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
GPR123	84435	broad.mit.edu	37	10	134916303	134916303	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:134916303C>T	uc001llx.3	+	c.358C>T	c.(358-360)CTG>TTG	p.L120L	GPR123_uc001llw.2_Silent_p.L840L	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	120	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)										0.208333	13.46153	15.352092	5	19	KEEP	---	---	---	---	capture		Silent	SNP	134916303	134916303	6911	10	C	T	T	T	311	24	GPR123	2	2
PRPF18	8559	broad.mit.edu	37	10	13655795	13655795	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:13655795C>T	uc001imp.2	+	c.634C>T	c.(634-636)CGC>TGC	p.R212C	PRPF18_uc001imq.2_Intron	NM_003675	NP_003666	Q99633	PRP18_HUMAN	PRP18 pre-mRNA processing factor 18 homolog	212					mRNA processing|RNA splicing	nuclear speck|spliceosomal complex				central_nervous_system(1)	1														0.144444	23.262358	34.17434	13	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13655795	13655795	13006	10	C	T	T	T	247	19	PRPF18	1	1
CDH23	64072	broad.mit.edu	37	10	73544768	73544768	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73544768G>T	uc001jrx.3	+	c.5623G>T	c.(5623-5625)GCC>TCC	p.A1875S		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1875	Cadherin 18.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.117647	17.371182	34.382524	14	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73544768	73544768	3237	10	G	T	T	T	546	42	CDH23	2	2
NDST2	8509	broad.mit.edu	37	10	75567627	75567627	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:75567627C>A	uc001jvk.2	-	c.520G>T	c.(520-522)GCC>TCC	p.A174S	NDST2_uc010qks.1_5'Flank|NDST2_uc010qkt.1_Missense_Mutation_p.A51S|NDST2_uc009xro.2_5'Flank|NDST2_uc010qku.1_Missense_Mutation_p.A51S	NM_003635	NP_003626	P52849	NDST2_HUMAN	heparan glucosaminyl	174	Lumenal (Potential).|Heparan sulfate N-deacetylase 2.					Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			ovary(1)	1	Prostate(51;0.0112)													0.150943	25.613524	38.024472	16	90	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75567627	75567627	10655	10	C	A	A	A	364	28	NDST2	2	2
PAFAH1B2	5049	broad.mit.edu	37	11	117038323	117038323	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117038323G>T	uc001pqe.1	+	c.598G>T	c.(598-600)GGG>TGG	p.G200W	PAFAH1B2_uc009yzk.1_Intron|PAFAH1B2_uc009yzl.1_Intron|PAFAH1B2_uc009yzm.2_Intron|PAFAH1B2_uc009yzn.2_Intron|PAFAH1B2_uc009yzj.1_Non-coding_Transcript	NM_002572	NP_002563	P68402	PA1B2_HUMAN	platelet-activating factor acetylhydrolase,	200					lipid catabolic process	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity			kidney(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;1.68e-05)|Epithelial(105;0.000162)|all cancers(92;0.00111)						104				0.208333	71.762609	83.113578	30	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117038323	117038323	11801	11	G	T	T	T	455	35	PAFAH1B2	2	2
SCN3B	55800	broad.mit.edu	37	11	123508905	123508905	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123508905G>T	uc001pza.1	-	c.573C>A	c.(571-573)GCC>GCA	p.A191A	SCN3B_uc001pzb.1_Silent_p.A191A	NM_001040151	NP_001035241	Q9NY72	SCN3B_HUMAN	voltage-gated sodium channel beta-3 subunit	191	Cytoplasmic (Potential).				axon guidance	integral to membrane|plasma membrane	voltage-gated sodium channel activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5		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;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)										0.153846	22.148819	31.085391	12	66	KEEP	---	---	---	---	capture		Silent	SNP	123508905	123508905	14401	11	G	T	T	T	548	43	SCN3B	2	2
SOX6	55553	broad.mit.edu	37	11	15994629	15994629	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:15994629C>A	uc001mme.2	-	c.2252G>T	c.(2251-2253)GGA>GTA	p.G751V	SOX6_uc001mmd.2_Missense_Mutation_p.G714V|SOX6_uc001mmf.2_Missense_Mutation_p.G711V|SOX6_uc001mmg.2_Missense_Mutation_p.G718V	NM_001145819	NP_001139291	P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6 isoform 4	738					muscle organ development	nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3														0.102113	23.956739	68.786722	29	255	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	15994629	15994629	15455	11	C	A	A	A	390	30	SOX6	2	2
LDLRAD3	143458	broad.mit.edu	37	11	36250716	36250716	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36250716G>T	uc001mwk.1	+	c.807G>T	c.(805-807)GCG>GCT	p.A269A	LDLRAD3_uc010rey.1_Silent_p.A220A|LDLRAD3_uc010rez.1_Silent_p.A148A|LDLRAD3_uc010rfa.1_Non-coding_Transcript	NM_174902	NP_777562	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain	269	Cytoplasmic (Potential).					integral to membrane	receptor activity			central_nervous_system(1)	1	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)												0.084388	7.924902	49.472334	20	217	KEEP	---	---	---	---	capture		Silent	SNP	36250716	36250716	9031	11	G	T	T	T	509	40	LDLRAD3	1	1
LRRC4C	57689	broad.mit.edu	37	11	40136265	40136265	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40136265G>T	uc001mxa.1	-	c.1578C>A	c.(1576-1578)ACC>ACA	p.T526T	LRRC4C_uc001mxc.1_Silent_p.T522T|LRRC4C_uc001mxd.1_Silent_p.T522T|LRRC4C_uc001mxb.1_Silent_p.T522T	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	526					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)												0.152074	66.032417	91.17742	33	184	KEEP	---	---	---	---	capture		Silent	SNP	40136265	40136265	9383	11	G	T	T	T	600	47	LRRC4C	2	2
OR4A47	403253	broad.mit.edu	37	11	48510590	48510590	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:48510590C>A	uc010rhx.1	+	c.246C>A	c.(244-246)GGC>GGA	p.G82G		NM_001005512	NP_001005512	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.101952	42.271575	115.107099	47	414	KEEP	---	---	---	---	capture		Silent	SNP	48510590	48510590	11448	11	C	A	A	A	353	28	OR4A47	2	2
OR4P4	81300	broad.mit.edu	37	11	55406314	55406314	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55406314A>G	uc010rij.1	+	c.481A>G	c.(481-483)ACC>GCC	p.T161A		NM_001004124	NP_001004124	Q8NGL7	OR4P4_HUMAN	olfactory receptor, family 4, subfamily P,	161	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1														0.109091	17.217749	42.221865	18	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55406314	55406314	11490	11	A	G	G	G	78	6	OR4P4	4	4
OR5F1	338674	broad.mit.edu	37	11	55761412	55761412	+	Silent	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55761412C>G	uc010riv.1	-	c.690G>C	c.(688-690)TCG>TCC	p.S230S		NM_003697	NP_003688	O95221	OR5F1_HUMAN	olfactory receptor, family 5, subfamily F,	230	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2	Esophageal squamous(21;0.00448)													0.149351	46.137629	64.287273	23	131	KEEP	---	---	---	---	capture		Silent	SNP	55761412	55761412	11568	11	C	G	G	G	288	23	OR5F1	3	3
OR5AP2	338675	broad.mit.edu	37	11	56409316	56409316	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56409316G>T	uc001njb.1	-	c.600C>A	c.(598-600)TTC>TTA	p.F200L		NM_001002925	NP_001002925	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP,	200	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|kidney(1)|central_nervous_system(1)	3														0.149015	214.192422	310.200959	121	691	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56409316	56409316	11554	11	G	T	T	T	581	45	OR5AP2	2	2
OR10W1	81341	broad.mit.edu	37	11	58035114	58035114	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:58035114G>T	uc001nmq.1	-	c.217C>A	c.(217-219)CTG>ATG	p.L73M		NM_207374	NP_997257	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W,	73	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.167235	105.0257	135.746534	49	244	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58035114	58035114	11327	11	G	T	T	T	451	35	OR10W1	2	2
OR52N2	390077	broad.mit.edu	37	11	5841641	5841641	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5841641C>A	uc010qzp.1	+	c.76C>A	c.(76-78)CAC>AAC	p.H26N	TRIM5_uc001mbq.1_Intron	NM_001005174	NP_001005174	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N,	26	Extracellular (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;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.101167	25.795388	66.557346	26	231	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5841641	5841641	11538	11	C	A	A	A	221	17	OR52N2	2	2
AHNAK	79026	broad.mit.edu	37	11	62287633	62287633	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:62287633G>A	uc001ntl.2	-	c.14256C>T	c.(14254-14256)GGC>GGT	p.G4752G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	4752					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)	14		Melanoma(852;0.155)												0.110843	40.636419	102.814683	46	369	KEEP	---	---	---	---	capture		Silent	SNP	62287633	62287633	417	11	G	A	A	A	535	42	AHNAK	2	2
C11orf68	83638	broad.mit.edu	37	11	65685409	65685409	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:65685409C>A	uc001ogi.2	-	c.403G>T	c.(403-405)GTG>TTG	p.V135L	C11orf68_uc009yqv.2_Missense_Mutation_p.V134L|DRAP1_uc001ogj.1_5'Flank	NM_001135635	NP_001129107	Q9H3H3	CK068_HUMAN	basophilic leukemia expressed protein BLES03	93											0				READ - Rectum adenocarcinoma(159;0.166)										0.190476	9.893138	11.76955	4	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65685409	65685409	1697	11	C	A	A	A	247	19	C11orf68	1	1
OR10A3	26496	broad.mit.edu	37	11	7960520	7960520	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7960520G>T	uc010rbi.1	-	c.548C>A	c.(547-549)CCG>CAG	p.P183Q		NM_001003745	NP_001003745	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A,	183	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)										0.121387	33.348727	57.649598	21	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7960520	7960520	11297	11	G	T	T	T	507	39	OR10A3	1	1
IPO7	10527	broad.mit.edu	37	11	9463643	9463643	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:9463643A>G	uc001mho.2	+	c.2918A>G	c.(2917-2919)AAT>AGT	p.N973S		NM_006391	NP_006382	O95373	IPO7_HUMAN	importin 7	973					interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)										0.142857	45.673087	63.740556	21	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9463643	9463643	8098	11	A	G	G	G	52	4	IPO7	4	4
SLC17A8	246213	broad.mit.edu	37	12	100787146	100787146	+	Splice_Site_SNP	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100787146G>A	uc010svi.1	+	c.474_splice	c.e4-1	p.R158_splice	SLC17A8_uc009ztx.2_Splice_Site_SNP_p.R158_splice	NM_139319	NP_647480			solute carrier family 17 (sodium-dependent						neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3														0.108108	18.28501	40.822723	16	132	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	100787146	100787146	14919	12	G	A	A	A	455	35	SLC17A8	5	2
SLC17A8	246213	broad.mit.edu	37	12	100787197	100787197	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:100787197C>T	uc010svi.1	+	c.524C>T	c.(523-525)CCC>CTC	p.P175L	SLC17A8_uc009ztx.2_Missense_Mutation_p.P175L	NM_139319	NP_647480	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (sodium-dependent	175	Vesicular (Potential).				neurotransmitter transport|sensory perception of sound|sodium ion transport	cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|symporter activity			ovary(3)	3														0.135231	70.545635	106.786151	38	243	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100787197	100787197	14919	12	C	T	T	T	286	22	SLC17A8	2	2
POLR3B	55703	broad.mit.edu	37	12	106821053	106821053	+	Nonsense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:106821053A>T	uc001tlp.2	+	c.1180A>T	c.(1180-1182)AAG>TAG	p.K394*	POLR3B_uc001tlq.2_Nonsense_Mutation_p.K336*	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	DNA-directed RNA polymerase III B isoform 1	394					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														0.140078	63.733692	95.872015	36	221	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	106821053	106821053	12657	12	A	T	T	T	169	13	POLR3B	5	3
TBX5	6910	broad.mit.edu	37	12	114804095	114804095	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:114804095T>A	uc001tvo.2	-	c.857A>T	c.(856-858)AAT>ATT	p.N286I	TBX5_uc001tvp.2_Missense_Mutation_p.N286I|TBX5_uc001tvq.2_Missense_Mutation_p.N236I|TBX5_uc010syv.1_Missense_Mutation_p.N286I	NM_181486	NP_852259	Q99593	TBX5_HUMAN	T-box 5 isoform 1	286					cardiac left ventricle formation|cell migration involved in coronary vasculogenesis|cell-cell signaling|embryonic arm morphogenesis|induction of apoptosis|negative regulation of cardiac muscle cell proliferation|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|pericardium development|positive regulation of cardioblast differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|ventricular septum development	cytoplasm|nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(6)|pancreas(1)	7	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		NSCLC(152;1358 1980 4050 23898 40356)								0.11336	34.309506	70.760429	28	219	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114804095	114804095	16187	12	T	A	A	A	676	52	TBX5	3	3
TMEM132B	114795	broad.mit.edu	37	12	126137133	126137133	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:126137133C>A	uc001uhe.1	+	c.2046C>A	c.(2044-2046)ATC>ATA	p.I682I	TMEM132B_uc001uhf.1_Silent_p.I194I	NM_052907	NP_443139	Q14DG7	T132B_HUMAN	transmembrane protein 132B	682	Extracellular (Potential).					integral to membrane				ovary(5)|large_intestine(1)|breast(1)|pancreas(1)	8	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)										0.119048	36.526309	66.445911	25	185	KEEP	---	---	---	---	capture		Silent	SNP	126137133	126137133	16577	12	C	A	A	A	395	31	TMEM132B	1	1
DDX11	1663	broad.mit.edu	37	12	31249876	31249876	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:31249876G>T	uc001rjt.1	+	c.1714G>T	c.(1714-1716)GCT>TCT	p.A572S	DDX11_uc001rjr.1_Missense_Mutation_p.A572S|DDX11_uc001rjs.1_Missense_Mutation_p.A572S|DDX11_uc001rju.1_Missense_Mutation_p.A250S|DDX11_uc001rjv.1_Missense_Mutation_p.A572S|DDX11_uc001rjw.1_Missense_Mutation_p.A546S|DDX11_uc009zjn.1_Non-coding_Transcript	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11	572					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)			0.090909	1.197689	6.767415	3	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31249876	31249876	4514	12	G	T	T	T	442	34	DDX11	2	2
IRAK4	51135	broad.mit.edu	37	12	44180315	44180315	+	Silent	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:44180315T>C	uc001rnu.3	+	c.1302T>C	c.(1300-1302)AGT>AGC	p.S434S	IRAK4_uc001rnt.3_Silent_p.S434S|IRAK4_uc001rnx.3_Silent_p.S310S|IRAK4_uc001rny.3_Silent_p.S310S|IRAK4_uc010sky.1_Silent_p.S310S|IRAK4_uc001rnv.3_Silent_p.S310S|IRAK4_uc001rnw.3_Silent_p.S310S	NM_001114182	NP_001107654	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	434	Protein kinase.				innate immune response|MyD88-dependent toll-like receptor signaling pathway|protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	ATP binding|magnesium ion binding|protein serine/threonine kinase activity				0	all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)						243				0.124224	38.183659	60.40778	20	141	KEEP	---	---	---	---	capture		Silent	SNP	44180315	44180315	8128	12	T	C	C	C	751	58	IRAK4	4	4
PCBP2	5094	broad.mit.edu	37	12	53853102	53853102	+	Missense_Mutation	SNP	C	T	T	rs111807426		TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53853102C>T	uc001sdc.3	+	c.290C>T	c.(289-291)CCG>CTG	p.P97L	PCBP2_uc001sdb.3_Missense_Mutation_p.P97L|PCBP2_uc001sdl.3_Missense_Mutation_p.P97L|PCBP2_uc001sde.3_Missense_Mutation_p.P97L|PCBP2_uc001sdi.3_Missense_Mutation_p.P97L|PCBP2_uc001sdd.3_Missense_Mutation_p.P97L|PCBP2_uc001sdf.3_Missense_Mutation_p.P97L|PCBP2_uc009zna.2_Missense_Mutation_p.P58L|PCBP2_uc010soh.1_Missense_Mutation_p.P97L|PCBP2_uc009zmz.1_Missense_Mutation_p.P39L|PCBP2_uc001sdg.1_Non-coding_Transcript	NM_005016	NP_005007	Q15366	PCBP2_HUMAN	poly(rC) binding protein 2 isoform a	97	KH 2.				innate immune response|negative regulation of defense response to virus|negative regulation of type I interferon production|nuclear mRNA splicing, via spliceosome|proteasomal ubiquitin-dependent protein catabolic process|response to virus	cytosol|nucleoplasm|ribonucleoprotein complex	DNA binding|RNA binding|ubiquitin protein ligase binding				0														0.131579	34.802804	54.845089	20	132	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53853102	53853102	11921	12	C	T	T	T	299	23	PCBP2	1	1
PAN2	9924	broad.mit.edu	37	12	56720127	56720127	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56720127C>T	uc001skx.2	-	c.1329G>A	c.(1327-1329)GCG>GCA	p.A443A	PAN2_uc001skw.2_5'Flank|PAN2_uc001skz.2_Silent_p.A443A|PAN2_uc001sky.2_Silent_p.A443A	NM_001127460	NP_001120932	Q504Q3	PAN2_HUMAN	PAN2 polyA specific ribonuclease subunit homolog	443					nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|ubiquitin-dependent protein catabolic process	cytosol|nucleus	nucleic acid binding|poly(A)-specific ribonuclease activity|ubiquitin thiolesterase activity			ovary(2)|large_intestine(1)|skin(1)	4														0.111111	4.372328	9.756504	4	32	KEEP	---	---	---	---	capture		Silent	SNP	56720127	56720127	11831	12	C	T	T	T	340	27	PAN2	1	1
RBMS2	5939	broad.mit.edu	37	12	56963712	56963712	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:56963712T>C	uc001sln.2	+	c.322T>C	c.(322-324)TCA>CCA	p.S108P	RBMS2_uc010sqp.1_5'UTR|RBMS2_uc010sqq.1_5'UTR|RBMS2_uc009zou.2_5'UTR	NM_002898	NP_002889	Q15434	RBMS2_HUMAN	RNA binding motif, single stranded interacting	108	RRM 1.				RNA processing	nucleus	nucleotide binding|RNA binding				0														0.15859	89.153428	114.366895	36	191	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56963712	56963712	13611	12	T	C	C	C	806	62	RBMS2	4	4
INHBC	3626	broad.mit.edu	37	12	57843212	57843212	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57843212G>T	uc001snv.1	+	c.466G>T	c.(466-468)GGT>TGT	p.G156C		NM_005538	NP_005529	P55103	INHBC_HUMAN	inhibin beta C chain preproprotein	156					growth	extracellular region	growth factor activity|hormone activity|transforming growth factor beta receptor binding				0														0.130053	117.452927	193.226549	74	495	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57843212	57843212	8044	12	G	T	T	T	559	43	INHBC	2	2
ANKS1B	56899	broad.mit.edu	37	12	99640640	99640640	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:99640640C>A	uc001tge.1	-	c.1759G>T	c.(1759-1761)GAC>TAC	p.D587Y	ANKS1B_uc001tgf.1_Missense_Mutation_p.D167Y|ANKS1B_uc001tgk.2_5'UTR|ANKS1B_uc009ztt.1_Missense_Mutation_p.D553Y	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a	587						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)										0.099593	42.435142	121.236505	49	443	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99640640	99640640	697	12	C	A	A	A	377	29	ANKS1B	2	2
