(4750-4752)AGC>AGT	p.S1584S	LRBA_uc003ilt.3_Silent_p.S243S|LRBA_uc003ilu.3_Silent_p.S1584S	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1584						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)	6	all_hematologic(180;0.151)													0.151575	121.145963	180.215293	77	431	KEEP	---	---	---	---	capture		Silent	SNP	151749751	151749751	9304	4	G	A	A	A	594	46	LRBA	2	2
SH3D19	152503	broad.mit.edu	37	4	152049490	152049490	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:152049490C>T	uc010ipl.1	-	c.1990G>A	c.(1990-1992)GAA>AAA	p.E664K	SH3D19_uc003imb.2_Missense_Mutation_p.E419K|SH3D19_uc003imc.2_Missense_Mutation_p.E605K|SH3D19_uc003ime.2_Missense_Mutation_p.E641K|SH3D19_uc010ipm.2_Missense_Mutation_p.E641K	NM_001009555	NP_001009555	Q5HYK7	SH319_HUMAN	SH3 domain containing 19 isoform a	664	SH3 4.				cellular membrane organization|positive regulation of membrane protein ectodomain proteolysis|post-Golgi vesicle-mediated transport	cytosol|Golgi apparatus|nucleus|plasma membrane	proline-rich region binding			ovary(1)	1	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)												0.133333	9.01748	14.890746	6	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152049490	152049490	14740	4	C	T	T	T	416	32	SH3D19	2	2
DCHS2	54798	broad.mit.edu	37	4	155219121	155219121	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155219121C>A	uc003inw.2	-	c.4980G>T	c.(4978-4980)CAG>CAT	p.Q1660H		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1660	Cadherin 14.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)										0.157143	13.55934	21.452287	11	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155219121	155219121	4459	4	C	A	A	A	311	24	DCHS2	2	2
DCHS2	54798	broad.mit.edu	37	4	155237050	155237050	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:155237050G>C	uc003inw.2	-	c.3745C>G	c.(3745-3747)CTT>GTT	p.L1249V		NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	1249	Cadherin 10.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)										0.5	75.254291	75.254291	22	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155237050	155237050	4459	4	G	C	C	C	468	36	DCHS2	3	3
GRIA2	2891	broad.mit.edu	37	4	158283966	158283966	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:158283966C>A	uc003ipm.3	+	c.2422C>A	c.(2422-2424)CTC>ATC	p.L808I	GRIA2_uc011cit.1_Missense_Mutation_p.L761I|GRIA2_uc003ipl.3_Missense_Mutation_p.L808I|GRIA2_uc003ipk.3_Missense_Mutation_p.L761I|GRIA2_uc011civ.1_Non-coding_Transcript|GRIA2_uc011ciw.1_Non-coding_Transcript|GRIA2_uc011cix.1_Silent_p.P79P|GRIA2_uc011ciy.1_3'UTR|GRIA2_uc011ciz.1_Non-coding_Transcript	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	808	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)									0.123077	9.45195	18.492062	8	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158283966	158283966	7046	4	C	A	A	A	312	24	GRIA2	2	2
TLL1	7092	broad.mit.edu	37	4	167020606	167020606	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:167020606G>T	uc011cjn.1	+	c.2903G>T	c.(2902-2904)GGC>GTC	p.G968V	TLL1_uc003irh.1_Missense_Mutation_p.G945V|TLL1_uc011cjo.1_Missense_Mutation_p.G769V	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	945	CUB 5.				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(2)|breast(1)|central_nervous_system(1)	4	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)										0.076389	-4.239572	22.19165	11	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167020606	167020606	16475	4	G	T	T	T	546	42	TLL1	2	2
GALNT7	51809	broad.mit.edu	37	4	174216973	174216973	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:174216973T>A	uc003isz.3	+	c.944T>A	c.(943-945)GTA>GAA	p.V315E	GALNT7_uc011ckb.1_Missense_Mutation_p.V92E	NM_017423	NP_059119	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	315	Catalytic subdomain A.|Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			central_nervous_system(1)	1		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)										0.316667	53.207176	54.99852	19	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	174216973	174216973	6482	4	T	A	A	A	741	57	GALNT7	3	3
ODZ3	55714	broad.mit.edu	37	4	183245189	183245189	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:183245189C>A	uc003ivd.1	+	c.16C>A	c.(16-18)CGC>AGC	p.R6S	ODZ3_uc010irv.1_Missense_Mutation_p.R6S	NM_001080477	NP_001073946	Q9P273	TEN3_HUMAN	odz, odd Oz/ten-m homolog 3	6	Cytoplasmic (Potential).|Teneurin N-terminal.				signal transduction	integral to membrane					0		all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184)		all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487)										0.098039	4.346886	12.584378	5	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	183245189	183245189	11241	4	C	A	A	A	247	19	ODZ3	1	1
HTT	3064	broad.mit.edu	37	4	3156033	3156033	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:3156033C>G	uc011bvq.1	+	c.3518C>G	c.(3517-3519)TCT>TGT	p.S1173C		NM_002111	NP_002102	P42858	HD_HUMAN	huntingtin	1171					establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule	autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex	beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding			ovary(1)|lung(1)	2		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)										0.285714	11.694357	12.27111	4	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3156033	3156033	7757	4	C	G	G	G	416	32	HTT	3	3
DCAF4L1	285429	broad.mit.edu	37	4	41984273	41984273	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:41984273G>A	uc003gwk.2	+	c.464G>A	c.(463-465)TGT>TAT	p.C155Y		NM_001029955	NP_001025126	Q3SXM0	DC4L1_HUMAN	WD repeat domain 21B	155											0														0.172043	29.338934	38.795241	16	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41984273	41984273	4442	4	G	A	A	A	624	48	DCAF4L1	2	2
KCTD8	386617	broad.mit.edu	37	4	44176901	44176901	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:44176901C>T	uc003gwu.2	-	c.1328G>A	c.(1327-1329)TGT>TAT	p.C443Y		NM_198353	NP_938167	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerisation domain	443						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity			central_nervous_system(2)|ovary(1)	3														0.08125	-0.639936	27.933711	13	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44176901	44176901	8421	4	C	T	T	T	221	17	KCTD8	2	2
CORIN	10699	broad.mit.edu	37	4	47808936	47808936	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47808936G>T	uc003gxm.2	-	c.192C>A	c.(190-192)ATC>ATA	p.I64I	CORIN_uc011bzg.1_Silent_p.I64I|CORIN_uc011bzh.1_Silent_p.I64I|CORIN_uc011bzi.1_Silent_p.I64I|CORIN_uc003gxn.3_Silent_p.I64I	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	64	Helical; Signal-anchor for type II membrane protein; (Potential).				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)	1														0.189655	21.888547	27.115793	11	47	KEEP	---	---	---	---	capture		Silent	SNP	47808936	47808936	3890	4	G	T	T	T	525	41	CORIN	2	2
CWH43	80157	broad.mit.edu	37	4	49019322	49019322	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:49019322T>C	uc003gyv.2	+	c.1243T>C	c.(1243-1245)TAT>CAT	p.Y415H	CWH43_uc011bzl.1_Missense_Mutation_p.Y388H	NM_025087	NP_079363	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog	415					GPI anchor biosynthetic process	integral to membrane				ovary(1)	1														0.269231	61.843956	65.589827	21	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49019322	49019322	4233	4	T	C	C	C	689	53	CWH43	4	4
PDGFRA	5156	broad.mit.edu	37	4	55136873	55136873	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55136873G>A	uc003han.3	+	c.1195G>A	c.(1195-1197)GAA>AAA	p.E399K	PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.E293K|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	399	Ig-like C2-type 4.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.131579	15.094628	25.122407	10	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55136873	55136873	12082	4	G	A	A	A	585	45	PDGFRA	2	2
AASDH	132949	broad.mit.edu	37	4	57204599	57204599	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57204599C>A	uc003hbn.2	-	c.3266G>T	c.(3265-3267)TGT>TTT	p.C1089F	AASDH_uc010ihb.2_Missense_Mutation_p.C604F|AASDH_uc011caa.1_3'UTR|AASDH_uc003hbo.2_Missense_Mutation_p.C989F|AASDH_uc011cab.1_Missense_Mutation_p.C604F|AASDH_uc010ihc.2_3'UTR	NM_181806	NP_861522	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1089					fatty acid metabolic process		acid-thiol ligase activity|acyl carrier activity|ATP binding|cofactor binding			ovary(4)	4	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)												0.144737	19.171709	28.404548	11	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57204599	57204599	23	4	C	A	A	A	221	17	AASDH	2	2
STAP1	26228	broad.mit.edu	37	4	68447163	68447163	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:68447163T>A	uc003hde.3	+	c.504T>A	c.(502-504)TAT>TAA	p.Y168*	STAP1_uc003hdf.2_Nonsense_Mutation_p.Y168*	NM_012108	NP_036240	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	168					cellular membrane fusion|intracellular protein transport	cytoplasm					0														0.297753	149.79657	156.312047	53	125	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	68447163	68447163	15771	4	T	A	A	A	660	51	STAP1	5	3
UGT2A1	10941	broad.mit.edu	37	4	70505157	70505158	+	Missense_Mutation	DNP	GA	TG	TG			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70505157_70505158GA>TG	uc011caq.1	-	c.804_805TC>CA	c.(802-807)ACTCTA>ACCATA	p.L269I	UGT2A1_uc010ihu.2_Intron|UGT2A1_uc003hem.3_Intron|UGT2A1_uc010iht.2_Intron|UGT2A1_uc010ihs.2_Missense_Mutation_p.L60I	NM_001105677	NP_001099147	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family,	59	Extracellular (Potential).				detection of chemical stimulus|sensory perception of smell	integral to membrane	glucuronosyltransferase activity|glucuronosyltransferase activity			ovary(1)	1														0.117978	18.65988	44.203472	21	157	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	70505157	70505158	17511	4	GA	TG	TG	TG	425	33	UGT2A1	2	2
SULT1B1	27284	broad.mit.edu	37	4	70615457	70615457	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70615457G>T	uc003hen.2	-	c.357C>A	c.(355-357)TTC>TTA	p.F119L		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	119					3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.318966	96.725874	100.108956	37	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70615457	70615457	15896	4	G	T	T	T	425	33	SULT1B1	2	2
PROL1	58503	broad.mit.edu	37	4	71275726	71275726	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:71275726C>A	uc003hfi.2	+	c.681C>A	c.(679-681)AAC>AAA	p.N227K		NM_021225	NP_067048	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	227	Thr-rich.				regulation of sensory perception of pain	extracellular region	endopeptidase inhibitor activity			large_intestine(1)	1		all_hematologic(202;0.196)												0.102564	5.038641	17.322471	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71275726	71275726	12997	4	C	A	A	A	233	18	PROL1	2	2
FRAS1	80144	broad.mit.edu	37	4	79447788	79447788	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79447788C>A	uc003hlb.2	+	c.10902C>A	c.(10900-10902)GCC>GCA	p.A3634A		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3629	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.421053	22.795586	22.899185	8	11	KEEP	---	---	---	---	capture		Silent	SNP	79447788	79447788	6288	4	C	A	A	A	301	24	FRAS1	2	2
SLC10A6	345274	broad.mit.edu	37	4	87770057	87770057	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:87770057C>A	uc003hqd.2	-	c.212G>T	c.(211-213)GGA>GTA	p.G71V		NM_197965	NP_932069	Q3KNW5	SOAT_HUMAN	sodium-dependent organic anion transporter	71	Helical; (Potential).					integral to membrane|plasma membrane	bile acid:sodium symporter activity				0		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)										0.153846	11.464153	17.427104	8	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87770057	87770057	14873	4	C	A	A	A	390	30	SLC10A6	2	2
PKD2	5311	broad.mit.edu	37	4	88940614	88940614	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:88940614C>T	uc003hre.2	+	c.600C>T	c.(598-600)CTC>CTT	p.L200L		NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	200	Cytoplasmic (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity				0		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)										0.357143	44.613012	45.368141	15	27	KEEP	---	---	---	---	capture		Silent	SNP	88940614	88940614	12391	4	C	T	T	T	405	32	PKD2	2	2
ATOH1	474	broad.mit.edu	37	4	94750176	94750176	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:94750176G>A	uc003hta.1	+	c.99G>A	c.(97-99)CCG>CCA	p.P33P		NM_005172	NP_005163	Q92858	ATOH1_HUMAN	atonal homolog 1	33	Poly-Pro.				transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity|transcription regulator activity				0		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)										0.6875	36.233795	36.738583	11	5	KEEP	---	---	---	---	capture		Silent	SNP	94750176	94750176	1131	4	G	A	A	A	483	38	ATOH1	1	1
PDHA2	5161	broad.mit.edu	37	4	96761995	96761995	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:96761995G>A	uc003htr.3	+	c.694G>A	c.(694-696)GAG>AAG	p.E232K		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase E1 alpha 2 precursor	232					glycolysis|oxidation-reduction process	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	NADH(DB00157)									0.28169	50.872839	53.912102	20	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96761995	96761995	12086	4	G	A	A	A	585	45	PDHA2	2	2
MARCH6	10299	broad.mit.edu	37	5	10415778	10415778	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:10415778C>T	uc003jet.1	+	c.2145C>T	c.(2143-2145)CTC>CTT	p.L715L	MARCH6_uc011cmu.1_Silent_p.L667L|MARCH6_uc003jeu.1_Silent_p.L413L|MARCH6_uc011cmv.1_Silent_p.L610L	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	715	Cytoplasmic (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding				0														0.059524	-7.387662	9.662021	5	79	KEEP	---	---	---	---	capture		Silent	SNP	10415778	10415778	9688	5	C	T	T	T	366	29	MARCH6	2	2
CTNND2	1501	broad.mit.edu	37	5	11018133	11018133	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:11018133G>T	uc003jfa.1	-	c.3037C>A	c.(3037-3039)CTC>ATC	p.L1013I	CTNND2_uc010itt.2_Missense_Mutation_p.L922I|CTNND2_uc011cmy.1_Missense_Mutation_p.L676I|CTNND2_uc011cmz.1_Missense_Mutation_p.L580I|CTNND2_uc010itu.1_Non-coding_Transcript|CTNND2_uc011cmx.1_Missense_Mutation_p.L605I	NM_001332	NP_001323	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	1013	ARM 9.				multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|pancreas(1)|lung(1)|skin(1)	7														0.06383	-5.403991	13.179023	6	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11018133	11018133	4179	5	G	T	T	T	455	35	CTNND2	2	2
CAMK4	814	broad.mit.edu	37	5	110814128	110814128	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:110814128T>A	uc011cvj.1	+	c.751T>A	c.(751-753)TTC>ATC	p.F251I	CAMK4_uc003kpf.2_Missense_Mutation_p.F251I|CAMK4_uc010jbv.2_Missense_Mutation_p.F54I	NM_001744	NP_001735	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	251	Protein kinase.				activation of phospholipase C activity|nerve growth factor receptor signaling pathway|protein phosphorylation|synaptic transmission	cytosol|nucleoplasm	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(3)|lung(2)	5		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)						687				0.210084	54.10711	63.364984	25	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110814128	110814128	2722	5	T	A	A	A	780	60	CAMK4	3	3
