Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
LYVE1	10894	broad.mit.edu	36	11	10537261	10537261	+	Silent	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:10537261G>A	uc001miv.2	-	c.942C>T	c.(940-942)ACC>ACT	p.T314T		NM_006691	NP_006682	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor	314	Cytoplasmic (Potential).				anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction		p.T314T(1)		central_nervous_system(1)	1														0.256148	340.873662	367.168532	125	363	GG		KEEP	---	---	---	---	capture		all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)	Silent	SNP	10537261	10537261	9506	11	G	A	A	39	39	LYVE1	A	1	1
DSCAML1	57453	broad.mit.edu	36	11	116811695	116811695	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:116811695C>T	uc001prh.1	-	c.4931G>A	c.(4930-4932)GGT>GAT	p.G1644D		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1584	Extracellular (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)	5	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)												0.278689	90.72058	96.081455	34	88	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)	Missense_Mutation	SNP	116811695	116811695	4953	11	C	T	T	18	18	DSCAML1	T	2	2
VPS11	55823	broad.mit.edu	36	11	118446264	118446264	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118446264C>T	uc001puy.1	+	c.583C>T	c.(583-585)CGC>TGC	p.R195C		NM_021729	NP_068375	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11	195					protein transport	cytoplasmic membrane-bounded vesicle|HOPS complex|late endosome membrane|lysosomal membrane	nucleotide binding|protein binding|zinc ion binding			ovary(2)|central_nervous_system(1)	3	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)												0.243243	22.69118	24.891392	9	28	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)	Missense_Mutation	SNP	118446264	118446264	17755	11	C	T	T	31	31	VPS11	T	1	1
ROBO4	54538	broad.mit.edu	36	11	124270967	124270967	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:124270967A>C	uc001qbg.1	-	c.731T>G	c.(730-732)CTG>CGG	p.L244R	ROBO4_uc001qbh.1_Missense_Mutation_p.L134R|ROBO4_uc001qbi.1_5'Flank	NM_019055	NP_061928	Q8WZ75	ROBO4_HUMAN	roundabout homolog 4, magic roundabout	244					angiogenesis|cell differentiation	integral to membrane	receptor activity			ovary(1)|skin(1)	2	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)												0.198198	47.881858	57.299087	22	89	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)	Missense_Mutation	SNP	124270967	124270967	13995	11	A	C	C	7	7	ROBO4	C	4	4
MRGPRX1	259249	broad.mit.edu	36	11	18912430	18912430	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18912430A>C	uc001mpg.1	-	c.478T>G	c.(478-480)TTA>GTA	p.L160V		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	160	Helical; Name=4; (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3														0.213235	62.666084	73.183076	29	107	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18912430	18912430	10159	11	A	C	C	2	2	MRGPRX1	C	4	4
OR51L1	119682	broad.mit.edu	36	11	4976974	4976974	+	Silent	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4976974T>C	uc001lzw.1	+	c.186T>C	c.(184-186)TAT>TAC	p.Y62Y		NM_001004755	NP_001004755	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L,	62	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)												0.096463	29.311597	80.079232	30	281	TT		KEEP	---	---	---	---	capture		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)	Silent	SNP	4976974	4976974	11512	11	T	C	C	52	52	OR51L1	C	4	4
GDPD5	81544	broad.mit.edu	36	11	74831892	74831892	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:74831892C>G	uc001owo.2	-	c.885G>C	c.(883-885)AGG>AGC	p.R295S	GDPD5_uc009yuc.1_Missense_Mutation_p.R157S|GDPD5_uc009yud.1_Missense_Mutation_p.R176S|GDPD5_uc001owp.2_Missense_Mutation_p.R295S|GDPD5_uc009yue.1_Missense_Mutation_p.R183S|GDPD5_uc001own.2_Missense_Mutation_p.R50S	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	295	Extracellular (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1														0.25	6.518366	7.200996	3	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74831892	74831892	6595	11	C	G	G	26	26	GDPD5	G	3	3
RAB21	23011	broad.mit.edu	36	12	70450651	70450651	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:70450651C>G	uc001swt.1	+	c.232C>G	c.(232-234)CAA>GAA	p.Q78E		NM_014999	NP_055814	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	78	GTP (By similarity).			Q->L: Defects in GTP hydrolysis.	protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0														0.173077	10.53402	15.968664	9	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70450651	70450651	13367	12	C	G	G	29	29	RAB21	G	3	3