NALCN	259232	broad.mit.edu	37	13	101755531	101755531	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:101755531T>A	uc001vox.1	-	c.3049A>T	c.(3049-3051)ATT>TTT	p.I1017F		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1017	Helical; Name=S5 of repeat III; (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.102703	15.612385	44.692474	19	166	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	101755531	101755531	10544	13	T	A	A	A	676	52	NALCN	3	3
UPF3A	65110	broad.mit.edu	37	13	115047559	115047559	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:115047559C>T	uc001vup.2	+	c.271C>T	c.(271-273)CTG>TTG	p.L91L	UPF3A_uc010tkn.1_Silent_p.L91L|UPF3A_uc001vuq.2_Silent_p.L91L|UPF3A_uc001vus.2_Non-coding_Transcript|UPF3A_uc001vur.2_Non-coding_Transcript	NM_023011	NP_075387	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A	91					mRNA transport|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation	cytoplasm|nucleus|plasma membrane	nucleocytoplasmic transporter activity|nucleotide binding|protein binding|RNA binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)										0.75	11.628199	11.854391	3	1	KEEP	---	---	---	---	capture		Silent	SNP	115047559	115047559	17565	13	C	T	T	T	363	28	UPF3A	2	2
SACS	26278	broad.mit.edu	37	13	23915491	23915491	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:23915491C>A	uc001uon.2	-	c.2524G>T	c.(2524-2526)GAC>TAC	p.D842Y	SACS_uc001uoo.2_Missense_Mutation_p.D695Y|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	842					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				0.151515	17.903347	25.582768	10	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23915491	23915491	14284	13	C	A	A	A	416	32	SACS	2	2
ZC3H13	23091	broad.mit.edu	37	13	46619113	46619113	+	Silent	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:46619113T>C	uc010tfw.1	-	c.204A>G	c.(202-204)AAA>AAG	p.K68K	ZC3H13_uc001vas.1_Silent_p.K68K|ZC3H13_uc001vat.1_Silent_p.K68K	NM_015070	NP_055885	Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	68							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)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		Esophageal Squamous(187;747 2077 11056 31291 44172)								0.027027	-48.014197	15.970944	7	252	KEEP	---	---	---	---	capture		Silent	SNP	46619113	46619113	18153	13	T	C	C	C	725	56	ZC3H13	4	4
CYSLTR2	57105	broad.mit.edu	37	13	49281203	49281203	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:49281203G>C	uc010acx.1	+	c.250G>C	c.(250-252)GAT>CAT	p.D84H	CYSLTR2_uc010acy.1_Missense_Mutation_p.D84H|CYSLTR2_uc010acz.1_Missense_Mutation_p.D84H|CYSLTR2_uc010ada.1_Missense_Mutation_p.D84H|CYSLTR2_uc010adb.1_Missense_Mutation_p.D84H|CYSLTR2_uc010adc.1_Missense_Mutation_p.D84H|CYSLTR2_uc010add.1_Missense_Mutation_p.D84H|CYSLTR2_uc010acw.1_Missense_Mutation_p.D84H|CYSLTR2_uc001vck.2_Missense_Mutation_p.D84H	NM_020377	NP_065110	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	84	Helical; Name=2; (Potential).				immune response	integral to membrane|plasma membrane				lung(2)	2		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)					46				0.050847	-9.955629	15.26522	6	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49281203	49281203	4367	13	G	C	C	C	429	33	CYSLTR2	3	3
SLITRK6	84189	broad.mit.edu	37	13	86369995	86369995	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:86369995C>T	uc001vll.1	-	c.649G>A	c.(649-651)GAC>AAC	p.D217N	SLITRK6_uc010afe.1_5'UTR	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	217	Extracellular (Potential).					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)										0.233831	121.815655	134.851746	47	154	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86369995	86369995	15245	13	C	T	T	T	390	30	SLITRK6	2	2
DZIP1	22873	broad.mit.edu	37	13	96274626	96274626	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:96274626G>A	uc001vmk.2	-	c.1081C>T	c.(1081-1083)CAT>TAT	p.H361Y	DZIP1_uc001vml.2_Missense_Mutation_p.H361Y	NM_198968	NP_945319	Q86YF9	DZIP1_HUMAN	DAZ interacting protein 1 isoform 2	361					germ cell development|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleic acid binding|protein binding|zinc ion binding			ovary(2)	2	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)											0.089674	18.275951	80.842491	33	335	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	96274626	96274626	5049	13	G	A	A	A	611	47	DZIP1	2	2
AHNAK2	113146	broad.mit.edu	37	14	105414735	105414735	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105414735G>T	uc010axc.1	-	c.7053C>A	c.(7051-7053)GAC>GAA	p.D2351E	AHNAK2_uc001ypx.2_Missense_Mutation_p.D2251E	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2351						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.102564	7.144479	19.421859	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	105414735	105414735	418	14	G	T	T	T	516	40	AHNAK2	1	1
NYNRIN	57523	broad.mit.edu	37	14	24885288	24885288	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24885288G>T	uc001wpf.3	+	c.4333G>T	c.(4333-4335)GCC>TCC	p.A1445S		NM_025081	NP_079357	Q9P2P1	NYNRI_HUMAN	hypothetical protein LOC57523	1445					DNA integration	integral to membrane	DNA binding			ovary(2)|central_nervous_system(1)	3										473				0.108108	3.770673	9.406169	4	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24885288	24885288	11201	14	G	T	T	T	546	42	NYNRIN	2	2
ARID4A	5926	broad.mit.edu	37	14	58832019	58832019	+	Splice_Site_SNP	SNP	G	A	A	rs62621193		TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:58832019G>A	uc001xdp.2	+	c.3211_splice	c.e20+1	p.G1071_splice	ARID4A_uc001xdo.2_Splice_Site_SNP_p.G1071_splice|ARID4A_uc001xdq.2_Splice_Site_SNP_p.G1071_splice	NM_002892	NP_002883			retinoblastoma-binding protein 1 isoform I						chromatin assembly or disassembly|negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|transcriptional repressor complex	chromatin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(3)|lung(1)	4														0.037736	-16.398594	8.120369	4	102	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	58832019	58832019	934	14	G	A	A	A	572	44	ARID4A	5	2
PAPLN	89932	broad.mit.edu	37	14	73725989	73725989	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:73725989A>G	uc010ttx.1	+	c.1721A>G	c.(1720-1722)CAG>CGG	p.Q574R	PAPLN_uc001xnw.3_Missense_Mutation_p.Q547R|PAPLN_uc010arl.2_Non-coding_Transcript|PAPLN_uc010ttw.1_Non-coding_Transcript|PAPLN_uc010tty.1_Missense_Mutation_p.Q574R|PAPLN_uc010arm.2_5'Flank	NM_173462	NP_775733	O95428	PPN_HUMAN	papilin	574						proteinaceous extracellular matrix	metalloendopeptidase activity|serine-type endopeptidase inhibitor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)										0.049505	-10.614598	11.147253	5	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73725989	73725989	11845	14	A	G	G	G	91	7	PAPLN	4	4
YLPM1	56252	broad.mit.edu	37	14	75265706	75265706	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75265706G>C	uc001xqj.3	+	c.3706G>C	c.(3706-3708)GAT>CAT	p.D1236H	YLPM1_uc001xql.3_Non-coding_Transcript	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1041	Arg-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)										0.044444	-13.96707	16.004852	6	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75265706	75265706	18069	14	G	C	C	C	429	33	YLPM1	3	3
YLPM1	56252	broad.mit.edu	37	14	75265919	75265919	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:75265919G>T	uc001xqj.3	+	c.3919G>T	c.(3919-3921)GAG>TAG	p.E1307*	YLPM1_uc001xql.3_Non-coding_Transcript	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	1112	Arg-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)										0.039106	-26.139175	14.913819	7	172	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	75265919	75265919	18069	14	G	T	T	T	585	45	YLPM1	5	2
C14orf166B	145497	broad.mit.edu	37	14	77332323	77332323	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77332323C>A	uc001xsx.2	+	c.1264C>A	c.(1264-1266)CAA>AAA	p.Q422K	C14orf166B_uc010asn.1_Missense_Mutation_p.Q182K|C14orf166B_uc001xsw.2_Non-coding_Transcript	NM_194287	NP_919263	Q0VAA2	CN16B_HUMAN	hypothetical protein LOC145497	422											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		Ovarian(165;1056 1958 32571 36789 48728)								0.2	7.616267	8.871806	3	12	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77332323	77332323	1805	14	C	A	A	A	273	21	C14orf166B	2	2
FLRT2	23768	broad.mit.edu	37	14	86089492	86089492	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:86089492G>T	uc001xvr.2	+	c.1634G>T	c.(1633-1635)GGC>GTC	p.G545V	FLRT2_uc010atd.2_Missense_Mutation_p.G545V	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	545	Helical; (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(234;0.0319)										0.218182	58.140167	66.192589	24	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86089492	86089492	6181	14	G	T	T	T	546	42	FLRT2	2	2
SERPINA12	145264	broad.mit.edu	37	14	94964180	94964180	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94964180G>T	uc001ydj.2	-	c.555C>A	c.(553-555)ACC>ACA	p.T185T		NM_173850	NP_776249	Q8IW75	SPA12_HUMAN	serine (or cysteine) proteinase inhibitor, clade	185					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			central_nervous_system(2)|ovary(1)|lung(1)	4				COAD - Colon adenocarcinoma(157;0.235)						148				0.1	14.841921	42.018431	17	153	KEEP	---	---	---	---	capture		Silent	SNP	94964180	94964180	14577	14	G	T	T	T	548	43	SERPINA12	2	2
SERPINA4	5267	broad.mit.edu	37	14	95034546	95034546	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95034546G>T	uc010avd.2	+	c.1115G>T	c.(1114-1116)AGG>ATG	p.R372M	SERPINA4_uc001ydk.2_Missense_Mutation_p.R335M|SERPINA4_uc001ydl.2_Missense_Mutation_p.R335M	NM_006215	NP_006206	P29622	KAIN_HUMAN	serine (or cysteine) proteinase inhibitor, clade	335					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity			ovary(3)	3				COAD - Colon adenocarcinoma(157;0.211)										0.141791	32.927757	49.516589	19	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95034546	95034546	14579	14	G	T	T	T	455	35	SERPINA4	2	2
TRPM1	4308	broad.mit.edu	37	15	31362381	31362381	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:31362381A>T	uc001zfm.2	-	c.66T>A	c.(64-66)AGT>AGA	p.S22R	TRPM1_uc010azy.2_5'Flank|TRPM1_uc001zfl.2_5'Flank|TRPM1_uc001zfn.3_Missense_Mutation_p.S22R	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	22	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)										0.141148	206.318224	310.16269	118	718	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31362381	31362381	17136	15	A	T	T	T	76	6	TRPM1	3	3
RYR3	6263	broad.mit.edu	37	15	33945030	33945030	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:33945030C>A	uc001zhi.2	+	c.4254C>A	c.(4252-4254)GCC>GCA	p.A1418A	RYR3_uc010bar.2_Silent_p.A1418A	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	1418	4 X approximate repeats.|B30.2/SPRY 3.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.161677	54.242464	72.404955	27	140	KEEP	---	---	---	---	capture		Silent	SNP	33945030	33945030	14250	15	C	A	A	A	262	21	RYR3	2	2
MGA	23269	broad.mit.edu	37	15	42042472	42042472	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:42042472G>T	uc010ucy.1	+	c.6667G>T	c.(6667-6669)GAC>TAC	p.D2223Y	MGA_uc010ucz.1_Missense_Mutation_p.D2014Y|MGA_uc010uda.1_Missense_Mutation_p.D839Y|MGA_uc001zoi.2_Missense_Mutation_p.D437Y	NM_001164273	NP_001157745	Q8IWI9	MGAP_HUMAN	MAX-interacting protein isoform 1	2184	Basic motif.				regulation of transcription, DNA-dependent	MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(6)|kidney(3)|upper_aerodigestive_tract(1)|skin(1)	11		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)						606				0.104396	17.279266	45.626754	19	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42042472	42042472	9930	15	G	T	T	T	585	45	MGA	2	2
IGDCC3	9543	broad.mit.edu	37	15	65625667	65625667	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:65625667C>T	uc002aos.2	-	c.910G>A	c.(910-912)GTC>ATC	p.V304I		NM_004884	NP_004875	Q8IVU1	IGDC3_HUMAN	putative neuronal cell adhesion molecule	304	Extracellular (Potential).|Ig-like C2-type 3.									ovary(3)	3														0.162162	11.126111	15.142485	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65625667	65625667	7869	15	C	T	T	T	247	19	IGDCC3	1	1
CHRNB4	1143	broad.mit.edu	37	15	78921890	78921890	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:78921890C>A	uc002bed.1	-	c.757G>T	c.(757-759)GTC>TTC	p.V253F	CHRNB4_uc002bee.1_Intron|CHRNB4_uc010blh.1_Missense_Mutation_p.V71F	NM_000750	NP_000741	P30926	ACHB4_HUMAN	cholinergic receptor, nicotinic, beta 4	253	Helical; (Potential).				regulation of neurotransmitter secretion|synaptic transmission involved in micturition|synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity				0										152				0.153086	127.811187	174.413443	62	343	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78921890	78921890	3527	15	C	A	A	A	247	19	CHRNB4	1	1
RASGRF1	5923	broad.mit.edu	37	15	79265681	79265681	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:79265681C>T	uc002beq.2	-	c.3624G>A	c.(3622-3624)ACG>ACA	p.T1208T	RASGRF1_uc002bep.2_Silent_p.T1192T|RASGRF1_uc002beo.2_Silent_p.T424T	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	1210	Ras-GEF.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(2)|ovary(1)|central_nervous_system(1)	4										694				0.042254	-18.971912	12.975868	6	136	KEEP	---	---	---	---	capture		Silent	SNP	79265681	79265681	13533	15	C	T	T	T	288	23	RASGRF1	1	1
KIAA1024	23251	broad.mit.edu	37	15	79750731	79750731	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:79750731G>A	uc002bew.1	+	c.2242G>A	c.(2242-2244)GAG>AAG	p.E748K	KIAA1024_uc010unk.1_Missense_Mutation_p.E748K	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN	hypothetical protein LOC23251	748						integral to membrane				pancreas(2)|ovary(1)|central_nervous_system(1)	4														0.137097	29.584298	45.39253	17	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79750731	79750731	8512	15	G	A	A	A	533	41	KIAA1024	2	2
IL16	3603	broad.mit.edu	37	15	81592014	81592015	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:81592014_81592015CC>AA	uc010unp.1	+	c.2473_2474CC>AA	c.(2473-2475)CCT>AAT	p.P825N	IL16_uc010blq.1_Missense_Mutation_p.P737N|IL16_uc002bge.3_Non-coding_Transcript|IL16_uc002bgh.3_Missense_Mutation_p.P783N|IL16_uc002bgg.2_Missense_Mutation_p.P783N|IL16_uc002bgi.1_Missense_Mutation_p.P173N|IL16_uc002bgj.2_Missense_Mutation_p.P277N|IL16_uc002bgk.2_Missense_Mutation_p.P82N|IL16_uc002bgl.1_Missense_Mutation_p.P82N|IL16_uc010unq.1_Missense_Mutation_p.P82N	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	783					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4														0.104651	8.20647	21.579449	9	77	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	81592014	81592015	7934	15	CC	AA	AA	AA	390	30	IL16	2	2
HDGFRP3	50810	broad.mit.edu	37	15	83826167	83826167	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:83826167C>A	uc002bjs.1	-	c.459G>T	c.(457-459)AAG>AAT	p.K153N		NM_016073	NP_057157	Q9Y3E1	HDGR3_HUMAN	hepatoma-derived growth factor, related protein	153					cell proliferation	nucleus	growth factor activity				0														0.112195	31.266393	61.722757	23	182	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	83826167	83826167	7304	15	C	A	A	A	311	24	HDGFRP3	2	2
ADAMTSL3	57188	broad.mit.edu	37	15	84611369	84611369	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:84611369G>T	uc002bjz.3	+	c.2139G>T	c.(2137-2139)GGG>GGT	p.G713G	ADAMTSL3_uc010bmt.1_Silent_p.G713G|ADAMTSL3_uc010bmu.1_Silent_p.G713G	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	713	TSP type-1 5.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			central_nervous_system(5)|ovary(5)|large_intestine(4)|lung(1)|breast(1)|kidney(1)|pancreas(1)	18			BRCA - Breast invasive adenocarcinoma(143;0.211)							580				0.106017	32.870498	86.647432	37	312	KEEP	---	---	---	---	capture		Silent	SNP	84611369	84611369	277	15	G	T	T	T	535	42	ADAMTSL3	2	2
NOMO1	23420	broad.mit.edu	37	16	14982998	14982998	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:14982998G>T	uc002dcv.2	+	c.3370G>T	c.(3370-3372)GAC>TAC	p.D1124Y		NM_014287	NP_055102	Q15155	NOMO1_HUMAN	nodal modulator 1 precursor	1124	Extracellular (Potential).					integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			ovary(1)	1														0.095679	15.45223	68.647833	31	293	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14982998	14982998	10934	16	G	T	T	T	585	45	NOMO1	2	2
SMG1	23049	broad.mit.edu	37	16	18881188	18881188	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:18881188G>C	uc002dfm.2	-	c.2621C>G	c.(2620-2622)TCT>TGT	p.S874C	SMG1_uc010bwb.2_Missense_Mutation_p.S734C	NM_015092	NP_055907	Q96Q15	SMG1_HUMAN	PI-3-kinase-related kinase SMG-1	874					DNA repair|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|peptidyl-serine phosphorylation|phosphatidylinositol phosphorylation|protein autophosphorylation	cytoplasm|nucleus	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			breast(5)|lung(4)|kidney(2)|stomach(1)|ovary(1)	13										1101				0.081633	3.05975	11.792354	4	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18881188	18881188	15293	16	G	C	C	C	429	33	SMG1	3	3
UMOD	7369	broad.mit.edu	37	16	20352502	20352502	+	Silent	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20352502C>G	uc002dhb.2	-	c.1587G>C	c.(1585-1587)CTG>CTC	p.L529L	UMOD_uc002dgz.2_Silent_p.L496L|UMOD_uc002dha.2_Silent_p.L496L	NM_003361	NP_003352	P07911	UROM_HUMAN	uromodulin precursor	496	ZP.				cellular defense response|negative regulation of cell proliferation	anchored to membrane|apical plasma membrane|basolateral plasma membrane|cilium membrane|extrinsic to membrane|primary cilium|spindle pole	calcium ion binding			ovary(1)	1														0.107843	17.645087	33.200534	11	91	KEEP	---	---	---	---	capture		Silent	SNP	20352502	20352502	17537	16	C	G	G	G	210	17	UMOD	3	3
TNRC6A	27327	broad.mit.edu	37	16	24834793	24834793	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:24834793A>T	uc002dmm.2	+	c.5554A>T	c.(5554-5556)AGT>TGT	p.S1852C	TNRC6A_uc010bxs.2_Missense_Mutation_p.S1599C|TNRC6A_uc002dmn.2_Missense_Mutation_p.S1550C|TNRC6A_uc002dmo.2_Missense_Mutation_p.S1491C|TNRC6A_uc002dmr.2_Missense_Mutation_p.S51C	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1852	Sufficient for interaction with EIF2C2.|RRM.				negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)										0.118881	50.95968	91.742925	34	252	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24834793	24834793	16881	16	A	T	T	T	91	7	TNRC6A	3	3