TSSK1B	83942	broad.mit.edu	37	5	112770252	112770252	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:112770252C>A	uc003kqm.2	-	c.285G>T	c.(283-285)CAG>CAT	p.Q95H	MCC_uc003kql.3_Intron	NM_032028	NP_114417	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1	95	Protein kinase.				cell differentiation|multicellular organismal development|protein phosphorylation|spermatogenesis		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			ovary(2)|skin(1)	3		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)						32				0.27907	30.580266	32.46886	12	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112770252	112770252	17221	5	C	A	A	A	311	24	TSSK1B	2	2
PRR16	51334	broad.mit.edu	37	5	120021732	120021732	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:120021732T>C	uc003ksq.2	+	c.243T>C	c.(241-243)AAT>AAC	p.N81N	PRR16_uc003ksp.2_Silent_p.N58N|PRR16_uc003ksr.2_Silent_p.N11N	NM_016644	NP_057728	Q569H4	PRR16_HUMAN	proline rich 16	81										pancreas(2)|ovary(1)	3		all_cancers(142;0.0464)|Prostate(80;0.00446)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.000126)|Epithelial(69;0.000331)|all cancers(49;0.00169)										0.23871	98.015432	107.666937	37	118	KEEP	---	---	---	---	capture		Silent	SNP	120021732	120021732	13032	5	T	C	C	C	634	49	PRR16	4	4
SNX24	28966	broad.mit.edu	37	5	122281795	122281795	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:122281795A>T	uc011cwo.1	+	c.190A>T	c.(190-192)AGG>TGG	p.R64W	SNX24_uc003ktf.2_Missense_Mutation_p.R64W|SNX24_uc010jcy.2_Missense_Mutation_p.R64W	NM_014035	NP_054754	Q9Y343	SNX24_HUMAN	SBBI31 protein	64	PX.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding				0		Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	OV - Ovarian serous cystadenocarcinoma(64;0.000654)|Epithelial(69;0.0016)|all cancers(49;0.0139)										0.137931	6.280041	9.957059	4	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122281795	122281795	15395	5	A	T	T	T	192	15	SNX24	3	3
MEGF10	84466	broad.mit.edu	37	5	126667082	126667082	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:126667082C>T	uc003kuh.3	+	c.82C>T	c.(82-84)CTT>TTT	p.L28F	MEGF10_uc010jdc.1_Missense_Mutation_p.L28F|MEGF10_uc010jdd.1_Missense_Mutation_p.L28F|MEGF10_uc003kui.3_Missense_Mutation_p.L28F	NM_032446	NP_115822	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10 precursor	28	Extracellular (Potential).|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				ovary(4)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)										0.304348	58.353221	60.707565	21	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126667082	126667082	9849	5	C	T	T	T	416	32	MEGF10	2	2
PRRC1	133619	broad.mit.edu	37	5	126860309	126860309	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:126860309C>T	uc003kuk.2	+	c.190C>T	c.(190-192)CCT>TCT	p.P64S	PRRC1_uc003kuj.3_Missense_Mutation_p.P64S	NM_130809	NP_570721	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	64	Pro-rich.					Golgi apparatus					0		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)										0.108527	11.851651	31.453177	14	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126860309	126860309	13053	5	C	T	T	T	390	30	PRRC1	2	2
FNIP1	96459	broad.mit.edu	37	5	131042107	131042107	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:131042107C>A	uc003kvs.1	-	c.911G>T	c.(910-912)AGA>ATA	p.R304I	RAPGEF6_uc003kvp.1_Intron|FNIP1_uc003kvt.1_Missense_Mutation_p.R276I|FNIP1_uc010jdm.1_Missense_Mutation_p.R259I|FNIP1_uc003kvu.2_Missense_Mutation_p.R304I	NM_133372	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1 isoform 1	304					regulation of protein phosphorylation	cytoplasm	protein binding			pancreas(1)	1		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)										0.245283	28.929302	32.081528	13	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131042107	131042107	6217	5	C	A	A	A	416	32	FNIP1	2	2
CDC25C	995	broad.mit.edu	37	5	137622186	137622186	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:137622186A>G	uc003lcs.1	-	c.1394T>C	c.(1393-1395)ATG>ACG	p.M465T	CDC25C_uc003lcp.1_Missense_Mutation_p.M387T|CDC25C_uc003lcq.1_Missense_Mutation_p.M314T|CDC25C_uc003lcr.1_Missense_Mutation_p.M387T|CDC25C_uc011cyp.1_Missense_Mutation_p.M404T	NM_001790	NP_001781	P30307	MPIP3_HUMAN	cell division cycle 25C isoform a	387	Rhodanese.				cell cycle checkpoint|cell division|cell proliferation|DNA replication|G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of mitosis|traversing start control point of mitotic cell cycle	cytosol|nucleoplasm	protein tyrosine phosphatase activity|WW domain binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)							669				0.208333	23.323868	27.105168	10	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137622186	137622186	3192	5	A	G	G	G	104	8	CDC25C	4	4
PCDHA3	56145	broad.mit.edu	37	5	140181097	140181097	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140181097C>A	uc003lhf.2	+	c.315C>A	c.(313-315)CAC>CAA	p.H105Q	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.H105Q	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	105	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.226415	24.070802	27.719218	12	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140181097	140181097	11945	5	C	A	A	A	233	18	PCDHA3	2	2
PCDHA11	56138	broad.mit.edu	37	5	140249750	140249750	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140249750G>T	uc003lia.2	+	c.1062G>T	c.(1060-1062)TTG>TTT	p.L354F	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Missense_Mutation_p.L354F	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	354	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.206897	14.033097	16.34255	6	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140249750	140249750	11941	5	G	T	T	T	620	48	PCDHA11	2	2
PCDHA11	56138	broad.mit.edu	37	5	140249785	140249785	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140249785C>A	uc003lia.2	+	c.1097C>A	c.(1096-1098)ACG>AAG	p.T366K	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc011dae.1_Missense_Mutation_p.T366K	NM_018902	NP_061725	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11 isoform 1 precursor	366	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.289474	28.710584	30.219994	11	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140249785	140249785	11941	5	C	A	A	A	247	19	PCDHA11	1	1
PCDHAC1	56135	broad.mit.edu	37	5	140307154	140307154	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140307154C>T	uc003lih.2	+	c.677C>T	c.(676-678)ACA>ATA	p.T226I	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lig.1_Missense_Mutation_p.T226I	NM_018898	NP_061721	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1 isoform 1	226	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(2)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.190476	15.77683	19.538039	8	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140307154	140307154	11952	5	C	T	T	T	221	17	PCDHAC1	2	2
PCDHB8	56128	broad.mit.edu	37	5	140559784	140559784	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140559784G>T	uc011dai.1	+	c.2169G>T	c.(2167-2169)GTG>GTT	p.V723V	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	723	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.303797	62.26438	64.981849	24	55	KEEP	---	---	---	---	capture		Silent	SNP	140559784	140559784	11968	5	G	T	T	T	600	47	PCDHB8	2	2
PCDHGA2	56113	broad.mit.edu	37	5	140720008	140720008	+	Silent	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140720008T>A	uc003ljk.1	+	c.1470T>A	c.(1468-1470)TCT>TCA	p.S490S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Silent_p.S490S	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	490	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.197674	34.536646	41.850321	17	69	KEEP	---	---	---	---	capture		Silent	SNP	140720008	140720008	11974	5	T	A	A	A	717	56	PCDHGA2	3	3
PCDHGA3	56112	broad.mit.edu	37	5	140725094	140725094	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140725094G>T	uc003ljm.1	+	c.1494G>T	c.(1492-1494)GGG>GGT	p.G498G	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Silent_p.G258G|PCDHGA3_uc011dap.1_Silent_p.G498G	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	498	Extracellular (Potential).|Cadherin 5.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.255556	50.808198	55.673156	23	67	KEEP	---	---	---	---	capture		Silent	SNP	140725094	140725094	11975	5	G	T	T	T	548	43	PCDHGA3	2	2
PCDHGB1	56104	broad.mit.edu	37	5	140730252	140730252	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140730252C>T	uc003ljo.1	+	c.425C>T	c.(424-426)TCA>TTA	p.S142L	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc011daq.1_Missense_Mutation_p.S142L	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1 isoform 1	142	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.104651	6.707928	20.083587	9	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140730252	140730252	11982	5	C	T	T	T	377	29	PCDHGB1	2	2
AFAP1L1	134265	broad.mit.edu	37	5	148699197	148699197	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:148699197T>A	uc003lqh.2	+	c.1532T>A	c.(1531-1533)ATG>AAG	p.M511K	AFAP1L1_uc010jgy.2_Missense_Mutation_p.M511K|AFAP1L1_uc003lqi.1_Missense_Mutation_p.M126K	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	511	PH 2.						protein binding			breast(1)|pancreas(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.294118	12.36212	13.011443	5	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148699197	148699197	355	5	T	A	A	A	663	51	AFAP1L1	3	3
ATP10B	23120	broad.mit.edu	37	5	160059293	160059293	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:160059293C>T	uc003lym.1	-	c.1463G>A	c.(1462-1464)AGA>AAA	p.R488K	ATP10B_uc003lyn.2_Missense_Mutation_p.R46K	NM_025153	NP_079429	O94823	AT10B_HUMAN	ATPase, class V, type 10B	488	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.254237	37.896638	41.130909	15	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160059293	160059293	1136	5	C	T	T	T	416	32	ATP10B	2	2
GABRA6	2559	broad.mit.edu	37	5	161116276	161116276	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:161116276G>T	uc003lyu.2	+	c.463G>T	c.(463-465)GAC>TAC	p.D155Y	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	155	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|large_intestine(1)|central_nervous_system(1)	9	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						TCGA Ovarian(5;0.080)			0.126582	10.406228	21.154624	10	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161116276	161116276	6416	5	G	T	T	T	585	45	GABRA6	2	2
ODZ2	57451	broad.mit.edu	37	5	167642069	167642069	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:167642069C>A	uc010jjd.2	+	c.3843C>A	c.(3841-3843)TAC>TAA	p.Y1281*	ODZ2_uc003lzr.3_Nonsense_Mutation_p.Y1051*|ODZ2_uc003lzt.3_Nonsense_Mutation_p.Y654*|ODZ2_uc010jje.2_Nonsense_Mutation_p.Y545*	NM_001122679	NP_001116151			odz, odd Oz/ten-m homolog 2											ovary(6)|central_nervous_system(4)	10	Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242)	Medulloblastoma(196;0.0241)|all_neural(177;0.026)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124)										0.266667	30.378317	32.592859	12	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	167642069	167642069	11240	5	C	A	A	A	259	20	ODZ2	5	2
TSPAN17	26262	broad.mit.edu	37	5	176083133	176083133	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:176083133G>T	uc003met.2	+	c.637G>T	c.(637-639)GGG>TGG	p.G213W	TSPAN17_uc003mes.3_Intron|TSPAN17_uc003meu.2_Intron|TSPAN17_uc003mev.2_Missense_Mutation_p.G213W|TSPAN17_uc003mew.2_Intron	NM_012171	NP_036303	Q96FV3	TSN17_HUMAN	transmembrane 4 superfamily member 17 isoform a	210	Extracellular (Potential).					integral to membrane|ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity				0	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.361111	35.362186	35.974605	13	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	176083133	176083133	17192	5	G	T	T	T	455	35	TSPAN17	2	2
PRDM9	56979	broad.mit.edu	37	5	23521200	23521200	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:23521200G>A	uc003jgo.2	+	c.420G>A	c.(418-420)CTG>CTA	p.L140L		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	140					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.469697	91.416682	91.469596	31	35	KEEP	---	---	---	---	capture		Silent	SNP	23521200	23521200	12906	5	G	A	A	A	574	45	PRDM9	2	2
PRDM9	56979	broad.mit.edu	37	5	23526560	23526560	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:23526560G>C	uc003jgo.2	+	c.1363G>C	c.(1363-1365)GAG>CAG	p.E455Q		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	455					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6														0.458824	136.120842	136.245887	39	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23526560	23526560	12906	5	G	C	C	C	429	33	PRDM9	3	3
SDHA	6389	broad.mit.edu	37	5	236605	236605	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:236605C>A	uc011clv.1	+	c.1323C>A	c.(1321-1323)GCC>GCA	p.A441A	SDHA_uc003jao.3_Silent_p.A441A|SDHA_uc011clw.1_Silent_p.A393A|SDHA_uc003jap.3_Silent_p.A441A|SDHA_uc003jaq.3_Silent_p.A216A|SDHA_uc003jar.3_Silent_p.A35A	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,	441					nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)									0.127273	9.62486	17.044116	7	48	KEEP	---	---	---	---	capture		Silent	SNP	236605	236605	14448	5	C	A	A	A	288	23	SDHA	1	1
CDH9	1007	broad.mit.edu	37	5	26988214	26988214	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:26988214T>A	uc003jgs.1	-	c.227A>T	c.(226-228)AAG>ATG	p.K76M	CDH9_uc010iug.2_Missense_Mutation_p.K76M	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	76	Extracellular (Potential).|Cadherin 1.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.090909	2.530769	11.811613	5	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26988214	26988214	3246	5	T	A	A	A	728	56	CDH9	3	3
NPR3	4883	broad.mit.edu	37	5	32712591	32712591	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:32712591G>T	uc003jhv.2	+	c.709G>T	c.(709-711)GAC>TAC	p.D237Y	NPR3_uc010iuo.2_Intron|NPR3_uc011cnz.1_Intron|NPR3_uc003jhu.2_Missense_Mutation_p.D237Y	NM_000908	NP_000899	P17342	ANPRC_HUMAN	natriuretic peptide receptor C/guanylate cyclase	237	Extracellular (Potential).				diuresis|osteoclast proliferation|regulation of blood pressure|regulation of osteoblast proliferation|skeletal system development	integral to membrane	hormone binding|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled			ovary(1)|central_nervous_system(1)	2					Nesiritide(DB04899)									0.075893	-0.92421	40.297405	17	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32712591	32712591	11001	5	G	T	T	T	481	37	NPR3	1	1