ZC3H13	23091	broad.mit.edu	36	13	45457438	45457438	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:45457438T>C	uc001vas.1	-	c.1715A>G	c.(1714-1716)GAA>GGA	p.E572G	ZC3H13_uc001vat.1_Missense_Mutation_p.E572G	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	572	Arg/Ser-rich.						nucleic acid binding|zinc ion binding			ovary(1)|lung(1)	2		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)				Esophageal Squamous(187;747 2077 11056 31291 44172)								0.282443	118.025318	123.591402	37	94	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)	Missense_Mutation	SNP	45457438	45457438	18153	13	T	C	C	62	62	ZC3H13	C	4	4
OR4K13	390433	broad.mit.edu	36	14	19572342	19572342	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19572342C>T	uc001vwm.1	-	c.416G>A	c.(415-417)CGG>CAG	p.R139Q		NM_001004714	NP_001004714	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K,	139	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)													0.278169	215.826947	228.385055	79	205	CC		KEEP	---	---	---	---	capture	Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)	Missense_Mutation	SNP	19572342	19572342	11478	14	C	T	T	23	23	OR4K13	T	1	1
MKRN3	7681	broad.mit.edu	36	15	21362415	21362415	+	Silent	SNP	C	T	T	rs36072495	unknown	TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:21362415C>T	uc001ywh.2	+	c.393C>T	c.(391-393)GGC>GGT	p.G131G	MKRN3_uc010ayi.1_Silent_p.G131G|MKRN3_uc001ywi.2_Intron	NM_005664	NP_005655	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	131						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)							p.G131G(JHUEM7-Tumor)|p.G131G(MM1S-Tumor)|p.G131G(NCIH2172-Tumor)	79				0.247706	65.576276	71.886697	27	82	CC		KEEP	---	---	---	---	capture		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)	Silent	SNP	21362415	21362415	9998	15	C	T	T	27	27	MKRN3	T	1	1
CLCN7	1186	broad.mit.edu	36	16	1447701	1447701	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1447701C>T	uc002clv.2	-	c.733G>A	c.(733-735)GGA>AGA	p.G245R	CLCN7_uc002clw.2_Missense_Mutation_p.G221R	NM_001287	NP_001278	P51798	CLCN7_HUMAN	chloride channel 7 isoform a	245	Selectivity filter part_2 (By similarity).					integral to membrane|lysosomal membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			ovary(1)	1		Hepatocellular(780;0.0893)												0.329412	83.577269	85.766782	28	57	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1447701	1447701	3604	16	C	T	T	22	22	CLCN7	T	2	2
GPR139	124274	broad.mit.edu	36	16	19950855	19950855	+	Silent	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:19950855C>T	uc002dgu.1	-	c.765G>A	c.(763-765)GCG>GCA	p.A255A		NM_001002911	NP_001002911	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	255	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(2)	2														0.234375	68.975869	77.177713	30	98	CC		KEEP	---	---	---	---	capture			Silent	SNP	19950855	19950855	6922	16	C	T	T	27	27	GPR139	T	1	1
PKD1	5310	broad.mit.edu	36	16	2087418	2087418	+	Silent	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:2087418C>T	uc002cos.1	-	c.10308G>A	c.(10306-10308)CAG>CAA	p.Q3436Q	PKD1_uc002cot.1_Silent_p.Q3435Q|PKD1_uc010bse.1_Non-coding_Transcript	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	3436	Cytoplasmic (Potential).				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(1)	1														0.189189	14.301242	17.647081	7	30	CC		KEEP	---	---	---	---	capture			Silent	SNP	2087418	2087418	12387	16	C	T	T	28	28	PKD1	T	2	2
KRT13	3860	broad.mit.edu	36	17	36913198	36913198	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36913198C>T	uc002hwu.1	-	c.602G>A	c.(601-603)CGC>CAC	p.R201H	KRT13_uc002hwv.1_Missense_Mutation_p.R201H|KRT13_uc002hww.1_Missense_Mutation_p.R94H|KRT13_uc010cxo.1_Missense_Mutation_p.R201H|KRT13_uc002hwx.1_Missense_Mutation_p.R189H	NM_153490	NP_705694	P13646	K1C13_HUMAN	keratin 13 isoform a	201	Coil 1B.|Rod.				epidermis development	intermediate filament	structural molecule activity			ovary(2)|pancreas(1)	3		Breast(137;0.000286)												0.273381	99.799555	106.225799	38	101	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36913198	36913198	8765	17	C	T	T	27	27	KRT13	T	1	1
KRT14	3861	broad.mit.edu	36	17	36994780	36994780	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36994780C>T	uc002hxf.1	-	c.581G>A	c.(580-582)CGT>CAT	p.R194H	KRT14_uc010cxp.1_Missense_Mutation_p.R194H	NM_000526	NP_000517	P02533	K1C14_HUMAN	keratin 14	194	Coil 1B.|Rod.				epidermis development|hemidesmosome assembly|intermediate filament bundle assembly	cytosol|keratin filament|mitochondrion|nucleus	protein binding|structural constituent of cytoskeleton			ovary(1)	1		Breast(137;0.000307)												0.177215	23.892784	31.670222	14	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36994780	36994780	8766	17	C	T	T	19	19	KRT14	T	1	1