CTCF	10664	broad.mit.edu	37	16	67662413	67662413	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:67662413G>T	uc002etl.2	+	c.1659G>T	c.(1657-1659)GCG>GCT	p.A553A	CTCF_uc010cek.2_Silent_p.A225A|CTCF_uc002etm.1_Silent_p.A42A	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	553					chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		Colon(175;1200 1966 6945 23069 27405)								0.113158	60.748204	116.864887	43	337	KEEP	---	---	---	---	capture		Silent	SNP	67662413	67662413	4159	16	G	T	T	T	496	39	CTCF	1	1
CTCF	10664	broad.mit.edu	37	16	67663408	67663408	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:67663408C>T	uc002etl.2	+	c.1809C>T	c.(1807-1809)CGC>CGT	p.R603R	CTCF_uc010cek.2_Silent_p.R275R|CTCF_uc002etm.1_Silent_p.R92R	NM_006565	NP_006556	P49711	CTCF_HUMAN	CCCTC-binding factor	603					chromatin modification|chromosome segregation|negative regulation of transcription, DNA-dependent|nucleosome positioning|positive regulation of transcription, DNA-dependent|regulation of centromeric sister chromatid cohesion|regulation of molecular function, epigenetic	chromosome, centromeric region|condensed chromosome|nucleolus|nucleoplasm	chromatin insulator sequence binding|promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		Colon(175;1200 1966 6945 23069 27405)								0.115152	25.198256	49.27783	19	146	KEEP	---	---	---	---	capture		Silent	SNP	67663408	67663408	4159	16	C	T	T	T	353	28	CTCF	2	2
PKD1L2	114780	broad.mit.edu	37	16	81155282	81155282	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:81155282C>A	uc002fgh.1	-	c.6521G>T	c.(6520-6522)CGC>CTC	p.R2174L	PKD1L2_uc002fgf.1_5'UTR|PKD1L2_uc002fgg.1_Non-coding_Transcript	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	2174	Cytoplasmic (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.075	0.793534	8.204718	3	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81155282	81155282	12389	16	C	A	A	A	351	27	PKD1L2	1	1
DNAH9	1770	broad.mit.edu	37	17	11656186	11656186	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11656186T>A	uc002gne.2	+	c.6647T>A	c.(6646-6648)ATC>AAC	p.I2216N	DNAH9_uc010coo.2_Missense_Mutation_p.I1510N	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	2216	AAA 2 (By similarity).			I -> T (in Ref. 4; BAA21573).	cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.117978	27.543486	53.080679	21	157	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11656186	11656186	4791	17	T	A	A	A	650	50	DNAH9	3	3
DHRS7B	25979	broad.mit.edu	37	17	21094259	21094259	+	Splice_Site_SNP	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:21094259A>T	uc002gyo.2	+	c.773_splice	c.e7-2	p.V258_splice		NM_015510	NP_056325			dehydrogenase/reductase (SDR family) member 7B						oxidation-reduction process	integral to membrane|peroxisomal membrane	binding|oxidoreductase activity			pancreas(1)	1														0.09434	3.250719	11.997669	5	48	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	21094259	21094259	4675	17	A	T	T	T	195	15	DHRS7B	5	3
FLOT2	2319	broad.mit.edu	37	17	27209238	27209238	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:27209238C>T	uc002hdc.2	-	c.597G>A	c.(595-597)AAG>AAA	p.K199K		NM_004475	NP_004466	Q14254	FLOT2_HUMAN	flotillin 2	199					cell adhesion|epidermis development	cell surface|endosome|membrane fraction					0	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;3.26e-06)|all cancers(11;1.76e-05)|BRCA - Breast invasive adenocarcinoma(11;0.00015)|OV - Ovarian serous cystadenocarcinoma(11;0.0602)											0.106061	18.658285	38.996257	14	118	KEEP	---	---	---	---	capture		Silent	SNP	27209238	27209238	6179	17	C	T	T	T	311	24	FLOT2	2	2
SYNRG	11276	broad.mit.edu	37	17	35913989	35913989	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:35913989C>T	uc002hoa.2	-	c.1836G>A	c.(1834-1836)CTG>CTA	p.L612L	SYNRG_uc010wde.1_Silent_p.L534L|SYNRG_uc010wdf.1_Silent_p.L534L|SYNRG_uc002hoc.2_Silent_p.L533L|SYNRG_uc002hoe.2_Silent_p.L534L|SYNRG_uc002hod.2_Silent_p.L534L|SYNRG_uc010wdg.1_Silent_p.L451L|SYNRG_uc002hob.2_Silent_p.L612L|SYNRG_uc002hof.2_Silent_p.L324L|SYNRG_uc010cvd.1_Silent_p.L412L	NM_007247	NP_009178	Q9UMZ2	SYNRG_HUMAN	synergin, gamma isoform 1	612	Interaction with A1P1G1 and A1P1G2.				endocytosis|intracellular protein transport	AP-1 adaptor complex	calcium ion binding			ovary(2)	2														0.028881	-51.962907	15.692006	8	269	KEEP	---	---	---	---	capture		Silent	SNP	35913989	35913989	15981	17	C	T	T	T	366	29	SYNRG	2	2
CCDC56	28958	broad.mit.edu	37	17	40948054	40948054	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40948054G>A	uc010wgz.1	-	c.204C>T	c.(202-204)CTC>CTT	p.L68L	WNK4_uc002ibj.2_Intron|WNK4_uc010wgx.1_Intron|CNTD1_uc002ibm.3_5'Flank|CNTD1_uc010wha.1_5'Flank	CCDC56		Q9Y2R0	CCD56_HUMAN	SubName: Full=cDNA FLJ50764;	Error:Variant_position_missing_in_Q9Y2R0_after_alignment						integral to membrane					0		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0741)										0.1875	49.913134	61.632122	24	104	KEEP	---	---	---	---	capture		Silent	SNP	40948054	40948054	2949	17	G	A	A	A	573	45	CCDC56	2	2
UTP18	51096	broad.mit.edu	37	17	49357467	49357467	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:49357467G>T	uc002its.2	+	c.1113_splice	c.e8+1	p.K371_splice		NM_016001	NP_057085			UTP18, small subunit processome component						rRNA processing	nucleolus					0			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)											0.116279	7.542017	13.774166	5	38	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	49357467	49357467	17663	17	G	T	T	T	572	44	UTP18	5	2
MC5R	4161	broad.mit.edu	37	18	13826463	13826463	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:13826463C>A	uc010xaf.1	+	c.699C>A	c.(697-699)AGC>AGA	p.S233R		NM_005913	NP_005904	P33032	MC5R_HUMAN	melanocortin 5 receptor	233	Cytoplasmic (Potential).			ALPGASSARQRTSM -> LCPGPALRGRGPAW (in Ref. 1).	G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocortin receptor activity|protein binding			ovary(3)	3														0.096774	3.7993	13.90759	6	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13826463	13826463	9756	18	C	A	A	A	324	25	MC5R	2	2
NETO1	81832	broad.mit.edu	37	18	70417550	70417550	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:70417550C>G	uc002lkw.2	-	c.1288G>C	c.(1288-1290)GAC>CAC	p.D430H	NETO1_uc002lkx.1_Missense_Mutation_p.D429H|NETO1_uc002lky.1_Missense_Mutation_p.D430H	NM_138966	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin- and tolloid-like protein 1 isoform 3	430	Cytoplasmic (Potential).				memory|regulation of long-term neuronal synaptic plasticity|visual learning	cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane	receptor activity			ovary(2)	2		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)										0.186667	75.207633	89.0049	28	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70417550	70417550	10738	18	C	G	G	G	377	29	NETO1	3	3
KEAP1	9817	broad.mit.edu	37	19	10610279	10610279	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10610279G>A	uc002moq.1	-	c.431C>T	c.(430-432)TCC>TTC	p.S144F	KEAP1_uc002mor.1_Missense_Mutation_p.S144F	NM_012289	NP_036421	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	144	BTB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|midbody|nucleus	protein binding			breast(2)|ovary(1)|pancreas(1)	4			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)											0.275862	45.177194	47.799038	16	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10610279	10610279	8447	19	G	A	A	A	533	41	KEAP1	2	2
CC2D1A	54862	broad.mit.edu	37	19	14029592	14029592	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:14029592C>T	uc002mxo.2	+	c.980C>T	c.(979-981)TCG>TTG	p.S327L	CC2D1A_uc002mxn.2_Missense_Mutation_p.S226L|CC2D1A_uc002mxp.2_Missense_Mutation_p.S327L|CC2D1A_uc010dzh.2_5'UTR|CC2D1A_uc002mxq.1_5'UTR	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	327	Pro-rich.				positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)											0.083333	0.895586	7.248233	3	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	14029592	14029592	2846	19	C	T	T	T	403	31	CC2D1A	1	1
CEACAM7	1087	broad.mit.edu	37	19	42191008	42191009	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42191008_42191009CC>AA	uc002ori.1	-	c.208_209GG>TT	c.(208-210)GGG>TTG	p.G70L	CEACAM7_uc010ehx.2_Missense_Mutation_p.G70L|CEACAM7_uc010ehy.1_Missense_Mutation_p.G70L	NM_006890	NP_008821	Q14002	CEAM7_HUMAN	carcinoembryonic antigen-related cell adhesion	70	Ig-like V-type.					anchored to membrane|integral to membrane|plasma membrane				ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(3;0.0027)|all cancers(3;0.00979)|Epithelial(262;0.0366)										0.141631	59.914037	88.776738	33	200	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	42191008	42191009	3330	19	CC	AA	AA	AA	286	22	CEACAM7	2	2
LAIR2	3904	broad.mit.edu	37	19	55014926	55014926	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:55014926G>T	uc002qgc.2	+	c.45G>T	c.(43-45)CTG>CTT	p.L15L	LAIR2_uc002qga.1_Non-coding_Transcript|LAIR2_uc002qgb.1_Intron|LAIR2_uc002qgd.2_Silent_p.L15L|LAIR2_uc010erl.2_Silent_p.L15L	NM_002288	NP_002279	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like	15						extracellular region	receptor activity			ovary(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)										0.116667	18.657328	36.010615	14	106	KEEP	---	---	---	---	capture		Silent	SNP	55014926	55014926	8926	19	G	T	T	T	600	47	LAIR2	2	2
NLRP8	126205	broad.mit.edu	37	19	56467169	56467169	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56467169G>T	uc002qmh.2	+	c.1745G>T	c.(1744-1746)GGT>GTT	p.G582V	NLRP8_uc010etg.2_Missense_Mutation_p.G582V	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	582						cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)										0.066667	-2.013743	6.746815	3	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56467169	56467169	10886	19	G	T	T	T	572	44	NLRP8	2	2
ZNF835	90485	broad.mit.edu	37	19	57176423	57176423	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57176423C>A	uc010ygo.1	-	c.210G>T	c.(208-210)GGG>GGT	p.G70G	ZNF835_uc010ygn.1_Silent_p.G48G	NM_001005850	NP_001005850	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	70					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(3)|skin(1)	4														0.12	7.615886	14.700943	6	44	KEEP	---	---	---	---	capture		Silent	SNP	57176423	57176423	18785	19	C	A	A	A	275	22	ZNF835	2	2
CAPS	828	broad.mit.edu	37	19	5915081	5915081	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:5915081G>A	uc002mdt.2	+	c.392G>A	c.(391-393)CGC>CAC	p.R131H	CAPS_uc002mdu.2_Intron	NM_004058	NP_004049	Q13938	CAYP1_HUMAN	calcyphosine isoform a	131					intracellular signal transduction	cytoplasm	calcium ion binding				0														0.102564	2.570199	8.711907	4	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5915081	5915081	2756	19	G	A	A	A	494	38	CAPS	1	1
MUC16	94025	broad.mit.edu	37	19	9046706	9046706	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9046706G>T	uc002mkp.2	-	c.34925C>A	c.(34924-34926)ACT>AAT	p.T11642N		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11644	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.132561	175.476403	277.381484	103	674	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9046706	9046706	10367	19	G	T	T	T	468	36	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9061615	9061615	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9061615G>T	uc002mkp.2	-	c.25831C>A	c.(25831-25833)CCT>ACT	p.P8611T		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	8613	Ser-rich.|Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.112903	41.589053	87.452233	35	275	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9061615	9061615	10367	19	G	T	T	T	572	44	MUC16	2	2
MUC16	94025	broad.mit.edu	37	19	9089295	9089295	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9089295G>T	uc002mkp.2	-	c.2520C>A	c.(2518-2520)CTC>CTA	p.L840L		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	840	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.162121	197.667188	269.352145	107	553	KEEP	---	---	---	---	capture		Silent	SNP	9089295	9089295	10367	19	G	T	T	T	522	41	MUC16	2	2
KCNA2	3737	broad.mit.edu	37	1	111146525	111146525	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:111146525G>A	uc001dzu.2	-	c.880C>T	c.(880-882)CGT>TGT	p.R294C	KCNA2_uc009wfv.1_Missense_Mutation_p.R294C|KCNA2_uc009wfw.2_Missense_Mutation_p.R294C	NM_004974	NP_004965	P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related	294	Helical; Voltage-sensor; Name=Segment S4; (Potential).					juxtaparanode region of axon|voltage-gated potassium channel complex	delayed rectifier potassium channel activity			ovary(1)	1		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)		Pancreas(18;568 735 10587 23710 36357)								0.145038	38.836451	54.714788	19	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111146525	111146525	8308	1	G	A	A	A	507	39	KCNA2	1	1
NBPF7	343505	broad.mit.edu	37	1	120384102	120384102	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120384102C>A	uc010oxk.1	-	c.460G>T	c.(460-462)GAT>TAT	p.D154Y		NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505	154						cytoplasm				ovary(1)	1	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)										0.151292	69.585886	101.162213	41	230	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120384102	120384102	10597	1	C	A	A	A	390	30	NBPF7	2	2
ADAM30	11085	broad.mit.edu	37	1	120438759	120438759	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120438759C>A	uc001eij.2	-	c.201G>T	c.(199-201)CAG>CAT	p.Q67H		NM_021794	NP_068566	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30 preproprotein	67					proteolysis	integral to membrane	metalloendopeptidase activity|zinc ion binding			ovary(2)|lung(1)	3	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)										0.139344	31.890998	47.2211	17	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120438759	120438759	249	1	C	A	A	A	259	20	ADAM30	2	2
SEMA4A	64218	broad.mit.edu	37	1	156126349	156126349	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:156126349C>G	uc001fnl.2	+	c.284C>G	c.(283-285)CCC>CGC	p.P95R	SEMA4A_uc009wrq.2_Missense_Mutation_p.P95R|SEMA4A_uc001fnm.2_Missense_Mutation_p.P95R|SEMA4A_uc001fnn.2_5'UTR|SEMA4A_uc001fno.2_Missense_Mutation_p.P95R	NM_022367	NP_071762	Q9H3S1	SEM4A_HUMAN	semaphorin B precursor	95	Sema.|Extracellular (Potential).				axon guidance|visual perception	integral to membrane|plasma membrane	receptor activity			ovary(1)	1	Hepatocellular(266;0.158)													0.146341	26.142074	36.001822	12	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	156126349	156126349	14517	1	C	G	G	G	286	22	SEMA4A	3	3
FCRL1	115350	broad.mit.edu	37	1	157771827	157771827	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:157771827G>A	uc001frg.2	-	c.764C>T	c.(763-765)CCC>CTC	p.P255L	FCRL1_uc001frf.2_Non-coding_Transcript|FCRL1_uc001frh.2_Missense_Mutation_p.P255L|FCRL1_uc001fri.2_Missense_Mutation_p.P255L|FCRL1_uc001frj.2_Non-coding_Transcript	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor	255	Ig-like C2-type 3.|Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(3)	3	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GBM(54;482 1003 11223 30131 35730)								0.204301	146.911373	169.552456	57	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157771827	157771827	6031	1	G	A	A	A	559	43	FCRL1	2	2
CD1D	912	broad.mit.edu	37	1	158152847	158152847	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158152847C>A	uc001frr.2	+	c.787C>A	c.(787-789)CTC>ATC	p.L263I	CD1D_uc009wss.2_Intron	NM_001766	NP_001757	P15813	CD1D_HUMAN	CD1D antigen precursor	263	Ig-like.|Extracellular (Potential).				antigen processing and presentation, endogenous lipid antigen via MHC class Ib|detection of bacterium|innate immune response|interspecies interaction between organisms|positive regulation of innate immune response|T cell selection	endosome membrane|integral to plasma membrane|lysosomal membrane	beta-2-microglobulin binding|exogenous lipid antigen binding|histone binding|receptor activity			ovary(1)	1	all_hematologic(112;0.0378)													0.171123	124.452433	162.718191	64	310	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158152847	158152847	3104	1	C	A	A	A	416	32	CD1D	2	2
OR6K6	128371	broad.mit.edu	37	1	158724748	158724748	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158724748C>A	uc001fsw.1	+	c.143C>A	c.(142-144)GCG>GAG	p.A48E		NM_001005184	NP_001005184	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K,	48	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_hematologic(112;0.0378)													0.116773	78.393151	146.429836	55	416	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158724748	158724748	11614	1	C	A	A	A	351	27	OR6K6	1	1
NIT1	4817	broad.mit.edu	37	1	161088936	161088937	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:161088936_161088937GG>TT	uc001fxv.1	+	c.111_112GG>TT	c.(109-114)ATGGCT>ATTTCT	p.37_38MA>IS	PFDN2_uc001fxu.2_5'Flank|NIT1_uc001fxw.2_Missense_Mutation_p.37_38MA>IS|NIT1_uc001fxx.1_Missense_Mutation_p.1_2MA>IS|NIT1_uc001fxy.1_Missense_Mutation_p.1_2MA>IS|NIT1_uc010pka.1_Missense_Mutation_p.22_23MA>IS	NM_005600	NP_005591	Q86X76	NIT1_HUMAN	nitrilase 1	37_38					nitrogen compound metabolic process	mitochondrion	nitrilase activity				0	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)											0.109091	14.515359	31.166404	12	98	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	161088936	161088937	10834	1	GG	TT	TT	TT	611	47	NIT1	2	2
DUSP27	92235	broad.mit.edu	37	1	167096659	167096659	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:167096659G>T	uc001geb.1	+	c.2291G>T	c.(2290-2292)GGG>GTG	p.G764V		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27	764					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.092593	9.194066	36.260205	15	147	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167096659	167096659	5009	1	G	T	T	T	559	43	DUSP27	2	2
TNR	7143	broad.mit.edu	37	1	175325510	175325510	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:175325510C>A	uc001gkp.1	-	c.3063G>T	c.(3061-3063)ATG>ATT	p.M1021I	TNR_uc009wwu.1_Missense_Mutation_p.M1021I	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	1021	Fibronectin type-III 8.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)													0.211503	285.742832	327.22871	114	425	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175325510	175325510	16879	1	C	A	A	A	221	17	TNR	2	2