SLC45A2	51151	broad.mit.edu	37	5	33947415	33947415	+	Silent	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33947415C>G	uc003jid.2	-	c.1221G>C	c.(1219-1221)CTG>CTC	p.L407L	SLC45A2_uc003jie.2_Silent_p.L407L	NM_016180	NP_057264	Q9UMX9	S45A2_HUMAN	membrane-associated transporter protein isoform	407	Helical; Name=9; (Potential).				melanin biosynthetic process|response to stimulus|transmembrane transport|visual perception	integral to membrane|melanosome membrane				ovary(2)	2						Ovarian(31;380 859 8490 22203 49048)								0.084699	12.429599	76.509543	31	335	KEEP	---	---	---	---	capture		Silent	SNP	33947415	33947415	15138	5	C	G	G	G	210	17	SLC45A2	3	3
SPEF2	79925	broad.mit.edu	37	5	35806992	35806992	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35806992A>T	uc003jjo.2	+	c.5194A>T	c.(5194-5196)AGT>TGT	p.S1732C	SPEF2_uc003jjp.1_Missense_Mutation_p.S1218C|SPEF2_uc003jjr.2_Missense_Mutation_p.S787C	NM_024867	NP_079143	Q9C093	SPEF2_HUMAN	KPL2 protein isoform 1	1732					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity			ovary(1)|central_nervous_system(1)	2	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)											0.542056	181.152799	181.316864	58	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35806992	35806992	15547	5	A	T	T	T	39	3	SPEF2	3	3
IL7R	3575	broad.mit.edu	37	5	35873614	35873614	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35873614C>A	uc003jjs.2	+	c.570C>A	c.(568-570)CTC>CTA	p.L190L	IL7R_uc011coo.1_Silent_p.L190L|IL7R_uc011cop.1_Intron	NM_002185	NP_002176	P16871	IL7RA_HUMAN	interleukin 7 receptor precursor	190	Extracellular (Potential).|Fibronectin type-III.				immune response|regulation of DNA recombination	extracellular region|integral to membrane	antigen binding|interleukin-7 receptor activity			ovary(3)|breast(1)	4	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)											0.3375	72.595073	74.466008	27	53	KEEP	---	---	---	---	capture		Silent	SNP	35873614	35873614	8006	5	C	A	A	A	379	30	IL7R	2	2
NIPBL	25836	broad.mit.edu	37	5	37000950	37000950	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:37000950G>C	uc003jkl.3	+	c.3534G>C	c.(3532-3534)CAG>CAC	p.Q1178H	NIPBL_uc003jkk.3_Missense_Mutation_p.Q1178H	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1178					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding|transcription repressor activity			ovary(3)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	8	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)							934				0.084507	3.691456	16.133258	6	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37000950	37000950	10829	5	G	C	C	C	425	33	NIPBL	3	3
NIPBL	25836	broad.mit.edu	37	5	37027499	37027499	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:37027499G>A	uc003jkl.3	+	c.5847G>A	c.(5845-5847)GAG>GAA	p.E1949E	NIPBL_uc003jkk.3_Silent_p.E1949E	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1949	HEAT 3.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of gene-specific transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding|transcription repressor activity			ovary(3)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	8	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)							934				0.098901	3.083174	17.813824	9	82	KEEP	---	---	---	---	capture		Silent	SNP	37027499	37027499	10829	5	G	A	A	A	438	34	NIPBL	2	2
C9	735	broad.mit.edu	37	5	39331799	39331799	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:39331799G>T	uc003jlv.3	-	c.594C>A	c.(592-594)AAC>AAA	p.N198K		NM_001737	NP_001728	P02748	CO9_HUMAN	complement component 9 precursor	198	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis|hemolysis by symbiont of host erythrocytes	extracellular region|membrane attack complex					0	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)											0.081967	5.031957	48.409376	20	224	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39331799	39331799	2556	5	G	T	T	T	516	40	C9	1	1
C7	730	broad.mit.edu	37	5	40981518	40981518	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:40981518G>T	uc003jmh.2	+	c.2375G>T	c.(2374-2376)CGA>CTA	p.R792L		NM_000587	NP_000578	P10643	CO7_HUMAN	complement component 7 precursor	792	Complement control factor I module 2.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	extracellular region|membrane attack complex					0		Ovarian(839;0.0112)												0.083333	0.208004	6.550451	3	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40981518	40981518	2482	5	G	T	T	T	481	37	C7	1	1
C6	729	broad.mit.edu	37	5	41143053	41143053	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41143053G>T	uc003jmk.2	-	c.2679C>A	c.(2677-2679)AAC>AAA	p.N893K	C6_uc003jml.1_Missense_Mutation_p.N893K	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	893	Complement control factor I module 2.|C5b-binding domain.|Kazal-like 2.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)	5		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)												0.126866	22.579703	40.782939	17	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41143053	41143053	2416	5	G	T	T	T	568	44	C6	2	2
FBXO4	26272	broad.mit.edu	37	5	41929975	41929975	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:41929975A>T	uc003jmq.2	+	c.602A>T	c.(601-603)GAG>GTG	p.E201V	FBXO4_uc003jmp.2_Missense_Mutation_p.E201V|FBXO4_uc003jmr.2_Missense_Mutation_p.E201V	NM_012176	NP_036308	Q9UKT5	FBX4_HUMAN	F-box only protein 4 isoform 1	201					positive regulation of protein ubiquitination|protein polyubiquitination|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process|telomere maintenance|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	protein binding|protein homodimerization activity|ubiquitin-protein ligase activity			liver(1)	1		Lung NSC(810;4.15e-05)|Breast(839;0.00093)|Ovarian(839;0.00965)|Myeloproliferative disorder(839;0.0255)|all_neural(839;0.0604)												0.075472	-6.829664	22.580795	12	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41929975	41929975	5985	5	A	T	T	T	143	11	FBXO4	3	3
GHR	2690	broad.mit.edu	37	5	42689017	42689017	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:42689017C>A	uc003jmt.2	+	c.162C>A	c.(160-162)ACC>ACA	p.T54T	GHR_uc011cpq.1_Intron	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	54	Extracellular (Potential).				2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(2)|kidney(1)	3		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)					274				0.449814	374.042767	374.632812	121	148	KEEP	---	---	---	---	capture		Silent	SNP	42689017	42689017	6639	5	C	A	A	A	262	21	GHR	2	2
ADAMTS16	170690	broad.mit.edu	37	5	5146398	5146398	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5146398G>C	uc003jdl.2	+	c.331G>C	c.(331-333)GAT>CAT	p.D111H	ADAMTS16_uc003jdk.1_Missense_Mutation_p.D111H|ADAMTS16_uc003jdj.1_Missense_Mutation_p.D111H	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	111					proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.180723	32.947198	40.94941	15	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5146398	5146398	262	5	G	C	C	C	533	41	ADAMTS16	3	3
ADAMTS16	170690	broad.mit.edu	37	5	5239937	5239937	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5239937C>T	uc003jdl.2	+	c.2422C>T	c.(2422-2424)CGG>TGG	p.R808W	ADAMTS16_uc003jdk.1_Missense_Mutation_p.R808W	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	808	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.050761	-22.693436	19.415083	10	187	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5239937	5239937	262	5	C	T	T	T	295	23	ADAMTS16	1	1
SNX18	112574	broad.mit.edu	37	5	53814569	53814569	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:53814569G>T	uc003jpj.3	+	c.787G>T	c.(787-789)GGG>TGG	p.G263W	SNX18_uc011cqg.1_Missense_Mutation_p.G263W|SNX18_uc003jpi.3_Missense_Mutation_p.G263W	NM_052870	NP_443102	Q96RF0	SNX18_HUMAN	sorting nexin 18 isoform b	263					cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding				0		Lung NSC(810;3.46e-05)|Breast(144;0.102)												0.136364	10.949145	19.390998	9	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53814569	53814569	15389	5	G	T	T	T	559	43	SNX18	2	2
ACTBL2	345651	broad.mit.edu	37	5	56778146	56778146	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:56778146G>T	uc003jrm.2	-	c.389C>A	c.(388-390)ACA>AAA	p.T130K		NM_001017992	NP_001017992	Q562R1	ACTBL_HUMAN	actin, beta-like 2	130						cytoplasm|cytoskeleton	ATP binding			ovary(3)	3		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)										0.061224	-6.72991	12.96631	6	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56778146	56778146	195	5	G	T	T	T	624	48	ACTBL2	2	2
MAP1B	4131	broad.mit.edu	37	5	71495423	71495423	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:71495423G>T	uc003kbw.3	+	c.6241G>T	c.(6241-6243)GAT>TAT	p.D2081Y	MAP1B_uc010iyw.1_Missense_Mutation_p.D2098Y|MAP1B_uc010iyx.1_Missense_Mutation_p.D1955Y|MAP1B_uc010iyy.1_Missense_Mutation_p.D1955Y	NM_005909	NP_005900	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2081						microtubule|microtubule associated complex	structural molecule activity			large_intestine(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		Melanoma(17;367 822 11631 31730 47712)								0.419643	286.225888	287.484111	94	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71495423	71495423	9611	5	G	T	T	T	481	37	MAP1B	1	1
ZNF366	167465	broad.mit.edu	37	5	71756118	71756118	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:71756118G>A	uc003kce.1	-	c.1206C>T	c.(1204-1206)TTC>TTT	p.F402F		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	402	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)										0.32	19.467374	20.200602	8	17	KEEP	---	---	---	---	capture		Silent	SNP	71756118	71756118	18462	5	G	A	A	A	529	41	ZNF366	2	2
ZNF366	167465	broad.mit.edu	37	5	71756208	71756208	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:71756208G>A	uc003kce.1	-	c.1116C>T	c.(1114-1116)CTC>CTT	p.L372L		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	372	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)										0.103448	1.804309	6.345201	3	26	KEEP	---	---	---	---	capture		Silent	SNP	71756208	71756208	18462	5	G	A	A	A	470	37	ZNF366	1	1
ZNF366	167465	broad.mit.edu	37	5	71757137	71757137	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:71757137C>A	uc003kce.1	-	c.187G>T	c.(187-189)GAC>TAC	p.D63Y		NM_152625	NP_689838	Q8N895	ZN366_HUMAN	zinc finger protein 366	63					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)										0.122449	12.741716	26.413353	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71757137	71757137	18462	5	C	A	A	A	416	32	ZNF366	2	2
CMYA5	202333	broad.mit.edu	37	5	79028950	79028950	+	Silent	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:79028950A>T	uc003kgc.2	+	c.4362A>T	c.(4360-4362)ATA>ATT	p.I1454I		NM_153610	NP_705838	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1454						perinuclear region of cytoplasm				ovary(6)|pancreas(2)|lung(1)	9		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)										0.206897	28.272243	32.886475	12	46	KEEP	---	---	---	---	capture		Silent	SNP	79028950	79028950	3728	5	A	T	T	T	189	15	CMYA5	3	3
MSH3	4437	broad.mit.edu	37	5	80064744	80064744	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:80064744G>T	uc003kgz.2	+	c.2175G>T	c.(2173-2175)GAG>GAT	p.E725D		NM_002439	NP_002430	P20585	MSH3_HUMAN	mutS homolog 3	725					maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding			ovary(1)	1		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		Melanoma(88;1010 1399 13793 26548 36275)				1101				0.229167	24.797742	28.028774	11	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80064744	80064744	10264	5	G	T	T	T	425	33	MSH3	2	2
RGMB	285704	broad.mit.edu	37	5	98128924	98128924	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:98128924G>A	uc003knc.2	+	c.904G>A	c.(904-906)GTG>ATG	p.V302M		NM_001012761	NP_001012779	Q6NW40	RGMB_HUMAN	RGM domain family, member B	261					axon guidance|BMP signaling pathway|cell adhesion|positive regulation of transcription, DNA-dependent	anchored to plasma membrane|ER-Golgi intermediate compartment|membrane raft	identical protein binding				0		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)										0.195652	18.459107	22.42369	9	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98128924	98128924	13754	5	G	A	A	A	520	40	RGMB	1	1
AIM1	202	broad.mit.edu	37	6	106967187	106967187	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:106967187A>T	uc003prh.2	+	c.880A>T	c.(880-882)AGG>TGG	p.R294W		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	294							sugar binding			breast(4)|ovary(2)|large_intestine(1)	7	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)						659				0.28	17.514012	18.602201	7	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106967187	106967187	433	6	A	T	T	T	36	3	AIM1	3	3
DSE	29940	broad.mit.edu	37	6	116758311	116758311	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:116758311C>T	uc011ebg.1	+	c.2737C>T	c.(2737-2739)CCA>TCA	p.P913S	DSE_uc003pws.2_Missense_Mutation_p.P894S|DSE_uc003pwt.2_Missense_Mutation_p.P894S|DSE_uc003pwu.2_Missense_Mutation_p.P561S	NM_013352	NP_037484	Q9UL01	DSE_HUMAN	dermatan sulfate epimerase precursor	894					dermatan sulfate biosynthetic process	endoplasmic reticulum|Golgi apparatus|integral to membrane	chondroitin-glucuronate 5-epimerase activity			ovary(1)	1		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)										0.20339	25.868187	30.688049	12	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116758311	116758311	4958	6	C	T	T	T	286	22	DSE	2	2
C6orf170	221322	broad.mit.edu	37	6	121615756	121615756	+	Silent	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:121615756A>G	uc003pyo.1	-	c.1191T>C	c.(1189-1191)ACT>ACC	p.T397T	C6orf170_uc003pyq.1_Non-coding_Transcript|C6orf170_uc003pyp.1_5'Flank	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	397					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3				GBM - Glioblastoma multiforme(226;0.00521)										0.283019	138.214192	144.9336	45	114	KEEP	---	---	---	---	capture		Silent	SNP	121615756	121615756	2449	6	A	G	G	G	184	15	C6orf170	4	4
GPR126	57211	broad.mit.edu	37	6	142741054	142741054	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:142741054G>T	uc010khe.2	+	c.3132G>T	c.(3130-3132)ATG>ATT	p.M1044I	GPR126_uc010khc.2_Missense_Mutation_p.M1044I|GPR126_uc010khd.2_Missense_Mutation_p.M1016I|GPR126_uc010khf.2_Missense_Mutation_p.M1016I|GPR126_uc011edv.1_Missense_Mutation_p.M104I	NM_198569	NP_940971	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126 beta 1 precursor	1044	Helical; Name=5; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)	1	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)										0.343915	182.016436	186.084002	65	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142741054	142741054	6914	6	G	T	T	T	611	47	GPR126	2	2
HIVEP2	3097	broad.mit.edu	37	6	143095280	143095280	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:143095280G>A	uc003qjd.2	-	c.596C>T	c.(595-597)GCC>GTC	p.A199V		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	199	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|central_nervous_system(1)	4				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		Esophageal Squamous(107;843 1510 13293 16805 42198)								0.209302	19.550029	22.914937	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143095280	143095280	7478	6	G	A	A	A	546	42	HIVEP2	2	2