PAPL	390928	broad.mit.edu	36	19	44283500	44283500	+	Silent	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44283500C>T	uc002oki.1	+	c.879C>T	c.(877-879)AAC>AAT	p.N293N	PAPL_uc010egl.1_Missense_Mutation_p.T252M	NM_001004318	NP_001004318	Q6ZNF0	PAPL_HUMAN	FLJ16165 protein	293						extracellular region	acid phosphatase activity|metal ion binding				0														0.297872	76.267434	79.698289	28	66	CC		KEEP	---	---	---	---	capture			Silent	SNP	44283500	44283500	11844	19	C	T	T	19	19	PAPL	T	1	1
TMEM146	257062	broad.mit.edu	36	19	5729542	5729542	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5729542G>A	uc002mda.1	+	c.2252G>A	c.(2251-2253)CGC>CAC	p.R751H		NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146	751	Cytoplasmic (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.265306	63.329581	68.19318	26	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5729542	5729542	16592	19	G	A	A	38	38	TMEM146	A	1	1
RFX2	5990	broad.mit.edu	36	19	5991035	5991035	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5991035T>G	uc002meb.1	-	c.478A>C	c.(478-480)ACC>CCC	p.T160P	RFX2_uc002mec.1_Missense_Mutation_p.T160P	NM_000635	NP_000626	P48378	RFX2_HUMAN	regulatory factor X2 isoform a	160					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription regulator activity			breast(4)|ovary(1)	5						Colon(38;171 817 19800 47433 48051)								0.5	7.179397	7.179397	7	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5991035	5991035	13735	19	T	G	G	59	59	RFX2	G	4	4
ATAD3B	83858	broad.mit.edu	36	1	1407512	1407512	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1407512T>G	uc001afv.1	+	c.646T>G	c.(646-648)TCC>GCC	p.S216A	ATAD3B_uc001afw.1_Missense_Mutation_p.S170A|ATAD3B_uc001afx.1_Missense_Mutation_p.S170A	NM_031921	NP_114127	Q5T9A4	ATD3B_HUMAN	AAA-ATPase  TOB3	216							ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)												0.142857	6.62398	9.193656	3	18	TT		KEEP	---	---	---	---	capture		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)	Missense_Mutation	SNP	1407512	1407512	1093	1	T	G	G	58	58	ATAD3B	G	4	4
BCAN	63827	broad.mit.edu	36	1	154884420	154884420	+	Silent	SNP	A	G	G			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:154884420A>G	uc001fpp.1	+	c.663A>G	c.(661-663)CGA>CGG	p.R221R	BCAN_uc001fpo.1_Silent_p.R221R	NM_021948	NP_068767	Q96GW7	PGCB_HUMAN	brevican isoform 1	221	Link 1.				cell adhesion	anchored to membrane|proteinaceous extracellular matrix	hyaluronic acid binding|sugar binding			ovary(1)|pancreas(1)	2	all_hematologic(923;0.088)|Hepatocellular(266;0.158)													0.19186	81.662667	96.939064	33	139	AA		KEEP	---	---	---	---	capture			Silent	SNP	154884420	154884420	1366	1	A	G	G	11	11	BCAN	G	4	4
PYHIN1	149628	broad.mit.edu	36	1	157181342	157181342	+	Silent	SNP	C	A	A			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:157181342C>A	uc001ftb.1	+	c.1245C>A	c.(1243-1245)CCC>CCA	p.P415P	PYHIN1_uc001ftc.1_Silent_p.P406P|PYHIN1_uc001ftd.1_Silent_p.P415P|PYHIN1_uc001fte.1_Silent_p.P406P	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1	415					cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)													0.325203	113.05644	116.391711	40	83	CC		KEEP	---	---	---	---	capture			Silent	SNP	157181342	157181342	13323	1	C	A	A	22	22	PYHIN1	A	3	3
OR2T6	254879	broad.mit.edu	36	1	246618216	246618216	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246618216G>T	uc001iei.1	+	c.684G>T	c.(682-684)ATG>ATT	p.M228I		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	228	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	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)													0.236842	108.670802	120.70262	45	145	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		Missense_Mutation	SNP	246618216	246618216	11435	1	G	T	T	45	45	OR2T6	T	3	3
SGIP1	84251	broad.mit.edu	36	1	66905804	66905804	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:66905804C>T	uc001dcr.1	+	c.475C>T	c.(475-477)CGC>TGC	p.R159C	SGIP1_uc001dcs.1_Intron|SGIP1_uc001dct.1_Intron	NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	159					intracellular protein transport|positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess|vesicle-mediated transport	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3														0.257353	174.366673	188.85944	70	202	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66905804	66905804	14697	1	C	T	T	27	27	SGIP1	T	1	1
GBP1	2633	broad.mit.edu	36	1	89294438	89294438	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89294438C>T	uc001dmx.2	-	c.1217G>A	c.(1216-1218)CGT>CAT	p.R406H		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	406					interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.123)												0.239316	210.632767	232.403885	84	267	CC		KEEP	---	---	---	---	capture		all cancers(265;0.0156)|Epithelial(280;0.0291)	Missense_Mutation	SNP	89294438	89294438	6539	1	C	T	T	19	19	GBP1	T	1	1