ANGPTL1	9068	broad.mit.edu	37	1	178834573	178834573	+	Silent	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:178834573C>G	uc001gma.2	-	c.339G>C	c.(337-339)GTG>GTC	p.V113V	RALGPS2_uc001gly.1_Intron|RALGPS2_uc001glz.2_Intron|RALGPS2_uc010pnb.1_Intron|ANGPTL1_uc001gmb.2_Silent_p.V113V|ANGPTL1_uc010pnc.1_Silent_p.V35V	NM_004673	NP_004664	O95841	ANGL1_HUMAN	angiopoietin-like 1 precursor	113	Potential.					extracellular space	receptor binding				0														0.030369	-78.16846	33.361014	14	447	KEEP	---	---	---	---	capture		Silent	SNP	178834573	178834573	616	1	C	G	G	G	366	29	ANGPTL1	3	3
TDRD5	163589	broad.mit.edu	37	1	179562935	179562935	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:179562935C>A	uc010pnp.1	+	c.573C>A	c.(571-573)ACC>ACA	p.T191T	TDRD5_uc001gnf.1_Silent_p.T191T	NM_173533	NP_775804	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	191	Lotus/OST-HTH 2.				DNA methylation involved in gamete generation|P granule organization|spermatid development	chromatoid body|pi-body	nucleic acid binding			ovary(2)|central_nervous_system(1)|skin(1)	4														0.330144	204.562386	209.878252	69	140	KEEP	---	---	---	---	capture		Silent	SNP	179562935	179562935	16260	1	C	A	A	A	262	21	TDRD5	2	2
FAM5C	339479	broad.mit.edu	37	1	190423996	190423996	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:190423996C>A	uc001gse.1	-	c.25G>T	c.(25-27)GCT>TCT	p.A9S	FAM5C_uc010pot.1_5'UTR	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	9						extracellular region				lung(2)|ovary(1)|kidney(1)	4	Prostate(682;0.198)													0.289855	55.955636	58.697907	20	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190423996	190423996	5817	1	C	A	A	A	325	25	FAM5C	2	2
ASPM	259266	broad.mit.edu	37	1	197057403	197057403	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197057403T>A	uc001gtu.2	-	c.10144A>T	c.(10144-10146)ACA>TCA	p.T3382S	ASPM_uc001gtv.2_Missense_Mutation_p.T1797S|ASPM_uc001gtw.3_Missense_Mutation_p.T1230S	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	3382					mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.078947	1.57857	29.099715	12	140	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197057403	197057403	1075	1	T	A	A	A	754	58	ASPM	3	3
PPP1R15B	84919	broad.mit.edu	37	1	204375279	204375279	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:204375279T>C	uc001hav.3	-	c.2083A>G	c.(2083-2085)ATG>GTG	p.M695V		NM_032833	NP_116222	Q5SWA1	PR15B_HUMAN	protein phosphatase 1, regulatory subunit 15B	695					regulation of translation					ovary(1)|pancreas(1)	2	all_cancers(21;0.0032)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.179)|all_epithelial(62;0.193)|Prostate(682;0.227)		all cancers(3;1.14e-29)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.139)											0.241071	412.546372	446.793622	135	425	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	204375279	204375279	12799	1	T	C	C	C	676	52	PPP1R15B	4	4
UBXN10	127733	broad.mit.edu	37	1	20517245	20517245	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:20517245C>T	uc001bdb.2	+	c.191C>T	c.(190-192)CCA>CTA	p.P64L		NM_152376	NP_689589	Q96LJ8	UBX10_HUMAN	UBX domain protein 10	64										ovary(1)	1														0.137143	39.988085	62.281786	24	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20517245	20517245	17470	1	C	T	T	T	273	21	UBXN10	2	2
SLC26A9	115019	broad.mit.edu	37	1	205897047	205897047	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:205897047C>T	uc001hdp.2	-	c.1084G>A	c.(1084-1086)GAC>AAC	p.D362N	SLC26A9_uc001hdo.2_Missense_Mutation_p.D30N|SLC26A9_uc001hdq.2_Missense_Mutation_p.D362N	NM_134325	NP_599152	Q7LBE3	S26A9_HUMAN	solute carrier family 26, member 9 isoform b	362						integral to membrane	chloride channel activity|secondary active sulfate transmembrane transporter activity			ovary(1)	1	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0458)											0.131579	49.199128	79.268546	30	198	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	205897047	205897047	15021	1	C	T	T	T	403	31	SLC26A9	1	1
TRIM11	81559	broad.mit.edu	37	1	228584677	228584677	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:228584677C>A	uc001hss.2	-	c.830G>T	c.(829-831)GGA>GTA	p.G277V	TRIM11_uc010pvx.1_Missense_Mutation_p.G276V|TRIM11_uc001hst.1_Missense_Mutation_p.G277V	NM_145214	NP_660215	Q96F44	TRI11_HUMAN	tripartite motif-containing 11	277	B30.2/SPRY.				response to virus	cytoplasm|nucleus	protein binding|zinc ion binding				0		Prostate(94;0.0724)												0.176471	29.26632	37.658918	15	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	228584677	228584677	17031	1	C	A	A	A	390	30	TRIM11	2	2
SIPA1L2	57568	broad.mit.edu	37	1	232574993	232574993	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:232574993C>A	uc001hvg.2	-	c.3892G>T	c.(3892-3894)GCT>TCT	p.A1298S	SIPA1L2_uc001hvf.2_Missense_Mutation_p.A372S	NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	1298					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.22619	46.280569	52.063611	19	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	232574993	232574993	14825	1	C	A	A	A	338	26	SIPA1L2	2	2
RYR2	6262	broad.mit.edu	37	1	237819276	237819276	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237819276T>A	uc001hyl.1	+	c.8121T>A	c.(8119-8121)GAT>GAA	p.D2707E		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2707	Modulator (Potential).|Cytoplasmic (By similarity).|3.|4 X approximate repeats.				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)											0.232877	45.538398	50.306228	17	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237819276	237819276	14249	1	T	A	A	A	634	49	RYR2	3	3
FMN2	56776	broad.mit.edu	37	1	240370817	240370817	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:240370817T>G	uc010pye.1	+	c.2717T>G	c.(2716-2718)CTG>CGG	p.L906R	FMN2_uc010pyd.1_Missense_Mutation_p.L902R	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	902	Pro-rich.|FH1.				actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)							1289				0.13253	17.564088	28.453702	11	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	240370817	240370817	6192	1	T	G	G	G	715	55	FMN2	4	4
OR6F1	343169	broad.mit.edu	37	1	247875730	247875730	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:247875730T>A	uc001idj.1	-	c.328A>T	c.(328-330)ACA>TCA	p.T110S		NM_001005286	NP_001005286	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F,	110	Helical; Name=3; (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;0.0168)											0.261364	129.070463	138.140112	46	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	247875730	247875730	11611	1	T	A	A	A	767	59	OR6F1	3	3
TRIM58	25893	broad.mit.edu	37	1	248020633	248020633	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248020633G>A	uc001ido.2	+	c.85G>A	c.(85-87)GTG>ATG	p.V29M		NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	29	RING-type.					intracellular	zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)											0.272727	8.720614	9.232403	3	8	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248020633	248020633	17077	1	G	A	A	A	520	40	TRIM58	1	1
OR2T6	254879	broad.mit.edu	37	1	248551067	248551067	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248551067C>A	uc001iei.1	+	c.158C>A	c.(157-159)CCT>CAT	p.P53H		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	53	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)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.276786	88.475718	93.498615	31	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248551067	248551067	11435	1	C	A	A	A	312	24	OR2T6	2	2
OR2T6	254879	broad.mit.edu	37	1	248551409	248551409	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248551409C>A	uc001iei.1	+	c.500C>A	c.(499-501)CCG>CAG	p.P167Q		NM_001005471	NP_001005471	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T,	167	Extracellular (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)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.289474	33.510892	35.019512	11	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248551409	248551409	11435	1	C	A	A	A	299	23	OR2T6	1	1
OR2T2	401992	broad.mit.edu	37	1	248616371	248616371	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248616371G>T	uc001iek.1	+	c.273G>T	c.(271-273)AAG>AAT	p.K91N		NM_001004136	NP_001004136	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T,	91	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)											0.102142	47.78551	143.593822	62	545	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248616371	248616371	11426	1	G	T	T	T	425	33	OR2T2	2	2
C1orf94	84970	broad.mit.edu	37	1	34677938	34677938	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:34677938C>A	uc001bxt.2	+	c.1652C>A	c.(1651-1653)TCT>TAT	p.S551Y	C1orf94_uc001bxs.3_Missense_Mutation_p.S361Y	NM_001134734	NP_001128206	Q6P1W5	CA094_HUMAN	hypothetical protein LOC84970 isoform a	361							protein binding				0		Myeloproliferative disorder(586;0.0393)												0.124031	21.004929	38.838646	16	113	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34677938	34677938	2147	1	C	A	A	A	416	32	C1orf94	2	2
FUBP1	8880	broad.mit.edu	37	1	78430042	78430042	+	Splice_Site_SNP	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:78430042C>A	uc010orm.1	-	c.901_splice	c.e12-1	p.V301_splice	FUBP1_uc001dih.3_Splice_Site_SNP|FUBP1_uc001dii.2_Splice_Site_SNP_p.V280_splice	NM_003902	NP_003893			far upstream element-binding protein						regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	protein binding|RNA binding|sequence-specific DNA binding transcription factor activity|single-stranded DNA binding			central_nervous_system(2)|lung(1)	3														0.068182	-2.722629	14.2538	6	82	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	78430042	78430042	6343	1	C	A	A	A	312	24	FUBP1	5	2
COL24A1	255631	broad.mit.edu	37	1	86512537	86512537	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:86512537G>T	uc001dlj.2	-	c.1921C>A	c.(1921-1923)CGT>AGT	p.R641S	COL24A1_uc010osd.1_5'UTR|COL24A1_uc001dlk.2_Non-coding_Transcript|COL24A1_uc010ose.1_Non-coding_Transcript|COL24A1_uc010osf.1_Non-coding_Transcript|COL24A1_uc009wcq.2_Missense_Mutation_p.R641S	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1 precursor	641					cell adhesion	collagen	extracellular matrix structural constituent			ovary(3)|central_nervous_system(1)	4				all cancers(265;0.0627)|Epithelial(280;0.0689)										0.170213	37.339797	47.011107	16	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	86512537	86512537	3821	1	G	T	T	T	507	39	COL24A1	1	1
LPPR5	163404	broad.mit.edu	37	1	99418685	99418685	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:99418685G>T	uc001dsb.2	-	c.562C>A	c.(562-564)CGA>AGA	p.R188R	LPPR5_uc001dsc.2_Silent_p.R188R	NM_001037317	NP_001032394	Q32ZL2	LPPR5_HUMAN	phosphatidic acid phosphatase type 2d isoform 1	188						integral to membrane	hydrolase activity				0														0.152381	59.268322	83.557284	32	178	KEEP	---	---	---	---	capture		Silent	SNP	99418685	99418685	9301	1	G	T	T	T	506	39	LPPR5	1	1
ANKRD5	63926	broad.mit.edu	37	20	10030593	10030593	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:10030593A>G	uc002wno.2	+	c.1376A>G	c.(1375-1377)TAC>TGC	p.Y459C	ANKRD5_uc002wnp.2_Missense_Mutation_p.Y459C|ANKRD5_uc010gbz.2_Missense_Mutation_p.Y270C	NM_022096	NP_071379	Q9NU02	ANKR5_HUMAN	ankyrin repeat domain protein 5	459							calcium ion binding			ovary(1)|breast(1)	2														0.131068	51.413333	78.645857	27	179	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10030593	10030593	684	20	A	G	G	G	182	14	ANKRD5	4	4
EDEM2	55741	broad.mit.edu	37	20	33714148	33714148	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33714148C>A	uc002xbo.2	-	c.875G>T	c.(874-876)CGC>CTC	p.R292L	EDEM2_uc010zuv.1_Missense_Mutation_p.R251L|EDEM2_uc010zus.1_Missense_Mutation_p.R71L|EDEM2_uc002xbq.2_Missense_Mutation_p.R255L|EDEM2_uc010zut.1_Missense_Mutation_p.R251L|EDEM2_uc002xbp.2_Missense_Mutation_p.R140L|EDEM2_uc002xbn.2_Missense_Mutation_p.R140L|EDEM2_uc002xbr.2_Non-coding_Transcript|EDEM2_uc010zuu.1_Missense_Mutation_p.R16L	NM_018217	NP_060687	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like	292					post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding				0			BRCA - Breast invasive adenocarcinoma(18;0.00936)			Esophageal Squamous(51;906 1021 24535 36410 39145)								0.074468	0.849125	18.322333	7	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33714148	33714148	5099	20	C	A	A	A	351	27	EDEM2	1	1
PHACTR3	116154	broad.mit.edu	37	20	58342383	58342384	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:58342383_58342384CC>AA	uc002yau.2	+	c.684_685CC>AA	c.(682-687)CTCCCC>CTAACC	p.P229T	PHACTR3_uc002yat.2_Missense_Mutation_p.P226T|PHACTR3_uc010zzw.1_Missense_Mutation_p.P188T|PHACTR3_uc002yav.2_Missense_Mutation_p.P188T|PHACTR3_uc002yaw.2_Missense_Mutation_p.P188T|PHACTR3_uc002yax.2_Intron	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	229	Pro-rich.					nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)											0.146667	37.786138	55.753727	22	128	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	58342383	58342384	12234	20	CC	AA	AA	AA	379	30	PHACTR3	2	2
TAF4	6874	broad.mit.edu	37	20	60575248	60575248	+	Nonsense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:60575248G>A	uc002ybs.2	-	c.2719C>T	c.(2719-2721)CAA>TAA	p.Q907*		NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4	907					interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|general RNA polymerase II transcription factor activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription coactivator activity|transcription initiation factor activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)											0.155844	43.991979	61.415957	24	130	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	60575248	60575248	16047	20	G	A	A	A	598	46	TAF4	5	2
PLCB1	23236	broad.mit.edu	37	20	8862361	8862361	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:8862361G>T	uc002wnb.2	+	c.3516G>T	c.(3514-3516)AAG>AAT	p.K1172N	PLCB1_uc002wna.2_3'UTR	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	1172					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of gene-specific transcription|negative regulation of monocyte extravasation|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of gene-specific transcription|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity|transcription repressor activity			ovary(4)|breast(3)|lung(1)	8														0.166987	173.988344	228.766899	87	434	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8862361	8862361	12453	20	G	T	T	T	425	33	PLCB1	2	2
C20orf103	24141	broad.mit.edu	37	20	9496207	9496207	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:9496207C>A	uc002wni.1	+	c.172C>A	c.(172-174)CTC>ATC	p.L58I	C20orf103_uc010zrc.1_Missense_Mutation_p.L58I	NM_012261	NP_036393	Q9UJQ1	CT103_HUMAN	chromosome 20 open reading frame 103 precursor	58	Extracellular (Potential).					integral to membrane				lung(1)|breast(1)	2			COAD - Colon adenocarcinoma(9;0.194)											0.098361	8.301644	28.001205	12	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9496207	9496207	2151	20	C	A	A	A	416	32	C20orf103	2	2
PAK7	57144	broad.mit.edu	37	20	9561009	9561009	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:9561009C>A	uc002wnl.2	-	c.773G>T	c.(772-774)GGA>GTA	p.G258V	PAK7_uc002wnk.2_Missense_Mutation_p.G258V|PAK7_uc002wnj.2_Missense_Mutation_p.G258V|PAK7_uc010gby.1_Missense_Mutation_p.G258V	NM_020341	NP_065074	Q9P286	PAK7_HUMAN	p21-activated kinase 7	258	Linker.				protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(7)|skin(3)|ovary(2)|central_nervous_system(2)|large_intestine(1)	15			COAD - Colon adenocarcinoma(9;0.194)							177				0.136213	59.453359	98.04976	41	260	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9561009	9561009	11821	20	C	A	A	A	390	30	PAK7	2	2
SEZ6L	23544	broad.mit.edu	37	22	26690378	26690378	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26690378G>T	uc003acb.2	+	c.956G>T	c.(955-957)GGG>GTG	p.G319V	SEZ6L_uc003acc.2_Missense_Mutation_p.G319V|SEZ6L_uc011akc.1_Missense_Mutation_p.G319V|SEZ6L_uc003acd.2_Missense_Mutation_p.G319V|SEZ6L_uc011akd.1_Missense_Mutation_p.G319V|SEZ6L_uc003ace.2_Missense_Mutation_p.G319V|SEZ6L_uc003acf.1_Missense_Mutation_p.G92V|SEZ6L_uc010gvc.1_Missense_Mutation_p.G92V	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	319	CUB 1.|Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.103896	57.796217	141.960385	56	483	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26690378	26690378	14632	22	G	T	T	T	559	43	SEZ6L	2	2
SEZ6L	23544	broad.mit.edu	37	22	26769422	26769422	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:26769422C>T	uc003acb.2	+	c.2800C>T	c.(2800-2802)CAA>TAA	p.Q934*	SEZ6L_uc003acc.2_Nonsense_Mutation_p.Q934*|SEZ6L_uc011akc.1_Intron|SEZ6L_uc003acd.2_Intron|SEZ6L_uc011akd.1_Intron|SEZ6L_uc003ace.2_Intron|SEZ6L_uc003acf.1_Nonsense_Mutation_p.Q707*|SEZ6L_uc010gvc.1_Intron|SEZ6L_uc011ake.1_Intron	NM_021115	NP_066938	Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	934	Extracellular (Potential).					endoplasmic reticulum membrane|integral to membrane				ovary(4)|central_nervous_system(1)|pancreas(1)	6														0.075	-0.518176	14.310819	6	74	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	26769422	26769422	14632	22	C	T	T	T	377	29	SEZ6L	5	2
EFCAB6	64800	broad.mit.edu	37	22	44028081	44028081	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:44028081C>T	uc003bdy.1	-	c.2136G>A	c.(2134-2136)CAG>CAA	p.Q712Q	EFCAB6_uc003bdz.1_Silent_p.Q560Q|EFCAB6_uc010gzi.1_Silent_p.Q560Q|EFCAB6_uc010gzj.1_Silent_p.Q10Q|EFCAB6_uc010gzk.1_Non-coding_Transcript	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	712					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|pancreas(1)	4		Ovarian(80;0.0247)|all_neural(38;0.025)												0.166667	48.332864	62.875471	23	115	KEEP	---	---	---	---	capture		Silent	SNP	44028081	44028081	5126	22	C	T	T	T	363	28	EFCAB6	2	2
ST6GAL2	84620	broad.mit.edu	37	2	107423373	107423373	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:107423373C>A	uc002tdq.2	-	c.1351G>T	c.(1351-1353)GTG>TTG	p.V451L	ST6GAL2_uc002tdr.2_Missense_Mutation_p.V451L	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	451	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.076923	0.093706	7.239882	3	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107423373	107423373	15740	2	C	A	A	A	234	18	ST6GAL2	2	2
SCN3A	6328	broad.mit.edu	37	2	165969467	165969467	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165969467G>T	uc002ucx.2	-	c.3771C>A	c.(3769-3771)CTC>CTA	p.L1257L	SCN3A_uc002ucy.2_Silent_p.L1208L|SCN3A_uc002ucz.2_Silent_p.L1208L|SCN3A_uc002uda.1_Silent_p.L1077L|SCN3A_uc002udb.1_Silent_p.L1077L	NM_006922	NP_008853	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha	1257	Helical; Name=S2 of repeat III; (Potential).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(4)|breast(3)|central_nervous_system(1)	8					Lamotrigine(DB00555)									0.111732	93.83767	200.529767	80	636	KEEP	---	---	---	---	capture		Silent	SNP	165969467	165969467	14400	2	G	T	T	T	574	45	SCN3A	2	2