GRM1	2911	broad.mit.edu	37	6	146720721	146720721	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:146720721C>T	uc010khw.1	+	c.2546C>T	c.(2545-2547)GCC>GTC	p.A849V	GRM1_uc010khv.1_Missense_Mutation_p.A849V|GRM1_uc003qll.2_Missense_Mutation_p.A849V|GRM1_uc011edz.1_Missense_Mutation_p.A849V|GRM1_uc011eea.1_Missense_Mutation_p.A849V	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	849	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			ovary(4)|central_nervous_system(3)|large_intestine(2)	9		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)									0.296296	62.666891	65.673948	24	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146720721	146720721	7075	6	C	T	T	T	338	26	GRM1	2	2
EZR	7430	broad.mit.edu	37	6	159188080	159188080	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:159188080C>G	uc003qrt.3	-	c.1627G>C	c.(1627-1629)GAT>CAT	p.D543H	EZR_uc011efr.1_Missense_Mutation_p.D150H|EZR_uc011efs.1_Missense_Mutation_p.D511H|EZR_uc003qru.3_Missense_Mutation_p.D543H	NM_003379	NP_003370	P15311	EZRI_HUMAN	ezrin	543	Interaction with SCYL3.				actin filament bundle assembly|axon guidance|cytoskeletal anchoring at plasma membrane|leukocyte cell-cell adhesion|membrane to membrane docking|regulation of cell shape	actin filament|apical plasma membrane|basolateral plasma membrane|cortical cytoskeleton|cytosol|extrinsic to membrane|filopodium|microvillus membrane|nucleolus|ruffle membrane	actin filament binding|cell adhesion molecule binding			ovary(1)	1		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-17)|BRCA - Breast invasive adenocarcinoma(81;6.58e-06)										0.072165	-1.51389	16.727788	7	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159188080	159188080	5529	6	C	G	G	G	416	32	EZR	3	3
TTLL2	83887	broad.mit.edu	37	6	167754214	167754214	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:167754214G>T	uc003qvs.1	+	c.826G>T	c.(826-828)GGG>TGG	p.G276W	TTLL2_uc011egr.1_Non-coding_Transcript	NM_031949	NP_114155	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	276	TTL.				protein modification process		ATP binding|tubulin-tyrosine ligase activity			ovary(1)|central_nervous_system(1)	2		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)										0.166667	46.761461	63.19318	26	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167754214	167754214	17282	6	G	T	T	T	455	35	TTLL2	2	2
HIST1H4C	8364	broad.mit.edu	37	6	26104274	26104274	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26104274G>T	uc003ngi.2	+	c.99G>T	c.(97-99)CCG>CCT	p.P33P		NM_003542	NP_003533	P62805	H4_HUMAN	histone cluster 1, H4c	33					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0														0.627119	120.787462	121.624865	37	22	KEEP	---	---	---	---	capture		Silent	SNP	26104274	26104274	7452	6	G	T	T	T	496	39	HIST1H4C	1	1
HIST1H4H	8365	broad.mit.edu	37	6	26285577	26285577	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26285577T>A	uc003nhm.2	-	c.151A>T	c.(151-153)ATC>TTC	p.I51F	HIST1H4H_uc003nhl.1_Non-coding_Transcript	NM_003543	NP_003534	P62805	H4_HUMAN	histone cluster 1, H4h	51					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(2)	2														0.554217	147.430157	147.64001	46	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26285577	26285577	7457	6	T	A	A	A	637	49	HIST1H4H	3	3
VARS2	57176	broad.mit.edu	37	6	30882661	30882661	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:30882661G>A	uc011dmz.1	+	c.138G>A	c.(136-138)CTG>CTA	p.L46L	GTF2H4_uc003nsb.1_3'UTR|VARS2_uc003nsc.1_Silent_p.L16L|VARS2_uc003nsd.2_Silent_p.L16L|VARS2_uc011dmx.1_Silent_p.L16L|VARS2_uc011dmy.1_Intron|VARS2_uc011dna.1_Silent_p.L16L|VARS2_uc011dnb.1_Non-coding_Transcript|VARS2_uc011dnc.1_Non-coding_Transcript	NM_020442	NP_065175	Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	16					valyl-tRNA aminoacylation	mitochondrion	ATP binding|valine-tRNA ligase activity			ovary(3)|central_nervous_system(1)	4														0.145455	12.060117	18.714307	8	47	KEEP	---	---	---	---	capture		Silent	SNP	30882661	30882661	17689	6	G	A	A	A	574	45	VARS2	2	2
CUL9	23113	broad.mit.edu	37	6	43152183	43152183	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152183G>A	uc003ouk.2	+	c.135G>A	c.(133-135)CTG>CTA	p.L45L	CUL9_uc003ouj.1_Silent_p.L45L|CUL9_uc003oul.2_Silent_p.L45L|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	45					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.142857	11.99312	20.617229	10	60	KEEP	---	---	---	---	capture		Silent	SNP	43152183	43152183	4221	6	G	A	A	A	574	45	CUL9	2	2
CUL9	23113	broad.mit.edu	37	6	43152229	43152229	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152229G>C	uc003ouk.2	+	c.181G>C	c.(181-183)GAG>CAG	p.E61Q	CUL9_uc003ouj.1_Missense_Mutation_p.E61Q|CUL9_uc003oul.2_Missense_Mutation_p.E61Q|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	61					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.126316	17.929776	30.880353	12	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43152229	43152229	4221	6	G	C	C	C	429	33	CUL9	3	3
CUL9	23113	broad.mit.edu	37	6	43152442	43152442	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152442G>A	uc003ouk.2	+	c.394G>A	c.(394-396)GAA>AAA	p.E132K	CUL9_uc003ouj.1_Missense_Mutation_p.E132K|CUL9_uc003oul.2_Missense_Mutation_p.E132K|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	132					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.100917	7.650784	24.975351	11	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43152442	43152442	4221	6	G	A	A	A	429	33	CUL9	2	2
CUL9	23113	broad.mit.edu	37	6	43152449	43152449	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152449G>A	uc003ouk.2	+	c.401G>A	c.(400-402)GGG>GAG	p.G134E	CUL9_uc003ouj.1_Missense_Mutation_p.G134E|CUL9_uc003oul.2_Missense_Mutation_p.G134E|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	134					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.092593	3.761109	21.831298	10	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43152449	43152449	4221	6	G	A	A	A	559	43	CUL9	2	2
CUL9	23113	broad.mit.edu	37	6	43152637	43152637	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152637G>T	uc003ouk.2	+	c.589G>T	c.(589-591)GAT>TAT	p.D197Y	CUL9_uc003ouj.1_Missense_Mutation_p.D197Y|CUL9_uc003oul.2_Missense_Mutation_p.D197Y|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	197					regulation of mitotic metaphase/anaphase transition|ubiquitin-dependent protein catabolic process	anaphase-promoting complex|cytoplasm	ATP binding|ubiquitin protein ligase binding|zinc ion binding			ovary(5)|central_nervous_system(1)	6														0.166667	10.927403	14.720317	6	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43152637	43152637	4221	6	G	T	T	T	481	37	CUL9	1	1
RSPH9	221421	broad.mit.edu	37	6	43638529	43638529	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43638529C>A	uc003ovw.1	+	c.674C>A	c.(673-675)TCC>TAC	p.S225Y	RSPH9_uc003ovx.1_Silent_p.V242V	NM_152732	NP_689945	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog	225					cilium axoneme assembly|cilium movement	cilium axoneme|cytoplasm|cytoskeleton|motile cilium					0														0.428571	23.969873	24.063531	9	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43638529	43638529	14188	6	C	A	A	A	390	30	RSPH9	2	2
RHAG	6005	broad.mit.edu	37	6	49586980	49586980	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49586980G>T	uc003ozk.3	-	c.253C>A	c.(253-255)CTC>ATC	p.L85I	RHAG_uc010jzl.2_Missense_Mutation_p.L85I|RHAG_uc010jzm.2_Missense_Mutation_p.L85I	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	85	Helical; (Potential).				carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)	1	Lung NSC(77;0.0255)					Ovarian(176;476 2003 7720 43408 44749)								0.136842	20.113822	32.239106	13	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49586980	49586980	13790	6	G	T	T	T	468	36	RHAG	2	2
CRISP1	167	broad.mit.edu	37	6	49825116	49825116	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49825116C>A	uc003ozw.2	-	c.-1_splice	c.e2-1		CRISP1_uc003ozx.2_Splice_Site_SNP	NM_001131	NP_001122			acidic epididymal glycoprotein-like 1 isoform 1						fusion of sperm to egg plasma membrane	extracellular space					0	Lung NSC(77;0.0358)													0.115385	6.910517	14.488753	6	46	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	49825116	49825116	4018	6	C	A	A	A	312	24	CRISP1	5	2
EXOC2	55770	broad.mit.edu	37	6	592520	592520	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:592520T>A	uc003mtd.2	-	c.1141A>T	c.(1141-1143)ATC>TTC	p.I381F	EXOC2_uc003mte.2_Missense_Mutation_p.I381F|EXOC2_uc011dho.1_Intron	NM_018303	NP_060773	Q96KP1	EXOC2_HUMAN	Sec5 protein	381					exocytosis|protein transport					ovary(2)|breast(2)|pancreas(1)	5	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)										0.150943	12.7651	18.953632	8	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	592520	592520	5495	6	T	A	A	A	650	50	EXOC2	3	3
KIAA1009	22832	broad.mit.edu	37	6	84856412	84856412	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:84856412C>G	uc010kbp.2	-	c.3864G>C	c.(3862-3864)CAG>CAC	p.Q1288H	KIAA1009_uc003pkj.3_Missense_Mutation_p.Q1212H|KIAA1009_uc003pki.3_Missense_Mutation_p.Q674H	NM_014895	NP_055710	Q5TB80	QN1_HUMAN	KIAA1009 protein	1288	Potential.				cell division|mitosis	centrosome|nucleus|plasma membrane|spindle	protein binding			ovary(1)	1		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)										0.428571	10.72415	10.755267	3	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84856412	84856412	8510	6	C	G	G	G	415	32	KIAA1009	3	3
ZNF292	23036	broad.mit.edu	37	6	87965088	87965088	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:87965088A>G	uc003plm.3	+	c.1741A>G	c.(1741-1743)AAA>GAA	p.K581E		NM_015021	NP_055836	O60281	ZN292_HUMAN	zinc finger protein 292	581	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)										0.144444	26.120158	37.065245	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87965088	87965088	18418	6	A	G	G	G	169	13	ZNF292	4	4
ORC3L	23595	broad.mit.edu	37	6	88375549	88375549	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:88375549C>T	uc003pmg.2	+	c.2031C>T	c.(2029-2031)ATC>ATT	p.I677I	ORC3L_uc003pmh.2_Silent_p.I676I|ORC3L_uc003pmi.2_Silent_p.I639I|ORC3L_uc011dzo.1_Silent_p.I533I|ORC3L_uc011dzp.1_Silent_p.I533I|ORC3L_uc003pmj.1_Non-coding_Transcript	NM_181837	NP_862820	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3 isoform 1	676					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0		all_cancers(76;9.05e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;5.29e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.0469)										0.411765	21.221586	21.337278	7	10	KEEP	---	---	---	---	capture		Silent	SNP	88375549	88375549	11674	6	C	T	T	T	382	30	ORC3L	2	2
EPHA7	2045	broad.mit.edu	37	6	93965714	93965714	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:93965714C>A	uc003poe.2	-	c.2214G>T	c.(2212-2214)ATG>ATT	p.M738I	EPHA7_uc003pof.2_Missense_Mutation_p.M733I|EPHA7_uc011eac.1_Missense_Mutation_p.M734I	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	738	Cytoplasmic (Potential).|Protein kinase.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity	p.M738I(1)		ovary(7)|lung(6)|central_nervous_system(3)|large_intestine(2)|skin(2)|pancreas(1)	21		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)						635				0.327586	53.818209	55.340566	19	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	93965714	93965714	5365	6	C	A	A	A	325	25	EPHA7	2	2
COQ3	51805	broad.mit.edu	37	6	99825363	99825363	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:99825363T>A	uc003ppk.2	-	c.387_splice	c.e4-1	p.R129_splice		NM_017421	NP_059117			hexaprenyldihydroxybenzoate methyltransferase						glycerol metabolic process|ubiquinone biosynthetic process	mitochondrial matrix	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity|3-demethylubiquinone-9 3-O-methyltransferase activity|hexaprenyldihydroxybenzoate methyltransferase activity				0		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)										0.190476	8.487217	10.368441	4	17	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	99825363	99825363	3884	6	T	A	A	A	728	56	COQ3	5	3
DNAJC2	27000	broad.mit.edu	37	7	102957423	102957425	+	Missense	Complex_substitution	CNC	TNT	TNT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:102957423C>T	uc003vbo.2	-	c.1281G>A	c.(1279-1281)GAG>GAA	p.E427E	PMPCB_uc011kll.1_Intron|DNAJC2_uc003vbn.2_Silent_p.E52E|DNAJC2_uc010lix.2_Silent_p.E374E|DNAJC2_uc003vbp.2_Silent_p.E52E	NM_014377	NP_055192	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	427					'de novo' cotranslational protein folding|chromatin modification|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nuclear membrane	chromatin binding|DNA binding|histone binding|Hsp70 protein binding|ubiquitin binding			kidney(1)	1														0.104651	8.909004	22.278901	9	77	KEEP	---	---	---	---	capture		Missense	Complex_substitution	102957423	102957425	4822	7	CNC	TNT	TNT	T	311	24	DNAJC2	5	5
PIK3CG	5294	broad.mit.edu	37	7	106508576	106508576	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:106508576C>A	uc003vdv.3	+	c.570C>A	c.(568-570)AGC>AGA	p.S190R	PIK3CG_uc003vdu.2_Missense_Mutation_p.S190R|PIK3CG_uc003vdw.2_Missense_Mutation_p.S190R	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	190					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.384615	38.018836	38.47204	15	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106508576	106508576	12340	7	C	A	A	A	337	26	PIK3CG	2	2
LAMB1	3912	broad.mit.edu	37	7	107580467	107580467	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107580467A>G	uc003vev.2	-	c.3800T>C	c.(3799-3801)CTG>CCG	p.L1267P	LAMB1_uc003vew.2_Missense_Mutation_p.L1243P	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1243	Potential.|Domain II.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)	4					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.041916	-25.416689	12.244991	7	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107580467	107580467	8933	7	A	G	G	G	91	7	LAMB1	4	4
LAMB4	22798	broad.mit.edu	37	7	107692543	107692543	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107692543C>A	uc010ljo.1	-	c.3915G>T	c.(3913-3915)GCG>GCT	p.A1305A	LAMB4_uc003vey.2_Silent_p.A1305A|LAMB4_uc010ljp.1_Silent_p.A274A	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4 precursor	1305	Domain II.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)	7														0.269231	76.459002	81.45358	28	76	KEEP	---	---	---	---	capture		Silent	SNP	107692543	107692543	8936	7	C	A	A	A	288	23	LAMB4	1	1
PTPRZ1	5803	broad.mit.edu	37	7	121659302	121659302	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:121659302G>T	uc003vjy.2	+	c.4968G>T	c.(4966-4968)GTG>GTT	p.V1656V	PTPRZ1_uc003vjz.2_Silent_p.V796V|PTPRZ1_uc011knt.1_Silent_p.V246V	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1656	Helical; (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9														0.238095	34.988908	39.04929	15	48	KEEP	---	---	---	---	capture		Silent	SNP	121659302	121659302	13272	7	G	T	T	T	600	47	PTPRZ1	2	2
CPA5	93979	broad.mit.edu	37	7	130008321	130008321	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130008321C>A	uc010lmd.1	+	c.1194C>A	c.(1192-1194)CTC>CTA	p.L398L	CPA5_uc003vps.2_Silent_p.L398L|CPA5_uc003vpt.2_Missense_Mutation_p.S370Y|CPA5_uc010lme.1_Silent_p.L398L|CPA5_uc003vpu.1_Silent_p.L398L	NM_001127441	NP_001120913	Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5 isoform 1	398					proteolysis	extracellular region	metallocarboxypeptidase activity|zinc ion binding			ovary(2)	2	Melanoma(18;0.0435)													0.393939	104.968843	105.953267	39	60	KEEP	---	---	---	---	capture		Silent	SNP	130008321	130008321	3931	7	C	A	A	A	390	30	CPA5	2	2