ZSWIM1	90204	broad.mit.edu	36	20	43945788	43945788	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43945788T>C	uc002xqe.1	+	c.1150T>C	c.(1150-1152)TGC>CGC	p.C384R	ZSWIM1_uc010ghi.1_Missense_Mutation_p.C384R	NM_080603	NP_542170	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	384	SWIM-type.						zinc ion binding				0		Myeloproliferative disorder(115;0.028)												0.215517	59.413879	68.077222	25	91	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43945788	43945788	18844	20	T	C	C	55	55	ZSWIM1	C	4	4
COL20A1	57642	broad.mit.edu	36	20	61409333	61409333	+	Silent	SNP	C	G	G			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61409333C>G	uc002yep.1	+	c.543C>G	c.(541-543)GTC>GTG	p.V181V	COL20A1_uc002yeq.1_Non-coding_Transcript	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	181	VWFA.				cell adhesion	collagen|extracellular space	structural molecule activity				0	all_cancers(38;1.39e-10)													0.145833	14.093498	19.881771	7	41	CC		KEEP	---	---	---	---	capture			Silent	SNP	61409333	61409333	3817	20	C	G	G	32	32	COL20A1	G	3	3
TMPRSS2	7113	broad.mit.edu	36	21	41764469	41764469	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:41764469C>T	uc010gor.1	-	c.1147G>A	c.(1147-1149)GGG>AGG	p.G383R	TMPRSS2_uc010gos.1_Missense_Mutation_p.G383R|TMPRSS2_uc002yzj.1_Missense_Mutation_p.G383R	NM_005656	NP_005647	O15393	TMPS2_HUMAN	transmembrane protease, serine 2 isoform 2	383	Peptidase S1.|Extracellular (Potential).				proteolysis	cytoplasm|extracellular region|integral to plasma membrane	scavenger receptor activity|serine-type endopeptidase activity		TMPRSS2/ERG(2058)|TMPRSS2/ETV1(24)	prostate(2082)|central_nervous_system(1)	2083		Prostate(19;4.48e-07)|all_epithelial(19;0.031)								848				0.244444	28.502823	31.180306	11	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41764469	41764469	16788	21	C	T	T	23	23	TMPRSS2	T	1	1
FBXO7	25793	broad.mit.edu	36	22	31217162	31217162	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:31217162C>T	uc003amq.1	+	c.961C>T	c.(961-963)CGA>TGA	p.R321*	FBXO7_uc003amp.1_3'UTR|FBXO7_uc003amr.1_Nonsense_Mutation_p.R207*|FBXO7_uc003ams.1_Nonsense_Mutation_p.R165*|FBXO7_uc003amt.1_Nonsense_Mutation_p.R242*|FBXO7_uc003amu.1_Nonsense_Mutation_p.R207*|FBXO7_uc003amv.1_5'Flank	NM_012179	NP_036311	Q9Y3I1	FBX7_HUMAN	F-box only protein 7 isoform 1	321					cell death|regulation of protein stability|ubiquitin-dependent protein catabolic process	ubiquitin ligase complex	protein binding|ubiquitin-protein ligase activity			ovary(1)	1														0.204545	61.85501	72.543583	27	105	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	31217162	31217162	5997	22	C	T	T	23	23	FBXO7	T	5	1
FAM123C	205147	broad.mit.edu	36	2	131238048	131238048	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131238048C>T	uc002trw.2	+	c.1933C>T	c.(1933-1935)CCT>TCT	p.P645S	FAM123C_uc010fms.1_Missense_Mutation_p.P645S|FAM123C_uc010fmt.1_Missense_Mutation_p.P645S|FAM123C_uc010fmu.1_Missense_Mutation_p.P645S|FAM123C_uc010fmv.1_Missense_Mutation_p.P645S	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	645										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)													0.361111	37.965714	38.576709	13	23	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.13)	Missense_Mutation	SNP	131238048	131238048	5621	2	C	T	T	26	26	FAM123C	T	2	2
SCN9A	6335	broad.mit.edu	36	2	166793553	166793553	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:166793553C>T	uc002udq.2	-	c.4067G>A	c.(4066-4068)CGT>CAT	p.R1356H		NM_002977	NP_002968	Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha	1367	III.					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|central_nervous_system(5)	11					Lamotrigine(DB00555)|Lidocaine(DB00281)									0.201835	196.854302	232.869817	88	348	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166793553	166793553	14407	2	C	T	T	19	19	SCN9A	T	1	1
MYT1L	23040	broad.mit.edu	36	2	1886028	1886028	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:1886028G>T	uc002qxe.1	-	c.1863C>A	c.(1861-1863)TAC>TAA	p.Y621*	MYT1L_uc002qxd.1_Nonsense_Mutation_p.Y619*|MYT1L_uc010ewl.1_Non-coding_Transcript	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	621					cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)												0.212766	9.883322	13.56195	10	37	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)	Nonsense_Mutation	SNP	1886028	1886028	10502	2	G	T	T	48	48	MYT1L	T	5	3