C2orf39	92749	broad.mit.edu	37	2	26667141	26667141	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26667141G>T	uc002rhg.2	+	c.1080G>T	c.(1078-1080)AAG>AAT	p.K360N	C2orf39_uc010eym.1_Non-coding_Transcript	NM_145038	NP_659475	Q96MC2	CC164_HUMAN	hypothetical protein LOC92749	360	Potential.										0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.170213	34.640109	44.311813	16	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26667141	26667141	2252	2	G	T	T	T	438	34	C2orf39	2	2
LTBP1	4052	broad.mit.edu	37	2	33488394	33488394	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:33488394T>A	uc002ros.2	+	c.2555T>A	c.(2554-2556)GTT>GAT	p.V852D	LTBP1_uc002rot.2_Missense_Mutation_p.V526D|LTBP1_uc002rou.2_Missense_Mutation_p.V525D|LTBP1_uc002rov.2_Missense_Mutation_p.V472D|LTBP1_uc010ymz.1_Missense_Mutation_p.V525D|LTBP1_uc010yna.1_Missense_Mutation_p.V472D	NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding	851					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)												0.120482	28.97728	52.426367	20	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33488394	33488394	9449	2	T	A	A	A	780	60	LTBP1	3	3
STON1-GTF2A1L	286749	broad.mit.edu	37	2	48818791	48818791	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:48818791G>T	uc002rwp.1	+	c.1931_splice	c.e3-1	p.S644_splice	STON1_uc002rwo.3_Splice_Site_SNP_p.S644_splice|STON1_uc010fbm.2_Splice_Site_SNP_p.S644_splice|STON1-GTF2A1L_uc010yol.1_Splice_Site_SNP_p.S644_splice|STON1_uc002rwr.2_Intron|STON1_uc002rwq.2_Splice_Site_SNP_p.S644_splice	NM_172311	NP_758515			STON1-GTF2A1L protein						endocytosis|intracellular protein transport|transcription initiation from RNA polymerase II promoter	clathrin adaptor complex|transcription factor TFIIA complex	RNA polymerase II transcription factor activity			ovary(3)|pancreas(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)											0.181818	48.175096	59.68443	22	99	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	48818791	48818791	15837	2	G	T	T	T	455	35	STON1-GTF2A1L	5	2
SNRNP200	23020	broad.mit.edu	37	2	96954407	96954407	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:96954407G>A	uc002svu.2	-	c.3252C>T	c.(3250-3252)GTC>GTT	p.V1084V	SNRNP200_uc002svw.1_Silent_p.V156V	NM_014014	NP_054733	O75643	U520_HUMAN	activating signal cointegrator 1 complex subunit	1084	SEC63 1.				cis assembly of pre-catalytic spliceosome|response to stimulus|visual perception	catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			ovary(5)|large_intestine(1)|skin(1)	7														0.164706	28.796819	37.867406	14	71	KEEP	---	---	---	---	capture		Silent	SNP	96954407	96954407	15352	2	G	A	A	A	574	45	SNRNP200	2	2
BOC	91653	broad.mit.edu	37	3	112993283	112993283	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:112993283C>A	uc003dzz.2	+	c.1296C>A	c.(1294-1296)CCC>CCA	p.P432P	BOC_uc003dzx.2_Silent_p.P432P|BOC_uc003dzy.2_Silent_p.P432P|BOC_uc003eab.2_Silent_p.P133P	NM_033254	NP_150279	Q9BWV1	BOC_HUMAN	brother of CDO precursor	432	Extracellular (Potential).				cell adhesion|muscle cell differentiation|positive regulation of myoblast differentiation	integral to membrane|plasma membrane	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|pancreas(1)	6			Epithelial(53;0.227)											0.111111	12.848661	27.65491	11	88	KEEP	---	---	---	---	capture		Silent	SNP	112993283	112993283	1506	3	C	A	A	A	301	24	BOC	2	2
CASR	846	broad.mit.edu	37	3	122002991	122002991	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:122002991C>A	uc003eew.3	+	c.2220C>A	c.(2218-2220)CTC>CTA	p.L740L	CASR_uc003eev.3_Silent_p.L730L	NM_000388	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor precursor	730	Helical; Name=4; (Potential).				anatomical structure morphogenesis|calcium ion import|cellular calcium ion homeostasis|chemosensory behavior|detection of calcium ion|ossification	integral to plasma membrane	G-protein coupled receptor activity|phosphatidylinositol phospholipase C activity			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)									0.104348	9.308077	27.225597	12	103	KEEP	---	---	---	---	capture		Silent	SNP	122002991	122002991	2801	3	C	A	A	A	405	32	CASR	2	2
COL6A6	131873	broad.mit.edu	37	3	130285781	130285781	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130285781C>A	uc010htl.2	+	c.1518C>A	c.(1516-1518)ATC>ATA	p.I506I		NM_001102608	NP_001096078	A6NMZ7	CO6A6_HUMAN	collagen type VI alpha 6 precursor	506	VWFA 3.|Nonhelical region.				axon guidance|cell adhesion	collagen				ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.16129	61.535577	81.832585	30	156	KEEP	---	---	---	---	capture		Silent	SNP	130285781	130285781	3841	3	C	A	A	A	369	29	COL6A6	2	2
NEK11	79858	broad.mit.edu	37	3	130881250	130881250	+	Splice_Site_SNP	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:130881250A>T	uc003eny.2	+	c.963_splice	c.e11-2	p.M321_splice	NEK11_uc003enx.2_Splice_Site_SNP_p.M321_splice|NEK11_uc003eoa.2_Splice_Site_SNP_p.M321_splice|NEK11_uc003enz.2_Splice_Site_SNP_p.M139_splice|NEK11_uc010htn.2_Splice_Site_SNP|NEK11_uc011blk.1_Splice_Site_SNP_p.M173_splice|NEK11_uc011bll.1_Splice_Site_SNP_p.W216_splice|NEK11_uc011blm.1_Splice_Site_SNP_p.M321_splice	NM_024800	NP_079076			NIMA-related kinase 11 isoform 1						cell cycle|intra-S DNA damage checkpoint|intracellular protein kinase cascade|protein phosphorylation	nucleolus	ATP binding|identical protein binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(4)|central_nervous_system(1)	5										271				0.164751	93.758671	121.602791	43	218	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	130881250	130881250	10722	3	A	T	T	T	195	15	NEK11	5	3
NUP210	23225	broad.mit.edu	37	3	13427851	13427851	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:13427851C>A	uc003bxv.1	-	c.741G>T	c.(739-741)CCG>CCT	p.P247P		NM_024923	NP_079199	Q8TEM1	PO210_HUMAN	nucleoporin 210 precursor	247	Lumenal (Probable).				carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	endoplasmic reticulum membrane|nuclear membrane|nuclear pore				ovary(3)|large_intestine(3)|skin(2)|pancreas(1)|liver(1)	10	all_neural(104;0.187)									587				0.125	16.301444	27.284613	10	70	KEEP	---	---	---	---	capture		Silent	SNP	13427851	13427851	11165	3	C	A	A	A	288	23	NUP210	1	1
GK5	256356	broad.mit.edu	37	3	141900397	141900397	+	Silent	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:141900397T>C	uc003euq.1	-	c.954A>G	c.(952-954)CCA>CCG	p.P318P	GK5_uc003eup.1_Silent_p.P39P|GK5_uc010hus.1_Non-coding_Transcript	NM_001039547	NP_001034636	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	318					glycerol metabolic process		ATP binding|glycerol kinase activity				0														0.120301	23.708657	42.511104	16	117	KEEP	---	---	---	---	capture		Silent	SNP	141900397	141900397	6690	3	T	C	C	C	652	51	GK5	4	4
SLC9A9	285195	broad.mit.edu	37	3	142985602	142985602	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:142985602C>A	uc003evn.2	-	c.1880G>T	c.(1879-1881)GGC>GTC	p.G627V		NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen	627					regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)	2														0.183908	73.090302	89.405755	32	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142985602	142985602	15218	3	C	A	A	A	338	26	SLC9A9	2	2
OTOL1	131149	broad.mit.edu	37	3	161221085	161221085	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:161221085G>T	uc011bpb.1	+	c.789G>T	c.(787-789)GGG>GGT	p.G263G		NM_001080440	NP_001073909	A6NHN0	OTOL1_HUMAN	otolin-1 precursor	263	Collagen-like 2.					collagen					0														0.235294	8.789927	9.880788	4	13	KEEP	---	---	---	---	capture		Silent	SNP	161221085	161221085	11716	3	G	T	T	T	548	43	OTOL1	2	2
SERPINI2	5276	broad.mit.edu	37	3	167164213	167164213	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:167164213G>T	uc003fes.1	-	c.1138C>A	c.(1138-1140)CCA>ACA	p.P380T	SERPINI2_uc003fer.1_Missense_Mutation_p.P370T|SERPINI2_uc003fet.1_Missense_Mutation_p.P370T	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	370					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			urinary_tract(1)	1														0.063492	-7.307513	17.684019	8	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	167164213	167164213	14607	3	G	T	T	T	533	41	SERPINI2	2	2
MECOM	2122	broad.mit.edu	37	3	168812877	168812877	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:168812877A>T	uc011bpj.1	-	c.3006T>A	c.(3004-3006)AAT>AAA	p.N1002K	MECOM_uc010hwk.1_Missense_Mutation_p.N828K|MECOM_uc003ffj.3_Missense_Mutation_p.N879K|MECOM_uc003ffi.3_Missense_Mutation_p.N814K|MECOM_uc011bpi.1_Missense_Mutation_p.N806K|MECOM_uc003ffn.3_Missense_Mutation_p.N814K|MECOM_uc003ffk.2_Missense_Mutation_p.N805K|MECOM_uc003ffl.2_Missense_Mutation_p.N965K|MECOM_uc011bpk.1_Missense_Mutation_p.N804K	NM_004991	NP_004982	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus isoform c	Error:Variant_position_missing_in_Q13465_after_alignment							sequence-specific DNA binding transcription factor activity			lung(3)|skin(2)|ovary(1)|pancreas(1)|central_nervous_system(1)	8										646				0.094118	7.532724	21.603073	8	77	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168812877	168812877	9811	3	A	T	T	T	102	8	MECOM	3	3
ARPP21	10777	broad.mit.edu	37	3	35835224	35835224	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:35835224C>A	uc011axy.1	+	c.2216C>A	c.(2215-2217)CCC>CAC	p.P739H	ARPP21_uc003cga.2_Missense_Mutation_p.P719H|ARPP21_uc003cgb.2_Missense_Mutation_p.P738H|ARPP21_uc003cgf.2_Missense_Mutation_p.P574H|ARPP21_uc003cgg.2_Missense_Mutation_p.P261H	NM_016300	NP_057384	Q9UBL0	ARP21_HUMAN	cyclic AMP-regulated phosphoprotein, 21 kD	738	Gln-rich.					cytoplasm	nucleic acid binding			ovary(2)	2														0.125926	25.872708	44.321286	17	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35835224	35835224	996	3	C	A	A	A	286	22	ARPP21	2	2
HHATL	57467	broad.mit.edu	37	3	42739015	42739015	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42739015G>T	uc003clw.2	-	c.850C>A	c.(850-852)CCA>ACA	p.P284T	HHATL_uc003clx.2_Missense_Mutation_p.P284T	NM_020707	NP_065758	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	284					negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)										0.128205	22.337557	38.101801	15	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42739015	42739015	7374	3	G	T	T	T	559	43	HHATL	2	2
KIF9	64147	broad.mit.edu	37	3	47288896	47288896	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47288896C>T	uc010hjp.2	-	c.1200G>A	c.(1198-1200)CGG>CGA	p.R400R	KIF9_uc003cqx.2_Silent_p.R400R|KIF9_uc003cqy.2_Silent_p.R400R|KIF9_uc011bat.1_Non-coding_Transcript|KIF9_uc011bau.1_Non-coding_Transcript	NM_001134878	NP_001128350	Q9HAQ2	KIF9_HUMAN	kinesin family member 9 isoform 2	400					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)								0.110294	16.115668	36.570104	15	121	KEEP	---	---	---	---	capture		Silent	SNP	47288896	47288896	8621	3	C	T	T	T	379	30	KIF9	2	2
FLNB	2317	broad.mit.edu	37	3	58110122	58110122	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:58110122G>T	uc010hne.2	+	c.3788G>T	c.(3787-3789)GGT>GTT	p.G1263V	FLNB_uc003djj.2_Missense_Mutation_p.G1263V|FLNB_uc003djk.2_Missense_Mutation_p.G1263V|FLNB_uc010hnf.2_Missense_Mutation_p.G1263V|FLNB_uc003djl.2_Missense_Mutation_p.G1094V|FLNB_uc003djm.2_Missense_Mutation_p.G1094V	NM_001164317	NP_001157789	O75369	FLNB_HUMAN	filamin B isoform 1	1263	Filamin 11.|Interaction with FBLP1.				actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction	cell cortex|integral to membrane|nucleus|sarcomere	actin binding			breast(6)|ovary(3)	9				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)						676				0.095808	8.965087	36.356794	16	151	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58110122	58110122	6176	3	G	T	T	T	572	44	FLNB	2	2
CPOX	1371	broad.mit.edu	37	3	98311879	98311879	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:98311879A>T	uc003dsx.2	-	c.470T>A	c.(469-471)CTG>CAG	p.L157Q	CPOX_uc011bgz.1_Missense_Mutation_p.L157Q	NM_000097	NP_000088	P36551	HEM6_HUMAN	coproporphyrinogen oxidase precursor	157					oxidation-reduction process	mitochondrial intermembrane space	coproporphyrinogen oxidase activity|protein homodimerization activity				0						Esophageal Squamous(75;7 1223 22300 43648 48951)								0.571429	13.500421	13.531454	4	3	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98311879	98311879	3959	3	A	T	T	T	91	7	CPOX	3	3
NPNT	255743	broad.mit.edu	37	4	106863785	106863785	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:106863785G>C	uc011cfd.1	+	c.1175G>C	c.(1174-1176)AGT>ACT	p.S392T	NPNT_uc003hya.2_Missense_Mutation_p.S362T|NPNT_uc011cfc.1_Missense_Mutation_p.S379T|NPNT_uc011cfe.1_Missense_Mutation_p.S392T|NPNT_uc010ilt.1_Missense_Mutation_p.S362T|NPNT_uc011cff.1_Missense_Mutation_p.S362T|NPNT_uc010ilu.1_Missense_Mutation_p.S258T	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor	362	Pro-rich.				cell differentiation	membrane	calcium ion binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)										0.130872	78.511989	117.995819	39	259	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106863785	106863785	10995	4	G	C	C	C	468	36	NPNT	3	3
FAT4	79633	broad.mit.edu	37	4	126240206	126240206	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:126240206C>A	uc003ifj.3	+	c.2640C>A	c.(2638-2640)AAC>AAA	p.N880K		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	880	Extracellular (Potential).|Cadherin 8.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(8)|pancreas(2)	10														0.170732	30.930376	39.312382	14	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	126240206	126240206	5928	4	C	A	A	A	220	17	FAT4	2	2
RNF150	57484	broad.mit.edu	37	4	141888839	141888839	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:141888839C>A	uc003iio.1	-	c.673G>T	c.(673-675)GCA>TCA	p.A225S	RNF150_uc010iok.1_Intron|RNF150_uc003iip.1_Missense_Mutation_p.A225S	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor	225	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)													0.139665	81.924644	126.809691	50	308	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141888839	141888839	13928	4	C	A	A	A	351	27	RNF150	1	1
TTC29	83894	broad.mit.edu	37	4	147796051	147796051	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:147796051C>T	uc003ikx.3	-	c.694G>A	c.(694-696)GAA>AAA	p.E232K	TTC29_uc003ikw.3_Missense_Mutation_p.E206K|TTC29_uc010ipc.2_Non-coding_Transcript|TTC29_uc010ipd.1_Missense_Mutation_p.E206K	NM_031956	NP_114162	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	206	TPR 1.						binding				0	all_hematologic(180;0.151)													0.085366	2.056053	16.356741	7	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	147796051	147796051	17251	4	C	T	T	T	377	29	TTC29	2	2
IRF2	3660	broad.mit.edu	37	4	185310048	185310048	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:185310048C>A	uc003iwf.3	-	c.914G>T	c.(913-915)TGG>TTG	p.W305L		NM_002199	NP_002190	P14316	IRF2_HUMAN	interferon regulatory factor 2	305					blood coagulation|cell proliferation|interferon-gamma-mediated signaling pathway|negative regulation of transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	focal adhesion|nucleoplasm	DNA binding|protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity			ovary(1)	1		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)										0.171271	69.009393	87.501166	31	150	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	185310048	185310048	8131	4	C	A	A	A	273	21	IRF2	2	2
BEND4	389206	broad.mit.edu	37	4	42127651	42127651	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:42127651C>T	uc003gwn.2	-	c.1095G>A	c.(1093-1095)CTG>CTA	p.L365L	BEND4_uc003gwm.2_Silent_p.L365L|BEND4_uc011byy.1_Silent_p.L365L	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a	365											0														0.08871	7.454337	49.850466	22	226	KEEP	---	---	---	---	capture		Silent	SNP	42127651	42127651	1423	4	C	T	T	T	314	25	BEND4	2	2
CSN2	1447	broad.mit.edu	37	4	70823356	70823356	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:70823356G>C	uc003hes.3	-	c.311C>G	c.(310-312)GCT>GGT	p.A104G	CSN2_uc003het.3_Missense_Mutation_p.A103G	NM_001891	NP_001882	P05814	CASB_HUMAN	casein beta precursor	104					calcium ion transport	extracellular region	calcium ion binding|enzyme inhibitor activity|transporter activity				0														0.091743	28.183478	83.086478	30	297	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70823356	70823356	4089	4	G	C	C	C	442	34	CSN2	3	3
FBXL21	26223	broad.mit.edu	37	5	135273223	135273223	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:135273223T>C	uc010jec.1	+	c.476T>C	c.(475-477)ATG>ACG	p.M159T	FBXL21_uc003lbc.2_Non-coding_Transcript	NM_012159	NP_036291	Q9UKT6	FXL21_HUMAN	F-box and leucine-rich repeat protein 21	159	LRR 1.				rhythmic process	ubiquitin ligase complex	ubiquitin-protein ligase activity			lung(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.108434	24.619635	49.857498	18	148	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135273223	135273223	5955	5	T	C	C	C	663	51	FBXL21	4	4
TRPC7	57113	broad.mit.edu	37	5	135692319	135692319	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:135692319C>A	uc003lbn.1	-	c.754G>T	c.(754-756)GCC>TCC	p.A252S	TRPC7_uc010jef.1_Missense_Mutation_p.A244S|TRPC7_uc010jeg.1_Non-coding_Transcript|TRPC7_uc010jeh.1_Missense_Mutation_p.A244S|TRPC7_uc010jei.1_Missense_Mutation_p.A244S|TRPC7_uc010jej.1_5'UTR	NM_020389	NP_065122	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel,	253	Cytoplasmic (Potential).				axon guidance|platelet activation	integral to membrane|plasma membrane	calcium channel activity|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)											0.074074	-0.346271	9.717823	4	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135692319	135692319	17135	5	C	A	A	A	364	28	TRPC7	2	2
PCDHB6	56130	broad.mit.edu	37	5	140531692	140531692	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140531692C>A	uc003lir.2	+	c.1854C>A	c.(1852-1854)CAC>CAA	p.H618Q	PCDHB6_uc011dah.1_Missense_Mutation_p.H482Q	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	618	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.081081	-1.461134	18.593199	9	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140531692	140531692	11966	5	C	A	A	A	220	17	PCDHB6	2	2