PLXNA4	91584	broad.mit.edu	37	7	131888148	131888148	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:131888148G>T	uc003vra.3	-	c.2329C>A	c.(2329-2331)CTG>ATG	p.L777M		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	777	Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1														0.165049	33.306373	44.276741	17	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131888148	131888148	12548	7	G	T	T	T	451	35	PLXNA4	2	2
CHRM2	1129	broad.mit.edu	37	7	136700435	136700435	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:136700435G>T	uc003vtf.1	+	c.823G>T	c.(823-825)GTT>TTT	p.V275F	CHRM2_uc003vtg.1_Missense_Mutation_p.V275F|CHRM2_uc003vtj.1_Missense_Mutation_p.V275F|CHRM2_uc003vtk.1_Missense_Mutation_p.V275F|CHRM2_uc003vtl.1_Missense_Mutation_p.V275F|CHRM2_uc003vtm.1_Missense_Mutation_p.V275F|CHRM2_uc003vti.1_Missense_Mutation_p.V275F|CHRM2_uc003vto.1_Missense_Mutation_p.V275F|CHRM2_uc003vtn.1_Missense_Mutation_p.V275F	NM_001006630	NP_001006631	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	275	Cytoplasmic (By similarity).				activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|nervous system development|regulation of heart contraction|response to virus	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|protein binding			ovary(4)|central_nervous_system(1)	5					Anisotropine Methylbromide(DB00517)|Atropine(DB00572)|Benzquinamide(DB00767)|Carbachol(DB00411)|Cryptenamine(DB00785)|Cyclizine(DB01176)|Desipramine(DB01151)|Diphenidol(DB01231)|Doxacurium(DB01334)|Doxacurium chloride(DB01135)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Ipratropium(DB00332)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pilocarpine(DB01085)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Rocuronium(DB00728)|Thiethylperazine(DB00372)|Tolterodine(DB01036)|Tridihexethyl(DB00505)|Triflupromazine(DB00508)									0.168421	33.937362	43.831037	16	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136700435	136700435	3511	7	G	T	T	T	624	48	CHRM2	2	2
PTN	5764	broad.mit.edu	37	7	137028346	137028346	+	De_novo_Start_OutOfFrame	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:137028346C>A	uc003vtq.2	-	c.-162G>T	c.(-164--160)GAGGG>GATGG		PTN_uc010lmx.2_De_novo_Start_OutOfFrame|PTN_uc003vtr.1_De_novo_Start_OutOfFrame	NM_002825	NP_002816			pleiotrophin						nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			pancreas(1)	1														0.092308	1.89678	12.78187	6	59	KEEP	---	---	---	---	capture		De_novo_Start_OutOfFrame	SNP	137028346	137028346	13223	7	C	A	A	A	300	24	PTN	5	2
KIAA1549	57670	broad.mit.edu	37	7	138555917	138555917	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:138555917T>A	uc011kql.1	-	c.4537A>T	c.(4537-4539)AAA>TAA	p.K1513*	KIAA1549_uc011kqi.1_Nonsense_Mutation_p.K297*|KIAA1549_uc003vuk.3_Nonsense_Mutation_p.K1463*|KIAA1549_uc011kqj.1_Nonsense_Mutation_p.K1513*|KIAA1549_uc011kqk.1_Nonsense_Mutation_p.K297*	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670 isoform 1	1513						integral to membrane			KIAA1549/BRAF(211)	central_nervous_system(211)|pancreas(1)	212						NSCLC(119;1534 1718 44213 46230 50068)				967				0.176471	5.915276	7.591777	3	14	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	138555917	138555917	8553	7	T	A	A	A	793	61	KIAA1549	5	3
CLCN1	1180	broad.mit.edu	37	7	143039110	143039110	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143039110G>A	uc003wcr.1	+	c.1671G>A	c.(1669-1671)CTG>CTA	p.L557L	CLCN1_uc011ktc.1_Silent_p.L169L	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	557	Helical; (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)|breast(1)|central_nervous_system(1)	3	Melanoma(164;0.205)													0.229167	21.820587	25.037414	11	37	KEEP	---	---	---	---	capture		Silent	SNP	143039110	143039110	3598	7	G	A	A	A	587	46	CLCN1	2	2
EPHA1	2041	broad.mit.edu	37	7	143088839	143088839	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143088839C>T	uc003wcz.2	-	c.2726G>A	c.(2725-2727)GGC>GAC	p.G909D		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1 precursor	909	Cytoplasmic (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379				0.240741	31.06577	34.366095	13	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143088839	143088839	5358	7	C	T	T	T	338	26	EPHA1	2	2
OR2A12	346525	broad.mit.edu	37	7	143793059	143793059	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143793059C>A	uc011kty.1	+	c.859C>A	c.(859-861)CTC>ATC	p.L287I		NM_001004135	NP_001004135	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A,	287	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3	Melanoma(164;0.0783)													0.360531	541.304606	550.328157	190	337	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143793059	143793059	11381	7	C	A	A	A	312	24	OR2A12	2	2
DGKB	1607	broad.mit.edu	37	7	14620523	14620523	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:14620523C>G	uc003ssz.2	-	c.1576G>C	c.(1576-1578)GGC>CGC	p.G526R	DGKB_uc011jxt.1_Missense_Mutation_p.G507R|DGKB_uc003sta.2_Missense_Mutation_p.G526R|DGKB_uc011jxu.1_Missense_Mutation_p.G525R	NM_004080	NP_004071	Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta isoform 1	526	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	cytoplasm|plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding			lung(5)|ovary(4)|breast(2)|skin(1)	12					Phosphatidylserine(DB00144)					800				0.169231	21.382135	28.117692	11	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14620523	14620523	4645	7	C	G	G	G	273	21	DGKB	3	3
CNTNAP2	26047	broad.mit.edu	37	7	146536953	146536953	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:146536953C>T	uc003weu.1	+	c.359C>T	c.(358-360)ACA>ATA	p.T120I		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	120	F5/8 type C.|Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)											0.170732	10.999066	15.207129	7	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146536953	146536953	3785	7	C	T	T	T	221	17	CNTNAP2	2	2
ZNF425	155054	broad.mit.edu	37	7	148802280	148802280	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:148802280C>A	uc003wfj.2	-	c.683G>T	c.(682-684)AGA>ATA	p.R228I		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	228					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)											0.288462	36.801122	38.889292	15	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	148802280	148802280	18492	7	C	A	A	A	416	32	ZNF425	2	2
WDR60	55112	broad.mit.edu	37	7	158677276	158677276	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:158677276G>T	uc003woe.3	+	c.901G>T	c.(901-903)GGT>TGT	p.G301C	WDR60_uc010lqv.2_Non-coding_Transcript|WDR60_uc010lqw.2_De_novo_Start_OutOfFrame	NM_018051	NP_060521	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	301										ovary(2)|breast(1)	3	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)										0.138889	12.996702	22.078328	10	62	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158677276	158677276	17884	7	G	T	T	T	455	35	WDR60	2	2
CCDC129	223075	broad.mit.edu	37	7	31683378	31683378	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31683378C>A	uc011kae.1	+	c.2472C>A	c.(2470-2472)TGC>TGA	p.C824*	CCDC129_uc011kad.1_Nonsense_Mutation_p.C808*|CCDC129_uc003tcj.1_Nonsense_Mutation_p.C798*|CCDC129_uc003tci.1_Nonsense_Mutation_p.C649*|CCDC129_uc003tck.1_Nonsense_Mutation_p.C706*	NM_194300	NP_919276	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	798	Cys-rich.										0														0.671233	154.493333	156.389457	49	24	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	31683378	31683378	2884	7	C	A	A	A	337	26	CCDC129	5	2
BMPER	168667	broad.mit.edu	37	7	34085917	34085917	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:34085917G>C	uc011kap.1	+	c.577_splice	c.e7-1	p.G193_splice		NM_133468	NP_597725			BMP-binding endothelial regulator precursor						blood vessel endothelial cell proliferation involved in sprouting angiogenesis|endothelial cell activation|negative regulation of BMP signaling pathway|positive regulation of ERK1 and ERK2 cascade|regulation of endothelial cell migration|regulation of pathway-restricted SMAD protein phosphorylation	extracellular space				ovary(2)|central_nervous_system(1)	3														0.12685	89.365794	153.618878	60	413	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	34085917	34085917	1493	7	G	C	C	C	455	35	BMPER	5	3
AOAH	313	broad.mit.edu	37	7	36616225	36616225	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:36616225T>A	uc003tfh.3	-	c.976A>T	c.(976-978)AGA>TGA	p.R326*	AOAH_uc010kxf.2_Nonsense_Mutation_p.R326*|AOAH_uc011kba.1_Nonsense_Mutation_p.R294*	NM_001637	NP_001628	P28039	AOAH_HUMAN	acyloxyacyl hydrolase precursor	326					inflammatory response|lipid metabolic process	extracellular region	acyloxyacyl hydrolase activity|lipoprotein lipase activity				0														0.169811	33.379659	44.321497	18	88	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	36616225	36616225	736	7	T	A	A	A	726	56	AOAH	5	3
ABCA13	154664	broad.mit.edu	37	7	48356826	48356826	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:48356826A>C	uc003toq.2	+	c.9932A>C	c.(9931-9933)AAA>ACA	p.K3311T	ABCA13_uc010kys.1_Missense_Mutation_p.K385T|ABCA13_uc003tos.1_Missense_Mutation_p.K137T	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	3311					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10														0.108696	13.104914	27.041067	10	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48356826	48356826	32	7	A	C	C	C	13	1	ABCA13	4	4
GRB10	2887	broad.mit.edu	37	7	50742190	50742190	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:50742190T>A	uc003tpi.2	-	c.305A>T	c.(304-306)CAG>CTG	p.Q102L	GRB10_uc003tph.3_Missense_Mutation_p.Q44L|GRB10_uc003tpj.2_Missense_Mutation_p.Q102L|GRB10_uc003tpk.2_Missense_Mutation_p.Q102L|GRB10_uc010kzb.2_Missense_Mutation_p.Q44L|GRB10_uc003tpl.2_Missense_Mutation_p.Q96L|GRB10_uc003tpm.2_Missense_Mutation_p.Q44L|GRB10_uc003tpn.2_Missense_Mutation_p.Q44L	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform	102					insulin receptor signaling pathway|insulin receptor signaling pathway|negative regulation of glucose import|negative regulation of glycogen biosynthetic process|negative regulation of insulin receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway	cytosol|plasma membrane	insulin receptor binding|insulin receptor binding|SH3/SH2 adaptor activity			upper_aerodigestive_tract(1)|ovary(1)	2	Glioma(55;0.08)|all_neural(89;0.245)													0.138889	8.853632	13.387564	5	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50742190	50742190	7033	7	T	A	A	A	715	55	GRB10	3	3
LANCL2	55915	broad.mit.edu	37	7	55493123	55493123	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:55493123G>T	uc003tqp.2	+	c.1185G>T	c.(1183-1185)AAG>AAT	p.K395N		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	395					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)	1	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)											0.177778	32.650149	41.445902	16	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55493123	55493123	8944	7	G	T	T	T	451	35	LANCL2	2	2
SBDS	51119	broad.mit.edu	37	7	66458404	66458404	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:66458404T>C	uc003tvm.1	-	c.259A>G	c.(259-261)ATT>GTT	p.I87V		NM_016038	NP_057122	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome protein	87			I -> S (in SDS).		bone marrow development|bone mineralization|inner cell mass cell proliferation|learning|leukocyte chemotaxis|mitotic spindle stabilization|positive regulation of translation|ribosomal large subunit biogenesis|rRNA processing	cytoplasm|nucleolus|spindle pole	microtubule binding|rRNA binding			ovary(1)	1										219				0.25	43.306108	46.707773	15	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66458404	66458404	14338	7	T	C	C	C	650	50	SBDS	4	4
MAGI2	9863	broad.mit.edu	37	7	77756547	77756547	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:77756547C>A	uc003ugx.2	-	c.3390G>T	c.(3388-3390)AGG>AGT	p.R1130S	MAGI2_uc003ugy.2_Missense_Mutation_p.R1116S|MAGI2_uc010ldx.1_Missense_Mutation_p.R723S	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1130						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)	5		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)												0.108696	8.510702	29.497643	15	123	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77756547	77756547	9574	7	C	A	A	A	337	26	MAGI2	2	2
GNAI1	2770	broad.mit.edu	37	7	79846622	79846622	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:79846622C>A	uc003uhb.1	+	c.878C>A	c.(877-879)TCA>TAA	p.S293*	GNAI1_uc011kgt.1_Nonsense_Mutation_p.S241*	NM_002069	NP_002060	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein),	293					cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission	centrosome|heterotrimeric G-protein complex|midbody	G-protein beta/gamma-subunit complex binding|GTP binding|metabotropic serotonin receptor binding|signal transducer activity			central_nervous_system(1)	1														0.293103	43.04906	45.273634	17	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	79846622	79846622	6773	7	C	A	A	A	377	29	GNAI1	5	2
CACNA2D1	781	broad.mit.edu	37	7	81634805	81634805	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81634805G>A	uc003uhr.1	-	c.1524C>T	c.(1522-1524)CCC>CCT	p.P508P		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	508	Extracellular (Potential).|Cache.					voltage-gated calcium channel complex	metal ion binding			ovary(5)|pancreas(1)	6					Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)									0.222222	9.089741	10.368057	4	14	KEEP	---	---	---	---	capture		Silent	SNP	81634805	81634805	2664	7	G	A	A	A	600	47	CACNA2D1	2	2
PCLO	27445	broad.mit.edu	37	7	82545566	82545566	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82545566T>G	uc003uhx.2	-	c.11736A>C	c.(11734-11736)CAA>CAC	p.Q3912H	PCLO_uc003uhv.2_Missense_Mutation_p.Q3912H|PCLO_uc010lec.2_Missense_Mutation_p.Q877H	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	3843	Gln-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.133816	132.888521	204.806199	74	479	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82545566	82545566	12003	7	T	G	G	G	829	64	PCLO	4	4
CDK14	5218	broad.mit.edu	37	7	90741857	90741857	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:90741857G>C	uc003uky.2	+	c.1155G>C	c.(1153-1155)AAG>AAC	p.K385N	CDK14_uc003ukz.1_Missense_Mutation_p.K367N|CDK14_uc010les.1_Missense_Mutation_p.K339N|CDK14_uc011khl.1_Missense_Mutation_p.K256N	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1	385	Protein kinase.				cell division|G2/M transition of mitotic cell cycle|protein phosphorylation|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity	p.K367N(1)		lung(3)|ovary(1)	4						GBM(83;1228 1256 8311 16577 31299)			p.K385N(BT549-Tumor)	302				0.221945	236.32165	264.734588	89	312	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90741857	90741857	3259	7	G	C	C	C	542	42	CDK14	3	3