APOB	338	broad.mit.edu	36	2	21079100	21079100	+	Silent	SNP	C	T	T	rs56675344	unknown	TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:21079100C>T	uc002red.1	-	c.12699G>A	c.(12697-12699)TCG>TCA	p.S4233S		NM_000384	NP_000375	P04114	APOB_HUMAN	apolipoprotein B precursor	4233					cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus|very-low-density lipoprotein particle assembly	chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle	cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity			ovary(11)|central_nervous_system(3)|large_intestine(2)|pancreas(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Atorvastatin(DB01076)									0.229268	116.618728	130.396501	47	158	CC		KEEP	---	---	---	---	capture			Silent	SNP	21079100	21079100	796	2	C	T	T	31	31	APOB	T	1	1
HDLBP	3069	broad.mit.edu	36	2	241821963	241821963	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:241821963A>G	uc002waz.2	-	c.3233T>C	c.(3232-3234)ATC>ACC	p.I1078T	HDLBP_uc002wba.2_Missense_Mutation_p.I1078T|HDLBP_uc002wbb.1_Missense_Mutation_p.I761T	NM_203346	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	1078	KH 13.				cholesterol metabolic process|lipid transport	cytoplasm|high-density lipoprotein particle|nucleus|plasma membrane	lipid binding|protein binding|RNA binding			breast(3)	3		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)								532				0.195402	91.269736	106.309918	34	140	AA		KEEP	---	---	---	---	capture		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)	Missense_Mutation	SNP	241821963	241821963	7308	2	A	G	G	12	12	HDLBP	G	4	4
DYSF	8291	broad.mit.edu	36	2	71724646	71724646	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:71724646T>C	uc010fen.1	+	c.4571T>C	c.(4570-4572)ATA>ACA	p.I1524T	DYSF_uc002sie.1_Missense_Mutation_p.I1485T|DYSF_uc002sig.2_Missense_Mutation_p.I1471T|DYSF_uc010fee.1_Missense_Mutation_p.I1506T|DYSF_uc010fef.1_Missense_Mutation_p.I1523T|DYSF_uc010feg.1_Missense_Mutation_p.I1516T|DYSF_uc010feh.1_Missense_Mutation_p.I1492T|DYSF_uc010fei.1_Missense_Mutation_p.I1502T|DYSF_uc010fej.1_Missense_Mutation_p.I1493T|DYSF_uc002sif.1_Missense_Mutation_p.I1486T|DYSF_uc010fek.1_Missense_Mutation_p.I1503T|DYSF_uc010fel.1_Missense_Mutation_p.I1472T|DYSF_uc010fem.1_Missense_Mutation_p.I1507T|DYSF_uc010feo.1_Missense_Mutation_p.I1517T	NM_003494	NP_003485	O75923	DYSF_HUMAN	dysferlin isoform 8	1485	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding			ovary(3)|breast(2)|pancreas(1)	6														0.259259	20.012421	21.429946	7	20	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71724646	71724646	5045	2	T	C	C	49	49	DYSF	C	4	4
CNTN4	152330	broad.mit.edu	36	3	3070493	3070493	+	Silent	SNP	C	G	G			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:3070493C>G	uc003bpc.1	+	c.2814C>G	c.(2812-2814)GTC>GTG	p.V938V	CNTN4_uc003bpe.1_Silent_p.V610V|CNTN4_uc003bpf.1_Silent_p.V609V|CNTN4_uc003bpg.1_Silent_p.V194V	NM_175607	NP_783302	Q8IWV2	CNTN4_HUMAN	contactin 4 isoform a precursor	938	Fibronectin type-III 4.				axon guidance|axonal fasciculation|brain development|negative regulation of neuron differentiation|neuron cell-cell adhesion|regulation of synaptic plasticity	anchored to membrane|axon|extracellular region|plasma membrane	protein binding			large_intestine(2)|ovary(2)|lung(1)|central_nervous_system(1)|pancreas(1)	7		Ovarian(110;0.156)												0.255814	20.40412	22.737682	11	32	CC		KEEP	---	---	---	---	capture		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)	Silent	SNP	3070493	3070493	3781	3	C	G	G	32	32	CNTN4	G	3	3
CCK	885	broad.mit.edu	36	3	42280015	42280015	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42280015C>T	uc003clc.1	-	c.112G>A	c.(112-114)GAG>AAG	p.E38K	CCK_uc003cld.1_Missense_Mutation_p.E38K	NM_000729	NP_000720	P06307	CCKN_HUMAN	cholecystokinin preproprotein	38					axonogenesis|eating behavior|neuron migration		neuropeptide hormone activity	p.E38K(1)		central_nervous_system(1)	1		Ovarian(412;0.0728)												0.276316	52.240539	55.670364	21	55	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.219)	Missense_Mutation	SNP	42280015	42280015	3004	3	C	T	T	30	30	CCK	T	2	2
MANF	7873	broad.mit.edu	36	3	51400346	51400346	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51400346T>C	uc003dbc.1	+	c.370T>C	c.(370-372)TAT>CAT	p.Y124H		NM_006010	NP_006001	P55145	MANF_HUMAN	arginine-rich, mutated in early stage tumors	121					response to unfolded protein	extracellular region	growth factor activity				0														0.27907	38.984307	40.870008	12	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51400346	51400346	9606	3	T	C	C	57	57	MANF	C	4	4