PCDHGA2	56113	broad.mit.edu	37	5	140719632	140719632	+	Missense_Mutation	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140719632T>C	uc003ljk.1	+	c.1094T>C	c.(1093-1095)ATA>ACA	p.I365T	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc011dao.1_Missense_Mutation_p.I365T	NM_018915	NP_061738	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2 isoform 1	365	Cadherin 4.|Extracellular (Potential).				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)											0.115	36.582119	65.787195	23	177	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140719632	140719632	11974	5	T	C	C	C	637	49	PCDHGA2	4	4
CSF1R	1436	broad.mit.edu	37	5	149449602	149449602	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:149449602C>A	uc003lrl.2	-	c.1344G>T	c.(1342-1344)CAG>CAT	p.Q448H	CSF1R_uc011dcd.1_Missense_Mutation_p.Q300H|CSF1R_uc010jhc.2_Non-coding_Transcript|CSF1R_uc003lrm.2_Missense_Mutation_p.Q448H	NM_005211	NP_005202	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor precursor	448	Ig-like C2-type 5.|Extracellular (Potential).				cell proliferation|multicellular organismal development|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane|receptor complex	ATP binding|cytokine binding|macrophage colony-stimulating factor receptor activity|protein homodimerization activity			haematopoietic_and_lymphoid_tissue(38)|lung(6)|central_nervous_system(3)|liver(3)|breast(2)|endometrium(1)|ovary(1)	54			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)					592				0.175758	60.866589	77.227482	29	136	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	149449602	149449602	4073	5	C	A	A	A	311	24	CSF1R	2	2
SLC36A3	285641	broad.mit.edu	37	5	150656993	150656993	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:150656993G>T	uc003ltx.2	-	c.1497C>A	c.(1495-1497)ATC>ATA	p.I499I	GM2A_uc011dcs.1_Intron|SLC36A3_uc003ltv.2_Silent_p.I443I|SLC36A3_uc003ltw.2_Silent_p.I458I	NM_001145017	NP_001138489	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3 isoform 1	458	Extracellular (Potential).					integral to membrane				ovary(2)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.09854	44.407276	132.786675	54	494	KEEP	---	---	---	---	capture		Silent	SNP	150656993	150656993	15092	5	G	T	T	T	577	45	SLC36A3	2	2
PRLR	5618	broad.mit.edu	37	5	35072726	35072726	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:35072726G>T	uc003jjm.2	-	c.494C>A	c.(493-495)ACG>AAG	p.T165K	PRLR_uc003jjg.1_Missense_Mutation_p.T165K|PRLR_uc003jjh.1_Missense_Mutation_p.T165K|PRLR_uc003jji.1_Missense_Mutation_p.T94K|PRLR_uc003jjj.1_Missense_Mutation_p.T165K|PRLR_uc003jjk.1_Missense_Mutation_p.T94K|PRLR_uc003jjl.3_Missense_Mutation_p.T64K|PRLR_uc010iuw.1_Missense_Mutation_p.T94K	NM_000949	NP_000940	P16471	PRLR_HUMAN	prolactin receptor precursor	165	Fibronectin type-III 2.|Extracellular (Potential).				activation of JAK2 kinase activity|activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|embryo implantation|lactation|steroid biosynthetic process|T cell activation	cell surface|extracellular region|integral to membrane	metal ion binding|ornithine decarboxylase activator activity|peptide hormone binding|prolactin receptor activity|protein homodimerization activity			ovary(2)	2	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Dromostanolone(DB00858)|Fluoxymesterone(DB01185)|Pegvisomant(DB00082)|Somatropin recombinant(DB00052)									0.145455	66.255663	92.848026	32	188	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35072726	35072726	12974	5	G	T	T	T	520	40	PRLR	1	1
ANKRD55	79722	broad.mit.edu	37	5	55412488	55412488	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:55412488A>T	uc003jqu.2	-	c.919T>A	c.(919-921)TAC>AAC	p.Y307N	ANKRD55_uc003jqt.2_Missense_Mutation_p.Y19N	NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	306	ANK 9.										0		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)												0.108434	29.645779	67.480352	27	222	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55412488	55412488	689	5	A	T	T	T	182	14	ANKRD55	3	3
ANKRD55	79722	broad.mit.edu	37	5	55439661	55439661	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:55439661T>A	uc003jqu.2	-	c.579A>T	c.(577-579)AAA>AAT	p.K193N		NM_024669	NP_078945	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55 isoform 1	192											0		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)												0.172093	159.368935	203.067382	74	356	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55439661	55439661	689	5	T	A	A	A	725	56	ANKRD55	3	3
IQGAP2	10788	broad.mit.edu	37	5	75989204	75989204	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:75989204G>T	uc003kek.2	+	c.3930G>T	c.(3928-3930)GTG>GTT	p.V1310V	IQGAP2_uc011csv.1_Silent_p.V806V|IQGAP2_uc003kel.2_Silent_p.V806V|IQGAP2_uc010izw.1_Silent_p.V11V	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1310					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			ovary(6)|central_nervous_system(1)	7		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)										0.068966	-1.150084	9.988799	4	54	KEEP	---	---	---	---	capture		Silent	SNP	75989204	75989204	8118	5	G	T	T	T	574	45	IQGAP2	2	2
RASA1	5921	broad.mit.edu	37	5	86672763	86672763	+	Silent	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:86672763A>T	uc003kiw.2	+	c.2250A>T	c.(2248-2250)ACA>ACT	p.T750T	RASA1_uc010jav.2_Non-coding_Transcript|RASA1_uc003kix.2_Silent_p.T573T|RASA1_uc011ctv.1_Silent_p.T583T|RASA1_uc011ctw.1_Silent_p.T584T|RASA1_uc010jaw.2_Silent_p.T572T	NM_002890	NP_002881	P20936	RASA1_HUMAN	RAS p21 protein activator 1 isoform 1	750	Ras-GAP.				cytokinesis|embryo development|intracellular signal transduction|negative regulation of cell-matrix adhesion|negative regulation of neuron apoptosis|negative regulation of Ras protein signal transduction|positive regulation of anti-apoptosis|regulation of actin filament polymerization|regulation of cell shape|regulation of RNA metabolic process|vasculogenesis	cytosol|intrinsic to internal side of plasma membrane	glycoprotein binding|GTPase binding|potassium channel inhibitor activity|Ras GTPase activator activity|receptor binding			upper_aerodigestive_tract(1)|ovary(1)	2		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)						386				0.076677	2.446793	59.885204	24	289	KEEP	---	---	---	---	capture		Silent	SNP	86672763	86672763	13520	5	A	T	T	T	67	6	RASA1	3	3
TRAF3IP2	10758	broad.mit.edu	37	6	111913163	111913163	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:111913163C>A	uc011ebc.1	-	c.127G>T	c.(127-129)GCA>TCA	p.A43S	TRAF3IP2_uc003pvg.2_Missense_Mutation_p.A43S|TRAF3IP2_uc003pvf.2_Missense_Mutation_p.A43S|TRAF3IP2_uc010kdw.2_Missense_Mutation_p.A43S|TRAF3IP2_uc010kdx.2_Missense_Mutation_p.A43S	NM_147686	NP_679211	O43734	CIKS_HUMAN	TRAF3 interacting protein 2 isoform 2	52					intracellular signal transduction|positive regulation of I-kappaB kinase/NF-kappaB cascade					ovary(2)|central_nervous_system(1)	3		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)										0.12605	19.035941	35.308398	15	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111913163	111913163	16985	6	C	A	A	A	338	26	TRAF3IP2	2	2
IFNGR1	3459	broad.mit.edu	37	6	137519214	137519214	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:137519214G>A	uc003qho.2	-	c.1424C>T	c.(1423-1425)TCC>TTC	p.S475F	IFNGR1_uc011edm.1_Missense_Mutation_p.S447F	NM_000416	NP_000407	P15260	INGR1_HUMAN	interferon gamma receptor 1 precursor	475	Cytoplasmic (Potential).				regulation of interferon-gamma-mediated signaling pathway|response to virus	integral to plasma membrane	interferon-gamma receptor activity				0	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)									0.073864	-1.675421	31.167249	13	163	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137519214	137519214	7850	6	G	A	A	A	533	41	IFNGR1	2	2
SYNE1	23345	broad.mit.edu	37	6	152949423	152949423	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:152949423G>T	uc010kiw.2	-	c.44C>A	c.(43-45)GCC>GAC	p.A15D	SYNE1_uc003qot.3_Missense_Mutation_p.A15D|SYNE1_uc003qou.3_Missense_Mutation_p.A15D|SYNE1_uc010kjb.1_Missense_Mutation_p.A15D|SYNE1_uc003qpa.1_Missense_Mutation_p.A15D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	15	Actin-binding.|Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding			central_nervous_system(15)|ovary(8)|large_intestine(5)|pancreas(2)	30		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)										0.119318	27.646587	52.685034	21	155	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	152949423	152949423	15966	6	G	T	T	T	546	42	SYNE1	2	2
SNX9	51429	broad.mit.edu	37	6	158317937	158317937	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:158317937G>C	uc003qqv.1	+	c.379G>C	c.(379-381)GCC>CCC	p.A127P		NM_016224	NP_057308	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	127					cell communication|intracellular protein transport|lipid tube assembly|positive regulation of GTPase activity|positive regulation of protein oligomerization|receptor-mediated endocytosis	clathrin-coated vesicle|cytoplasmic vesicle membrane|extrinsic to internal side of plasma membrane|ruffle|trans-Golgi network	1-phosphatidylinositol binding|protein homodimerization activity|ubiquitin protein ligase binding				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)										0.140625	34.964371	51.140565	18	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158317937	158317937	15409	6	G	C	C	C	546	42	SNX9	3	3
SOD2	6648	broad.mit.edu	37	6	160103667	160103667	+	Missense_Mutation	SNP	A	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:160103667A>C	uc003qsg.2	-	c.527T>G	c.(526-528)CTT>CGT	p.L176R	SOD2_uc003qsf.3_5'Flank|SOD2_uc003qsh.2_Missense_Mutation_p.L137R|SOD2_uc003qsi.1_Missense_Mutation_p.L176R|SOD2_uc011efu.1_Missense_Mutation_p.L116R|SOD2_uc011efv.1_Missense_Mutation_p.L137R	NM_001024465	NP_001019636	P04179	SODM_HUMAN	manganese superoxide dismutase isoform A	176					age-dependent response to reactive oxygen species|negative regulation of neuron apoptosis|oxygen homeostasis|protein homotetramerization|regulation of transcription from RNA polymerase II promoter|release of cytochrome c from mitochondria|removal of superoxide radicals|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure		manganese ion binding|superoxide dismutase activity				0		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)										0.080645	0.923026	12.040725	5	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160103667	160103667	15421	6	A	C	C	C	39	3	SOD2	4	4
LPA	4018	broad.mit.edu	37	6	161022092	161022092	+	Missense_Mutation	SNP	A	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:161022092A>G	uc003qtl.2	-	c.2984T>C	c.(2983-2985)GTG>GCG	p.V995A		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	3503	Kringle 31.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)									0.079498	0.33186	43.474023	19	220	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	161022092	161022092	9276	6	A	G	G	G	78	6	LPA	4	4
ALDH5A1	7915	broad.mit.edu	37	6	24503644	24503644	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:24503644G>C	uc003nef.2	+	c.592G>C	c.(592-594)GCT>CCT	p.A198P	ALDH5A1_uc003neg.2_Missense_Mutation_p.A198P	NM_170740	NP_733936	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5A1 isoform 1 precursor	198					acetate metabolic process|central nervous system development|galactosylceramide metabolic process|gamma-aminobutyric acid catabolic process|glucose metabolic process|glutamate metabolic process|glutamine metabolic process|glutathione metabolic process|glycerophospholipid metabolic process|neurotransmitter catabolic process|neurotransmitter secretion|protein homotetramerization|respiratory electron transport chain|short-chain fatty acid metabolic process|succinate metabolic process	mitochondrial matrix|soluble fraction	protein homodimerization activity|succinate-semialdehyde dehydrogenase activity				0					Chlormerodrin(DB00534)|NADH(DB00157)|Succinic acid(DB00139)									0.107843	14.506626	30.011561	11	91	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24503644	24503644	505	6	G	C	C	C	546	42	ALDH5A1	3	3
ZNF165	7718	broad.mit.edu	37	6	28056964	28056964	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28056964C>T	uc003nkg.2	+	c.1174C>T	c.(1174-1176)CGA>TGA	p.R392*	ZNF165_uc003nkh.2_Nonsense_Mutation_p.R392*|ZNF165_uc003nki.3_Nonsense_Mutation_p.R392*|ZSCAN12P1_uc003nkj.3_5'Flank	NM_003447	NP_003438	P49910	ZN165_HUMAN	zinc finger protein 165	392	C2H2-type 3.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0														0.032895	-25.862957	10.343196	5	147	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	28056964	28056964	18331	6	C	T	T	T	347	27	ZNF165	5	1
OR12D2	26529	broad.mit.edu	37	6	29364990	29364990	+	Missense_Mutation	SNP	A	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29364990A>C	uc003nmf.3	+	c.514A>C	c.(514-516)ATC>CTC	p.I172L		NM_013936	NP_039224	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.061329	-26.883403	91.050525	36	551	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29364990	29364990	11337	6	A	C	C	C	208	16	OR12D2	4	4
RIPK1	8737	broad.mit.edu	37	6	3105762	3105762	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:3105762G>T	uc010jni.2	+	c.1053G>T	c.(1051-1053)ATG>ATT	p.M351I	RIPK1_uc003muv.3_Missense_Mutation_p.M188I|RIPK1_uc003muw.3_Missense_Mutation_p.M286I|RIPK1_uc011dhs.1_Missense_Mutation_p.M305I|RIPK1_uc003mux.2_Missense_Mutation_p.M351I	NM_003804	NP_003795	Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine	351	Interaction with SQSTM1.				activation of caspase activity|activation of JUN kinase activity|activation of pro-apoptotic gene products|induction of apoptosis by extracellular signals|induction of necroptosis by extracellular signals|innate immune response|MyD88-independent toll-like receptor signaling pathway|positive regulation of anti-apoptosis|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 production|positive regulation of NF-kappaB transcription factor activity|positive regulation of tumor necrosis factor production|protein autophosphorylation|regulation of ATP:ADP antiporter activity|regulation of oxygen and reactive oxygen species metabolic process|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|tumor necrosis factor-mediated signaling pathway	cytosol|death-inducing signaling complex|endosome membrane|mitochondrion|receptor complex	ATP binding|death domain binding|death receptor binding|protein serine/threonine kinase activity			large_intestine(3)|lung(1)|skin(1)	5	Ovarian(93;0.0386)	all_hematologic(90;0.0895)								138				0.10984	58.656829	124.516785	48	389	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	3105762	3105762	13857	6	G	T	T	T	611	47	RIPK1	2	2
TNXB	7148	broad.mit.edu	37	6	32052275	32052275	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32052275C>A	uc003nzl.2	-	c.3360G>T	c.(3358-3360)CTG>CTT	p.L1120L		NM_019105	NP_061978	P22105	TENX_HUMAN	tenascin XB isoform 1 precursor	1207	Fibronectin type-III 4.				actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction	extracellular space|intracellular|proteinaceous extracellular matrix	heparin binding|integrin binding				0														0.131148	12.654919	20.725311	8	53	KEEP	---	---	---	---	capture		Silent	SNP	32052275	32052275	16887	6	C	A	A	A	262	21	TNXB	2	2
NOTCH4	4855	broad.mit.edu	37	6	32187987	32187987	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:32187987G>A	uc003obb.2	-	c.1234C>T	c.(1234-1236)CTC>TTC	p.L412F	NOTCH4_uc011dpu.1_Non-coding_Transcript|NOTCH4_uc011dpv.1_Non-coding_Transcript|NOTCH4_uc003obc.2_Missense_Mutation_p.L412F	NM_004557	NP_004548	Q99466	NOTC4_HUMAN	notch4 preproprotein	412	EGF-like 10.|Extracellular (Potential).				cell fate determination|embryo development|hemopoiesis|mammary gland development|negative regulation of endothelial cell differentiation|Notch receptor processing|Notch signaling pathway|patterning of blood vessels|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|protein heterodimerization activity|receptor activity			ovary(5)|lung(5)|central_nervous_system(2)|upper_aerodigestive_tract(1)|breast(1)	14										693				0.08589	5.61592	33.951739	14	149	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	32187987	32187987	10954	6	G	A	A	A	455	35	NOTCH4	2	2
HLA-DPB1	3115	broad.mit.edu	37	6	33053644	33053644	+	Silent	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:33053644C>T	uc003ocu.1	+	c.735C>T	c.(733-735)TTC>TTT	p.F245F	HLA-DPB1_uc011dqo.1_Non-coding_Transcript|HLA-DPB1_uc011dqp.1_Silent_p.F244F|HLA-DPB1_uc011dqq.1_Silent_p.F141F	NM_002121	NP_002112	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP	245	Helical; (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to membrane|lysosomal membrane|MHC class II protein complex				ovary(1)	1														0.04142	-23.916198	14.29398	7	162	KEEP	---	---	---	---	capture		Silent	SNP	33053644	33053644	7494	6	C	T	T	T	376	29	HLA-DPB1	2	2
CUL9	23113	broad.mit.edu	37	6	43152465	43152465	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43152465G>A	uc003ouk.2	+	c.417G>A	c.(415-417)ACG>ACA	p.T139T	CUL9_uc003ouj.1_Silent_p.T139T|CUL9_uc003oul.2_Silent_p.T139T|CUL9_uc010jyk.2_5'UTR|CUL9_uc003oum.1_5'Flank	NM_015089	NP_055904	Q8IWT3	CUL9_HUMAN	p53-associated parkin-like cytoplasmic protein	139					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														0.104839	16.085964	35.334813	13	111	KEEP	---	---	---	---	capture		Silent	SNP	43152465	43152465	4221	6	G	A	A	A	496	39	CUL9	1	1
RARS2	57038	broad.mit.edu	37	6	88228554	88228554	+	Silent	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:88228554T>A	uc003pme.2	-	c.1293A>T	c.(1291-1293)GCA>GCT	p.A431A	RARS2_uc003pmb.2_Silent_p.A256A|RARS2_uc003pmc.2_Silent_p.A256A|RARS2_uc003pmd.2_Silent_p.A68A|RARS2_uc003pmf.2_Non-coding_Transcript	NM_020320	NP_064716	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	431					arginyl-tRNA aminoacylation	mitochondrial matrix	arginine-tRNA ligase activity|ATP binding|protein binding			ovary(2)|central_nervous_system(1)	3		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)										0.153846	39.613621	54.508259	20	110	KEEP	---	---	---	---	capture		Silent	SNP	88228554	88228554	13519	6	T	A	A	A	756	59	RARS2	3	3
GABRR1	2569	broad.mit.edu	37	6	89891759	89891759	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:89891759A>T	uc003pna.2	-	c.814T>A	c.(814-816)TAC>AAC	p.Y272N	GABRR1_uc011dzv.1_Missense_Mutation_p.Y249N	NM_002042	NP_002033	P24046	GBRR1_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 1	272	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			pancreas(1)	1		all_cancers(76;9.49e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.46e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00917)	Picrotoxin(DB00466)									0.109145	43.000649	94.357588	37	302	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89891759	89891759	6427	6	A	T	T	T	195	15	GABRR1	3	3