DYNC1I1	1780	broad.mit.edu	37	7	95657570	95657570	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:95657570G>T	uc003uoc.3	+	c.1104G>T	c.(1102-1104)TGG>TGT	p.W368C	DYNC1I1_uc003uod.3_Missense_Mutation_p.W351C|DYNC1I1_uc003uob.2_Missense_Mutation_p.W331C|DYNC1I1_uc003uoe.3_Missense_Mutation_p.W348C|DYNC1I1_uc010lfl.2_Missense_Mutation_p.W357C	NM_004411	NP_004402	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	368	WD 2.				vesicle transport along microtubule	condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|perinuclear region of cytoplasm|spindle pole	microtubule binding|microtubule motor activity			ovary(3)|kidney(1)	4	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)											0.125604	33.603598	61.941081	26	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95657570	95657570	5028	7	G	T	T	T	559	43	DYNC1I1	2	2
LMTK2	22853	broad.mit.edu	37	7	97821992	97821992	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:97821992A>C	uc003upd.1	+	c.2215A>C	c.(2215-2217)AAA>CAA	p.K739Q		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	739					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(8)|pancreas(2)|large_intestine(1)	11	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)									547				0.129032	13.658653	21.964898	8	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97821992	97821992	9188	7	A	C	C	C	65	5	LMTK2	4	4
PVRIG	79037	broad.mit.edu	37	7	99817788	99817788	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:99817788C>A	uc003uue.2	+	c.170C>A	c.(169-171)TCC>TAC	p.S57Y	GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uuf.1_Missense_Mutation_p.S57Y	NM_024070	NP_076975	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin	57						integral to membrane					0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.222222	8.389694	9.668265	4	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99817788	99817788	13296	7	C	A	A	A	390	30	PVRIG	2	2
RP1L1	94137	broad.mit.edu	37	8	10466151	10466151	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10466151C>A	uc003wtc.2	-	c.5457G>T	c.(5455-5457)GCG>GCT	p.A1819A		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	1819					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.469136	237.408138	237.539912	76	86	KEEP	---	---	---	---	capture		Silent	SNP	10466151	10466151	14012	8	C	A	A	A	288	23	RP1L1	1	1
RP1L1	94137	broad.mit.edu	37	8	10466368	10466368	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10466368T>A	uc003wtc.2	-	c.5240A>T	c.(5239-5241)GAG>GTG	p.E1747V		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	1747					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.526316	86.146146	86.180248	30	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10466368	10466368	14012	8	T	A	A	A	702	54	RP1L1	3	3
RP1L1	94137	broad.mit.edu	37	8	10470657	10470657	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10470657C>A	uc003wtc.2	-	c.951G>T	c.(949-951)GAG>GAT	p.E317D		NM_178857	NP_849188	A6NKC6	A6NKC6_HUMAN	retinitis pigmentosa 1-like 1	317					intracellular signal transduction					ovary(4)|breast(3)|central_nervous_system(1)	8				COAD - Colon adenocarcinoma(149;0.0811)										0.333333	24.067939	24.731187	9	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10470657	10470657	14012	8	C	A	A	A	311	24	RP1L1	2	2
RIMS2	9699	broad.mit.edu	37	8	104897987	104897987	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:104897987G>T	uc003yls.2	+	c.494G>T	c.(493-495)AGG>ATG	p.R165M	RIMS2_uc003ylp.2_Missense_Mutation_p.R387M|RIMS2_uc003ylw.2_Missense_Mutation_p.R195M|RIMS2_uc003ylq.2_Missense_Mutation_p.R195M|RIMS2_uc003ylr.2_Missense_Mutation_p.R195M	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	418					intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)							728				0.328947	65.842443	67.817496	25	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	104897987	104897987	13845	8	G	T	T	T	455	35	RIMS2	2	2
ZFPM2	23414	broad.mit.edu	37	8	106813563	106813565	+	Missense	Complex_substitution	GNG	TNT	TNT			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:106813563G>T	uc003ymd.2	+	c.1253G>T	c.(1252-1254)AGC>ATC	p.S418I	ZFPM2_uc011lhs.1_Missense_Mutation_p.S149I	NM_012082	NP_036214	Q8WW38	FOG2_HUMAN	zinc finger protein, multitype 2	418					blood coagulation|transcription, DNA-dependent	nucleoplasm	DNA binding|RNA polymerase II transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)											0.123967	18.775672	35.478064	15	106	KEEP	---	---	---	---	capture		Missense	Complex_substitution	106813563	106813565	18248	8	GNG	TNT	TNT	T	442	34	ZFPM2	5	5
PKHD1L1	93035	broad.mit.edu	37	8	110477130	110477130	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110477130C>A	uc003yne.2	+	c.8069C>A	c.(8068-8070)GCT>GAT	p.A2690D		NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor	2690	Extracellular (Potential).				immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)											0.147059	46.814887	71.247485	30	174	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110477130	110477130	12397	8	C	A	A	A	364	28	PKHD1L1	2	2
CSMD3	114788	broad.mit.edu	37	8	113266537	113266537	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113266537C>G	uc003ynu.2	-	c.10055G>C	c.(10054-10056)TGT>TCT	p.C3352S	CSMD3_uc003yns.2_Missense_Mutation_p.C2554S|CSMD3_uc003ynt.2_Missense_Mutation_p.C3312S|CSMD3_uc011lhx.1_Missense_Mutation_p.C3183S	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3352	Extracellular (Potential).|Sushi 27.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.236686	114.613977	125.323001	40	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113266537	113266537	4087	8	C	G	G	G	221	17	CSMD3	3	3
CSMD3	114788	broad.mit.edu	37	8	113392686	113392686	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113392686C>A	uc003ynu.2	-	c.6032_splice	c.e38-1	p.G2011_splice	CSMD3_uc003yns.2_Splice_Site_SNP_p.G1213_splice|CSMD3_uc003ynt.2_Splice_Site_SNP_p.G1971_splice|CSMD3_uc011lhx.1_Splice_Site_SNP_p.G1907_splice	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.134831	18.235507	29.743502	12	77	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	113392686	113392686	4087	8	C	A	A	A	312	24	CSMD3	5	2
CSMD3	114788	broad.mit.edu	37	8	113563015	113563015	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:113563015C>G	uc003ynu.2	-	c.4449G>C	c.(4447-4449)AAG>AAC	p.K1483N	CSMD3_uc003yns.2_Missense_Mutation_p.K755N|CSMD3_uc003ynt.2_Missense_Mutation_p.K1443N|CSMD3_uc011lhx.1_Missense_Mutation_p.K1379N	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	1483	Extracellular (Potential).|CUB 8.					integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.197674	35.134872	42.45146	17	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113563015	113563015	4087	8	C	G	G	G	311	24	CSMD3	3	3
CSMD3	114788	broad.mit.edu	37	8	114111193	114111193	+	Splice_Site_SNP	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:114111193C>G	uc003ynu.2	-	c.710_splice	c.e5-1	p.A237_splice	CSMD3_uc003ynt.2_Splice_Site_SNP_p.A197_splice|CSMD3_uc011lhx.1_Splice_Site_SNP_p.A237_splice|CSMD3_uc010mcx.1_Splice_Site_SNP_p.A237_splice	NM_198123	NP_937756			CUB and Sushi multiple domains 3 isoform 1							integral to membrane|plasma membrane				ovary(20)|lung(11)|kidney(8)|large_intestine(6)|skin(3)|central_nervous_system(2)|urinary_tract(1)|breast(1)	52										2888	TCGA Ovarian(7;0.080)			0.115385	4.105552	7.893976	3	23	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	114111193	114111193	4087	8	C	G	G	G	364	28	CSMD3	5	3
USP17L2	377630	broad.mit.edu	37	8	11995836	11995836	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:11995836G>T	uc003wvc.1	-	c.434C>A	c.(433-435)CCC>CAC	p.P145H	FAM66D_uc011kxp.1_Intron|FAM66D_uc011kxo.1_Intron	NM_201402	NP_958804	Q6R6M4	U17L2_HUMAN	deubiquitinating enzyme 3	145					apoptosis|cell cycle|G2/M transition checkpoint|mitotic cell cycle G1/S transition checkpoint|protein deubiquitination|ubiquitin-dependent protein catabolic process	nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity				0														0.2	15.69756	19.031727	8	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11995836	11995836	17611	8	G	T	T	T	559	43	USP17L2	2	2
NOV	4856	broad.mit.edu	37	8	120435364	120435364	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:120435364A>G	uc003yoq.2	+	c.1066A>G	c.(1066-1068)AAA>GAA	p.K356E		NM_002514	NP_002505	P48745	NOV_HUMAN	nephroblastoma overexpressed precursor	356					regulation of cell growth		growth factor activity|insulin-like growth factor binding			ovary(2)|skin(2)|kidney(1)	5	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)		Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)					71				0.10687	23.871814	64.196735	28	234	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120435364	120435364	10957	8	A	G	G	G	117	9	NOV	4	4
ATAD2	29028	broad.mit.edu	37	8	124371495	124371495	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124371495C>T	uc003yqh.3	-	c.1348G>A	c.(1348-1350)GAA>AAA	p.E450K	ATAD2_uc011lii.1_Missense_Mutation_p.E241K|ATAD2_uc003yqi.3_Non-coding_Transcript|ATAD2_uc003yqj.2_Missense_Mutation_p.E450K	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	450					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)											0.104839	10.678751	29.941012	13	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124371495	124371495	1090	8	C	T	T	T	416	32	ATAD2	2	2
KLHL38	340359	broad.mit.edu	37	8	124663935	124663935	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124663935C>T	uc003yqs.1	-	c.1232G>A	c.(1231-1233)TGG>TAG	p.W411*		NM_001081675	NP_001075144	Q2WGJ6	KLH38_HUMAN	kelch-like 38	411	Kelch 3.										0														0.244681	55.07485	60.660848	23	71	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	124663935	124663935	8704	8	C	T	T	T	273	21	KLHL38	5	2
TG	7038	broad.mit.edu	37	8	133895170	133895170	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133895170G>T	uc003ytw.2	+	c.1001G>T	c.(1000-1002)GGG>GTG	p.G334V		NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	334	Thyroglobulin type-1 4.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.088889	0.876233	8.552618	4	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133895170	133895170	16341	8	G	T	T	T	559	43	TG	2	2
TG	7038	broad.mit.edu	37	8	134144116	134144116	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:134144116G>T	uc003ytw.2	+	c.7923G>T	c.(7921-7923)GAG>GAT	p.E2641D	TG_uc010mdw.2_Missense_Mutation_p.E1400D|TG_uc011ljb.1_Missense_Mutation_p.E1010D|TG_uc011ljc.1_Missense_Mutation_p.E774D	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	2641					hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.125	9.42026	19.319785	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134144116	134144116	16341	8	G	T	T	T	451	35	TG	2	2
ST3GAL1	6482	broad.mit.edu	37	8	134488142	134488142	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:134488142C>T	uc003yuk.2	-	c.126G>A	c.(124-126)ATG>ATA	p.M42I	ST3GAL1_uc003yum.2_Missense_Mutation_p.M42I	NM_173344	NP_775479	Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase	42	Lumenal (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,3-sialyltransferase activity				0	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)											0.090909	2.496699	13.6361	6	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134488142	134488142	15732	8	C	T	T	T	273	21	ST3GAL1	2	2
COL22A1	169044	broad.mit.edu	37	8	139636013	139636013	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139636013C>G	uc003yvd.2	-	c.3733G>C	c.(3733-3735)GAG>CAG	p.E1245Q	COL22A1_uc011ljo.1_Missense_Mutation_p.E525Q	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1245	Pro-rich.|Gly-rich.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(10)|pancreas(1)	11	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)											0.036697	-34.297664	16.436539	8	210	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139636013	139636013	3819	8	C	G	G	G	416	32	COL22A1	3	3
CYP11B2	1585	broad.mit.edu	37	8	143999131	143999131	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:143999131G>T	uc003yxk.1	-	c.126C>A	c.(124-126)CCC>CCA	p.P42P		NM_000498	NP_000489	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B,	42					aldosterone biosynthetic process|oxidation-reduction process|potassium ion homeostasis|regulation of blood volume by renal aldosterone|renal water homeostasis|sodium ion homeostasis|xenobiotic metabolic process	mitochondrial inner membrane	corticosterone 18-monooxygenase activity|electron carrier activity|heme binding|steroid 11-beta-monooxygenase activity				0	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Candesartan(DB00796)|Metyrapone(DB01011)									0.212121	14.609387	17.136883	7	26	KEEP	---	---	---	---	capture		Silent	SNP	143999131	143999131	4311	8	G	T	T	T	548	43	CYP11B2	2	2
ZNF623	9831	broad.mit.edu	37	8	144733541	144733541	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144733541C>A	uc003yzd.2	+	c.1499C>A	c.(1498-1500)ACA>AAA	p.T500K	ZNF623_uc011lkp.1_Missense_Mutation_p.T460K|ZNF623_uc003yzc.2_Missense_Mutation_p.T460K	NM_014789	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623 isoform 1	500					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)											0.038835	-32.48544	14.854563	8	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144733541	144733541	18642	8	C	A	A	A	221	17	ZNF623	2	2
RHOBTB2	23221	broad.mit.edu	37	8	22873257	22873257	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:22873257G>T	uc003xcp.2	+	c.2032_splice	c.e11+1	p.E678_splice	RHOBTB2_uc011kzp.1_Splice_Site_SNP_p.E663_splice|RHOBTB2_uc003xcq.2_Splice_Site_SNP_p.E656_splice	NM_001160036	NP_001153508			Rho-related BTB domain containing 2 isoform 1						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|plasma membrane	GTP binding			ovary(1)|lung(1)	2		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)										0.176471	6.814496	8.491319	3	14	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	22873257	22873257	13809	8	G	T	T	T	572	44	RHOBTB2	5	2
EXTL3	2137	broad.mit.edu	37	8	28573653	28573653	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28573653G>T	uc003xgz.1	+	c.77G>T	c.(76-78)CGC>CTC	p.R26L		NM_001440	NP_001431	O43909	EXTL3_HUMAN	exostoses-like 3	26	Cytoplasmic (Potential).					integral to membrane|intrinsic to endoplasmic reticulum membrane	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|metal ion binding|protein binding				0		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)										0.352941	50.22685	51.202617	18	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28573653	28573653	5521	8	G	T	T	T	494	38	EXTL3	1	1
KCNU1	157855	broad.mit.edu	37	8	36671880	36671880	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:36671880C>T	uc010lvw.2	+	c.888C>T	c.(886-888)TTC>TTT	p.F296F	KCNU1_uc003xjw.2_Non-coding_Transcript	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	296	Helical; Name=Segment S6; (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)										0.1	1.600673	6.398303	3	27	KEEP	---	---	---	---	capture		Silent	SNP	36671880	36671880	8398	8	C	T	T	T	376	29	KCNU1	2	2