PPA2	27068	broad.mit.edu	36	4	106614635	106614635	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:106614635G>C	uc003hxl.1	-	c.22C>G	c.(22-24)CTG>GTG	p.L8V	PPA2_uc003hxm.1_Missense_Mutation_p.L8V|PPA2_uc003hxn.1_Missense_Mutation_p.L8V|PPA2_uc003hxo.1_Missense_Mutation_p.L8V|PPA2_uc003hxp.1_Missense_Mutation_p.L8V|PPA2_uc003hxq.1_5'UTR|PPA2_uc003hxr.1_5'UTR|PPA2_uc003hxs.1_5'Flank	NM_176869	NP_789845	Q9H2U2	IPYR2_HUMAN	inorganic pyrophosphatase 2 isoform 1 precursor	8					diphosphate metabolic process|tRNA aminoacylation for protein translation	mitochondrial matrix	inorganic diphosphatase activity|magnesium ion binding			pancreas(1)	1		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)										OREG0016281	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.571429	8.69759	8.714014	4	3	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)	Missense_Mutation	SNP	106614635	106614635	12717	4	G	C	C	34	34	PPA2	C	3	3
DKK2	27123	broad.mit.edu	36	4	108066496	108066496	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:108066496G>T	uc003hyi.1	-	c.282C>A	c.(280-282)CAC>CAA	p.H94Q	DKK2_uc003hyj.1_Missense_Mutation_p.H94Q|DKK2_uc010ilw.1_Non-coding_Transcript	NM_014421	NP_055236	Q9UBU2	DKK2_HUMAN	dickkopf homolog 2 precursor	94	DKK-type Cys-1.				multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)												0.268293	117.333027	125.27904	44	120	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)	Missense_Mutation	SNP	108066496	108066496	4725	4	G	T	T	44	44	DKK2	T	3	3
DCHS2	54798	broad.mit.edu	36	4	155524994	155524994	+	Silent	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155524994G>A	uc003inw.1	-	c.210C>T	c.(208-210)AAC>AAT	p.N70N	DCHS2_uc003inx.1_Intron	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	70	Cadherin 1.				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)												0.284091	63.734869	67.420413	25	63	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(193;0.107)	Silent	SNP	155524994	155524994	4459	4	G	A	A	40	40	DCHS2	A	1	1
PCDHB9	56127	broad.mit.edu	36	5	140548417	140548417	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140548417G>A	uc003liw.1	+	c.1342G>A	c.(1342-1344)GCC>ACC	p.A448T		NM_019119	NP_061992	Q9Y5E1	PCDB9_HUMAN	protocadherin beta 9 precursor	448	Extracellular (Potential).|Cadherin 4.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding				0														0.283721	152.527175	161.535689	61	154	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140548417	140548417	11969	5	G	A	A	38	38	PCDHB9	A	1	1
FAT2	2196	broad.mit.edu	36	5	150904076	150904076	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:150904076G>T	uc003lue.2	-	c.6805C>A	c.(6805-6807)CCT>ACT	p.P2269T		NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	FAT tumor suppressor 2 precursor	2269	Cadherin 19.|Extracellular (Potential).				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding			ovary(4)	4		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)												0.251572	96.254472	105.150301	40	119	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Missense_Mutation	SNP	150904076	150904076	5926	5	G	T	T	43	43	FAT2	T	3	3
FAM71B	153745	broad.mit.edu	36	5	156525502	156525502	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:156525502C>T	uc003lwn.1	-	c.256G>A	c.(256-258)GTC>ATC	p.V86I		NM_130899	NP_570969	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	86						nucleus				ovary(3)|pancreas(1)	4	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)												0.181818	50.252639	63.872038	26	117	CC		KEEP	---	---	---	---	capture	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Missense_Mutation	SNP	156525502	156525502	5831	5	C	T	T	19	19	FAM71B	T	1	1
GPR98	84059	broad.mit.edu	36	5	90005682	90005682	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:90005682G>A	uc003kju.1	+	c.4985G>A	c.(4984-4986)CGT>CAT	p.R1662H	GPR98_uc003kjt.1_De_novo_Start_InFrame|GPR98_uc010jba.1_Non-coding_Transcript	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	1662	Calx-beta 11.|Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.263889	47.231206	50.91564	19	53	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Missense_Mutation	SNP	90005682	90005682	6997	5	G	A	A	40	40	GPR98	A	1	1
TCP10	6953	broad.mit.edu	36	6	167710108	167710108	+	Silent	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:167710108G>A	uc003qvv.1	-	c.492C>T	c.(490-492)CCC>CCT	p.P164P	TCP10_uc003qvu.2_Silent_p.P164P|TCP10_uc003qvw.2_Silent_p.P140P	NM_004610	NP_004601	Q12799	TCP10_HUMAN	t-complex 10	191						cytosol				breast(1)	1		Breast(66;1.53e-05)|Ovarian(120;0.024)												0.360656	132.579012	134.658767	44	78	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)	Silent	SNP	167710108	167710108	16236	6	G	A	A	39	39	TCP10	A	1	1