NRCAM	4897	broad.mit.edu	37	7	107808728	107808728	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:107808728C>A	uc003vfb.2	-	c.3307G>T	c.(3307-3309)GCA>TCA	p.A1103S	NRCAM_uc003vfc.2_Intron|NRCAM_uc011kmk.1_Intron|NRCAM_uc003vfd.2_Intron|NRCAM_uc003vfe.2_Intron|NRCAM_uc011kmj.1_Intron	NM_001037132	NP_001032209	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule isoform A	1103	Fibronectin type-III 5.|Extracellular (Potential).				angiogenesis|axon guidance|axonal fasciculation|cell-cell adhesion|central nervous system development|clustering of voltage-gated sodium channels|neuron migration|positive regulation of neuron differentiation|regulation of axon extension|synapse assembly	external side of plasma membrane|integral to plasma membrane	ankyrin binding			ovary(3)|breast(2)	5														0.111111	7.607532	15.683612	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107808728	107808728	11049	7	C	A	A	A	364	28	NRCAM	2	2
CFTR	1080	broad.mit.edu	37	7	117232483	117232483	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117232483G>A	uc003vjd.2	+	c.2262G>A	c.(2260-2262)GTG>GTA	p.V754V	CFTR_uc011knq.1_Silent_p.V160V	NM_000492	NP_000483	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance	754	Cytoplasmic (Potential).		V -> M (in CF).		respiratory gaseous exchange	apical plasma membrane|basolateral plasma membrane|chloride channel complex|early endosome membrane	ATP binding|ATP-binding and phosphorylation-dependent chloride channel activity|channel-conductance-controlling ATPase activity|chloride channel regulator activity|enzyme binding|PDZ domain binding			central_nervous_system(2)|ovary(1)	3	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Glibenclamide(DB01016)									0.208333	22.619538	26.404928	10	38	KEEP	---	---	---	---	capture		Silent	SNP	117232483	117232483	3427	7	G	A	A	A	574	45	CFTR	2	2
CPA1	1357	broad.mit.edu	37	7	130025716	130025716	+	Missense_Mutation	SNP	T	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:130025716T>G	uc003vpx.2	+	c.1024T>G	c.(1024-1026)TCT>GCT	p.S342A	CPA1_uc003vpw.2_Missense_Mutation_p.S176A	NM_001868	NP_001859	P15085	CBPA1_HUMAN	carboxypeptidase A1 precursor	342					proteolysis	extracellular space	metallocarboxypeptidase activity|zinc ion binding			ovary(1)	1	Melanoma(18;0.0435)													0.068182	-2.112626	6.37829	3	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130025716	130025716	3927	7	T	G	G	G	702	54	CPA1	4	4
KEL	3792	broad.mit.edu	37	7	142641424	142641424	+	Missense_Mutation	SNP	G	T	T	rs61729050		TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142641424G>T	uc003wcb.2	-	c.1477C>A	c.(1477-1479)CAA>AAA	p.Q493K		NM_000420	NP_000411	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	493	Extracellular (Potential).				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding			ovary(3)|central_nervous_system(1)	4	Melanoma(164;0.059)													0.164516	110.216363	143.348304	51	259	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142641424	142641424	8448	7	G	T	T	T	624	48	KEL	2	2
OR2A5	393046	broad.mit.edu	37	7	143748277	143748277	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143748277C>A	uc011ktw.1	+	c.783C>A	c.(781-783)GCC>GCA	p.A261A		NM_012365	NP_036497	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A,	261	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)	3	Melanoma(164;0.0783)													0.10566	21.905826	62.865402	28	237	KEEP	---	---	---	---	capture		Silent	SNP	143748277	143748277	11387	7	C	A	A	A	275	22	OR2A5	2	2
ZNF777	27153	broad.mit.edu	37	7	149153030	149153030	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:149153030G>A	uc003wfv.2	-	c.84C>T	c.(82-84)CCC>CCT	p.P28P		NM_015694	NP_056509	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	28					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)											0.117647	5.98021	10.861759	4	30	KEEP	---	---	---	---	capture		Silent	SNP	149153030	149153030	18748	7	G	A	A	A	548	43	ZNF777	2	2
PTPRN2	5799	broad.mit.edu	37	7	157475536	157475536	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:157475536C>A	uc011kwa.1	-	c.1951G>T	c.(1951-1953)GGC>TGC	p.G651C	PTPRN2_uc003wno.2_Missense_Mutation_p.G628C|PTPRN2_uc003wnp.2_Missense_Mutation_p.G611C|PTPRN2_uc003wnq.2_Missense_Mutation_p.G599C|PTPRN2_uc003wnr.2_Missense_Mutation_p.G590C	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	628	Helical; (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.16	7.883317	10.635586	4	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157475536	157475536	13265	7	C	A	A	A	286	22	PTPRN2	2	2
TMEM184A	202915	broad.mit.edu	37	7	1590517	1590517	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:1590517G>A	uc003skv.3	-	c.321C>T	c.(319-321)AGC>AGT	p.S107S	TMEM184A_uc003skt.3_5'UTR|TMEM184A_uc003skw.3_5'UTR	NM_001097620	NP_001091089	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	107	Helical; (Potential).					integral to membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)										0.142857	4.809614	7.391999	3	18	KEEP	---	---	---	---	capture		Silent	SNP	1590517	1590517	16638	7	G	A	A	A	542	42	TMEM184A	2	2
CRHR2	1395	broad.mit.edu	37	7	30693085	30693085	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30693085G>A	uc003tbp.2	-	c.1308C>T	c.(1306-1308)GCC>GCT	p.A436A	CRHR2_uc003tbn.2_Silent_p.A409A|CRHR2_uc010kvw.1_3'UTR|CRHR2_uc010kvx.1_Silent_p.A408A|CRHR2_uc010kvy.1_Silent_p.A245A|CRHR2_uc003tbo.2_Silent_p.A395A	NM_001883	NP_001874	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	409	Cytoplasmic (Potential).				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding			ovary(1)	1														0.1341	57.65452	91.541176	35	226	KEEP	---	---	---	---	capture		Silent	SNP	30693085	30693085	4011	7	G	A	A	A	496	39	CRHR2	1	1
RALA	5898	broad.mit.edu	37	7	39730128	39730128	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:39730128G>T	uc003thd.2	+	c.262G>T	c.(262-264)GGG>TGG	p.G88W		NM_005402	NP_005393	P11233	RALA_HUMAN	ras related v-ral simian leukemia viral oncogene	88					actin cytoskeleton reorganization|cell cycle|chemotaxis|cytokinesis|exocytosis|interspecies interaction between organisms|membrane raft localization|nerve growth factor receptor signaling pathway|positive regulation of filopodium assembly|Ras protein signal transduction|regulation of exocytosis	cell surface|cleavage furrow|cytosol|midbody|plasma membrane	Edg-2 lysophosphatidic acid receptor binding|GTP binding|GTPase activity			lung(1)|skin(1)	2										17				0.157895	48.096932	65.063412	24	128	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	39730128	39730128	13470	7	G	T	T	T	559	43	RALA	2	2
GRB10	2887	broad.mit.edu	37	7	50742267	50742267	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:50742267C>A	uc003tpi.2	-	c.228G>T	c.(226-228)ACG>ACT	p.T76T	GRB10_uc003tph.3_Silent_p.T18T|GRB10_uc003tpj.2_Silent_p.T76T|GRB10_uc003tpk.2_Silent_p.T76T|GRB10_uc010kzb.2_Silent_p.T18T|GRB10_uc003tpl.2_Silent_p.T70T|GRB10_uc003tpm.2_Silent_p.T18T|GRB10_uc003tpn.2_Silent_p.T18T	NM_005311	NP_005302	Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10 isoform	76					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)													0.075	0.585619	15.410049	6	74	KEEP	---	---	---	---	capture		Silent	SNP	50742267	50742267	7033	7	C	A	A	A	288	23	GRB10	1	1
CACNA2D1	781	broad.mit.edu	37	7	81662148	81662148	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:81662148G>T	uc003uhr.1	-	c.1108C>A	c.(1108-1110)CAG>AAG	p.Q370K		NM_000722	NP_000713	P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha	370	Extracellular (Potential).|VWFA.					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)									0.141844	36.998611	54.443903	20	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81662148	81662148	2664	7	G	T	T	T	611	47	CACNA2D1	2	2
ABCB4	5244	broad.mit.edu	37	7	87031499	87031499	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:87031499C>G	uc003uiv.1	-	c.3774G>C	c.(3772-3774)AAG>AAC	p.K1258N	ABCB4_uc003uiw.1_Missense_Mutation_p.K1251N|ABCB4_uc003uix.1_Missense_Mutation_p.K1204N	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	1258	ABC transporter 2.|Cytoplasmic (By similarity).				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.098802	35.707796	89.484578	33	301	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87031499	87031499	44	7	C	G	G	G	311	24	ABCB4	3	3
UBR5	51366	broad.mit.edu	37	8	103266711	103266711	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:103266711G>A	uc003ykr.1	-	c.8219C>T	c.(8218-8220)CCA>CTA	p.P2740L	UBR5_uc003yks.1_Missense_Mutation_p.P2739L|UBR5_uc003ykq.2_Missense_Mutation_p.P251L	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	2740	Pro-rich.|HECT.				cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(5)|ovary(3)|large_intestine(3)|kidney(1)|central_nervous_system(1)	13	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			Ovarian(131;96 1741 5634 7352 27489)				1024				0.155039	44.714692	59.379434	20	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103266711	103266711	17463	8	G	A	A	A	611	47	UBR5	2	2
PHF20L1	51105	broad.mit.edu	37	8	133823374	133823374	+	Splice_Site_SNP	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133823374G>T	uc003ytt.2	+	c.930_splice	c.e9+1	p.Q310_splice	PHF20L1_uc003ytr.2_Missense_Mutation_p.V285L|PHF20L1_uc010mdv.2_Missense_Mutation_p.V285L|PHF20L1_uc003yts.2_Splice_Site_SNP_p.Q310_splice|PHF20L1_uc011lja.1_Splice_Site_SNP_p.Q284_splice|PHF20L1_uc003ytu.1_Splice_Site_SNP|PHF20L1_uc003ytv.2_Missense_Mutation_p.V150L	NM_016018	NP_057102			PHD finger protein 20-like 1 isoform 1								nucleic acid binding|zinc ion binding			ovary(2)	2	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)											0.175439	46.933776	58.254384	20	94	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	133823374	133823374	12255	8	G	T	T	T	572	44	PHF20L1	5	2
COL22A1	169044	broad.mit.edu	37	8	139737684	139737684	+	Splice_Site_SNP	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139737684C>A	uc003yvd.2	-	c.2140_splice	c.e24-1	p.G714_splice	COL22A1_uc011ljo.1_Splice_Site_SNP_p.G14_splice	NM_152888	NP_690848			collagen, type XXII, alpha 1						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)											0.222222	26.825147	30.019572	10	35	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	139737684	139737684	3819	8	C	A	A	A	312	24	COL22A1	5	2
ZNF251	90987	broad.mit.edu	37	8	145948533	145948533	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:145948533C>A	uc003zdv.3	-	c.512G>T	c.(511-513)GGC>GTC	p.G171V		NM_138367	NP_612376	Q9BRH9	ZN251_HUMAN	zinc finger protein 251	171					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(97;3.54e-11)|all_epithelial(106;2.65e-10)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.75e-39)|Epithelial(56;7.54e-38)|all cancers(56;6.19e-33)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.11)	GBM - Glioblastoma multiforme(99;0.198)										0.125654	32.959819	59.102116	24	167	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145948533	145948533	18387	8	C	A	A	A	338	26	ZNF251	2	2
DLGAP2	9228	broad.mit.edu	37	8	1581080	1581080	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:1581080G>T	uc003wpl.2	+	c.1438G>T	c.(1438-1440)GAC>TAC	p.D480Y	DLGAP2_uc003wpm.2_Missense_Mutation_p.D480Y	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	559					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)										0.065574	-4.755968	19.102404	8	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1581080	1581080	4740	8	G	T	T	T	481	37	DLGAP2	1	1
FGL1	2267	broad.mit.edu	37	8	17722223	17722223	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:17722223C>A	uc003wye.2	-	c.967G>T	c.(967-969)GGC>TGC	p.G323C	FGL1_uc003wxx.2_Missense_Mutation_p.G273C|FGL1_uc003wxy.2_Missense_Mutation_p.G273C|FGL1_uc003wxz.2_Missense_Mutation_p.G272C|FGL1_uc003wya.2_Missense_Mutation_p.G273C|FGL1_uc003wyb.2_Missense_Mutation_p.G273C|FGL1_uc003wyc.2_Missense_Mutation_p.G273C|FGL1_uc003wyd.2_Non-coding_Transcript|FGL1_uc003wyf.2_Missense_Mutation_p.G243C	NM_201553	NP_963847	Q08830	FGL1_HUMAN	fibrinogen-like 1 precursor	273	Fibrinogen C-terminal.				signal transduction	fibrinogen complex	receptor binding				0				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)										0.171429	13.130116	16.700573	6	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	17722223	17722223	6109	8	C	A	A	A	299	23	FGL1	1	1
FZD3	7976	broad.mit.edu	37	8	28385432	28385432	+	Silent	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:28385432T>A	uc003xgx.2	+	c.1155T>A	c.(1153-1155)GTT>GTA	p.V385V	FZD3_uc010lvb.2_Silent_p.V385V	NM_017412	NP_059108	Q9NPG1	FZD3_HUMAN	frizzled 3 precursor	385	Helical; Name=5; (Potential).				canonical Wnt receptor signaling pathway|cell proliferation in midbrain|commissural neuron axon guidance|establishment of planar polarity|facial nucleus development|G-protein signaling, coupled to cGMP nucleotide second messenger|gonad development|inner ear morphogenesis|neural tube closure|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development	apical part of cell|axon|cytoplasm|dendrite|integral to membrane|neuron projection membrane|neuronal cell body|presynaptic active zone	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)										0.127962	39.474116	67.943709	27	184	KEEP	---	---	---	---	capture		Silent	SNP	28385432	28385432	6382	8	T	A	A	A	808	63	FZD3	3	3
KIF13B	23303	broad.mit.edu	37	8	29035078	29035078	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:29035078C>A	uc003xhh.3	-	c.738G>T	c.(736-738)GTG>GTT	p.V246V	KIF13B_uc003xhj.2_Silent_p.V143V|KIF13B_uc010lvf.1_Silent_p.V182V	NM_015254	NP_056069	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	246	Kinesin-motor.				microtubule-based movement|protein targeting|signal transduction|T cell activation	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein kinase binding				0		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)										0.129032	77.423036	127.295023	48	324	KEEP	---	---	---	---	capture		Silent	SNP	29035078	29035078	8586	8	C	A	A	A	262	21	KIF13B	2	2
UNC5D	137970	broad.mit.edu	37	8	35608274	35608274	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:35608274C>G	uc003xjr.1	+	c.2110C>G	c.(2110-2112)CTG>GTG	p.L704V	UNC5D_uc003xjs.1_Missense_Mutation_p.L699V|UNC5D_uc003xju.1_Missense_Mutation_p.L280V	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	704	Cytoplasmic (Potential).|Interaction with DCC (By similarity).				apoptosis|axon guidance	integral to membrane	receptor activity			ovary(2)|pancreas(1)	3				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)										0.106628	38.990036	92.343714	37	310	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35608274	35608274	17553	8	C	G	G	G	311	24	UNC5D	3	3
IKBKB	3551	broad.mit.edu	37	8	42178306	42178306	+	Silent	SNP	T	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42178306T>C	uc003xow.1	+	c.1632T>C	c.(1630-1632)ATT>ATC	p.I544I	IKBKB_uc010lxh.1_3'UTR|IKBKB_uc011lco.1_Non-coding_Transcript|IKBKB_uc010lxj.1_Silent_p.I321I|IKBKB_uc003xox.1_Silent_p.I265I|IKBKB_uc011lcp.1_Non-coding_Transcript|IKBKB_uc011lcq.1_Silent_p.I542I|IKBKB_uc010lxi.1_Non-coding_Transcript|IKBKB_uc011lcr.1_Silent_p.I485I	NM_001556	NP_001547	O14920	IKKB_HUMAN	inhibitor of nuclear factor kappa B kinase beta	544					anti-apoptosis|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein phosphorylation|T cell receptor signaling pathway|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	CD40 receptor complex|cytosol|internal side of plasma membrane|membrane raft	ATP binding|identical protein binding|IkappaB kinase activity|transcription activator activity			breast(3)|ovary(2)|lung(1)|skin(1)	7	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Arsenic trioxide(DB01169)|Auranofin(DB00995)					402				0.044534	-35.310109	19.676566	11	236	KEEP	---	---	---	---	capture		Silent	SNP	42178306	42178306	7912	8	T	C	C	C	809	63	IKBKB	4	4
SLC20A2	6575	broad.mit.edu	37	8	42287590	42287590	+	Silent	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:42287590C>A	uc010lxl.2	-	c.1701G>T	c.(1699-1701)ACG>ACT	p.T567T	SLC20A2_uc010lxm.2_Silent_p.T567T|SLC20A2_uc003xpe.2_Silent_p.T567T|SLC20A2_uc011lcu.1_Silent_p.T369T	NM_006749	NP_006740	Q08357	S20A2_HUMAN	solute carrier family 20, member 2	567	Cytoplasmic (Potential).				interspecies interaction between organisms	integral to plasma membrane|membrane fraction	inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			ovary(2)	2	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)											0.128205	7.147434	12.402154	5	34	KEEP	---	---	---	---	capture		Silent	SNP	42287590	42287590	14935	8	C	A	A	A	340	27	SLC20A2	1	1
ZFHX4	79776	broad.mit.edu	37	8	77618186	77618186	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77618186G>T	uc003yav.2	+	c.1863G>T	c.(1861-1863)GTG>GTT	p.V621V	ZFHX4_uc003yat.1_Silent_p.V621V|ZFHX4_uc003yau.1_Silent_p.V621V|ZFHX4_uc003yaw.1_Silent_p.V621V	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	621	C2H2-type 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)											0.141935	40.638052	59.805481	22	133	KEEP	---	---	---	---	capture		Silent	SNP	77618186	77618186	18223	8	G	T	T	T	613	48	ZFHX4	2	2
ZFHX4	79776	broad.mit.edu	37	8	77690667	77690667	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77690667A>T	uc003yav.2	+	c.3239A>T	c.(3238-3240)AAT>ATT	p.N1080I	ZFHX4_uc003yau.1_Missense_Mutation_p.N1106I|ZFHX4_uc003yaw.1_Missense_Mutation_p.N1080I	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1080					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)											0.160156	83.92754	112.063487	41	215	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77690667	77690667	18223	8	A	T	T	T	52	4	ZFHX4	3	3
ACTL7B	10880	broad.mit.edu	37	9	111618088	111618088	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:111618088C>T	uc004bdi.2	-	c.123G>A	c.(121-123)ATG>ATA	p.M41I		NM_006686	NP_006677	Q9Y614	ACL7B_HUMAN	actin-like 7B	41						actin cytoskeleton|cytoplasm	structural constituent of cytoskeleton			pancreas(1)	1														0.096154	6.665379	23.679272	10	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	111618088	111618088	202	9	C	T	T	T	377	29	ACTL7B	2	2
TNC	3371	broad.mit.edu	37	9	117803262	117803262	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:117803262C>T	uc004bjj.3	-	c.5350G>A	c.(5350-5352)GGC>AGC	p.G1784S	TNC_uc010mvf.2_Missense_Mutation_p.G1511S	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	1784	Fibronectin type-III 13.				cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|ovary(1)	5														0.245833	162.322609	176.434408	59	181	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117803262	117803262	16811	9	C	T	T	T	286	22	TNC	2	2