MYST3	7994	broad.mit.edu	37	8	41790452	41790452	+	Silent	SNP	G	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:41790452G>A	uc010lxb.2	-	c.5286C>T	c.(5284-5286)ACC>ACT	p.T1762T	MYST3_uc010lxc.2_Silent_p.T1762T|MYST3_uc003xon.3_Silent_p.T1762T	NM_001099412	NP_001092882	Q92794	MYST3_HUMAN	MYST histone acetyltransferase (monocytic	1762					histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription activator activity|transcription coactivator activity|transcription factor binding|zinc ion binding			ovary(3)|central_nervous_system(1)|pancreas(1)	5	all_epithelial(6;1.12e-27)|all_lung(13;3.94e-12)|Lung NSC(13;6.54e-11)|Ovarian(28;0.00744)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000294)|Lung NSC(58;0.00105)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	Epithelial(1;2.82e-19)|all cancers(1;1.15e-16)|BRCA - Breast invasive adenocarcinoma(8;9.17e-11)|OV - Ovarian serous cystadenocarcinoma(14;9.4e-05)|Colorectal(10;0.000728)|Lung(22;0.00153)|LUSC - Lung squamous cell carcinoma(45;0.00741)|COAD - Colon adenocarcinoma(11;0.0171)							476				0.267148	189.207335	202.785835	74	203	KEEP	---	---	---	---	capture		Silent	SNP	41790452	41790452	10499	8	G	A	A	A	600	47	MYST3	2	2
PRKDC	5591	broad.mit.edu	37	8	48772321	48772321	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:48772321C>T	uc003xqi.2	-	c.6059_splice	c.e47-1	p.D2020_splice	PRKDC_uc003xqj.2_Splice_Site_SNP_p.D2020_splice|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835			protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of gene-specific transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				Esophageal Squamous(79;1091 1253 12329 31680 40677)				1566				0.088889	1.864939	9.54865	4	41	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	48772321	48772321	12964	8	C	T	T	T	416	32	PRKDC	5	2
PXDNL	137902	broad.mit.edu	37	8	52320774	52320774	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:52320774G>T	uc003xqu.3	-	c.3410C>A	c.(3409-3411)TCG>TAG	p.S1137*	PXDNL_uc003xqt.3_Non-coding_Transcript	NM_144651	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog-like precursor	1137					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)												0.360656	59.769495	60.754223	22	39	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52320774	52320774	13306	8	G	T	T	T	481	37	PXDNL	5	1
XKR4	114786	broad.mit.edu	37	8	56015490	56015490	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:56015490A>T	uc003xsf.2	+	c.442A>T	c.(442-444)ACG>TCG	p.T148S		NM_052898	NP_443130	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related	148	Helical; (Potential).					integral to membrane				pancreas(2)	2			Epithelial(17;0.000117)|all cancers(17;0.000836)											0.304348	19.217294	20.00231	7	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56015490	56015490	18014	8	A	T	T	T	78	6	XKR4	3	3
TRPA1	8989	broad.mit.edu	37	8	72951990	72951990	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:72951990C>A	uc003xza.2	-	c.2104G>T	c.(2104-2106)GTG>TTG	p.V702L		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	702	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6			Epithelial(68;0.223)		Menthol(DB00825)									0.071429	-0.37498	7.541824	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	72951990	72951990	17128	8	C	A	A	A	221	17	TRPA1	2	2
ZFHX4	79776	broad.mit.edu	37	8	77765642	77765642	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77765642T>A	uc003yav.2	+	c.6350T>A	c.(6349-6351)ATG>AAG	p.M2117K	ZFHX4_uc003yau.1_Missense_Mutation_p.M2162K|ZFHX4_uc003yaw.1_Missense_Mutation_p.M2117K	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2117	Homeobox 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.28	97.878101	103.313503	35	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77765642	77765642	18223	8	T	A	A	A	663	51	ZFHX4	3	3
ZFHX4	79776	broad.mit.edu	37	8	77776276	77776276	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77776276C>A	uc003yav.2	+	c.10191C>A	c.(10189-10191)GTC>GTA	p.V3397V		NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	3393					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.221154	47.842456	55.237082	23	81	KEEP	---	---	---	---	capture		Silent	SNP	77776276	77776276	18223	8	C	A	A	A	379	30	ZFHX4	2	2
STMN2	11075	broad.mit.edu	37	8	80553737	80553737	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:80553737C>A	uc003ybj.2	+	c.240C>A	c.(238-240)TCC>TCA	p.S80S	STMN2_uc010lzp.2_Non-coding_Transcript|STMN2_uc011lfn.1_Silent_p.S80S	NM_007029	NP_008960	Q93045	STMN2_HUMAN	superiorcervical ganglia, neural specific 10	80	Potential.|Regulatory/phosphorylation domain (Potential).				intracellular signal transduction|negative regulation of microtubule depolymerization|negative regulation of microtubule polymerization|negative regulation of neuron projection development|neuron differentiation|positive regulation of microtubule depolymerization|positive regulation of neuron projection development	axon|growth cone|membrane|membrane fraction|perinuclear region of cytoplasm|soluble fraction	protein binding			ovary(1)|central_nervous_system(1)	2	all_lung(9;8.34e-05)		Epithelial(68;0.0229)|all cancers(69;0.0874)											0.054945	-9.175456	9.784717	5	86	KEEP	---	---	---	---	capture		Silent	SNP	80553737	80553737	15829	8	C	A	A	A	275	22	STMN2	2	2
PSKH2	85481	broad.mit.edu	37	8	87076703	87076703	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87076703C>A	uc011lfy.1	-	c.343G>T	c.(343-345)GTT>TTT	p.V115F		NM_033126	NP_149117	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	115	Protein kinase.				protein phosphorylation		ATP binding|protein serine/threonine kinase activity			lung(2)|ovary(1)	3			STAD - Stomach adenocarcinoma(118;0.129)							100				0.207792	35.754357	41.849121	16	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87076703	87076703	13118	8	C	A	A	A	234	18	PSKH2	2	2
CNBD1	168975	broad.mit.edu	37	8	88365987	88365987	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:88365987G>T	uc003ydy.2	+	c.1276G>T	c.(1276-1278)GCA>TCA	p.A426S		NM_173538	NP_775809	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	426	cNMP.									ovary(3)	3														0.096154	3.233255	11.739491	5	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88365987	88365987	3729	8	G	T	T	T	546	42	CNBD1	2	2
SLC26A7	115111	broad.mit.edu	37	8	92307883	92307883	+	Silent	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:92307883A>G	uc003yez.2	+	c.429A>G	c.(427-429)CAA>CAG	p.Q143Q	SLC26A7_uc003yex.2_Silent_p.Q143Q|SLC26A7_uc003yey.2_Non-coding_Transcript|SLC26A7_uc003yfa.2_Silent_p.Q143Q	NM_134266	NP_599028	Q8TE54	S26A7_HUMAN	solute carrier family 26, member 7 isoform b	143	Extracellular (Potential).					basolateral plasma membrane|integral to membrane|recycling endosome membrane	anion:anion antiporter activity|bicarbonate transmembrane transporter activity|chloride channel activity|oxalate transmembrane transporter activity|sulfate transmembrane transporter activity			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(11;0.00802)											0.277108	69.103756	72.805573	23	60	KEEP	---	---	---	---	capture		Silent	SNP	92307883	92307883	15019	8	A	G	G	G	11	1	SLC26A7	4	4
KIAA1429	25962	broad.mit.edu	37	8	95503860	95503860	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95503860C>A	uc003ygo.1	-	c.5086G>T	c.(5086-5088)GGA>TGA	p.G1696*	KIAA1429_uc010maz.1_Intron	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	hypothetical protein LOC25962 isoform 1	1696					mRNA processing|RNA splicing	nucleus				ovary(1)	1	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)											0.241071	63.160071	70.019707	27	85	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	95503860	95503860	8540	8	C	A	A	A	312	24	KIAA1429	5	2
KIAA1529	57653	broad.mit.edu	37	9	100077004	100077004	+	Silent	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:100077004C>A	uc011lut.1	+	c.1242C>A	c.(1240-1242)ACC>ACA	p.T414T	KIAA1529_uc004axe.1_Silent_p.T414T|KIAA1529_uc004axg.1_Silent_p.T275T|KIAA1529_uc011lus.1_Silent_p.T232T|KIAA1529_uc010msm.1_Non-coding_Transcript|KIAA1529_uc004axf.2_Silent_p.T275T|KIAA1529_uc011luv.1_Silent_p.T272T	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)	6		Acute lymphoblastic leukemia(62;0.154)												0.5	19.551393	19.551393	6	6	KEEP	---	---	---	---	capture		Silent	SNP	100077004	100077004	8549	9	C	A	A	A	288	23	KIAA1529	1	1
GABBR2	9568	broad.mit.edu	37	9	101216263	101216263	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:101216263C>T	uc004ays.2	-	c.1236G>A	c.(1234-1236)ACG>ACA	p.T412T		NM_005458	NP_005449	O75899	GABR2_HUMAN	G protein-coupled receptor 51 precursor	412	Extracellular (Potential).				negative regulation of adenylate cyclase activity|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	G-protein coupled receptor activity|GABA-B receptor activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)									0.057692	-8.107774	13.208041	6	98	KEEP	---	---	---	---	capture		Silent	SNP	101216263	101216263	6407	9	C	T	T	T	288	23	GABBR2	1	1
TMEM38B	55151	broad.mit.edu	37	9	108536317	108536317	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:108536317G>T	uc004bcu.1	+	c.832G>T	c.(832-834)GCC>TCC	p.A278S	TMEM38B_uc010mtn.1_3'UTR	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	278	Cytoplasmic (Potential).					integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)	1														0.243243	21.454787	23.680192	9	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108536317	108536317	16699	9	G	T	T	T	598	46	TMEM38B	2	2
ACTL7B	10880	broad.mit.edu	37	9	111617731	111617731	+	Silent	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:111617731C>T	uc004bdi.2	-	c.480G>A	c.(478-480)CGG>CGA	p.R160R		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	160						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1														0.1875	6.317973	7.779326	3	13	KEEP	---	---	---	---	capture		Silent	SNP	111617731	111617731	202	9	C	T	T	T	275	22	ACTL7B	2	2
TNC	3371	broad.mit.edu	37	9	117840453	117840453	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:117840453T>C	uc004bjj.3	-	c.2443A>G	c.(2443-2445)ACA>GCA	p.T815A	TNC_uc010mvf.2_Missense_Mutation_p.T815A	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	815	Fibronectin type-III 3.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|ovary(1)	5														0.377049	58.698265	59.511244	23	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117840453	117840453	16811	9	T	C	C	C	767	59	TNC	4	4
PAPPA	5069	broad.mit.edu	37	9	118982343	118982343	+	Silent	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:118982343G>T	uc004bjn.2	+	c.2046G>T	c.(2044-2046)CTG>CTT	p.L682L	PAPPA_uc011lxp.1_Silent_p.L377L|PAPPA_uc011lxq.1_Intron	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	682					cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|pancreas(1)	5										611				0.444444	167.678252	168.017854	56	70	KEEP	---	---	---	---	capture		Silent	SNP	118982343	118982343	11849	9	G	T	T	T	600	47	PAPPA	2	2
NUP214	8021	broad.mit.edu	37	9	134026140	134026140	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:134026140A>C	uc004cag.2	+	c.2265A>C	c.(2263-2265)AAA>AAC	p.K755N	NUP214_uc004cah.2_Missense_Mutation_p.K745N|NUP214_uc004cai.2_Missense_Mutation_p.K185N|NUP214_uc004caf.1_Missense_Mutation_p.K744N|NUP214_uc010mzf.2_Missense_Mutation_p.K53N	NM_005085	NP_005076	P35658	NU214_HUMAN	nucleoporin 214kDa	755	Leucine-zipper 1.|11 X 5 AA approximate repeats.				carbohydrate metabolic process|glucose transport|mRNA metabolic process|protein export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore|nucleoplasm	protein binding			breast(3)|ovary(2)|lung(1)|central_nervous_system(1)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		Pancreas(4;24 48 25510 30394 32571)				1058				0.378049	84.698285	85.770686	31	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134026140	134026140	11167	9	A	C	C	C	37	3	NUP214	4	4
TTF1	7270	broad.mit.edu	37	9	135277845	135277845	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135277845C>G	uc004cbl.2	-	c.364G>C	c.(364-366)GAT>CAT	p.D122H	TTF1_uc011mcp.1_Non-coding_Transcript|TTF1_uc004cbm.2_Intron	NM_007344	NP_031370	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase	122	N-terminal region (NRD) (By similarity).				negative regulation of DNA replication|regulation of transcription, DNA-dependent|termination of RNA polymerase I transcription	nucleolus|nucleoplasm	DNA binding			ovary(2)|pancreas(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)										0.226667	47.334895	52.479006	17	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135277845	135277845	17273	9	C	G	G	G	390	30	TTF1	3	3
BNC2	54796	broad.mit.edu	37	9	16436469	16436469	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:16436469T>G	uc003zml.2	-	c.1723A>C	c.(1723-1725)AGT>CGT	p.S575R	BNC2_uc011lmw.1_Missense_Mutation_p.S480R|BNC2_uc003zmm.2_Missense_Mutation_p.S533R|BNC2_uc003zmq.1_Missense_Mutation_p.S589R|BNC2_uc003zmr.1_Missense_Mutation_p.S612R|BNC2_uc003zmp.1_Missense_Mutation_p.S603R|BNC2_uc010mij.1_Missense_Mutation_p.S497R|BNC2_uc011lmv.1_Missense_Mutation_p.S401R|BNC2_uc003zmo.1_Missense_Mutation_p.S497R|BNC2_uc003zmj.2_Missense_Mutation_p.S340R|BNC2_uc003zmk.2_Non-coding_Transcript|BNC2_uc003zmi.2_Missense_Mutation_p.S340R|BNC2_uc003zmn.1_Missense_Mutation_p.S340R	NM_017637	NP_060107	Q6ZN30	BNC2_HUMAN	basonuclin 2	575	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	zinc ion binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(50;9.01e-08)										0.283019	37.121981	39.426311	15	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16436469	16436469	1500	9	T	G	G	G	728	56	BNC2	4	4
ADAMTSL1	92949	broad.mit.edu	37	9	18662046	18662046	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:18662046T>A	uc003zne.3	+	c.1060T>A	c.(1060-1062)TGC>AGC	p.C354S	ADAMTSL1_uc003znb.2_Missense_Mutation_p.C354S|ADAMTSL1_uc003znc.3_Missense_Mutation_p.C354S	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	354						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|lung(1)	4				GBM - Glioblastoma multiforme(50;1.29e-17)										0.235294	30.478827	33.743634	12	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18662046	18662046	275	9	T	A	A	A	767	59	ADAMTSL1	3	3
DDX58	23586	broad.mit.edu	37	9	32488878	32488878	+	Silent	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:32488878T>A	uc003zra.2	-	c.807A>T	c.(805-807)GGA>GGT	p.G269G	DDX58_uc010mjj.2_Non-coding_Transcript|DDX58_uc010mjk.1_Silent_p.G224G|DDX58_uc011lnr.1_Silent_p.G66G|DDX58_uc010mji.2_Silent_p.G198G	NM_014314	NP_055129	O95786	DDX58_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide	269	ATP (Probable).|Helicase ATP-binding.				innate immune response|negative regulation of type I interferon production|positive regulation of defense response to virus by host|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|response to virus	cytosol	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|zinc ion binding			ovary(2)|liver(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)										0.24	13.336455	14.880036	6	19	KEEP	---	---	---	---	capture		Silent	SNP	32488878	32488878	4546	9	T	A	A	A	795	62	DDX58	3	3