HLA-B	3106	broad.mit.edu	36	6	31430390	31430390	+	Silent	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31430390C>T	uc003nth.2	-	c.1044G>A	c.(1042-1044)GCG>GCA	p.A348A	HLA-C_uc003ntb.1_Intron|HLA-C_uc003ntc.1_5'Flank|HLA-B_uc010jsm.1_Intron|HLA-B_uc003ntf.2_Intron|HLA-B_uc003ntg.1_Silent_p.A227A|HLA-B_uc003nti.1_Non-coding_Transcript	NM_005514	NP_005505	P01889	1B07_HUMAN	major histocompatibility complex, class I, B	348	Cytoplasmic (Potential).				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity				0														0.214953	52.286078	60.298218	23	84	CC		KEEP	---	---	---	---	capture			Silent	SNP	31430390	31430390	7487	6	C	T	T	19	19	HLA-B	T	1	1
RELN	5649	broad.mit.edu	36	7	103057691	103057691	+	Silent	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:103057691C>T	uc003vca.1	-	c.2634G>A	c.(2632-2634)GAG>GAA	p.E878E	RELN_uc010liz.1_Silent_p.E878E	NM_005045	NP_005036	P78509	RELN_HUMAN	reelin isoform a	878					axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity			ovary(8)|large_intestine(2)|central_nervous_system(2)|pancreas(1)|skin(1)	14						NSCLC(146;835 1944 15585 22231 52158)								0.143443	63.656171	93.538624	35	209	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	Silent	SNP	103057691	103057691	13689	7	C	T	T	24	24	RELN	T	2	2
THSD7A	221981	broad.mit.edu	36	7	11388711	11388711	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:11388711G>A	uc003ssf.2	-	c.4469C>T	c.(4468-4470)ACA>ATA	p.T1490I	THSD7A_uc003ssd.2_5'Flank	NM_015204	NP_056019	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1490	Extracellular (Potential).					integral to membrane				ovary(3)	3														0.181818	31.4457	39.817176	16	72	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.163)	Missense_Mutation	SNP	11388711	11388711	16407	7	G	A	A	48	48	THSD7A	A	2	2
TAS2R39	259285	broad.mit.edu	36	7	142591384	142591384	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142591384G>A	uc003wcg.1	+	c.751G>A	c.(751-753)GAC>AAC	p.D251N		NM_176881	NP_795362	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	251	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity				0	Melanoma(164;0.059)													0.180602	111.683318	140.350397	54	245	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142591384	142591384	16098	7	G	A	A	37	37	TAS2R39	A	1	1
OR2A5	393046	broad.mit.edu	36	7	143379095	143379095	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143379095C>T	uc003wdu.1	+	c.668C>T	c.(667-669)GCG>GTG	p.A223V		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	223	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)													0.22973	197.400213	222.169874	85	285	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143379095	143379095	11387	7	C	T	T	27	27	OR2A5	T	1	1
DNAH11	8701	broad.mit.edu	36	7	21565759	21565759	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21565759G>A	uc003svc.1	+	c.706G>A	c.(706-708)GAA>AAA	p.E236K		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	236	Stem (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.24	31.075108	34.15987	12	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21565759	21565759	4781	7	G	A	A	37	37	DNAH11	A	1	1
GRB10	2887	broad.mit.edu	36	7	50709666	50709666	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:50709666C>G	uc003tpi.1	-	c.323G>C	c.(322-324)AGG>ACG	p.R108T	GRB10_uc003tph.2_Missense_Mutation_p.R50T|GRB10_uc003tpj.1_Missense_Mutation_p.R108T|GRB10_uc003tpk.1_Missense_Mutation_p.R108T|GRB10_uc010kzb.1_Missense_Mutation_p.R50T|GRB10_uc003tpl.1_Missense_Mutation_p.R102T|GRB10_uc003tpm.1_Missense_Mutation_p.R50T|GRB10_uc003tpn.1_Missense_Mutation_p.R50T	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform	108					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)													0.253333	46.884689	51.031937	19	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	50709666	50709666	7033	7	C	G	G	24	24	GRB10	G	3	3
PCLO	27445	broad.mit.edu	36	7	82601729	82601729	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0169-01	TCGA-06-0169-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:82601729T>C	uc003uhx.2	-	c.3073A>G	c.(3073-3075)AAA>GAA	p.K1025E	PCLO_uc003uhv.2_Missense_Mutation_p.K1025E	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	971	Pro-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														0.206522	48.973783	56.317838	19	73	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82601729	82601729	12003	7	T	C	C	64	64	PCLO	C	4	4
NXPH1	30010	broad.mit.edu	36	7	8757643	8757643	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:8757643G>C	uc003srv.1	+	c.535G>C	c.(535-537)GCA>CCA	p.A179P		NM_152745	NP_689958	P58417	NXPH1_HUMAN	neurexophilin 1 precursor	179	IV (linker domain).					extracellular region				ovary(1)|central_nervous_system(1)	2		Ovarian(82;0.0628)												0.094737	10.300286	25.967158	9	86	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)	Missense_Mutation	SNP	8757643	8757643	11195	7	G	C	C	42	42	NXPH1	C	3	3