CEP110	11064	broad.mit.edu	37	9	123920082	123920082	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:123920082G>T	uc004bkx.1	+	c.4561G>T	c.(4561-4563)GAA>TAA	p.E1521*	CEP110_uc004bla.1_Nonsense_Mutation_p.E969*|CEP110_uc010mvo.1_Nonsense_Mutation_p.E190*|CEP110_uc004blb.1_Nonsense_Mutation_p.E190*|CEP110_uc010mvp.1_5'UTR	NM_007018	NP_008949	Q7Z7A1	CE110_HUMAN	centrosomal protein 110kDa	1521	Potential.				cell division|G2/M transition of mitotic cell cycle	centrosome|cytosol	protein binding			ovary(3)|skin(1)	4										584				0.181818	42.83018	53.295387	20	90	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	123920082	123920082	3378	9	G	T	T	T	429	33	CEP110	5	2
LCN2	3934	broad.mit.edu	37	9	130911883	130911883	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:130911883C>A	uc011map.1	+	c.79C>A	c.(79-81)CTG>ATG	p.L27M	LCN2_uc010mxq.1_Missense_Mutation_p.L27M|LCN2_uc004bto.1_Missense_Mutation_p.L27M	NM_005564	NP_005555	P80188	NGAL_HUMAN	lipocalin 2 precursor	27					apoptosis|innate immune response|regulation of apoptosis|siderophore transport		iron ion binding|transporter activity				0														0.142857	6.679648	10.12239	4	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130911883	130911883	9008	9	C	A	A	A	311	24	LCN2	2	2
GLIPR2	152007	broad.mit.edu	37	9	36162380	36162380	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:36162380G>T	uc003zyz.2	+	c.326G>T	c.(325-327)TGG>TTG	p.W109L	GLIPR2_uc010mlf.1_3'UTR|GLIPR2_uc003zza.2_Non-coding_Transcript|GLIPR2_uc003zyy.1_Intron	NM_022343	NP_071738	Q9H4G4	GAPR1_HUMAN	GLI pathogenesis-related 2	109				TGHFTAMVWKNTKKMGVGKASASDGSSFVVARYFPAGNVVN EGFFEENVLPPKK -> IRFFFFNFLLFLSKPLLYFSYF (in Ref. 3; BAC11019).		extracellular region|Golgi membrane				central_nervous_system(1)	1														0.169355	134.049102	172.497107	63	309	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36162380	36162380	6712	9	G	T	T	T	611	47	GLIPR2	2	2
PCSK5	5125	broad.mit.edu	37	9	78772069	78772069	+	Missense_Mutation	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:78772069G>A	uc004ajz.2	+	c.1421G>A	c.(1420-1422)CGA>CAA	p.R474Q	PCSK5_uc004ajy.2_Missense_Mutation_p.R474Q|PCSK5_uc004aka.2_Non-coding_Transcript	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	474	Homo B/P.				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3														0.038278	-31.882665	16.285342	8	201	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	78772069	78772069	12024	9	G	A	A	A	481	37	PCSK5	1	1
S1PR3	1903	broad.mit.edu	37	9	91617197	91617197	+	Nonsense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:91617197C>A	uc004aqe.2	+	c.1082C>A	c.(1081-1083)TCA>TAA	p.S361*		NM_005226	NP_005217	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	361	Cytoplasmic (By similarity).				anatomical structure morphogenesis|elevation of cytosolic calcium ion concentration|inflammatory response|positive regulation of cell proliferation	integral to plasma membrane	lipid binding|lysosphingolipid and lysophosphatidic acid receptor activity			ovary(2)|central_nervous_system(1)	3														0.261905	57.704591	62.018889	22	62	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	91617197	91617197	14275	9	C	A	A	A	377	29	S1PR3	5	2
HTR2C	3358	broad.mit.edu	37	X	114141816	114141816	+	Silent	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:114141816T>A	uc004epu.1	+	c.1215T>A	c.(1213-1215)GCT>GCA	p.A405A	HTR2C_uc010nqc.1_Silent_p.A405A|HTR2C_uc004epv.1_3'UTR	NM_000868	NP_000859	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C	405	Cytoplasmic (By similarity).				cGMP biosynthetic process|ERK1 and ERK2 cascade|feeding behavior|phosphatidylinositol biosynthetic process|release of sequestered calcium ion into cytosol|response to drug|serotonin receptor signaling pathway|synaptic transmission	cytoplasm|integral to membrane|nucleus|plasma membrane	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding|drug binding|phosphatidylinositol phospholipase C activity|protein binding|serotonin binding|serotonin receptor activity			ovary(3)	3					Chlorprothixene(DB01239)|Clozapine(DB00363)|Dexfenfluramine(DB01191)|Fenfluramine(DB00574)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Thiethylperazine(DB00372)|Tramadol(DB00193)|Ziprasidone(DB00246)									0.195804	64.812859	77.150539	28	115	KEEP	---	---	---	---	capture		Silent	SNP	114141816	114141816	7743	23	T	A	A	A	717	56	HTR2C	3	3
KIAA1210	57481	broad.mit.edu	37	X	118220652	118220652	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:118220652C>A	uc004era.3	-	c.4541G>T	c.(4540-4542)AGG>ATG	p.R1514M		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1514										ovary(4)|skin(1)	5														0.259259	57.834992	62.088257	21	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118220652	118220652	8522	23	C	A	A	A	312	24	KIAA1210	2	2
DCAF12L2	340578	broad.mit.edu	37	X	125298619	125298619	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:125298619G>C	uc004euk.1	-	c.1289C>G	c.(1288-1290)GCG>GGG	p.A430G		NM_001013628	NP_001013650	Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	430										lung(2)|large_intestine(1)|ovary(1)|pancreas(1)	5														0.123457	35.385293	57.85185	20	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	125298619	125298619	4436	23	G	C	C	C	494	38	DCAF12L2	3	3
ARHGEF6	9459	broad.mit.edu	37	X	135770094	135770094	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:135770094G>T	uc004fab.2	-	c.1242C>A	c.(1240-1242)CTC>CTA	p.L414L	ARHGEF6_uc011mwd.1_Silent_p.L287L|ARHGEF6_uc011mwe.1_Silent_p.L260L	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	414	DH.				apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)													0.034884	-27.911793	12.565762	6	166	KEEP	---	---	---	---	capture		Silent	SNP	135770094	135770094	925	23	G	T	T	T	574	45	ARHGEF6	2	2
ZIC3	7547	broad.mit.edu	37	X	136649500	136649500	+	Missense_Mutation	SNP	C	G	G			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:136649500C>G	uc004fak.2	+	c.650C>G	c.(649-651)CCT>CGT	p.P217R		NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3	217			P -> A (in a patient with atrial septal defect and pulmonic stenosis not associated with heterotaxy; lacks DNA- binding; does not inhibit transcriptional activation and interaction with GLI3).		cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)													0.21875	18.607378	20.939797	7	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136649500	136649500	18271	23	C	G	G	G	312	24	ZIC3	3	3
BCOR	54880	broad.mit.edu	37	X	39932097	39932097	+	Silent	SNP	G	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:39932097G>A	uc004den.3	-	c.2502C>T	c.(2500-2502)AGC>AGT	p.S834S	BCOR_uc004dep.3_Silent_p.S834S|BCOR_uc004deo.3_Silent_p.S834S|BCOR_uc004dem.3_Silent_p.S834S|BCOR_uc004deq.3_Silent_p.S834S	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	BCL-6 interacting corepressor isoform c	834					chromatin modification|heart development|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|odontogenesis|palate development|protein ubiquitination|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|promoter binding|transcription corepressor activity|transcription factor binding			ovary(2)|kidney(1)|central_nervous_system(1)	4														0.166667	10.257793	13.41674	5	25	KEEP	---	---	---	---	capture		Silent	SNP	39932097	39932097	1407	23	G	A	A	A	490	38	BCOR	1	1
PHF16	9767	broad.mit.edu	37	X	46918161	46918161	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46918161G>T	uc004dgx.2	+	c.2154G>T	c.(2152-2154)GAG>GAT	p.E718D	PHF16_uc004dgy.2_Missense_Mutation_p.E718D	NM_001077445	NP_001070913	Q92613	JADE3_HUMAN	PHD finger protein 16	718					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.160494	26.220753	35.109677	13	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46918161	46918161	12250	23	G	T	T	T	425	33	PHF16	2	2
RBM10	8241	broad.mit.edu	37	X	47044719	47044719	+	Nonsense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47044719C>T	uc004dhi.2	+	c.2314C>T	c.(2314-2316)CAG>TAG	p.Q772*	RBM10_uc004dhf.2_Nonsense_Mutation_p.Q707*|RBM10_uc004dhg.2_Nonsense_Mutation_p.Q629*|RBM10_uc004dhh.2_Nonsense_Mutation_p.Q706*|RBM10_uc010nhq.2_Nonsense_Mutation_p.Q630*	NM_005676	NP_005667	P98175	RBM10_HUMAN	RNA binding motif protein 10 isoform 1	707					mRNA processing|RNA splicing	chromatin remodeling complex	nucleotide binding|RNA binding|zinc ion binding			large_intestine(1)|ovary(1)|pancreas(1)	3						Melanoma(171;120 2705 19495 39241)								0.1875	6.614851	8.078457	3	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47044719	47044719	13572	23	C	T	T	T	221	17	RBM10	5	2
FOXP3	50943	broad.mit.edu	37	X	49108150	49108150	+	Missense_Mutation	SNP	A	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:49108150A>T	uc010niq.1	-	c.1016T>A	c.(1015-1017)TTC>TAC	p.F339Y	FOXP3_uc011mnb.1_Missense_Mutation_p.F397Y|FOXP3_uc011mnc.1_Missense_Mutation_p.F347Y|FOXP3_uc004dnf.3_Missense_Mutation_p.F374Y|FOXP3_uc004dne.3_Missense_Mutation_p.F339Y	NM_001114377	NP_001107849	Q9BZS1	FOXP3_HUMAN	forkhead box P3 isoform b	374	Fork-head.				B cell homeostasis|cerebellum development|chromatin remodeling|embryo development|myeloid cell homeostasis|negative regulation of activated T cell proliferation|negative regulation of chronic inflammatory response|negative regulation of CREB transcription factor activity|negative regulation of cytokine secretion|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of histone acetylation|negative regulation of histone deacetylation|negative regulation of interferon-gamma biosynthetic process|negative regulation of interferon-gamma production|negative regulation of interleukin-10 production|negative regulation of interleukin-2 biosynthetic process|negative regulation of interleukin-2 production|negative regulation of interleukin-4 production|negative regulation of interleukin-5 production|negative regulation of interleukin-6 production|negative regulation of isotype switching to IgE isotypes|negative regulation of NF-kappaB transcription factor activity|negative regulation of T cell cytokine production|negative regulation of tumor necrosis factor production|pattern specification process|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone acetylation|positive regulation of immature T cell proliferation in thymus|positive regulation of peripheral T cell tolerance induction|positive regulation of T cell anergy|positive regulation of transforming growth factor-beta1 production|post-embryonic development|regulation of isotype switching to IgG isotypes|T cell homeostasis|T cell receptor signaling pathway|tolerance induction to self antigen	cytoplasm|cytoplasm|nucleus|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|histone acetyltransferase binding|histone deacetylase binding|NF-kappaB binding|NFAT protein binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription corepressor activity|zinc ion binding				0	Ovarian(276;0.236)					GBM(182;1432 2112 16160 23073 31774)								0.225	21.153441	23.933182	9	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49108150	49108150	6274	23	A	T	T	T	117	9	FOXP3	3	3
HUWE1	10075	broad.mit.edu	37	X	53581722	53581722	+	Missense_Mutation	SNP	G	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53581722G>C	uc004dsp.2	-	c.8366C>G	c.(8365-8367)TCT>TGT	p.S2789C	HUWE1_uc004dsn.2_Missense_Mutation_p.S1613C	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	2789					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17														0.065041	-3.408172	20.773402	8	115	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53581722	53581722	7761	23	G	C	C	C	429	33	HUWE1	3	3
PFKFB1	5207	broad.mit.edu	37	X	54964098	54964098	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54964098C>A	uc004dty.1	-	c.1158G>T	c.(1156-1158)GAG>GAT	p.E386D	PFKFB1_uc010nkd.1_Missense_Mutation_p.E194D|PFKFB1_uc011mol.1_Missense_Mutation_p.E321D	NM_002625	NP_002616	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,	386	Fructose-2,6-bisphosphatase.				energy reserve metabolic process|fructose 2,6-bisphosphate metabolic process|gluconeogenesis|glycolysis|intracellular protein kinase cascade	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex	6-phosphofructo-2-kinase activity|ATP binding|fructose-2,6-bisphosphate 2-phosphatase activity|identical protein binding			ovary(1)	1														0.12766	35.860036	61.276157	24	164	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54964098	54964098	12182	23	C	A	A	A	415	32	PFKFB1	2	2
ARHGEF9	23229	broad.mit.edu	37	X	62926160	62926160	+	Missense_Mutation	SNP	T	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:62926160T>A	uc004dvl.2	-	c.359A>T	c.(358-360)AAG>ATG	p.K120M	ARHGEF9_uc004dvj.1_Missense_Mutation_p.K9M|ARHGEF9_uc004dvk.1_De_novo_Start_OutOfFrame|ARHGEF9_uc011mos.1_Missense_Mutation_p.K99M|ARHGEF9_uc004dvm.1_Missense_Mutation_p.K99M|ARHGEF9_uc011mot.1_Missense_Mutation_p.K67M|ARHGEF9_uc004dvn.2_Missense_Mutation_p.K127M	NM_015185	NP_056000	O43307	ARHG9_HUMAN	Cdc42 guanine exchange factor 9	120	DH.				apoptosis|induction of apoptosis by extracellular signals|ion transmembrane transport|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol	Rho guanyl-nucleotide exchange factor activity			ovary(5)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	8														0.144068	31.491211	45.886449	17	101	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	62926160	62926160	927	23	T	A	A	A	728	56	ARHGEF9	3	3
MAGEE1	57692	broad.mit.edu	37	X	75650121	75650121	+	Nonsense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:75650121G>T	uc004ecm.1	+	c.1798G>T	c.(1798-1800)GAG>TAG	p.E600*		NM_020932	NP_065983	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	600	MAGE 1.					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane				breast(3)|ovary(1)|pancreas(1)|skin(1)	6														0.172414	10.355689	13.296712	5	24	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	75650121	75650121	9568	23	G	T	T	T	533	41	MAGEE1	5	2
BRWD3	254065	broad.mit.edu	37	X	79978240	79978240	+	Missense_Mutation	SNP	C	A	A			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79978240C>A	uc004edt.2	-	c.1697G>T	c.(1696-1698)CGT>CTT	p.R566L	BRWD3_uc004edo.2_Missense_Mutation_p.R162L|BRWD3_uc004edp.2_Missense_Mutation_p.R395L|BRWD3_uc004edq.2_Missense_Mutation_p.R162L|BRWD3_uc010nmj.1_Missense_Mutation_p.R162L|BRWD3_uc004edr.2_Missense_Mutation_p.R236L|BRWD3_uc004eds.2_Missense_Mutation_p.R162L|BRWD3_uc004edu.2_Missense_Mutation_p.R236L|BRWD3_uc004edv.2_Missense_Mutation_p.R162L|BRWD3_uc004edw.2_Missense_Mutation_p.R162L|BRWD3_uc004edx.2_Missense_Mutation_p.R162L|BRWD3_uc004edy.2_Missense_Mutation_p.R162L|BRWD3_uc004edz.2_Missense_Mutation_p.R236L|BRWD3_uc004eea.2_Missense_Mutation_p.R236L|BRWD3_uc004eeb.2_Missense_Mutation_p.R162L	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	566										ovary(4)	4														0.101266	19.281961	44.341341	16	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79978240	79978240	1557	23	C	A	A	A	247	19	BRWD3	1	1
SATL1	340562	broad.mit.edu	37	X	84362715	84362715	+	Silent	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:84362715G>T	uc011mqx.1	-	c.1260C>A	c.(1258-1260)GGC>GGA	p.G420G	SATL1_uc004een.2_Silent_p.G420G	NM_001163541	NP_001157013	Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	233	Gln-rich.						N-acetyltransferase activity			breast(2)	2														0.111732	47.435925	100.76509	40	318	KEEP	---	---	---	---	capture		Silent	SNP	84362715	84362715	14336	23	G	T	T	T	535	42	SATL1	2	2
POF1B	79983	broad.mit.edu	37	X	84606415	84606415	+	Missense_Mutation	SNP	C	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:84606415C>T	uc004ees.2	-	c.481G>A	c.(481-483)GGA>AGA	p.G161R	POF1B_uc004eer.2_Missense_Mutation_p.G161R	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	161							actin binding				0														0.109091	17.113193	33.764821	12	98	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	84606415	84606415	12610	23	C	T	T	T	312	24	POF1B	2	2
PCDH11X	27328	broad.mit.edu	37	X	91132563	91132563	+	Missense_Mutation	SNP	G	T	T			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91132563G>T	uc004efk.1	+	c.1324G>T	c.(1324-1326)GGC>TGC	p.G442C	PCDH11X_uc004efl.1_Missense_Mutation_p.G442C|PCDH11X_uc004efo.1_Missense_Mutation_p.G442C|PCDH11X_uc010nmv.1_Missense_Mutation_p.G442C|PCDH11X_uc004efm.1_Missense_Mutation_p.G442C|PCDH11X_uc004efn.1_Missense_Mutation_p.G442C|PCDH11X_uc004efh.1_Missense_Mutation_p.G442C|PCDH11X_uc004efj.1_Missense_Mutation_p.G442C	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	442	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.202128	46.568718	54.318878	19	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	91132563	91132563	11928	23	G	T	T	T	611	47	PCDH11X	2	2
SCNN1A	6337	broad.mit.edu	37	12	6457044	6457045	+	Frame_Shift_Ins	INS	-	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:6457044_6457045insC	uc001qnw.2	-	c.2181_2182insG	c.(2179-2184)GGGCCCfs	p.G727fs	SCNN1A_uc001qnv.2_Frame_Shift_Ins_p.G368fs|SCNN1A_uc001qnx.2_Frame_Shift_Ins_p.G668fs|SCNN1A_uc010sfb.1_Frame_Shift_Ins_p.G691fs	NM_001159576	NP_001153048	P37088	SCNNA_HUMAN	sodium channel, nonvoltage-gated 1 alpha isoform	668_669	Cytoplasmic (By similarity).				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding				0					Amiloride(DB00594)|Triamterene(DB00384)									0.38			3	5		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	6457044	6457045	14409	12	-	C	C	C	546	42	SCNN1A	5	5
KLHL26	55295	broad.mit.edu	37	19	18780017	18780018	+	Frame_Shift_Ins	INS	-	C	C			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:18780017_18780018insC	uc002njz.1	+	c.1810_1811insC	c.(1810-1812)GCCfs	p.A604fs		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	604	Kelch 6.									ovary(1)	1														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	18780017	18780018	8693	19	-	C	C	C	494	38	KLHL26	5	5
ETAA1	54465	broad.mit.edu	37	2	67624591	67624591	+	Frame_Shift_Del	DEL	G	-	-			TCGA-44-2655-01	TCGA-44-2655-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:67624591_67624591delG	uc002sdz.1	+	c.11_11delG	c.(10-12)CGAfs	p.R4fs		NM_019002	NP_061875	Q9NY74	ETAA1_HUMAN	ETAA16 protein	4						cytoplasm|nucleus				ovary(3)|large_intestine(1)	4														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	67624591	67624591	5460	2	G	-	-	-	481	37	ETAA1	5	5