CNTNAP3	79937	broad.mit.edu	37	9	39178266	39178266	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:39178266C>A	uc004abi.2	-	c.630G>T	c.(628-630)TTG>TTT	p.L210F	CNTNAP3_uc004abj.2_Missense_Mutation_p.L210F|CNTNAP3_uc011lqr.1_Non-coding_Transcript|CNTNAP3_uc004abk.1_Missense_Mutation_p.L210F|CNTNAP3_uc011lqs.1_Missense_Mutation_p.L210F|CNTNAP3_uc004abl.1_Missense_Mutation_p.L122F	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor	210	Extracellular (Potential).|Laminin G-like 1.				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)										0.367089	82.350369	83.578871	29	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39178266	39178266	3786	9	C	A	A	A	376	29	CNTNAP3	2	2
PSAT1	29968	broad.mit.edu	37	9	80919661	80919661	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:80919661G>T	uc004ala.2	+	c.202G>T	c.(202-204)GAC>TAC	p.D68Y	PSAT1_uc004alb.2_Missense_Mutation_p.D68Y	NM_058179	NP_478059	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1 isoform 1	68					L-serine biosynthetic process|pyridoxine biosynthetic process		O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding			ovary(1)	1					L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)	Colon(34;187 791 10662 18313 37609)								0.371429	36.865531	37.373999	13	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80919661	80919661	13097	9	G	T	T	T	429	33	PSAT1	2	2
ROR2	4920	broad.mit.edu	37	9	94487276	94487276	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:94487276C>A	uc004arj.1	-	c.1500G>T	c.(1498-1500)CAG>CAT	p.Q500H	ROR2_uc004ari.1_Missense_Mutation_p.Q360H	NM_004560	NP_004551	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	500	Cytoplasmic (Potential).|Protein kinase.				negative regulation of cell proliferation|positive regulation of cell migration|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding			lung(6)|central_nervous_system(5)|ovary(3)|large_intestine(2)	16										461				0.170984	54.266016	74.029272	33	160	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	94487276	94487276	14006	9	C	A	A	A	415	32	ROR2	2	2
HNRNPH2	3188	broad.mit.edu	37	X	100667366	100667366	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:100667366C>A	uc004ehm.2	+	c.390C>A	c.(388-390)TTC>TTA	p.F130L	HNRNPH2_uc004ehn.2_Missense_Mutation_p.F130L	NM_019597	NP_062543	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2	130	RRM 2.				nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding				0														0.276596	31.955941	34.066874	13	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100667366	100667366	7559	23	C	A	A	A	415	32	HNRNPH2	2	2
RAB40AL	282808	broad.mit.edu	37	X	102193080	102193080	+	Silent	SNP	T	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:102193080T>C	uc004ejs.2	+	c.834T>C	c.(832-834)TCT>TCC	p.S278S		NM_001031834	NP_001027004	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	278					protein transport|small GTPase mediated signal transduction	mitochondrion|plasma membrane	GTP binding			ovary(2)	2														0.068966	-1.045744	10.089204	4	54	KEEP	---	---	---	---	capture		Silent	SNP	102193080	102193080	13399	23	T	C	C	C	717	56	RAB40AL	4	4
CXorf61	203413	broad.mit.edu	37	X	115593079	115593079	+	Silent	SNP	A	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:115593079A>G	uc004eqj.1	-	c.171T>C	c.(169-171)CTT>CTC	p.L57L		NM_001017978	NP_001017978	Q5H943	KKLC1_HUMAN	chromosome X open reading frame 61	57	Extracellular (Potential).					integral to membrane|plasma membrane					0														0.359375	60.592607	61.712681	23	41	KEEP	---	---	---	---	capture		Silent	SNP	115593079	115593079	4280	23	A	G	G	G	54	5	CXorf61	4	4
GPR112	139378	broad.mit.edu	37	X	135432188	135432188	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135432188C>T	uc004ezu.1	+	c.6323C>T	c.(6322-6324)TCC>TTC	p.S2108F	GPR112_uc010nsb.1_Missense_Mutation_p.S1903F|GPR112_uc010nsc.1_Missense_Mutation_p.S1875F	NM_153834	NP_722576	Q8IZF6	GP112_HUMAN	G-protein coupled receptor 112	2108	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(5)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	11	Acute lymphoblastic leukemia(192;0.000127)									487				0.640351	238.401172	240.376964	73	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135432188	135432188	6903	23	C	T	T	T	390	30	GPR112	2	2
SLITRK2	84631	broad.mit.edu	37	X	144906230	144906230	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:144906230G>T	uc004fcd.2	+	c.2287G>T	c.(2287-2289)GTC>TTC	p.V763F	SLITRK2_uc010nsp.2_Missense_Mutation_p.V763F|SLITRK2_uc010nso.2_Missense_Mutation_p.V763F|SLITRK2_uc011mwq.1_Missense_Mutation_p.V763F|SLITRK2_uc011mwr.1_Missense_Mutation_p.V763F|SLITRK2_uc011mws.1_Missense_Mutation_p.V763F|SLITRK2_uc004fcg.2_Missense_Mutation_p.V763F|SLITRK2_uc011mwt.1_Missense_Mutation_p.V763F|CXorf1_uc004fch.2_5'Flank	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2 precursor	763	Cytoplasmic (Potential).					integral to membrane				ovary(4)|pancreas(1)	5	Acute lymphoblastic leukemia(192;6.56e-05)													0.3375	79.599156	81.468115	27	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144906230	144906230	15241	23	G	T	T	T	468	36	SLITRK2	2	2
ATP2B3	492	broad.mit.edu	37	X	152806888	152806888	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:152806888C>T	uc004fht.1	+	c.280C>T	c.(280-282)CAA>TAA	p.Q94*	ATP2B3_uc004fhs.1_Nonsense_Mutation_p.Q94*	NM_001001344	NP_001001344	Q16720	AT2B3_HUMAN	plasma membrane calcium ATPase 3 isoform 3b	94	Cytoplasmic (Potential).				ATP biosynthetic process|platelet activation	integral to membrane|plasma membrane	ATP binding|calcium-transporting ATPase activity|calmodulin binding|metal ion binding			pancreas(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.875	22.551106	23.628627	7	1	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	152806888	152806888	1160	23	C	T	T	T	325	25	ATP2B3	5	2
CXorf21	80231	broad.mit.edu	37	X	30577880	30577880	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30577880C>A	uc004dcg.1	-	c.593G>T	c.(592-594)AGC>ATC	p.S198I		NM_025159	NP_079435	Q9HAI6	CX021_HUMAN	hypothetical protein LOC80231	198										ovary(1)	1														0.409091	52.639264	52.957605	18	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30577880	30577880	4261	23	C	A	A	A	364	28	CXorf21	2	2
DMD	1756	broad.mit.edu	37	X	31497208	31497208	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:31497208C>T	uc004dda.1	-	c.8560G>A	c.(8560-8562)GAA>AAA	p.E2854K	DMD_uc004dcq.1_Missense_Mutation_p.E125K|DMD_uc004dcr.1_Missense_Mutation_p.E394K|DMD_uc004dcs.1_Missense_Mutation_p.E394K|DMD_uc004dct.1_Missense_Mutation_p.E394K|DMD_uc004dcu.1_Missense_Mutation_p.E394K|DMD_uc004dcv.1_Missense_Mutation_p.E394K|DMD_uc004dcw.2_Missense_Mutation_p.E1510K|DMD_uc004dcx.2_Missense_Mutation_p.E1513K|DMD_uc004dcz.2_Missense_Mutation_p.E2731K|DMD_uc004dcy.1_Missense_Mutation_p.E2850K|DMD_uc004ddb.1_Missense_Mutation_p.E2846K	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	2854	Spectrin 20.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.428571	18.447786	18.510096	6	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31497208	31497208	4760	23	C	T	T	T	390	30	DMD	2	2
DMD	1756	broad.mit.edu	37	X	32632478	32632478	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:32632478T>A	uc004dda.1	-	c.1424A>T	c.(1423-1425)GAG>GTG	p.E475V	DMD_uc004dcz.2_Missense_Mutation_p.E352V|DMD_uc004dcy.1_Missense_Mutation_p.E471V|DMD_uc004ddb.1_Missense_Mutation_p.E467V|DMD_uc010ngo.1_Intron|DMD_uc004ddf.2_Missense_Mutation_p.E467V|DMD_uc010ngp.1_Intron|DMD_uc010ngq.1_Intron	NM_004006	NP_003997	P11532	DMD_HUMAN	dystrophin Dp427m isoform	475	Spectrin 2.				muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)												0.416667	26.841383	26.987734	10	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32632478	32632478	4760	23	T	A	A	A	702	54	DMD	3	3
PPP1R3F	89801	broad.mit.edu	37	X	49142834	49142834	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:49142834G>T	uc004dnh.1	+	c.1682G>T	c.(1681-1683)GGG>GTG	p.G561V	PPP1R3F_uc011mnd.1_Missense_Mutation_p.G232V|PPP1R3F_uc004dni.2_Missense_Mutation_p.G215V|PPP1R3F_uc004dnj.1_Missense_Mutation_p.G215V	NM_033215	NP_149992	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory (inhibitor)	561	Extracellular (Potential).					integral to membrane				ovary(2)	2	Ovarian(276;0.236)													0.736842	44.156222	45.119423	14	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49142834	49142834	12810	23	G	T	T	T	559	43	PPP1R3F	2	2
KIF4A	24137	broad.mit.edu	37	X	69521901	69521901	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:69521901G>C	uc004dyg.2	+	c.668G>C	c.(667-669)AGA>ACA	p.R223T	KIF4A_uc010nkw.2_Missense_Mutation_p.R223T|KIF4A_uc004dyf.1_Missense_Mutation_p.R223T	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	223	Kinesin-motor.			R -> G (in Ref. 2; AAD05492).	anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4														0.343137	112.395874	114.612244	35	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69521901	69521901	8614	23	G	C	C	C	429	33	KIF4A	3	3
ABCB7	22	broad.mit.edu	37	X	74291487	74291487	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:74291487C>A	uc004ebz.2	-	c.1067G>T	c.(1066-1068)AGA>ATA	p.R356I	ABCB7_uc004eca.2_Missense_Mutation_p.R355I|ABCB7_uc011mqn.1_Missense_Mutation_p.R329I|ABCB7_uc010nls.2_Missense_Mutation_p.R316I|ABCB7_uc010nlt.2_Missense_Mutation_p.R315I	NM_004299	NP_004290	O75027	ABCB7_HUMAN	ATP-binding cassette, sub-family B, member 7	355	ABC transmembrane type-1.				cellular iron ion homeostasis	integral to membrane|mitochondrial inner membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances|heme transporter activity			ovary(1)	1														0.380952	44.788114	45.310796	16	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74291487	74291487	47	23	C	A	A	A	416	32	ABCB7	2	2
ATRX	546	broad.mit.edu	37	X	76855270	76855270	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:76855270C>T	uc004ecp.3	-	c.5717G>A	c.(5716-5718)AGT>AAT	p.S1906N	ATRX_uc004ecq.3_Missense_Mutation_p.S1868N|ATRX_uc004eco.3_Missense_Mutation_p.S1691N	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	1906					DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)					2				0.125	4.919279	8.206597	3	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76855270	76855270	1227	23	C	T	T	T	260	20	ATRX	2	2
GPR174	84636	broad.mit.edu	37	X	78426508	78426508	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:78426508C>G	uc004edg.1	+	c.4C>G	c.(4-6)CCT>GCT	p.P2A		NM_032553	NP_115942	Q9BXC1	GP174_HUMAN	putative purinergic receptor FKSG79	2	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			lung(1)|central_nervous_system(1)	2														0.34375	32.512463	33.203843	11	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78426508	78426508	6947	23	C	G	G	G	338	26	GPR174	3	3
PABPC5	140886	broad.mit.edu	37	X	90690787	90690787	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:90690787G>T	uc004efg.2	+	c.211G>T	c.(211-213)GAT>TAT	p.D71Y	PABPC5_uc004eff.1_Intron	NM_080832	NP_543022	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	71	RRM 1.					cytoplasm	nucleotide binding|RNA binding			ovary(1)|lung(1)|pancreas(1)	3														0.666667	48.006411	48.599463	16	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90690787	90690787	11783	23	G	T	T	T	533	41	PABPC5	2	2
PCDH11X	27328	broad.mit.edu	37	X	91873877	91873877	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91873877C>A	uc004efk.1	+	c.3982C>A	c.(3982-3984)CCA>ACA	p.P1328T	PCDH11X_uc004efl.1_Missense_Mutation_p.P1318T|PCDH11X_uc004efo.1_Missense_Mutation_p.P1291T|PCDH11X_uc010nmv.1_3'UTR|PCDH11X_uc004efm.1_Missense_Mutation_p.P1320T|PCDH11X_uc004efn.1_Missense_Mutation_p.P1310T	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	1328	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.528736	137.750103	137.812353	46	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91873877	91873877	11928	23	C	A	A	A	390	30	PCDH11X	2	2
NLGN4Y	22829	broad.mit.edu	37	Y	16936082	16936082	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chrY:16936082G>T	uc011nas.1	+	c.700G>T	c.(700-702)GGT>TGT	p.G234C	NLGN4Y_uc004fte.2_Missense_Mutation_p.G46C|NLGN4Y_uc004ftg.2_Missense_Mutation_p.G214C|NLGN4Y_uc004ftf.2_5'UTR|NLGN4Y_uc004fth.2_Missense_Mutation_p.G214C	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked isoform 1	214	Extracellular (Potential).				brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of synaptic transmission|social behavior|territorial aggressive behavior|vocalization behavior	integral to membrane|plasma membrane|synapse	carboxylesterase activity|protein binding				0														0.214286	14.338379	16.447377	6	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16936082	16936082	10868	24	G	T	T	T	507	39	NLGN4Y	1	1
OVCH1	341350	broad.mit.edu	37	12	29617462	29617462	+	Frame_Shift_Del	DEL	G	-	-	rs117919494	by1000genomes	TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:29617462_29617462delG	uc001rix.1	-	c.2103_2103delC	c.(2101-2103)ACCfs	p.T701fs		NM_183378	NP_899234	Q7RTY7	OVCH1_HUMAN	ovochymase 1 precursor	701	Peptidase S1 2.				proteolysis	extracellular region	metal ion binding|serine-type endopeptidase activity			ovary(3)|central_nervous_system(3)|pancreas(3)|large_intestine(1)	10	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)													0.40			19	29		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	29617462	29617462	11736	12	G	-	-	-	496	39	OVCH1	5	5
HS3ST3A1	9955	broad.mit.edu	37	17	13399670	13399671	+	Frame_Shift_Ins	INS	-	T	T			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:13399670_13399671insT	uc002gob.1	-	c.1064_1065insA	c.(1063-1065)GCGfs	p.A355fs		NM_006042	NP_006033	Q9Y663	HS3SA_HUMAN	heparan sulfate D-glucosaminyl	355	Lumenal (Potential).					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity			ovary(1)|central_nervous_system(1)	2		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)										0.31			8	18		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	13399670	13399671	7659	17	-	T	T	T	288	23	HS3ST3A1	5	5
ZNF607	84775	broad.mit.edu	37	19	38189751	38189751	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:38189751_38189751delC	uc002ohc.1	-	c.1281_1281delG	c.(1279-1281)GGGfs	p.G427fs	ZNF607_uc002ohb.1_Frame_Shift_Del_p.G426fs	NM_032689	NP_116078	Q96SK3	ZN607_HUMAN	zinc finger protein 607	427	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)											0.37			17	29		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	38189751	38189751	18628	19	C	-	-	-	379	30	ZNF607	5	5
DYSF	8291	broad.mit.edu	37	2	71740450	71740450	+	Frame_Shift_Del	DEL	C	-	-			TCGA-17-Z028-01	TCGA-17-Z028-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:71740450_71740450delC	uc010fen.2	+	c.541_541delC	c.(541-543)CCGfs	p.P181fs	DYSF_uc010feg.2_Frame_Shift_Del_p.P180fs|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Frame_Shift_Del_p.P180fs|DYSF_uc002sie.2_Intron|DYSF_uc010fei.2_Frame_Shift_Del_p.P180fs|DYSF_uc010fek.2_Frame_Shift_Del_p.P181fs|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Frame_Shift_Del_p.P181fs|DYSF_uc010fem.2_Intron|DYSF_uc002sif.2_Intron	NM_001130987	NP_001124459	O75923	DYSF_HUMAN	dysferlin isoform 1	152	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.43			3	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	71740450	71740450	5045	2	C	-	-	-	338	26	DYSF	5	5