GPR20	2843	broad.mit.edu	36	8	142436177	142436177	+	Silent	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:142436177G>A	uc003ywf.1	-	c.1029C>T	c.(1027-1029)GCC>GCT	p.A343A	GPR20_uc010mer.1_Silent_p.A343A	NM_005293	NP_005284	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	343	Cytoplasmic (Potential).					integral to plasma membrane	G-protein coupled receptor activity				0	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)													0.2	24.69531	29.297906	11	44	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0415)		Silent	SNP	142436177	142436177	6955	8	G	A	A	39	39	GPR20	A	1	1
TEX15	56154	broad.mit.edu	36	8	30815042	30815042	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:30815042G>A	uc003xil.1	-	c.7151C>T	c.(7150-7152)ACG>ATG	p.T2384M		NM_031271	NP_112561	Q9BXT5	TEX15_HUMAN	testis expressed 15	2384										ovary(3)	3														0.208211	158.840794	185.727198	71	270	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)	Missense_Mutation	SNP	30815042	30815042	16306	8	G	A	A	40	40	TEX15	A	1	1
IL7	3574	broad.mit.edu	36	8	79872878	79872878	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0169-01	TCGA-06-0169-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:79872878C>T	uc003ybg.1	-	c.131G>A	c.(130-132)AGC>AAC	p.S44N	IL7_uc003ybe.1_Missense_Mutation_p.S3N|IL7_uc003ybf.1_Missense_Mutation_p.S3N|IL7_uc003ybh.1_Intron|IL7_uc003ybi.2_Non-coding_Transcript	NM_000880	NP_000871	P13232	IL7_HUMAN	interleukin 7 precursor	44					bone resorption|cell-cell signaling|humoral immune response|organ morphogenesis|positive regulation of B cell proliferation|positive regulation of T cell differentiation	extracellular space	cytokine activity|growth factor activity|interleukin-7 receptor binding				0														0.225806	86.833609	97.544938	35	120	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79872878	79872878	8005	8	C	T	T	28	28	IL7	T	2	2
COL15A1	1306	broad.mit.edu	36	9	100837152	100837152	+	Silent	SNP	G	A	A			TCGA-06-0169-01	TCGA-06-0169-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:100837152G>A	uc004azb.1	+	c.2115G>A	c.(2113-2115)CCG>CCA	p.P705P		NM_001855	NP_001846	P39059	COFA1_HUMAN	alpha 1 type XV collagen precursor	705	Triple-helical region 2 (COL2).				angiogenesis|cell adhesion|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding|extracellular matrix structural constituent			ovary(6)	6		Acute lymphoblastic leukemia(62;0.0562)												0.230263	88.850908	98.98444	35	117	GG		KEEP	---	---	---	---	capture			Silent	SNP	100837152	100837152	3810	9	G	A	A	39	39	COL15A1	A	1	1
C9orf131	138724	broad.mit.edu	36	9	35035456	35035456	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:35035456A>G	uc003zvw.1	+	c.2830A>G	c.(2830-2832)AAG>GAG	p.K944E	C9orf131_uc003zvu.1_Missense_Mutation_p.K896E|C9orf131_uc003zvv.1_Missense_Mutation_p.K871E|C9orf131_uc003zvx.1_Missense_Mutation_p.K909E	NM_203299	NP_976044	Q5VYM1	CI131_HUMAN	hypothetical protein LOC138724 isoform A	944											0	all_epithelial(49;0.22)													0.36	212.58329	215.600395	63	112	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(32;0.00117)|Lung(28;0.00309)		Missense_Mutation	SNP	35035456	35035456	2570	9	A	G	G	1	1	C9orf131	G	4	4
FGD3	89846	broad.mit.edu	36	9	94822502	94822502	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0169-01	TCGA-06-0169-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:94822502A>C	uc004asw.2	+	c.1469A>C	c.(1468-1470)GAC>GCC	p.D490A	FGD3_uc004asx.2_Missense_Mutation_p.D490A|FGD3_uc004asz.2_Missense_Mutation_p.D490A|FGD3_uc004ata.2_Missense_Mutation_p.D293A	NM_001083536	NP_149077	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	490					actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|ruffle	Rho guanyl-nucleotide exchange factor activity|small GTPase binding|zinc ion binding			ovary(1)|breast(1)	2														0.35	7.148048	7.620516	7	13	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94822502	94822502	6071	9	A	C	C	10	10	FGD3	C	4	4
EIF2S3	1968	broad.mit.edu	36	X	24004795	24004798	+	Frame_Shift_Del	DEL	CAAT	-	-			TCGA-06-0169-01	TCGA-06-0169-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24004795_24004798delCAAT	uc004dbc.1	+	c.1391_1394delCAAT	c.(1390-1395)ACAATCfs	p.T464fs		NM_001415	NP_001406	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2,	464_465						cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity			lung(1)	1														0.47			57	65				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	24004795	24004798	5200	23	CAAT	-	-	17	17	EIF2S3	-	5	5
